From 645caf36dfb92dcba140abe25f13b9eff06ed329 Mon Sep 17 00:00:00 2001
From: Dimitar Tasev <dimtasev@gmail.com>
Date: Fri, 19 May 2017 17:47:14 +0100
Subject: [PATCH] Re #xxx remove tomo files
---
Framework/Algorithms/CMakeLists.txt | 11 -
.../MantidAlgorithms/Tomography/FBPTomopy.h | 45 -
.../MantidAlgorithms/Tomography/tomopy/fbp.h | 34 -
.../Tomography/tomopy/utils.h | 103 -
.../src/ImggTomographicReconstruction.cpp | 405 ----
.../Algorithms/src/Tomography/FBPTomopy.cpp | 15 -
.../Algorithms/src/Tomography/tomopy/fbp.c | 160 --
.../Algorithms/src/Tomography/tomopy/utils.c | 207 --
.../test/Tomography/FBPTomopyTest.h | 114 -
Framework/DataHandling/CMakeLists.txt | 3 -
.../MantidDataHandling/LoadSavuTomoConfig.h | 75 -
.../src/ImggAggregateWavelengths.cpp | 906 --------
.../DataHandling/src/LoadSavuTomoConfig.cpp | 206 --
.../DataHandling/src/SaveSavuTomoConfig.cpp | 206 --
.../test/LoadSavuTomoConfigTest.h | 189 --
.../test/SaveSavuTomoConfigTest.h | 177 --
.../src/SCARFTomoReconstruction.cpp | 1498 -------------
.../test/SCARFTomoReconstructionTest.h | 683 ------
MantidQt/CustomInterfaces/CMakeLists.txt | 65 -
.../Tomography/IImggFormatsConvertPresenter.h | 60 -
.../Tomography/IImggFormatsConvertView.h | 183 --
.../Tomography/ITomographyIfacePresenter.h | 73 -
.../Tomography/ITomographyIfaceView.h | 323 ---
.../Tomography/ITomographyROIPresenter.h | 85 -
.../Tomography/ITomographyROIView.h | 290 ---
.../Tomography/ImageSelectCoRAndRegions.ui | 933 --------
.../Tomography/ImageStackPreParams.h | 62 -
.../Tomography/ImggFormats.h | 55 -
.../Tomography/ImggFormatsConvert.ui | 350 ---
.../Tomography/ImggFormatsConvertPresenter.h | 105 -
.../ImggFormatsConvertViewQtWidget.h | 129 --
.../Tomography/StackOfImagesDirs.h | 102 -
.../Tomography/TomoPathsConfig.h | 145 --
.../Tomography/TomoRecToolConfig.h | 121 --
.../Tomography/TomoReconFiltersSettings.h | 52 -
.../Tomography/TomoReconPostprocSettings.h | 44 -
.../Tomography/TomoReconPreprocSettings.h | 58 -
.../Tomography/TomoReconToolsUserSettings.h | 55 -
.../Tomography/TomoSystemSettings.h | 75 -
.../Tomography/TomoSystemSettingsLocal.h | 58 -
.../Tomography/TomoSystemSettingsRemote.h | 53 -
.../Tomography/TomoToolConfigAstra.ui | 206 --
.../Tomography/TomoToolConfigCustom.ui | 135 --
.../Tomography/TomoToolConfigDialogAstra.h | 38 -
.../Tomography/TomoToolConfigDialogBase.h | 153 --
.../Tomography/TomoToolConfigDialogCustom.h | 37 -
.../Tomography/TomoToolConfigDialogSavu.h | 71 -
.../Tomography/TomoToolConfigDialogTomoPy.h | 37 -
.../Tomography/TomoToolConfigSavu.ui | 392 ----
.../Tomography/TomoToolConfigTomoPy.ui | 210 --
.../Tomography/TomographyIfaceModel.h | 330 ---
.../Tomography/TomographyIfacePresenter.h | 185 --
.../Tomography/TomographyIfaceQtGUI.ui | 106 -
.../Tomography/TomographyIfaceQtTabEnergy.ui | 400 ----
.../TomographyIfaceQtTabFiltersSettings.ui | 604 ------
.../Tomography/TomographyIfaceQtTabRun.ui | 802 -------
.../TomographyIfaceQtTabSystemSettings.ui | 790 -------
.../TomographyIfaceQtTabVisualize.ui | 236 --
.../Tomography/TomographyIfaceViewQtGUI.h | 402 ----
.../Tomography/TomographyProcess.h | 105 -
.../Tomography/TomographyROIPresenter.h | 158 --
.../Tomography/TomographyROIViewQtWidget.h | 311 ---
.../Tomography/TomographyThread.h | 115 -
.../Tomography/ToolConfigAstraToolbox.h | 74 -
.../Tomography/ToolConfigCustom.h | 63 -
.../Tomography/ToolConfigTomoPy.h | 69 -
.../src/Tomography/EnergyBandsViewQtGUI.cpp | 163 --
.../src/Tomography/ImageStackPreParams.cpp | 12 -
.../src/Tomography/ImggFormats.cpp | 94 -
.../ImggFormatsConvertPresenter.cpp | 359 ----
.../ImggFormatsConvertViewQtWidget.cpp | 375 ----
.../src/Tomography/StackOfImagesDirs.cpp | 208 --
.../src/Tomography/TomoPathsConfig.cpp | 18 -
.../Tomography/TomoReconPostprocSettings.cpp | 15 -
.../Tomography/TomoReconPreprocSettings.cpp | 17 -
.../src/Tomography/TomoSystemSettings.cpp | 28 -
.../Tomography/TomoSystemSettingsLocal.cpp | 55 -
.../Tomography/TomoSystemSettingsRemote.cpp | 21 -
.../Tomography/TomoToolConfigDialogAstra.cpp | 45 -
.../Tomography/TomoToolConfigDialogBase.cpp | 36 -
.../Tomography/TomoToolConfigDialogCustom.cpp | 71 -
.../Tomography/TomoToolConfigDialogSavu.cpp | 632 ------
.../Tomography/TomoToolConfigDialogTomoPy.cpp | 47 -
.../src/Tomography/TomographyIfaceModel.cpp | 1048 ---------
.../Tomography/TomographyIfacePresenter.cpp | 929 --------
.../Tomography/TomographyIfaceViewQtGUI.cpp | 1894 -----------------
.../src/Tomography/TomographyROIPresenter.cpp | 603 ------
.../Tomography/TomographyROIViewQtWidget.cpp | 1366 ------------
.../src/Tomography/ToolConfig.cpp | 85 -
.../test/ImggFormatsConvertPresenterTest.h | 108 -
.../test/ImggFormatsConvertViewMock.h | 74 -
.../test/StackOfImagesDirsTest.h | 111 -
.../test/TomographyIfaceModelTest.h | 406 ----
.../test/TomographyIfacePresenterTest.h | 732 -------
.../test/TomographyROIPresenterTest.h | 679 ------
.../test/TomographyROIViewMock.h | 112 -
.../test/TomographyViewMock.h | 139 --
.../ImggAggregateWavelengths-v1.rst | 163 --
.../ImggTomographicReconstruction-v1.rst | 125 --
.../algorithms/LoadSavuTomoConfig-v1.rst | 76 -
.../algorithms/SCARFTomoReconstruction-v1.rst | 89 -
.../algorithms/SaveSavuTomoConfig-v1.rst | 66 -
.../interfaces/Tomographic_Reconstruction.rst | 497 -----
scripts/Imaging/IMAT/__init__.py | 23 -
scripts/Imaging/IMAT/agg_energy_bands.py | 87 -
scripts/Imaging/IMAT/prep/__init__.py | 36 -
.../IMAT/prep/energy_bands_aggregator.py | 365 ----
scripts/Imaging/IMAT/prep/filters.py | 208 --
scripts/Imaging/IMAT/prep/filters_adv.py | 135 --
scripts/Imaging/IMAT/tomo_reconstruct.py | 411 ----
scripts/Imaging/IMAT/tomorec/__init__.py | 54 -
scripts/Imaging/IMAT/tomorec/configs.py | 195 --
scripts/Imaging/IMAT/tomorec/io.py | 578 -----
.../IMAT/tomorec/reconstruction_command.py | 1365 ------------
scripts/Imaging/IMAT/tomorec/tool_imports.py | 69 -
115 files changed, 29566 deletions(-)
delete mode 100644 Framework/Algorithms/inc/MantidAlgorithms/Tomography/FBPTomopy.h
delete mode 100644 Framework/Algorithms/inc/MantidAlgorithms/Tomography/tomopy/fbp.h
delete mode 100644 Framework/Algorithms/inc/MantidAlgorithms/Tomography/tomopy/utils.h
delete mode 100644 Framework/Algorithms/src/ImggTomographicReconstruction.cpp
delete mode 100644 Framework/Algorithms/src/Tomography/FBPTomopy.cpp
delete mode 100644 Framework/Algorithms/src/Tomography/tomopy/fbp.c
delete mode 100644 Framework/Algorithms/src/Tomography/tomopy/utils.c
delete mode 100644 Framework/Algorithms/test/Tomography/FBPTomopyTest.h
delete mode 100644 Framework/DataHandling/inc/MantidDataHandling/LoadSavuTomoConfig.h
delete mode 100644 Framework/DataHandling/src/ImggAggregateWavelengths.cpp
delete mode 100644 Framework/DataHandling/src/LoadSavuTomoConfig.cpp
delete mode 100644 Framework/DataHandling/src/SaveSavuTomoConfig.cpp
delete mode 100644 Framework/DataHandling/test/LoadSavuTomoConfigTest.h
delete mode 100644 Framework/DataHandling/test/SaveSavuTomoConfigTest.h
delete mode 100644 Framework/RemoteAlgorithms/src/SCARFTomoReconstruction.cpp
delete mode 100644 Framework/RemoteAlgorithms/test/SCARFTomoReconstructionTest.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertPresenter.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyIfacePresenter.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyROIPresenter.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyROIView.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImageSelectCoRAndRegions.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormats.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvert.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertPresenter.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertViewQtWidget.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/StackOfImagesDirs.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconFiltersSettings.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconPostprocSettings.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconPreprocSettings.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsLocal.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsRemote.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigAstra.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigCustom.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogAstra.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogCustom.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogSavu.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogTomoPy.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigSavu.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigTomoPy.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtGUI.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabEnergy.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabFiltersSettings.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabRun.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabSystemSettings.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabVisualize.ui
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyProcess.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyROIViewQtWidget.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyThread.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h
delete mode 100644 MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/EnergyBandsViewQtGUI.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/ImggFormats.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/ImggFormatsConvertPresenter.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/ImggFormatsConvertViewQtWidget.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/StackOfImagesDirs.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoPathsConfig.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoReconPostprocSettings.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoReconPreprocSettings.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettings.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettingsLocal.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettingsRemote.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogAstra.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogBase.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogCustom.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogSavu.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogTomoPy.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomographyIfacePresenter.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceViewQtGUI.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomographyROIPresenter.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/TomographyROIViewQtWidget.cpp
delete mode 100644 MantidQt/CustomInterfaces/src/Tomography/ToolConfig.cpp
delete mode 100644 MantidQt/CustomInterfaces/test/ImggFormatsConvertPresenterTest.h
delete mode 100644 MantidQt/CustomInterfaces/test/ImggFormatsConvertViewMock.h
delete mode 100644 MantidQt/CustomInterfaces/test/StackOfImagesDirsTest.h
delete mode 100644 MantidQt/CustomInterfaces/test/TomographyIfaceModelTest.h
delete mode 100644 MantidQt/CustomInterfaces/test/TomographyIfacePresenterTest.h
delete mode 100644 MantidQt/CustomInterfaces/test/TomographyROIPresenterTest.h
delete mode 100644 MantidQt/CustomInterfaces/test/TomographyROIViewMock.h
delete mode 100644 MantidQt/CustomInterfaces/test/TomographyViewMock.h
delete mode 100644 docs/source/algorithms/ImggAggregateWavelengths-v1.rst
delete mode 100644 docs/source/algorithms/ImggTomographicReconstruction-v1.rst
delete mode 100644 docs/source/algorithms/LoadSavuTomoConfig-v1.rst
delete mode 100644 docs/source/algorithms/SCARFTomoReconstruction-v1.rst
delete mode 100644 docs/source/algorithms/SaveSavuTomoConfig-v1.rst
delete mode 100644 docs/source/interfaces/Tomographic_Reconstruction.rst
delete mode 100644 scripts/Imaging/IMAT/__init__.py
delete mode 100644 scripts/Imaging/IMAT/agg_energy_bands.py
delete mode 100644 scripts/Imaging/IMAT/prep/__init__.py
delete mode 100644 scripts/Imaging/IMAT/prep/energy_bands_aggregator.py
delete mode 100644 scripts/Imaging/IMAT/prep/filters.py
delete mode 100644 scripts/Imaging/IMAT/prep/filters_adv.py
delete mode 100644 scripts/Imaging/IMAT/tomo_reconstruct.py
delete mode 100644 scripts/Imaging/IMAT/tomorec/__init__.py
delete mode 100644 scripts/Imaging/IMAT/tomorec/configs.py
delete mode 100644 scripts/Imaging/IMAT/tomorec/io.py
delete mode 100644 scripts/Imaging/IMAT/tomorec/reconstruction_command.py
delete mode 100644 scripts/Imaging/IMAT/tomorec/tool_imports.py
diff --git a/Framework/Algorithms/CMakeLists.txt b/Framework/Algorithms/CMakeLists.txt
index a770b9938ec..6a30372e559 100644
--- a/Framework/Algorithms/CMakeLists.txt
+++ b/Framework/Algorithms/CMakeLists.txt
@@ -293,7 +293,6 @@ set ( SRC_FILES
src/TimeAtSampleStrategyDirect.cpp
src/TimeAtSampleStrategyElastic.cpp
src/TimeAtSampleStrategyIndirect.cpp
- src/Tomography/FBPTomopy.cpp
src/Transpose.cpp
src/UnGroupWorkspace.cpp
src/UnaryOperation.cpp
@@ -311,12 +310,6 @@ set ( SRC_FILES
src/XDataConverter.cpp
)
-# C as they originally come from a different project (tomopy)
-set ( C_SRC_FILES
- src/Tomography/tomopy/fbp.c
- src/Tomography/tomopy/utils.c
-)
-
set ( INC_FILES
inc/MantidAlgorithms/AbsorptionCorrection.h
inc/MantidAlgorithms/AddLogDerivative.h
@@ -619,9 +612,6 @@ set ( INC_FILES
inc/MantidAlgorithms/TimeAtSampleStrategyDirect.h
inc/MantidAlgorithms/TimeAtSampleStrategyElastic.h
inc/MantidAlgorithms/TimeAtSampleStrategyIndirect.h
- inc/MantidAlgorithms/Tomography/FBPTomopy.h
- inc/MantidAlgorithms/Tomography/tomopy/fbp.h
- inc/MantidAlgorithms/Tomography/tomopy/utils.h
inc/MantidAlgorithms/Transpose.h
inc/MantidAlgorithms/UnGroupWorkspace.h
inc/MantidAlgorithms/UnaryOperation.h
@@ -924,7 +914,6 @@ set ( TEST_FILES
TimeAtSampleStrategyDirectTest.h
TimeAtSampleStrategyElasticTest.h
TimeAtSampleStrategyIndirectTest.h
- Tomography/FBPTomopyTest.h
TransposeTest.h
UnGroupWorkspaceTest.h
UnaryOperationTest.h
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/Tomography/FBPTomopy.h b/Framework/Algorithms/inc/MantidAlgorithms/Tomography/FBPTomopy.h
deleted file mode 100644
index 0d295f82a82..00000000000
--- a/Framework/Algorithms/inc/MantidAlgorithms/Tomography/FBPTomopy.h
+++ /dev/null
@@ -1,45 +0,0 @@
-#ifndef MANTID_ALGORITHMS_TOMOGRAPHY_FBPTOMOPY_H_
-#define MANTID_ALGORITHMS_TOMOGRAPHY_FBPTOMOPY_H_
-
-#include "MantidAlgorithms/DllConfig.h"
-
-namespace Mantid {
-namespace Algorithms {
-namespace Tomography {
-
-/**
- Wrapper for C function(s) that implement tomopy reconstruction
- methods.
-
- Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
- National Laboratory & European Spallation Source
-
- This file is part of Mantid.
-
- Mantid is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- Mantid is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- File change history is stored at: <https://github.com/mantidproject/mantid>
- Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-
-/// FBP - Filtered Back-Projection routine as implemented in tomopy
-void MANTID_ALGORITHMS_DLL FBPTomopy(const float *data, int dy, int dt, int dx,
- const float *center, const float *theta,
- float *recon, int ngridx, int ngridy);
-
-} // namespace Tomography
-} // namespace Algorithms
-} // namespace Mantid
-
-#endif /* MANTID_ALGORITHMS_TOMOGRAPHY_FBPTOMOPY_H_ */
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/Tomography/tomopy/fbp.h b/Framework/Algorithms/inc/MantidAlgorithms/Tomography/tomopy/fbp.h
deleted file mode 100644
index ade127406da..00000000000
--- a/Framework/Algorithms/inc/MantidAlgorithms/Tomography/tomopy/fbp.h
+++ /dev/null
@@ -1,34 +0,0 @@
-/**
- fbp function from Tomopy - FBP reconstruction method
-
- Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
- National Laboratory & European Spallation Source
-
- This file is part of Mantid.
-
- Mantid is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- Mantid is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- File change history is stored at: <https://github.com/mantidproject/mantid>
- Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-#ifndef MANTID_ALGORITHMS_TOMOGRAPHY_TOMOPY_FBP_H_
-#define MANTID_ALGORITHMS_TOMOGRAPHY_TOMOPY_FBP_H_
-
-extern "C" {
-void fbp(const float *data, int dy, int dt, int dx, const float *center,
- const float *theta, float *recon, int ngridx, int ngridy,
- const char * /*fname*/, const float * /*filter_par*/);
-}
-
-#endif /* MANTID_ALGORITHMS_TOMOGRAPHY_TOMOPY_FBP_H_ */
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/Tomography/tomopy/utils.h b/Framework/Algorithms/inc/MantidAlgorithms/Tomography/tomopy/utils.h
deleted file mode 100644
index 607160a3be2..00000000000
--- a/Framework/Algorithms/inc/MantidAlgorithms/Tomography/tomopy/utils.h
+++ /dev/null
@@ -1,103 +0,0 @@
-/**
- Common functions for different reconstruction methods in Tomopy
-
- Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
- National Laboratory & European Spallation Source
-
- This file is part of Mantid.
-
- Mantid is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- Mantid is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http:www.gnu.org/licenses/>.
-
- File change history is stored at: <https:github.com/mantidproject/mantid>
- Code Documentation is available at: <http:doxygen.mantidproject.org>
-*/
-/**
- * This file is substantially modified but originally based on the
- * file utils.h from tomopy (available from
- * https:github.com/tomopy/tomopy/blob/master/src/utils.h) which is:
- */
-/*
- Copyright (c) 2015, UChicago Argonne, LLC. All rights reserved.
-
- Copyright 2015. UChicago Argonne, LLC. This software was produced
- under U.S. Government contract DE-AC02-06CH11357 for Argonne National
- Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
- U.S. Department of Energy. The U.S. Government has rights to use,
- reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR
- UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
- ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is
- modified to produce derivative works, such modified software should
- be clearly marked, so as not to confuse it with the version available
- from ANL.
-
- Additionally, redistribution and use in source and binary forms, with
- or without modification, are permitted provided that the following
- conditions are met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in
- the documentation and/or other materials provided with the
- distribution.
-
- * Neither the name of UChicago Argonne, LLC, Argonne National
- Laboratory, ANL, the U.S. Government, nor the names of its
- contributors may be used to endorse or promote products derived
- from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago
- Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGE.
-*/
-#ifndef MANTID_ALGORITHMS_TOMOGRAPHY_TOMOPY_UTILS_H_
-#define MANTID_ALGORITHMS_TOMOGRAPHY_TOMOPY_UTILS_H_
-
-void preprocessing(int ngridx, int ngridy, int dz, float center, float *mov,
- float *gridx, float *gridy);
-
-int calc_quadrant(float theta_p);
-
-void calc_coords(int ngridx, int ngridy, float xi, float yi, float sin_p,
- float cos_p, const float *gridx, const float *gridy,
- float *coordx, float *coordy);
-
-void trim_coords(int ngridx, int ngridy, const float *coordx,
- const float *coordy, const float *gridx, const float *gridy,
- int *asize, float *ax, float *ay, int *bsize, float *bx,
- float *by);
-
-void sort_intersections(int ind_condition, int asize, const float *ax,
- const float *ay, int bsize, const float *bx,
- const float *by, int *csize, float *coorx,
- float *coory);
-
-void calc_dist(int ngridx, int ngridy, int csize, const float *coorx,
- const float *coory, int *indi, float *dist);
-
-void calc_simdata(int s, int p, int d, int ngridx, int ngridy, int dt, int dx,
- int csize, const int *indi, const float *dist,
- const float *model, float *simdata);
-
-#endif /* MANTID_ALGORITHMS_TOMOGRAPHY_TOMOPY_UTILS_H_ */
diff --git a/Framework/Algorithms/src/ImggTomographicReconstruction.cpp b/Framework/Algorithms/src/ImggTomographicReconstruction.cpp
deleted file mode 100644
index 9f7657ae22a..00000000000
--- a/Framework/Algorithms/src/ImggTomographicReconstruction.cpp
+++ /dev/null
@@ -1,405 +0,0 @@
-#include "MantidAlgorithms/ImggTomographicReconstruction.h"
-#include "MantidAlgorithms/Tomography/FBPTomopy.h"
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/CommonBinsValidator.h"
-#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/HistogramValidator.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceUnitValidator.h"
-#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidDataObjects/Workspace2D.h"
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/CompositeValidator.h"
-#include "MantidKernel/ListValidator.h"
-#include "MantidKernel/make_unique.h"
-
-namespace Mantid {
-namespace Algorithms {
-
-// Register the algorithm into the AlgorithmFactory
-DECLARE_ALGORITHM(ImggTomographicReconstruction)
-
-namespace {
-// Just to have explicit double => float casts in std::copy/transform
-struct DoubleToFloatStd {
- float operator()(const double &dblValue) const {
- return static_cast<float>(dblValue);
- }
-};
-}
-
-//----------------------------------------------------------------------------------------------
-
-/// Algorithms name for identification. @see Algorithm::name
-const std::string ImggTomographicReconstruction::name() const {
- return "ImggTomographicReconstruction";
-}
-
-/// Algorithm's version for identification. @see Algorithm::version
-int ImggTomographicReconstruction::version() const { return 1; }
-
-/// Algorithm's category for identification. @see Algorithm::category
-const std::string ImggTomographicReconstruction::category() const {
- return "Diffraction\\Imaging;Diffraction\\Tomography";
-}
-
-/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
-const std::string ImggTomographicReconstruction::summary() const {
- return "Reconstruct a 3D volume from 2D imaging projection data";
-}
-
-namespace {
-const std::string PROP_INPUT_WS = "InputWorkspace";
-const std::string PROP_METHOD = "Method";
-const std::string PROP_OUTPUT_WS = "OutputWorkspace";
-const std::string PROP_COR = "CenterOfRotation";
-const std::string PROP_RELAXATION_PARAM = "RelaxationParameter";
-const std::string PROP_MAX_CORES = "MaximumCores";
-const std::string PROP_MIN_PROJ_ANGLE = "MinProjectionAngle";
-const std::string PROP_MAX_PROJ_ANGLE = "MaxProjectionAngle";
-}
-
-//----------------------------------------------------------------------------------------------
-/** Initialize the algorithm's properties.
- */
-void ImggTomographicReconstruction::init() {
-
- declareProperty(
- Kernel::make_unique<API::WorkspaceProperty<API::Workspace>>(
- PROP_INPUT_WS, "", Kernel::Direction::Input),
- "Group of workspace holding images (with one spectrum per pixel row).");
-
- std::vector<std::string> methods{"FBP (tomopy)"};
- declareProperty(
- PROP_METHOD, methods.front(),
- boost::make_shared<Kernel::ListValidator<std::string>>(methods),
- "Reconstruction method", Kernel::Direction::Input);
-
- declareProperty(
- Kernel::make_unique<API::WorkspaceProperty<API::WorkspaceGroup>>(
- PROP_OUTPUT_WS, "", Kernel::Direction::Output),
- "Output reconstructed volume, as a group of workspaces where "
- "each workspace holds one slice of the volume.");
-
- auto zeroOrPosInt = boost::make_shared<Kernel::BoundedValidator<int>>();
- zeroOrPosInt->setLower(-1);
- declareProperty(PROP_COR, -1, zeroOrPosInt,
- "Center of rotation for the reconstruction (in pixels).");
-
- auto zeroOrPosDbl = boost::make_shared<Kernel::BoundedValidator<double>>();
- zeroOrPosDbl->setLower(0.0);
- declareProperty(PROP_RELAXATION_PARAM, 0.5, zeroOrPosDbl,
- "Relaxation parameter for the reconstruction method.");
-
- zeroOrPosInt->setLower(0);
- declareProperty(PROP_MAX_CORES, 0, zeroOrPosInt,
- "Maximum number of cores to use for parallel runs. Leave "
- "empty to use all available cores.");
-
- declareProperty(PROP_MIN_PROJ_ANGLE, 0.0, zeroOrPosDbl,
- "Minimum projection angle.");
-
- declareProperty(PROP_MAX_PROJ_ANGLE, 180.0, zeroOrPosDbl,
- "Maximum projection angle (assuming a uniform angle increase "
- "from first to last projection.");
-}
-
-std::map<std::string, std::string>
-ImggTomographicReconstruction::validateInputs() {
- std::map<std::string, std::string> result;
-
- API::Workspace_const_sptr inWks = getProperty(PROP_INPUT_WS);
- API::WorkspaceGroup_const_sptr inGrp =
- boost::dynamic_pointer_cast<const API::WorkspaceGroup>(inWks);
- if (!inGrp) {
- result[PROP_INPUT_WS] = "The current version of this algorithm only "
- "supports input workspaces of type WorkspaceGroup";
- } else {
- if (inGrp->size() < 2) {
- result[PROP_INPUT_WS] = "The input workspace must have at least two "
- "workspaces (projection images)";
- }
-
- auto first = inGrp->getItem(0);
- auto fwks = boost::dynamic_pointer_cast<API::MatrixWorkspace>(first);
- if (!fwks) {
- result[PROP_INPUT_WS] =
- "Unable to get a matrix workspace from the first "
- "item of the input workspace group " +
- first->getTitle() +
- ". It must contain workspaces of type MatrixWorkspace";
- } else {
- int cor = getProperty(PROP_COR);
- size_t bsize = fwks->blocksize();
- if (cor < 0 || cor >= static_cast<int>(bsize)) {
- result[PROP_COR] =
- "The center of rotation must be between 0 and the "
- "number of columns in the input projection images (0 to " +
- std::to_string(bsize - 1) + ")";
- }
- }
- // Not validating requirements on all input workspaces here (there could be
- // many)
- }
-
- double minAngle = getProperty(PROP_MIN_PROJ_ANGLE);
- double maxAngle = getProperty(PROP_MAX_PROJ_ANGLE);
-
- if (minAngle >= maxAngle) {
- result[PROP_MIN_PROJ_ANGLE] = PROP_MIN_PROJ_ANGLE +
- " cannot be equal to or lower than " +
- PROP_MAX_PROJ_ANGLE;
- }
- return result;
-}
-
-//----------------------------------------------------------------------------------------------
-/** Execute the algorithm.
- */
-void ImggTomographicReconstruction::exec() {
- throw std::runtime_error(
- "This algorithm cannot be executed with a single workspace as input");
-}
-
-bool ImggTomographicReconstruction::processGroups() {
- API::Workspace_const_sptr inWks = getProperty("InputWorkspace");
-
- API::WorkspaceGroup_const_sptr wks =
- boost::dynamic_pointer_cast<const API::WorkspaceGroup>(inWks);
-
- if (!wks) {
- g_log.error(
- "Could not retrieve the input workspace as a workspace group: ");
- return false;
- }
-
- // TODO: apply validators here on every input image/workspace
- for (size_t idx = 0; idx < wks->size(); idx++) {
- auto item = wks->getItem(0);
- auto mWS = boost::dynamic_pointer_cast<API::MatrixWorkspace>(item);
- if (!mWS) {
- throw std::runtime_error("Unable to get a matrix workspace from the "
- "element of te workspace group with title " +
- item->getTitle());
- }
-
- auto wsValidator = boost::make_shared<Kernel::CompositeValidator>();
- wsValidator->add<API::CommonBinsValidator>();
- wsValidator->add<API::HistogramValidator>();
- // Probably we won't need this:
- // wsValidator->add<API::WorkspaceUnitValidator>("Label");
- const std::string validation = wsValidator->isValid(mWS);
- if (validation != "") {
- throw std::runtime_error(
- "Validation of input image / matrix workspace failed: " + validation);
- }
- }
-
- double minAngle = getProperty(PROP_MIN_PROJ_ANGLE);
- double maxAngle = getProperty(PROP_MAX_PROJ_ANGLE);
- auto angles = prepareProjectionAngles(wks, minAngle, maxAngle);
-
- // these values are expected as 'int' by the tompy routines
- const int ysize = static_cast<int>(ySizeProjections(wks));
- const int projSize = static_cast<int>(angles->size());
- const int xsize = static_cast<int>(xSizeProjections(wks));
- // total size of input data in voxels
- size_t totalInSize = ysize * projSize * xsize;
- // total size of the reconstructed volume
- size_t totalReconSize = ysize * ysize * xsize;
-
- auto inVol = prepareInputData(totalInSize, wks);
- auto reconVol = prepareDataVol(totalReconSize);
-
- int cor = getProperty(PROP_COR);
- auto centers = prepareCenters(cor, ysize);
-
- Mantid::Algorithms::Tomography::FBPTomopy(
- inVol->data(), ysize, projSize, xsize, centers->data(), angles->data(),
- reconVol->data(), xsize, ysize);
-
- size_t expectedVox = ysize * ysize * xsize;
- if (reconVol->size() != expectedVox) {
- std::stringstream stream;
- stream << std::string("The reconstructed volume data block does not "
- "have the expected dimensions. It has ")
- << reconVol->size() << " voxels, whereas I was expecting: " << ysize
- << " slices by " << ysize << " rows by " << xsize
- << " columns = " << expectedVox << " voxels in total";
- throw std::runtime_error(stream.str());
- }
-
- const auto outputGrp = buildOutputWks(*reconVol, xsize, ysize, ysize);
- setProperty(PROP_OUTPUT_WS, outputGrp);
-
- g_log.notice() << "Finished reconstruction of volume from workspace "
- << wks->getTitle() << " with " << projSize
- << " input projections, " << ysize << " rows by " << xsize
- << " columns.\n";
-
- return true;
-}
-
-std::unique_ptr<std::vector<float>>
-ImggTomographicReconstruction::prepareProjectionAngles(
- API::WorkspaceGroup_const_sptr wks, double minAngle,
- double maxAngle) const {
-
- auto projCount = wks->size();
- auto angles = Kernel::make_unique<std::vector<float>>(projCount);
-
- auto vec = *angles;
- if (vec.empty())
- return angles;
-
- double factor = (maxAngle - minAngle);
- vec[0] = static_cast<float>(minAngle);
- for (size_t idx = 1; idx < projCount; ++idx) {
- vec[idx] = static_cast<float>(minAngle +
- factor * static_cast<double>(idx) /
- static_cast<double>(projCount - 1));
- }
-
- return angles;
-}
-
-std::unique_ptr<std::vector<float>>
-ImggTomographicReconstruction::prepareInputData(
- size_t totalSize, API::WorkspaceGroup_const_sptr wksg) {
- auto data = prepareDataVol(totalSize);
-
- if (!wksg || 0 == wksg->size())
- return data;
-
- auto first = wksg->getItem(0);
- auto fwks = boost::dynamic_pointer_cast<API::MatrixWorkspace>(first);
- if (!fwks) {
- throw std::runtime_error(
- "Unable to get a matrix workspace from the first "
- "item of the input workspace group " +
- first->getTitle() +
- ". It must contain workspaces of type MatrixWorkspace");
- }
-
- size_t ysize = fwks->getNumberHistograms();
- size_t xsize = fwks->blocksize();
- const size_t oneSliceSize = xsize * ysize;
-
- PARALLEL_FOR_NO_WSP_CHECK()
- for (int slice = 0; slice < static_cast<int>(wksg->size()); ++slice) {
- size_t startSlice = slice * oneSliceSize;
- for (size_t row = 0; row < ysize; ++row) {
- const auto &dataY = fwks->getSpectrum(row).readY();
- size_t startRow = startSlice + row * ysize;
- // MSVC will produce C4244 warnings in <xutility> (double=>float
- // converstion)
- // std::copy(dataY.begin(), dataY.end(), data->begin() + startRow);
- std::transform(dataY.begin(), dataY.end(), data->begin() + startRow,
- DoubleToFloatStd());
- }
- }
-
- return data;
-}
-
-std::unique_ptr<std::vector<float>>
-ImggTomographicReconstruction::prepareDataVol(size_t totalSize) {
- return Kernel::make_unique<std::vector<float>>(totalSize);
-}
-
-std::unique_ptr<std::vector<float>>
-ImggTomographicReconstruction::prepareCenters(int cor, size_t totalSize) {
- auto centers = Kernel::make_unique<std::vector<float>>(totalSize);
-
- for (auto &cnt : *centers) {
- cnt = static_cast<float>(cor);
- }
-
- return centers;
-}
-
-size_t ImggTomographicReconstruction::xSizeProjections(
- API::WorkspaceGroup_const_sptr wks) const {
- auto first = wks->getItem(0);
-
- auto wksItem = boost::dynamic_pointer_cast<API::MatrixWorkspace>(first);
- if (!wksItem) {
- throw std::runtime_error("Unable to get a matrix workspace from the first "
- "item of the workspace group " +
- first->getTitle());
- }
-
- return wksItem->getNumberHistograms();
-}
-
-size_t ImggTomographicReconstruction::pSizeProjections(
- API::WorkspaceGroup_const_sptr wks) const {
- return wks->size();
-}
-
-size_t ImggTomographicReconstruction::ySizeProjections(
- API::WorkspaceGroup_const_sptr wks) const {
- auto first = wks->getItem(0);
-
- auto wksItem = boost::dynamic_pointer_cast<API::MatrixWorkspace>(first);
- if (!wksItem) {
- throw std::runtime_error("Unable to get a matrix workspace from the first "
- "item of the workspace group " +
- first->getTitle());
- }
-
- return wksItem->blocksize();
-}
-
-/**
- * Transfer data from a numpy/tomopy style data volume to a workspace
- * group of MatrixWorkspaces. This will typically have ysize slices
- * (images) of dimensions ysize rows by xsize columns.
-
- *
- * @param dataVol a 3D data volume that may have been generated as
- * output from a reconstruction
- * @param xsize image x dimension or number of columns (bins)
- * @param ysize image y dimension or number of rows (spectra)
- * @param sliceSize number of slices
- *
- * @return a workspace group with reconstruction slices
- */
-API::WorkspaceGroup_sptr
-ImggTomographicReconstruction::buildOutputWks(const std::vector<float> &dataVol,
- size_t xsize, size_t ysize,
- size_t sliceSize) {
-
- // auto wsGroup = boost::make_shared<API::WorkspaceGroup>();
- auto wsGroup = API::WorkspaceGroup_sptr(new API::WorkspaceGroup());
- wsGroup->setTitle("Reconstructed volume from imaging projection data");
-
- const size_t oneSliceSize = xsize * ysize;
- PARALLEL_FOR_NO_WSP_CHECK()
- for (int slice = 0; slice < static_cast<int>(sliceSize); ++slice) {
- // individual slices as Workspace2D/MatrixWorkspace
- DataObjects::Workspace2D_sptr sliceWS =
- boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
- API::WorkspaceFactory::Instance().create("Workspace2D", ysize,
- xsize + 1, xsize));
- size_t startSlice = slice * oneSliceSize;
- for (size_t row = 0; row < ysize; ++row) {
- auto &specRow = sliceWS->getSpectrum(row);
- auto &dataX = specRow.dataX();
- std::fill(dataX.begin(), dataX.end(), static_cast<double>(row));
-
- size_t startRow = startSlice + row * ysize;
- size_t endRow = startRow + xsize;
- auto &dataY = specRow.dataY();
- std::transform(dataVol.begin() + startRow, dataVol.begin() + endRow,
- dataY.begin(), DoubleToFloatStd());
- }
- wsGroup->addWorkspace(sliceWS);
- }
-
- return wsGroup;
-}
-
-} // namespace Algorithms
-} // namespace Mantid
diff --git a/Framework/Algorithms/src/Tomography/FBPTomopy.cpp b/Framework/Algorithms/src/Tomography/FBPTomopy.cpp
deleted file mode 100644
index 807ece8f292..00000000000
--- a/Framework/Algorithms/src/Tomography/FBPTomopy.cpp
+++ /dev/null
@@ -1,15 +0,0 @@
-#include "MantidAlgorithms/Tomography/FBPTomopy.h"
-#include "MantidAlgorithms/Tomography/tomopy/fbp.h"
-
-namespace Mantid {
-namespace Algorithms {
-namespace Tomography {
-
-void FBPTomopy(const float *data, int dy, int dt, int dx, const float *center,
- const float *theta, float *recon, int ngridx, int ngridy) {
- fbp(data, dy, dt, dx, center, theta, recon, ngridx, ngridy, nullptr, nullptr);
-}
-
-} // namespace Tomography
-} // namespace Algorithms
-} // namespace Mantid
diff --git a/Framework/Algorithms/src/Tomography/tomopy/fbp.c b/Framework/Algorithms/src/Tomography/tomopy/fbp.c
deleted file mode 100644
index b0451a11807..00000000000
--- a/Framework/Algorithms/src/Tomography/tomopy/fbp.c
+++ /dev/null
@@ -1,160 +0,0 @@
-/**
- This file is originally based on the implementation of the FBP (Filtered
- Back-Projection) method of tomopy, available from
- https:github.com/tomopy/tomopy/blob/master/src/fbp.c, which is:
- */
-/*
- Copyright (c) 2015, UChicago Argonne, LLC. All rights reserved.
-
- Copyright 2015. UChicago Argonne, LLC. This software was produced
- under U.S. Government contract DE-AC02-06CH11357 for Argonne National
- Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
- U.S. Department of Energy. The U.S. Government has rights to use,
- reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR
- UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
- ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is
- modified to produce derivative works, such modified software should
- be clearly marked, so as not to confuse it with the version available
- from ANL.
-
- Additionally, redistribution and use in source and binary forms, with
- or without modification, are permitted provided that the following
- conditions are met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in
- the documentation and/or other materials provided with the
- distribution.
-
- * Neither the name of UChicago Argonne, LLC, Argonne National
- Laboratory, ANL, the U.S. Government, nor the names of its
- contributors may be used to endorse or promote products derived
- from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago
- Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGE.
-*/
-
-#include "MantidAlgorithms/Tomography/tomopy/utils.h"
-
-#include <assert.h>
-#include <math.h>
-#include <stdlib.h>
-
-void fbp(const float *data, int dy, int dt, int dx, const float *center,
- const float *theta, float *recon, int ngridx, int ngridy,
- const char *fname, const float *filter_par) {
-
- int s, p, d, n;
- int quadrant;
- float theta_p, sin_p, cos_p;
- float mov, xi, yi;
- int asize, bsize, csize;
- int ind_data, ind_recon;
-
- float *gridx, *gridy, *coordx, *coordy, *ax, *ay, *bx, *by, *coorx, *coory,
- *dist;
- int *indi;
-
- gridx = (float *)malloc((size_t)(ngridx + 1) * sizeof(float));
- gridy = (float *)malloc((size_t)(ngridy + 1) * sizeof(float));
- coordx = (float *)malloc((size_t)(ngridy + 1) * sizeof(float));
- coordy = (float *)malloc((size_t)(ngridx + 1) * sizeof(float));
- ax = (float *)malloc((size_t)(ngridx + ngridy) * sizeof(float));
- ay = (float *)malloc((size_t)(ngridx + ngridy) * sizeof(float));
- bx = (float *)malloc((size_t)(ngridx + ngridy) * sizeof(float));
- by = (float *)malloc((size_t)(ngridx + ngridy) * sizeof(float));
- coorx = (float *)malloc((size_t)(ngridx + ngridy) * sizeof(float));
- coory = (float *)malloc((size_t)(ngridx + ngridy) * sizeof(float));
- dist = (float *)malloc((size_t)(ngridx + ngridy) * sizeof(float));
- indi = (int *)malloc((size_t)(ngridx + ngridy) * sizeof(int));
-
- /* unused arguments: */
- (void)fname;
- (void)filter_par;
-
- assert(coordx != NULL && coordy != NULL && ax != NULL && ay != NULL &&
- by != NULL && bx != NULL && coorx != NULL && coory != NULL &&
- dist != NULL && indi != NULL);
-
- /* For each slice */
- for (s = 0; s < dy; s++) {
- preprocessing(ngridx, ngridy, dx, center[s], &mov, gridx,
- gridy); /* Outputs: mov, gridx, gridy */
-
- /* For each projection angle */
- for (p = 0; p < dt; p++) {
- /*
- Calculate the sin and cos values
- of the projection angle and find
- at which quadrant on the cartesian grid.
- */
- theta_p = (float)fmod(theta[p], 2 * M_PI);
- quadrant = calc_quadrant(theta_p);
- sin_p = sinf(theta_p);
- cos_p = cosf(theta_p);
-
- /* For each detector pixel */
- for (d = 0; d < dx; d++) {
- /* Calculate coordinates */
- xi = (float)(-ngridx - ngridy);
- yi = (float)(1 - dx) / 2.0f + (float)d + mov;
- calc_coords(ngridx, ngridy, xi, yi, sin_p, cos_p, gridx, gridy, coordx,
- coordy);
-
- /* Merge the (coordx, gridy) and (gridx, coordy) */
- trim_coords(ngridx, ngridy, coordx, coordy, gridx, gridy, &asize, ax,
- ay, &bsize, bx, by);
-
- /*
- Sort the array of intersection points (ax, ay) and
- (bx, by). The new sorted intersection points are
- stored in (coorx, coory). Total number of points
- are csize.
- */
- sort_intersections(quadrant, asize, ax, ay, bsize, bx, by, &csize,
- coorx, coory);
-
- /*
- Calculate the distances (dist) between the
- intersection points (coorx, coory). Find the
- indices of the pixels on the reconstruction grid.
- */
- calc_dist(ngridx, ngridy, csize, coorx, coory, indi, dist);
-
- /* Update */
- ind_recon = s * ngridx * ngridy;
- ind_data = d + p * dx + s * dt * dx;
- for (n = 0; n < csize - 1; n++) {
- recon[indi[n] + ind_recon] += data[ind_data] * dist[n];
- }
- }
- }
- }
-
- free(gridx);
- free(gridy);
- free(coordx);
- free(coordy);
- free(ax);
- free(ay);
- free(bx);
- free(by);
- free(coorx);
- free(coory);
- free(dist);
- free(indi);
-}
diff --git a/Framework/Algorithms/src/Tomography/tomopy/utils.c b/Framework/Algorithms/src/Tomography/tomopy/utils.c
deleted file mode 100644
index 6b5248d5bac..00000000000
--- a/Framework/Algorithms/src/Tomography/tomopy/utils.c
+++ /dev/null
@@ -1,207 +0,0 @@
-/**
- This file is originally based on the implementation of the FBP (Filtered
- Back-Projection) method of tomopy, available from
- https:github.com/tomopy/tomopy/blob/master/src/fbp.c, which is:
- */
-/*
- Copyright (c) 2015, UChicago Argonne, LLC. All rights reserved.
-
- Copyright 2015. UChicago Argonne, LLC. This software was produced
- under U.S. Government contract DE-AC02-06CH11357 for Argonne National
- Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
- U.S. Department of Energy. The U.S. Government has rights to use,
- reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR
- UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
- ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is
- modified to produce derivative works, such modified software should
- be clearly marked, so as not to confuse it with the version available
- from ANL.
-
- Additionally, redistribution and use in source and binary forms, with
- or without modification, are permitted provided that the following
- conditions are met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in
- the documentation and/or other materials provided with the
- distribution.
-
- * Neither the name of UChicago Argonne, LLC, Argonne National
- Laboratory, ANL, the U.S. Government, nor the names of its
- contributors may be used to endorse or promote products derived
- from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago
- Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGE.
-*/
-
-#include "MantidAlgorithms/Tomography/tomopy/utils.h"
-
-#include <math.h>
-
-void preprocessing(int ry, int rz, int num_pixels, float center, float *mov,
- float *gridx, float *gridy) {
- int i;
-
- for (i = 0; i <= ry; i++) {
- gridx[i] = ((float)-ry / 2.f + (float)i);
- }
-
- for (i = 0; i <= rz; i++) {
- gridy[i] = ((float)-rz / 2.f + (float)i);
- }
-
- *mov = ((float)num_pixels - 1) / 2.0f - center;
- if (*mov - floor(*mov) < 0.01f) {
- *mov += 0.01f;
- }
- *mov += 0.5f;
-}
-
-int calc_quadrant(float theta_p) {
- int quadrant;
- if ((theta_p >= 0 && theta_p < M_PI / 2) ||
- (theta_p >= M_PI && theta_p < 3 * M_PI / 2) ||
- (theta_p >= -M_PI && theta_p < -M_PI / 2) ||
- (theta_p >= -2 * M_PI && theta_p < -3 * M_PI / 2)) {
- quadrant = 1;
- } else {
- quadrant = 0;
- }
- return quadrant;
-}
-
-void calc_coords(int ry, int rz, float xi, float yi, float sin_p, float cos_p,
- const float *gridx, const float *gridy, float *coordx,
- float *coordy) {
- float srcx, srcy, detx, dety;
- float slope, islope;
- int n;
-
- srcx = xi * cos_p - yi * sin_p;
- srcy = xi * sin_p + yi * cos_p;
- detx = -xi * cos_p - yi * sin_p;
- dety = -xi * sin_p + yi * cos_p;
-
- slope = (srcy - dety) / (srcx - detx);
- islope = 1 / slope;
- for (n = 0; n <= ry; n++) {
- coordy[n] = slope * (gridx[n] - srcx) + srcy;
- }
- for (n = 0; n <= rz; n++) {
- coordx[n] = islope * (gridy[n] - srcy) + srcx;
- }
-}
-
-void trim_coords(int ry, int rz, const float *coordx, const float *coordy,
- const float *gridx, const float *gridy, int *asize, float *ax,
- float *ay, int *bsize, float *bx, float *by) {
- int n;
-
- *asize = 0;
- *bsize = 0;
- for (n = 0; n <= rz; n++) {
- if (coordx[n] >= gridx[0] + 1e-2) {
- if (coordx[n] <= gridx[ry] - 1e-2) {
- ax[*asize] = coordx[n];
- ay[*asize] = gridy[n];
- (*asize)++;
- }
- }
- }
- for (n = 0; n <= ry; n++) {
- if (coordy[n] >= gridy[0] + 1e-2) {
- if (coordy[n] <= gridy[rz] - 1e-2) {
- bx[*bsize] = gridx[n];
- by[*bsize] = coordy[n];
- (*bsize)++;
- }
- }
- }
-}
-
-void sort_intersections(int ind_condition, int asize, const float *ax,
- const float *ay, int bsize, const float *bx,
- const float *by, int *csize, float *coorx,
- float *coory) {
- int i = 0, j = 0, k = 0;
- int a_ind;
- while (i < asize && j < bsize) {
- a_ind = (ind_condition) ? i : (asize - 1 - i);
- if (ax[a_ind] < bx[j]) {
- coorx[k] = ax[a_ind];
- coory[k] = ay[a_ind];
- i++;
- k++;
- } else {
- coorx[k] = bx[j];
- coory[k] = by[j];
- j++;
- k++;
- }
- }
- while (i < asize) {
- a_ind = (ind_condition) ? i : (asize - 1 - i);
- coorx[k] = ax[a_ind];
- coory[k] = ay[a_ind];
- i++;
- k++;
- }
- while (j < bsize) {
- coorx[k] = bx[j];
- coory[k] = by[j];
- j++;
- k++;
- }
- *csize = asize + bsize;
-}
-
-void calc_dist(int ry, int rz, int csize, const float *coorx,
- const float *coory, int *indi, float *dist) {
- int n;
-
- for (n = 0; n < csize - 1; n++) {
- int i1, i2;
- float x1, x2;
- float diffx, diffy, midx, midy;
- int indx, indy;
-
- diffx = coorx[n + 1] - coorx[n];
- diffy = coory[n + 1] - coory[n];
- dist[n] = (float)sqrt(diffx * diffx + diffy * diffy);
- midx = (coorx[n + 1] + coorx[n]) / 2;
- midy = (coory[n + 1] + coory[n]) / 2;
- x1 = midx + (float)ry / 2.f;
- x2 = midy + (float)rz / 2.f;
- i1 = (int)(midx + ry / 2.);
- i2 = (int)(midy + rz / 2.);
- indx = i1 - (i1 > x1);
- indy = i2 - (i2 > x2);
- indi[n] = indy + (indx * rz);
- }
-}
-
-void calc_simdata(int s, int p, int d, int ry, int rz, int dt, int dx,
- int csize, const int *indi, const float *dist,
- const float *model, float *simdata) {
- int n;
-
- int index_model = s * ry * rz;
- int index_data = d + p * dx + s * dt * dx;
- for (n = 0; n < csize - 1; n++) {
- simdata[index_data] += model[indi[n] + index_model] * dist[n];
- }
-}
diff --git a/Framework/Algorithms/test/Tomography/FBPTomopyTest.h b/Framework/Algorithms/test/Tomography/FBPTomopyTest.h
deleted file mode 100644
index 091844e6134..00000000000
--- a/Framework/Algorithms/test/Tomography/FBPTomopyTest.h
+++ /dev/null
@@ -1,114 +0,0 @@
-#ifndef MANTID_ALGORITHMS_FBPTOMOPYTEST_H_
-#define MANTID_ALGORITHMS_FBPTOMOPYTEST_H_
-
-#include <cxxtest/TestSuite.h>
-
-#include "MantidAlgorithms/Tomography/FBPTomopy.h"
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidKernel/Exception.h"
-
-#include "MantidTestHelpers/WorkspaceCreationHelper.h"
-
-#include <numeric>
-
-using namespace Mantid::Algorithms::Tomography;
-
-class FBPTomopyTest : public CxxTest::TestSuite {
-
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static FBPTomopyTest *createSuite() { return new FBPTomopyTest(); }
-
- static void destroySuite(FBPTomopyTest *suite) { delete suite; }
-
- void test_null() {
- FBPTomopy(nullptr, 0, 0, 0, nullptr, nullptr, nullptr, 0, 0);
- }
-
- void test_small_buffer_flat() {
- const size_t numProj = 3;
- const size_t ysize = 8;
- const size_t xsize = 8;
- const size_t projSize = numProj * ysize * xsize;
- std::array<float, projSize> projImages;
- std::fill(projImages.begin(), projImages.end(), 33.0f);
-
- const size_t reconSize = ysize * ysize * xsize;
- std::array<float, reconSize> reconVol;
- std::fill(reconVol.begin(), reconVol.end(), 0.0f);
-
- const size_t numAngles = numProj;
- std::array<float, numAngles> angles{{0.0, 90.0, 180.0}};
-
- const size_t numCenters = ysize;
- std::array<float, numCenters> centers{{4, 3, 3, 4, 4, 4, 4, 3}};
-
- FBPTomopy(projImages.data(), ysize, numProj, xsize, centers.data(),
- angles.data(), reconVol.data(), xsize, ysize);
-
- TS_ASSERT_DELTA(reconVol.front(), 66.7519, 1);
- TS_ASSERT_DELTA(reconVol[1], 67.9431, 1);
- TS_ASSERT_DELTA(reconVol[2], 90.9802, 1);
- TS_ASSERT_DELTA(reconVol[3], 111.1035, 1);
- TS_ASSERT_DELTA(reconVol[4], 88.6847, 1);
- TS_ASSERT_DELTA(reconVol[20], 102.3709, 1);
- TS_ASSERT_DELTA(reconVol[50], 97.4173, 1);
- TS_ASSERT_DELTA(reconVol[100], 97.4172, 1);
- TS_ASSERT_DELTA(reconVol[150], 99.8273, 1);
- TS_ASSERT_DELTA(reconVol[projSize - 5], 82.4248, 1);
- TS_ASSERT_DELTA(reconVol[projSize - 4], 74.1906, 1);
- TS_ASSERT_DELTA(reconVol[projSize - 3], 60.5043, 1);
- TS_ASSERT_DELTA(reconVol[projSize - 2], 67.9431, 1);
- TS_ASSERT_DELTA(reconVol.back(), 66.7519, 1);
- }
-
- void test_buffer_idx() {
- const size_t numProj = 8;
- const size_t ysize = 16;
- const size_t xsize = 16;
- const size_t projSize = numProj * ysize * xsize;
- std::array<float, projSize> projImages;
- std::iota(projImages.begin(), projImages.end(), 0.0f);
-
- // inconsistent/stressing values
- std::fill(projImages.begin() + 300, projImages.begin() + 400, 333.0f);
- std::fill(projImages.begin() + 600, projImages.begin() + 850, 999.0f);
- std::fill(projImages.begin() + 990, projImages.begin() + 1100, 1000.0f);
- std::fill(projImages.begin() + 1500, projImages.begin() + 1700, -444.0f);
- std::fill(projImages.begin() + 1900, projImages.begin() + 2000, 765.0f);
-
- const size_t reconSize = ysize * ysize * xsize;
- std::array<float, reconSize> reconVol;
- std::fill(reconVol.begin(), reconVol.end(), 0.0f);
-
- const size_t numAngles = numProj;
- std::array<float, numAngles> angles{
- {0.0, 45.0, 90.0, 135.0, 180.0, 225.0, 270.0, 315.0}};
-
- const size_t numCenters = ysize;
- std::array<float, numCenters> centers;
- std::fill(centers.begin(), centers.end(), 7.5f);
-
- FBPTomopy(projImages.data(), ysize, numProj, xsize, centers.data(),
- angles.data(), reconVol.data(), xsize, ysize);
-
- TS_ASSERT_DELTA(reconVol.front(), 241.6610, 1);
- TS_ASSERT_DELTA(reconVol[1], 286.6727, 1);
- TS_ASSERT_DELTA(reconVol[2], 392.6853, 1);
- TS_ASSERT_DELTA(reconVol[3], 350.0282, 1);
- TS_ASSERT_DELTA(reconVol[4], 429.8395, 1);
- TS_ASSERT_DELTA(reconVol[200], 516.5272, 1);
- TS_ASSERT_DELTA(reconVol[500], 1202.6435, 1);
- TS_ASSERT_DELTA(reconVol[1000], 3604.5090, 1);
- TS_ASSERT_DELTA(reconVol[1500], 8092.9765, 1);
- TS_ASSERT_DELTA(reconVol[1900], 7941.9135, 1);
- TS_ASSERT_DELTA(reconVol[projSize - 5], 6829.1318, 1);
- TS_ASSERT_DELTA(reconVol[projSize - 4], 5662.6342, 1);
- TS_ASSERT_DELTA(reconVol[projSize - 3], 5747.1845, 1);
- TS_ASSERT_DELTA(reconVol[projSize - 2], 6034.2163, 1);
- TS_ASSERT_DELTA(reconVol.back(), 3736.5483, 1);
- }
-};
-
-#endif /* MANTID_ALGORITHM_FBPTOMOPYTEST_H_ */
diff --git a/Framework/DataHandling/CMakeLists.txt b/Framework/DataHandling/CMakeLists.txt
index 5c2c065eb7e..c6ee3ac5eb9 100644
--- a/Framework/DataHandling/CMakeLists.txt
+++ b/Framework/DataHandling/CMakeLists.txt
@@ -101,7 +101,6 @@ set ( SRC_FILES
src/LoadSPE.cpp
src/LoadSampleDetailsFromRaw.cpp
src/LoadSassena.cpp
- src/LoadSavuTomoConfig.cpp
src/LoadSpec.cpp
src/LoadSpice2D.cpp
src/LoadSpiceAscii.cpp
@@ -271,7 +270,6 @@ set ( INC_FILES
inc/MantidDataHandling/LoadSPE.h
inc/MantidDataHandling/LoadSampleDetailsFromRaw.h
inc/MantidDataHandling/LoadSassena.h
- inc/MantidDataHandling/LoadSavuTomoConfig.h
inc/MantidDataHandling/LoadSpec.h
inc/MantidDataHandling/LoadSpice2D.h
inc/MantidDataHandling/LoadSpiceAscii.h
@@ -440,7 +438,6 @@ set ( TEST_FILES
LoadSampleDetailsFromRawTest.h
LoadSassenaTest.h
LoadSaveAsciiTest.h
- LoadSavuTomoConfigTest.h
LoadSpice2dTest.h
LoadSpiceAsciiTest.h
LoadSpiceXML2DDetTest.h
diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadSavuTomoConfig.h b/Framework/DataHandling/inc/MantidDataHandling/LoadSavuTomoConfig.h
deleted file mode 100644
index 9e9e34655d7..00000000000
--- a/Framework/DataHandling/inc/MantidDataHandling/LoadSavuTomoConfig.h
+++ /dev/null
@@ -1,75 +0,0 @@
-#ifndef MANTID_DATAHANDLING_LOADSAVUTOMOCONFIG_H_
-#define MANTID_DATAHANDLING_LOADSAVUTOMOCONFIG_H_
-
-#include "MantidAPI/Algorithm.h"
-#include "MantidAPI/ITableWorkspace_fwd.h"
-
-namespace NeXus {
-class File;
-}
-
-namespace Mantid {
-namespace DataHandling {
-
-/**
- LoadSavuTomoConfig : Load a tomographic reconstruction parameters
- file (as used in the savu tomography reconstructin pipeline) into a
- TableWorkspace
-
- Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
- National Laboratory & European Spallation Source
-
- This file is part of Mantid.
-
- Mantid is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- Mantid is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- File change history is stored at: <https://github.com/mantidproject/mantid>
- Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class DLLExport LoadSavuTomoConfig : public API::Algorithm {
-public:
- /// Algorithm's name for identification overriding a virtual method
- const std::string name() const override { return "LoadSavuTomoConfig"; }
- /// Summary of algorithms purpose
- const std::string summary() const override {
- return "Load configuration parameters from a tomographic "
- "reconstruction parameter file.";
- }
-
- /// Algorithm's version for identification overriding a virtual method
- int version() const override { return 1; }
-
- /// Algorithm's category for identification overriding a virtual method
- const std::string category() const override {
- return "DataHandling\\Imaging";
- }
-
-private:
- /// Implement abstract Algorithm methods
- void init() override;
- /// Implement abstract Algorithm methods
- void exec() override;
-
- // do the real loading
- Mantid::API::ITableWorkspace_sptr loadFile(std::string &fname,
- std::string &wsName);
-
- // open file safely and carefully checking potential issues
- bool checkOpenFile(std::string fname, boost::shared_ptr<NeXus::File> &f);
-};
-
-} // namespace DataHandling
-} // namespace Mantid
-
-#endif /* MANTID_DATAHANDLING_LOADSAVUTOMOCONFIG_H_ */
diff --git a/Framework/DataHandling/src/ImggAggregateWavelengths.cpp b/Framework/DataHandling/src/ImggAggregateWavelengths.cpp
deleted file mode 100644
index 63273b693ec..00000000000
--- a/Framework/DataHandling/src/ImggAggregateWavelengths.cpp
+++ /dev/null
@@ -1,906 +0,0 @@
-#include "MantidDataHandling/ImggAggregateWavelengths.h"
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidKernel/BoundedValidator.h"
-#include "MantidKernel/ListValidator.h"
-#include "MantidKernel/make_unique.h"
-#include "MantidKernel/MandatoryValidator.h"
-#include "MantidKernel/StringTokenizer.h"
-
-#include <fstream>
-#include <iomanip>
-
-#include <Poco/File.h>
-#include <Poco/DirectoryIterator.h>
-#include <Poco/Path.h>
-
-namespace Mantid {
-namespace DataHandling {
-
-const std::string ImggAggregateWavelengths::outPrefixProjections =
- "sum_projection_";
-const std::string ImggAggregateWavelengths::outPrefixBands = "bands_";
-const std::string ImggAggregateWavelengths::indexRangesPrefix = "idx_";
-const std::string ImggAggregateWavelengths::tofRangesPrefix = "tof_";
-const std::string ImggAggregateWavelengths::outSubdirsPrefixUniformBands =
- "bands_uniform_";
-const std::string ImggAggregateWavelengths::outSubdirsPrefixIndexBands =
- "bands_by_index_";
-const std::string ImggAggregateWavelengths::outSubdirsPrefixToFBands =
- "bands_by_tof_";
-
-using Mantid::Kernel::Direction;
-using Mantid::API::WorkspaceProperty;
-
-// Register the algorithm into the AlgorithmFactory
-DECLARE_ALGORITHM(ImggAggregateWavelengths)
-
-//----------------------------------------------------------------------------------------------
-
-/// Algorithms name for identification. @see Algorithm::name
-const std::string ImggAggregateWavelengths::name() const {
- return "ImggAggregateWavelengths";
-}
-
-/// Algorithm's version for identification. @see Algorithm::version
-int ImggAggregateWavelengths::version() const { return 1; }
-
-/// Algorithm's category for identification. @see Algorithm::category
-const std::string ImggAggregateWavelengths::category() const {
- return "DataHandling\\Imaging";
-}
-
-/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
-const std::string ImggAggregateWavelengths::summary() const {
- return "Aggregates images from multiple energy bands or wavelengths";
-}
-
-namespace {
-const std::string PROP_INPUT_PATH = "InputPath";
-const std::string PROP_OUTPUT_PATH = "OutputPath";
-const std::string PROP_UNIFORM_BANDS = "UniformBands";
-const std::string PROP_INDEX_RANGES = "IndexRanges";
-const std::string PROP_TOF_RANGES = "ToFRanges";
-const std::string PROP_NUM_PROJECTIONS_PROCESSED = "NumProjections";
-const std::string PROP_NUM_BANDS_PROCESSED = "NumBands";
-const std::string PROP_OUTPUT_PREFIX_PROJECTIONS = "OutputProjectionsPrefix";
-const std::string PROP_OUTPUT_PREFIX_BANDS = "OutputBandPrefix";
-const std::string PROP_OUTPUT_SUBDIRS_PREFIX_UNIFORM_BANDS =
- "OutputSubdirsPrefixUniformBands";
-const std::string PROP_OUTPUT_SUBDIRS_PREFIX_INDEX_BANDS =
- "OutputSubdirsPrefixIndexBands";
-const std::string PROP_OUTPUT_SUBDIRS_PREFIX_TOF_BANDS =
- "OutputSubdirsPrefixToFBands";
-const std::string PROP_INPUT_IMAGE_FORMAT = "InputImageFormat";
-const std::string PROP_OUTPUT_IMAGE_FORMAT = "OutputImageFormat";
-const std::string PROP_OUTPUT_BIT_DEPTH = "OutputBitDepth";
-
-// just to compare two Poco::Path objects, used for std algorithms
-struct PocoPathComp
- : public std::binary_function<Poco::Path, Poco::Path, bool> {
- bool operator()(const Poco::Path &lhs, const Poco::Path &rhs) const {
- return lhs.toString() < rhs.toString();
- }
-};
-}
-
-//----------------------------------------------------------------------------------------------
-/** Initialize the algorithm's properties.
- */
-void ImggAggregateWavelengths::init() {
- declareProperty(Mantid::Kernel::make_unique<API::FileProperty>(
- PROP_INPUT_PATH, "", API::FileProperty::Directory),
- "The path (directory) to the input image files. It must "
- "contain image files (radiography) or subdirectories "
- "containing image files (radiography, one directory per "
- "projection angle)");
-
- declareProperty(
- Kernel::make_unique<API::FileProperty>(PROP_OUTPUT_PATH, "",
- API::FileProperty::Directory),
- "The path (directory) where to generate the output image(s).");
-
- auto positive = boost::make_shared<Kernel::BoundedValidator<int>>();
- positive->setLower(0);
- declareProperty(
- PROP_UNIFORM_BANDS, 1, positive,
- "The number of output bands. The input bands are divided into uniform "
- "non-overlapping blocks and each of the output bands correspond to one "
- "block. This is a convenience particular case of the property " +
- PROP_INDEX_RANGES,
- Direction::Input);
-
- declareProperty(
- PROP_INDEX_RANGES, "",
- "A comma separated list of ranges of indices, where the "
- "indices refer to the input images, counting from 1. For "
- "example: 1-100, 101-200, 201-300. The number of ranges "
- "given will set the number of output bands. If you just need a "
- "certain"
- "number of bands split uniformly you can alternatively use "
- "the simple property " +
- PROP_UNIFORM_BANDS);
-
- // TODO: for later, when we have the required headers to do this
- declareProperty(
- PROP_TOF_RANGES, "",
- "A comma separated list of time-of-flight ranges given as for example "
- "5000-10000. These will be the boundaries in ToF that delimit the output "
- "bands. The units are as specified in the input images headers or "
- "metainformation (normally units of microseconds). The algorithm will "
- "produce as many output bands as ranges are "
- "given in this property. The ranges can overlap");
-
- declareProperty(PROP_NUM_PROJECTIONS_PROCESSED, 0,
- "The number of projections (subdirectories with images) "
- "found in the input path and successfully processed",
- Direction::Output);
-
- declareProperty(PROP_NUM_BANDS_PROCESSED, 0,
- "The number of wavelength or energy bands found in the "
- "inputs and successfully processed (aggregated) into the "
- "output(s)",
- Direction::Output);
-
- const std::string grpPrefixes = "Naming (prefixes for the outputs)";
- declareProperty(
- PROP_OUTPUT_PREFIX_PROJECTIONS, outPrefixProjections,
- Kernel::make_unique<Kernel::MandatoryValidator<std::string>>(),
- "This prefix is added in the output file names to precede the projection "
- "sequence number (or angle, or simply the input directory index). The "
- "names of the output files then look like: " +
- outPrefixProjections + outPrefixBands + indexRangesPrefix + "1_1200" +
- ", as in addition to this prefix, another prefix is added with the "
- "indices of the input images included (see option " +
- PROP_OUTPUT_PREFIX_BANDS,
- Direction::Input);
-
- declareProperty(
- PROP_OUTPUT_PREFIX_BANDS, outPrefixBands,
- Kernel::make_unique<Kernel::MandatoryValidator<std::string>>(),
- "This prefix is used for the output file names in addition to the prefix "
- "that specifies the projection or input "
- "directory sequence number, (" +
- PROP_OUTPUT_PREFIX_PROJECTIONS +
- "). "
- "The output bands will be written into subdirectories with names "
- "where the prefix is prepended. In addition to this prefix, a second "
- "prefix that specifies whether the input bands were aggregated by "
- "indices or by time of flight is also appended. For example when "
- "running this algorithm using the property " +
- PROP_UNIFORM_BANDS + " or " + PROP_INDEX_RANGES +
- " the output subdirectoy names will look like '" +
- outPrefixProjections + outPrefixBands + indexRangesPrefix +
- "1_1200' (where the 1 and 1200 derive from the "
- "division into uniform non-overlaping blocks of "
- "input bands, or the index ranges given. When "
- "running the algorithm using the property " +
- PROP_TOF_RANGES + " the output names will look like '" +
- outPrefixBands + tofRangesPrefix +
- "10000_50000' (where the 10000 and 50000 are the time of flight "
- "boundaries of the output band, using the same units as in the image "
- "headers).",
- Direction::Input);
-
- declareProperty(PROP_OUTPUT_SUBDIRS_PREFIX_UNIFORM_BANDS,
- outSubdirsPrefixUniformBands,
- "This prefix will be "
- "used for the name of the output subdirectories of every "
- "output band when producing uniform output bands (property " +
- PROP_UNIFORM_BANDS + ")",
- Direction::Input);
-
- declareProperty(
- PROP_OUTPUT_SUBDIRS_PREFIX_INDEX_BANDS, outSubdirsPrefixIndexBands,
- "This prefix will be "
- "used for the name of the output subdirectories of every "
- "output band when producing output bands using index ranges (property " +
- PROP_INDEX_RANGES + ")",
- Direction::Input);
-
- declareProperty(
- PROP_OUTPUT_SUBDIRS_PREFIX_TOF_BANDS, outSubdirsPrefixToFBands,
- "This prefix will be "
- "used for the name of the output subdirectories of every "
- "output band when producing output bands using ToF ranges (property " +
- PROP_TOF_RANGES + ")",
- Direction::Input);
-
- setPropertyGroup(PROP_OUTPUT_PREFIX_PROJECTIONS, grpPrefixes);
- setPropertyGroup(PROP_OUTPUT_PREFIX_BANDS, grpPrefixes);
- setPropertyGroup(PROP_OUTPUT_SUBDIRS_PREFIX_UNIFORM_BANDS, grpPrefixes);
- setPropertyGroup(PROP_OUTPUT_SUBDIRS_PREFIX_INDEX_BANDS, grpPrefixes);
- setPropertyGroup(PROP_OUTPUT_SUBDIRS_PREFIX_TOF_BANDS, grpPrefixes);
-
- const std::string grpImgFormat = "Image format";
-
- std::vector<std::string> imgFormat{"FITS"};
- declareProperty(
- PROP_INPUT_IMAGE_FORMAT, "FITS", "From the input directory(ies) use "
- "images in this format and ignore any "
- "other files",
- boost::make_shared<Mantid::Kernel::StringListValidator>(imgFormat),
- Direction::Input);
-
- declareProperty(
- PROP_OUTPUT_IMAGE_FORMAT, "FITS", "Produce output images in this format",
- boost::make_shared<Mantid::Kernel::StringListValidator>(imgFormat),
- Direction::Input);
-
- const std::vector<int> bitDepths{16};
- declareProperty(PROP_OUTPUT_BIT_DEPTH, 16,
- boost::make_shared<Kernel::ListValidator<int>>(bitDepths),
- "The bit depth or number of bits per pixel to use for the "
- "output image(s). Only 16 bits is supported at the "
- "moment.",
- Direction::Input);
-
- setPropertyGroup(PROP_INPUT_IMAGE_FORMAT, grpImgFormat);
- setPropertyGroup(PROP_OUTPUT_IMAGE_FORMAT, grpImgFormat);
- setPropertyGroup(PROP_OUTPUT_BIT_DEPTH, grpImgFormat);
-}
-
-std::map<std::string, std::string> ImggAggregateWavelengths::validateInputs() {
- std::map<std::string, std::string> result;
-
- size_t optCount = 0;
- const int uniformBands = getProperty(PROP_UNIFORM_BANDS);
- if (uniformBands > 0)
- optCount++;
- const std::string indexRanges = getPropertyValue(PROP_INDEX_RANGES);
- if (!indexRanges.empty())
- optCount++;
- const std::string tofRanges = getPropertyValue(PROP_TOF_RANGES);
- if (!tofRanges.empty())
- optCount++;
-
- // Prevent for now. When we enable this option, remove this if
- if (!tofRanges.empty())
- result[PROP_TOF_RANGES] =
- "This property is not supported in this version of the algorithm";
-
- if (1 != optCount) {
- result[PROP_UNIFORM_BANDS] = "One and only one of the options " +
- PROP_UNIFORM_BANDS + ", " + PROP_INDEX_RANGES +
- ", " + PROP_TOF_RANGES + " has to be set.";
- }
-
- const std::string inputPath = getPropertyValue(PROP_INPUT_PATH);
- const std::string outputPath = getPropertyValue(PROP_OUTPUT_PATH);
- if (inputPath == outputPath)
- result[PROP_INPUT_PATH] = "The input and output paths should be different.";
-
- return result;
-}
-
-//----------------------------------------------------------------------------------------------
-/** Execute the algorithm.
- */
-void ImggAggregateWavelengths::exec() {
- const std::string inputPath = getPropertyValue(PROP_INPUT_PATH);
- const std::string outputPath = getPropertyValue(PROP_OUTPUT_PATH);
- const std::string indexRanges = getPropertyValue(PROP_INDEX_RANGES);
- const std::string tofRanges = getPropertyValue(PROP_TOF_RANGES);
- const int uniformBands = getProperty(PROP_UNIFORM_BANDS);
-
- if (uniformBands > 0)
- aggUniformBands(inputPath, outputPath, uniformBands);
- else if (!indexRanges.empty())
- aggIndexBands(inputPath, outputPath, indexRanges);
- else if (!tofRanges.empty())
- aggToFBands(inputPath, outputPath, tofRanges);
-
- g_log.notice() << "Saved output aggregated images into: " << outputPath
- << ". They are now ready for further processing. \n";
-}
-
-void ImggAggregateWavelengths::aggUniformBands(const std::string &inputPath,
- const std::string &outputPath,
- size_t bands) {
-
- Poco::Path path(inputPath);
- auto inputSubDirs = findInputSubdirs(path);
-
- if (inputSubDirs.empty()) {
- g_log.warning() << "Could not find any input files or directories in "
- << inputPath
- << " when trying to split the input bands into a uniform "
- "number of output bands. Nothing will be produced in "
- "the output path.\n";
- }
-
- auto outputSubdirs =
- buildOutputSubdirNamesFromUniformBands(inputSubDirs, bands);
-
- size_t count = 0;
- for (const auto &subdir : inputSubDirs) {
- processDirectory(subdir, bands, outputPath, outputSubdirs, outPrefixBands,
- count++);
- }
- setProperty(PROP_NUM_PROJECTIONS_PROCESSED, static_cast<int>(count));
-}
-
-void ImggAggregateWavelengths::aggIndexBands(const std::string &inputPath,
- const std::string &outputPath,
- const std::string &rangesSpec) {
-
- Poco::Path path(inputPath);
- auto inputSubDirs = findInputSubdirs(path);
-
- if (inputSubDirs.empty()) {
- g_log.warning() << "Could not find any input files or directories in "
- << inputPath << " when looking for input bands. Nothing "
- "will be produced in the output path.\n";
- }
-
- auto outRanges = rangesFromStringProperty(rangesSpec, PROP_INDEX_RANGES);
-
- auto outputSubdirs = buildOutputSubdirNamesFromIndexRangesBands(outRanges);
-
- size_t count = 0;
- for (const auto &subdir : inputSubDirs) {
- processDirectory(subdir, outRanges, outputPath, outputSubdirs,
- outPrefixBands, count++);
- }
- setProperty(PROP_NUM_PROJECTIONS_PROCESSED, static_cast<int>(count));
-}
-
-void ImggAggregateWavelengths::aggToFBands(const std::string & /*inputPath*/,
- const std::string & /*outputPath*/,
- const std::string & /*ranges*/) {
-
- throw std::runtime_error("The property " + PROP_TOF_RANGES +
- "is not supported at the moment");
-}
-
-/**
- * Aggregate the images found in an input directory (can be all the
- * images from a radiography experiment, or all the images
- * corresponding to a single projection angle from a tomography
- * experiment). This is the version that processed the "UniformBands"
- * property, splitting the input images into uniform bands or blocks
- * (as many as given in the property).
- *
- * @param inDir where to find the input images.
- *
- * @param bands number of output bands, or number of bands into
- * which the input bands should be aggregated, non-overlapping and
- * uniformly distributed.
- *
- * @param outDir where to write the output image(s).
- *
- * @param outSubdirs subdirectories for every output range (given in the
- * input parameter rages)
- *
- * @param prefix prefix for the image names. The indices will be
- * appended to the prefix
- *
- * @param outImgIndex index of the directory/angle/projection, for
- * file naming purposes
- */
-void ImggAggregateWavelengths::processDirectory(
- const Poco::Path &inDir, size_t bands, const std::string &outDir,
- const std::vector<std::string> &outSubdirs, const std::string &prefix,
- size_t outImgIndex) {
- Mantid::API::MatrixWorkspace_sptr aggImg;
-
- auto images = findInputImages(inDir);
-
- if (images.empty()) {
- g_log.warning()
- << "Could not find any input image files in the subdirectory '"
- << inDir.toString() << "'. It will be ignored.\n";
- return;
- }
-
- auto ranges = splitSizeIntoRanges(images.size(), bands);
-
- processDirectory(inDir, ranges, outDir, outSubdirs, prefix, outImgIndex);
-}
-
-/**
- * Produces the output images (bands) from a directory. The directory
- * may hold the images for radiography data, or one projection angle
- * from tomography data. Multiple output bands (images) can be
- * produced as specified in ranges.
- *
- * This passes through the images one by one (only once), but every
- * images can be aggregated into multiple output bands (as the bands
- * or min-max ranges can overlap)
- *
- * @param inDir where to load images from
- * @param ranges min-max pairs that define the limits of the output bands
- * @param prefix to prepend to all the file names
- * @param outDir where to write the output images/bands
- *
- * @param outSubdirs subdirectories for every output range (given in the
- * input parameter rages)
- *
- * @param outImgIndex an index in the sequence of directories being
- * processed
- */
-void ImggAggregateWavelengths::processDirectory(
- const Poco::Path &inDir,
- const std::vector<std::pair<size_t, size_t>> &ranges,
- const std::string outDir, const std::vector<std::string> &outSubdirs,
- const std::string &prefix, size_t outImgIndex) {
-
- auto imgFiles = findInputImages(inDir);
-
- const size_t maxProgress = imgFiles.size() + 1;
- API::Progress prog(this, 0, 1, maxProgress);
-
- const std::string wsName = "__ImggAggregateWavelengths_fits_seq";
- const std::string wsNameFirst = wsName + "_first";
-
- prog.report(0, "Loading first input image file");
- auto it = std::begin(imgFiles);
- std::vector<API::MatrixWorkspace_sptr> outAccums;
- outAccums.resize(ranges.size());
- outAccums[0] = loadFITS(*it, wsNameFirst);
-
- prog.report(1, "Preparing workspaces for the output images");
- for (size_t idx = 1; idx < ranges.size(); ++idx) {
- outAccums[idx] = outAccums[0]->clone();
- }
- ++it;
-
- prog.report(1, "Loading input image files");
- size_t inputIdx = 1;
- for (auto end = std::end(imgFiles); it != end; ++it, ++inputIdx) {
- // load one more
- const API::MatrixWorkspace_sptr img = loadFITS(*it, wsName);
-
- // add into output
- for (size_t idx = 0; idx < outAccums.size(); ++idx) {
- if (idx >= ranges[idx].first && idx <= ranges[idx].second) {
- aggImage(outAccums[idx], img);
- }
- }
-
- // clear image/workspace. TODO: This is a big waste of
- // allocations/deallocations
- Mantid::API::AnalysisDataService::Instance().remove(wsName);
- prog.reportIncrement(1);
- }
-
- prog.report("Saving output image file(s)");
- for (size_t idx = 0; idx < outAccums.size(); ++idx) {
- // call the file like: bands_idx_0_1000...
- const std::string indicesName = indexRangesPrefix +
- std::to_string(ranges[idx].first) + "_to_" +
- std::to_string(ranges[idx].second);
-
- Poco::Path outPath(outDir);
- outPath.append(outSubdirs[idx]);
- Poco::File fileOutDir(outPath);
- if (!fileOutDir.exists()) {
- fileOutDir.createDirectory();
- }
-
- const std::string extendedPrefix = prefix + indicesName;
- saveAggImage(outAccums[idx], outPath.toString(), extendedPrefix,
- outImgIndex);
- }
- Mantid::API::AnalysisDataService::Instance().remove(wsNameFirst);
-
- // output just the number of bands founds for the first subdirectory
- int nBands = getProperty(PROP_NUM_BANDS_PROCESSED);
- if (0 == nBands) {
- setProperty(PROP_NUM_BANDS_PROCESSED, static_cast<int>(imgFiles.size()));
- }
- prog.reportIncrement(1, "Finished processing input subdirectory/projection");
-}
-
-std::vector<std::pair<size_t, size_t>>
-ImggAggregateWavelengths::rangesFromStringProperty(
- const std::string &rangesSpec, const std::string &propName) {
- Mantid::Kernel::StringTokenizer rangeTokens(
- rangesSpec, ",", Mantid::Kernel::StringTokenizer::TOK_IGNORE_EMPTY |
- Mantid::Kernel::StringTokenizer::TOK_TRIM);
-
- if (rangeTokens.count() <= 0) {
- throw std::invalid_argument(
- "Could not find any valid range of values in the property " + propName);
- }
-
- std::vector<std::pair<size_t, size_t>> ranges;
- for (const auto &str : rangeTokens) {
- const std::string sep = "-";
- Mantid::Kernel::StringTokenizer minMaxTokens(
- str, sep, Mantid::Kernel::StringTokenizer::TOK_IGNORE_EMPTY |
- Mantid::Kernel::StringTokenizer::TOK_TRIM);
- if (2 != minMaxTokens.count()) {
- throw std::invalid_argument(
- std::string(
- "Could not parse a minimum and maximum value separated by '")
- .append(sep)
- .append("' from the string: ")
- .append(str));
- }
-
- try {
- ranges.emplace_back(boost::lexical_cast<size_t>(minMaxTokens[0]),
- boost::lexical_cast<size_t>(minMaxTokens[1]));
- } catch (std::runtime_error &rexc) {
- throw std::runtime_error("Failed to parse this index range: " + str +
- " . Details: " + std::string(rexc.what()));
- }
- }
-
- return ranges;
-}
-
-/**
- * Find the (sub)directories that need processing. Each subdirectory
- * would normally correspond to a projection (angle). If an
- * (apparently) image file is found in the input path, it is assumed
- * that the input path is the only that needs processing (it should
- * contain images from a radiography or single projection) and
- * subdirectories are then ignored. Other files (for example .txt
- * files) are ignored in any case.
- *
- * @param path input path which may contain subdirectories
- *
- * @return subdirectories of the input path to process (or the input
- * path itself if it is the only one that will b processed).
- */
-std::vector<Poco::Path>
-ImggAggregateWavelengths::findInputSubdirs(const Poco::Path &path) {
- // Note: sorted directory iterators available only in poco >= 1.5.2
- std::vector<Poco::Path> dirsFound;
-
- Poco::File dir(path);
- if (!dir.isDirectory() || !dir.exists())
- return dirsFound;
-
- // could also use Poco::Glob to find the files as an alternative
- Poco::DirectoryIterator it(dir);
- Poco::DirectoryIterator end;
- while (it != end) {
-
- // there is at least one image file: take just the first level directory
- if (it->isFile()) {
- const std::string &name = it.name();
- const std::string extShort = name.substr(name.size() - 3);
- const std::string extLong = name.substr(name.size() - 4);
-
- if (isSupportedExtension(extShort, extLong)) {
- // the input path contiains image files, take it
- dirsFound = {path};
- break;
- }
- }
-
- if (it->isDirectory()) {
- dirsFound.push_back(it.path());
- }
-
- ++it;
- }
-
- // this assumes the usual sorting of images of a stack (directory): a prefix,
- // and a sequence number (with a fixed number of digits).
- std::sort(dirsFound.begin(), dirsFound.end(), PocoPathComp());
-
- return dirsFound;
-}
-
-/**
- * Find images in a directory. It takes the (image) files that have
- * the expected/supported extension. Anything else (other files,
- * directories) is ignored.
- *
- * @param path directory where to look for images
- */
-std::vector<Poco::Path>
-ImggAggregateWavelengths::findInputImages(const Poco::Path &path) {
- // Note: sorted directory iterators available only in poco >= 1.5.2
- std::vector<Poco::Path> imgsFound;
-
- Poco::File dir(path);
- if (!dir.isDirectory() || !dir.exists())
- return imgsFound;
-
- Poco::DirectoryIterator it(dir);
- Poco::DirectoryIterator end;
- while (it != end) {
-
- if (it->isFile()) {
- const std::string summedSkipStr = "_SummedImg.";
- const std::string name = it.name();
- if (std::string::npos != name.find(summedSkipStr)) {
- ++it;
- continue;
- }
-
- const std::string extShort = name.substr(name.size() - 3);
- const std::string extLong = name.substr(name.size() - 4);
- if (isSupportedExtension(extShort, extLong)) {
- imgsFound.emplace_back(it.path());
- }
- }
-
- if (it->isDirectory()) {
- imgsFound.push_back(it.path());
- }
-
- ++it;
- }
-
- // this assumes the usual sorting of images of a stack (directory): a prefix,
- // and a sequence number (with a fixed number of digits).
- std::sort(imgsFound.begin(), imgsFound.end(), PocoPathComp());
-
- return imgsFound;
-}
-
-/**
- * Split into uniform blocks, for when producing multiple output bands
- * from the input images/bands. If the division is not exact, a few
- * images at the end will be ignored, so the number of input bands
- * that will go into every output band is the same for all of
- * them. For example, if 1000 input images/bands are aggregated into 3
- * output bands, From 1000/3: 333 (output band 1), 333 (output band
- * 2), 333 (output band 3), and 1 last image is not considered.
- *
- * @param availableCount how many input elements there are @param
- * bands into how many uniform blocks they should be split
- *
- * @returns pairs of min-max for the output blocks
- */
-std::vector<std::pair<size_t, size_t>>
-ImggAggregateWavelengths::splitSizeIntoRanges(size_t availableCount,
- size_t bands) {
- std::vector<std::pair<size_t, size_t>> ranges;
- size_t inc = availableCount / bands;
- if (inc < 1) {
- throw std::runtime_error(
- "The number of output bands requested (" + std::to_string(bands) +
- ") is bigger than the number of available input images (" +
- std::to_string(availableCount) +
- "). It should be equal or smaller, and "
- "normally it is much smaller. Please "
- "check that you are providing the "
- "correct input parameters");
- }
-
- for (size_t count = 0; count < availableCount; count += inc) {
- size_t max =
- ((count + inc) > availableCount) ? availableCount : count + inc;
- ranges.emplace_back(count, max);
- }
-
- return ranges;
-}
-
-/**
- * Builds the names of the output subdirectories (bands) given the
- * input subdirectories, when splitting the input bands/images into
- * uniform blocks. It has to look for the number of available input
- * images from the first input subdirectory that has any images.
- *
- * @param inputSubDirs input subdirectories (one or more)
- * @param bands how many output bands will be produced
- *
- * @returns list of names that can be used to create subdirectories
- * for the outputs, derived from the ranges that split the input bands
- * into uniform blocks. For example
- */
-std::vector<std::string>
-ImggAggregateWavelengths::buildOutputSubdirNamesFromUniformBands(
- const std::vector<Poco::Path> &inputSubDirs, size_t bands) {
- std::vector<std::string> outputSubdirs;
- // get number of available images from first effective subdirectory
- std::vector<Poco::Path> images;
- for (size_t idx = 0; idx < inputSubDirs.size() && images.empty(); ++idx) {
- images = findInputImages(inputSubDirs[idx]);
- }
- auto outRanges = splitSizeIntoRanges(images.size(), bands);
-
- const std::string subdirsPrefix =
- getProperty(PROP_OUTPUT_SUBDIRS_PREFIX_UNIFORM_BANDS);
- for (const auto &range : outRanges) {
- // one different subdirectory for every output band
- outputSubdirs.emplace_back(subdirsPrefix + indexRangesPrefix +
- std::to_string(range.first) + "_to_" +
- std::to_string(range.second));
- }
-
- return outputSubdirs;
-}
-
-/**
- * Builds the names of the output subdirectories (bands) given a
- * sequence of image index ranges, when splitting the input
- * bands/images into a sequence of ranges. It has to look for the
- * number of available input images from the first input subdirectory
- * that has any images.
- *
- * @param outRanges min-max pairs with ranges of image indices to use
- * for the output bands
- *
- * @returns list of names that can be used to create subdirectories
- * for the outputs, derived from the ranges
- */
-std::vector<std::string>
-ImggAggregateWavelengths::buildOutputSubdirNamesFromIndexRangesBands(
- const std::vector<std::pair<size_t, size_t>> &outRanges) {
- std::vector<std::string> outputSubdirs;
- const std::string subdirsPrefix =
- getProperty(PROP_OUTPUT_SUBDIRS_PREFIX_INDEX_BANDS);
- for (const auto &range : outRanges) {
- // one different subdirectory for every output band
- outputSubdirs.emplace_back(subdirsPrefix + indexRangesPrefix +
- std::to_string(range.first) + "_to_" +
- std::to_string(range.second));
- }
-
- return outputSubdirs;
-}
-
-bool ImggAggregateWavelengths::isSupportedExtension(
- const std::string &extShort, const std::string &extLong) {
- const std::vector<std::string> formatExtensionsShort{"fit"};
- const std::vector<std::string> formatExtensionsLong{"fits"};
-
- bool found = (formatExtensionsShort.cend() !=
- std::find(formatExtensionsShort.cbegin(),
- formatExtensionsShort.cend(), extShort)) ||
- (formatExtensionsLong.cend() !=
- std::find(formatExtensionsLong.cbegin(),
- formatExtensionsLong.cend(), extLong));
- return found;
-}
-
-/**
- * Add a workspace into an accumulator workspace ('toAdd' into
- * 'accum'). This method blatantly ignores the X values and the E
- * (error) values. We're only interested in the Y values (pixels,
- * counts).
- *
- * @param accum workspace where to add a new workspace
- * @param toAdd workspace to add
- */
-void ImggAggregateWavelengths::aggImage(API::MatrixWorkspace_sptr accum,
- const API::MatrixWorkspace_sptr toAdd) {
- const size_t sizeX = accum->blocksize();
- const size_t sizeY = accum->getNumberHistograms();
-
- const size_t sizeXIn = accum->blocksize();
- const size_t sizeYIn = accum->getNumberHistograms();
-
- if (sizeX != sizeXIn || sizeY != sizeYIn) {
- throw std::runtime_error(
- "Cannot add images of different dimensions. The first image has "
- "dimensions " +
- std::to_string(sizeY) + " rows by " + std::to_string(sizeX) +
- " columns whereas the second image has dimensions " +
- std::to_string(sizeYIn) + " rows by " + std::to_string(sizeXIn) +
- " columns.");
- }
-
- for (size_t row = 0; row < sizeY; row++) {
- accum->mutableY(row) += toAdd->y(row);
- }
-}
-
-/**
- * Save an image workspace into an image file.
- *
- * @param accum workspace with image data
- * @param outDir where the file goes
- * @param prefix prefix to use in the file name
- * @param outImgIndex index of the directory/angle/projection which
- * will be used in the filename
- */
-void ImggAggregateWavelengths::saveAggImage(
- const API::MatrixWorkspace_sptr accum, const std::string &outDir,
- const std::string &prefix, size_t outImgIndex) {
- // for example 'sum_projection_00003_bands_indices_0_1000'
- std::ostringstream sstr;
- sstr << std::setw(5) << std::setfill('0') << outImgIndex;
- const std::string outName = outPrefixProjections + sstr.str() + "_" + prefix;
-
- Poco::Path outPath(outDir);
- Poco::File dirFile(outPath);
- if (!dirFile.isDirectory() || !dirFile.exists()) {
- g_log.information() << "Cannot save output image into '"
- << outPath.toString()
- << "'. It is not an existing directory.\n";
- return;
- }
-
- outPath.append(outName);
- std::string fullName = outPath.toString();
- // only FITS support for now
- fullName += ".fits";
- saveFITS(accum, fullName);
- g_log.information() << "Saved output aggregated image into: " << fullName
- << '\n';
-}
-
-API::MatrixWorkspace_sptr
-ImggAggregateWavelengths::loadFITS(const Poco::Path &imgPath,
- const std::string &outName) {
-
- auto loader =
- Mantid::API::AlgorithmManager::Instance().createUnmanaged("LoadFITS");
- try {
- loader->initialize();
- loader->setChild(true);
- loader->setPropertyValue("Filename", imgPath.toString());
- loader->setProperty("OutputWorkspace", outName);
- // this is way faster when loading into a MatrixWorkspace
- loader->setProperty("LoadAsRectImg", true);
- } catch (std::exception &e) {
- throw std::runtime_error("Failed to initialize the algorithm to "
- "load images. Error description: " +
- std::string(e.what()));
- }
-
- try {
- loader->execute();
- } catch (std::exception &e) {
- throw std::runtime_error(
- "Failed to load image. Could not load this file as a "
- "FITS image: " +
- std::string(e.what()));
- }
-
- if (!loader->isExecuted()) {
- throw std::runtime_error(
- "Failed to load image correctly. Note that even though "
- "the image file has been loaded it seems to contain errors.");
- }
-
- API::MatrixWorkspace_sptr ws;
- try {
- API::Workspace_sptr outWS = loader->getProperty("OutputWorkspace");
- API::WorkspaceGroup_sptr wsg =
- boost::dynamic_pointer_cast<API::WorkspaceGroup>(outWS);
- ws = boost::dynamic_pointer_cast<API::MatrixWorkspace>(
- wsg->getItem(wsg->size() - 1));
- } catch (std::exception &e) {
- throw std::runtime_error(
- "Could not load image contents for file '" + imgPath.toString() +
- "'. An unrecoverable error "
- "happened when trying to load the image contents. Cannot "
- "display it. Error details: " +
- std::string(e.what()));
- }
-
- return ws;
-}
-
-void ImggAggregateWavelengths::saveFITS(const API::MatrixWorkspace_sptr accum,
- const std::string &filename) {
- auto writer =
- Mantid::API::AlgorithmManager::Instance().createUnmanaged("SaveFITS");
- try {
- writer->initialize();
- writer->setChild(true);
- writer->setPropertyValue("Filename", filename);
- writer->setProperty("InputWorkspace", accum);
- // this is way faster when loading into a MatrixWorkspace
- writer->setProperty("BitDepth", 16);
- } catch (std::exception &e) {
- throw std::runtime_error("Failed to initialize the algorithm to "
- "save images in FITS format. Error description: " +
- std::string(e.what()));
- }
-
- try {
- writer->execute();
- } catch (std::exception &e) {
- throw std::runtime_error(
- "Failed to write image. Could not write this file as a"
- "FITS image: " +
- std::string(e.what()));
- }
-}
-
-} // namespace DataHandling
-} // namespace Mantid
diff --git a/Framework/DataHandling/src/LoadSavuTomoConfig.cpp b/Framework/DataHandling/src/LoadSavuTomoConfig.cpp
deleted file mode 100644
index 6b75a28a3de..00000000000
--- a/Framework/DataHandling/src/LoadSavuTomoConfig.cpp
+++ /dev/null
@@ -1,206 +0,0 @@
-#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/ITableWorkspace.h"
-#include "MantidAPI/TableRow.h"
-#include "MantidAPI/WorkspaceProperty.h"
-#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidDataHandling/LoadSavuTomoConfig.h"
-#include "MantidKernel/PropertyWithValue.h"
-
-#include <nexus/NeXusException.hpp>
-
-namespace Mantid {
-namespace DataHandling {
-
-// Register the algorithm into the algorithm factory
-DECLARE_ALGORITHM(LoadSavuTomoConfig)
-
-using namespace Mantid::API;
-
-/**
- * Standard Initialisation method. Declares properties.
- */
-void LoadSavuTomoConfig::init() {
- // Required input properties
- const std::vector<std::string> exts{".nxs", ".nx5", ".xml"};
- declareProperty(
- Kernel::make_unique<FileProperty>("Filename", "", FileProperty::Load,
- exts),
- "The name of the Nexus parameterization file to read, as a full "
- "or relative path.");
-
- declareProperty(Kernel::make_unique<WorkspaceProperty<ITableWorkspace>>(
- "OutputWorkspace", "savuTomoConfig",
- Kernel::Direction::Output, PropertyMode::Mandatory),
- "The name of the workspace to be created as output of "
- "the algorithm, a workspace with this name will be created "
- "and stored in the Analysis Data Service.");
-}
-
-/**
- * Executes the algorithm: reads in the parameters file and creates
- * and fills the output workspace
- *
- * @throw runtime_error Thrown if execution fails
- */
-void LoadSavuTomoConfig::exec() {
- progress(0, "Opening file...");
-
- // Will throw an approriate exception if there is a problem with the
- // properties
- std::string fname = getPropertyValue("Filename");
- std::string wsName = getPropertyValue("OutputWorkspace");
-
- ITableWorkspace_sptr ws;
- try {
- // Do the real load. Throws exception if issues found
- ws = loadFile(fname, wsName);
- if (ws) {
- setProperty("OutputWorkspace", ws);
- }
- } catch (std::exception &e) {
- g_log.error() << "Failed to load savu tomography reconstruction "
- "parameterization file: " << e.what() << '\n';
- return;
- }
-
- progress(1.0, "Loading finished.");
-}
-
-/**
- * Can it be openend in the expected format, and does it seem to have
- * sensible contents?
- *
- * @param fname name of file
- * @param f nexus file object, created if file is fine
- *
- * @return true if everything seems fine, false otherwise
- */
-bool LoadSavuTomoConfig::checkOpenFile(std::string fname,
- boost::shared_ptr<NeXus::File> &f) {
- try {
- f = boost::make_shared<NeXus::File>(fname);
- if (f)
- f->getEntries();
- } catch (NeXus::Exception &e) {
- g_log.error() << "Failed to open as a NeXus file: '" << fname
- << "', error description: " << e.what() << '\n';
- return false;
- }
- return true;
-}
-
-/**
- * Loads a tomography parameterization file into a newly created table
- * workspace. The file must have the following syntax:
- *
- * @verbatim
- <NXentry name="entry1">
- <NXprocess name="processing">
- <NXnote name="id">
- <values id="ID VALUE" params="..." name="..." cite="...">
- </values>
- </NXnote>
- </NXprocess>
- </NXentry>
-@endverbatim
- *
- * @param fname name of the parameterization file
- * @param wsName name of workspace where to load the file data
- *
- * @return table workspace with parameters (plugins) found in the
- * loaded file
- */
-ITableWorkspace_sptr LoadSavuTomoConfig::loadFile(std::string &fname,
- std::string &wsName) {
- // Throws an exception if there is a problem with file access
- // Mantid::NeXus::NXRoot root(fname);
- boost::shared_ptr<NeXus::File> f;
- if (!checkOpenFile(fname, f)) {
- throw std::runtime_error(
- "Failed to recognize this file as a NeXus file, cannot continue.");
- }
-
- ITableWorkspace_sptr ws = API::WorkspaceFactory::Instance().createTable();
- if (!ws)
- throw std::runtime_error("Could not create TableWorkspace for "
- "workspace with name '" +
- wsName + "'");
-
- // init workspace
- ws->setTitle("Table with tomography parameters from file " + fname);
- ws->addColumn("str", "ID");
- ws->addColumn("str", "Parameters");
- ws->addColumn("str", "Name");
- ws->addColumn("str", "Cite");
-
- // a bit of file consistency check, check at least there's a
- // 'entry1'
- // it could be more strict and demand entries.size()==1
- std::map<std::string, std::string> entries = f->getEntries();
- std::string mainEntryName = "entry";
- auto it = entries.find(mainEntryName);
- if (entries.end() == it) {
- throw std::runtime_error(
- "Could not find the '" + mainEntryName +
- "' "
- "entry. Even though this file looks like a valid NeXus file, it is "
- "not in the correct format for tomography reconstruction "
- "parameterization files.");
- }
-
- // go through the input file plugin entries
- f->openGroup(mainEntryName, "NXentry");
- f->openGroup("process", "NXprocess");
- size_t pluginsLen = f->getEntries().size();
- for (size_t j = 0; j < pluginsLen; j++) {
- API::TableRow table = ws->appendRow();
-
- std::string entryIdx = std::to_string(j);
- try {
- f->openGroup(entryIdx, "NXnote");
- } catch (NeXus::Exception &e) {
- // detailed NeXus error message and throw...
- g_log.error() << "Failed to load plugin '" << j
- << "' from"
- "NeXus file. Error description: " << e.what() << '\n';
- throw std::runtime_error(
- "Could not load one or more plugin "
- "entries from the tomographic reconstruction parameterization "
- "file. Please check that the file is correct.");
- }
-
- // TODO: check final 'schema', get these 4 fields from the file
- std::string id;
- std::string params;
- std::string name;
- std::string cite;
- try {
- f->readData("data", params);
- f->readData("id", id);
- f->readData("name", name);
- // cite not available for now
- // f->readData("cite", cite);
- // This might be extended to an NXcite group that would be included
- // not here but inside an "intermediate" NXcollection group. That
- // NXcite would have 4 arrays: description, doi, endnote, bibtex.
- // But this is what we have so far.
- cite = "Not available";
- } catch (NeXus::Exception &e) {
- // permissive, just error message but carry on
- g_log.warning()
- << "Failed to read some fields in tomographic "
- "reconstruction plugin line. The file seems to be wrong. Error "
- "description: " << e.what() << '\n';
- }
-
- table << id << params << name << cite;
- f->closeGroup();
- progress(static_cast<double>(j) / static_cast<double>(pluginsLen));
- }
- f->close();
-
- return ws;
-}
-
-} // namespace DataHandling
-} // namespace Mantid
diff --git a/Framework/DataHandling/src/SaveSavuTomoConfig.cpp b/Framework/DataHandling/src/SaveSavuTomoConfig.cpp
deleted file mode 100644
index 80c331018d6..00000000000
--- a/Framework/DataHandling/src/SaveSavuTomoConfig.cpp
+++ /dev/null
@@ -1,206 +0,0 @@
-#include "MantidAPI/AnalysisDataService.h"
-#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/ITableWorkspace.h"
-#include "MantidDataHandling/SaveSavuTomoConfig.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/MandatoryValidator.h"
-
-#include <nexus/NeXusFile.hpp>
-#include <Poco/File.h>
-
-namespace Mantid {
-namespace DataHandling {
-// Register the algorithm into the algorithm factory
-DECLARE_ALGORITHM(SaveSavuTomoConfig)
-
-using namespace Kernel;
-using namespace API;
-
-SaveSavuTomoConfig::SaveSavuTomoConfig()
- : API::Algorithm(), m_pluginInfoCount(4) {}
-
-/**
- * Initialise the algorithm
- */
-void SaveSavuTomoConfig::init() {
- // Get a list of table workspaces which contain the plugin information
- declareProperty(
- Kernel::make_unique<ArrayProperty<std::string>>(
- "InputWorkspaces",
- boost::make_shared<MandatoryValidator<std::vector<std::string>>>()),
- "The names of the table workspaces containing plugin information.");
-
- declareProperty(Kernel::make_unique<API::FileProperty>(
- "Filename", "", FileProperty::Save,
- std::vector<std::string>(1, ".nxs")),
- "The name of the tomographic config file to write, as a full "
- "or relative path. This will overwrite existing files.");
-}
-
-/**
- * Execute the algorithm
- */
-void SaveSavuTomoConfig::exec() {
- // Prepare properties for writing to file
- std::string fileName = getPropertyValue("Filename");
-
- progress(0, "Checking workspace (tables)...");
-
- std::vector<ITableWorkspace_sptr> wss =
- checkTables(getProperty("InputWorkspaces"));
-
- try {
- saveFile(fileName, wss);
- } catch (std::exception &e) {
- g_log.error()
- << "Failed to save savu tomography reconstruction parameterization "
- "file, error description: " << e.what() << '\n';
- return;
- }
-
- progress(0, "File saved.");
-}
-
-/**
- * Do a basic check that the table seems to be what we need to save a
- * savu configuration file.
- *
- * @param tws Table workspace that should contain plugin/processing
- * steps information (a savu configuration)
- *
- * @return True if the table passed seems to be a savu configuration table
- */
-bool SaveSavuTomoConfig::tableLooksGenuine(const ITableWorkspace_sptr &tws) {
- // note that more columns might be added in the relatively near future
- if (!(tws->columnCount() >= m_pluginInfoCount))
- return false;
-
- std::vector<std::string> names = tws->getColumnNames();
- return (4 <= names.size() && "ID" == names[0] && "Parameters" == names[1] &&
- "Name" == names[2] && "Cite" == names[3]);
-}
-
-/**
- * Check that the list of workspace names identifies table workspaces
- * with (approximately) the expected information (4 columns), and
- * return the corresponding (table) workspace objects.
- *
- * @param workspaces Table workspace names that should contain plugin/processing
- * steps information
- *
- * @return Table workspaces retrieved from the ADS, corresponding to
- * the names passed
- */
-std::vector<ITableWorkspace_sptr>
-SaveSavuTomoConfig::checkTables(const std::vector<std::string> &workspaces) {
- std::vector<ITableWorkspace_sptr> wss;
- for (const auto &workspace : workspaces) {
- if (AnalysisDataService::Instance().doesExist(workspace)) {
- ITableWorkspace_sptr table =
- AnalysisDataService::Instance().retrieveWS<ITableWorkspace>(
- workspace);
- // Check it's valid. Very permissive check for the time being
- if (table && tableLooksGenuine(table)) {
- wss.push_back(table);
- } else {
- throw std::runtime_error("Invalid workspace provided: " + workspace +
- ". This algorithm requires a table "
- "workspace with correct savu plugin/ "
- "pipeline process information.");
- }
- } else {
- throw std::runtime_error(
- "One or more specified table workspaces don't exist. I could not "
- "find this one: " +
- workspace);
- }
- }
- return wss;
-}
-
-/**
- * Check that the list of workspace names identifies table workspaces
- * with (approximately) the expected information (4 columns), and
- * return the corresponding (table) workspace objects.
- *
- * @param fname Destination file name (can be ammended if needed and that
- * will be logged)
- * @param wss Table workspaces that apparently contain plugin/processing
- * steps information
- */
-void SaveSavuTomoConfig::saveFile(
- const std::string fname, const std::vector<ITableWorkspace_sptr> &wss) {
- // Ensure it has a .nxs extension
- std::string fileName = fname;
- if (!boost::ends_with(fileName, ".nxs")) {
- const std::string ext = ".nxs";
- g_log.notice() << "Adding extension '" << ext
- << "' to the output "
- "file name given (it is a NeXus file). \n";
- fileName = fileName + ".nxs";
- }
-
- // If file exists, delete it.
- Poco::File f(fileName);
- if (f.exists()) {
- g_log.notice() << "Overwriting existing file: '" << fileName << "'\n";
- f.remove();
- } else {
- g_log.notice() << "Creating file: '" << fileName << ";\n";
- }
-
- // Create the file handle
- NXhandle fileHandle;
- NXstatus status = NXopen(fileName.c_str(), NXACC_CREATE5, &fileHandle);
-
- if (status == NX_ERROR)
- throw std::runtime_error("Unable to create file.");
-
- NeXus::File nxFile(fileHandle);
-
- std::string topLevelEntry = "entry";
- nxFile.makeGroup(topLevelEntry, "NXentry", true);
-
- const std::string processingEntry = "processing";
- nxFile.makeGroup(processingEntry, "NXprocess", true);
-
- // Iterate through all plugin entries (number sub groups 0....n-1)
- size_t procCount = 0;
- for (const auto &w : wss) {
- // Concatenate table contents, putting pipeline processing steps in the same
- // sequence
- // as they come in the seq of table workspaces
- for (size_t ti = 0; ti < w->rowCount(); ++ti) {
- // Column info order is [ID / Params {as json string} / name {description}
- // /
- // citation info]
- std::string id = w->cell<std::string>(ti, 0);
- std::string params = w->cell<std::string>(ti, 1);
- std::string name = w->cell<std::string>(ti, 2);
- // Unused for now, until file format is finalized/documented.
- // std::string cite = w->cell<std::string>(ti, 3);
-
- // but in the file it goes as: data (params), id, name
- nxFile.makeGroup(std::to_string(procCount++), "NXnote", true);
- nxFile.writeData("data", params);
- nxFile.writeData("id", id);
- nxFile.writeData("name", name);
- // Ignore citation information for now. Format not fixed yet.
- // nxFile.writeData("cite", cite);
- nxFile.closeGroup(); // close NXnote
- }
- }
-
- nxFile.closeGroup(); // processing NXprocess
-
- // This seems to be required for certain extensions that can be appended
- // to these files. Not fixed for now.
- nxFile.makeGroup("intermediate", "NXcollection", false);
-
- nxFile.closeGroup(); // Top level entry (NXentry)
-
- nxFile.close();
-}
-
-} // namespace DataHandling
-} // namespace Mantid
diff --git a/Framework/DataHandling/test/LoadSavuTomoConfigTest.h b/Framework/DataHandling/test/LoadSavuTomoConfigTest.h
deleted file mode 100644
index 013669f1ae6..00000000000
--- a/Framework/DataHandling/test/LoadSavuTomoConfigTest.h
+++ /dev/null
@@ -1,189 +0,0 @@
-#ifndef LOADSAVUTOMOCONFIGTEST_H_
-#define LOADSAVUTOMOCONFIGTEST_H_
-
-#include <cxxtest/TestSuite.h>
-
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/AnalysisDataService.h"
-#include "MantidAPI/ITableWorkspace.h"
-#include "MantidDataHandling/LoadSavuTomoConfig.h"
-
-using namespace Mantid::API;
-using Mantid::DataHandling::LoadSavuTomoConfig;
-
-class LoadSavuTomoConfigTest : public CxxTest::TestSuite {
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static LoadSavuTomoConfigTest *createSuite() {
- return new LoadSavuTomoConfigTest();
- }
- static void destroySuite(LoadSavuTomoConfigTest *suite) { delete suite; }
-
- /// Tests casting, general algorithm properties: name, version, etc.
- void test_algorithm() {
- testAlg = Mantid::API::AlgorithmManager::Instance().create(
- "LoadSavuTomoConfig" /*, 1*/);
- TS_ASSERT(testAlg);
- TS_ASSERT_EQUALS(testAlg->name(), "LoadSavuTomoConfig");
- TS_ASSERT_EQUALS(testAlg->version(), 1);
- }
-
- void test_init() {
- if (!testAlg->isInitialized())
- testAlg->initialize();
-
- TS_ASSERT_THROWS_NOTHING(testAlg->initialize());
- TS_ASSERT(testAlg->isInitialized());
- }
-
- void test_wrongExec() {
- IAlgorithm_sptr testFail = Mantid::API::AlgorithmManager::Instance().create(
- "LoadSavuTomoConfig" /*, 1*/);
- TS_ASSERT(testFail);
- TS_ASSERT_THROWS_NOTHING(testFail->initialize());
- // exec without Filename property set -> should throw
- TS_ASSERT_THROWS(testFail->execute(), std::runtime_error);
- // try to set empty filename
- TS_ASSERT_THROWS(testFail->setPropertyValue("Filename", ""),
- std::invalid_argument);
- TS_ASSERT(!testFail->isExecuted());
-
- // exec with Filename but empty OutputWorkspace -> should throw
- IAlgorithm_sptr fail2 = Mantid::API::AlgorithmManager::Instance().create(
- "LoadSavuTomoConfig" /*, 1*/);
- TS_ASSERT_THROWS_NOTHING(fail2->initialize());
- TS_ASSERT_THROWS_NOTHING(fail2->setPropertyValue("Filename", testFilename));
- TS_ASSERT_THROWS(fail2->setPropertyValue("OutputWorkspace", ""),
- std::invalid_argument);
- TS_ASSERT_THROWS(fail2->execute(), std::runtime_error);
- TS_ASSERT(!fail2->isExecuted());
-
- // exec with Filename but no OutputWorkspace -> should not finish
- IAlgorithm_sptr fail3 = Mantid::API::AlgorithmManager::Instance().create(
- "LoadSavuTomoConfig" /*, 1*/);
- TS_ASSERT_THROWS_NOTHING(fail3->initialize());
- TS_ASSERT_THROWS_NOTHING(fail3->setPropertyValue("Filename", testFilename));
- TS_ASSERT_THROWS_NOTHING(fail3->execute());
- TS_ASSERT(!fail2->isExecuted());
- }
-
- // one file with errors/unrecognized content
- void test_wrongContentsFile() {
- // TODO: wait until we have a final spec of the format, then try to fool
- // the loader here
- }
-
- // one example file that should load fine
- void test_loadOK() {
- // Uses examples from the savu repository:
- // https://github.com/DiamondLightSource/Savu/tree/master/test_data
-
- // TODO: At the moment load just one file to test basic
- // functionality. Probably more files should be added here as we
- // have more certainty about the format
- std::string inWSName = "LoadSavuTomoConfig_test_ws";
- // Load examples from
- // https://github.com/DiamondLightSource/Savu/tree/master/test_data
- TS_ASSERT_THROWS_NOTHING(
- testAlg->setPropertyValue("Filename", testFilename));
- TS_ASSERT_THROWS_NOTHING(
- testAlg->setPropertyValue("OutputWorkspace", inWSName));
-
- if (!testAlg->isInitialized())
- testAlg->initialize();
- TS_ASSERT(testAlg->isInitialized());
-
- TS_ASSERT_THROWS_NOTHING(testAlg->execute());
- TS_ASSERT(testAlg->isExecuted());
-
- AnalysisDataServiceImpl &ads = AnalysisDataService::Instance();
-
- TS_ASSERT(ads.doesExist(inWSName));
- ITableWorkspace_sptr ws;
- TS_ASSERT_THROWS_NOTHING(ws = ads.retrieveWS<ITableWorkspace>(inWSName));
-
- // general format: 3 columns (data, id, name)
- TS_ASSERT_EQUALS(ws->columnCount(), 4);
- TS_ASSERT_EQUALS(ws->rowCount(), 3);
-
- checkColumns(ws);
-
-#if (defined __APPLE__ && defined __INTEL_COMPILER)
- // This is a horror, an exception needed for osx 10.8 where lib nexus does
- // not behave
- // Bug in NeXus strings: the last character is trimmed
- // TODO: remove this when osx 10.8 extinguishes (theres a ticket being
- // created for that).
- // ID
- TS_ASSERT_EQUALS(ws->cell<std::string>(0, 0),
- "savu.plugins.timeseries_field_correction");
- TS_ASSERT_EQUALS(ws->cell<std::string>(1, 0), "savu.plugins.median_filte");
- TS_ASSERT_EQUALS(ws->cell<std::string>(2, 0), "savu.plugins.simple_reco");
-
- // data entry in NeXus file (Params column)
- TS_ASSERT_EQUALS(ws->cell<std::string>(0, 1), "{");
- TS_ASSERT_EQUALS(ws->cell<std::string>(1, 1),
- "{\"kernel_size\": [1, 3, 3]");
- TS_ASSERT_EQUALS(ws->cell<std::string>(2, 1),
- "{\"center_of_rotation\": 86");
-
- // name entry in NeXus file
- TS_ASSERT_EQUALS(ws->cell<std::string>(0, 2),
- "Timeseries Field Correction");
- TS_ASSERT_EQUALS(ws->cell<std::string>(1, 2), "Median Filte");
- TS_ASSERT_EQUALS(ws->cell<std::string>(2, 2), "Simple Reconstructio");
-
-#else
- // this example has 3 plugins: savu.plugins.timeseries_fields_corrections,
- // savu.median_filter,
- // savu.plugins.simple_recon
- // ID
- TS_ASSERT_EQUALS(ws->cell<std::string>(0, 0),
- "savu.plugins.timeseries_field_corrections");
- TS_ASSERT_EQUALS(ws->cell<std::string>(1, 0), "savu.plugins.median_filter");
- TS_ASSERT_EQUALS(ws->cell<std::string>(2, 0), "savu.plugins.simple_recon");
-
- // data entry in NeXus file (Params column)
- TS_ASSERT_EQUALS(ws->cell<std::string>(0, 1), "{}");
- TS_ASSERT_EQUALS(ws->cell<std::string>(1, 1),
- "{\"kernel_size\": [1, 3, 3]}");
- TS_ASSERT_EQUALS(ws->cell<std::string>(2, 1),
- "{\"center_of_rotation\": 86}");
-
- // name entry in NeXus file
- TS_ASSERT_EQUALS(ws->cell<std::string>(0, 2),
- "Timeseries Field Corrections");
- TS_ASSERT_EQUALS(ws->cell<std::string>(1, 2), "Median Filter");
- TS_ASSERT_EQUALS(ws->cell<std::string>(2, 2), "Simple Reconstruction");
-#endif
-
- // cite information, not presently available in example files
- for (size_t i = 0; i < nRows; i++) {
- TS_ASSERT_EQUALS(ws->cell<std::string>(i, 3), "Not available");
- }
- }
-
-private:
- void checkColumns(ITableWorkspace_sptr &table) {
- // each row of the workspace should have: ID, Params, Name, Cite
- std::vector<std::string> names = table->getColumnNames();
- TS_ASSERT_EQUALS(names.size(), 4);
- TS_ASSERT_EQUALS(names[0], "ID");
- TS_ASSERT_EQUALS(names[1], "Parameters");
- TS_ASSERT_EQUALS(names[2], "Name");
- TS_ASSERT_EQUALS(names[3], "Cite");
- }
-
- IAlgorithm_sptr testAlg;
- static const size_t nRows;
- static const size_t nCols;
- static const std::string testFilename;
-};
-
-const size_t LoadSavuTomoConfigTest::nRows = 3;
-const size_t LoadSavuTomoConfigTest::nCols = 4;
-const std::string LoadSavuTomoConfigTest::testFilename =
- "savu_test_data_process03.nxs";
-
-#endif /* LOADSAVUTOMOCONFIGTEST_H__*/
diff --git a/Framework/DataHandling/test/SaveSavuTomoConfigTest.h b/Framework/DataHandling/test/SaveSavuTomoConfigTest.h
deleted file mode 100644
index c3f301f5033..00000000000
--- a/Framework/DataHandling/test/SaveSavuTomoConfigTest.h
+++ /dev/null
@@ -1,177 +0,0 @@
-#ifndef SAVESAVUTOMOCONFIGTEST_H_
-#define SAVESAVUTOMOCONFIGTEST_H_
-
-#include <cxxtest/TestSuite.h>
-
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/AnalysisDataService.h"
-#include "MantidAPI/ITableWorkspace.h"
-#include "MantidAPI/TableRow.h"
-#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidDataHandling/SaveSavuTomoConfig.h"
-
-#include <Poco/File.h>
-
-using namespace Mantid::API;
-using namespace Mantid::DataHandling;
-
-class SaveSavuTomoConfigTest : public CxxTest::TestSuite {
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static SaveSavuTomoConfigTest *createSuite() {
- return new SaveSavuTomoConfigTest();
- }
- static void destroySuite(SaveSavuTomoConfigTest *suite) { delete suite; }
-
- /// Tests casting, general algorithm properties: name, version, etc.
- void test_algorithm() {
- testSave = Mantid::API::AlgorithmManager::Instance().create(
- "SaveSavuTomoConfig" /*, 1*/);
- TS_ASSERT(testSave);
- TS_ASSERT_EQUALS(testSave->name(), "SaveSavuTomoConfig");
- TS_ASSERT_EQUALS(testSave->version(), 1);
- }
-
- void test_init() {
- if (!testSave->isInitialized())
- testSave->initialize();
-
- TS_ASSERT_THROWS_NOTHING(testSave->initialize());
- TS_ASSERT(testSave->isInitialized());
- }
-
- /// this is the first test that uses the good workspace (wsName) so it creates
- /// it
- void test_wrongExec() {
- ITableWorkspace_sptr ws = makeTableWorkspace(wsName);
-
- IAlgorithm_sptr testFail = Mantid::API::AlgorithmManager::Instance().create(
- "SaveSavuTomoConfig" /*, 1*/);
- TS_ASSERT(testFail);
- TS_ASSERT_THROWS_NOTHING(testFail->initialize());
- // exec without InputWorkspaces property set -> should throw
- TS_ASSERT_THROWS(testFail->execute(), std::runtime_error);
- // try to set empty InputWorkspaces
- TS_ASSERT_THROWS(testFail->setPropertyValue("InputWorkspaces", ""),
- std::invalid_argument);
- TS_ASSERT(!testFail->isExecuted());
-
- // exec with InputWorkspaces but empty Filename -> should throw
- IAlgorithm_sptr fail2 = Mantid::API::AlgorithmManager::Instance().create(
- "SaveSavuTomoConfig" /*, 1*/);
- TS_ASSERT_THROWS_NOTHING(fail2->initialize());
- TS_ASSERT_THROWS_NOTHING(
- fail2->setPropertyValue("InputWorkspaces", wsName));
- TS_ASSERT_THROWS(fail2->setPropertyValue("Filename", ""),
- std::invalid_argument);
- TS_ASSERT_THROWS(fail2->execute(), std::runtime_error);
- TS_ASSERT(!fail2->isExecuted());
-
- // exec with InputWorkspaces but no Filename -> should throw
- IAlgorithm_sptr fail3 = Mantid::API::AlgorithmManager::Instance().create(
- "SaveSavuTomoConfig" /*, 1*/);
- TS_ASSERT_THROWS_NOTHING(fail3->initialize());
- TS_ASSERT_THROWS_NOTHING(
- fail3->setPropertyValue("InputWorkspaces", wsName));
- TS_ASSERT_THROWS(fail3->execute(), std::runtime_error);
- }
-
- void test_wrongTableFormat() {
- std::string badWSName = "bad_table";
- ITableWorkspace_sptr ws = makeWrongTableWorkspace(badWSName);
-
- // using wrong table: should fail
- IAlgorithm_sptr fail = Mantid::API::AlgorithmManager::Instance().create(
- "SaveSavuTomoConfig" /*, 1*/);
- TS_ASSERT_THROWS_NOTHING(fail->initialize());
- TS_ASSERT_THROWS_NOTHING(
- fail->setPropertyValue("InputWorkspaces", badWSName));
- TS_ASSERT_THROWS_NOTHING(fail->setPropertyValue("Filename", outFilename));
- TS_ASSERT_THROWS_NOTHING(fail->execute());
- TS_ASSERT(!fail->isExecuted());
-
- AnalysisDataService::Instance().remove(badWSName);
- }
-
- /// this is the last test that uses the good workspace (wsName) so it removes
- /// it from teh ADS
- void test_saveOK() {
- TS_ASSERT(testSave->isInitialized());
- TS_ASSERT_THROWS_NOTHING(
- testSave->setPropertyValue("InputWorkspaces", wsName));
- TS_ASSERT_THROWS_NOTHING(
- testSave->setPropertyValue("Filename", outFilename));
- TS_ASSERT_THROWS_NOTHING(testSave->execute());
- TS_ASSERT(testSave->isExecuted());
-
- // very basic test, to do more than this use the sibling LoadSavuTomo
- // algorithm
- TS_ASSERT(Poco::File(outFilename).exists());
- boost::shared_ptr<NeXus::File> file;
- // can open as NeXus and find one of the entries
- TS_ASSERT_THROWS_NOTHING(file =
- boost::make_shared<NeXus::File>(outFilename));
- TS_ASSERT_THROWS_NOTHING(file->openPath("/entry/processing/0"));
- TS_ASSERT_THROWS_NOTHING(file->close());
-
- cleanup();
- }
-
-private:
- /// removes the output file and the input workspace
- void cleanup() {
- TS_ASSERT_THROWS_NOTHING(Poco::File(outFilename).remove());
- TS_ASSERT_THROWS_NOTHING(AnalysisDataService::Instance().remove(wsName));
- }
-
- /// helper: specific table format here for savu pipeline configurations
- ITableWorkspace_sptr makeTableWorkspace(const std::string &name) {
- ITableWorkspace_sptr ws = WorkspaceFactory::Instance().createTable();
- AnalysisDataService::Instance().addOrReplace(name, ws);
- ws->addColumn("str", "ID");
- ws->addColumn("str", "Parameters");
- ws->addColumn("str", "Name");
- ws->addColumn("str", "Cite");
-
- Mantid::API::TableRow row = ws->appendRow();
- row << "savu.id1"
- << "{\"param1\": val1}"
- << "name 1"
- << "cite 1";
- row = ws->appendRow();
- row << "savu.id2"
- << "{\"param2\": val2}"
- << "name 2"
- << "cite 2";
-
- return ws;
- }
-
- // helper to build a bad table: intentionally forgets to add some columns
- ITableWorkspace_sptr makeWrongTableWorkspace(const std::string &name) {
- ITableWorkspace_sptr ws = WorkspaceFactory::Instance().createTable();
- AnalysisDataService::Instance().addOrReplace(name, ws);
- ws->addColumn("str", "ID");
- ws->addColumn("str", "Name");
-
- Mantid::API::TableRow row = ws->appendRow();
- row << "savu.id1"
- << "{\"param1\": val1}";
- row = ws->appendRow();
- row << "savu.id2"
- << "{\"param2\": val2}";
-
- return ws;
- }
-
- IAlgorithm_sptr testSave;
- static const std::string outFilename;
- static const std::string wsName;
-};
-
-const std::string SaveSavuTomoConfigTest::wsName = "simple_table";
-const std::string SaveSavuTomoConfigTest::outFilename =
- "savu_tomo_save_test.nxs";
-
-#endif /* SAVESAVUTOMOCONFIGTEST_H */
diff --git a/Framework/RemoteAlgorithms/src/SCARFTomoReconstruction.cpp b/Framework/RemoteAlgorithms/src/SCARFTomoReconstruction.cpp
deleted file mode 100644
index 78c7e4df572..00000000000
--- a/Framework/RemoteAlgorithms/src/SCARFTomoReconstruction.cpp
+++ /dev/null
@@ -1,1498 +0,0 @@
-#include <fstream>
-
-#include "MantidAPI/FileProperty.h"
-#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidAPI/WorkspaceProperty.h"
-#include "MantidKernel/ArrayProperty.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidKernel/FacilityInfo.h"
-#include "MantidKernel/InternetHelper.h"
-#include "MantidKernel/ListValidator.h"
-#include "MantidKernel/MandatoryValidator.h"
-#include "MantidKernel/MaskedProperty.h"
-#include "MantidKernel/NullValidator.h"
-#include "MantidKernel/RemoteJobManager.h"
-#include "MantidKernel/VisibleWhenProperty.h"
-#include "MantidRemoteAlgorithms/SCARFTomoReconstruction.h"
-
-#include <Poco/File.h>
-#include <Poco/DOM/Document.h>
-#include <Poco/DOM/DOMParser.h>
-#include <Poco/DOM/Element.h>
-#include <Poco/DOM/NodeList.h>
-#include <Poco/Net/HTTPRequest.h>
-#include <Poco/StreamCopier.h>
-
-#include <boost/algorithm/string/replace.hpp>
-
-namespace Mantid {
-namespace RemoteAlgorithms {
-
-// Register the algorithm into the AlgorithmFactory
-DECLARE_ALGORITHM(SCARFTomoReconstruction)
-
-using namespace Mantid::Kernel;
-
-std::map<std::string, SCARFTomoReconstruction::Token>
- SCARFTomoReconstruction::m_tokenStash;
-
-std::string SCARFTomoReconstruction::m_acceptType =
- "text/plain,application/xml,text/xml";
-
-const std::string SCARFTomoReconstruction::m_SCARFComputeResource =
- "SCARF@STFC";
-
-int SCARFTomoReconstruction::m_jobSeq = 1;
-
-SCARFTomoReconstruction::SCARFTomoReconstruction()
- : Mantid::API::Algorithm(), m_action() {}
-
-void SCARFTomoReconstruction::init() {
- // list of all actions
- std::vector<std::string> actions{"LogIn", "LogOut", "Ping",
- "Upload", "SubmitJob", "JobStatus",
- "JobStatusByID", "Download", "CancelJob"};
-
- auto listValue = boost::make_shared<StringListValidator>(actions);
- auto nullV = boost::make_shared<Kernel::NullValidator>();
-
- // Username always visible, it doesn't hurt and it is required to know the
- // web service base URL for most LSF commands
- auto requireStrValue = boost::make_shared<MandatoryValidator<std::string>>();
- declareProperty("UserName", "", requireStrValue,
- "Name of the user to authenticate as", Direction::Input);
-
- // Action to perform
- declareProperty("Action", "LogIn", listValue,
- "Choose the operation to perform "
- "on the compute resource " +
- m_SCARFComputeResource,
- Direction::Input);
-
- // - Action: login
- declareProperty(make_unique<MaskedProperty<std::string>>("Password", "",
- Direction::Input),
- "The password for the user");
- setPropertySettings("Password", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "LogIn"));
-
- // - Action: submit
- declareProperty(make_unique<PropertyWithValue<std::string>>(
- "RunnablePath",
- "/work/imat/webservice_test/tomopy/imat_recon_FBP.py",
- Direction::Input),
- "The path (on the remote compute resource) of a file to run "
- "(example: shell or python script)");
- setPropertySettings("RunnablePath", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "SubmitJob"));
-
- declareProperty(
- make_unique<PropertyWithValue<std::string>>(
- "JobOptions", "/work/imat/webservice_test/remote_output/test_",
- Direction::Input),
- "Options for the job command line, application dependent. It "
- "can include for example the NXTomo input file when using savu "
- "for tomographic reconstruction.");
- setPropertySettings("JobOptions", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "SubmitJob"));
-
- declareProperty(
- "JobName", "", nullV,
- "Optional name for the job, if not given then a "
- "name will be generated internally or at the compute resource",
- Direction::Input);
- setPropertySettings("JobName", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "SubmitJob"));
-
- // - Action: upload file
- declareProperty(
- make_unique<API::FileProperty>("FileToUpload", "",
- API::FileProperty::OptionalLoad, "",
- Direction::Input),
- "Name of the file (local, full path) to upload to the compute "
- "resource/server ");
- setPropertySettings("FileToUpload", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "Upload"));
-
- declareProperty(
- make_unique<PropertyWithValue<std::string>>(
- "DestinationDirectory", "/work/imat", Direction::Input),
- "Path where to upload the file on the compute resource/server");
- setPropertySettings(
- "DestinationDirectory",
- make_unique<VisibleWhenProperty>("Action", IS_EQUAL_TO, "Upload"));
-
- // - Action: query status and info (of implicitly all jobs)
- declareProperty(make_unique<ArrayProperty<std::string>>("RemoteJobsID",
- Direction::Output),
- "ID strings for the jobs");
- declareProperty(make_unique<ArrayProperty<std::string>>("RemoteJobsNames",
- Direction::Output),
- "Names of the jobs");
- declareProperty(make_unique<ArrayProperty<std::string>>("RemoteJobsStatus",
- Direction::Output),
- "Strings describing the current status of the jobs");
- declareProperty(make_unique<ArrayProperty<std::string>>("RemoteJobsCommands",
- Direction::Output),
- "Strings with the command line run for the jobs");
-
- // - Action: query status and info by ID
- declareProperty(
- make_unique<PropertyWithValue<int>>("JobID", 0, Direction::Input),
- "The ID of a job currently running or recently run on the "
- "compute resource");
- setPropertySettings("JobID", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "JobStatusByID"));
-
- declareProperty("RemoteJobName", "", nullV, "Name of the remote job",
- Direction::Output);
- declareProperty("RemoteJobStatus", "", nullV, "Current status of the job "
- "(running, exited, etc.)",
- Direction::Output);
- declareProperty("RemoteJobCommand", "", nullV, "Command line run remotely "
- "for this job ",
- Direction::Output);
-
- // - Action: download file
- declareProperty(
- make_unique<PropertyWithValue<std::string>>("RemoteJobFilename", "",
- Direction::Input),
- "Name of the job file to download - you can give an empty name "
- "to download all the files of this job.");
- setPropertySettings(
- "RemoteJobFilename",
- make_unique<VisibleWhenProperty>("Action", IS_EQUAL_TO, "Download"));
-
- declareProperty(
- make_unique<API::FileProperty>("LocalDirectory", "",
- API::FileProperty::OptionalDirectory, "",
- Direction::Input),
- "Path to a local directory/folder where to download files from "
- "the compute resource/server");
- setPropertySettings("LocalDirectory", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "Download"));
-
- declareProperty(
- make_unique<PropertyWithValue<int>>("DownloadJobID", 0, Direction::Input),
- "ID of the job for which to download files. A job with this ID "
- "must be running or have been run on the compute resource.");
- setPropertySettings("DownloadJobID", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "Download"));
-
- // - Action: cancel job by ID
- declareProperty(
- make_unique<PropertyWithValue<int>>("CancelJobID", 0, Direction::Input),
- "The ID for a currently running job on " + m_SCARFComputeResource);
- setPropertySettings("CancelJobID", make_unique<VisibleWhenProperty>(
- "Action", IS_EQUAL_TO, "CancelJob"));
-}
-
-/**
- * Execute algorithm: check what action/command has to be run and call
- * specific methods.
- *
- * The implementation of the more specific methods is based on:
- * Mantid::Kernel::InternetHelper.
- */
-void SCARFTomoReconstruction::exec() {
-
- m_action = getAction();
-
- g_log.information("Running SCARFTomoReconstruction");
-
- // only action that doesn't require any credentials
- if (Action::PING == m_action) {
- doPing();
- return;
- }
-
- // otherwise, check first username and then action-specific parameters
- std::string username;
- try {
- username = getPropertyValue("UserName");
- } catch (std::runtime_error & /*e*/) {
- g_log.error()
- << "To use this algorithm to perform the requested action "
- "you need to give a valid username on the compute resource" +
- m_SCARFComputeResource << '\n';
- throw;
- }
- // all actions that require at least a username
- if (Action::LOGIN == m_action) {
- std::string password;
- try {
- password = getPropertyValue("Password");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "To log in using this algorithm you need to give a "
- "valid username and password on the compute resource "
- << m_SCARFComputeResource << ".\n";
- throw;
- }
- if (password.empty()) {
- throw std::runtime_error("You have given an empty password but the "
- "current login mechanism on " +
- m_SCARFComputeResource +
- " does not support "
- "this. This may change in the future. For the "
- "time being you need to provide a password.");
- }
- doLogin(username, password);
- } else if (Action::LOGOUT == m_action) {
- doLogout(username);
- } else if (Action::SUBMIT == m_action) {
- doSubmit(username);
- } else if (Action::QUERYSTATUS == m_action) {
- doQueryStatus(username);
- } else if (Action::QUERYSTATUSBYID == m_action) {
- std::string jobId;
- try {
- jobId = getPropertyValue("JobID");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "To query the detailed status of a job by its ID you "
- "need to give the ID of a job running on "
- << m_SCARFComputeResource << ".\n";
- throw;
- }
- doQueryStatusById(username, jobId);
- } else if (Action::CANCEL == m_action) {
- std::string jobId;
- try {
- jobId = getPropertyValue("CancelJobID");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "To cancel a job you need to give the ID of a job "
- "running on " << m_SCARFComputeResource << ".\n";
- throw;
- }
- doCancel(username, jobId);
- } else if (Action::UPLOAD == m_action) {
- std::string filename, destDir;
- try {
- filename = getPropertyValue("FileToUpload");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "To upload a file you need to provide an existing "
- "local file.\n";
- throw;
- }
- try {
- destDir = getPropertyValue("DestinationDirectory");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "To upload a file you need to provide a destination "
- "directory on " << m_SCARFComputeResource << ".\n";
- throw;
- }
- doUploadFile(username, destDir, filename);
- } else if (Action::DOWNLOAD == m_action) {
- std::string jobId, fname, localDir;
- try {
- jobId = getPropertyValue("DownloadJobID");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "To download a file you need to give the ID of a job "
- "running on " << m_SCARFComputeResource << ".\n";
- throw;
- }
- try {
- fname = getPropertyValue("RemoteJobFilename");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "To download a file you need to provide the name of a "
- "file from the remote job.\n";
- throw;
- }
- try {
- localDir = getPropertyValue("LocalDirectory");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "To download a file you need to provide a destination "
- "(local) directory.\n";
- throw;
- }
- doDownload(username, jobId, fname, localDir);
- }
-}
-
-/**
- * Log into SCARF. If it goes well, it will produce a token that can
- * be reused for a while in subsequent queries. Internally it relies
- * on the InternetHelper to send an HTTP request and obtain the
- * response.
- *
- * @param username normally an STFC federal ID
- * @param password user password
- */
-void SCARFTomoReconstruction::doLogin(const std::string &username,
- const std::string &password) {
- // log into "https://portal.scarf.rl.ac.uk/cgi-bin/token.py";
-
- // this should go away and obtained from 'computeResourceInfo' (like
- // a very simple InstrumentInfo) or similar. What we need here is
- // computeResourceInfo::baseURL()
- const std::string SCARFLoginBaseURL = "https://portal.scarf.rl.ac.uk/";
- const std::string SCARFLoginPath = "/cgi-bin/token.py";
-
- std::vector<std::string> res =
- ConfigService::Instance().getFacility().computeResources();
- auto it = std::find(res.begin(), res.end(), m_SCARFComputeResource);
- if (res.end() == it)
- throw std::runtime_error(
- std::string("Failed to find a compute resource "
- "for " +
- m_SCARFComputeResource + " (facility: " +
- ConfigService::Instance().getFacility().name() + ")."));
-
- std::string httpsURL = SCARFLoginBaseURL + SCARFLoginPath + "?username=" +
- username + "&password=" + password;
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error("Error while sending HTTP request to authenticate "
- "(log in): " +
- std::string(ie.what()));
- }
- // We would check (Poco::Net::HTTPResponse::HTTP_OK == code) but the SCARF
- // login script (token.py) seems to return 200 whatever happens, as far as the
- // request is well formed. So this is how to know if authentication succeeded:
- const std::string expectedSubstr = "https://portal.scarf.rl.ac.uk";
- std::string resp = ss.str();
- if (InternetHelper::HTTP_OK == code &&
- resp.find(expectedSubstr) != std::string::npos) {
- // it went fine, stash cookie/token which looks like this (2 lines):
- // https://portal.scarf.rl.ac.uk:8443/platform/
- // scarf362"2015-02-10T18:50:00Z"Mv2ncX8Z0TpH0lZHxMyXNVCb7ucT6jHNOx...
- std::string url, token_str;
- std::getline(ss, url);
- std::getline(ss, token_str);
- // note that the token needs a substring replace and a prefix, like this:
- boost::replace_all(token_str, "\"", "#quote#");
- token_str = "platform_token=" + token_str;
- // insert in the token stash
- UsernameToken tok(username, Token(url, token_str));
- m_tokenStash.insert(tok); // the password is never stored
- g_log.notice() << "Got authentication token. You are now logged into "
- << m_SCARFComputeResource << '\n';
- } else {
- throw std::runtime_error("Login failed. Please check your username and "
- "password. Got this response: " +
- resp);
- }
-}
-
-/**
- * Log out from SCARF. In practice, it trashes the cookie (if we were
- * successfully logged in).
- *
- * @param username Username to use (should have authenticated before)
- */
-void SCARFTomoReconstruction::doLogout(const std::string &username) {
- auto it = m_tokenStash.find(username);
- if (m_tokenStash.end() == it) {
- throw std::runtime_error(
- "Logout failed. You do not seem to be logged in. "
- "I do not remember this username. Please check your "
- "username.");
- }
-
- // logout query, needs headers = {'Content-Type': 'text/plain', 'Cookie':
- // token,
- // 'Accept': 'text/plain,application/xml,text/xml'}
- const std::string logoutPath = "webservice/pacclient/logout/";
- const std::string baseURL = it->second.m_url;
- const std::string token = it->second.m_token_str;
-
- std::string httpsURL = baseURL + logoutPath;
- std::map<std::string, std::string> headers{{"Content-Type", "text/plain"},
- {"Cookie", token},
- {"Accept", m_acceptType}};
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss, headers);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error("Error while sending HTTP request to log out: " +
- std::string(ie.what()));
- }
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- g_log.notice() << "Logged out.\n";
- g_log.debug() << "Response from server: " << ss.str() << '\n';
- } else {
- throw std::runtime_error("Failed to logout from the web service at: " +
- httpsURL + ". Please check your username.");
- }
-
- // successfully logged out, forget the token
- m_tokenStash.erase(it);
-}
-
-/**
- * Submits a job to SCARF. The different ways jobs could be submitted
- * (supported toolkits, LSF PAC submission forms, launcher scripts,
- * supported options, etc.) are not well defined at the moment.
- *
- * @param username Username to use (should have authenticated before)
- */
-void SCARFTomoReconstruction::doSubmit(const std::string &username) {
- auto it = m_tokenStash.find(username);
- if (m_tokenStash.end() == it) {
- throw std::runtime_error(
- "Job submission failed. You do not seem to be logged "
- "in. I do not remember this username. Please check "
- "your username.");
- }
-
- // Not sure at this point if there could be commands without options
- // For the time being it's possible.
- std::string jobOptions;
- try {
- jobOptions = getPropertyValue("JobOptions");
- } catch (std::runtime_error & /*e*/) {
- g_log.warning() << "You did not specify any options for the job. Maybe you "
- "forgot to pass the options?\n";
- m_jobOptions = "";
- }
-
- std::string runnablePath;
- try {
- runnablePath = getPropertyValue("RunnablePath");
- } catch (std::runtime_error & /*e*/) {
- g_log.error() << "You did not specify a the path to the parameter file "
- "which is required to create a new reconstruction job. "
- "Please provide "
- "a valid tomography reconstruction parameter file\n";
- throw;
- }
-
- std::string jobName;
- try {
- jobName = getPropertyValue("JobName");
- } catch (std::runtime_error & /*e*/) {
- jobName = "";
- }
-
- progress(0, "Starting job...");
-
- // Job submit query, requires specific parameters for LSF submit
- // Example params passed to python submit utility:
- // $ pacclient.py submit --app TOMOPY_0_0_3 --param "INPUT_FILE=
- // /work/imat/webservice_test/tomopy/imat_recon_FBP.py;INPUT_ARGS=
- // /work/imat/scripts/test_;JOB_NAME=01_test_job;OUTPUT_FILE=%J.output;ERROR_FILE=
- // %J.error"
-
- // Two applications are for now registered on SCARF:
- // TOMOPY_0_0_3, PYASTRATOOLBOX_1_1 - old versions
- // TOMOPY_0_1_9, PYASTRATOOLBOX_1_6 - newer versions (Dec 2015)
- std::string appName = "TOMOPY_0_1_9";
- // Basic attempt at guessing the app that we might really need. This
- // is not fixed/unstable at the moment
- if (runnablePath.find("--tool astra") != std::string::npos ||
- runnablePath.find("--tool=astra") != std::string::npos) {
- appName = "PYASTRATOOLBOX_1_6";
- }
-
- // this gets executed (for example via 'exec' or 'python', depending on the
- // appName
- const std::string boundary = "bqJky99mlBWa-ZuqjC53mG6EzbmlxB";
- const std::string &body =
- buildSubmitBody(appName, boundary, runnablePath, jobOptions, jobName);
-
- // Job submit, needs these headers:
- // headers = {'Content-Type': 'multipart/mixed; boundary='+boundary,
- // 'Accept': 'text/xml,application/xml;', 'Cookie': token,
- // 'Content-Length': str(len(body))}
- // Content-Length is added by InternetHelper/Poco HTTP request
- const std::string submitPath = "webservice/pacclient/submitapp";
- const std::string baseURL = it->second.m_url;
- const std::string token = it->second.m_token_str;
-
- std::string httpsURL = baseURL + submitPath;
- std::map<std::string, std::string> headers{
- {"Content-Type", "multipart/mixed; boundary=" + boundary},
- {"Accept", m_acceptType},
- {"Cookie", token}};
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss, headers,
- Poco::Net::HTTPRequest::HTTP_POST, body);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error(
- "Error while sending HTTP request to submit a job: " +
- std::string(ie.what()));
- }
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- std::string resp = ss.str();
- if (std::string::npos != resp.find("<errMsg>")) {
- g_log.warning()
- << "Submitted job but got a a response that seems to contain "
- "an error message from " << m_SCARFComputeResource << ": "
- << extractPACErrMsg(ss.str()) << '\n';
- } else {
- g_log.notice() << "Submitted job successfully.\n";
- g_log.debug() << "Response from server: " << resp << '\n';
- }
- } else {
- throw std::runtime_error(
- "Failed to submit a job through the web service at:" + httpsURL +
- ". Please check your username, credentials, "
- "and parameters.");
- }
-
- progress(1.0, "Job started on " + m_SCARFComputeResource);
-}
-
-/**
- * Query the status of jobs running (if successful will return info on
- * jobs running for our user)
- *
- * @param username Username to use (should have authenticated before)
- */
-void SCARFTomoReconstruction::doQueryStatus(const std::string &username) {
- auto it = m_tokenStash.find(username);
- if (m_tokenStash.end() == it) {
- throw std::runtime_error(
- "Job status query failed. You do not seem to be logged "
- "in. I do not remember this username. Please check "
- "your username.");
- }
-
- progress(0, "Checking the status of jobs...");
-
- // Job query status, needs these headers:
- // headers = {'Content-Type': 'application/xml', 'Cookie': token,
- // 'Accept': ACCEPT_TYPE}
- const std::string jobStatusPath = "webservice/pacclient/jobs?";
- const std::string baseURL = it->second.m_url;
- const std::string token = it->second.m_token_str;
-
- std::string httpsURL = baseURL + jobStatusPath;
- std::map<std::string, std::string> headers{
- {"Content-Type", "application/xml"},
- {"Accept", m_acceptType},
- {"Cookie", token}};
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss, headers);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error(
- "Error while sending HTTP request to query the status "
- "of jobs: " +
- std::string(ie.what()));
- }
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- std::string resp = ss.str();
- if (std::string::npos != resp.find("<Jobs>") &&
- std::string::npos != resp.find("<extStatus>")) {
- genOutputStatusInfo(resp);
- g_log.notice() << "Queried the status of jobs and stored the "
- "information in output properties.\n";
- } else {
- g_log.warning() << "Queried the status of jobs but got what looks "
- "like an error message as response: " << resp << '\n';
- }
- g_log.notice() << "Queried job status successfully.\n";
- g_log.debug() << "Response from server: " << resp << '\n';
- } else {
- throw std::runtime_error(
- "Failed to obtain job status information through the "
- "web service at:" +
- httpsURL + ". Please check your "
- "username, credentials, and parameters.");
- }
-
- progress(1.0, "Status of jobs retrived.");
-}
-
-/**
- * Query the status of jobs running (if successful will return info on
- * jobs running for our user)
- *
- * @param username Username to use (should have authenticated before)
- * @param jobId Identifier of a job as used by the job scheduler (integer
- *number)
- */
-void SCARFTomoReconstruction::doQueryStatusById(const std::string &username,
- const std::string &jobId) {
- auto it = m_tokenStash.find(username);
- if (m_tokenStash.end() == it) {
- throw std::runtime_error(
- "Job status query failed. You do not seem to be logged "
- "in. I do not remember this username. Please check "
- "your username.");
- }
-
- progress(0, "Checking the status of job with Id " + jobId);
-
- // Job query status, needs these headers:
- // headers = {'Content-Type': 'application/xml', 'Cookie': token,
- // 'Accept': ACCEPT_TYPE}
- const std::string jobIdStatusPath = "webservice/pacclient/jobs/";
- const std::string baseURL = it->second.m_url;
- const std::string token = it->second.m_token_str;
-
- std::string httpsURL = baseURL + jobIdStatusPath;
- std::map<std::string, std::string> headers{
- {"Content-Type", "application/xml"},
- {"Accept", m_acceptType},
- {"Cookie", token}};
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss, headers);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error(
- "Error while sending HTTP request to query the status "
- "of a job: " +
- std::string(ie.what()));
- }
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- std::string resp = ss.str();
- if (std::string::npos != resp.find("<Jobs>") &&
- std::string::npos != resp.find("<extStatus>")) {
- genOutputStatusInfo(resp, jobId);
- g_log.notice() << "Queried job status (Id " << jobId
- << ") and stored "
- "information into output properties.\n";
- g_log.debug() << "Response from server: " << resp << '\n';
- } else {
- g_log.warning() << "Queried job status (Id " << jobId
- << " ) but got what "
- "looks like an error message as response: " << resp
- << '\n';
- }
- } else {
- throw std::runtime_error("Failed to obtain job (Id:" + jobId +
- " ) status "
- "information through the web service at:" +
- httpsURL +
- ". Please check your username, credentials, and "
- "parameters.");
- }
-
- progress(1.0, "Status of job " + jobId + "retrived.");
-}
-
-/**
- * Ping the server to see if the web service is active/available.
- *
- * @return true if the web service responds.
- */
-bool SCARFTomoReconstruction::doPing() {
- progress(0, "Pinging compute resource " + m_SCARFComputeResource);
-
- // Job ping, needs these headers:
- // headers = {'Content-Type': 'application/xml', 'Accept': ACCEPT_TYPE}
- const std::string pingPath = "platform/webservice/pacclient/ping/";
- // This could be retrieved from facilities or similar
- // (like SCARFLoginBaseURL above) - TODO: clarify that in Facilities.xml
- // the port number is known only after logging in
- const std::string baseURL = "https://portal.scarf.rl.ac.uk:8443/";
-
- std::string httpsURL = baseURL + pingPath;
- std::map<std::string, std::string> headers{
- {"Content-Type", "application/xml"}, {"Accept", m_acceptType}};
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss, headers);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error("Error while sending HTTP request to ping the "
- "server " +
- std::string(ie.what()));
- }
- bool ok = false;
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- std::string resp = ss.str();
- if (std::string::npos != resp.find("Web Services are ready")) {
- g_log.notice()
- << "Pinged compute resource with apparently good response: " << resp
- << '\n';
- ok = true;
- } else {
- g_log.warning() << "Pinged compute resource but got what looks like an "
- "error message: " << resp << '\n';
- }
- } else {
- throw std::runtime_error(
- "Failed to ping the web service at: " + httpsURL +
- ". Please check your parameters, software version, "
- "etc.");
- }
-
- progress(1.0, "Ping compute resource " + m_SCARFComputeResource + " done.");
-
- return ok;
-}
-
-/**
- * Cancel a submitted job, identified by its ID in the job queue.
- *
- * @param username Username to use (should have authenticated before)
- * @param jobId Identifier of a job as used by the job scheduler (integer
- *number)
- */
-void SCARFTomoReconstruction::doCancel(const std::string &username,
- const std::string &jobId) {
- auto it = m_tokenStash.find(username);
- if (m_tokenStash.end() == it) {
- throw std::runtime_error(
- "Job status query failed. You do not seem to be logged "
- "in. I do not remember this username. Please check "
- "your username.");
- }
-
- progress(0, "Cancelling/killing job " + jobId);
-
- // Job kill, needs these headers:
- // headers = {'Content-Type': 'text/plain', 'Cookie': token, 'Accept':
- // ACCEPT_TYPE}
- const std::string killPath =
- "webservice/pacclient/jobOperation/kill/" + jobId;
- const std::string baseURL = it->second.m_url;
- const std::string token = it->second.m_token_str;
-
- std::string httpsURL = baseURL + killPath;
- std::map<std::string, std::string> headers{
- {"Content-Type", "application/xml"},
- {"Cookie", token},
- {"Accept", m_acceptType}};
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss, headers);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error(
- "Error while sending HTTP request to cancel a job: " +
- std::string(ie.what()));
- }
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- std::string resp = ss.str();
- if (std::string::npos != resp.find("<errMsg>")) {
- g_log.warning() << "Killed job with Id" << jobId
- << " but got what looks like an "
- "error message as response: " << extractPACErrMsg(resp)
- << '\n';
- } else if (std::string::npos != resp.find("<actionMsg>")) {
- g_log.notice() << "Killed job with Id" << jobId << ".\n";
- g_log.debug() << "Response from server: " << resp << '\n';
- } else {
- g_log.warning() << "Killed job with Id" << jobId
- << " but got what a response "
- "that I do not recognize: " << resp << '\n';
- }
- } else {
- throw std::runtime_error(
- "Failed to kill job (Id: " + jobId + " ) through the web "
- "service at:" +
- httpsURL + ". Please check your "
- "existing jobs, username, and parameters.");
- }
-
- progress(1.0, "Killed job with Id " + jobId + ".");
-}
-
-/**
- * Upload a file to a directory on the server.
- *
- * @param username Username to use (should have authenticated before)
- * @param destDir Destination directory on the server
- * @param filename File name of the local file to upload
- */
-void SCARFTomoReconstruction::doUploadFile(const std::string &username,
- const std::string &destDir,
- const std::string &filename) {
- auto it = m_tokenStash.find(username);
- if (m_tokenStash.end() == it) {
- throw std::runtime_error(
- "File upload failed. You do not seem to be logged "
- "in. I do not remember this username. Please check "
- "your username.");
- }
-
- progress(0, "Uploading file: " + filename);
-
- // File upload, needs these headers:
- // headers = {'Content-Type': 'multipart/mixed; boundary='+boundary,
- // 'Accept': 'text/plain;', 'Cookie': token,
- // 'Content-Length': str(len(body))}
- // Content-Length is added by InternetHelper/Poco HTTP request
- // The 0 at the end of the upload path is 'jobId' 0, if a jobId is given the
- // upload goes to a path relative to the job path.
- const std::string uploadPath = "webservice/pacclient/upfile/0";
- const std::string boundary = "4k89ogja023oh1-gkdfk903jf9wngmujfs95m";
- const std::string baseURL = it->second.m_url;
- const std::string token = it->second.m_token_str;
-
- InternetHelper session;
- std::string httpsURL = baseURL + uploadPath;
- std::map<std::string, std::string> headers{
- {"Content-Type", "multipart/mixed; boundary=" + boundary},
- {"Accept", m_acceptType},
- {"Cookie", token}};
-
- const std::string &body = buildUploadBody(boundary, destDir, filename);
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss, headers,
- Poco::Net::HTTPRequest::HTTP_POST, body);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error(
- "Error while sending HTTP request to upload a file: " +
- std::string(ie.what()));
- }
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- std::string resp = ss.str();
- g_log.notice() << "Uploaded file, response from server: " << resp << '\n';
- } else {
- throw std::runtime_error(
- "Failed to upload file through the web service at:" + httpsURL +
- ". Please check your username, credentials, "
- "and parameters.");
- }
-
- progress(1.0, "File uploaded to " + m_SCARFComputeResource);
-}
-
-/**
- * Download a file or a set of files from a remote job into a local
- * directory. Note that this download as supported by LSF at SCARF is
- * job-specific: you download a file from a job and not a file in the
- * file system in general. When downloading multiple files this action
- * requires two steps: one first HTTP request to get the remote
- * path(s) for all the job file(s), and a second request or series of
- * requests to actually download the file(s).
- *
- * @param username Username to use (should have authenticated before)
- * @param jobId Identifier of a job as used by the job scheduler (integer
- *number)
- * @param fname File name (of a job file on the compute resource). If no name is
- * given then all the job files are downloaded into localDir
- * @param localDir Local directory where to download the file(s)
- */
-void SCARFTomoReconstruction::doDownload(const std::string &username,
- const std::string &jobId,
- const std::string &fname,
- const std::string &localDir) {
- auto it = m_tokenStash.find(username);
- if (m_tokenStash.end() == it) {
- throw std::runtime_error(
- "File upload failed. You do not seem to be logged "
- "in. I do not remember this username. Please check "
- "your username.");
- }
-
- progress(0, "Downloading file: " + fname + " in " + localDir);
-
- if (fname.empty()) {
- // no/empty name implies we want all the files of a remote job
- getAllJobFiles(jobId, localDir, it->second);
- } else {
- // name given, so we directly download this single file
- getOneJobFile(jobId, fname, localDir, it->second);
- }
-}
-
-/**
- * Send the HHTP(S) request required to perform one of the actions.
- *
- * @param url Full URL, including request string
- * @param rss Response body stream
- * @param headers HTTP headers given as key-value pairs
- * @param method By default GET (Poco::Net::HTTPRequest::HTTP_POST), also
- *accepts
- * POST (Poco::Net::HTTPRequest::HTTP_POST)
- * @param body HTTP message body
- *
- * @return HTTP(S) response code
- */
-int SCARFTomoReconstruction::doSendRequestGetResponse(
- const std::string &url, std::ostream &rss, const StringToStringMap &headers,
- const std::string &method, const std::string &body) {
- InternetHelper session;
-
- std::string ContTypeName = "Content-Type";
- auto it = headers.find(ContTypeName);
- if (headers.end() != it) {
- session.setContentType(it->second);
- }
- session.headers() = headers;
- if (!method.empty())
- session.setMethod(method);
- if (!body.empty()) {
- session.setBody(body);
- // beware, the inet helper will set method=POST if body not empty!
- // But here, for example to download, we need a GET with non-empty body
- if (Poco::Net::HTTPRequest::HTTP_GET == method) {
- session.setMethod(method);
- }
- }
- return session.sendRequest(url, rss);
-}
-
-/**
- * Adds one param to a submit request body (first argument). This is
- * part of a multipart body content.
- *
- * @param body Body string being built for an HTTP request
- * @param boundary Boundary string between parameters, for request encoding
- * @param paramName Name of a parameter, for example INPUT_FILE
- * @param paramVal Value of the parameter
- */
-void SCARFTomoReconstruction::encodeParam(std::string &body,
- const std::string &boundary,
- const std::string ¶mName,
- const std::string ¶mVal) {
- body += "--" + boundary + "\r\n";
- body += "Content-Disposition: form-data; name=\"" + paramName + "\"\r\n";
- body += "Content-Type: application/xml; charset=US-ASCII\r\n";
- body += "Content-Transfer-Encoding: 8bit\r\n";
- body += "\r\n";
- body += "<AppParam><id>" + paramName + "</id><value>" + paramVal +
- "</value><type></type></AppParam>\r\n";
-}
-
-/**
- * Tiny helper to generate an integer sequence number for the job
- * names.
- */
-int SCARFTomoReconstruction::jobSeqNo() { return m_jobSeq++; }
-
-/**
- * Helper method to do the somewhat ugly encoding of parameters for
- * submit requests.
- *
- * @param appName A registered app name/form form SCARF, example: TOMOPY_0_0_3
- * @param boundary Boundary string between parts of the multi-part body
- * @param inputFile Input file parameter, this file will be run
- * @param inputArgs Arguments to the command (application specific)
- * @param jobName Name passed by the user (can be empty == no preference)
- *
- * @return A string ready to be used as body of a 'job submit' HTTP request
- */
-std::string SCARFTomoReconstruction::buildSubmitBody(
- const std::string &appName, const std::string &boundary,
- const std::string &inputFile, const std::string &inputArgs,
- const std::string &jobName) {
- // BLOCK: start and encode app name like this:
- // --bqJky99mlBWa-ZuqjC53mG6EzbmlxB
- // Content-Disposition: form-data; name="AppName"
- // Content-ID: <AppName>
- //
- // TOMOPY_0_0_3
- std::string body = "--" + boundary + "\r\n";
- body += "Content-Disposition: form-data; name=\"AppName\"\r\n"
- "Content-ID: <AppName>\r\n"
- "\r\n" +
- appName + "\r\n";
-
- // BLOCK: encode params head like this:
- // --bqJky99mlBWa-ZuqjC53mG6EzbmlxB
- // Content-Disposition: form-data; name="data"
- // Content-Type: multipart/mixed; boundary=_Part_1_701508.1145579811786
- // Content-ID: <data>
- //
- body += "--" + boundary + "\r\n";
- const std::string boundaryInner = "_Part_1_701508.1145579811786";
- body += "Content-Disposition: form-data; name=\"data\"\r\n";
- body += "Content-Type: multipart/mixed; boundary=" + boundaryInner + "\r\n";
- body += "Content-ID: <data>\r\n";
- body += "\r\n";
-
- // BLOCKS: encode params like this:
- {
- // BLOCK: encode INPUT_ARGS like this:
- // --_Part_1_701508.1145579811786
- // Content-Disposition: form-data; name="INPUT_ARGS"
- // Content-Type: application/xml; charset=US-ASCII
- // Content-Transfer-Encoding: 8bit
- // <AppParam><id>INPUT_ARGS</id><value>
- // /work/imat/scripts/test_</value><type></type></AppParam>
- encodeParam(body, boundaryInner, "INPUT_ARGS", inputArgs);
- }
- {
- // BLOCK: encode OUTPUT_FILE like this:
- // --_Part_1_701508.1145579811786
- // Content-Disposition: form-data; name="OUTPUT_FILE"
- // Content-Type: application/xml; charset=US-ASCII
- // Content-Transfer-Encoding: 8bit
- // <AppParam><id>OUTPUT_FILE</id><value>%J.output</value>
- // <type></type></AppParam>
- encodeParam(body, boundaryInner, "OUTPUT_FILE", "%J.output");
- }
- {
- // BLOCK: encode ERROR_FILE like this:
- // --_Part_1_701508.1145579811786
- // Content-Disposition: form-data; name="ERROR_FILE"
- // Content-Type: application/xml; charset=US-ASCII
- // Content-Transfer-Encoding: 8bit
- // <AppParam><id>ERROR_FILE</id><value>%J.error</value>
- // <type></type></AppParam>
- encodeParam(body, boundaryInner, "ERROR_FILE", "%J.error");
- }
- {
- // BLOCK: encode JOB_NAME like this:
- // --_Part_1_701508.1145579811786
- // Content-Disposition: form-data; name="JOB_NAME"
- // Content-Type: application/xml; charset=US-ASCII
- // Content-Transfer-Encoding: 8bit
- // <AppParam><id>JOB_NAME</id><value>foo</value><type></type></AppParam>
- std::string name;
- if (jobName.empty()) {
- name = "Mantid_tomography_" + std::to_string(jobSeqNo());
- } else {
- name = jobName;
- }
- encodeParam(body, boundaryInner, "JOB_NAME", name);
- }
- {
- // BLOCK: encode INPUT_FILE (this is what will be run,
- // if appName=TOMOPY_0_0_3) like this:
- // --_Part_1_701508.1145579811786
- // Content-Disposition: form-data; name="INPUT_FILE"
- // Content-Type: application/xml; charset=US-ASCII
- // Content-Transfer-Encoding: 8bit
- // <AppParam><id>INPUT_FILE</id><value>
- // /work/imat/webservice_test/tomopy/imat_recon_FBP.py</value>
- // <type></type></AppParam>
- encodeParam(body, boundaryInner, "INPUT_FILE", inputFile);
- }
- // BLOCK: params end like this:
- // --_Part_1_701508.1145579811786--
- //
- body += "--" + boundaryInner + "--\r\n\r\n";
-
- // BLOCK: end like this:
- body += "--" + boundary + "--\r\n\r\n";
-
- return body;
-}
-
-/**
- * Helper method to encode the body of file upload requests.
- *
- * @param boundary Boundary string between parts of the multi-part body
- * @param destDir Path where to upload the file on the remote compute
- *resource/server
- * @param filename Name (path) of the local file to upload
- *
- * @return A string ready to be used as body of a 'file upload' HTTP request
- */
-std::string
-SCARFTomoReconstruction::buildUploadBody(const std::string &boundary,
- const std::string &destDir,
- const std::string &filename) {
- // build file name as given in the request body
- std::string upName = filename;
- std::replace(upName.begin(), upName.end(), '\\', '/');
- // discard up to last / (path)
- upName = upName.substr(upName.rfind('/') + 1);
-
- // BLOCK: start and encode destination directory like this:
- // --4k89ogja023oh1-gkdfk903jf9wngmujfs95m
- // Content-Disposition: form-data; name="DirName"
- // Content-ID: <DirName>
- //
- // /work/imat/foo_test
- std::string body = "--" + boundary + "\r\n";
- body += "Content-Disposition: form-data; name=\"DirName\"\r\n"
- "Content-ID: <DirName>\r\n"
- "\r\n" +
- destDir + "\r\n";
-
- // BLOCK: encode file like this (could be repeated for multi-file uploads):
- // --4k89ogja023oh1-gkdfk903jf9wngmujfs95m
- // Content-Disposition: form-data; name="bar.txt"; filename=bar.txt
- // Content-Type: application/octet-stream
- // Content-ID: <bar.txt>
- //
- body += "--" + boundary + "\r\n";
- body += "Content-Disposition: form-data; name=\"" + upName + "\"\r\n";
- body += "Content-Type: application/octet-stream \r\n";
- body += "Content-Transfer-Encoding: UTF-8\r\n";
- body += "Content-ID: <" + upName + ">\r\n";
- body += "\r\n";
-
- // BLOCK: the file
- std::ifstream fileStream(filename.c_str(),
- std::ios_base::binary | std::ios_base::in);
- Poco::StreamCopier::copyToString(fileStream, body);
-
- // BLOCK: end like this:
- body += "--" + boundary + "--" + "\r\n\r\n";
-
- return body;
-}
-
-/**
- * Fills in a table workspace with job status information from an LSC
- * PAC response in ~xml format. Assumes that the workspace passed is
- * empty and ready to be filled. This guarantees that a non-null (I)
- * table workspace object is returned.
- *
- * @param resp Body of an HHTP response to a status query
- * @param jobIDFilter ID of one job (empty string immplies all jobs)
- */
-void SCARFTomoReconstruction::genOutputStatusInfo(
- const std::string &resp, const std::string &jobIDFilter) {
- Poco::XML::DOMParser parser;
- Poco::AutoPtr<Poco::XML::Document> doc;
- try {
- doc = parser.parseString(resp);
- } catch (Poco::Exception &e) {
- throw std::runtime_error("Unable to parse response in XML format: " +
- e.displayText());
- } catch (std::exception &e) {
- throw std::runtime_error("Unable to parse response in XML format: " +
- std::string(e.what()));
- }
-
- Poco::XML::Element *pRootElem = doc->documentElement();
- if (!pRootElem || !pRootElem->hasChildNodes()) {
- g_log.error("XML response from compute resouce contains no root element.");
- throw std::runtime_error("No root element was found in XML response, "
- "cannot parse it.");
- }
-
- Poco::AutoPtr<Poco::XML::NodeList> jobs =
- pRootElem->getElementsByTagName("Job");
- if (!jobs) {
- g_log.error("XML response from compute resouce contains no root element.");
- throw std::runtime_error("No root element was found in XML response, "
- "cannot parse it.");
- }
-
- size_t n = jobs->length();
- if (0 == jobs->length()) {
- g_log.notice() << "Got information about 0 jobs. You may not have any jobs "
- "currently running on the compute resource. The output "
- "workspace will not "
- "have any rows/information";
- }
-
- // This is the information that is usually available for running/recently
- // run jobs
- std::vector<std::string> jobIds;
- std::vector<std::string> jobNames;
- std::vector<std::string> jobStatus;
- std::vector<std::string> jobCommands;
- for (size_t i = 0; i < n; i++) {
- Poco::XML::Element *el = static_cast<Poco::XML::Element *>(
- jobs->item(static_cast<unsigned long>(i)));
- if (!el)
- throw std::runtime_error("Error while trying to parse job with index " +
- std::to_string(i) +
- "could not produce a complete table workspace.");
-
- Poco::XML::Element *id = el->getChildElement("id");
- if (id) {
- const std::string &IdStr = id->innerText();
- if (!jobIDFilter.empty() && IdStr != jobIDFilter)
- continue;
-
- jobIds.push_back(IdStr);
- }
-
- Poco::XML::Element *name = el->getChildElement("name");
- if (name) {
- jobNames.push_back(name->innerText());
- } else {
- jobNames.emplace_back("Unknown!");
- }
-
- Poco::XML::Element *status = el->getChildElement("status");
- if (status) {
- jobStatus.push_back(status->innerText());
- } else {
- jobStatus.emplace_back("Unknown!");
- }
-
- Poco::XML::Element *cmd = el->getChildElement("cmd");
- if (cmd) {
- jobCommands.push_back(cmd->innerText());
- } else {
- jobCommands.emplace_back("Unknown!");
- }
- }
-
- if (jobIds.size() != jobNames.size() || jobIds.size() != jobStatus.size() ||
- jobIds.size() != jobCommands.size()) {
- throw std::runtime_error(
- "There was an unexpected error while filling output "
- "properties the information retrieved from the remote "
- "compute resource. Failed to assign properties.");
- }
- if (jobIDFilter.empty()) {
- // multi-job query
- setProperty("RemoteJobsID", jobIds);
- setProperty("RemoteJobsNames", jobNames);
- setProperty("RemoteJobsStatus", jobStatus);
- setProperty("RemoteJobsCommands", jobCommands);
- } else {
- // Single job query. Here the job ID is an input
- if (jobIds.empty()) {
- setProperty("RemoteJobName", "Unknown!");
- setProperty("RemoteJobStatus", "Unknown!");
- setProperty("RemoteJobCommand", "Unknown!");
- } else {
- setProperty("RemoteJobName", jobNames.front());
- setProperty("RemoteJobStatus", jobStatus.front());
- setProperty("RemoteJobCommand", jobCommands.front());
- }
- }
-}
-
-/**
- * Gets action code in m_action, if input argument is valid. Otherwise
- * show error message and get undefined action.
- *
- * @return A valid action code (including 'undefined' code, if action
- * not known).
- */
-SCARFTomoReconstruction::Action::Type SCARFTomoReconstruction::getAction() {
- std::string par = getPropertyValue("Action");
- Action::Type act = Action::UNDEF;
- if (par == "LogIn") {
- act = Action::LOGIN;
- } else if (par == "LogOut") {
- act = Action::LOGOUT;
- } else if (par == "SubmitJob") {
- act = Action::SUBMIT;
- } else if (par == "JobStatus") {
- act = Action::QUERYSTATUS;
- } else if (par == "JobStatusByID") {
- act = Action::QUERYSTATUSBYID;
- } else if (par == "Ping") {
- act = Action::PING;
- } else if (par == "CancelJob") {
- act = Action::CANCEL;
- } else if (par == "Upload") {
- act = Action::UPLOAD;
- } else if (par == "Download") {
- act = Action::DOWNLOAD;
- } else {
- g_log.error() << "Unknown action specified: '" << m_action
- << "', ignoring it.";
- }
- return act;
-}
-
-/**
- * Helper to check if it's possible to write an output file and give
- * informative messages.
- *
- * @param localPath Destination directory
- * @param fname Name of the file being downloaded
- *
- * @return The full patch checked
- */
-const std::string SCARFTomoReconstruction::checkDownloadOutputFile(
- const std::string &localPath, const std::string &fname) const {
- std::string outName = localPath + "/" + fname;
- Poco::File f(outName);
- if (f.exists()) {
- if (f.canWrite()) {
- g_log.notice() << "Overwriting output file: " << outName << '\n';
- } else {
- g_log.warning() << "It is not possible to write into the output file: "
- << outName << ", you may not have the required "
- "permissions. Please check.\n";
- }
- }
- return f.path();
-}
-
-/**
- * Turns the esoteric name used in LSF PAC web service into a normal
- * filename (as a basename + extention, discarding the path to
- * it). For example, this method translates:
- * 'PAC Server* /home/isisg/scarf362/../scarf362/
- * Mantid_tomography_1_1423743450375PtlPj/417666.error*FILE*281*true'
- * into '417666.error'.
- *
- * @param PACName A file name specification as returned by PAC LSF
- * when downloading multiple files from jobs
- *
- * @return A filename ready to be used to save the file locally. Empty
- * string if fails.
- */
-const std::string
-SCARFTomoReconstruction::filterPACFilename(const std::string PACName) const {
- // discard up to last / (path)
- std::string name = PACName.substr(PACName.rfind('/') + 1);
- // remove trailing parameters
- size_t ast = name.find('*');
- name.replace(ast, std::string::npos, "");
- return name;
-}
-
-/**
- * Download a job file once we have obtained the remote path.
- *
- * @param jobId Identifier of a job as used by the job scheduler (integer
- *number)
- * @param remotePath File name (of a job file on the compute resource)
- * @param localPath Local path where to download the file (already checked)
- * @param t Authentication token/cookie including url+string
- */
-void SCARFTomoReconstruction::getOneJobFile(const std::string &jobId,
- const std::string &remotePath,
- const std::string &localPath,
- const Token &t) {
- // Job download (one) file once we know the remote path, needs these headers:
- // headers = {'Content-Type': 'text/plain', 'Cookie': token, 'Accept':
- // ACCEPT_TYPE}
- // - and as request body the name of the file
- const std::string downloadOnePath = "webservice/pacclient/file/" + jobId;
- const std::string baseURL = t.m_url;
- const std::string token = t.m_token_str;
-
- std::string httpsURL = baseURL + downloadOnePath;
-
- std::map<std::string, std::string> headers{
- {"Content-Type", "application/xml"},
- {"Cookie", token},
- {"Accept", m_acceptType}};
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(
- httpsURL, ss, headers, Poco::Net::HTTPRequest::HTTP_GET, remotePath);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error(
- "Error while sending HTTP request to download a file: " +
- std::string(ie.what()));
- }
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- // this is what indicates success/failure: response content empty/not empty
- if (ss.rdbuf()->in_avail() > 0) {
- // check file is writeable and inform user
- // get basename from 'PAC' name
- std::string name = filterPACFilename(remotePath);
- if (name.empty()) {
- g_log.notice() << "Could not download remote file " << remotePath
- << " into " << localPath
- << ", a problem with its name was found\n";
- }
- std::string outName = checkDownloadOutputFile(localPath, name);
- std::ofstream file(outName.c_str(),
- std::ios_base::binary | std::ios_base::out);
- Poco::StreamCopier::copyStream(ss, file);
- g_log.notice() << "Downloaded remote file " << outName << " into "
- << localPath << ".\n";
- // do this only if you want to log the file contents!
- // g_log.debug() << "Response from server: " << ss.str() << '\n';
- } else {
- // log an error but potentially continue with other files
- g_log.error()
- << "Download failed. You may not have the required permissions "
- "or the file may not be available on " << m_SCARFComputeResource
- << ": " << remotePath << '\n';
- }
- } else {
- throw std::runtime_error(
- "Failed to download a file for job Id:" + jobId +
- " through the web service at:" + httpsURL +
- ". Please "
- "check your existing jobs, username, and parameters.");
- }
-}
-
-/**
- * Download all files for a remote job.
- *
- * @param jobId Identifier of a job as used by the job scheduler (integer
- *number)
- * @param localDir Local directory where to download the file (already checked)
- * @param t Authentication token/cookie including url+string
- */
-void SCARFTomoReconstruction::getAllJobFiles(const std::string &jobId,
- const std::string &localDir,
- const Token &t) {
- // Job download (multiple) files, needs these headers:
- // headers = {'Content-Type': 'text/plain', 'Cookie': token, 'Accept':
- // ACCEPT_TYPE}
- const std::string downloadPath = "webservice/pacclient/jobfiles/" + jobId;
- const std::string baseURL = t.m_url;
- const std::string token = t.m_token_str;
-
- std::string httpsURL = baseURL + downloadPath;
- std::map<std::string, std::string> headers{
- {"Content-Type", "application/xml"},
- {"Cookie", token},
- {"Accept", m_acceptType}};
- int code;
- std::stringstream ss;
- try {
- code = doSendRequestGetResponse(httpsURL, ss, headers);
- } catch (Kernel::Exception::InternetError &ie) {
- throw std::runtime_error(
- "Error while sending HTTP request to download files: " +
- std::string(ie.what()));
- }
- // what you get in this response is one line with text like this:
- // 'PAC Server*/home/isisg/scarf362/../scarf362/
- // Mantid_tomography_1_1423743450375PtlPj/417666.error*FILE*281*true;PAC
- // Server*/
- // home/isisg/scarf362/../scarf362/
- // Mantid_tomography_1_1423743450375PtlPj/417666.output*FILE*1145*true;'
- // (the number between *FILE* and *true is the size in bytes)
- std::vector<std::string> filePACNames;
- if (Poco::Net::HTTPResponse::HTTP_OK == code) {
- std::string resp = ss.str();
- // this is what indicates success/failure: presence of '/' or '\'
- if (std::string::npos != resp.find('/') ||
- std::string::npos != resp.find('\\')) {
- // you can get multiple files, as remote file names listed separated by
- // ';'
- std::string PACname;
- while (std::getline(ss, PACname, ';')) {
- filePACNames.push_back(PACname);
- }
- for (auto &filePACName : filePACNames) {
- getOneJobFile(jobId, filePACName, localDir, t);
- }
- }
- } else {
- throw std::runtime_error(
- "Failed to download job files (Id:" + jobId + " ) through "
- "the web service at:" +
- httpsURL + ". Please check your "
- "existing jobs, username, and parameters.");
- }
-
- progress(1.0, "Download of " + std::to_string(filePACNames.size()) +
- " file(s) completed in " + localDir);
-}
-
-/**
- * Gets the error message from a more or less xml response body. Sometimes these
- *error
- * responses may read like this:
- * <?xml version="1.0" encoding="UTF-8" standalone="yes"?><Job>
- * <errMsg>Job <417940>: Job has already finished</errMsg><id>0</id></Job>
- *
- * @param response Body of an HHTP response that apparently contains some error
- *message
- *
- * @return Part of the response that seems to contain the specific error message
- */
-std::string
-SCARFTomoReconstruction::extractPACErrMsg(const std::string &response) const {
- // discard up to last errMsg start tag
- const std::string openTag = "<errMsg>";
- std::string msg = response.substr(response.rfind(openTag) + openTag.size());
- if (msg.empty())
- return response;
-
- // remove close tags
- size_t tags = msg.rfind("</errMsg>");
- msg.replace(tags, std::string::npos, "");
-
- // avoid/translate common entities
- boost::replace_all(msg, "<", "<");
- boost::replace_all(msg, ">", ">");
-
- return msg;
-}
-
-} // end namespace RemoteAlgorithms
-} // end namespace Mantid
diff --git a/Framework/RemoteAlgorithms/test/SCARFTomoReconstructionTest.h b/Framework/RemoteAlgorithms/test/SCARFTomoReconstructionTest.h
deleted file mode 100644
index 207592a1dcd..00000000000
--- a/Framework/RemoteAlgorithms/test/SCARFTomoReconstructionTest.h
+++ /dev/null
@@ -1,683 +0,0 @@
-#ifndef MANTID_REMOTEALGORITHMS_SCARFTOMORECONSTRUCTION_H_
-#define MANTID_REMOTEALGORITHMS_SCARFTOMORECONSTRUCTION_H_
-
-#include <cxxtest/TestSuite.h>
-
-#include "MantidAPI/ITableWorkspace.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidKernel/FacilityInfo.h"
-#include "MantidRemoteAlgorithms/SCARFTomoReconstruction.h"
-
-using namespace Mantid::RemoteAlgorithms;
-
-/**
- * Very crude mock up for the interaction with the remote compute
- * resource (in real life, through the PAC web service of the LSF job
- * scheduler on SCARF). This one returns 200 OK and a simple response
- * string.
- */
-class MockedSCARFTomo : public SCARFTomoReconstruction {
-protected:
- int doSendRequestGetResponse(
- const std::string &url, std::ostream &response,
- const StringToStringMap &headers = StringToStringMap(),
- const std::string &method = std::string(),
- const std::string &body = "") override {
- UNUSED_ARG(url);
- UNUSED_ARG(headers);
- UNUSED_ARG(method);
- UNUSED_ARG(body);
-
- response << "response OK - mocked up";
- return 200;
- }
-};
-
-/**
- * One more crude mock up for the interaction with the remote compute
- * resource. This one returns an error (the connection is fine, but
- * the response from the server is an error; example: wrong path,
- * server bug, etc.).
- */
-class MockedErrorResponse_SCARFTomo : public SCARFTomoReconstruction {
-protected:
- int doSendRequestGetResponse(
- const std::string &url, std::ostream &response,
- const StringToStringMap &headers = StringToStringMap(),
- const std::string &method = std::string(),
- const std::string &body = "") override {
- UNUSED_ARG(url);
- UNUSED_ARG(response);
- UNUSED_ARG(headers);
- UNUSED_ARG(method);
- UNUSED_ARG(body);
-
- response << "Error response - mocked up";
- return 404;
- }
-};
-
-/**
- * One more crude mock up for the interaction with the remote compute
- * resource. This one raises an exception as if the (underlying)
- * InternetHelper had found a connection issue.
- */
-class MockedConnectionError_SCARFTomo : public SCARFTomoReconstruction {
-protected:
- int doSendRequestGetResponse(
- const std::string &url, std::ostream &response,
- const StringToStringMap &headers = StringToStringMap(),
- const std::string &method = std::string(),
- const std::string &body = "") override {
- UNUSED_ARG(url);
- UNUSED_ARG(response);
- UNUSED_ARG(headers);
- UNUSED_ARG(method);
- UNUSED_ARG(body);
-
- // throw as if there was a connection error
- throw Mantid::Kernel::Exception::InternetError(
- "Mocked up exception - connection error");
- }
-};
-
-/**
- * One more crude mock up for the interaction with the remote compute
- * resource. This one returns an OK code and a string that reads like
- * what we expect when doing a successful login request.
- */
-class MockedGoodLoginResponse_SCARFTomo : public SCARFTomoReconstruction {
-protected:
- int doSendRequestGetResponse(
- const std::string &url, std::ostream &response,
- const StringToStringMap &headers = StringToStringMap(),
- const std::string &method = std::string(),
- const std::string &body = "") override {
- UNUSED_ARG(url);
- UNUSED_ARG(response);
- UNUSED_ARG(headers);
- UNUSED_ARG(method);
- UNUSED_ARG(body);
-
- response << "https://portal.scarf.rl.ac.uk - response OK and login "
- "successful - mocked up";
- return 200;
- }
-};
-
-/**
- * One more crude mock up for the interaction with the remote compute
- * resource. This one returns an OK code and a string that reads like
- * a response with basic job status information.
- */
-class MockedGoodJobStatus_SCARFTomo : public SCARFTomoReconstruction {
-public:
- MockedGoodJobStatus_SCARFTomo(const std::string &id)
- : SCARFTomoReconstruction(), jobID(id){};
-
-protected:
- int doSendRequestGetResponse(
- const std::string &url, std::ostream &response,
- const StringToStringMap &headers = StringToStringMap(),
- const std::string &method = std::string(),
- const std::string &body = "") override {
- UNUSED_ARG(url);
- UNUSED_ARG(response);
- UNUSED_ARG(headers);
- UNUSED_ARG(method);
- UNUSED_ARG(body);
-
- response
- << "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>"
- "<Jobs><Job><cmd>python /work/imat/webservice_test/test.py.py "
- "/work/imat/webservice_test/test_out/</cmd><extStatus>-</extStatus>"
- "<id>" << jobID
- << "</id><name>Mantid_tomography_1</name><status>Running</status>"
- "</Job></Jobs>";
- return 200;
- }
-
-private:
- std::string jobID;
-};
-
-class SCARFTomoReconstructionTest : public CxxTest::TestSuite {
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static SCARFTomoReconstructionTest *createSuite() {
- return new SCARFTomoReconstructionTest();
- }
-
- static void destroySuite(SCARFTomoReconstructionTest *suite) { delete suite; }
-
- void setUp() override {
- const Mantid::Kernel::FacilityInfo &fac =
- Mantid::Kernel::ConfigService::Instance().getFacility();
- m_facility = fac.name();
- }
-
- void test_castAlgorithm() {
- // can create
- boost::shared_ptr<MockedSCARFTomo> a;
- TS_ASSERT(a = boost::make_shared<MockedSCARFTomo>());
- // can cast to inherited interfaces and base classes
-
- MockedSCARFTomo alg;
- TS_ASSERT(dynamic_cast<Mantid::RemoteAlgorithms::SCARFTomoReconstruction *>(
- &alg));
- TS_ASSERT(dynamic_cast<Mantid::API::Algorithm *>(&alg));
- TS_ASSERT(dynamic_cast<Mantid::Kernel::PropertyManagerOwner *>(&alg));
- TS_ASSERT(dynamic_cast<Mantid::API::IAlgorithm *>(&alg));
- TS_ASSERT(dynamic_cast<Mantid::Kernel::IPropertyManager *>(&alg));
- }
-
- void test_initAlgorithm() {
- MockedSCARFTomo tomo;
- TS_ASSERT_THROWS_NOTHING(tomo.initialize());
- }
-
- void test_propertiesMissing() {
- MockedSCARFTomo alg1;
- TS_ASSERT_THROWS_NOTHING(alg1.initialize());
- // password missing
- TS_ASSERT_THROWS_NOTHING(alg1.setPropertyValue("UserName", "anything"));
- TS_ASSERT_THROWS_NOTHING(alg1.setPropertyValue("Action", "LogIn"));
-
- TS_ASSERT_THROWS_NOTHING(alg1.execute());
- TS_ASSERT(!alg1.isExecuted());
-
- MockedSCARFTomo alg2;
- TS_ASSERT_THROWS_NOTHING(alg2.initialize());
- // username missing
- TS_ASSERT_THROWS_NOTHING(alg2.setPropertyValue("Password", "whatever"));
- TS_ASSERT_THROWS_NOTHING(alg2.setPropertyValue("Action", "LogIn"));
-
- TS_ASSERT_THROWS(alg2.execute(), std::runtime_error);
- TS_ASSERT(!alg2.isExecuted());
-
- MockedSCARFTomo alg3;
- TS_ASSERT_THROWS_NOTHING(alg3.initialize());
- // mispellings...
- // these try to set inexistent propeties => runtime_error
- TS_ASSERT_THROWS(alg3.setPropertyValue("sername", "anything"),
- std::runtime_error);
- TS_ASSERT_THROWS(alg3.setPropertyValue("Passw", "anything"),
- std::runtime_error);
- // these try to set wrong values for valid properties => invalid_argument
- TS_ASSERT_THROWS(alg3.setPropertyValue("Action", "Loggin"),
- std::invalid_argument);
- TS_ASSERT_THROWS(alg3.setProperty("Action", "unknown_opt"),
- std::invalid_argument);
- TS_ASSERT_THROWS(alg3.setPropertyValue("JobID", "strings_not_allowed"),
- std::invalid_argument);
- }
-
- void test_actionWithoutUsernameBeforeLogin() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
-
- // Forget the username and you should get an exception
- // alg.setProperty("UserName", "foo_user"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "JobStatus"));
-
- TS_ASSERT_THROWS(alg.execute(), std::runtime_error);
- TS_ASSERT(!alg.isExecuted());
-
- MockedSCARFTomo tomo;
- TS_ASSERT_THROWS_NOTHING(tomo.initialize());
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("Action", "SubmitJob"));
-
- TS_ASSERT_THROWS(tomo.execute(), std::runtime_error);
- TS_ASSERT(!tomo.isExecuted());
- }
-
- void test_actionWithoutLogin() {
- MockedSCARFTomo alg;
-
- // Even if you provide all required params, you should get an exception
- // if not logged in
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "JobStatus"));
-
- TS_ASSERT_THROWS(alg.execute(), std::runtime_error);
- TS_ASSERT(!alg.isExecuted());
-
- MockedSCARFTomo tomo;
- TS_ASSERT_THROWS_NOTHING(tomo.initialize());
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("UserName", "anyone"));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("Action", "SubmitJob"));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("RunnablePath", "/foo/bar.sh"));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("JobOptions", "--test --baz"));
-
- TS_ASSERT_THROWS_NOTHING(tomo.execute());
- TS_ASSERT(!tomo.isExecuted());
- }
-
- /// Login is required before running the other actions (except ping)
- // The good username is: foo_user
- void test_login() {
- m_goodUsername = "foo_user";
- m_goodPassword = "foo_password";
-
- // severe (connection) error
- MockedConnectionError_SCARFTomo err;
- TS_ASSERT_THROWS_NOTHING(err.initialize());
- TS_ASSERT_THROWS_NOTHING(err.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(err.setProperty("Password", m_goodPassword));
- TS_ASSERT_THROWS_NOTHING(err.setProperty("Action", "LogIn"));
-
- TS_ASSERT_THROWS_NOTHING(err.execute());
- TS_ASSERT(!err.isExecuted());
-
- // standard mocked response: looks like an unsuccessful login attempt
- MockedSCARFTomo tomo;
- TS_ASSERT_THROWS_NOTHING(tomo.initialize());
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("Password", m_goodPassword));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("Action", "LogIn"));
-
- TS_ASSERT_THROWS_NOTHING(tomo.execute());
- TS_ASSERT(!tomo.isExecuted());
-
- // successful login attempt
- MockedGoodLoginResponse_SCARFTomo login;
- TS_ASSERT_THROWS_NOTHING(login.initialize());
- TS_ASSERT_THROWS_NOTHING(login.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(login.setProperty("Password", m_goodPassword));
- TS_ASSERT_THROWS_NOTHING(login.setProperty("Action", "LogIn"));
-
- TS_ASSERT_THROWS_NOTHING(login.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT(
- "This algorithm / login should fail when the facility is not " +
- g_supportedFacility,
- !login.isExecuted());
- return;
- }
-
- TS_ASSERT(login.isExecuted());
- }
-
- void test_actionWithoutUsernameAfterLogin() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
-
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "JobStatus"));
-
- TS_ASSERT_THROWS(alg.execute(), std::runtime_error);
- TS_ASSERT(!alg.isExecuted());
-
- MockedSCARFTomo tomo;
- TS_ASSERT_THROWS_NOTHING(tomo.initialize());
- // Forget this and you should get an exception
- // tomo.setProperty("UserName", 3));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("Action", "SubmitJob"));
-
- TS_ASSERT_THROWS(tomo.execute(), std::runtime_error);
- TS_ASSERT(!tomo.isExecuted());
- }
-
- void test_actionWrongUsername() {
- // Once you log out all actions should produce an exception
- MockedSCARFTomo tomo;
- TS_ASSERT_THROWS_NOTHING(tomo.initialize());
- TS_ASSERT_THROWS_NOTHING(
- tomo.setProperty("UserName", "fail_" + m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("Action", "JobStatus"));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("RunnablePath", "/foo/bar.sh"));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("JobOptions", "--test --baz"));
-
- TS_ASSERT_THROWS_NOTHING(tomo.execute());
- TS_ASSERT(!tomo.isExecuted());
- }
-
- void test_wrongExec() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS(alg.setProperty("RandomName", 32), std::runtime_error);
-
- TS_ASSERT_THROWS(alg.execute(), std::runtime_error);
- TS_ASSERT(!alg.isExecuted());
- }
-
- void test_ping() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(alg.setPropertyValue("Action", "Ping"));
- TS_ASSERT_THROWS_NOTHING(alg.setPropertyValue("Username", m_goodUsername));
-
- TS_ASSERT_THROWS_NOTHING(alg.execute());
- TS_ASSERT(alg.isExecuted());
- }
-
- void test_submit() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "SubmitJob"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("RunnablePath", "/foo/bar.sh"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("JobOptions", "--test --baz"));
-
- TS_ASSERT_THROWS_NOTHING(alg.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT(
- "This algorithm / submit should fail when the facility is not " +
- g_supportedFacility,
- !alg.isExecuted());
- return;
- }
-
- TS_ASSERT(alg.isExecuted());
-
- // second submit in a row
- MockedSCARFTomo tomo;
- TS_ASSERT_THROWS_NOTHING(tomo.initialize());
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("Action", "SubmitJob"));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("RunnablePath", "/foo/bar.sh"));
- TS_ASSERT_THROWS_NOTHING(tomo.setProperty("JobOptions", "--random --baz"));
-
- TS_ASSERT_THROWS_NOTHING(tomo.execute());
- TS_ASSERT(tomo.isExecuted());
- }
-
- void test_queryStatus() {
- // this one is the basic mock up which doesn't provide the response content
- // that we need
- MockedSCARFTomo err;
- TS_ASSERT_THROWS_NOTHING(err.initialize());
- TS_ASSERT_THROWS_NOTHING(err.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(err.setProperty("Action", "JobStatus"));
-
- TS_ASSERT_THROWS_NOTHING(err.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT(
- "This algorithm / queryStatus should fail when the facility is not " +
- g_supportedFacility,
- !err.isExecuted());
- return;
- }
-
- TS_ASSERT(err.isExecuted());
-
- std::vector<std::string> vec;
- TS_ASSERT_THROWS_NOTHING(vec = err.getProperty("RemoteJobsID"));
- TS_ASSERT_EQUALS(vec.size(), 0);
- TS_ASSERT_THROWS_NOTHING(vec = err.getProperty("RemoteJobsNames"));
- TS_ASSERT_EQUALS(vec.size(), 0);
- TS_ASSERT_THROWS_NOTHING(vec = err.getProperty("RemoteJobsStatus"));
- TS_ASSERT_EQUALS(vec.size(), 0);
- TS_ASSERT_THROWS_NOTHING(vec = err.getProperty("RemoteJobsCommands"));
- TS_ASSERT_EQUALS(vec.size(), 0);
-
- // this one gives a basic/sufficient response with job status information
- MockedGoodJobStatus_SCARFTomo alg("wrong id");
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "JobStatus"));
-
- TS_ASSERT_THROWS_NOTHING(alg.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT(
- "This algorithm / queryStatus should fail when the facility is not " +
- g_supportedFacility,
- !alg.isExecuted());
- return;
- }
-
- TS_ASSERT(alg.isExecuted());
-
- // the mock produces info on one job
- TS_ASSERT_THROWS_NOTHING(vec = alg.getProperty("RemoteJobsID"));
- TS_ASSERT_EQUALS(vec.size(), 1);
- TS_ASSERT(vec.size() > 0 && !vec.front().empty());
- TS_ASSERT_THROWS_NOTHING(vec = alg.getProperty("RemoteJobsNames"));
- TS_ASSERT_EQUALS(vec.size(), 1);
- TS_ASSERT(vec.size() > 0 && !vec.front().empty());
- TS_ASSERT_THROWS_NOTHING(vec = alg.getProperty("RemoteJobsStatus"));
- TS_ASSERT_EQUALS(vec.size(), 1);
- TS_ASSERT(vec.size() > 0 && !vec.front().empty());
- TS_ASSERT_THROWS_NOTHING(vec = alg.getProperty("RemoteJobsCommands"));
- TS_ASSERT_EQUALS(vec.size(), 1);
- TS_ASSERT(vec.size() > 0 && !vec.front().empty());
- }
-
- void test_queryStatusByID() {
- // this one is the basic mockup: doesn't provide the response content that
- // we need
- MockedSCARFTomo err;
- TS_ASSERT_THROWS_NOTHING(err.initialize());
- TS_ASSERT_THROWS_NOTHING(err.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(err.setProperty("Action", "JobStatusByID"));
- TS_ASSERT_THROWS_NOTHING(err.setProperty("JobID", 123456789));
-
- TS_ASSERT_THROWS_NOTHING(err.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT("This algorithm / queryStatusByID should fail when the "
- "facility is not " +
- g_supportedFacility,
- !err.isExecuted());
- return;
- }
-
- TS_ASSERT(err.isExecuted());
-
- std::string tmp;
- TS_ASSERT_THROWS_NOTHING(tmp = err.getPropertyValue("RemoteJobName"));
- TS_ASSERT(tmp.empty());
- TS_ASSERT_THROWS_NOTHING(tmp = err.getPropertyValue("RemoteJobStatus"));
- TS_ASSERT(tmp.empty());
- TS_ASSERT_THROWS_NOTHING(tmp = err.getPropertyValue("RemoteJobsCommands"));
- TS_ASSERT(tmp.empty());
-
- // this one gives a basic/sufficient response with job status information
- std::string jobID = "444449";
- MockedGoodJobStatus_SCARFTomo alg(jobID);
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "JobStatusByID"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("JobID", jobID));
-
- TS_ASSERT_THROWS_NOTHING(alg.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT("This algorithm / queryStatusByID should fail when the "
- "facility is not " +
- g_supportedFacility,
- !alg.isExecuted());
- return;
- }
-
- TS_ASSERT(alg.isExecuted());
-
- // It could also check that it gets the names, etc. that the mock-up
- // produces
- TS_ASSERT_THROWS_NOTHING(tmp = alg.getPropertyValue("RemoteJobName"));
- TS_ASSERT(!tmp.empty());
- TS_ASSERT_THROWS_NOTHING(tmp = alg.getPropertyValue("RemoteJobStatus"));
- TS_ASSERT(!tmp.empty());
- TS_ASSERT_THROWS_NOTHING(tmp = alg.getPropertyValue("RemoteJobCommand"));
- TS_ASSERT(!tmp.empty());
- }
-
- void test_cancel() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "CancelJob"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("CancelJobID", 123456789));
-
- TS_ASSERT_THROWS_NOTHING(alg.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT(
- "This algorithm / cancel should fail when the facility is not " +
- g_supportedFacility,
- !alg.isExecuted());
- return;
- }
-
- TS_ASSERT(alg.isExecuted());
- }
-
- void test_upload() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Username", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "Upload"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("FileToUpload", "random_file"));
- TS_ASSERT_THROWS_NOTHING(
- alg.setProperty("DestinationDirectory", "random_path/"));
-
- TS_ASSERT_THROWS_NOTHING(alg.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT(
- "This algorithm / upload should fail when the facility is not " +
- g_supportedFacility,
- !alg.isExecuted());
- return;
- }
-
- TS_ASSERT(alg.isExecuted());
- }
-
- void test_download() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
-
- // Download with empty filename (get all files)
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "Download"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("DownloadJobID", 12345));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("RemoteJobFilename", ""));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("LocalDirectory", "/tmp/foo"));
- TS_ASSERT_THROWS_NOTHING(alg.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT(
- "This algorithm / download should fail when the facility is not " +
- g_supportedFacility,
- !alg.isExecuted());
- return;
- }
-
- TS_ASSERT(alg.isExecuted());
-
- MockedSCARFTomo alg2;
- TS_ASSERT_THROWS_NOTHING(alg2.initialize());
-
- // Download a single file (giving its name)
- TS_ASSERT_THROWS_NOTHING(alg2.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg2.setProperty("Action", "Download"));
- TS_ASSERT_THROWS_NOTHING(alg2.setProperty("DownloadJobID", 12345));
- TS_ASSERT_THROWS_NOTHING(
- alg2.setProperty("RemoteJobFilename", "inexistent_test_name.nxs.foo"));
- TS_ASSERT_THROWS_NOTHING(alg2.setProperty("LocalDirectory", "/tmp/foo"));
- TS_ASSERT_THROWS_NOTHING(alg2.execute());
- TS_ASSERT(!alg2.isExecuted());
- }
-
- void test_errorResponseFromServer() {
- MockedErrorResponse_SCARFTomo err;
- TS_ASSERT_THROWS_NOTHING(err.initialize());
- TS_ASSERT_THROWS_NOTHING(err.setPropertyValue("Username", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(err.setPropertyValue("Action", "JobStatus"));
-
- TS_ASSERT_THROWS_NOTHING(err.execute());
- TS_ASSERT(!err.isExecuted());
- }
-
- // logout must run after all the (positive) tests
- void test_logout() {
- MockedSCARFTomo alg;
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "LogOut"));
-
- TS_ASSERT_THROWS_NOTHING(alg.execute());
-
- if (g_supportedFacility != m_facility) {
- TSM_ASSERT(
- "This algorithm / logout should fail when the facility is not " +
- g_supportedFacility,
- !alg.isExecuted());
- return;
- }
-
- TS_ASSERT(alg.isExecuted());
- }
-
- void test_actionAfterLogout() {
- MockedSCARFTomo alg;
- // Once you log out all actions should produce an exception, regardless of
- // the username given
- TS_ASSERT_THROWS_NOTHING(alg.initialize());
- TS_ASSERT_THROWS_NOTHING(
- alg.setProperty("UserName", "fail_" + m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("Action", "JobStatus"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("RunnablePath", "/foo/bar.sh"));
- TS_ASSERT_THROWS_NOTHING(alg.setProperty("JobOptions", "--test --baz"));
-
- TS_ASSERT_THROWS_NOTHING(alg.execute());
- TS_ASSERT(!alg.isExecuted());
-
- MockedSCARFTomo alg2;
- TS_ASSERT_THROWS_NOTHING(alg2.initialize());
- TS_ASSERT_THROWS_NOTHING(alg2.setProperty("UserName", m_goodUsername));
- TS_ASSERT_THROWS_NOTHING(alg2.setProperty("Action", "JobStatus"));
- TS_ASSERT_THROWS_NOTHING(alg2.setProperty("RunnablePath", "/foo/bar.sh"));
- TS_ASSERT_THROWS_NOTHING(alg2.setProperty("JobOptions", "--test --baz"));
-
- TS_ASSERT_THROWS_NOTHING(alg2.execute());
- TS_ASSERT(!alg2.isExecuted());
- }
-
- void test_failConnect() {
- MockedConnectionError_SCARFTomo fail;
- TS_ASSERT_THROWS_NOTHING(fail.initialize());
- TS_ASSERT_THROWS_NOTHING(fail.setPropertyValue("Action", "Ping"));
-
- TS_ASSERT_THROWS(fail.execute(), std::runtime_error);
- TS_ASSERT(!fail.isExecuted());
-
- MockedConnectionError_SCARFTomo fail2;
- TS_ASSERT_THROWS_NOTHING(fail2.initialize());
- // username missing
- TS_ASSERT_THROWS_NOTHING(fail2.setPropertyValue("Username", "uname"));
- TS_ASSERT_THROWS_NOTHING(fail2.setPropertyValue("Password", "whatever"));
- TS_ASSERT_THROWS_NOTHING(fail2.setPropertyValue("Action", "LogIn"));
-
- TS_ASSERT_THROWS_NOTHING(fail2.execute());
- TS_ASSERT(!fail2.isExecuted());
- }
-
- void test_errorResponseFromServerAfterLogout() {
- MockedErrorResponse_SCARFTomo err;
- TS_ASSERT_THROWS_NOTHING(err.initialize());
- TS_ASSERT_THROWS_NOTHING(err.setPropertyValue("Username", "foo"));
- TS_ASSERT_THROWS_NOTHING(err.setPropertyValue("Action", "Ping"));
-
- TS_ASSERT_THROWS_NOTHING(err.execute());
- TS_ASSERT(!err.isExecuted());
- }
-
-private:
- std::string m_goodUsername;
- std::string m_goodPassword;
- std::string m_facility;
- static const std::string g_supportedFacility;
- static const std::string g_SCARFName;
-};
-
-const std::string SCARFTomoReconstructionTest::g_SCARFName = "SCARF@STFC";
-// This algorithm work only for ISIS
-const std::string SCARFTomoReconstructionTest::g_supportedFacility = "ISIS";
-
-#endif // MANTID_REMOTEALGORITHMS_SCARFTOMORECONSTRUCTION_H_
diff --git a/MantidQt/CustomInterfaces/CMakeLists.txt b/MantidQt/CustomInterfaces/CMakeLists.txt
index ef32f9a65cb..a4ecfad17c0 100644
--- a/MantidQt/CustomInterfaces/CMakeLists.txt
+++ b/MantidQt/CustomInterfaces/CMakeLists.txt
@@ -123,29 +123,6 @@ set ( SRC_FILES
src/SANSRunWindow.cpp
src/SampleTransmission.cpp
src/StepScan.cpp
- src/Tomography/EnergyBandsViewQtGUI.cpp
- src/Tomography/TomographyROIPresenter.cpp
- src/Tomography/TomographyROIViewQtWidget.cpp
- src/Tomography/ImageStackPreParams.cpp
- src/Tomography/ImggFormats.cpp
- src/Tomography/ImggFormatsConvertPresenter.cpp
- src/Tomography/ImggFormatsConvertViewQtWidget.cpp
- src/Tomography/StackOfImagesDirs.cpp
- src/Tomography/TomoPathsConfig.cpp
- src/Tomography/TomoReconPostprocSettings.cpp
- src/Tomography/TomoReconPreprocSettings.cpp
- src/Tomography/TomoSystemSettings.cpp
- src/Tomography/TomoSystemSettingsLocal.cpp
- src/Tomography/TomoSystemSettingsRemote.cpp
- src/Tomography/TomoToolConfigDialogBase.cpp
- src/Tomography/TomoToolConfigDialogTomoPy.cpp
- src/Tomography/TomoToolConfigDialogCustom.cpp
- src/Tomography/TomoToolConfigDialogSavu.cpp
- src/Tomography/TomoToolConfigDialogAstra.cpp
- src/Tomography/TomographyIfaceModel.cpp
- src/Tomography/TomographyIfacePresenter.cpp
- src/Tomography/TomographyIfaceViewQtGUI.cpp
- src/Tomography/ToolConfig.cpp
src/UserInputValidator.cpp
src/background.cpp
src/deltaECalc.cpp
@@ -300,40 +277,6 @@ set ( INC_FILES
inc/MantidQtCustomInterfaces/SANSRunWindow.h
inc/MantidQtCustomInterfaces/SampleTransmission.h
inc/MantidQtCustomInterfaces/StepScan.h
- inc/MantidQtCustomInterfaces/Tomography/ITomographyROIPresenter.h
- inc/MantidQtCustomInterfaces/Tomography/ITomographyROIView.h
- inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertPresenter.h
- inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h
- inc/MantidQtCustomInterfaces/Tomography/ITomographyIfacePresenter.h
- inc/MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyROIViewQtWidget.h
- inc/MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h
- inc/MantidQtCustomInterfaces/Tomography/ImggFormats.h
- inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertPresenter.h
- inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertViewQtWidget.h
- inc/MantidQtCustomInterfaces/Tomography/StackOfImagesDirs.h
- inc/MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h
- inc/MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h
- inc/MantidQtCustomInterfaces/Tomography/TomoReconPostprocSettings.h
- inc/MantidQtCustomInterfaces/Tomography/TomoReconPreprocSettings.h
- inc/MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h
- inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h
- inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsLocal.h
- inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsRemote.h
- inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h
- inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogTomoPy.h
- inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogCustom.h
- inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogSavu.h
- inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogAstra.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyThread.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyProcess.h
- inc/MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h
- inc/MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h
- inc/MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h
inc/MantidQtCustomInterfaces/Updateable.h
inc/MantidQtCustomInterfaces/UserInputValidator.h
inc/MantidQtCustomInterfaces/deltaECalc.h
@@ -441,14 +384,6 @@ set ( MOC_FILES inc/MantidQtCustomInterfaces/Background.h
inc/MantidQtCustomInterfaces/SANSEventSlicing.h
inc/MantidQtCustomInterfaces/SANSDiagnostics.h
inc/MantidQtCustomInterfaces/StepScan.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyROIViewQtWidget.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h
- inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertViewQtWidget.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h
- inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogSavu.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyProcess.h
- inc/MantidQtCustomInterfaces/Tomography/TomographyThread.h
)
set ( UI_FILES inc/MantidQtCustomInterfaces/DataComparison.ui
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertPresenter.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertPresenter.h
deleted file mode 100644
index 7fc3ea532d5..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertPresenter.h
+++ /dev/null
@@ -1,60 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IIMGGFORMATSCONVERTPRESENTER_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IIMGGFORMATSCONVERTPRESENTER_H_
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Presenter for the widget to convert images and stacks of images
-between different formats.
-
-Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class IImggFormatsConvertPresenter {
-
-public:
- IImggFormatsConvertPresenter(){};
- virtual ~IImggFormatsConvertPresenter(){};
-
- /// These are user actions, triggered from the (passive) view, that need
- /// handling by the presenter
- enum Notification {
- Init, ///< interface is initing (reload settings, set defaults, etc.)
- Convert, ///< User starts a conversion
- ShutDown ///< The widget is being closed/destroyed
- };
-
- /**
- * Notifications sent through the presenter when an (smart) action
- * is required to respond to user requests or something changes in
- * the view. This plays the role of signals emitted by the view to
- * this presenter.
- *
- * @param notif Type of notification to process.
- */
- virtual void notify(IImggFormatsConvertPresenter::Notification notif) = 0;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IIMGGFORMATSCONVERTPRESENTER_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h
deleted file mode 100644
index 31d34f7ab0a..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h
+++ /dev/null
@@ -1,183 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IIMGGFORMATSCONVERTVIEW_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IIMGGFORMATSCONVERTVIEW_H_
-
-#include "MantidAPI/MatrixWorkspace_fwd.h"
-
-#include <string>
-#include <vector>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Widget to convert images and stacks of images between different image
-formats.
-
-Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class IImggFormatsConvertView {
-
-public:
- IImggFormatsConvertView() {}
-
- virtual ~IImggFormatsConvertView() {}
-
- /**
- * Display a warning to the user (normally as a pop-up).
- *
- * @param warn warning title, should be short and would normally be
- * shown as the title of the window or a big banner.
- *
- * @param description longer, free form and human readable
- * description of the issue.
- */
- virtual void userWarning(const std::string &warn,
- const std::string &description) = 0;
-
- /**
- * Display a visible error message (normally as a pop-up).
- *
- * @param err error title, should be short and would normally be
- * shown as the title of the pop-up window or a big banner.
- *
- * @param description longer, free form description of the issue, as
- * user-understandable and detailed as posssible.
- */
- virtual void userError(const std::string &err,
- const std::string &description) = 0;
-
- /**
- * Set the list of formats that should be shown to the user
- *
- * @param fmts list of formats (identified by a (short) name).
- *
- * @param enableLoad (optional) whether to enable the loading of
- * each of the formats. If not given all of them will be enabled.
- *
- * @param enableSave (optional) whether to enable saving of
- * each of the formats. If not given all of them will be enabled.
- */
- virtual void setFormats(const std::vector<std::string> &fmts,
- const std::vector<bool> &enableLoad = {},
- const std::vector<bool> &enableSave = {}) = 0;
-
- /**
- * The input path to the files to convert, as selected by the user
- *
- * @return path as a string / validation is not done here
- */
- virtual std::string inputPath() const = 0;
-
- /**
- * Name of the format selected to pick input files.
- *
- * @return format name as a string
- */
- virtual std::string inputFormatName() const = 0;
-
- /**
- * The output / destination path for the converted files, as
- * selected by the user
- *
- * @return path as a string / validation is not done here
- */
- virtual std::string outputPath() const = 0;
-
- /**
- * Name of the output format selected.
- *
- * @return format name as a string
- */
- virtual std::string outputFormatName() const = 0;
-
- /**
- * User preference as to whether to compress the output images/data
- * files.
- *
- * @return compress or not
- */
- virtual bool compressHint() const = 0;
-
- /**
- * Maximum depth (subdirectories) to search for file from the input path.
- *
- * @return maximum depth set by the user
- */
- virtual size_t maxSearchDepth() const = 0;
-
- /**
- * Convert image (format A) to image (format B) when both formats
- * are only supported via Qt QImage and related classes. TODO: This
- * should not be here. Move to presenter when we have the
- * Load/SaveImage algorithm:
- * https://github.com/mantidproject/mantid/issues/6843
- *
- * @param inputName name of a readable image file(assuming Qt format
- * guess by header probing + extension)
- *
- * @param inputFormat image format to read
- *
- * @param outputName name of an output image file (assuming Qt
- * format guessing by suffix/extension)
- *
- * @param outputFormat image format to write
- */
- virtual void convert(const std::string &inputName,
- const std::string &inputFormat,
- const std::string &outputName,
- const std::string &outputFormat) const = 0;
-
- /**
- * Write an image that has been loaded in a matrix workspace. As
- * with convert(), move out of here when we have a Load/SaveImage
- * algorithm.
- *
- * @param inWks workspace holding image data
- * @param outputName name for the output file
- * @param outFormat image format
- */
- virtual void writeImg(Mantid::API::MatrixWorkspace_sptr inWks,
- const std::string &outputName,
- const std::string &outFormat) const = 0;
-
- /**
- * Load an image in a matrix workspace. As with convert(), move out
- * of here when we have a Load/SaveImage algorithm.
- *
- * @param inputName name for the output file
- * @param inFormat image format
- *
- * @return a workspace with image data loaded from file
- */
- virtual Mantid::API::MatrixWorkspace_sptr
- loadImg(const std::string &inputName, const std::string &inFormat) const = 0;
-
- /**
- * Save this widget settings (when closing this widget).
- */
- virtual void saveSettings() const = 0;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IIMGGFORMATSCONVERTVIEW_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyIfacePresenter.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyIfacePresenter.h
deleted file mode 100644
index a97f414c83f..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyIfacePresenter.h
+++ /dev/null
@@ -1,73 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYIFACEPRESENTER_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYIFACEPRESENTER_H_
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Interface for what the presenter of the tomography GUI needs to
-implement. Here the term presenter is used as in the MVP
-(Model-View-Presenter) pattern. The (passive) view will use this.
-
-Copyright © 2014-2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class ITomographyIfacePresenter {
-public:
- virtual ~ITomographyIfacePresenter() {}
-
- /// These are user actions, triggered from the (passive) view, that need
- /// handling by the presenter
- enum Notification {
- SystemSettingsUpdated, ///< Change in the system settings (local or remote)
- SetupResourcesAndTools, ///< Setup what are available, normally at startup
- CompResourceChanged, ///< 'current' compute resource changed
- ToolChanged, ///< 'current' tomographic reconstruction tool changed
- TomoPathsChanged, ///< user selects tomography data paths
- TomoPathsEditedByUser, ///< user edits manually paths that may modify other
- /// paths
- LogInRequested, ///< user hits 'log in' or similar
- LogOutRequested, ///< user hits 'log out' or similar
- SetupReconTool, ///< To start the setup (open dialog, etc.)
- RunReconstruct, ///< user hits 'reconstruct' or similar
- RunExternalProcess, /// M run external process using the cached parameters
- RefreshJobs, ///< get updated jobs info in the table/tree
- CancelJobFromTable, ///< cancel one job from the list
- VisualizeJobFromTable, ///< open visualization window for one job
- AggregateEnergyBands, ///< run aggregate bands (in the background)
- LogMsg, ///< need to send a message to the Mantid log system
- ShutDown ///< closing the interface
- };
-
- /**
- * Notifications sent through the presenter when something changes
- * in the view. This plays the role of signals emitted by the view
- * to this presenter.
- *
- * @param notif Type of notification to process.
- */
- virtual void notify(ITomographyIfacePresenter::Notification notif) = 0;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYIFACEPRESENTER_H_
\ No newline at end of file
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h
deleted file mode 100644
index 4cf862a8713..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h
+++ /dev/null
@@ -1,323 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYIFACEVIEW_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYIFACEVIEW_H_
-
-#include "MantidAPI/IAlgorithm_fwd.h"
-#include "MantidAPI/IRemoteJobManager.h"
-#include "MantidAPI/MatrixWorkspace_fwd.h"
-#include "MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoReconFiltersSettings.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h"
-
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-
-#include <QString>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Tomography GUI. Base class / interface for the view of the tomo GUI
-(view in the sense of the MVP pattern). This class is Qt-free. Qt
-specific functionality/dependencies are added in a class derived from
-this.
-
-Copyright © 2014-2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class ITomographyIfaceView {
-
-public:
- ITomographyIfaceView(){};
- virtual ~ITomographyIfaceView(){};
-
- /**
- * Display a warning to the user (for example as a pop-up window).
- *
- * @param warn warning title, should be short and would normally be
- * shown as the title of the window or a big banner.
- *
- * @param description longer, free form description of the issue.
- */
- virtual void userWarning(const std::string &warn,
- const std::string &description) = 0;
-
- /**
- * Display an error message (for example as a pop-up window).
- *
- * @param err Error title, should be short and would normally be
- * shown as the title of the window or a big banner.
- *
- * @param description longer, free form description of the issue.
- */
- virtual void userError(const std::string &err,
- const std::string &description) = 0;
-
- /**
- * Set the compute resources available (remote and/or local). Note
- * that the order of the list is/can be important.
- *
- * @param resources identifiers for the resources (their display names
- * normally). Order matters
- *
- * @param enabled tell if the resources are enabled or usable (which
- * should have an effect on how they are displayed and if they can be
- * used (for example, selected) in the interface.
- */
- virtual void setComputeResources(const std::vector<std::string> &resources,
- const std::vector<bool> &enabled) = 0;
-
- /**
- * Set the tools available on a compute resource.
- *
- * @param tools identifiers of the tools that can or could be run.
- * Order matters
- *
- * @param enabled tells if the tools are actually usable (which
- * should have an effect on how they are displayed and if they can
- * be used in the GUI (for example, if they can be selected at all).
- */
- virtual void setReconstructionTools(const std::vector<std::string> &tools,
- const std::vector<bool> &enabled) = 0;
-
- /**
- * Gives messages that this View wants to send to the logging
- * system.
- *
- * @return list of messages to log, one by one.
- */
- virtual std::vector<std::string> logMsgs() const = 0;
-
- /**
- * Reference or ID of the experiment entered/selected by the
- * user. The ID is effectively the RBNumber (defined at ISIS as the
- * "experiment reference number from the proposal"). The RBNumber
- * identifies one experiment or a set of experiments from an
- * approved experiment proposal. See for example:
- * www.isis.stfc.ac.uk/groups/computing/data/problems-finding-your-data11691.html
- *
- * @return identifier as a string
- */
- virtual std::string experimentReference() const = 0;
-
- /**
- * Username entered by the user
- *
- * @return username to log in to the compute resource
- */
- virtual std::string getUsername() const = 0;
-
- /**
- * Password entered by the user
- *
- * @return password to authenticate / log in to the compute resource
- */
- virtual std::string getPassword() const = 0;
-
- virtual std::vector<std::string> processingJobsIDs() const = 0;
-
- /**
- * Get the current system settings. This includes several
- * parameters. Most of them are paths or path components them, but
- * there are also some naming conventions and other parameters.
- *
- * @return Settings with current values (possibly modified by the
- * user).
- */
- virtual TomoSystemSettings systemSettings() const = 0;
-
- /**
- * The filters settings defined by the user. These options are
- * general pre-/post-processing options.
- *
- * @return Pre-/post-processing filters settings
- */
- virtual TomoReconFiltersSettings prePostProcSettings() const = 0;
-
- /**
- * Gets the compute resource that is currently selected by the user.
- * This calls a validation method that can throw in case of
- * inconsistencies.
- *
- * @return Name of the compute resource as a string.
- */
- virtual std::string currentComputeResource() const = 0;
-
- /**
- * What's the reconstruction tool currently used and/or set up by
- * the user.
- *
- * @return name of the tool as a human readable string
- */
- virtual std::string currentReconTool() const = 0;
-
- /**
- * Updates buttons and banners related to the current login
- * status. For example, when we are logged in, the 'log in' button
- * should be disabled, but some other widget may be enabled or some
- * way displaying the 'in' status.
- *
- * @param loggedIn if we're logged in.
- */
- virtual void updateLoginControls(bool loggedIn) = 0;
-
- /**
- * To enable/disable the actions that require being logged in. This
- * can include for example: submit jobs, get or refresh status of
- * jobs, setup parameters for the remote compute resource, logout,
- * etc.
- *
- * @param enable True to enable, or allow the user to use buttons
- * and widgets to trigger those actions.
- */
- virtual void enableLoggedActions(bool enable) = 0;
-
- /**
- * Whether to enable (allow the user to open or use) the tool
- * specific configuration dialog.
- *
- * @param on enable the button or mechanism to open the dialog
- */
- virtual void enableConfigTool(bool on) = 0;
-
- /**
- * Set the state of the 'reconstruct' button or similar to start
- * reconstruction jobs.
- *
- * @param on whether to enable / allow the user to run it
- */
- virtual void enableRunReconstruct(bool on) = 0;
-
- /**
- * Paths to the sample, open beam, etc. data (image) files.
- *
- * @return paths configuration object
- */
- virtual TomoPathsConfig currentPathsConfig() const = 0;
-
- /**
- * Takes paths produces programmatically and displays them to the
- * user. This can be used for example when modifying the paths based
- * on some logic/consistency checks outside of this view.
- *
- * @param cfg configuration to use from now on
- */
- virtual void updatePathsConfig(const TomoPathsConfig &cfg) = 0;
-
- /**
- * Regions and center of rotation, normally defined by the user with
- * a graphical rectangle selection tool.
- *
- * @return current user selection of regions
- */
- virtual ImageStackPreParams currentROIEtcParams() const = 0;
-
- /**
- * Show a tool specific configuration dialog for the user to set it up
- *
- * @param dialog The pointer to the current dialog
- */
- virtual void showToolConfig(TomoToolConfigDialogBase &dialog) = 0;
-
- /**
- * Refresh the table, tree etc. that displays info on the running/finished
- *jobs.
- *
- * @param status Job information, as produced for example by the
- * Mantid remote algorithms.
- *
- * @param localStatus similar information but for local runs
- */
- virtual void updateJobsInfoDisplay(
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &status,
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &
- localStatus) = 0;
-
- /**
- * Save settings (normally when closing the interface). This refers
- * to purely GUI settings, such as window max/min status and geometry,
- * preferences and niceties of the user interface.
- */
- virtual void saveSettings() const = 0;
-
- /**
- * If using the keep alive mechanism, what's the period for the
- * query to the remote compute resources? 0 == disabled (by default)
- *
- * @return period (in seconds) for the keep alive mechanism, when
- * using it; 0 otherwise.
- */
- virtual int keepAlivePeriod() { return 0; }
-
- /**
- * Get parameters for wavelength/energy bands aggregation. Provides
- * all the parameters needed to run the aggregation algorithm.
- *
- * @return parameters for an algorithm, as key-value strings
- * for every required parameter and optinal parameter set to
- * non-default values.
- */
- virtual std::map<std::string, std::string>
- currentAggregateBandsParams() const = 0;
-
- /**
- * Run the wavelength/energy bands aggregation algorithm in the
- * background.
- *
- * @param alg algorithm initialized and ready to run.
- */
- virtual void runAggregateBands(Mantid::API::IAlgorithm_sptr alg) = 0;
-
- /**
- * Prompts the user for confirmation with a yes/no dialogue.
- * The body can use HTML formatting.
- *
- * @param title The title that the message has
- * @param body The body that the message has. This CAN use HTML formatting
- */
- virtual bool userConfirmation(const std::string &title,
- const std::string &body) = 0;
-
- /**
- * Returns the cached executable string. This will be cached by calls from the
- * tabs, and allow the execution of any external program
- */
- virtual std::string getCachedExecutable() const = 0;
-
- /**
- * Returns the cached arguments string. This will be cached by calls from the
- * tabs, and allow the execution of any external program
- */
- virtual std::vector<std::string> getCachedArguments() const = 0;
-
- /**
- * Emit the external process output signal so that it can be processed by it's
- * receivers. The signals are connected inside the View's concrete class'
- * @param str the output string of the process
- */
- virtual void emitExternalProcessFinished(const QString &str) = 0;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYIFACEVIEW_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyROIPresenter.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyROIPresenter.h
deleted file mode 100644
index c34bb28324d..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyROIPresenter.h
+++ /dev/null
@@ -1,85 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYROIPRESENTER_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYROIPRESENTER_H_
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Presenter for the widget that handles the selection of the center of
-rotation, region of interest, region for normalization, etc. from an
-image or stack of images. This is the abstract base class / interface
-for the presenter (in the sense of the MVP pattern). The name
-ImageROI refers to the Center-of-Rotation, which is the most basic
-parameter that users can select via this widget. This class is
-QtGUI-free as it uses the interface of the view. The model is simply
-the ImageStackPreParams class which holds coordinates selected by the
-user.
-
-Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class ITomographyROIPresenter {
-
-public:
- ITomographyROIPresenter(){};
- virtual ~ITomographyROIPresenter(){};
-
- /// These are user actions, triggered from the (passive) view, that need
- /// handling by the presenter
- enum Notification {
- Init, ///< interface is initing (set, defaults, etc.)
- BrowseImage, ///< User browses for a single image file
- BrowseStack, ///< User browses for a stack (with
- ///< possibly many files)
- ChangeImageType, ///< Change between sample/flat/dark images
- ChangeRotation, ///< Modify the rotation in the images displayed
- UpdateImgIndex, ///< Sliding/scrolling through the stack
- PlayStartStop, ///< User starts or stops the "play images"
- UpdateColorMap, ///< When the user wants to change the
- ///< image colormap
- ColorRangeUpdated, ///< The uses changes the values or options of the
- ///< color range
- SelectCoR, ///< Start picking of the center of rotation
- SelectROI, ///< Start selection of the region of interest
- SelectNormalization, ///< Start selection of the normalization region
- FinishedCoR, ///< A CoR has been picked
- FinishedROI, ///< The ROI is selected
- FinishedNormalization, ///< The normalization region is selected
- ResetCoR, ///< Reset CoR to default/none/middle
- ResetROI, ///< Reset ROI to default/empty
- ResetNormalization, ///< Reet the normalization region to default/empty
- ShutDown ///< The widget is being closed/destroyed
- };
-
- /**
- * Notifications sent through the presenter when something changes
- * in the view. This plays the role of signals emitted by the view
- * to this presenter.
- *
- * @param notif Type of notification to process.
- */
- virtual void notify(ITomographyROIPresenter::Notification notif) = 0;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYROIPRESENTER_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyROIView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyROIView.h
deleted file mode 100644
index 447661f4a8d..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ITomographyROIView.h
+++ /dev/null
@@ -1,290 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYROIVIEW_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYROIVIEW_H_
-
-#include "MantidAPI/WorkspaceGroup_fwd.h"
-#include "MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Widget to handle the selection of the center of rotation, region of
-interest, region for normalization, etc. from an image or stack of
-images. This is the abstract base class / interface for the view of
-this widget (in the sense of the MVP pattern). The name ImageROI
-refers to the Center-of-Rotation, which is the most basic parameter
-that users can select via this widget. This class is Qt-free. Qt
-specific functionality and dependencies are added in a class derived
-from this.
-
-Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class ITomographyROIView {
-
-public:
- ITomographyROIView(){};
- virtual ~ITomographyROIView(){};
-
- // Selection states
- enum SelectionState {
- SelectNone, ///< Init, or after any reset
- SelectCoR,
- SelectROIFirst,
- SelectROISecond,
- SelectNormAreaFirst,
- SelectNormAreaSecond
- };
-
- /**
- * Sets the user selection. This should guarantee that all widgets
- * are updated (including spin boxes, image, slider through the
- * image stack, etc.
- *
- * @param params all user-modifyable parameters (coordinates for the
- * CoR, ROI and area for normalization).
- *
- */
- virtual void setParams(ImageStackPreParams ¶ms) = 0;
-
- /**
- * Provides the current user selection.
- *
- * @return parameters as set/edited by the user.
- */
- virtual ImageStackPreParams userSelection() const = 0;
-
- /**
- * The current selection state. For example: nothin/initialized,
- * selecting CoR, selecting second corner of the normalization area,
- * selecting first corner of the ROI.
- *
- * @return current state
- */
- virtual SelectionState selectionState() const = 0;
-
- /**
- * Update to a new state (for example select CoR).
- *
- * @param state new state we're transitioning into.
- */
- virtual void changeSelectionState(const SelectionState &state) = 0;
-
- /**
- * Display a special case of stack of images: individual image, from
- * a path to a recognized directory structure (sample/dark/white) or
- * image format. Here recognized format means something that is
- * supported natively by the widgets library, in practice
- * Qt. Normally you can expect that .tiff and .png images are
- * supported.
- *
- * @param path path to the stack (directory) or individual image file.
- */
- virtual void showStack(const std::string &path) = 0;
-
- /**
- * Display a stack of images (or individual image as a particular
- * case), from a workspace group containing matrix workspaces. It
- * assumes that the workspace contains an image in the form in which
- * LoadFITS loads FITS images (or spectrum per row, all of them with
- * the same number of data points (columns)).
- *
- * @param wsg Workspace group where every workspace is a FITS or
- * similar image that has been loaded with LoadFITS or similar
- * algorithm. This holds the sample images.
- *
- * @param wsgFlats Workspace group with flat (open beam) images.
- *
- * @param wsgDarks Workspace group with dark images.
- */
- virtual void showStack(const Mantid::API::WorkspaceGroup_sptr &wsg,
- const Mantid::API::WorkspaceGroup_sptr &wsgFlats,
- const Mantid::API::WorkspaceGroup_sptr &wsgDarks) = 0;
-
- /**
- * Get the stack of (sample) images currently being displayed (it
- * has been shown using showStack()), as a workspace group.
- *
- * @return workspace group containing the individual images, which
- * can be empty if no stack has been loaded.
- */
- virtual const Mantid::API::WorkspaceGroup_sptr stackSamples() const = 0;
-
- /**
- * Normally one image (projection for tomography stacks) will be
- * shown on a 2D display. Show there a particular projection from a
- * stack contained in a workspace group.
- *
- * @param wsg workspace holding a stack of images
- *
- * @param idx index (in the group) of the image to show
- *
- */
- virtual void showProjection(const Mantid::API::WorkspaceGroup_sptr &wsg,
- size_t idx) = 0;
-
- /**
- * Display a warning to the user (for example as a pop-up window).
- *
- * @param warn warning title, should be short and would normally be
- * shown as the title of the window or a big banner.
- *
- * @param description longer, free form description of the issue.
- */
- virtual void userWarning(const std::string &warn,
- const std::string &description) = 0;
-
- /**
- * Display an error message (for example as a pop-up window).
- *
- * @param err Error title, should be short and would normally be
- * shown as the title of the window or a big banner.
- *
- * @param description longer, free form description of the issue.
- */
- virtual void userError(const std::string &err,
- const std::string &description) = 0;
-
- /**
- * To enable/disable all actions in the view. Useful when it is
- * necessary to prevent the user from requesting actions. For
- * example, during a lenghty execution of a process, drawing, etc.
- *
- * @param enable whether to enable or disable actions.
- */
- virtual void enableActions(bool enable) = 0;
-
- /**
- * The images of the type selected by the user (samples/flats/darks).
- *
- * @return a workspace group with the images of the current type
- */
- virtual Mantid::API::WorkspaceGroup_sptr currentImageTypeStack() const = 0;
-
- /**
- * Sets the type of image (sample/flat/dark).
- *
- * @param wsg workspace group that contains the type of image
- */
- virtual void updateImageType(const Mantid::API::WorkspaceGroup_sptr wsg) = 0;
-
- /**
- * The index of the image currently shown (from the current stack if there's
- * any).
- *
- * @return index from 0 to the total number of images in the
- * stack-1, as used for example when indexing workspaces in
- * workspacegroups
- */
- virtual size_t currentImgIndex() const = 0;
-
- /**
- * Display now this image (idx) from the stack.
- *
- * @param idx index of the image to display.
- */
- virtual void updateImgWithIndex(size_t idx) = 0;
-
- /**
- * Start to play/animate the stack currently displayed.
- */
- virtual void playStart() = 0;
-
- /**
- * Stop playing/animating the stack currently displayed, and goes
- * back to the default status.
- */
- virtual void playStop() = 0;
-
- /**
- * The rotation angle selected.
- *
- * @return angle in degrees.
- */
- virtual float currentRotationAngle() const = 0;
-
- /**
- * Modify the rotation angle selection and update the image display
- * to match the new rotation.
- *
- * @param angle rotation angle in degrees
- */
- virtual void updateRotationAngle(float angle) = 0;
-
- /**
- * Get the WHOLE path/location of a single image file. This includes the
- * filename and the whole path of directories to it. If you want only the
- * directories the filename must be trimmed.
- *
- * @return location as a string
- */
- virtual std::string
- askImagePath(const std::string &windowTitle = "Open image") = 0;
-
- /**
- * Get the path of a color map file from the user.
- *
- * @return path as a string (empty if the selection is canceled or
- * fails otherwise)
- */
- virtual std::string askColorMapFile() = 0;
-
- /**
- * Update the current color map (and refresh the image with it).
- *
- * @param filename name of a color map file
- */
- virtual void updateColorMap(const std::string &filename) = 0;
-
- /**
- * Save settings (normally when closing this widget).
- */
- virtual void saveSettings() const = 0;
-
- /**
- * Forget the current center-of-rotation selection and set to
- * default.
- */
- virtual void resetCoR() = 0;
-
- /**
- * Forget the current region-of-interest selection and set to
- * default (all).
- */
- virtual void resetROI() = 0;
-
- /**
- * Forget the current selection of region-for-normalization and set
- * to default (none).
- */
- virtual void resetNormArea() = 0;
-
- /**
- * Notifies the main view that an image has been loaded, so that it can update
- * the paths
- */
- virtual void imageOrStackLoaded(const std::string &path) = 0;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_ITOMOGRAPHYROIVIEW_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImageSelectCoRAndRegions.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImageSelectCoRAndRegions.ui
deleted file mode 100644
index 4dc019ab85e..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImageSelectCoRAndRegions.ui
+++ /dev/null
@@ -1,933 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>ImageSelectCoRAndRegions</class>
- <widget class="QWidget" name="ImageSelectCoRAndRegions">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>800</width>
- <height>600</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="windowTitle">
- <string>Form</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_8">
- <item row="0" column="0">
- <widget class="QSplitter" name="splitter_main_horiz">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <widget class="QSplitter" name="splitter_img_vertical">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Expanding">
- <horstretch>2</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <widget class="QWidget" name="layoutWidget">
- <layout class="QGridLayout" name="gridLayout_5">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <item row="0" column="4">
- <widget class="QPushButton" name="pushButton_browse_stack">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>28</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>28</height>
- </size>
- </property>
- <property name="text">
- <string>Stack...</string>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="label_img_seq">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>28</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>28</height>
- </size>
- </property>
- <property name="text">
- <string>Image:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="2">
- <widget class="QLabel" name="label_img_name">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>28</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>28</height>
- </size>
- </property>
- <property name="text">
- <string>none</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLineEdit" name="lineEdit_img_seq">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>28</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>100</width>
- <height>28</height>
- </size>
- </property>
- <property name="text">
- <string>0/0</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="0" column="3">
- <widget class="QPushButton" name="pushButton_browse_img">
- <property name="text">
- <string>Image...</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="layoutWidget1">
- <layout class="QGridLayout" name="gridLayout_7" rowstretch="0,0">
- <property name="sizeConstraint">
- <enum>QLayout::SetMaximumSize</enum>
- </property>
- <property name="spacing">
- <number>3</number>
- </property>
- <item row="0" column="0">
- <widget class="QScrollArea" name="scrollArea">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>2</horstretch>
- <verstretch>2</verstretch>
- </sizepolicy>
- </property>
- <property name="widgetResizable">
- <bool>true</bool>
- </property>
- <widget class="QWidget" name="scrollAreaWidgetContents">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>496</width>
- <height>412</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>2</horstretch>
- <verstretch>2</verstretch>
- </sizepolicy>
- </property>
- <layout class="QGridLayout" name="gridLayout" rowstretch="0" columnstretch="0">
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <property name="spacing">
- <number>1</number>
- </property>
- <item row="0" column="0">
- <widget class="QLabel" name="label_img">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>3</horstretch>
- <verstretch>3</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QScrollBar" name="horizontalScrollBar_img_stack">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>2</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="invertedControls">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QSplitter" name="splitter_right_horiz">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <widget class="QWidget" name="layoutWidget_2">
- <layout class="QGridLayout" name="gridLayout_6">
- <property name="sizeConstraint">
- <enum>QLayout::SetDefaultConstraint</enum>
- </property>
- <property name="spacing">
- <number>4</number>
- </property>
- <item row="3" column="0">
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Minimum</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="2" column="0">
- <widget class="QGroupBox" name="groupBox_cor">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Minimum">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="maximumSize">
- <size>
- <width>250</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="title">
- <string>Center of rotation</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_2">
- <property name="leftMargin">
- <number>3</number>
- </property>
- <property name="topMargin">
- <number>3</number>
- </property>
- <property name="rightMargin">
- <number>3</number>
- </property>
- <property name="bottomMargin">
- <number>3</number>
- </property>
- <property name="spacing">
- <number>4</number>
- </property>
- <item row="1" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>Column:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinBox_cor_x">
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Row:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinBox_cor_y">
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="2" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QPushButton" name="pushButton_cor">
- <property name="toolTip">
- <string>After pushing this button, click on the image to select</string>
- </property>
- <property name="text">
- <string>Select</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_3">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>108</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_cor_reset">
- <property name="text">
- <string>Reset</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <spacer name="horizontalSpacer_4">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>78</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_center_find">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Auto-find</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_center_method">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <item>
- <property name="text">
- <string>TomoPy</string>
- </property>
- </item>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- <item row="5" column="0">
- <spacer name="verticalSpacer_3">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Minimum</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="7" column="0">
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>68</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QPushButton" name="pushButton_play">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Play</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QLabel" name="label_image_type">
- <property name="text">
- <string>Display:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_image_type">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <item>
- <property name="text">
- <string>Samples</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Flat</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Dark</string>
- </property>
- </item>
- </widget>
- </item>
- </layout>
- </item>
- <item row="1" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_6">
- <item>
- <spacer name="horizontalSpacer_6">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>80</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QLabel" name="label_rotation">
- <property name="text">
- <string>Rotate (clockwise):</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_rotation">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="editable">
- <bool>false</bool>
- </property>
- <property name="minimumContentsLength">
- <number>3</number>
- </property>
- <item>
- <property name="text">
- <string>0°</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>90°</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>180°</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>270°</string>
- </property>
- </item>
- </widget>
- </item>
- </layout>
- </item>
- <item row="4" column="0">
- <widget class="QGroupBox" name="groupBox_roi">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>250</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>250</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="title">
- <string>Region of interest:</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_3">
- <property name="leftMargin">
- <number>3</number>
- </property>
- <property name="topMargin">
- <number>3</number>
- </property>
- <property name="rightMargin">
- <number>3</number>
- </property>
- <property name="bottomMargin">
- <number>3</number>
- </property>
- <property name="spacing">
- <number>2</number>
- </property>
- <item row="0" column="0">
- <widget class="QLabel" name="spinbox_roi_left_label">
- <property name="text">
- <string> Left</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLabel" name="spinbox_roi_top_label">
- <property name="text">
- <string> Top</string>
- </property>
- </widget>
- </item>
- <item row="0" column="2">
- <widget class="QLabel" name="spinbox_roi_right_label">
- <property name="text">
- <string> Right</string>
- </property>
- </widget>
- </item>
- <item row="0" column="3">
- <widget class="QLabel" name="spinbox_roi_bottom_label">
- <property name="text">
- <string> Bottom</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QSpinBox" name="spinBox_roi_left">
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QSpinBox" name="spinBox_roi_top">
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <widget class="QSpinBox" name="spinBox_roi_right">
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item row="1" column="3">
- <widget class="QSpinBox" name="spinBox_roi_bottom">
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>4</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item row="7" column="0" colspan="4">
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QPushButton" name="pushButton_roi">
- <property name="toolTip">
- <string>After pushing this button, click and drag on the image to select</string>
- </property>
- <property name="text">
- <string>Select</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>80</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_roi_reset">
- <property name="toolTip">
- <string>Reset to the whole field of view</string>
- </property>
- <property name="text">
- <string>Reset</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- <item row="6" column="0">
- <widget class="QGroupBox" name="groupBox_norm">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>250</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>250</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="title">
- <string>Area for normalization:</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_4">
- <property name="leftMargin">
- <number>3</number>
- </property>
- <property name="topMargin">
- <number>3</number>
- </property>
- <property name="rightMargin">
- <number>3</number>
- </property>
- <property name="bottomMargin">
- <number>3</number>
- </property>
- <property name="spacing">
- <number>2</number>
- </property>
- <item row="0" column="0">
- <widget class="QLabel" name="spinbox_norm_left_label">
- <property name="text">
- <string> Left</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLabel" name="spinbox_norm_top_label">
- <property name="text">
- <string> Top</string>
- </property>
- </widget>
- </item>
- <item row="0" column="2">
- <widget class="QLabel" name="spinbox_norm_right_label">
- <property name="text">
- <string> Right</string>
- </property>
- </widget>
- </item>
- <item row="0" column="3">
- <widget class="QLabel" name="spinbox_norm_bottom_label">
- <property name="text">
- <string> Bottom</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QSpinBox" name="spinBox_norm_left">
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QSpinBox" name="spinBox_norm_top">
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <widget class="QSpinBox" name="spinBox_norm_right">
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item row="1" column="3">
- <widget class="QSpinBox" name="spinBox_norm_bottom">
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>9999</number>
- </property>
- </widget>
- </item>
- <item row="3" column="0" colspan="4">
- <layout class="QHBoxLayout" name="horizontalLayout_8">
- <item>
- <widget class="QPushButton" name="pushButton_norm_area">
- <property name="toolTip">
- <string>After pushing this button, click and drag on the image to select</string>
- </property>
- <property name="text">
- <string>Select</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>80</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_norm_area_reset">
- <property name="toolTip">
- <string>Reset to empty/none</string>
- </property>
- <property name="text">
- <string>Reset</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="layoutWidget_10">
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="MantidQt::MantidWidgets::ColorBarWidget" name="colorBarWidget" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>1</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </widget>
- </widget>
- </item>
- </layout>
- </widget>
- <customwidgets>
- <customwidget>
- <class>MantidQt::MantidWidgets::ColorBarWidget</class>
- <extends>QWidget</extends>
- <header>MantidQtMantidWidgets/ColorBarWidget.h</header>
- </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h
deleted file mode 100644
index 8b966e60183..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h
+++ /dev/null
@@ -1,62 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMAGESTACKPREPARAMS_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMAGESTACKPREPARAMS_H_
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-#include "MantidKernel/V2D.h"
-
-#include <utility>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-This holds parameters for pre-processing images or stacks of images
-for tomographic reconstruction. These parameters are used in different
-pre-processing steps in the tomographic reconstruction pipeline, and
-also for the reconstruction algorithms (iternative methods, FBP,
-etc.).
-
-The parameters include:
-- center of rotation
-- region of interest (clip from original or raw images)
-- region for normalization (where the beam is not blocked by any sample
- object throughout the stack of images) other parameters describing
- the stack of images:
-
-Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL ImageStackPreParams {
-public:
- ImageStackPreParams();
-
- typedef std::pair<Mantid::Kernel::V2D, Mantid::Kernel::V2D> Box2D;
-
- Mantid::Kernel::V2D cor;
- Box2D roi;
- Box2D normalizationRegion; //< also known as 'air' region
- float rotation; //< rotation angle in degrees
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMAGESTACKPREPARAMS_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormats.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormats.h
deleted file mode 100644
index 50061993400..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormats.h
+++ /dev/null
@@ -1,55 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGFORMATS_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGFORMATS_H_
-
-#include <string>
-#include <vector>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-File formats used to store imaging data (image file formats and
-generic imaging formats such as NXTomo
-http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html).
-
-Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-namespace ImggFormats {
-enum Format { FITS = 0, TIFF = 1, PNG = 2, JPG = 3, NXTomo = 4 };
-
-std::string shortName(Format fmt);
-
-std::vector<std::string> fileExtension(Format fmt);
-
-std::string fileExtension(const std::string &format);
-
-bool isFileExtension(const std::string &extension,
- const std::string &shortName);
-
-std::string description(Format fmt);
-
-} // namespace ImggFormats
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGFORMATS_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvert.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvert.ui
deleted file mode 100644
index da24f8a5c46..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvert.ui
+++ /dev/null
@@ -1,350 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>ImggFormatsConvert</class>
- <widget class="QWidget" name="ImggFormatsConvert">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>654</width>
- <height>426</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>ImgFormatsConversion</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_3">
- <item row="0" column="0">
- <widget class="QGroupBox" name="groupBox">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="title">
- <string>Input:</string>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="1" column="3">
- <widget class="QPushButton" name="pushButton_browse_input">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Path:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="2" colspan="2">
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>268</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>Pick format:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QComboBox" name="comboBox_input_format">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <item>
- <property name="text">
- <string>FITS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>TIFF</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>PNG</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>NXTomo</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="1" column="1" colspan="2">
- <widget class="QLineEdit" name="lineEdit_input_path">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>2</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QGroupBox" name="groupBox_2">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="title">
- <string>Output</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_2">
- <item row="1" column="0">
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Pixel bit-depth in outputs:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QComboBox" name="comboBox_output_format">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <item>
- <property name="text">
- <string>PNG</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>TIFF</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>FITS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>NXTomo</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_6">
- <property name="text">
- <string>Compression:</string>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QComboBox" name="comboBox_compression">
- <item>
- <property name="text">
- <string>Enable</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Disable</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="2" column="2">
- <spacer name="horizontalSpacer_4">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>362</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="4" column="0" colspan="3">
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLabel" name="label_5">
- <property name="text">
- <string>Path:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_output_path">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>2</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_browse_output">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string>Format:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QComboBox" name="comboBox_bit_depth">
- <item>
- <property name="text">
- <string>16 bits</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="1" column="2">
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>362</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="0" column="2">
- <spacer name="horizontalSpacer_3">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>362</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="3" column="0">
- <widget class="QLabel" name="label_7">
- <property name="text">
- <string>Maximum search depth:</string>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QSpinBox" name="spinBox_max_search_depth">
- <property name="toolTip">
- <string>How many subdirectory levels should be processed at most</string>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>10</number>
- </property>
- <property name="value">
- <number>3</number>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="2" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <spacer name="horizontalSpacer_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>278</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_convert">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="text">
- <string>Convert</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="3" column="0">
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertPresenter.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertPresenter.h
deleted file mode 100644
index c18a91663b2..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertPresenter.h
+++ /dev/null
@@ -1,105 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGFORMATSCONVERTPRESENTER_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGFORMATSCONVERTPRESENTER_H_
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/IImggFormatsConvertPresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h"
-#include "MantidAPI/MatrixWorkspace_fwd.h"
-
-// forward declarations for Poco classes
-namespace Poco {
-class File;
-class Path;
-}
-
-namespace MantidQt {
-
-namespace API {
-class BatchAlgorithmRunner;
-}
-
-namespace CustomInterfaces {
-
-/**
-Presenter for the widget to convert images and stacks of images
-between formats.
-
-Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL ImggFormatsConvertPresenter
- : public IImggFormatsConvertPresenter {
-
-public:
- /// Default constructor - normally used from the concrete view
- ImggFormatsConvertPresenter(IImggFormatsConvertView *view);
- ~ImggFormatsConvertPresenter() override;
-
- void notify(IImggFormatsConvertPresenter::Notification notif) override;
-
-protected:
- void initialize();
-
- /// clean shut down of model, view, etc.
- void cleanup();
-
- // Methods that process notifications from view->presenter
- void processInit();
- void processConvert();
- void processShutDown();
-
-private:
- size_t goThroughDirRecur(const Poco::File &inFilePath,
- const std::string &inFormat,
- const Poco::File &outFilePath,
- const std::string &outExt, size_t depth);
-
- void convert(const std::string &inputName, const std::string &inFormat,
- const std::string &outputName,
- const std::string &outFormat) const;
-
- void convertToFITS(const std::string &inputName, const std::string &inFormat,
- const std::string &outputName) const;
-
- void convertToNXTomo(const std::string &inputName,
- const std::string &inFormat,
- const std::string &outputName) const;
-
- Mantid::API::MatrixWorkspace_sptr loadImg(const std::string &inputName,
- const std::string inFormat) const;
-
- Mantid::API::MatrixWorkspace_sptr
- loadFITS(const std::string &inputName) const;
-
- void saveFITS(Mantid::API::MatrixWorkspace_sptr image,
- const std::string &outputName) const;
-
- void saveNXTomo(Mantid::API::MatrixWorkspace_sptr image,
- const std::string &outputName) const;
-
- /// Associated view for this presenter (MVP pattern)
- IImggFormatsConvertView *const m_view;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGGFORMATSCONVERTPRESENTER_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertViewQtWidget.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertViewQtWidget.h
deleted file mode 100644
index 3d1dbd7d746..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ImggFormatsConvertViewQtWidget.h
+++ /dev/null
@@ -1,129 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGFORMATSCONVERTVIEWQTWIDGET_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGFORMATSCONVERTVIEWQTWIDGET_H_
-
-#include "MantidAPI/MatrixWorkspace_fwd.h"
-#include "MantidQtCustomInterfaces/DllConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/IImggFormatsConvertPresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h"
-
-#include "ui_ImggFormatsConvert.h"
-
-#include <QWidget>
-
-// forward declarations for Qt
-class QComboBox;
-class QImage;
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Qt view of a widget to convert images and stacks of images between
-different formats.
-
-Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL ImggFormatsConvertViewQtWidget
- : public QWidget,
- public IImggFormatsConvertView {
- Q_OBJECT
-
-public:
- ImggFormatsConvertViewQtWidget(QWidget *parent = 0);
-
- ~ImggFormatsConvertViewQtWidget() override;
-
- void userWarning(const std::string &err,
- const std::string &description) override;
-
- void userError(const std::string &err,
- const std::string &description) override;
-
- void setFormats(const std::vector<std::string> &fmts,
- const std::vector<bool> &enableLoad,
- const std::vector<bool> &enableSave) override;
-
- std::string inputPath() const override;
- std::string inputFormatName() const override;
-
- std::string outputPath() const override;
- std::string outputFormatName() const override;
-
- bool compressHint() const override;
-
- size_t maxSearchDepth() const override;
-
- void convert(const std::string &inputName, const std::string &inputFormat,
- const std::string &outputName,
- const std::string &outputFormat) const override;
-
- void writeImg(Mantid::API::MatrixWorkspace_sptr inWks,
- const std::string &outputName,
- const std::string &outFormat) const override;
-
- Mantid::API::MatrixWorkspace_sptr
- loadImg(const std::string &inputName,
- const std::string &inFormat) const override;
-
-protected:
- void initLayout();
-
- void saveSettings() const override;
- void readSettings();
- void setup();
-
-private slots:
- void browseImgInputConvertClicked();
- void browseImgOutputConvertClicked();
- void convertClicked();
-
-private:
- void writeImgFile(const QImage &img, const std::string &outputName,
- const std::string &outFormat) const;
-
- QImage loadImgFile(const std::string &inputName,
- const std::string inFormat) const;
-
- void setFormatsCombo(QComboBox *cbox, const std::vector<std::string> &fmts,
- const std::vector<bool> &enable);
-
- std::string
- grabUserBrowseDir(QLineEdit *le,
- const std::string &userMsg = "Open directory/folder",
- bool remember = true);
- std::string askImgOrStackPath();
-
- void closeEvent(QCloseEvent *event) override;
-
- Ui::ImggFormatsConvert m_ui;
-
- // path name for persistent settings
- const static std::string m_settingsGroup;
-
- // presenter as in the model-view-presenter
- std::unique_ptr<IImggFormatsConvertPresenter> m_presenter;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_IMGGFORMATSCONVERTVIEWQTWIDGET_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/StackOfImagesDirs.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/StackOfImagesDirs.h
deleted file mode 100644
index 9aa221bdfcf..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/StackOfImagesDirs.h
+++ /dev/null
@@ -1,102 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_STACKOFIMAGESDIR_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_STACKOFIMAGESDIR_H_
-
-#include "MantidKernel/System.h"
-
-#include <string>
-#include <vector>
-
-// forward declarations
-namespace Poco {
-class File;
-}
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Represents the structure of directories where a stack of images is
-stored on disk: data/flat/dark + processed + pre_filtered, etc.
-
-Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class DLLExport StackOfImagesDirs {
-public:
- /// constructor from a path (to a directory)
- StackOfImagesDirs(const std::string &path, bool allowSimpleLayout = true);
-
- /// The current (simple) concept of valid is: there at least a
- /// sample/data directory with at least one file in it.
- bool isValid() const { return m_valid; }
-
- // human readable description of the expected structure of directories
- std::string description() const;
-
- // string that describes the status/error message about this directory
- std::string status() const;
-
- std::string sampleImagesDir() const { return m_sampleDir; };
- std::string flatImagesDir() const { return m_flatDir; };
- std::string darkImagesDir() const { return m_darkDir; };
-
- std::vector<std::string> sampleFiles() const;
- std::vector<std::string> flatFiles() const;
- std::vector<std::string> darkFiles() const;
-
-private:
- /// tries to find the expected data_/dark_/flat_ directories
- void findStackDirs(const std::string &path, bool allowSimpleLayout);
-
- /// simple version: just files (sample data)
- bool findStackFilesSimple(Poco::File &dir);
-
- /// complex version: sample (data), flat, and dark
- bool findStackDirsComplex(Poco::File &dir);
-
- /// finds images in a directory
- std::vector<std::string> findImgFiles(const std::string &path) const;
-
- /// passes basic validity checks
- bool m_valid;
- /// string with informative messages specially when not valid
- std::string m_statusDescStr;
-
- std::string m_sampleDir;
- std::string m_flatDir;
- std::string m_darkDir;
-
- std::string m_descr;
-
- static const std::string g_descrComplex;
- static const std::string g_descrSimple;
- static const std::string g_descrBoth;
- static const std::string g_sampleNamePrefix;
- static const std::string g_flatNamePrefix;
- static const std::string g_darkNamePrefix;
- static const std::string g_processedNamePrefix;
- static const std::string g_prefilteredNamePrefix;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_STACKOFIMAGESDIR_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h
deleted file mode 100644
index 4c079cf53e8..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h
+++ /dev/null
@@ -1,145 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOPATHSCONFIG_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOPATHSCONFIG_H_
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h"
-
-#include <string>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Represents one particular configuration of paths for tomography
-jobs. These paths point to sample, open bean, flat etc. data (images)
-that define where the data for a particular dataset can be found, and
-that are normally required to run reconstruction tools but also pre-
-and post- processing steps.
-
-Copyright © 2015,2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL TomoPathsConfig {
-public:
- /**
- * Default constructor, makes a paths configuration which probably
- * needs additional input from the user before being usable (see
- * validate()).
- */
- TomoPathsConfig();
-
- /**
- * If the result of this validation is true, that must be
- * interpreted as: "this is ready to be used to run reconstruction
- * or other types of tools." Answers the question: is it non-empty
- * and apparently correct and usable? This will be false if it is
- * not initialized or any inconsistency can be detected.
- *
- * @return whether this configuration seems to be ready to be used.
- */
- bool validate() const;
-
- /**
- * Path to the sample files (sample images, typically FITS files)
- *
- * @return path (full or relative) as a string.
- */
- std::string pathSamples() const { return m_pathFITS; }
-
- void updatePathSamples(const std::string &p) { m_pathFITS = p; }
-
- /**
- * Path to the open beam / flat file(s) (sample images, typically
- * FITS files) Note: open bean a.k.a. 'flat' or 'white'
- *
- * @return path (full or relative, directory or file) as a string.
- */
- std::string pathOpenBeam() const { return m_pathFlat; }
-
- /**
- * Set a new path to open beam/flat images, and whether it is
- * enabled.
- *
- * @param p new path string
- *
- * @param enable whether to effectively use the path for the
- * "normalize by flats" option with the current setup
- */
- void updatePathOpenBeam(const std::string &p, bool enable) {
- m_pathFlat = p;
- m_pathOpenBeamEnabled = enable;
- }
-
- /**
- * Path to the dark image file(s)
- *
- * @return path (full or relative, directory or file) as a string.
- */
- std::string pathDarks() const { return m_pathDark; }
-
- /**
- * Set a new path to dark images, and whether it is
- * enabled.
- *
- * @param p new path string
- *
- * @param enable whether to effectively use the path for the
- * "normalize by dark images" option with the current setup
- */
- void updatePathDarks(const std::string &p, bool enable) {
- m_pathDark = p;
- m_pathDarkEnabled = enable;
- }
-
- /**
- * Path to a base directory (for data usually). All other paths
- * could be absolute or relative to this one.
- *
- * @return path (full, directory) as a string.
- */
- std::string pathBase() const { return m_pathBase; }
-
- void updatePathBase(const std::string &p) { m_pathBase = p; }
-
- std::string pathSavuConfig() const;
-
- /// Whether the flat/open beam option is enabled by the user
- bool m_pathOpenBeamEnabled;
- /// Whether the "use dark images" option is enabled for this setup
- bool m_pathDarkEnabled;
-
-private:
- /// file paths, base dir on scarf
- std::string m_pathBase;
- /// path to fits file (sample data)
- std::string m_pathFITS;
- /// path to flat/open beam/bright image
- std::string m_pathFlat;
- /// path to dark image
- std::string m_pathDark;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOPATHSCONFIG_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h
deleted file mode 100644
index 485e585d3a6..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h
+++ /dev/null
@@ -1,121 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECTOOLCONFIG_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECTOOLCONFIG_H_
-
-#include <string>
-#include <vector>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Configuration of a third party tomographic reconstruction tool. This
-is under development, and as it is not necessarily related to custom
-interfaces this class and some derived ones might be moved out of
-here.
-
-Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-
-/**
- * General tomographic reconstruction tool configuration. This class
- * represents the configuration (or run options/settings) of a third
- * party or external tool/program/module/etc. that Mantid would run
- * either locally or on a remote computer. The purpose here is to
- * produce the command line or similar that will run the third party
- * tool for certain user requirements/settings/options/preferences.
- *
- * TODO: a related class to represent third party tools should be
- * added that would take care of platform specificities, tool
- * availability, execute permissions, etc.
- */
-class TomoRecToolConfig {
-public:
- /**
- * Construct a config object, given a 'runnable', which can be an
- * application, executable, script, etc. - the access point to a
- * third party tool. If this class is developed to be smart enough,
- * and with the help of the additional '3rd party tool' class, it
- * should be able to translate application names into binary paths
- * and similar internally.
- *
- * @param runnable name of the runnable object (application, executable,
- * etc.). This can be a full path, an application name, etc. At
- * present it is used in its simplest form: platform and machine
- * dependent full path to an execuatable or script.
- */
- TomoRecToolConfig(const std::string &runnable = "") : m_runnable(runnable) {}
-
- virtual ~TomoRecToolConfig() {}
-
- /**
- * validate that it is possible to produce a sensible command line
- * from this config object.
- *
- * @return the tool and its config are consistent and it looks
- * like it should be possible to run it.
- */
- virtual bool valid() const { return true; }
-
- /// A vector of tomographic reconstruction algorithms described by a
- /// name-in-tool and a human-readable-name
- typedef std::vector<std::pair<std::string, std::string>> TomoReconAlgs;
-
- virtual TomoReconAlgs algorithmsAvailable() const { return m_algs; };
-
- virtual void appendOptions(std::string &opts) {
- m_appendix = m_appendix + " " + opts;
- };
-
- /**
- * Produce a command line to run this tool with this configuration.
- *
- * @return command line ready to run on a certain platform
- */
- virtual std::string toCommand() const {
- return makeExecutable() + " " + makeCmdLineOptions();
- }
-
- /**
- * Produces a string with the command line options derived from the
- * different options set.
- *
- * @return command line options string
- */
- virtual std::string makeCmdLineOptions() const = 0;
-
- /**
- * Produces an string that describes the executable, ready to run
- * as a binary, python or other type of scripts, etc. Normally you
- * append command line options to this.
- */
- virtual std::string makeExecutable() const = 0;
-
-protected:
- std::string m_runnable;
- std::string m_appendix;
- TomoReconAlgs m_algs;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECTOOLCONFIG_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconFiltersSettings.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconFiltersSettings.h
deleted file mode 100644
index 2097585aff5..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconFiltersSettings.h
+++ /dev/null
@@ -1,52 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONFILTERSETTINGS_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONFILTERSETTINGS_H_
-
-#include "MantidQtCustomInterfaces/Tomography/TomoReconPreprocSettings.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoReconPostprocSettings.h"
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Settings for pre-/post-/other-processing filters to run a
-reconstruction jobs. Note this has been defined as general processing
-steps, not tied to any particular tool.
-
-Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-struct MANTIDQT_CUSTOMINTERFACES_DLL TomoReconFiltersSettings {
- MantidQt::CustomInterfaces::TomoReconPreprocSettings prep;
- MantidQt::CustomInterfaces::TomoReconPostprocSettings postp;
-
- /// whether to write pre-processed images in addition to the output
- /// reconstructed volume (slices/images)
- bool outputPreprocImages;
-
- TomoReconFiltersSettings() : prep(), postp(), outputPreprocImages(true) {}
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONFILTERSETTINGS_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconPostprocSettings.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconPostprocSettings.h
deleted file mode 100644
index 9fa1122258f..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconPostprocSettings.h
+++ /dev/null
@@ -1,44 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONPOSTPROCSETTINGS_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONPOSTPROCSETTINGS_H_
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Settings for post-processing a reconstructed volume.
-Note this is in principle not tied to any particular tool.
-
-Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-struct MANTIDQT_CUSTOMINTERFACES_DLL TomoReconPostprocSettings {
- double circMaskRadius;
- double cutOffLevel;
-
- TomoReconPostprocSettings();
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONPOSTPROCSETTINGS_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconPreprocSettings.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconPreprocSettings.h
deleted file mode 100644
index f201d2c76d0..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconPreprocSettings.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONPREPROCSETTINGS_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONPREPROCSETTINGS_H_
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-
-#include <cstddef>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Settings for pre-processing of the raw input images before
-reconstructing a volume. Note this is in principle not tied to any
-particular tool.
-
-Copyright © 2015,2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-struct MANTIDQT_CUSTOMINTERFACES_DLL TomoReconPreprocSettings {
- bool normalizeByAirRegion;
- bool normalizeByProtonCharge;
- bool normalizeByFlats;
- bool normalizeByDarks;
-
- // block-size in pixels
- size_t medianFilterWidth;
- // rotation to correct raw images, in degrees. Only multiples of 90
- int rotation;
- // maximum angle, in degrees
- double maxAngle;
- // block size in pixels
- size_t scaleDownFactor;
-
- TomoReconPreprocSettings();
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONPREPROCSETTINGS_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h
deleted file mode 100644
index 4466cad265e..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h
+++ /dev/null
@@ -1,55 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONTOOLSUSERSETTINGS_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONTOOLSUSERSETTINGS_H_
-
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h"
-
-#include <string>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Settings for a set of tomographic reconstruction tools supported.
-
-Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-struct TomoReconToolsUserSettings {
- // This is just too basic at the moment. We probably want to store
- // here the real settings objects for all the tools, and rather than
- // this horror have a dictionary of tools-settings or
- // similar. Waiting to see what happens with Savu and others.
- MantidQt::CustomInterfaces::ToolConfigTomoPy tomoPy;
- MantidQt::CustomInterfaces::ToolConfigAstraToolbox astra;
- MantidQt::CustomInterfaces::ToolConfigCustom custom;
-
- // savu not ready
- std::string savu;
- // CCPi not ready
- std::string CCPi;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMORECONTOOLSUSERSETTINGS_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h
deleted file mode 100644
index ee1ce8ecf66..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h
+++ /dev/null
@@ -1,75 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGS_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGS_H_
-
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettingsLocal.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettingsRemote.h"
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-
-#include <string>
-#include <vector>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Settings for the paths on the local and remote machines, path
-components, and related parameters. Most of these options could be
-hardcoded but it is convenient to be able to manipulate them, for
-flexibility and for testing purposes. Consists of "local" and "remote"
-parameters as well as other parameters that are global.
-
-Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-struct MANTIDQT_CUSTOMINTERFACES_DLL TomoSystemSettings {
- // TODO use dictionary(es) for the string settings when they settle down
- TomoSystemSettingsLocal m_local;
- TomoSystemSettingsRemote m_remote;
-
- std::vector<std::string> m_pathComponents;
-
- std::string m_samplesDirPrefix;
- std::string m_flatsDirPrefix;
- std::string m_darksDirPrefix;
-
- /// path component for the pre-processed file (outputs)
- std::string m_outputPathCompPreProcessed;
- /// path component for the reconstructed files (outputs)
- std::string m_outputPathCompReconst;
-
- /// experiment reference from the Run tab
- std::string m_experimentReference;
-
- static const std::string g_defSamplesDirPrefix;
- static const std::string g_defFlatsDirPrefix;
- static const std::string g_defDarksDirPrefix;
-
- static const std::string g_defOutputPathCompPreProcessed;
- static const std::string g_defOutputPathCompReconst;
-
- TomoSystemSettings();
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGS_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsLocal.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsLocal.h
deleted file mode 100644
index 9842f517f93..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsLocal.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGSLOCAL_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGSLOCAL_H_
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-
-#include <string>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Settings for the paths and other parameters on the local machine. Most
-of these options could be hardcoded but it is convenient to be able to
-manipulate them, for flexibility and for testing/commissioning.
-
-Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-struct MANTIDQT_CUSTOMINTERFACES_DLL TomoSystemSettingsLocal {
- std::string m_basePathTomoData;
- std::string m_remoteDriveOrMountPoint;
-
- std::string m_reconScriptsPath;
- std::string m_externalInterpreterPath;
-
- int m_processes;
- int m_cores;
-
- static const std::string g_defBasePathTomoData;
- static const std::string g_defRemoteDriveOrMountPoint;
- static const std::string g_defReconScriptsPath;
- static const std::string g_defExternalInterpreterPath;
-
- TomoSystemSettingsLocal();
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGSLOCAL_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsRemote.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsRemote.h
deleted file mode 100644
index d86778deb7e..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoSystemSettingsRemote.h
+++ /dev/null
@@ -1,53 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGSREMOTE_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGSREMOTE_H_
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-
-#include <string>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Settings for the paths and other parameters on the remote
-machine/compute resource/cluster. Some of these options could be
-hardcoded but it is convenient to be able to manipulate them, for
-flexibility and for testing/commissioning.
-
-Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-struct MANTIDQT_CUSTOMINTERFACES_DLL TomoSystemSettingsRemote {
- std::string m_basePathTomoData;
- std::string m_basePathReconScripts;
- int m_nodes;
- int m_cores;
-
- static const std::string g_defBasePathTomoData;
- static const std::string g_defBasePathReconScripts;
-
- TomoSystemSettingsRemote();
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOSYSTEMSETTINGSREMOTE_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigAstra.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigAstra.ui
deleted file mode 100644
index 6a279bfe7ca..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigAstra.ui
+++ /dev/null
@@ -1,206 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomoToolConfigAstra</class>
- <widget class="QDialog" name="TomoToolConfigAstra">
- <property name="windowModality">
- <enum>Qt::WindowModal</enum>
- </property>
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>545</width>
- <height>179</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Astra Toolbox Configuration</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QLabel" name="label_method">
- <property name="text">
- <string>Method:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_method">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <item>
- <property name="text">
- <string>FBP: filtered back propagation</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>SIRT: statistical image reconstruction</string>
- </property>
- </item>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QGroupBox" name="groupBox">
- <property name="title">
- <string>Advanced options</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QLabel" name="label_iter">
- <property name="text">
- <string>Iterations:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QSpinBox" name="spinBox_iter">
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>999</number>
- </property>
- <property name="value">
- <number>5</number>
- </property>
- </widget>
- </item>
- <item row="0" column="2" colspan="2">
- <spacer name="horizontalSpacer_4">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>178</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_cli_options">
- <property name="text">
- <string>Regularization:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1" colspan="2">
- <widget class="QDoubleSpinBox" name="doubleSpinBox_regularization">
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="maximum">
- <double>180.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="1" column="3">
- <spacer name="horizontalSpacer_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>305</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>178</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QDialogButtonBox" name="buttonBox">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="standardButtons">
- <set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections>
- <connection>
- <sender>buttonBox</sender>
- <signal>accepted()</signal>
- <receiver>TomoToolConfigAstra</receiver>
- <slot>accept()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>248</x>
- <y>254</y>
- </hint>
- <hint type="destinationlabel">
- <x>157</x>
- <y>274</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>buttonBox</sender>
- <signal>rejected()</signal>
- <receiver>TomoToolConfigAstra</receiver>
- <slot>reject()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>316</x>
- <y>260</y>
- </hint>
- <hint type="destinationlabel">
- <x>286</x>
- <y>274</y>
- </hint>
- </hints>
- </connection>
- </connections>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigCustom.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigCustom.ui
deleted file mode 100644
index def36df933b..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigCustom.ui
+++ /dev/null
@@ -1,135 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomoToolConfigCustom</class>
- <widget class="QDialog" name="TomoToolConfigCustom">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>802</width>
- <height>278</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Custom tool configuration</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_2">
- <item row="0" column="0">
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QLabel" name="label_runnable">
- <property name="text">
- <string>Runnable:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="2">
- <widget class="QLineEdit" name="lineEdit_runnable">
- <property name="toolTip">
- <string>Script or binary that can run on the remote environment</string>
- </property>
- <property name="text">
- <string>/work/imat/phase_commissioning/scripts/Imaging/IMAT/tomo_reconstruct.py</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0" colspan="2">
- <widget class="QLabel" name="label_cli_options">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Command line options:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <widget class="QTextEdit" name="textEdit_cl_opts">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string>Command line options to the script or binary</string>
- </property>
- <property name="html">
- <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
-<html><head><meta name="qrichtext" content="1" /><style type="text/css">
-p, li { white-space: pre-wrap; }
-</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">--help</p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="2" column="1" colspan="2">
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>17</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QDialogButtonBox" name="buttonBox">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="standardButtons">
- <set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections>
- <connection>
- <sender>buttonBox</sender>
- <signal>accepted()</signal>
- <receiver>TomoToolConfigCustom</receiver>
- <slot>accept()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>248</x>
- <y>254</y>
- </hint>
- <hint type="destinationlabel">
- <x>157</x>
- <y>274</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>buttonBox</sender>
- <signal>rejected()</signal>
- <receiver>TomoToolConfigCustom</receiver>
- <slot>reject()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>316</x>
- <y>260</y>
- </hint>
- <hint type="destinationlabel">
- <x>286</x>
- <y>274</y>
- </hint>
- </hints>
- </connection>
- </connections>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogAstra.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogAstra.h
deleted file mode 100644
index 34fa4233bd4..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogAstra.h
+++ /dev/null
@@ -1,38 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGASTRA_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGASTRA_H_
-
-#include "ui_TomoToolConfigAstra.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-class TomoToolConfigDialogAstra : public TomoToolConfigDialogBase {
-public:
- TomoToolConfigDialogAstra()
- : TomoToolConfigDialogBase(DEFAULT_TOOL_NAME, DEFAULT_TOOL_METHOD) {}
-
- ~TomoToolConfigDialogAstra() override {
- if (m_dialog) {
- delete m_dialog;
- }
- }
-
-private:
- void initialiseDialog() override;
- void setupMethodSelected() override;
- void setupToolSettingsFromPaths() override;
- void setupDialogUi() override;
- int executeQt() override;
- std::vector<std::pair<std::string, std::string>> getToolMethods() override;
-
- // initialised in .cpp file
- static const std::string DEFAULT_TOOL_NAME;
- static const std::string DEFAULT_TOOL_METHOD;
-
- QDialog *m_dialog = nullptr;
- Ui::TomoToolConfigAstra m_astraUi;
-};
-
-} // CustomInterfaces
-} // MantidQt
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGASTRA_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h
deleted file mode 100644
index 4933973efc7..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h
+++ /dev/null
@@ -1,153 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGBASE_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGBASE_H_
-
-#include "MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h"
-
-#include <memory>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Third party tool configuration dialog(s) for the tomographic reconstruction
-GUI.
-
-Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class TomoToolConfigDialogBase {
-public:
- TomoToolConfigDialogBase(const std::string toolName = "",
- const std::string toolMethod = "")
- : m_toolName(toolName), m_toolMethod(toolMethod), m_isInitialised(false) {
- }
- virtual ~TomoToolConfigDialogBase() {}
-
- /// public static function accessor to create dialogues
- static std::unique_ptr<TomoToolConfigDialogBase>
- getToolDialogFor(const std::string &toolName);
-
- /// Sets up the dialogue settings, but does not initialise a QDialog
- void setupDialog(const std::string &runPath, const TomoPathsConfig &paths,
- const std::string &pathOut,
- const std::string &localOutNameAppendix) {
-
- setupPaths(runPath, paths, pathOut, localOutNameAppendix);
- setupToolSettingsFromPaths();
- }
-
- /// initialises a QDialog and handles the returns
- virtual int initialiseGUIandExecute() {
- if (!isInitialised()) {
- // set up the tool's method on the first run
- // this prevents from creating and destroying many dialogues if the user
- // decides to scroll quickly, and the dialogue is only initialised if the
- // user clicks the "Setup" button. If the tool is not setup the default
- // settings will be provided if the user clicks Reconstruct
- initialiseDialog();
- setupDialogUi();
- setupMethodSelected();
-
- m_isInitialised = true;
- }
-
- const int res = this->executeQt();
- this->handleDialogResult(res);
- return res;
- }
-
- virtual bool isInitialised() const { return m_isInitialised; }
-
- std::string getSelectedToolMethod() const { return m_toolMethod; }
-
- /// return pointer and transfer ownership
- std::shared_ptr<TomoRecToolConfig> getSelectedToolSettings() const {
- return m_toolSettings;
- }
-
- std::string getSelectedToolName() const { return m_toolName; }
-
-protected:
- virtual void initialiseDialog() = 0;
-
- virtual void handleDialogResult(const int result);
-
- virtual void setScriptRunPath(const std::string run) { m_runPath = run; }
-
- virtual void setTomoPathsConfig(const TomoPathsConfig paths) {
- m_paths = paths;
- }
-
- virtual void setPathOut(const std::string pathOut) { m_pathOut = pathOut; }
-
- virtual void setLocalOutNameAppendix(const std::string localOutNameAppendix) {
- m_localOutNameAppendix = localOutNameAppendix;
- }
-
- virtual void setupPaths(const std::string &runPath,
- const TomoPathsConfig &paths,
- const std::string &pathOut,
- const std::string &localOutNameAppendix) {
- this->setScriptRunPath(runPath);
- this->setTomoPathsConfig(paths);
- this->setPathOut(pathOut);
- this->setLocalOutNameAppendix(localOutNameAppendix);
- }
-
- virtual void setupDialogUi() = 0;
-
- /// setup the selected method member variable
- virtual void setupMethodSelected() = 0;
-
- /// setup the tool config with the correct paths, must be called after the
- /// paths have been set!
- virtual void setupToolSettingsFromPaths() = 0;
-
- /// provided virtual function to add Qt execute behaviour as necessary
- virtual int executeQt() = 0; // this class doesn't inherit from Qt and doesnt
- // have this->exec()
-
- // empty function body as not all tools have methods
- virtual std::vector<std::pair<std::string, std::string>> getToolMethods() {
- return {};
- }
-
- std::shared_ptr<TomoRecToolConfig> m_toolSettings;
-
- const std::string m_toolName;
-
- std::string m_toolMethod;
-
- std::string m_runPath;
-
- std::string m_localOutNameAppendix;
-
- std::string m_pathOut;
-
- TomoPathsConfig m_paths;
-
- bool m_isInitialised;
-};
-}
-}
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGBASE_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogCustom.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogCustom.h
deleted file mode 100644
index 98f493470a0..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogCustom.h
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGCUSTOM_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGCUSTOM_H_
-
-#include "ui_TomoToolConfigCustom.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-class TomoToolConfigDialogCustom : public TomoToolConfigDialogBase {
-public:
- TomoToolConfigDialogCustom()
- : TomoToolConfigDialogBase(DEFAULT_TOOL_NAME, DEFAULT_TOOL_METHOD) {}
- ~TomoToolConfigDialogCustom() override {
- if (m_dialog) {
- delete m_dialog;
- }
- }
-
-private:
- void initialiseDialog() override;
- void setupMethodSelected() override;
- void setupToolSettingsFromPaths() override;
- void setupDialogUi() override;
- void handleDialogResult(int result) override;
- int executeQt() override;
-
- // initialised in .cpp file
- static const std::string DEFAULT_TOOL_NAME;
- static const std::string DEFAULT_TOOL_METHOD;
- static std::string m_backupCommandLine;
-
- QDialog *m_dialog = nullptr;
- Ui::TomoToolConfigCustom m_customUi;
-};
-} // CustomInterfaces
-} // MantidQt
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGCUSTOM_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogSavu.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogSavu.h
deleted file mode 100644
index fc6f242f538..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogSavu.h
+++ /dev/null
@@ -1,71 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGSAVU_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGSAVU_H_
-
-#include "ui_TomoToolConfigSavu.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-#include <MantidAPI/ITableWorkspace.h>
-
-namespace Mantid {
-namespace API {
-class TableRow;
-}
-}
-
-namespace MantidQt {
-namespace CustomInterfaces {
-class TomoToolConfigDialogSavu : public QMainWindow,
- public TomoToolConfigDialogBase {
- Q_OBJECT
-public:
- TomoToolConfigDialogSavu(QWidget *parent = 0);
-
-private:
- void setupMethodSelected() override;
- void setupToolSettingsFromPaths() override;
- void setupDialogUi() override;
- void initialiseDialog() override;
- int executeQt() override;
-
- void initSavuWindow();
- void loadAvailablePlugins();
- void refreshAvailablePluginListUI();
- void refreshCurrentPluginListUI();
- void availablePluginSelected();
-
- void createPluginTreeEntry(Mantid::API::TableRow &row);
- void createPluginTreeEntries(Mantid::API::ITableWorkspace_sptr table);
- void paramValModified(QTreeWidgetItem *item, int /*column*/);
- void currentPluginSelected();
- std::string paramValStringFromArray(const Json::Value &jsonVal,
- const std::string &name);
-
- std::string pluginParamValString(const Json::Value &jsonVal,
- const std::string &name);
-
- void loadSavuTomoConfig(std::string &filePath,
- Mantid::API::ITableWorkspace_sptr ¤tPlugins);
- void moveUpClicked();
- void moveDownClicked();
- void removeClicked();
- void menuOpenClicked();
- void menuSaveClicked();
- void menuSaveAsClicked();
- QString tableWSRowToString(Mantid::API::ITableWorkspace_sptr table, size_t i);
- void expandedItem(QTreeWidgetItem *item);
- void transferClicked();
- std::string createUniqueNameHidden();
-
- void userWarning(const std::string &err, const std::string &description);
- void userError(const std::string &err, const std::string &description);
-
- static size_t g_nameSeqNo;
-
- Ui::TomoToolConfigSavu m_savuUi;
- Mantid::API::ITableWorkspace_sptr m_availPlugins;
- Mantid::API::ITableWorkspace_sptr m_currPlugins;
- std::string m_currentParamPath;
-};
-
-} // CustomInterfaces
-} // MantidQt
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGSAVU_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogTomoPy.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogTomoPy.h
deleted file mode 100644
index bdd5b63e3aa..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogTomoPy.h
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGTOMOPY_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGTOMOPY_H_
-
-#include "ui_TomoToolConfigTomoPy.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-class TomoToolConfigDialogTomoPy : public TomoToolConfigDialogBase {
-
-public:
- TomoToolConfigDialogTomoPy()
- : TomoToolConfigDialogBase(DEFAULT_TOOL_NAME, DEFAULT_TOOL_METHOD) {}
-
- ~TomoToolConfigDialogTomoPy() override {
- if (m_dialog) {
- delete m_dialog;
- }
- }
-
-private:
- void initialiseDialog() override;
- void setupMethodSelected() override;
- void setupToolSettingsFromPaths() override;
- void setupDialogUi() override;
- int executeQt() override;
- std::vector<std::pair<std::string, std::string>> getToolMethods() override;
- // initialised in .cpp file
- static const std::string DEFAULT_TOOL_NAME;
- static const std::string DEFAULT_TOOL_METHOD;
-
- QDialog *m_dialog = nullptr;
- Ui::TomoToolConfigTomoPy m_tomoPyUi;
-};
-} // CustomInterfaces
-} // MantidQt
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOTOOLCONFIGDIALOGTOMOPY_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigSavu.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigSavu.ui
deleted file mode 100644
index 633f346ec3f..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigSavu.ui
+++ /dev/null
@@ -1,392 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomoToolConfigSavu</class>
- <widget class="QMainWindow" name="MainWindow">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>800</width>
- <height>600</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Savu configuration</string>
- </property>
- <widget class="QWidget" name="savuConfigCentralWidget">
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <widget class="QMenuBar" name="menubar_2">
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>21</height>
- </size>
- </property>
- <widget class="QMenu" name="menuFile">
- <property name="title">
- <string>File</string>
- </property>
- <addaction name="separator"/>
- </widget>
- <addaction name="menuFile"/>
- </widget>
- </item>
- <item>
- <widget class="QFrame" name="frame_2">
- <property name="frameShape">
- <enum>QFrame::Box</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <property name="margin">
- <number>0</number>
- </property>
- <item>
- <widget class="QSplitter" name="splitterPlugins">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <widget class="QFrame" name="frame_3">
- <property name="frameShape">
- <enum>QFrame::Box</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <widget class="QFrame" name="pluginBar">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>32</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>32</height>
- </size>
- </property>
- <property name="baseSize">
- <size>
- <width>0</width>
- <height>32</height>
- </size>
- </property>
- <property name="frameShape">
- <enum>QFrame::NoFrame</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <property name="margin">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="lblFilename">
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="text">
- <string>Available Plugins:</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>284</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="btnTransfer">
- <property name="font">
- <font>
- <pointsize>26</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>→</string>
- </property>
- <property name="autoDefault">
- <bool>false</bool>
- </property>
- <property name="default">
- <bool>false</bool>
- </property>
- <property name="flat">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QListWidget" name="listAvailablePlugins">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>3</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QTextBrowser" name="availablePluginDesc">
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>120</height>
- </size>
- </property>
- <property name="baseSize">
- <size>
- <width>0</width>
- <height>120</height>
- </size>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <widget class="QFrame" name="frame_4">
- <property name="frameShape">
- <enum>QFrame::Box</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_5">
- <item>
- <widget class="QFrame" name="currentBar">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>32</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>32</height>
- </size>
- </property>
- <property name="baseSize">
- <size>
- <width>0</width>
- <height>32</height>
- </size>
- </property>
- <property name="frameShape">
- <enum>QFrame::NoFrame</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <property name="margin">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="label">
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="text">
- <string>Current configuration</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>239</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="btnMoveUp">
- <property name="maximumSize">
- <size>
- <width>45</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>18</pointsize>
- <weight>75</weight>
- <italic>false</italic>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>â–²</string>
- </property>
- <property name="flat">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="btnMoveDown">
- <property name="maximumSize">
- <size>
- <width>45</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>18</pointsize>
- <weight>75</weight>
- <italic>false</italic>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>â–¼</string>
- </property>
- <property name="flat">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="btnRemove">
- <property name="maximumSize">
- <size>
- <width>45</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>16</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>X</string>
- </property>
- <property name="flat">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QTreeWidget" name="treeCurrentPlugins">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string>Here you can modify the parameters of the plugins.
-Double-click on them to modify their values.</string>
- </property>
- <column>
- <property name="text">
- <string notr="true">1</string>
- </property>
- </column>
- </widget>
- </item>
- <item>
- <widget class="QTextBrowser" name="currentPluginDesc">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>120</height>
- </size>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QPushButton" name="pushButton_Help">
- <property name="maximumSize">
- <size>
- <width>23</width>
- <height>23</height>
- </size>
- </property>
- <property name="text">
- <string>?</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_3">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>728</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QStatusBar" name="statusbar"/>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigTomoPy.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigTomoPy.ui
deleted file mode 100644
index c285f5b3791..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomoToolConfigTomoPy.ui
+++ /dev/null
@@ -1,210 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomoToolConfigTomoPy</class>
- <widget class="QDialog" name="TomoToolConfigTomoPy">
- <property name="windowModality">
- <enum>Qt::WindowModal</enum>
- </property>
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>547</width>
- <height>177</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>TomoPy Configuration</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Method:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_method">
- <item>
- <property name="text">
- <string>gridrec: Fourier grid reconstruction</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>SIRT: Simultaneous algebraic reconstruction technique</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>FBP: filtered back-propagation</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>MLEM: Maximum-likelihood expectation maximization</string>
- </property>
- </item>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QGroupBox" name="groupBox">
- <property name="title">
- <string>Advanced options</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QLabel" name="label_iter">
- <property name="text">
- <string>Iterations:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QSpinBox" name="spinBox_iter">
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>999</number>
- </property>
- <property name="value">
- <number>5</number>
- </property>
- </widget>
- </item>
- <item row="0" column="2" colspan="2">
- <spacer name="horizontalSpacer_4">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>178</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_cli_options">
- <property name="text">
- <string>Regularization:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1" colspan="2">
- <widget class="QDoubleSpinBox" name="doubleSpinBox_regularization">
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="maximum">
- <double>180.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="1" column="3">
- <spacer name="horizontalSpacer_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>305</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>178</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QDialogButtonBox" name="buttonBox">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="standardButtons">
- <set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections>
- <connection>
- <sender>buttonBox</sender>
- <signal>accepted()</signal>
- <receiver>TomoToolConfigTomoPy</receiver>
- <slot>accept()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>434</x>
- <y>200</y>
- </hint>
- <hint type="destinationlabel">
- <x>291</x>
- <y>111</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>buttonBox</sender>
- <signal>rejected()</signal>
- <receiver>TomoToolConfigTomoPy</receiver>
- <slot>reject()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>434</x>
- <y>200</y>
- </hint>
- <hint type="destinationlabel">
- <x>291</x>
- <y>111</y>
- </hint>
- </hints>
- </connection>
- </connections>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h
deleted file mode 100644
index 7167c8ca59d..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h
+++ /dev/null
@@ -1,330 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEMODEL_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEMODEL_H_
-
-#include "MantidAPI/IRemoteJobManager.h"
-#include "MantidAPI/ITableWorkspace_fwd.h"
-#include "MantidAPI/WorkspaceGroup_fwd.h"
-#include "MantidKernel/System.h"
-#include "MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoReconFiltersSettings.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h"
-
-// Include instead of forward declare so we have definition of qint64
-#include <QMutex>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-class TomographyProcess;
-class TomographyThread;
-/**
-Tomography GUI. Model for the interface (as in the MVP
-(Model-View-Presenter) pattern). In principle, in a strict MVP setup,
-signals from this model should always be handled through the presenter
-and never go directly to the view.
-
-Copyright © 2014,2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL TomographyIfaceModel {
- // For now, there is no need to make this a Q_OBJECT (and derive from
- // QObject, but this class may become a "full" Q_OBJECT as soon as a Qt
- // model (table, tree, etc.), with its signals, is used here
- // Q_OBJECT
-
-public:
- /// Default constructor
- TomographyIfaceModel();
- virtual ~TomographyIfaceModel();
-
- void setupComputeResource();
- void setupRunTool(const std::string &compRes);
-
- /// is the current facility supported? (only ISIS for now)
- bool facilitySupported();
-
- /// the compure resources supported and their status/availability
- std::vector<std::string> computeResources() { return m_computeRes; }
- std::vector<bool> computeResourcesStatus() { return m_computeResStatus; }
-
- /// the reconstruction tools supported and their status/availability
- std::vector<std::string> reconTools() { return m_reconTools; }
- std::vector<bool> reconToolsStatus() { return m_reconToolsStatus; }
-
- // Mantid::Kernel::Logger & logger() const;
-
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo>
- jobsStatus() const {
- return m_jobsStatus;
- }
-
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo>
- jobsStatusLocal() const {
- return m_jobsStatusLocal;
- }
-
- /// Username last logged in, if any.
- std::string loggedIn() const { return m_loggedInUser; }
-
- // TODO: add companion currentComputeResource where LoggedIn() is in
- //--------------------------------------------
- // Current tool Settings
- //--------------------------------------------
- void usingTool(const std::string &tool) { m_currentToolName = tool; }
- std::string usingTool() const { return m_currentToolName; }
-
- void setCurrentToolMethod(std::string toolMethod) {
- m_currentToolMethod = toolMethod;
- }
- std::string getCurrentToolMethod() const { return m_currentToolMethod; }
-
- void setCurrentToolSettings(std::shared_ptr<TomoRecToolConfig> settings) {
- m_currentToolSettings = settings;
- }
-
- //--------------------------------------------
- // Access to the system settings information
- //--------------------------------------------
- // get the remote scripts base dir from the system settings
- std::string getCurrentRemoteScriptsBasePath() const {
- return m_systemSettings.m_remote.m_basePathReconScripts;
- }
-
- /// get the local paths from the system settings
- std::string getCurrentLocalScriptsBasePath() const {
- return m_systemSettings.m_local.m_reconScriptsPath;
- }
-
- std::string getExeternalInterpreterPath() const {
- return m_systemSettings.m_local.m_externalInterpreterPath;
- }
-
- /// get the experiment reference currently selected
- std::string getCurrentExperimentReference() const {
- return m_systemSettings.m_experimentReference;
- }
-
- /// returns the scripts folder, used for remote path
- std::string getTomoScriptFolderPath() const { return g_tomoScriptFolderPath; }
-
- /// returns the tomo script location path inside the scripts folder
- std::string getTomoScriptLocationPath() const {
- return g_mainReconstructionScript;
- }
-
- /// ping the (remote) compute resource
- bool doPing(const std::string &compRes);
- /// Log into the (remote or local) compute resource
- void doLogin(const std::string &compRes, const std::string &user,
- const std::string &pw);
- /// Log out from the (remote or local) compute resource
- void doLogout(const std::string &compRes, const std::string &username);
- /// Query the status of running (and recent) jobs
- void doQueryJobStatus(const std::string &compRes,
- std::vector<std::string> &ids,
- std::vector<std::string> &names,
- std::vector<std::string> &status,
- std::vector<std::string> &cmds);
- /// Submit a new job to the (remote or local) compute resource
- void prepareSubmissionArguments(const bool local, std::string &runnable,
- std::vector<std::string> &args,
- std::string &allOpts);
-
- void doLocalRunReconstructionJob(
- const std::string &runnable, const std::vector<std::string> &args,
- const std::string &allOpts,
- MantidQt::CustomInterfaces::TomographyThread &thread,
- MantidQt::CustomInterfaces::TomographyProcess &worker,
- const std::string &workerName = "Mantid_Local");
-
- void doRemoteRunReconstructionJob(const std::string &compRes,
- const std::string &runnable,
- const std::string &allOpts);
-
- /// Cancel a previously submitted job
- void doCancelJobs(const std::string &compRes,
- const std::vector<std::string> &id);
-
- void addJobToStatus(const qint64 pid, const std::string &runnable,
- const std::string &allOpts,
- const std::string &workerName);
- /// Get fresh status information on running/recent jobs
- void doRefreshJobsInfo(const std::string &compRes);
-
- void refreshLocalJobsInfo();
-
- void setExperimentReference(const std::string ref) { m_experimentRef = ref; }
-
- /// Update to the current setings given by the user
- void setSystemSettings(const TomoSystemSettings &settings) {
- m_systemSettings = settings;
- }
-
- void setPrePostProcSettings(const TomoReconFiltersSettings &filters) {
- m_prePostProcSettings = filters;
- }
-
- void setImageStackPreParams(const ImageStackPreParams &roiEtc) {
- m_imageStackPreParams = roiEtc;
- }
-
- /// loads an image/picture in FITS format
- Mantid::API::WorkspaceGroup_sptr loadFITSImage(const std::string &path);
-
- /// Log this message through the system logging
- void logMsg(const std::string &msg);
- void logErrMsg(const std::string &msg);
-
- /// for clean destruction
- void cleanup();
-
- std::string localComputeResource() const { return g_LocalResourceName; }
-
- void setTomoPathsConfig(const TomoPathsConfig &tc) { m_pathsConfig = tc; }
- void updateProcessInJobList(const qint64 pid, const int exitCode);
- void terminateProcess();
-
- // Names of reconstruction tools
- static const std::string g_TomoPyTool;
- static const std::string g_AstraTool;
- static const std::string g_customCmdTool;
- // not supported yet
- static const std::string g_CCPiTool;
- static const std::string g_SavuTool;
-
- // Name of the remote compute resource
- static const std::string g_SCARFName;
- static const std::string g_LocalResourceName;
-
- // The main tomo_reconstruct.py or similar script (as it is distributed with
- // Mantid). This is the entry point for reconstruction jobs.
- static const std::string g_mainReconstructionScript;
- static const std::string g_tomoScriptFolderPath;
-
-protected: // protected to expose everything to testing
- std::string
- constructSingleStringFromVector(const std::vector<std::string> args) const;
-
- /// retrieve info from compute resource into status table
- void getJobStatusInfo(const std::string &compRes);
-
- std::string validateCompResource(const std::string &res) const;
-
- bool checkIfToolIsSetupProperly(const std::string &tool,
- const std::string &cmd,
- const std::vector<std::string> &args) const;
-
- void makeTomoRecScriptOptions(const bool local,
- std::vector<std::string> &opts) const;
-
- void filtersCfgToCmdOpts(const TomoReconFiltersSettings &filters,
- const ImageStackPreParams &corRegions,
- const bool local,
- std::vector<std::string> &opts) const;
-
- void splitCmdLine(const std::string &cmd, std::string &runnable,
- std::string &opts) const;
-
- /// process the tool name to be appropriate for the command line arg
- std::string prepareToolNameForArgs(const std::string &toolName) const;
-
- void checkDataPathsSet() const;
-
- std::string adaptInputPathForExecution(const std::string &path,
- const bool local) const;
-
- std::string buildOutReconstructionDir(const std::string &samplesDir,
- bool) const;
-
- bool processIsRunning(qint64 pid) const;
-
- std::string
- buildOutReconstructionDirFromSystemRoot(const std::string &samplesDir,
- bool local) const;
-
- std::string
- buildOutReconstructionDirFromSamplesDir(const std::string &samplesDir) const;
-
-private:
- /// facility for the remote compute resource
- const std::string m_facility;
-
- /// Experiment reference (RBNumber for example)
- std::string m_experimentRef;
-
- /// username last logged in (empty if not in login status), from local
- /// perspective
- std::string m_loggedInUser;
- std::string m_loggedInComp;
-
- /// compute resources suppoted by this GUI (remote ones, clusters, etc.)
- std::vector<std::string> m_computeRes;
- /// status of the compute resources: availalbe/unavailable or usable/unusable
- std::vector<bool> m_computeResStatus;
- /// identifiers of reconstruction tools supported, given a compute resource
- std::vector<std::string> m_reconTools;
- std::vector<bool> m_reconToolsStatus;
-
- // status of remote jobs
- std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> m_jobsStatus;
- // status of local runs/jobs
- std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> m_jobsStatusLocal;
-
- /// reconstruction tools available on SCARF
- std::vector<std::string> m_SCARFtools;
-
- // Paths for the sample, flat and dark images
- TomoPathsConfig m_pathsConfig;
-
- // System settting including several paths and parameters (local and remote)
- TomoSystemSettings m_systemSettings;
-
- //--------------------------------
- // Current tool variables
- //--------------------------------
-
- // current tool's name, updated from the presenter on change
- std::string m_currentToolName;
-
- // the tool settings so we can use it for reconstruction params
- std::shared_ptr<TomoRecToolConfig> m_currentToolSettings;
-
- // current tool's method, updated from the presenter on change
- std::string m_currentToolMethod;
-
- // Settings for the pre-/post-processing filters
- TomoReconFiltersSettings m_prePostProcSettings;
-
- // Parameters set for the ROI, normalization region, etc.
- ImageStackPreParams m_imageStackPreParams;
-
- // mutex for the job status info update operations
- // TODO: replace with std::mutex+std::lock_guard
- QMutex *m_statusMutex;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEMODEL_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h
deleted file mode 100644
index 3a874640a08..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h
+++ /dev/null
@@ -1,185 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEPRESENTER_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEPRESENTER_H_
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyIfacePresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h"
-
-#include <QMutex>
-#include <QObject>
-#include <boost/scoped_ptr.hpp>
-
-// Qt classes forward declarations
-class QThread;
-class QTimer;
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-class TomoPathsConfig;
-class TomoToolConfigDialogBase;
-
-/**
-Tomography GUI. Presenter for the GUI (as in the MVP
-(Model-View-Presenter) pattern). In principle, in a strict MVP setup,
-signals from the model should always be handled through this presenter
-and never go directly to the view, and viceversa.
-
-Copyright © 2014-2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL TomographyIfacePresenter
- : public QObject,
- public ITomographyIfacePresenter {
- Q_OBJECT
-
-public:
- /// Default constructor - normally used from the concrete view
- TomographyIfacePresenter(ITomographyIfaceView *view);
- ~TomographyIfacePresenter() override;
-
- void notify(ITomographyIfacePresenter::Notification notif) override;
-
-protected:
- void initialize();
-
- /// clean shut down of model, view, etc.
- void cleanup();
-
- // notification methods
- void processSystemSettingsUpdated();
- void processSetupResourcesAndTools();
- void processCompResourceChanged();
- void processToolChanged();
- void processTomoPathsChanged();
- void processTomoPathsEditedByUser();
- void processRunExternalProcess();
- void processLogin();
- void processLogout();
- void processSetupReconTool();
- void processRunRecon();
- void processCancelJobs();
- void processVisualizeJobs();
- void processLogMsg();
- void processAggregateEnergyBands();
- void processShutDown();
-
- void doVisualize(const std::vector<std::string> &ids);
-
- /// auto-guess additional directories when the user gives the samples path
- void findFlatsDarksFromSampleGivenByUser(TomoPathsConfig &cfg);
-
- bool
- usableEnergyBandsPaths(const std::map<std::string, std::string> &algParams);
-
- /// Starts a periodic query just to keep sessions alive when logged in
- void startKeepAliveMechanism(int period);
-
- /// Stops/kills the periodic query (for example if the user logs out)
- void killKeepAliveMechanism();
-
- bool isLocalResourceSelected() const;
-signals:
- void terminated();
-
-protected slots:
- /// It may be run on user request, or periodically from a timer/thread
- void processRefreshJobs();
- void readWorkerStdOut(const QString &workerString);
- void readWorkerStdErr(const QString &workerString);
- void addProcessToJobList();
- void reconProcessFailedToStart();
- void workerFinished(const qint64 pid, const int exitCode);
- void emitExternalProcessOutput(const qint64 pid, const int exitCode);
-
-private:
- /// Update the model's filter, COR and ROI/Area of norm settings
- /// and build the runnable and arguments
- void prepareSubmissionArguments(const bool local, std::string &runnable,
- std::vector<std::string> &args,
- std::string &allOpts);
- /// Asks the user for permission to cancel the running reconstruction
- bool userConfirmationToCancelRecon();
- void setupAndRunLocalReconstruction(const std::string &runnable,
- const std::vector<std::string> &args,
- const std::string &allOpts);
-
- void setupAndRunLocalExternalProcess(const std::string &runnable,
- const std::vector<std::string> &args,
- const std::string &allOpts);
- /// creates the correct dialog pointer and sets it to the member variable
- void createConfigDialogUsingToolName(const std::string &toolName);
-
- /// sets up the dialog and uses the settings to update the model
- void
- setupConfigDialogSettingsAndUpdateModel(TomoToolConfigDialogBase *dialog);
-
- /// configures up the dialog using the view
- void setupConfigDialogSettings(TomoToolConfigDialogBase &dialog);
-
- /// does the actual path configuration for local resource
- void setupConfigDialogSettingsForLocal(TomoToolConfigDialogBase &dialog);
-
- /// does the actual path configuration for remote resource
- void setupConfigDialogSettingsForRemote(TomoToolConfigDialogBase &dialog);
-
- /// update all the model information after the tool's been changed
- void updateModelAfterToolChanged(const TomoToolConfigDialogBase &dialog);
-
- /// update the model's current tool name using the dialog
- void updateModelCurrentToolName(const TomoToolConfigDialogBase &dialog);
-
- /// update the model's current tool method using the dialog
- void updateModelCurrentToolMethod(const TomoToolConfigDialogBase &dialog);
-
- /// update the model's current tool settings using the dialog
- void updateModelCurrentToolSettings(const TomoToolConfigDialogBase &dialog);
-
- /// Associated view for this presenter (MVP pattern)
- ITomographyIfaceView *const m_view;
-
- /// Associated model for this presenter (MVP pattern)
- const boost::scoped_ptr<TomographyIfaceModel> m_model;
-
- // TODO: replace this with an std::mutex. Also below for threads.
- // mutex for the job status info update operations on the view
- QMutex *m_statusMutex;
-
- // for periodic update of the job status table/tree
- QTimer *m_keepAliveTimer;
-
- std::unique_ptr<TomographyThread> m_workerThread;
- QString m_workerOutputCache;
- QString m_workerErrorCache;
-
- std::unique_ptr<TomoToolConfigDialogBase> m_configDialog;
-
- static const std::string g_defOutPathLocal;
- static const std::string g_defOutPathRemote;
-
- bool m_reconRunning = false;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEPRESENTER_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtGUI.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtGUI.ui
deleted file mode 100644
index 0c3e4253364..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtGUI.ui
+++ /dev/null
@@ -1,106 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomographyIfaceQtGUI</class>
- <widget class="QMainWindow" name="TomographyIfaceQtGUI">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>1059</width>
- <height>700</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>IMAT Imaging and Tomography</string>
- </property>
- <widget class="QWidget" name="mainWidget">
- <layout class="QGridLayout" name="gridLayout_4">
- <property name="margin">
- <number>3</number>
- </property>
- <property name="spacing">
- <number>1</number>
- </property>
- <item row="1" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QPushButton" name="pushButton_help">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="maximumSize">
- <size>
- <width>25</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>?</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>158</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_close">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Close</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="0" column="0">
- <widget class="QTabWidget" name="tabMain">
- <property name="toolTip">
- <string/>
- </property>
- <property name="currentIndex">
- <number>-1</number>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <action name="actionOpen">
- <property name="text">
- <string>&Open...</string>
- </property>
- </action>
- <action name="actionSave">
- <property name="text">
- <string>&Save</string>
- </property>
- </action>
- <action name="actionSaveAs">
- <property name="text">
- <string>Save As</string>
- </property>
- </action>
- </widget>
- <tabstops>
- <tabstop>tabMain</tabstop>
- </tabstops>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabEnergy.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabEnergy.ui
deleted file mode 100644
index 2a250fefa8d..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabEnergy.ui
+++ /dev/null
@@ -1,400 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomographyIfaceQtTabEnergy</class>
- <widget class="QWidget" name="TomographyIfaceQtTabEnergy">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>822</width>
- <height>574</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Form</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_4">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <widget class="QGroupBox" name="groupBox_inputs">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="title">
- <string>Input:</string>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="1" column="3">
- <widget class="QPushButton" name="pushButton_browse_input">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Path:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="2" colspan="2">
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>268</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>Pick format:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QComboBox" name="comboBox_input_format">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <item>
- <property name="text">
- <string>FITS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>TIFF</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>PNG</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="1" column="1" colspan="2">
- <widget class="QLineEdit" name="lineEdit_input_path">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>2</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QGroupBox" name="groupBox_outputs">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="title">
- <string>Output:</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QGridLayout" name="gridLayout_3">
- <item row="0" column="0">
- <widget class="QRadioButton" name="radioButton_uniform_bands">
- <property name="text">
- <string>Uniform</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="0" column="1" colspan="2">
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Number of bands:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="3">
- <widget class="QSpinBox" name="spinBox_uniform_bands">
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>1000</number>
- </property>
- </widget>
- </item>
- <item row="0" column="4">
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>326</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="1" column="0" colspan="2">
- <widget class="QRadioButton" name="radioButton_index_ranges">
- <property name="text">
- <string>Indices of boundaries:</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="2" colspan="3">
- <widget class="QLineEdit" name="lineEdit_index_ranges"/>
- </item>
- <item row="2" column="0" colspan="2">
- <widget class="QRadioButton" name="radioButton_tof_ranges">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>ToF boundaries:</string>
- </property>
- </widget>
- </item>
- <item row="2" column="2" colspan="3">
- <widget class="QLineEdit" name="lineEdit_tof_ranges"/>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QLabel" name="label_7">
- <property name="text">
- <string>Image format:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_output_format">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <item>
- <property name="text">
- <string>FITS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>TIFF</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>PNG</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_3">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <widget class="QLabel" name="label_6">
- <property name="text">
- <string>Path</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_output_path">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_browse_output">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <spacer name="horizontalSpacer_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>278</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_agg">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="text">
- <string>Aggregate</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>88</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QGroupBox" name="groupBox_config">
- <property name="title">
- <string>Configuration for remote:</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_2">
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string>Path:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_script">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>2</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>C:\MantidInstall\scrips\imaging\IMAT\agg_energy_bands.py</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_browse_script">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <tabstops>
- <tabstop>comboBox_input_format</tabstop>
- <tabstop>lineEdit_input_path</tabstop>
- <tabstop>pushButton_browse_input</tabstop>
- <tabstop>radioButton_uniform_bands</tabstop>
- <tabstop>spinBox_uniform_bands</tabstop>
- <tabstop>radioButton_index_ranges</tabstop>
- <tabstop>lineEdit_index_ranges</tabstop>
- <tabstop>radioButton_tof_ranges</tabstop>
- <tabstop>lineEdit_tof_ranges</tabstop>
- <tabstop>comboBox_output_format</tabstop>
- <tabstop>lineEdit_output_path</tabstop>
- <tabstop>pushButton_browse_output</tabstop>
- <tabstop>pushButton_agg</tabstop>
- <tabstop>groupBox_config</tabstop>
- <tabstop>lineEdit_script</tabstop>
- <tabstop>pushButton_browse_script</tabstop>
- </tabstops>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabFiltersSettings.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabFiltersSettings.ui
deleted file mode 100644
index 639ba999b67..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabFiltersSettings.ui
+++ /dev/null
@@ -1,604 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomographyIfaceQtTabFiltersSettings</class>
- <widget class="QWidget" name="TomographyIfaceQtTabFiltersSettings">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>826</width>
- <height>578</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Form</string>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QScrollArea" name="scrollArea">
- <property name="widgetResizable">
- <bool>true</bool>
- </property>
- <widget class="QWidget" name="scrollAreaWidgetContents">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>788</width>
- <height>671</height>
- </rect>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QGroupBox" name="groupBox">
- <property name="title">
- <string>Pre-processing (raw images)</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_5">
- <item row="10" column="2">
- <widget class="QDoubleSpinBox" name="doubleSpinBox_prep_max_angle">
- <property name="toolTip">
- <string>Maximum angle to use for reconstruction</string>
- </property>
- <property name="decimals">
- <number>3</number>
- </property>
- <property name="minimum">
- <double>1.000000000000000</double>
- </property>
- <property name="maximum">
- <double>360.000000000000000</double>
- </property>
- <property name="value">
- <double>360.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="11" column="0">
- <widget class="QLabel" name="label_prep_scale_factor">
- <property name="text">
- <string>Scale down factor:</string>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QCheckBox" name="checkBox_normalize_by_flats">
- <property name="statusTip">
- <string>Normalize every image with respect to the reference flat and dark images, if available</string>
- </property>
- <property name="text">
- <string>Normalize by flat (open beam) mages</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="5" column="1">
- <spacer name="horizontalSpacer_13">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>399</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="11" column="1">
- <spacer name="horizontalSpacer_14">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>399</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="10" column="1">
- <spacer name="horizontalSpacer_15">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>399</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="11" column="2">
- <widget class="QSpinBox" name="spinBox_prep_scale_factor">
- <property name="toolTip">
- <string>Sets the size of block to downscale. For example with 2, blocks of 2x2 pixels will be combined into a (median value) pixel</string>
- </property>
- <property name="minimum">
- <number>0</number>
- </property>
- <property name="maximum">
- <number>100</number>
- </property>
- <property name="value">
- <number>0</number>
- </property>
- </widget>
- </item>
- <item row="5" column="0">
- <widget class="QLabel" name="label_prep_median">
- <property name="text">
- <string>Dots removal (median filter width):</string>
- </property>
- </widget>
- </item>
- <item row="10" column="0">
- <widget class="QLabel" name="label_prep_max_angle">
- <property name="text">
- <string>Maximum angle:</string>
- </property>
- </widget>
- </item>
- <item row="5" column="2">
- <widget class="QSpinBox" name="spinBox_prep_median_filter_width">
- <property name="toolTip">
- <string>Set size of the blocks to calculate a median filter. Bigger size implies more smoothing.</string>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>1000</number>
- </property>
- </widget>
- </item>
- <item row="6" column="0" colspan="3">
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>Sinogram stripes removal / ring artifacts removal</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_3">
- <item>
- <property name="text">
- <string>Wavelet-Fourier</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>None</string>
- </property>
- </item>
- </widget>
- </item>
- </layout>
- </item>
- <item row="4" column="0">
- <widget class="QCheckBox" name="checkBox_corrections_MCP_detector">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Corrections for MCP detector</string>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QCheckBox" name="checkBox_normalize_by_darks">
- <property name="statusTip">
- <string>Normalize every image with respect to the reference flat and dark images, if available</string>
- </property>
- <property name="text">
- <string>Normalize by dark field images</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QCheckBox" name="checkBox_normalize_by_air_region">
- <property name="statusTip">
- <string>Normalize every image by their relative proton charges</string>
- </property>
- <property name="text">
- <string>Normalize by air region / proton charge</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QCheckBox" name="checkBox_normalize_by_proton_charge">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Normalize by proton charge</string>
- </property>
- </widget>
- </item>
- <item row="8" column="2">
- <widget class="QComboBox" name="comboBox_prep_rotation">
- <property name="toolTip">
- <string>Rotate all images in the input stacks by this angle</string>
- </property>
- <item>
- <property name="text">
- <string>0</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>90</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>180</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>270</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="8" column="1">
- <spacer name="horizontalSpacer_12">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>399</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="8" column="0">
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Rotation (°, clockwise)</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>15</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QGroupBox" name="groupBox_2">
- <property name="title">
- <string>Post-processing (reconstructed volume)</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_4">
- <item row="0" column="0">
- <widget class="QLabel" name="label_post_cir_mask">
- <property name="text">
- <string>Circular mask radius [0,1]:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <spacer name="horizontalSpacer_9">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>487</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="0" column="2">
- <widget class="QDoubleSpinBox" name="doubleSpinBox_post_circ_mask">
- <property name="toolTip">
- <string>Set the radius (relative to the smaller edge of the images). All pixels outside the mask are zeroed.</string>
- </property>
- <property name="decimals">
- <number>3</number>
- </property>
- <property name="maximum">
- <double>1.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>0.940000000000000</double>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_post_cutoff">
- <property name="text">
- <string>Cut-off level (%)</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <spacer name="horizontalSpacer_10">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>487</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="1" column="2">
- <widget class="QDoubleSpinBox" name="doubleSpinBox_post_cutoff">
- <property name="toolTip">
- <string>Cut-off (zeroes) low pixel values, below this level</string>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_3">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>15</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QGroupBox" name="groupBox_3">
- <property name="title">
- <string>Output options:</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLabel" name="label_out_img_format">
- <property name="text">
- <string>Output image format:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_out_img_format">
- <item>
- <property name="text">
- <string>PNG</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_6">
- <item>
- <widget class="QLabel" name="label_out_bit_depth">
- <property name="text">
- <string>Pixel bit-depth in outputs:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_out_bit_depth">
- <item>
- <property name="text">
- <string>16 bits</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_16">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_out_preproc_images">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="toolTip">
- <string>Write pre-processed images in addition to reconstructed volume</string>
- </property>
- <property name="text">
- <string>Produce pre-processed images stack</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QGroupBox" name="groupBox_out_intermediate_prep">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="title">
- <string>Produce intermediate pre-processed images</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_6">
- <item row="3" column="0">
- <widget class="QCheckBox" name="checkBox_output_dot_removal">
- <property name="text">
- <string>Dots removed (median filter)</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QCheckBox" name="checkBox_output_normalized_flat_images">
- <property name="text">
- <string>Normalized - flat, dark images</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QCheckBox" name="checkBox_output_normalized_proton_images">
- <property name="text">
- <string>Normalized - proton charge</string>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QCheckBox" name="checkBox_output_cropped_images">
- <property name="text">
- <string>Cropped</string>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <widget class="QCheckBox" name="checkBox_output_sinograms">
- <property name="text">
- <string>sinograms</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>14</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <spacer name="horizontalSpacer_11">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>608</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_reset">
- <property name="text">
- <string>Reset all</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </widget>
- <tabstops>
- <tabstop>scrollArea</tabstop>
- <tabstop>checkBox_normalize_by_air_region</tabstop>
- <tabstop>checkBox_normalize_by_proton_charge</tabstop>
- <tabstop>checkBox_normalize_by_flats</tabstop>
- <tabstop>checkBox_normalize_by_darks</tabstop>
- <tabstop>checkBox_corrections_MCP_detector</tabstop>
- <tabstop>spinBox_prep_median_filter_width</tabstop>
- <tabstop>comboBox_3</tabstop>
- <tabstop>comboBox_prep_rotation</tabstop>
- <tabstop>doubleSpinBox_prep_max_angle</tabstop>
- <tabstop>spinBox_prep_scale_factor</tabstop>
- <tabstop>doubleSpinBox_post_circ_mask</tabstop>
- <tabstop>doubleSpinBox_post_cutoff</tabstop>
- <tabstop>comboBox_out_img_format</tabstop>
- <tabstop>comboBox_out_bit_depth</tabstop>
- <tabstop>checkBox_out_preproc_images</tabstop>
- <tabstop>groupBox_out_intermediate_prep</tabstop>
- <tabstop>checkBox_output_cropped_images</tabstop>
- <tabstop>checkBox_output_normalized_proton_images</tabstop>
- <tabstop>checkBox_output_normalized_flat_images</tabstop>
- <tabstop>checkBox_output_dot_removal</tabstop>
- <tabstop>checkBox_output_sinograms</tabstop>
- <tabstop>pushButton_reset</tabstop>
- </tabstops>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabRun.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabRun.ui
deleted file mode 100644
index 4d62147b85b..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabRun.ui
+++ /dev/null
@@ -1,802 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomographyIfaceQtTabRun</class>
- <widget class="QWidget" name="TomographyIfaceQtTabRun">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>965</width>
- <height>764</height>
- </rect>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QSplitter" name="splitter_run_main_vertical">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <widget class="QSplitter" name="splitter_image_resource">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>220</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="opaqueResize">
- <bool>true</bool>
- </property>
- <widget class="QWidget" name="layoutWidget_5">
- <layout class="QGridLayout" name="gridLayout_11">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <item row="1" column="1">
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Fixed</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>6</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QGroupBox" name="experiment_reference">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>400</width>
- <height>49</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>400</width>
- <height>79</height>
- </size>
- </property>
- <property name="layoutDirection">
- <enum>Qt::LeftToRight</enum>
- </property>
- <property name="title">
- <string/>
- </property>
- <property name="flat">
- <bool>false</bool>
- </property>
- <property name="checkable">
- <bool>false</bool>
- </property>
- <widget class="QLabel" name="label_experiment_reference">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>20</y>
- <width>141</width>
- <height>40</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>39</width>
- <height>40</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>40</height>
- </size>
- </property>
- <property name="text">
- <string>Exp. reference (RB number)</string>
- </property>
- </widget>
- <widget class="QLineEdit" name="lineEdit_experiment_reference">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="geometry">
- <rect>
- <x>160</x>
- <y>30</y>
- <width>221</width>
- <height>20</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>RB0000XXX</string>
- </property>
- </widget>
- </widget>
- </item>
- <item>
- <widget class="QGroupBox" name="compute_resource">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>400</width>
- <height>130</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>400</width>
- <height>129</height>
- </size>
- </property>
- <property name="title">
- <string>Compute resource</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_15">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <item row="1" column="0">
- <widget class="QComboBox" name="comboBox_run_compute_resource">
- <item>
- <property name="text">
- <string>SCARF</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Local</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="1" column="1">
- <layout class="QHBoxLayout" name="horizontalLayout_6">
- <item>
- <widget class="QLabel" name="label_SCARF_username">
- <property name="minimumSize">
- <size>
- <width>90</width>
- <height>20</height>
- </size>
- </property>
- <property name="text">
- <string>Username:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_SCARF_username">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>140</width>
- <height>20</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Type your username on the remote compute resource</string>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="2" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <spacer name="horizontalSpacer_8">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QLabel" name="remote_status">
- <property name="text">
- <string>Remote status:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_remote_status">
- <property name="text">
- <string>Offline</string>
- </property>
- <property name="autoDefault">
- <bool>false</bool>
- </property>
- <property name="default">
- <bool>false</bool>
- </property>
- <property name="flat">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_9">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item row="2" column="1">
- <layout class="QHBoxLayout" name="horizontalLayout_7">
- <item>
- <widget class="QLabel" name="label_SCARF_password">
- <property name="minimumSize">
- <size>
- <width>90</width>
- <height>20</height>
- </size>
- </property>
- <property name="text">
- <string>Password:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_SCARF_password">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>140</width>
- <height>20</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Type your password. It will be used just for authentication. It won't be displayed or saved anywhere</string>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="echoMode">
- <enum>QLineEdit::Password</enum>
- </property>
- <property name="cursorPosition">
- <number>0</number>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="3" column="1">
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QPushButton" name="pushButton_SCARF_login">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>22</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>27</height>
- </size>
- </property>
- <property name="text">
- <string>Log in</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_SCARF_logout">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>22</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>27</height>
- </size>
- </property>
- <property name="text">
- <string>Log out</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </item>
- <item row="1" column="0">
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QGroupBox" name="reconstruction_tool">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>535</width>
- <height>50</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>535</width>
- <height>90</height>
- </size>
- </property>
- <property name="title">
- <string>Reconstruction tool</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_18">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <item row="0" column="1">
- <widget class="QComboBox" name="comboBox_run_tool">
- <item>
- <property name="text">
- <string>TomoPy</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Astra</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>CCPi CGLS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Savu</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Custom command</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="0" column="2">
- <widget class="QPushButton" name="pushButton_run_tool_setup">
- <property name="toolTip">
- <string>Define specific settings for the tool selected</string>
- </property>
- <property name="statusTip">
- <string/>
- </property>
- <property name="text">
- <string>Setup</string>
- </property>
- <property name="autoRepeat">
- <bool>false</bool>
- </property>
- <property name="autoExclusive">
- <bool>false</bool>
- </property>
- <property name="flat">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <widget class="QPushButton" name="pushButton_reconstruct">
- <property name="toolTip">
- <string/>
- </property>
- <property name="statusTip">
- <string/>
- </property>
- <property name="text">
- <string>Reconstruct</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QGroupBox" name="input_directories">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>535</width>
- <height>129</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>535</width>
- <height>129</height>
- </size>
- </property>
- <property name="title">
- <string>Directories/folders for the input images:</string>
- </property>
- <widget class="QWidget" name="horizontalLayoutWidget">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>20</y>
- <width>521</width>
- <height>31</height>
- </rect>
- </property>
- <layout class="QHBoxLayout" name="sample_dir">
- <item>
- <widget class="QLabel" name="label_samples">
- <property name="minimumSize">
- <size>
- <width>120</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>101</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Samples directory:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_path_samples">
- <property name="text">
- <string>D:/data/RB000000/experiment1/sample</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_samples_dir">
- <property name="maximumSize">
- <size>
- <width>75</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Browse...</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="horizontalLayoutWidget_2">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>50</y>
- <width>521</width>
- <height>31</height>
- </rect>
- </property>
- <layout class="QHBoxLayout" name="flat_dir">
- <property name="spacing">
- <number>6</number>
- </property>
- <item>
- <widget class="QCheckBox" name="checkBox_path_flats">
- <property name="text">
- <string>Flat/open beam</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_path_flats">
- <property name="text">
- <string>D:/data/RB000000/experiment1/flat</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_flats_dir">
- <property name="maximumSize">
- <size>
- <width>75</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Browse...</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="horizontalLayoutWidget_3">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>80</y>
- <width>521</width>
- <height>31</height>
- </rect>
- </property>
- <layout class="QHBoxLayout" name="dark_dir">
- <item>
- <widget class="QCheckBox" name="checkBox_path_darks">
- <property name="text">
- <string>Dark field:</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_path_darks">
- <property name="text">
- <string>D:/data/RB000000/experiment1/dark</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_darks_dir">
- <property name="maximumSize">
- <size>
- <width>75</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>Browse...</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="layoutWidget_7">
- <layout class="QVBoxLayout" name="verticalLayout_7">
- <property name="sizeConstraint">
- <enum>QLayout::SetMaximumSize</enum>
- </property>
- <item>
- <widget class="QLabel" name="label_11">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Reconstruction jobs:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSplitter" name="splitter_run_jobs">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <widget class="QTableWidget" name="tableWidget_run_jobs">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>1</horstretch>
- <verstretch>1</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>500</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="selectionBehavior">
- <enum>QAbstractItemView::SelectRows</enum>
- </property>
- <attribute name="horizontalHeaderStretchLastSection">
- <bool>true</bool>
- </attribute>
- <column>
- <property name="text">
- <string>Running on</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>Name</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>ID</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>Status</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>Command line</string>
- </property>
- </column>
- </widget>
- <widget class="QWidget" name="layoutWidget_8">
- <layout class="QGridLayout" name="gridLayout_16">
- <item row="5" column="0">
- <widget class="QPushButton" name="pushButton_run_job_cancel">
- <property name="text">
- <string>Cancel</string>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <spacer name="verticalSpacer_5">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="1" column="0">
- <widget class="QPushButton" name="pushButton_run_refresh">
- <property name="text">
- <string>Refresh</string>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QPushButton" name="pushButton_showProcessOutput">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Show Output</string>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QPushButton" name="pushButton_run_job_visualize">
- <property name="text">
- <string>Visualize</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </widget>
- <tabstops>
- <tabstop>comboBox_run_tool</tabstop>
- <tabstop>pushButton_run_tool_setup</tabstop>
- <tabstop>pushButton_reconstruct</tabstop>
- <tabstop>lineEdit_experiment_reference</tabstop>
- <tabstop>comboBox_run_compute_resource</tabstop>
- <tabstop>lineEdit_SCARF_username</tabstop>
- <tabstop>lineEdit_SCARF_password</tabstop>
- <tabstop>pushButton_SCARF_login</tabstop>
- <tabstop>pushButton_SCARF_logout</tabstop>
- <tabstop>tableWidget_run_jobs</tabstop> <!-- not sure we want this-->
- <tabstop>pushButton_run_refresh</tabstop>
- <tabstop>pushButton_run_job_visualize</tabstop>
- <tabstop>pushButton_run_job_cancel</tabstop>
- </tabstops>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabSystemSettings.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabSystemSettings.ui
deleted file mode 100644
index 910e59df411..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabSystemSettings.ui
+++ /dev/null
@@ -1,790 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomographyIfaceQtTabSystemSettings</class>
- <widget class="QWidget" name="TomographyIfaceQtTabSystemSettings">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>738</width>
- <height>571</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Form</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_9">
- <item row="0" column="0">
- <widget class="QScrollArea" name="scrollArea">
- <property name="lineWidth">
- <number>0</number>
- </property>
- <property name="widgetResizable">
- <bool>true</bool>
- </property>
- <widget class="QWidget" name="scrollAreaWidgetContents">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>-161</y>
- <width>700</width>
- <height>710</height>
- </rect>
- </property>
- <layout class="QGridLayout" name="gridLayout_8">
- <item row="1" column="0">
- <widget class="QGroupBox" name="groupBox_10">
- <property name="title">
- <string>Execution of reconstruction jobs:</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_6">
- <item row="0" column="0">
- <widget class="QGroupBox" name="groupBox_5">
- <property name="title">
- <string>Remote runs:</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_12">
- <item row="4" column="0">
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>51</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="2" column="1">
- <widget class="QSpinBox" name="spinBox_remote_cores">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>20</height>
- </size>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>99</number>
- </property>
- <property name="value">
- <number>8</number>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_24">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Number of cores:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="label_23">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Number of nodes:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QSpinBox" name="spinBox_remote_nodes">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>20</height>
- </size>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>99</number>
- </property>
- <property name="value">
- <number>1</number>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QGroupBox" name="groupBox_4">
- <property name="title">
- <string>Local runs:</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_11">
- <item row="1" column="0" colspan="2">
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <widget class="QLabel" name="label_recon_scripts">
- <property name="text">
- <string>Reconstruction scripts:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_local_recon_scripts">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>2</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>C:/MantidInstall/scripts/</string>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_local_recon_scripts_dir">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="0" column="0">
- <layout class="QGridLayout" name="gridLayout_10">
- <item row="0" column="0">
- <widget class="QLabel" name="label_3">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Max. processes:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QSpinBox" name="spinBox_local_processes">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>10</number>
- </property>
- <property name="value">
- <number>4</number>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_25">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Number of cores:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QSpinBox" name="spinBox_local_cores">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>10</height>
- </size>
- </property>
- <property name="maximum">
- <number>99</number>
- </property>
- <property name="value">
- <number>4</number>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="0" column="1">
- <spacer name="horizontalSpacer_7">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>259</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="2" column="0" colspan="2">
- <layout class="QHBoxLayout" name="horizontalLayout_6">
- <item>
- <widget class="QLabel" name="label_13_local_external_interpreter">
- <property name="text">
- <string>External interpreter:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_local_external_interpreter">
- <property name="text">
- <string>C:\local\Anaconda\python.exe</string>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_local_external_interpreter">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QGroupBox" name="groupBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>1</verstretch>
- </sizepolicy>
- </property>
- <property name="title">
- <string>File system and paths of the tomography system:</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_7">
- <item row="0" column="0">
- <widget class="QGroupBox" name="groupBox_2">
- <property name="title">
- <string>Path components of the inputs and outputs:</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_5">
- <item row="0" column="0">
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string>1st level:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLineEdit" name="lineEdit_path_comp_1st">
- <property name="text">
- <string>data</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_5">
- <property name="text">
- <string>2nd level:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QComboBox" name="comboBox_path_comp_2nd">
- <item>
- <property name="text">
- <string>Experiment Reference (RB number)</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_6">
- <property name="text">
- <string>3rd level:</string>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QComboBox" name="comboBox_path_comp_3rd">
- <item>
- <property name="text">
- <string>Sample/experiment name (free form)</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QLabel" name="label_7">
- <property name="text">
- <string>4th level:</string>
- </property>
- </widget>
- </item>
- <item row="4" column="0" colspan="2">
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QGroupBox" name="groupBox_7">
- <property name="title">
- <string>Path components (prefixes) of the inputs:</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_4">
- <item row="2" column="1">
- <widget class="QLineEdit" name="lineEdit_path_comp_input_darks">
- <property name="text">
- <string>dark</string>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QLineEdit" name="lineEdit_path_comp_input_flats">
- <property name="text">
- <string>flat</string>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_11">
- <property name="text">
- <string>Dark images:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="label_9">
- <property name="text">
- <string>Sample images</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_10">
- <property name="text">
- <string>Flat images:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLineEdit" name="lineEdit_path_comp_input_samples">
- <property name="text">
- <string>data</string>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <spacer name="horizontalSpacer_6">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QGroupBox" name="groupBox_6">
- <property name="title">
- <string>Path components of the outputs:</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_3">
- <item row="0" column="0">
- <widget class="QLabel" name="label_8">
- <property name="text">
- <string>Pre-processed data::</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLineEdit" name="lineEdit_path_comp_out_preprocessed">
- <property name="text">
- <string>pre_processed</string>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="0" column="2">
- <spacer name="horizontalSpacer_4">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Reconstructed data::</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QLineEdit" name="lineEdit_path_comp_out_processed">
- <property name="text">
- <string>processed</string>
- </property>
- <property name="readOnly">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <spacer name="horizontalSpacer_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>18</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QGroupBox" name="groupBox_3">
- <property name="title">
- <string>Paths on the remote (SCARF) file system</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_2">
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_10">
- <item>
- <widget class="QLabel" name="label_22">
- <property name="text">
- <string>Base path for tomography data:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_remote_base_path_data">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>20</height>
- </size>
- </property>
- <property name="text">
- <string>/work/imat</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item row="1" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Base path for reconstruction tools/scripts:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_remote_scripts_base_dir">
- <property name="text">
- <string>/work/imat/phase_commissioning</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_reset_scripts_base_dir_remote">
- <property name="text">
- <string>Reset</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QGroupBox" name="groupBox_8">
- <property name="title">
- <string>Root paths on the local system</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_11">
- <item>
- <widget class="QLabel" name="label_26">
- <property name="text">
- <string>Base drive / path for tomography data (in/out)::</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_on_local_data_drive_or_path">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>20</height>
- </size>
- </property>
- <property name="text">
- <string>D:\</string>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_on_local_data_drive_or_path">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item row="1" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QLabel" name="label_12">
- <property name="text">
- <string>Network drive or mount point for the remote:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_on_local_remote_data_drive_path">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>S:</string>
- </property>
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_on_local_remote_data_drive_path">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_3">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="2" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <spacer name="horizontalSpacer_8">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_reset_all">
- <property name="text">
- <string>Reset all</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </widget>
- <tabstops>
- <tabstop>groupBox</tabstop>
- <tabstop>lineEdit_path_comp_1st</tabstop>
- <tabstop>comboBox_path_comp_2nd</tabstop>
- <tabstop>comboBox_path_comp_3rd</tabstop>
- <tabstop>lineEdit_path_comp_input_samples</tabstop>
- <tabstop>lineEdit_path_comp_input_flats</tabstop>
- <tabstop>lineEdit_path_comp_input_darks</tabstop>
- <tabstop>lineEdit_path_comp_out_preprocessed</tabstop>
- <tabstop>lineEdit_path_comp_out_processed</tabstop>
- <tabstop>groupBox_3</tabstop>
- <tabstop>lineEdit_remote_base_path_data</tabstop>
- <tabstop>lineEdit_remote_scripts_base_dir</tabstop>
- <tabstop>pushButton_reset_scripts_base_dir_remote</tabstop>
- <tabstop>groupBox_8</tabstop>
- <tabstop>lineEdit_on_local_data_drive_or_path</tabstop>
- <tabstop>pushButton_on_local_data_drive_or_path</tabstop>
- <tabstop>lineEdit_on_local_remote_data_drive_path</tabstop>
- <tabstop>pushButton_on_local_remote_data_drive_path</tabstop>
- <tabstop>groupBox_10</tabstop>
- <tabstop>groupBox_5</tabstop>
- <tabstop>spinBox_remote_cores</tabstop>
- <tabstop>groupBox_4</tabstop>
- <tabstop>spinBox_local_processes</tabstop>
- <tabstop>spinBox_local_cores</tabstop>
- <tabstop>lineEdit_local_recon_scripts</tabstop>
- <tabstop>pushButton_local_recon_scripts_dir</tabstop>
- <tabstop>scrollArea</tabstop>
- </tabstops>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabVisualize.ui b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabVisualize.ui
deleted file mode 100644
index 89b22407306..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceQtTabVisualize.ui
+++ /dev/null
@@ -1,236 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>TomographyIfaceQtTabVisualize</class>
- <widget class="QWidget" name="TomographyIfaceQtTabVisualize">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>733</width>
- <height>569</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Form</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_2">
- <item row="0" column="0">
- <widget class="QSplitter" name="splitter">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <widget class="QWidget" name="layoutWidget">
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout" stretch="0,1">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QPushButton" name="pushButton_local_default_dir">
- <property name="text">
- <string>Local default</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_remote_default_dir">
- <property name="text">
- <string>Remote default</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_browse_files">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QTreeView" name="treeView_files">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>1</horstretch>
- <verstretch>1</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_paraview">
- <property name="text">
- <string>>ParaView</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_octopus">
- <property name="text">
- <string>>Octopus Vis.</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_vgstudio">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>>VGStudio</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>148</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QGroupBox" name="groupBox">
- <property name="title">
- <string>Configuration</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout" rowstretch="0,0" rowminimumheight="1,0">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <property name="margin">
- <number>3</number>
- </property>
- <property name="spacing">
- <number>2</number>
- </property>
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <property name="spacing">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>ParaView:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_paraview_location">
- <property name="text">
- <string>C:\Program Files\ParaView</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_browse_paraview">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="1" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <property name="spacing">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>Octopus Vis.</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_octopus_vis_location">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>C:/Program Files/Octopus Imaging/Octopus Visualisation</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_browse_octopus">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </widget>
- <tabstops>
- <tabstop>pushButton_local_default_dir</tabstop>
- <tabstop>pushButton_remote_default_dir</tabstop>
- <tabstop>pushButton_browse_files</tabstop>
- <tabstop>treeView_files</tabstop>
- <tabstop>pushButton_paraview</tabstop>
- <tabstop>pushButton_octopus</tabstop>
- <tabstop>pushButton_vgstudio</tabstop>
- <tabstop>groupBox</tabstop>
- <tabstop>lineEdit_paraview_location</tabstop>
- <tabstop>pushButton_browse_paraview</tabstop>
- <tabstop>lineEdit_octopus_vis_location</tabstop>
- <tabstop>pushButton_browse_octopus</tabstop>
- </tabstops>
- <resources/>
- <connections/>
-</ui>
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h
deleted file mode 100644
index 446294d2ce7..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h
+++ /dev/null
@@ -1,402 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEVIEWQTGUI_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEVIEWQTGUI_H_
-
-#include "MantidAPI/IRemoteJobManager.h"
-#include "MantidAPI/ITableWorkspace_fwd.h"
-#include "MantidAPI/MatrixWorkspace_fwd.h"
-#include "MantidAPI/TableRow.h"
-#include "MantidQtAPI/BatchAlgorithmRunner.h"
-#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/DllConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyIfacePresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h"
-#include "MantidQtCustomInterfaces/Tomography/ImggFormatsConvertViewQtWidget.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyROIViewQtWidget.h"
-
-#include "ui_ImageSelectCoRAndRegions.h"
-#include "ui_TomographyIfaceQtGUI.h"
-#include "ui_TomographyIfaceQtTabEnergy.h"
-#include "ui_TomographyIfaceQtTabFiltersSettings.h"
-#include "ui_TomographyIfaceQtTabRun.h"
-#include "ui_TomographyIfaceQtTabSystemSettings.h"
-#include "ui_TomographyIfaceQtTabVisualize.h"
-#include <boost/scoped_ptr.hpp>
-#include <json/json.h>
-
-// widgets used in this interface
-class QMutex;
-
-namespace MantidQt {
-namespace API {
-class BatchAlgorithmRunner;
-}
-}
-// Qt classes forward declarations
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Qt-based view of the Tomography GUI. Provides a concrete view for the
-graphical interface for tomography functionality in Mantid. This view
-is Qt-based and it is probably the only one that will be implemented
-in a foreseeable horizon. The interface of this class is given by
-ITomographyIfaceView so that it fits in the MVP (Model-View-Presenter)
-design of the tomography GUI.
-
-Copyright © 2014-2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL TomographyIfaceViewQtGUI
- : public MantidQt::API::UserSubWindow,
- public ITomographyIfaceView {
- Q_OBJECT
-
-public:
- /// Default Constructor
- TomographyIfaceViewQtGUI(QWidget *parent = 0);
- /// Destructor
- ~TomographyIfaceViewQtGUI() override;
-
- /// Interface name
- static std::string name() { return "Tomographic Reconstruction"; }
- /// This interface's categories.
- static QString categoryInfo() { return "Diffraction"; }
-
- void userWarning(const std::string &warn,
- const std::string &description) override;
-
- void userError(const std::string &err,
- const std::string &description) override;
-
- std::vector<std::string> logMsgs() const override { return m_logMsgs; }
-
- void setComputeResources(const std::vector<std::string> &resources,
- const std::vector<bool> &enabled) override;
-
- void setReconstructionTools(const std::vector<std::string> &tools,
- const std::vector<bool> &enabled) override;
-
- std::string experimentReference() const override {
- return m_setupExperimentRef;
- }
-
- std::string getUsername() const override;
-
- std::string getPassword() const override;
-
- void updateLoginControls(bool loggedIn) override;
-
- void enableLoggedActions(bool enable) override;
-
- /// possible for the user to define the configuration of a tool
- void enableConfigTool(bool on) override;
-
- /// possible for the user to run / submit a job
- void enableRunReconstruct(bool on) override;
-
- void updateCompResourceStatus(bool online);
-
- void updateJobsInfoDisplay(
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &status,
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &
- localStatus) override;
-
- std::vector<std::string> processingJobsIDs() const override {
- return m_processingJobsIDs;
- }
-
- TomoSystemSettings systemSettings() const override;
-
- TomoReconFiltersSettings prePostProcSettings() const override;
-
- std::string currentComputeResource() const override {
- return m_currentComputeRes;
- }
- std::string currentReconTool() const override { return m_currentReconTool; }
-
- int keepAlivePeriod() override { return m_settings.useKeepAlive; }
-
- TomoPathsConfig currentPathsConfig() const override { return m_pathsConfig; }
-
- ImageStackPreParams currentROIEtcParams() const override {
- return m_tabROIWidget->userSelection();
- }
-
- std::map<std::string, std::string>
- currentAggregateBandsParams() const override {
- return grabCurrentAggParams();
- }
-
- void runAggregateBands(Mantid::API::IAlgorithm_sptr alg) override;
-
- bool userConfirmation(const std::string &title,
- const std::string &body) override;
-
- std::string getCachedExecutable() const override { return m_extExec; }
-
- std::vector<std::string> getCachedArguments() const override {
- return m_extArgs;
- }
-
- void emitExternalProcessFinished(const QString &str) override;
-
-signals:
- void externalProcessFinished(const QString &str);
-
-private slots:
- void reconstructClicked();
- void toolSetupClicked();
- void runVisualizeClicked();
- void jobCancelClicked();
- void jobTableRefreshClicked();
- void updatedExperimentReference();
-
- void compResourceIndexChanged(int);
- void runToolIndexChanged(int);
- void SCARFLoginClicked();
- void SCARFLogoutClicked();
-
- void browseLocalInOutDirClicked();
- void browseLocalRemoteDriveOrPath();
- void browseLocalReconScriptsDirClicked();
- void browseLocalExternalInterpreterClicked();
-
- void flatsPathCheckStatusChanged(int status);
- void darksPathCheckStatusChanged(int status);
-
- void samplesPathBrowseClicked();
- void flatsPathBrowseClicked();
- void darksPathBrowseClicked();
-
- void samplesPathEditedByUser();
- void flatsPathEditedByUser();
- void darksPathEditedByUser();
-
- /// For the filters tab
- void resetPrePostFilters();
-
- /// open the MantidQT help window for this interface
- void openHelpWin();
-
- // visualization tools / short-cuts
- void browseFilesToVisualizeClicked();
- void sendToParaviewClicked();
- void sendToOctopusVisClicked();
- void defaultDirLocalVisualizeClicked();
- void defaultDirRemoteVisualizeClicked();
- void browseVisToolParaviewClicked();
- void browseVisToolOctopusClicked();
-
- // processing of energy bands
- void browseEnergyInputClicked();
- void browseEnergyOutputClicked();
-
- void systemSettingsEdited();
- void systemSettingsNumericEdited();
-
- // part of the system / advanced settings
- void resetRemoteSetup();
-
- // reset all system / advanced settings
- void resetSystemSettings();
-
- // start aggregation of energy/wavelength bands
- void pushButtonAggClicked();
- void browseAggScriptClicked();
- // aggregation run finished
- void finishedAggBands(bool error);
-
- // If the exec string is empty then the executable will be the one from the
- // system settings tab
- void runExternalProcess(const std::string &exec,
- const std::vector<std::string> &args);
-
- void imageOrStackLoadedInRoi(const std::string &path);
-
-private:
- /// Setup the interface (tab UI)
- void initLayout() override;
-
- void doSetupSectionRun();
- void doSetupSectionFilters();
- void doSetupSectionVisualize();
- void doSetupSectionEnergy();
- void doSetupSectionSystemSettings();
- void doSetupGeneralWidgets();
- void doSetupSectionRoi();
-
- /// Load default interface settings for each tab, normally on startup
- void readSettings();
- /// for the energy bands tab/widget
- void readSettingsEnergy();
- /// save settings (before closing)
- void saveSettings() const override;
- /// for the energy bands tab/widget
- void saveSettingsEnergy() const;
-
- void updateSystemSettingsTabFields(const TomoSystemSettings &setts);
-
- void updatePathsConfig(const TomoPathsConfig &cfg) override;
-
- void showToolConfig(
- MantidQt::CustomInterfaces::TomoToolConfigDialogBase &dialog) override;
-
- void closeEvent(QCloseEvent *ev) override;
-
- void processPathBrowseClick(QLineEdit *le, std::string &data);
-
- void updateFlatsDarksFromSamplePath(const std::string &path);
-
- TomoSystemSettings grabSystemSettingsFromUser() const;
-
- TomoReconFiltersSettings grabPrePostProcSettings() const;
-
- void setPrePostProcSettings(const TomoReconFiltersSettings &opts);
-
- std::string
- checkUserBrowseDir(QLineEdit *le,
- const std::string &userMsg = "Open directory/folder",
- bool remember = true);
-
- std::string checkUserBrowseFile(QLineEdit *le,
- const std::string &userMsg = "Open file",
- bool remember = true);
-
- std::string checkDefaultVisualizeDir(const std::string &basePath,
- const std::string &appendComp);
-
- void sendToVisTool(const std::string &toolName, const std::string &pathString,
- const std::string &appendBin);
-
- std::map<std::string, std::string> grabCurrentAggParams() const;
-
- void sendLog(const std::string &msg);
-
- static const std::string g_styleSheetOffline;
- static const std::string g_styleSheetOnline;
-
- /// Interface definition with widgets for the main interface window
- Ui::TomographyIfaceQtGUI m_ui;
- // And its sections/tabs. Note that for compactness they're called simply
- // 'tabs' but they could be separate dialogs, widgets, etc. combined in
- // different ways.
- Ui::TomographyIfaceQtTabRun m_uiTabRun;
- Ui::TomographyIfaceQtTabFiltersSettings m_uiTabFilters;
- Ui::ImageSelectCoRAndRegions m_uiTabCoR;
- Ui::TomographyIfaceQtTabVisualize m_uiTabVisualize;
- Ui::TomographyIfaceQtTabEnergy m_uiTabEnergy;
- Ui::TomographyIfaceQtTabSystemSettings m_uiTabSystemSettings;
-
- TomographyROIViewQtWidget *m_tabROIWidget;
- ImggFormatsConvertViewQtWidget *m_tabImggFormats;
-
- std::vector<std::string> m_processingJobsIDs;
-
- std::string m_currentComputeRes;
- std::string m_currentReconTool;
-
- std::string m_imgPath;
-
- std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> m_localJobsStatus;
-
- // Settings for external tools. where to find the system Python
- static std::vector<std::string> g_defAddPathPython;
- std::vector<std::string> m_defAddPathPython;
-
- static const std::string g_SCARFName;
- // a general (all tools in principle) default output path
- static const std::string g_defOutPathLocal;
- static const std::string g_defOutPathRemote;
-
- TomoPathsConfig m_pathsConfig;
-
- // several paths or path components related to where the files are found
- // (raw files, reconstructions, pre-post processed files, etc.)
- // These are the defaults
- static const std::string g_defPathComponentPhase;
- static const std::string g_defExperimentRef;
- // reconstruction scripts (external, but shipped with Mantid)
- static const std::string g_defPathReconScripts;
- // base dir for the reconstruction outputs
- static const std::string g_defPathReconOut;
- static const std::string g_defParaviewPath;
- static const std::string g_defParaviewAppendPath;
- static const std::string g_defOctopusVisPath;
- static const std::string g_defOctopusAppendPath;
- static const std::string g_defProcessedSubpath;
- // And these are the paths set up
- std::string m_setupPathComponentPhase;
- std::string m_setupExperimentRef;
- std::string m_setupParaviewPath;
- std::string m_setupOctopusVisPath;
- std::string m_setupProcessedSubpath;
-
- // here the view puts messages before notifying the presenter to show them
- std::vector<std::string> m_logMsgs;
-
- /// The not-so-small set of paths, path compnents and related parameters for
- /// the local and remote machines
- TomoSystemSettings m_systemSettings;
-
- // Basic representation of user settings, read/written on startup/close.
- // TODO: this could be done more sophisticated, with a class using
- // QDataStream and in/out stream operators for example. Keeping
- // it simple for now
- struct UserSettings {
- std::string SCARFBasePath;
- int useKeepAlive; // use if >0, number of seconds for a periodic query
- bool onCloseAskForConfirmation;
-
- UserSettings()
- : SCARFBasePath("/work/imat/runs/test/"), useKeepAlive(60),
- onCloseAskForConfirmation(false) {}
- };
- UserSettings m_settings;
-
- // path name for persistent settings
- std::string m_settingsGroup;
- std::string m_settingsSubGroupEnergy;
-
- // To run aggregation of wavelength/energy bands
- std::unique_ptr<MantidQt::API::BatchAlgorithmRunner> m_aggAlgRunner;
-
- // TODO? move to TomographyIfaceModel or TomographyIfaceSavuModel.h
- // plugins for Savu config files
- Mantid::API::ITableWorkspace_sptr m_availPlugins;
- Mantid::API::ITableWorkspace_sptr m_currPlugins;
- std::string m_currentParamPath;
-
- // presenter as in the model-view-presenter
- boost::scoped_ptr<ITomographyIfacePresenter> m_presenter;
-
- // holders for the external process' arguments
- // as the connection to the presenter is not done via Qt Signals we have no
- // other way of transfering data between them
- std::string m_extExec = "";
- std::vector<std::string> m_extArgs;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYIFACEVIEWQTGUI_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyProcess.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyProcess.h
deleted file mode 100644
index 17311d6c905..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyProcess.h
+++ /dev/null
@@ -1,105 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYPROCESS_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYPROCESS_H_
-
-#include <QProcess>
-#include <QString>
-#include <QStringList>
-#include <vector>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/*
-TomographyProcess class that run external processes and provides some helper
-functions. This class was designed to be used with TomographyThread to run
-external processes asyncronously to the main thread of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class TomographyProcess : public QProcess {
- Q_OBJECT
-public:
- // we want a nullptr for parent so we can move it to a thread
- TomographyProcess() : QProcess(nullptr) {}
-
- // intentionally copy the vector
- void setup(const std::string &runnable, const std::vector<std::string> &args,
- const std::string &allOpts,
- const std::string &workerName = "Mantid_Local") {
- m_runnable = QString::fromStdString(runnable);
- m_args = buildArguments(args);
- m_allArgs = allOpts;
- m_workerName = workerName;
- }
-
- std::string getRunnable() const { return m_runnable.toStdString(); }
- std::string getArgs() const { return m_allArgs; }
- std::string getName() const { return m_workerName; }
-
- /**
- * This method must be called after the process has emitted started().
- * Otherwise the returned PID is wrong, as it has not been assigned
- * a PID from the OS.
- *
- * The PID here is read after the process emits started()
- * by a connection to addJobToStatus() by the Presenter.
- */
- qint64 getPID() const {
- auto pid = this->pid();
-
- // qt connect could sometimes try to read the terminated process' PID
- if (!pid) {
- return 0;
- }
-
-#ifdef _WIN32
- // windows gets a struct object with more info
- auto actualpid = static_cast<qint64>(pid->dwProcessId);
-#else
- // linux just gets the PID
- auto actualpid = static_cast<qint64>(pid);
-#endif
- return actualpid;
- }
-
-public slots:
- /** This method should be used to start the worker as it passes the setup
- * runnable and args parameters into the base start method
- */
- void startWorker() { start(m_runnable, m_args); }
-
-private:
- QStringList buildArguments(const std::vector<std::string> &args) const {
- QStringList list;
- list.reserve(static_cast<int>(args.size()));
-
- for (const auto &arg : args) {
- list << QString::fromStdString(arg);
- }
-
- return list;
- }
-
- QString m_runnable;
- QStringList m_args;
-
- std::string m_allArgs;
- std::string m_workerName;
-};
-} // CustomInterfaces
-} // MantidQt
-#endif
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h
deleted file mode 100644
index 192ae80611f..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h
+++ /dev/null
@@ -1,158 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYROIPRESENTER_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYROIPRESENTER_H_
-
-#include "MantidAPI/WorkspaceGroup_fwd.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyROIPresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyROIView.h"
-#include "MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h"
-#include "MantidQtCustomInterfaces/Tomography/StackOfImagesDirs.h"
-#include <memory>
-#include <boost/scoped_ptr.hpp>
-
-#include <QObject>
-
-namespace MantidQt {
-
-namespace API {
-class BatchAlgorithmRunner;
-}
-
-namespace CustomInterfaces {
-class TomographyThread;
-
-/**
-Presenter for the image center of rotation (and other parameters)
-selection widget. In principle, in a strict MVP setup, signals from
-the model should always be handled through this presenter and never go
-directly to the view, and viceversa.
-
-Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL TomographyROIPresenter
- : public QObject,
- public ITomographyROIPresenter {
- // Q_OBJECT for the 'algorithm runner' signals
- // TODO: move the AlgorithmRunner to the view? Have a different, non-Qt
- // runner?
- // Remove Q_OBJECT and take this file out out MOC_FILES in CMakeLists.txt
- Q_OBJECT
-
-public:
- /// Default constructor - normally used from the concrete view
- TomographyROIPresenter(ITomographyROIView *view);
- ~TomographyROIPresenter() override;
-
- void notify(ITomographyROIPresenter::Notification notif) override;
-
-protected:
- void initialize();
-
- /// clean shut down of model, view, etc.
- void cleanup();
-
- // Methods that process notifications from view->presenter
- void processInit();
-
- void processBrowseImage();
- void processBrowseStack();
- void processNewStack(bool singleImage);
- void processLoadSingleImage();
- void processLoadStackOfImages();
- void processFindCoR();
- void setupAlgorithmRunnerAfterLoad();
- void processChangeImageType();
- void processChangeRotation();
- void processPlayStartStop();
- void processUpdateImgIndex();
- void processUpdateColorMap();
- void processColorRangeUpdated();
-
- void processSelectCoR();
- void processSelectROI();
- void processSelectNormalization();
- void processFinishedCoR();
- void processFinishedROI();
- void processFinishedNormalization();
- void processResetCoR();
- void processResetROI();
- void processResetNormalization();
-
- void processShutDown();
-
-private slots:
- void finishedLoadStack(bool error);
-
-private:
- inline std::string trimFileNameFromPath(const std::string &path) {
- return path.substr(0, path.find_last_of("/\\"));
- }
-
- StackOfImagesDirs checkInputStack(const std::string &path);
-
- /// loads a list of images from a stack, from their individual paths
- void loadFITSStack(const StackOfImagesDirs &soid, const std::string &wsgName,
- const std::string &wsgFlatsName,
- const std::string &wsgDarksName);
-
- void loadFITSList(const std::vector<std::string> &imgs,
- const std::string &wsName);
-
- void loadFITSImage(const std::string &path, const std::string &wsName);
-
- std::string
- filterImagePathsForFITSStack(const std::vector<std::string> &paths);
-
- /// the workspaces being visualized
- Mantid::API::WorkspaceGroup_sptr m_stackSamples, m_stackFlats, m_stackDarks;
-
- /// whether 'playing' the current stack of images
- bool m_playStatus;
-
- /// whether to show (potentially too many and too annoying) warning pop-ups or
- /// messages
- static bool g_warnIfUnexpectedFileExtensions;
-
- /// path to the image stack being visualized
- std::string m_stackPath;
-
- /// To run sequences of algorithms in a separate thread
- std::unique_ptr<MantidQt::API::BatchAlgorithmRunner> m_algRunner;
-
- /// Names used by the widget to store workspace groups
- static const std::string g_wsgName;
- static const std::string g_wsgFlatsName;
- static const std::string g_wsgDarksName;
-
- /// Associated view for this presenter (MVP pattern)
- ITomographyROIView *const m_view;
-
- /// Associated model for this presenter (MVP pattern). This is just
- /// a set of coordinates
- const boost::scoped_ptr<ImageStackPreParams> m_model;
-
- std::unique_ptr<TomographyThread> m_workerThread;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYROIPRESENTER_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyROIViewQtWidget.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyROIViewQtWidget.h
deleted file mode 100644
index a42d94725d9..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyROIViewQtWidget.h
+++ /dev/null
@@ -1,311 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYROIVIEWQTWIDGET_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYROIVIEWQTWIDGET_H_
-
-#include "MantidAPI/MatrixWorkspace_fwd.h"
-#include "MantidAPI/WorkspaceGroup_fwd.h"
-#include "MantidQtCustomInterfaces/DllConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyROIPresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyROIView.h"
-
-#include "ui_ImageSelectCoRAndRegions.h"
-
-#include <boost/scoped_ptr.hpp>
-
-#include <QTimer>
-// forward declarations for Qt
-class QWidget;
-class QPixmap;
-
-namespace Mantid {
-namespace Kernel {
-class V2D;
-}
-}
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Qt-based view of the widget to handle the selection of the center of
-rotation, region of interest, region for normalization, etc. from an
-image or stack of images. Provides a concrete view for the graphical
-interface for tomography functionality in Mantid. This view is
-Qt-based and it is probably the only one that will be implemented in a
-foreseeable horizon. The interface of this class is given by
-ITomographyROIView so that it fits in the MVP (Model-View-Presenter) design
-of the TomographyROI widget.
-
-Copyright © 2015-2016 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL TomographyROIViewQtWidget
- : public QWidget,
- public ITomographyROIView {
- Q_OBJECT
-
-public:
- TomographyROIViewQtWidget(QWidget *parent = 0);
- ~TomographyROIViewQtWidget() override;
-
- void setParams(ImageStackPreParams ¶ms) override;
-
- ImageStackPreParams userSelection() const override;
-
- SelectionState selectionState() const override { return m_selectionState; }
-
- void changeSelectionState(const SelectionState &state) override;
-
- /// show a stack of images given the path to the files
- void showStack(const std::string &path) override;
-
- /// show a (new) stack of images that have been loaded into groups of
- /// workspaces (samples, flats, darks)
- void showStack(const Mantid::API::WorkspaceGroup_sptr &wsg,
- const Mantid::API::WorkspaceGroup_sptr &wsgFlats,
- const Mantid::API::WorkspaceGroup_sptr &wsgDarks) override;
-
- const Mantid::API::WorkspaceGroup_sptr stackSamples() const override {
- return m_stackSamples;
- }
-
- void showProjection(const Mantid::API::WorkspaceGroup_sptr &wsg,
- size_t idx) override;
-
- void userWarning(const std::string &warn,
- const std::string &description) override;
-
- void userError(const std::string &err,
- const std::string &description) override;
-
- void enableActions(bool enable) override;
-
- size_t currentImgIndex() const override;
-
- void updateImgWithIndex(size_t idx) override;
-
- void playStart() override;
-
- void playStop() override;
-
- float currentRotationAngle() const override;
-
- void updateRotationAngle(float angle) override;
-
- Mantid::API::WorkspaceGroup_sptr currentImageTypeStack() const override;
-
- void updateImageType(const Mantid::API::WorkspaceGroup_sptr wsg) override;
-
- std::string askImagePath(const std::string &windowTitle) override;
-
- std::string askColorMapFile() override;
-
- void updateColorMap(const std::string &filename) override;
-
- void saveSettings() const override;
- void imageOrStackLoaded(const std::string &path) override;
-
-signals:
- void findCORClickedSignal(const std::string &exec,
- const std::vector<std::string> &args);
-
- void imageOrStackLoadedSignal(const std::string &path);
-
-public slots:
- void readCoRFromProcessOutput(const QString &str);
-
-protected:
- void initLayout();
-
- void resetCoR() override;
- void resetROI() override;
- void resetNormArea() override;
-
- void resetWidgetsOnNewStack();
-
- /// update coordinates from mouse event
- void mouseUpdateCoR(const int x, const int y);
-
- // get the coordinates on the first click of selection
- void mouseUpdateROICornersStartSelection(const int x, const int y);
- // update the coordinates while dragging the mouse
- void mouseUpdateROICornerContinuedSelection(const int x, const int y);
- // notify the presenter that the user has stopped selection
- void mouseFinishROI(const int x, const int y);
-
- // get the coordinates on the first click of selection
- void mouseUpdateNormAreaCornersStartSelection(const int x, const int y);
- // update the coordinates while dragging the mouse
- void mouseUpdateNormAreaCornerContinuedSelection(const int x, const int y);
- // notify the presenter that the user has stopped selection
- void mouseFinishNormArea(const int x, const int y);
-
-private slots:
- void browseImageClicked();
- void browseStackClicked();
-
- void rotationUpdated(int idx);
- void autoCoRToolChanged(int idx);
-
- void imageTypeUpdated(int idx);
-
- void loadColorMapRequest();
- void colorRangeChanged();
-
- void corClicked();
- void corResetClicked();
- void roiClicked();
- void roiResetClicked();
- void normAreaClicked();
- void normAreaResetClicked();
-
- void playClicked();
- void updatePlay();
-
- void updateFromImagesSlider(int current);
-
- void valueUpdatedCoR(int v);
- void valueUpdatedROI(int v);
- void valueUpdatedNormArea(int v);
- void findCORClicked();
-
-private:
- void setupConnections();
-
- void readSettings();
-
- /// enable types of images (sample, flat, dark)
- /// depending on their
- /// availability
- void enableImageTypes(bool enableSamples, bool enableFlats, bool enableDarks);
-
- /// enable/disable the groups with spin boxes for the
- /// center and corners
- void enableParamWidgets(bool enable);
-
- // widget closing
- void closeEvent(QCloseEvent *ev) override;
-
- /// initialize values to defaults and set max/min for
- /// the spin boxes
- void initParamWidgets(size_t maxWidth, size_t maxHeight);
-
- /// Set coordinates in the widgets from a params object
- void setParamWidgets(ImageStackPreParams ¶ms);
-
- // shows the image in a widget
- void showProjectionImage(const Mantid::API::WorkspaceGroup_sptr &wsg,
- size_t idx, float rotationAngle = 0);
-
- void getCheckedDimensions(const Mantid::API::MatrixWorkspace_sptr ws,
- size_t &width, size_t &height);
-
- void checkNewProjectionImage(const Mantid::API::WorkspaceGroup_sptr &wsg,
- size_t idx, size_t &width, size_t &height,
- Mantid::API::MatrixWorkspace_sptr &imgWS,
- std::string &imgName);
-
- void getPixelMinMax(Mantid::API::MatrixWorkspace_sptr ws, double &min,
- double &max);
-
- QPixmap transferWSImageToQPixmap(const Mantid::API::MatrixWorkspace_sptr ws,
- size_t width, size_t height,
- float rotationAngle);
-
- void grabCoRFromWidgets();
- void grabROIFromWidgets();
- void grabNormAreaFromWidgets();
-
- void grabCoRFromMousePoint(int x, int y);
- void grabROICorner1FromMousePoint(int x, int y);
- void grabROICorner2FromMousePoint(int x, int y);
- void grabNormAreaCorner1FromMousePoint(int x, int y);
- void grabNormAreaCorner2FromMousePoint(int x, int y);
-
- /// repaint the image with new positions of points and
- /// rectangles
- void refreshImage();
- void refreshCoR();
- void refreshROI();
- void refreshNormArea();
-
- /// draw a cross/target symbol
- void drawCenterCrossSymbol(QPainter &painter,
- const Mantid::Kernel::V2D ¢er) const;
-
- /// draw a rectangle/box to highlight the ROI: region of
- /// interest
- void drawBoxROI(QPainter &painter, const Mantid::Kernel::V2D &first,
- const Mantid::Kernel::V2D &second) const;
-
- /// draw a rectangle/box to highlight the normalization
- /// ("air") region
- void drawBoxNormalizationRegion(QPainter &painter,
- const Mantid::Kernel::V2D &first,
- const Mantid::Kernel::V2D &second) const;
-
- bool eventFilter(QObject *obj, QEvent *event) override;
-
- struct RectangleXY {
- int right;
- int top;
- } m_startOfRectangle;
-
- void updateValuesForSpinBoxes(
- const int x, const int y,
- const struct TomographyROIViewQtWidget::RectangleXY startPositions,
- QSpinBox *spinLeft, QSpinBox *spinTop, QSpinBox *spinRight,
- QSpinBox *spinBottom);
-
- Ui::ImageSelectCoRAndRegions m_ui;
-
- Mantid::API::WorkspaceGroup_sptr m_stackSamples, m_stackFlats, m_stackDarks;
-
- /// this holds the base image on top of which rectangles
- /// and other
- /// objects are drawn
- boost::scoped_ptr<QPixmap> m_basePixmap;
-
- /// current color map used to visualize the image/slice
- std::string m_colorMapFilename;
-
- /// persistent settings
- static const std::string m_settingsGroup;
-
- /// parameters currently set by the user
- ImageStackPreParams m_params;
-
- /// Timer for the "play" function
- std::unique_ptr<QTimer> m_playTimer;
-
- /// max image size for the current stack
- int m_imgWidth, m_imgHeight;
-
- /// are we picking the CoR, or the first point of the
- /// ROI, etc.
- SelectionState m_selectionState;
-
- // presenter as in the model-view-presenter
- boost::scoped_ptr<ITomographyROIPresenter> m_presenter;
-};
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYROIVIEWQTWIDGET_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyThread.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyThread.h
deleted file mode 100644
index 97699ecc194..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/TomographyThread.h
+++ /dev/null
@@ -1,115 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYTHREAD_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOMOGRAPHYTHREAD_H_
-
-#include "MantidQtCustomInterfaces/Tomography/TomographyProcess.h"
-#include <QString>
-#include <QThread>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-/*
-TomographyThread class that can handle a single worker, and get all the standard
-output and standard error content from the process.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class TomographyThread : public QThread {
- Q_OBJECT
-public:
- TomographyThread(QObject *parent, TomographyProcess *worker)
- : QThread(parent), m_worker(worker) {
- // interactions between the thread and the worker are defined here
- connect(this, SIGNAL(started()), worker, SLOT(startWorker()));
- connect(this, SIGNAL(started()), this, SLOT(startWorker()));
-
- connect(worker, SIGNAL(readyReadStandardOutput()), this,
- SLOT(readWorkerStdOut()));
- connect(worker, SIGNAL(readyReadStandardError()), this,
- SLOT(readWorkerStdErr()));
-
- connect(worker, SIGNAL(finished(int)), this, SLOT(finished(int)));
-
- connect(this, SIGNAL(finished()), this, SLOT(deleteLater()),
- Qt::DirectConnection);
-
- connect(this, SIGNAL(terminated()), worker, SLOT(terminate()));
- m_worker->moveToThread(this);
- }
-
- ~TomographyThread() override {
- // this will terminate the process if another reconstruction is started,
- // thus not allowing to have multiple reconstructions running at the same
- // time
- emit terminated();
-
- // this causes segfault in processRefreshJobs if the check isnt here
- if (m_workerRunning || !m_worker) {
- // emit that the worker has been forcefully closed, exit with error code 1
- // this is bad, find a way to notify without an explicit emit on thread
- // destroy
- emit workerFinished(m_workerPID, 1);
- }
- }
-
- /// this method is called after the worker's process has been successfully
- /// initialised. It is necessary to do that after the initialisation of the
- /// worker, because otherwise it does not have an assigned PID yet, as it is
- /// not running on the OS
- void setProcessPID(const qint64 pid) { m_workerPID = pid; }
-
- qint64 getProcessPID() const { return m_workerPID; }
-
-public slots:
- void finished(const int exitCode) {
- // queue up object deletion
- m_worker->deleteLater();
- m_workerRunning = false;
- // emit the exit code to the presenter so the process info can be updated
- emit workerFinished(m_workerPID, exitCode);
- }
-
- void readWorkerStdOut() const {
- auto *worker = qobject_cast<TomographyProcess *>(sender());
- QString out(worker->readAllStandardOutput());
- if (!out.isEmpty())
- emit stdOutReady(out.trimmed());
- }
-
- void readWorkerStdErr() const {
- auto *worker = qobject_cast<TomographyProcess *>(sender());
- QString out(worker->readAllStandardError());
-
- if (!out.isEmpty())
- emit stdErrReady(out.trimmed());
- }
-
- void startWorker() { m_workerRunning = true; }
-
-signals:
- void workerFinished(const qint64, const int);
- void stdOutReady(const QString &) const;
- void stdErrReady(const QString &) const;
-
-private:
- bool m_workerRunning = false;
- /// Holder for the current running process' PID
- qint64 m_workerPID = 0;
- TomographyProcess *const m_worker;
-};
-} // CustomInterfaces
-} // MantidQt
-#endif
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h
deleted file mode 100644
index 233947c42c7..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h
+++ /dev/null
@@ -1,74 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGATRATOOLBOX_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGATRATOOLBOX_H_
-
-#include <string>
-
-#include "MantidQtCustomInterfaces/DllConfig.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-
-Configuration of a third party tomographic reconstruction tool
-specialized for the Astra Toolbox tomographic reconstruction tool
-(C++, CUDA): Astra Toolbox <http://sourceforge.net/p/astra-toolbox/wiki/Home/
-
-Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL ToolConfigAstraToolbox
- : public TomoRecToolConfig {
-public:
- ToolConfigAstraToolbox();
-
- ToolConfigAstraToolbox(const std::string &runnable,
- const std::string &pathOut,
- const std::string &pathDark,
- const std::string &pathOpen,
- const std::string &pathSample);
-
- ~ToolConfigAstraToolbox() override {}
-
- // gives the list of methods (reconstruction algorithms) available
- static const std::vector<std::pair<std::string, std::string>> methods() {
- return g_astraMethods;
- }
-
-protected:
- std::string makeCmdLineOptions() const override;
-
- std::string makeExecutable() const override { return m_runnable; };
-
-private:
- static const std::vector<std::pair<std::string, std::string>> g_astraMethods;
-
- std::string m_pathOut;
- std::string m_pathDark;
- std::string m_pathOpen;
- std::string m_pathSample;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGATRATOOLBOX_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h
deleted file mode 100644
index e1409bb0fed..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h
+++ /dev/null
@@ -1,63 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGCUSTOM_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGCUSTOM_H_
-
-#include <string>
-
-#include "MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Configuration of a third party tomographic reconstruction tool as a
-Custom command line. To run a reconstruction tool via a command of the
-user's choice with free-form options.
-
-This is under development, and as it is not necessarily related to
-custom interfaces might be moved out of here. Tools of other type
-might be added, and then this should not be a sublcass of
-TomoRecToolConfig but of a more general ToolConfig class.
-
-Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class ToolConfigCustom : public TomoRecToolConfig {
-public:
- ToolConfigCustom() {}
-
- ToolConfigCustom(const std::string &runnable, const std::string &cmdOptions)
- : TomoRecToolConfig(runnable), m_opts(cmdOptions) {}
-
- ~ToolConfigCustom() override {}
-
-protected:
- std::string makeCmdLineOptions() const override { return m_opts; }
-
- std::string makeExecutable() const override { return m_runnable; };
-
-private:
- std::string m_opts;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGCUSTOM_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h
deleted file mode 100644
index 1af2c729ff3..00000000000
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGTOMOPY_H_
-#define MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGTOMOPY_H_
-
-#include "MantidQtCustomInterfaces/Tomography/TomoRecToolConfig.h"
-#include "MantidQtCustomInterfaces/DllConfig.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
-Third party tomographic reconstruction tool configuration class
-specialized for TomoPy (Python + C++):
-https://www1.aps.anl.gov/Science/Scientific-Software/TomoPy
-
-Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-Oak Ridge National Laboratory & European Spallation Source
-
-This file is part of Mantid.
-
-Mantid is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or
-(at your option) any later version.
-
-Mantid is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-File change history is stored at: <https://github.com/mantidproject/mantid>
-Code Documentation is available at: <http://doxygen.mantidproject.org>
-*/
-class MANTIDQT_CUSTOMINTERFACES_DLL ToolConfigTomoPy
- : public TomoRecToolConfig {
-public:
- ToolConfigTomoPy();
-
- ToolConfigTomoPy(const std::string &runnable, const std::string &pathOut,
- const std::string &pathDark, const std::string &pathOpen,
- const std::string &pathSample);
-
- ~ToolConfigTomoPy() override {}
-
- // gives the list of methods (reconstruction algorithms) available
- static const std::vector<std::pair<std::string, std::string>> methods() {
- return g_tomopyMethods;
- }
-
-protected:
- std::string makeCmdLineOptions() const override;
-
- std::string makeExecutable() const override { return m_runnable; };
-
-private:
- static const std::vector<std::pair<std::string, std::string>> g_tomopyMethods;
-
- std::string m_pathOut;
- std::string m_pathDark;
- std::string m_pathOpen;
- std::string m_pathSample;
-};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
-
-#endif // MANTIDQTCUSTOMINTERFACES_TOMOGRAPHY_TOOLCONFIGTOMOPY_H_
diff --git a/MantidQt/CustomInterfaces/src/Tomography/EnergyBandsViewQtGUI.cpp b/MantidQt/CustomInterfaces/src/Tomography/EnergyBandsViewQtGUI.cpp
deleted file mode 100644
index 80a2a433786..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/EnergyBandsViewQtGUI.cpp
+++ /dev/null
@@ -1,163 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h"
-#include "MantidAPI/AlgorithmManager.h"
-
-#include <QSettings>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-// Tomo GUI methods that process the energy bands tab. This
-// could/should become a class of its own, as the tab evolves.
-
-void TomographyIfaceViewQtGUI::readSettingsEnergy() {
- QSettings qs;
- qs.beginGroup(QString::fromStdString(m_settingsSubGroupEnergy));
-
- m_uiTabEnergy.lineEdit_input_path->setText(
- qs.value("input-path", "").toString());
-
- m_uiTabEnergy.lineEdit_output_path->setText(
- qs.value("output-path", "").toString());
-
- m_uiTabEnergy.radioButton_uniform_bands->setChecked(
- qs.value("uniform-bands-on", true).toBool());
- m_uiTabEnergy.radioButton_index_ranges->setChecked(
- qs.value("index-ranges-on", false).toBool());
- m_uiTabEnergy.radioButton_tof_ranges->setChecked(
- qs.value("tof-ranges-on", false).toBool());
-
- m_uiTabEnergy.spinBox_uniform_bands->setValue(
- qs.value("uniform-bands-value", 1).toInt());
- m_uiTabEnergy.lineEdit_index_ranges->setText(
- qs.value("index-ranges-value", "").toString());
- m_uiTabEnergy.lineEdit_tof_ranges->setText(
- qs.value("tof-ranges-value", "").toString());
-
- m_uiTabEnergy.comboBox_input_format->setCurrentIndex(
- qs.value("input-image-format", 0).toInt());
- m_uiTabEnergy.comboBox_output_format->setCurrentIndex(
- qs.value("output-image-format", 0).toInt());
-
- qs.endGroup();
-}
-
-void TomographyIfaceViewQtGUI::saveSettingsEnergy() const {
- QSettings qs;
- qs.beginGroup(QString::fromStdString(m_settingsSubGroupEnergy));
-
- qs.setValue("input-path", m_uiTabEnergy.lineEdit_input_path->text());
- qs.setValue("output-path", m_uiTabEnergy.lineEdit_output_path->text());
-
- qs.setValue("uniform-bands-on",
- m_uiTabEnergy.radioButton_uniform_bands->isChecked());
- qs.setValue("index-ranges-on",
- m_uiTabEnergy.radioButton_index_ranges->isChecked());
- qs.setValue("tof-ranges-on",
- m_uiTabEnergy.radioButton_tof_ranges->isChecked());
-
- qs.setValue("uniform-bands-value",
- m_uiTabEnergy.spinBox_uniform_bands->value());
- qs.setValue("index-ranges-value",
- m_uiTabEnergy.lineEdit_index_ranges->text());
- qs.setValue("tof-ranges-value", m_uiTabEnergy.lineEdit_tof_ranges->text());
-
- qs.setValue("input-image-format",
- m_uiTabEnergy.comboBox_input_format->currentIndex());
- qs.setValue("output-image-format",
- m_uiTabEnergy.comboBox_output_format->currentIndex());
-
- qs.endGroup();
-}
-
-void TomographyIfaceViewQtGUI::doSetupSectionEnergy() {
- m_aggAlgRunner =
- Mantid::Kernel::make_unique<MantidQt::API::BatchAlgorithmRunner>();
-
- connect(m_uiTabEnergy.pushButton_browse_input, SIGNAL(released()), this,
- SLOT(browseEnergyInputClicked()));
-
- connect(m_uiTabEnergy.pushButton_browse_output, SIGNAL(released()), this,
- SLOT(browseEnergyOutputClicked()));
-
- connect(m_uiTabEnergy.pushButton_agg, SIGNAL(released()), this,
- SLOT(pushButtonAggClicked()));
-
- connect(m_uiTabEnergy.pushButton_browse_script, SIGNAL(released()), this,
- SLOT(browseAggScriptClicked()));
-}
-
-std::map<std::string, std::string>
-TomographyIfaceViewQtGUI::grabCurrentAggParams() const {
- std::map<std::string, std::string> params;
-
- params["InputPath"] = m_uiTabEnergy.lineEdit_input_path->text().toStdString();
- params["OutputPath"] =
- m_uiTabEnergy.lineEdit_output_path->text().toStdString();
-
- if (m_uiTabEnergy.radioButton_uniform_bands->isChecked()) {
- params["UniformBands"] =
- std::to_string(m_uiTabEnergy.spinBox_uniform_bands->value());
- } else if (m_uiTabEnergy.radioButton_index_ranges->isChecked()) {
- params["IndexRanges"] =
- m_uiTabEnergy.lineEdit_index_ranges->text().toStdString();
- } else if (m_uiTabEnergy.radioButton_tof_ranges->isChecked()) {
- params["ToFRanges"] =
- m_uiTabEnergy.lineEdit_tof_ranges->text().toStdString();
- }
-
- params["InputImageFormat"] = "FITS";
- params["OutputImageFormat"] = "FITS";
-
- return params;
-}
-
-void TomographyIfaceViewQtGUI::browseEnergyInputClicked() {
- checkUserBrowseDir(m_uiTabEnergy.lineEdit_input_path);
-}
-
-void TomographyIfaceViewQtGUI::browseEnergyOutputClicked() {
- checkUserBrowseDir(m_uiTabEnergy.lineEdit_output_path);
-}
-
-void TomographyIfaceViewQtGUI::pushButtonAggClicked() {
- m_presenter->notify(ITomographyIfacePresenter::AggregateEnergyBands);
-}
-
-void TomographyIfaceViewQtGUI::browseAggScriptClicked() {
- checkUserBrowseFile(
- m_uiTabEnergy.lineEdit_script,
- "Select script to aggregate bands on the remote compute resource", false);
-}
-
-void TomographyIfaceViewQtGUI::runAggregateBands(
- Mantid::API::IAlgorithm_sptr alg) {
-
- // reset any previous connections
- m_aggAlgRunner.get()->disconnect();
- connect(m_aggAlgRunner.get(), SIGNAL(batchComplete(bool)), this,
- SLOT(finishedAggBands(bool)), Qt::QueuedConnection);
-
- m_aggAlgRunner->addAlgorithm(alg);
-
- // run lengthy I/O intensive algorithm async
- m_uiTabEnergy.pushButton_agg->setEnabled(false);
- m_aggAlgRunner->executeBatchAsync();
-}
-
-void TomographyIfaceViewQtGUI::finishedAggBands(bool error) {
- if (error) {
- userWarning("Process failed", "Could not run or finish the aggregation of "
- "bands. Please check the log messages for "
- "details.");
- } else {
- userWarning("Process finished",
- "Aggregation of bands finished. The "
- "results should now be available from the output path given. "
- "You can check the logs for more information and (detailed "
- "warning/error messages if there were any issues).");
- }
- m_uiTabEnergy.pushButton_agg->setEnabled(true);
-}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp b/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
deleted file mode 100644
index 784dc8ed98c..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
+++ /dev/null
@@ -1,12 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h"
-
-using namespace MantidQt::CustomInterfaces;
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-ImageStackPreParams::ImageStackPreParams()
- : cor(), roi(), normalizationRegion(), rotation(-1.0f) {}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/ImggFormats.cpp b/MantidQt/CustomInterfaces/src/Tomography/ImggFormats.cpp
deleted file mode 100644
index 45ba954d80b..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/ImggFormats.cpp
+++ /dev/null
@@ -1,94 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/ImggFormats.h"
-
-#include <algorithm>
-#include <map>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-namespace ImggFormats {
-
-// Names are often acronyms, so writing them uppercase
-const static std::vector<std::string> shortNames{"FITS", "TIFF", "PNG", "JPEG",
- "NXTomo"};
-
-// Map format name to vector of accepted/recognized extensions
-const static std::map<std::string, std::vector<std::string>> extensions{
- {"FITS", {"fits", "fit"}},
- {"TIFF", {"tiff", "tif"}},
- {"PNG", {"png"}},
- {"JPEG", {"jpg", "jpeg"}},
- {"NXTomo", {"nxs"}}};
-
-const static std::vector<std::string> descriptions{
- "FITS: Flexible Image Transport System.",
- "TIFF: - Tagged Image File Format", "PNG: Portable Network Graphics",
- "JPEG: Joint Photographic Experts Group",
- "NXTomo: NXTomo NeXus application definition"};
-
-/**
- * Possible common/accepted file extensions for a format
- *
- * @return extensions (without the dot, like "fits") in no particular
- * order, lowercase
- */
-std::string shortName(Format fmt) { return shortNames.at(fmt); }
-
-/**
- * Get sequence number or ID of the format
- *
- * @param shortName short name of the format (example: "FITS")
- *
- * @return the format id number, -1 if it is unknown
- */
-size_t formatID(const std::string &shortName) {
- auto pos = std::find(shortNames.begin(), shortNames.end(), shortName);
-
- if (shortNames.end() == pos) {
- return 0;
- }
-
- return pos - shortNames.begin();
-}
-
-/**
- * The first-choice file extension for a format (given by
- * name). Example: FITS => fit
- *
- * @param format name of the format (short string)
- *
- * @return extension as a string, empty if the format is unknown.
- */
-std::string fileExtension(const std::string &format) {
- const auto &exts = extensions.at(format);
-
- return exts.front();
-}
-
-/**
- * Find out whether this extension is one of the accepted format
- * extensions. This is case insensitive
- *
- * @param extension a file name extension like .fits, or a filename
- * @param shortName name of a file format
- */
-bool isFileExtension(const std::string &extension,
- const std::string &shortName) {
- size_t pos = extension.find_last_of('.');
- std::string lowExt = extension.substr(pos + 1);
- std::transform(lowExt.begin(), lowExt.end(), lowExt.begin(), ::tolower);
-
- const auto &valid = extensions.at(shortName);
- return (valid.end() != std::find(valid.begin(), valid.end(), lowExt));
-}
-
-/**
- * Human readable description / long name of the format
- *
- * @return description string to show in log messages, interfaces,
- * etc.
- */
-std::string description(Format fmt) { return descriptions.at(fmt); }
-
-} // namespace ImggFormats
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/ImggFormatsConvertPresenter.cpp b/MantidQt/CustomInterfaces/src/Tomography/ImggFormatsConvertPresenter.cpp
deleted file mode 100644
index a4fb00fff43..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/ImggFormatsConvertPresenter.cpp
+++ /dev/null
@@ -1,359 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/ImggFormatsConvertPresenter.h"
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/AnalysisDataService.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h"
-#include "MantidQtCustomInterfaces/Tomography/ImggFormats.h"
-
-#include <Poco/DirectoryIterator.h>
-#include <Poco/File.h>
-#include <Poco/Path.h>
-
-using namespace MantidQt::CustomInterfaces;
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-namespace {
-Mantid::Kernel::Logger g_log("ImggFormatsConvert");
-}
-
-ImggFormatsConvertPresenter::ImggFormatsConvertPresenter(
- IImggFormatsConvertView *view)
- : m_view(view) {
- if (!m_view) {
- throw std::runtime_error(
- "Severe inconsistency found. Presenter created "
- "with an empty/null view (formats conversion interface). "
- "Cannot continue.");
- }
-}
-
-ImggFormatsConvertPresenter::~ImggFormatsConvertPresenter() { cleanup(); }
-
-void ImggFormatsConvertPresenter::cleanup() {}
-
-void ImggFormatsConvertPresenter::notify(Notification notif) {
-
- switch (notif) {
-
- case IImggFormatsConvertPresenter::Init:
- processInit();
- break;
-
- case IImggFormatsConvertPresenter::Convert:
- processConvert();
- break;
-
- case IImggFormatsConvertPresenter::ShutDown:
- processShutDown();
- break;
- }
-}
-
-void ImggFormatsConvertPresenter::processInit() {
- const std::vector<std::string> formats{
- shortName(ImggFormats::FITS), shortName(ImggFormats::TIFF),
- shortName(ImggFormats::PNG), shortName(ImggFormats::JPG),
- shortName(ImggFormats::NXTomo)};
-
- const std::vector<bool> enableLoads{true, true, true, true, false};
-
- m_view->setFormats(formats, enableLoads);
-}
-
-void ImggFormatsConvertPresenter::processConvert() {
- const std::string inPS = m_view->inputPath();
- const std::string outPS = m_view->outputPath();
- size_t depth = m_view->maxSearchDepth();
-
- g_log.information() << "Trying to convert images from path: " << inPS
- << " into " << outPS << ", with depth " << depth << '\n';
-
- const std::string emptyMsg = "Please specify an input and and output path.";
- if (inPS.empty()) {
- m_view->userError("Empty imput path", emptyMsg);
- return;
- }
- if (outPS.empty()) {
- m_view->userError("Empty output path", emptyMsg);
- return;
- }
-
- Poco::File inFilePath(inPS);
- if (!inFilePath.exists() || !inFilePath.isDirectory() ||
- !inFilePath.canRead()) {
- m_view->userError(
- "Cannot read from input path",
- "Please check the input path given: " + inPS +
- ". It must be an existing directory and it must be readable.");
- return;
- }
-
- Poco::File outFilePath(outPS);
- if (!outFilePath.exists() || !outFilePath.isDirectory() ||
- !outFilePath.canWrite()) {
- m_view->userError(
- "Cannot write into the output path",
- "Please check the output path given: " + outPS +
- ". It must be an existing directory and it must be writeable.");
- return;
- }
-
- const std::string inFormat = m_view->inputFormatName();
- const std::string outFormat = m_view->outputFormatName();
-
- try {
- size_t count = goThroughDirRecur(inPS, inFormat, outPS, outFormat, depth);
- if (count > 0) {
- std::stringstream msg;
- msg << "Finished converstion of images from path: " << inPS << " into "
- << outPS << ", with depth " << depth << ". Converted " << count
- << " images from format " << inFormat << " to format " << outFormat
- << '\n';
- g_log.notice() << msg.str();
- m_view->userWarning("Conversion finished successfully", msg.str());
- } else {
- std::stringstream msg;
- msg << "No images could be found in input path: " << inPS
- << " with format " << inFormat << ". 0 images converted.\n";
- g_log.notice() << msg.str();
- m_view->userWarning("No images could be found", msg.str());
- }
- } catch (std::runtime_error &rexc) {
- m_view->userError("Error while converting files",
- "There was an error in the conversion process: " +
- std::string(rexc.what()));
- }
-}
-
-void ImggFormatsConvertPresenter::processShutDown() { m_view->saveSettings(); }
-
-/**
- * Search for images in the input path and transfers them to the
- * output path in the output format. For subdirectories, it recurs
- * through subdirectories "depth" levels.
- *
- * @param inFilePath input path where to search for image/stack files
- * @param inFormat input format to consider
- * @param outFilePath output path to write converted files
- * @param outFormat format for the output images
- * @param depth search depth remaining (for recursive calls).
- *
- * @return count of images processed/converted
- */
-size_t ImggFormatsConvertPresenter::goThroughDirRecur(
- const Poco::File &inFilePath, const std::string &inFormat,
- const Poco::File &outFilePath, const std::string &outFormat, size_t depth) {
-
- const std::string outExt = ImggFormats::fileExtension(outFormat);
-
- size_t count = 0;
- Poco::DirectoryIterator end;
- for (Poco::DirectoryIterator it(inFilePath); it != end; ++it) {
- if (it->isDirectory()) {
-
- if (1 == depth)
- continue;
-
- // skip the output directory if it is nested in the input path!
- if (it.path().toString() == outFilePath.path())
- continue;
-
- // append, to delve into subdirectory:
- Poco::Path outPath(outFilePath.path());
- outPath.append(it.name());
- // create subdirectory in output path
- Poco::File(outPath).createDirectory();
-
- count +=
- goThroughDirRecur(it.path(), inFormat, outPath, outFormat, depth - 1);
- } else if (it->isFile()) {
-
- const std::string fname = it.name();
- if (ImggFormats::isFileExtension(fname, inFormat)) {
- // intentionally not removing source/original extension
- Poco::Path path(outFilePath.path());
- path.append(it.name());
- const std::string outFilename = path.toString() + "." + outExt;
- convert(it.path().toString(), inFormat, outFilename, outFormat);
- ++count;
- }
- }
- }
- return count;
-}
-
-/**
- * Create an output image from an input image, converting
- * formats. This uses the view (Qt classes) to process images in
- * traditional formats like TIFF, PNG, JPG. That should be moved to
- * this presenter when we have the Load/SaveImage algorithm.
- *
- * @param inputName name of input image
- * @param inFormat format the input image is in
- * @param outputName name of the output image to produce
- * @param outFormat format for the output image
- */
-void ImggFormatsConvertPresenter::convert(const std::string &inputName,
- const std::string &inFormat,
- const std::string &outputName,
- const std::string &outFormat) const {
-
- if ("NXTomo" == outFormat) {
- convertToNXTomo(inputName, inFormat, outputName);
- } else if ("FITS" == outFormat) {
- convertToFITS(inputName, inFormat, outputName);
- } else {
- if ("FITS" == inFormat) {
- auto inWks = loadFITS(inputName);
- m_view->writeImg(inWks, outputName, outFormat);
- } else {
- // other image formats
- try {
- m_view->convert(inputName, inFormat, outputName, outFormat);
- } catch (std::runtime_error &rexc) {
- m_view->userError("Error in conversion",
- "There was an error when converting the image " +
- inputName + " from format " + inFormat +
- " to format " + outFormat +
- " into the output file " + outputName +
- ". Details: " + rexc.what());
- }
- }
- }
-}
-
-void ImggFormatsConvertPresenter::convertToFITS(
- const std::string &inputName, const std::string &inFormat,
- const std::string &outputName) const {
-
- auto inWks = loadImg(inputName, inFormat);
- try {
- saveFITS(inWks, outputName);
- } catch (std::runtime_error &rexc) {
- m_view->userError(
- "Error in conversion",
- "There was an error when converting the image " + inputName +
- " (format " + inFormat +
- "), trying to write it into FITS format in the output file " +
- outputName + ". Details: " + rexc.what());
- }
-}
-
-void ImggFormatsConvertPresenter::convertToNXTomo(
- const std::string &inputName, const std::string &inFormat,
- const std::string &outputName) const {
-
- // loadNXTomo is not enabled (and there is no LoadNXTomo algorithm for now)
- auto inWks = loadImg(inputName, inFormat);
- try {
- saveNXTomo(inWks, outputName);
- } catch (std::runtime_error &rexc) {
- m_view->userError(
- "Error in conversion",
- "There was an error when converting the image " + inputName +
- " (format " + inFormat +
- "), trying to write it into NXTomo format in the output file " +
- outputName + ". Details: " + rexc.what());
- }
-}
-
-Mantid::API::MatrixWorkspace_sptr
-ImggFormatsConvertPresenter::loadImg(const std::string &inputName,
- const std::string inFormat) const {
- Mantid::API::MatrixWorkspace_sptr wks;
- // TODO: This should become the algorithm LoadImage:
- // https://github.com/mantidproject/mantid/issues/6843
- if ("FITS" == inFormat) {
- wks = loadFITS(inputName);
- } else {
- wks = m_view->loadImg(inputName, inFormat);
- }
- return wks;
-}
-
-Mantid::API::MatrixWorkspace_sptr
-ImggFormatsConvertPresenter::loadFITS(const std::string &inputName) const {
-
- const std::string wksGrpName = "__fits_img_to_convert";
- if (Mantid::API::AnalysisDataService::Instance().doesExist(wksGrpName)) {
- auto algDel =
- Mantid::API::AlgorithmManager::Instance().create("DeleteWorkspace");
- algDel->setChild(true);
- algDel->setPropertyValue("Workspace", wksGrpName);
- algDel->execute();
- }
- // Just run LoadFITS
- auto alg = Mantid::API::AlgorithmManager::Instance().create("LoadFITS");
- alg->initialize();
- alg->setChild(true);
- alg->setProperty("Filename", inputName);
- alg->setProperty("OutputWorkspace", wksGrpName);
- alg->setProperty("LoadAsRectImg", true);
- alg->execute();
-
- if (!alg->isExecuted()) {
- throw std::runtime_error("Failed to execute the algorithm "
- "LoadFITS to load the image file '" +
- inputName + "' in FITS format.");
- }
-
- Mantid::API::Workspace_sptr wks = alg->getProperty("OutputWorkspace");
- auto grp = boost::dynamic_pointer_cast<Mantid::API::WorkspaceGroup>(wks);
- if (!grp) {
- throw std::runtime_error(
- "When loading a FITS image: " + inputName +
- ", failed to retrieve the output workspace (group) after "
- "executing the algorithm LoadFITS.");
- }
- auto imgWorkspace = boost::dynamic_pointer_cast<Mantid::API::MatrixWorkspace>(
- grp->getItem(grp->size() - 1));
-
- return imgWorkspace;
-}
-
-void ImggFormatsConvertPresenter::saveFITS(
- Mantid::API::MatrixWorkspace_sptr image,
- const std::string &outputName) const {
- // Just run LoadFITS
- auto alg = Mantid::API::AlgorithmManager::Instance().create("SaveFITS");
- alg->initialize();
- alg->setProperty("InputWorkspace", image);
- alg->setProperty("Filename", outputName);
- alg->execute();
-
- if (!alg->isExecuted()) {
- throw std::runtime_error("Failed to execute the algorithm SaveFITS to save "
- "an image in FITS format into the file '" +
- outputName + ".");
- }
-}
-
-void ImggFormatsConvertPresenter::saveNXTomo(
- Mantid::API::MatrixWorkspace_sptr image,
- const std::string &outputName) const {
-
- // Run the algorithm SaveNXTomo
- auto alg = Mantid::API::AlgorithmManager::Instance().create("SaveNXTomo");
- alg->initialize();
- alg->setProperty("InputWorkspaces", image);
- alg->setProperty("Filename", outputName);
- alg->setProperty("OverwriteFile", false);
- alg->execute();
-
- if (!alg->isExecuted()) {
- throw std::runtime_error(
- "Failed to execute the algorithm SaveNXTomo to save "
- "images in NXTomo format into the file '" +
- outputName + ".");
- }
-
- g_log.information()
- << "Save NXTomo file (overwriting if the file already existed: "
- << outputName << '\n';
-}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/ImggFormatsConvertViewQtWidget.cpp b/MantidQt/CustomInterfaces/src/Tomography/ImggFormatsConvertViewQtWidget.cpp
deleted file mode 100644
index 0c709bdea1e..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/ImggFormatsConvertViewQtWidget.cpp
+++ /dev/null
@@ -1,375 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/ImggFormatsConvertViewQtWidget.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidQtAPI/AlgorithmInputHistory.h"
-#include "MantidQtCustomInterfaces/Tomography/ImggFormatsConvertPresenter.h"
-
-using namespace Mantid::API;
-using namespace MantidQt::CustomInterfaces;
-
-#include <QCloseEvent>
-#include <QFileDialog>
-#include <QImageReader>
-#include <QImageWriter>
-#include <QMessageBox>
-#include <QSettings>
-
-#include <QImage>
-#include <iostream>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-// this would be more like a CustomWidget if it's eventually moved there
-const std::string ImggFormatsConvertViewQtWidget::m_settingsGroup =
- "CustomInterfaces/ImggFormatsConvertView";
-
-ImggFormatsConvertViewQtWidget::ImggFormatsConvertViewQtWidget(QWidget *parent)
- : QWidget(parent), IImggFormatsConvertView(), m_presenter(nullptr) {
- initLayout();
-}
-
-ImggFormatsConvertViewQtWidget::~ImggFormatsConvertViewQtWidget() {
- m_presenter->notify(IImggFormatsConvertPresenter::ShutDown);
-}
-
-void ImggFormatsConvertViewQtWidget::initLayout() {
- // setup container ui
- m_ui.setupUi(this);
-
- setup();
- // presenter that knows how to handle a view like this. It should
- // take care of all the logic. Note the view needs to now the
- // concrete presenter here
- m_presenter.reset(new ImggFormatsConvertPresenter(this));
-
- // it will know what compute resources and tools we have available:
- // This view doesn't even know the names of compute resources, etc.
- m_presenter->notify(IImggFormatsConvertPresenter::Init);
-
- // some combo boxes are re-populated by the init process, reload
- // settings now:
- readSettings();
-}
-
-void ImggFormatsConvertViewQtWidget::setup() {
-
- connect(m_ui.pushButton_browse_input, SIGNAL(released()), this,
- SLOT(browseImgInputConvertClicked()));
-
- connect(m_ui.pushButton_browse_output, SIGNAL(released()), this,
- SLOT(browseImgOutputConvertClicked()));
-
- connect(m_ui.pushButton_convert, SIGNAL(released()), this,
- SLOT(convertClicked()));
-}
-
-void ImggFormatsConvertViewQtWidget::readSettings() {
- QSettings qs;
- qs.beginGroup(QString::fromStdString(m_settingsGroup));
-
- m_ui.comboBox_input_format->setCurrentIndex(
- qs.value("input-format", 0).toInt());
- m_ui.lineEdit_input_path->setText(qs.value("input-path", "").toString());
-
- m_ui.comboBox_output_format->setCurrentIndex(
- qs.value("output-format", 0).toInt());
- m_ui.comboBox_bit_depth->setCurrentIndex(qs.value("bit-depth", 0).toInt());
- m_ui.comboBox_compression->setCurrentIndex(
- qs.value("compression", 0).toInt());
- m_ui.spinBox_max_search_depth->setValue(
- qs.value("max-search-depth", 0).toInt());
- m_ui.lineEdit_output_path->setText(qs.value("output-path", "").toString());
-
- restoreGeometry(qs.value("interface-win-geometry").toByteArray());
- qs.endGroup();
-}
-
-void ImggFormatsConvertViewQtWidget::saveSettings() const {
- QSettings qs;
- qs.beginGroup(QString::fromStdString(m_settingsGroup));
-
- qs.setValue("input-format", m_ui.comboBox_input_format->currentIndex());
- qs.setValue("input-path", m_ui.lineEdit_input_path->text());
-
- qs.setValue("output-format", m_ui.comboBox_output_format->currentIndex());
- qs.setValue("bit-depth", m_ui.comboBox_bit_depth->currentIndex());
- qs.setValue("compression", m_ui.comboBox_compression->currentIndex());
- qs.setValue("max-search-depth", m_ui.spinBox_max_search_depth->value());
- qs.setValue("output-path", m_ui.lineEdit_output_path->text());
-
- qs.setValue("interface-win-geometry", saveGeometry());
- qs.endGroup();
-}
-
-void ImggFormatsConvertViewQtWidget::browseImgInputConvertClicked() {
- grabUserBrowseDir(m_ui.lineEdit_input_path);
-}
-
-void ImggFormatsConvertViewQtWidget::browseImgOutputConvertClicked() {
- grabUserBrowseDir(m_ui.lineEdit_output_path);
-}
-
-void ImggFormatsConvertViewQtWidget::convertClicked() {
- m_presenter->notify(IImggFormatsConvertPresenter::Convert);
-}
-
-void ImggFormatsConvertViewQtWidget::userWarning(
- const std::string &warn, const std::string &description) {
- QMessageBox::warning(this, QString::fromStdString(warn),
- QString::fromStdString(description), QMessageBox::Ok,
- QMessageBox::Ok);
-}
-
-void ImggFormatsConvertViewQtWidget::userError(const std::string &err,
- const std::string &description) {
- QMessageBox::critical(this, QString::fromStdString(err),
- QString::fromStdString(description), QMessageBox::Ok,
- QMessageBox::Ok);
-}
-
-void ImggFormatsConvertViewQtWidget::setFormats(
- const std::vector<std::string> &fmts, const std::vector<bool> &enableLoad,
- const std::vector<bool> &enableSave) {
- // same formats for inputs and outputs
- setFormatsCombo(m_ui.comboBox_input_format, fmts, enableLoad);
- setFormatsCombo(m_ui.comboBox_output_format, fmts, enableSave);
-
- m_ui.spinBox_max_search_depth->setValue(3);
- if (m_ui.comboBox_output_format->count() > 0) {
- m_ui.comboBox_output_format->setCurrentIndex(1);
- }
-}
-
-void ImggFormatsConvertViewQtWidget::setFormatsCombo(
- QComboBox *cbox, const std::vector<std::string> &fmts,
- const std::vector<bool> &enable) {
- cbox->clear();
- for (const auto &name : fmts) {
- cbox->addItem(QString::fromStdString(name));
- }
-
- if (enable.empty() || enable.size() != fmts.size())
- return;
-
- for (size_t fmtIdx = 0; fmtIdx < fmts.size(); fmtIdx++) {
- if (!enable[fmtIdx]) {
- // to display the text in this row as "disabled"
- QModelIndex rowIdx = cbox->model()->index(static_cast<int>(fmtIdx), 0);
- QVariant disabled(0);
- cbox->model()->setData(rowIdx, disabled, Qt::UserRole - 1);
- }
- }
-}
-
-std::string ImggFormatsConvertViewQtWidget::inputPath() const {
- return m_ui.lineEdit_input_path->text().toStdString();
-}
-
-std::string ImggFormatsConvertViewQtWidget::inputFormatName() const {
- const auto cbox = m_ui.comboBox_input_format;
- if (!cbox)
- return "";
-
- return cbox->currentText().toStdString();
-}
-
-std::string ImggFormatsConvertViewQtWidget::outputPath() const {
- return m_ui.lineEdit_output_path->text().toStdString();
-}
-
-std::string ImggFormatsConvertViewQtWidget::outputFormatName() const {
- const auto cbox = m_ui.comboBox_output_format;
- if (!cbox)
- return "";
-
- return cbox->currentText().toStdString();
-}
-
-bool ImggFormatsConvertViewQtWidget::compressHint() const {
- return 0 == m_ui.comboBox_compression->currentIndex();
-}
-
-void ImggFormatsConvertViewQtWidget::convert(
- const std::string &inputName, const std::string &inputFormat,
- const std::string &outputName, const std::string &outputFormat) const {
-
- QImage img = loadImgFile(inputName, inputFormat);
-
- if (!img.isGrayscale()) {
- // Qt5 has QImage::Format_Alpha8;
- QImage::Format toFormat = QImage::Format_RGB32;
- Qt::ImageConversionFlag toFlags = Qt::MonoOnly;
- img = img.convertToFormat(toFormat, toFlags);
- }
-
- writeImgFile(img, outputName, outputFormat);
-}
-
-void ImggFormatsConvertViewQtWidget::writeImg(
- MatrixWorkspace_sptr inWks, const std::string &outputName,
- const std::string &outFormat) const {
- if (!inWks)
- return;
- auto width = inWks->getNumberHistograms();
- if (0 == width)
- return;
- auto height = inWks->blocksize();
-
- QImage img(QSize(static_cast<int>(width), static_cast<int>(height)),
- QImage::Format_Indexed8);
-
- int tableSize = 256;
- QVector<QRgb> grayscale(tableSize);
- for (int i = 0; i < grayscale.size(); i++) {
- int level = i; // would be equivalent: qGray(i, i, i);
- grayscale[i] = qRgb(level, level, level);
- }
- img.setColorTable(grayscale);
-
- // only 16 to 8 bits color map supported with current libraries
- const double scaleFactor = std::numeric_limits<unsigned short int>::max() /
- std::numeric_limits<unsigned char>::max();
- for (int yi = 0; yi < static_cast<int>(width); ++yi) {
- const auto &row = inWks->y(yi);
- for (int xi = 0; xi < static_cast<int>(width); ++xi) {
- int scaled = static_cast<int>(row[xi] / scaleFactor);
- // Images not from IMAT, just crop. This needs much improvement when
- // we have proper Load/SaveImage algorithms
- if (scaled > 255)
- scaled = 255;
- if (scaled < 0)
- scaled = 0;
- img.setPixel(xi, yi, scaled);
- }
- }
-
- writeImgFile(img, outputName, outFormat);
-}
-
-/**
- * Write an image using a QImageWriter
- *
- * @param img QImage with data ready to be saved
- * @param outputName output filename
- * @param outFormat format for the image file
- */
-void ImggFormatsConvertViewQtWidget::writeImgFile(
- const QImage &img, const std::string &outputName,
- const std::string &outFormat) const {
- // With (simpler but less flexible) QImage:
- // img.save(QString::fromStdString(outputName));
-
- QImageWriter writer(QString::fromStdString(outputName));
- writer.setFormat(outFormat.c_str());
- if (compressHint())
- writer.setCompression(1);
- writer.write(img);
-}
-
-MatrixWorkspace_sptr
-ImggFormatsConvertViewQtWidget::loadImg(const std::string &inputName,
- const std::string &inFormat) const {
-
- QImage img = loadImgFile(inputName, inFormat);
- int width = img.width();
- int height = img.height();
-
- MatrixWorkspace_sptr imgWks = boost::dynamic_pointer_cast<MatrixWorkspace>(
- WorkspaceFactory::Instance().create("Workspace2D", height, width + 1,
- width));
- imgWks->setTitle(inputName);
- const double scaleFactor = std::numeric_limits<unsigned char>::max();
- for (int yi = 0; yi < static_cast<int>(width); ++yi) {
- auto &row = imgWks->getSpectrum(yi);
- auto &dataY = row.mutableY();
- row.mutableX() = static_cast<double>(yi);
- for (int xi = 0; xi < static_cast<int>(width); ++xi) {
- QRgb vRgb = img.pixel(xi, yi);
- dataY[xi] = scaleFactor * qGray(vRgb);
- }
- }
-
- return imgWks;
-}
-
-/**
- * Load an image using a QImageReader
- *
- * @param inputName filename
- * @param inFormat format for the image file
- *
- * @return QImage object with image data read from file
- */
-QImage
-ImggFormatsConvertViewQtWidget::loadImgFile(const std::string &inputName,
- const std::string inFormat) const {
- // Simpler but less flexible load with QImage:
- // img.load(QString::fromStdString(inputName));
-
- QImageReader reader(inputName.c_str());
- if (!reader.autoDetectImageFormat()) {
- reader.setFormat(inFormat.c_str());
- }
-
- return reader.read();
-}
-
-size_t ImggFormatsConvertViewQtWidget::maxSearchDepth() const {
- return static_cast<size_t>(m_ui.spinBox_max_search_depth->value());
-}
-
-std::string ImggFormatsConvertViewQtWidget::grabUserBrowseDir(
- QLineEdit *le, const std::string &userMsg, bool remember) {
-
- QString prev;
- if (le->text().isEmpty()) {
- prev =
- MantidQt::API::AlgorithmInputHistory::Instance().getPreviousDirectory();
- } else {
- prev = le->text();
- }
-
- QString path(
- QFileDialog::getExistingDirectory(this, tr(userMsg.c_str()), prev));
-
- if (!path.isEmpty()) {
- le->setText(path);
- if (remember) {
- MantidQt::API::AlgorithmInputHistory::Instance().setPreviousDirectory(
- path);
- }
- }
-
- return path.toStdString();
-}
-
-std::string ImggFormatsConvertViewQtWidget::askImgOrStackPath() {
- // get path
- QString fitsStr = QString("Supported formats: FITS, TIFF and PNG "
- "(*.fits *.fit *.tiff *.tif *.png);;"
- "FITS, Flexible Image Transport System images "
- "(*.fits *.fit);;"
- "TIFF, Tagged Image File Format "
- "(*.tif *.tiff);;"
- "PNG, Portable Network Graphics "
- "(*.png);;"
- "Other extensions/all files (*)");
- QString prevPath =
- MantidQt::API::AlgorithmInputHistory::Instance().getPreviousDirectory();
- QString path(QFileDialog::getExistingDirectory(
- this, tr("Open stack of images"), prevPath, QFileDialog::ShowDirsOnly));
- if (!path.isEmpty()) {
- MantidQt::API::AlgorithmInputHistory::Instance().setPreviousDirectory(path);
- }
-
- return path.toStdString();
-}
-
-void ImggFormatsConvertViewQtWidget::closeEvent(QCloseEvent *event) {
- m_presenter->notify(IImggFormatsConvertPresenter::ShutDown);
- event->accept();
-}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/StackOfImagesDirs.cpp b/MantidQt/CustomInterfaces/src/Tomography/StackOfImagesDirs.cpp
deleted file mode 100644
index 1cfcc3d0443..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/StackOfImagesDirs.cpp
+++ /dev/null
@@ -1,208 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/StackOfImagesDirs.h"
-
-#include <boost/algorithm/string.hpp>
-
-#include <Poco/DirectoryIterator.h>
-#include <Poco/Path.h>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string StackOfImagesDirs::g_descrComplex =
- "A directory (folder) that contains subdirectories with names "
- "starting with:\n- 'Data' (for sample images),\n- 'Flat' (for white "
- "bean images),\n- 'Dark' (for dark images)\nThe first one is "
- "mandatory whereas the other two are optional.";
-
-const std::string StackOfImagesDirs::g_descrSimple =
- "A directory containing (readable) image files.";
-
-const std::string StackOfImagesDirs::g_descrBoth = "Two alternatives: \n\n"
- "Simple: " +
- g_descrSimple +
- "\n\n"
- "Or Full:\n\n" +
- g_descrComplex + "\n";
-
-const std::string StackOfImagesDirs::g_sampleNamePrefix = "data";
-const std::string StackOfImagesDirs::g_flatNamePrefix = "flat";
-const std::string StackOfImagesDirs::g_darkNamePrefix = "dark";
-const std::string StackOfImagesDirs::g_processedNamePrefix = "processed";
-const std::string StackOfImagesDirs::g_prefilteredNamePrefix = "pre_filtered";
-
-StackOfImagesDirs::StackOfImagesDirs(const std::string &path,
- bool allowSimpleLayout)
- : m_valid(false), m_statusDescStr("Constructed, no checks done yet.") {
- findStackDirs(path, allowSimpleLayout);
-}
-
-std::string StackOfImagesDirs::description() const { return m_descr; }
-
-std::string StackOfImagesDirs::status() const {
- if (m_valid)
- return "Stack of images is correct";
- else
- return "There are errors in the directories and/or files. " +
- m_statusDescStr;
-}
-
-std::vector<std::string> StackOfImagesDirs::sampleFiles() const {
- return findImgFiles(m_sampleDir);
-}
-std::vector<std::string> StackOfImagesDirs::flatFiles() const {
- return findImgFiles(m_flatDir);
-}
-std::vector<std::string> StackOfImagesDirs::darkFiles() const {
- return findImgFiles(m_darkDir);
-}
-
-void StackOfImagesDirs::findStackDirs(const std::string &path,
- bool allowSimpleLayout) {
- if (allowSimpleLayout) {
- m_descr = g_descrBoth;
- } else {
- m_descr = g_descrComplex;
- }
-
- if (path.empty())
- return;
-
- Poco::File dir(path);
- if (!dir.isDirectory() || !dir.exists())
- return;
-
- bool found = false;
- // go for the simple layout first (just image files in a flat tree).
- if (allowSimpleLayout) {
- found = findStackFilesSimple(dir);
- }
-
- if (!found) {
- findStackDirsComplex(dir);
- }
-}
-
-/**
- * Tries to find a stack of images with the simple layout: all sample
- * files are in the directory given.
- *
- * @param dir directory which is the base path for the stack of images, that is,
- * which contains image files.
- *
- * @return whether the stack has been found succesfully
- */
-bool StackOfImagesDirs::findStackFilesSimple(Poco::File &dir) {
- Poco::DirectoryIterator end;
- for (Poco::DirectoryIterator it(dir); it != end; ++it) {
- // presence of one regular file is enough
- if (it->isFile()) {
- m_sampleDir = dir.path();
- m_flatDir = "";
- m_darkDir = "";
- m_valid = true;
- }
- }
-
- return m_valid;
-}
-
-/**
- * Tries to find a stack of images with the full or complex
- * layout. Assumes that the path given has been checked. In a full
- * layout the files are arranged in up to three subdirectories:
- *
- * - path/data*: sample images
- * - path/flat*: flat images
- * - path/dark*: dark images
- *
- * @param dir directory to use as base path for the stack of images
- *
- * @return whether the stack has been found succesfully
- */
-bool StackOfImagesDirs::findStackDirsComplex(Poco::File &dir) {
- Poco::DirectoryIterator end;
- for (Poco::DirectoryIterator it(dir); it != end; ++it) {
- if (!it->isDirectory()) {
- continue;
- }
-
- const std::string name = it.name();
-
- // case insensitive comparison against expected pattersn: data_*, flat_*,
- // dark_*, etc.
- if (boost::iequals(name.substr(0, g_sampleNamePrefix.length()),
- g_sampleNamePrefix)) {
- m_sampleDir = it.path().toString();
- } else if (boost::iequals(name.substr(0, g_flatNamePrefix.length()),
- g_flatNamePrefix)) {
- m_flatDir = it.path().toString();
- } else if (boost::iequals(name.substr(0, g_darkNamePrefix.length()),
- g_darkNamePrefix)) {
- m_darkDir = it.path().toString();
- }
- }
-
- if (m_sampleDir.empty()) {
- m_statusDescStr = "The the sample images directory (" + g_sampleNamePrefix +
- "...) has not been found.";
- return false;
- }
-
- // can be valid only if we get here. There must be at least one entry that is
- // a file
- Poco::Path samplesPath(m_sampleDir);
- for (Poco::DirectoryIterator it(samplesPath); it != end; ++it) {
- if (it->isFile()) {
- m_valid = true;
- break;
- }
- }
-
- if (m_valid) {
- m_statusDescStr = "all checks passed";
- } else {
- m_statusDescStr = "No files were found in the sample images directory (" +
- g_sampleNamePrefix + "...).";
- }
-
- return m_valid;
-}
-
-std::vector<std::string>
-StackOfImagesDirs::findImgFiles(const std::string &path) const {
- std::vector<std::string> fnames;
- if (path.empty()) {
- return fnames;
- }
-
- try {
- Poco::File dir(path);
- if (!dir.isDirectory() || !dir.exists())
- return fnames;
-
- // as an alternative could also use Poco::Glob to find the files
- Poco::DirectoryIterator it(dir);
- Poco::DirectoryIterator end;
- while (it != end) {
- // TODO: filter names by extension?
- // const std::string name = it.name();
- if (it->isFile()) {
- fnames.push_back(it.path().toString());
- }
-
- ++it;
- }
-
- // this assumes the usual sorting of images of a stack (directory): a
- // prefix,
- // and a sequence number (with a fixed number of digits).
- std::sort(fnames.begin(), fnames.end());
- } catch (std::runtime_error &) {
- // it's fine if the files are not found, not readable, etc.
- }
-
- return fnames;
-}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoPathsConfig.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoPathsConfig.cpp
deleted file mode 100644
index 15b84c0fade..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoPathsConfig.cpp
+++ /dev/null
@@ -1,18 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoPathsConfig.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-TomoPathsConfig::TomoPathsConfig()
- : m_pathOpenBeamEnabled(true), m_pathDarkEnabled(true),
- m_pathBase("/work/imat/phase_commissioning/"),
- m_pathFITS(m_pathBase + "data"), m_pathFlat(m_pathBase + "flat"),
- m_pathDark(m_pathBase + "dark") {}
-
-bool TomoPathsConfig::validate() const {
- // TODO: too simple for now
- return (!m_pathFITS.empty() && !m_pathFlat.empty() && !m_pathDark.empty());
-}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoReconPostprocSettings.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoReconPostprocSettings.cpp
deleted file mode 100644
index cd3bd710c97..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoReconPostprocSettings.cpp
+++ /dev/null
@@ -1,15 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoReconPostprocSettings.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
- * Default initialization of post-processing options. This should
- * represent sensible first time usage defaults that can be used by
- * GUIs, etc.
- */
-TomoReconPostprocSettings::TomoReconPostprocSettings()
- : circMaskRadius(0.94), cutOffLevel(0.0) {}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoReconPreprocSettings.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoReconPreprocSettings.cpp
deleted file mode 100644
index 919e098f8e3..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoReconPreprocSettings.cpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoReconPreprocSettings.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-/**
- * Default initialization of pre-processing options. This should
- * represent sensible first time usage defaults that can be used by
- * GUIs, etc.
- */
-TomoReconPreprocSettings::TomoReconPreprocSettings()
- : normalizeByAirRegion(true), normalizeByProtonCharge(false),
- normalizeByFlats(true), normalizeByDarks(true), medianFilterWidth(3),
- rotation(0), maxAngle(360.0), scaleDownFactor(0) {}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettings.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettings.cpp
deleted file mode 100644
index b1899615e47..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettings.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string TomoSystemSettings::g_defSamplesDirPrefix = "data";
-const std::string TomoSystemSettings::g_defFlatsDirPrefix = "flat";
-const std::string TomoSystemSettings::g_defDarksDirPrefix = "dark";
-
-const std::string TomoSystemSettings::g_defOutputPathCompPreProcessed =
- "pre_processed";
-
-const std::string TomoSystemSettings::g_defOutputPathCompReconst = "processed";
-
-/**
- * Default initialization which should be enough in most cases.
- */
-TomoSystemSettings::TomoSystemSettings()
- : m_local(), m_remote(),
- m_pathComponents({"data", "RB number", "experiment name", "input type"}),
- m_samplesDirPrefix(g_defSamplesDirPrefix),
- m_flatsDirPrefix(g_defFlatsDirPrefix),
- m_darksDirPrefix(g_defDarksDirPrefix),
- m_outputPathCompPreProcessed(g_defOutputPathCompPreProcessed),
- m_outputPathCompReconst(g_defOutputPathCompReconst) {}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettingsLocal.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettingsLocal.cpp
deleted file mode 100644
index 02bd0db9000..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettingsLocal.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettingsLocal.h"
-#include "MantidKernel/ConfigService.h"
-
-#include <Poco/Path.h>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string TomoSystemSettingsLocal::g_defBasePathTomoData =
-#ifdef _WIN32
- "D:\\";
-#else
- "${HOME}/imat-data";
-#endif
-
-const std::string TomoSystemSettingsLocal::g_defRemoteDriveOrMountPoint =
-#ifdef _WIN32
- "S:\\imat";
-#else
- "/media/scarf";
-#endif
-
-const std::string TomoSystemSettingsLocal::g_defReconScriptsPath =
-#ifdef _WIN32
- "C:/MantidInstall/scripts";
-#else
- Poco::Path(
- Mantid::Kernel::ConfigService::Instance().getDirectoryOfExecutable())
- .parent()
- .append("scripts")
- .toString();
-#endif
-
-const std::string TomoSystemSettingsLocal::g_defExternalInterpreterPath =
-#ifdef _WIN32
- // assume we're using Aanconda Python and it is installed in c:/local
- // could also be c:/local/anaconda/scripts/ipython
- "c:/local/anaconda/python.exe";
-#else
- // just use the system Python, assuming is in the system path
- "python";
-#endif
-
-/**
- * Default initialization which should be enough in most cases.
- */
-TomoSystemSettingsLocal::TomoSystemSettingsLocal()
- : m_basePathTomoData(g_defBasePathTomoData),
- m_remoteDriveOrMountPoint(g_defRemoteDriveOrMountPoint),
- m_reconScriptsPath(g_defReconScriptsPath),
- m_externalInterpreterPath(g_defExternalInterpreterPath), m_processes(4),
- m_cores(4) {}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettingsRemote.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettingsRemote.cpp
deleted file mode 100644
index d2de7dccfbe..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoSystemSettingsRemote.cpp
+++ /dev/null
@@ -1,21 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettingsRemote.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string TomoSystemSettingsRemote::g_defBasePathTomoData =
- "/work/imat";
-
-const std::string TomoSystemSettingsRemote::g_defBasePathReconScripts =
- "/work/imat/phase_commissioning";
-
-/**
- * Default initialization which should be enough in most cases.
- */
-TomoSystemSettingsRemote::TomoSystemSettingsRemote()
- : m_basePathTomoData(g_defBasePathTomoData),
- m_basePathReconScripts(g_defBasePathReconScripts), m_nodes(2),
- m_cores(4) {}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogAstra.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogAstra.cpp
deleted file mode 100644
index 61cf5f5c3ef..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogAstra.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogAstra.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string TomoToolConfigDialogAstra::DEFAULT_TOOL_NAME = "Astra";
-const std::string TomoToolConfigDialogAstra::DEFAULT_TOOL_METHOD = "FBP3D_CUDA";
-
-void TomoToolConfigDialogAstra::setupDialogUi() {
- m_astraUi.setupUi(m_dialog);
- m_astraUi.comboBox_method->clear();
- const auto &methods = getToolMethods();
- for (auto &method : methods) {
- m_astraUi.comboBox_method->addItem(QString::fromStdString(method.second));
- }
-}
-
-void TomoToolConfigDialogAstra::initialiseDialog() { m_dialog = new QDialog; }
-
-void TomoToolConfigDialogAstra::setupToolSettingsFromPaths() {
- m_toolSettings = std::make_shared<ToolConfigAstraToolbox>(
- m_runPath, m_pathOut + m_localOutNameAppendix, m_paths.pathDarks(),
- m_paths.pathOpenBeam(), m_paths.pathSamples());
-}
-
-void TomoToolConfigDialogAstra::setupMethodSelected() {
- const auto &methods = getToolMethods();
-
- const int mi = m_astraUi.comboBox_method->currentIndex();
- m_toolMethod = methods[mi].first;
-}
-
-/** Calls the execute of the QDialog
-*/
-int TomoToolConfigDialogAstra::executeQt() { return m_dialog->exec(); }
-
-std::vector<std::pair<std::string, std::string>>
-TomoToolConfigDialogAstra::getToolMethods() {
- return ToolConfigAstraToolbox::methods();
-}
-
-} // CustomInterfaces
-} // MantidQt
\ No newline at end of file
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogBase.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogBase.cpp
deleted file mode 100644
index 5d95af10cf4..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogBase.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogTomoPy.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogAstra.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogSavu.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogCustom.h"
-
-#include "MantidKernel/make_unique.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-std::unique_ptr<TomoToolConfigDialogBase>
-TomoToolConfigDialogBase::getToolDialogFor(const std::string &toolName) {
-
- if (toolName == "TomoPy") {
- return Mantid::Kernel::make_unique<TomoToolConfigDialogTomoPy>();
- } else if (toolName == "Astra") {
- return Mantid::Kernel::make_unique<TomoToolConfigDialogAstra>();
- } else if (toolName == "Savu") {
- return Mantid::Kernel::make_unique<TomoToolConfigDialogSavu>();
- } else if (toolName == "Custom command") {
- return Mantid::Kernel::make_unique<TomoToolConfigDialogCustom>();
- }
- // tool doesn't exist, return nullptr
- return nullptr;
-}
-
-void TomoToolConfigDialogBase::handleDialogResult(const int result) {
- if (QDialog::Accepted == result) {
- // setup the new settings if the user has Accepted
- setupMethodSelected();
- setupToolSettingsFromPaths();
- }
-}
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogCustom.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogCustom.cpp
deleted file mode 100644
index f8e31af5914..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogCustom.cpp
+++ /dev/null
@@ -1,71 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogCustom.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string TomoToolConfigDialogCustom::DEFAULT_TOOL_NAME =
- "Custom command";
-
-// custom tool doesn't have a default method
-const std::string TomoToolConfigDialogCustom::DEFAULT_TOOL_METHOD = "";
-
-std::string TomoToolConfigDialogCustom::m_backupCommandLine = "";
-
-/** Reads the current strings in the dialogue and creates
-* the tool settings from them. If the dialogue is not initialised yet
-* the strings will be empty, thus we put the default values
-*/
-void TomoToolConfigDialogCustom::setupToolSettingsFromPaths() {
-
- if (m_isInitialised) {
- // None of the other paths matter, because the user could've changed
- // them, so ignore them and load the current ones on the dialogue
- const std::string run =
- m_customUi.lineEdit_runnable->text().toStdString(); // current path
- const std::string opts = m_customUi.textEdit_cl_opts->toPlainText()
- .toStdString(); // current commands
-
- // update the settings with the newest information
- m_toolSettings = std::make_shared<ToolConfigCustom>(run, opts);
- } else {
- // create settings with the default values
- m_toolSettings = std::make_shared<ToolConfigCustom>(m_runPath, "--help");
- }
-}
-
-void TomoToolConfigDialogCustom::setupMethodSelected() {
-
- // sets the current runnable path, overriding the default one
- m_customUi.lineEdit_runnable->setText(QString::fromStdString(m_runPath));
-}
-
-void TomoToolConfigDialogCustom::setupDialogUi() {
- m_customUi.setupUi(m_dialog);
-
- if (m_backupCommandLine != "") {
- m_customUi.textEdit_cl_opts->setText(
- QString::fromStdString(m_backupCommandLine));
- }
-
- // get default options from command line
- const std::string opts =
- m_customUi.textEdit_cl_opts->toPlainText().toStdString();
-
- // create the default settings
- m_toolSettings = std::make_shared<ToolConfigCustom>(m_runPath, opts);
-}
-
-void TomoToolConfigDialogCustom::initialiseDialog() { m_dialog = new QDialog; }
-
-void TomoToolConfigDialogCustom::handleDialogResult(int result) {
- if (QDialog::Accepted == result) {
- // if accepted we want to save the information
- m_backupCommandLine =
- m_customUi.textEdit_cl_opts->toPlainText().toStdString();
- setupToolSettingsFromPaths();
- }
-}
-int TomoToolConfigDialogCustom::executeQt() { return m_dialog->exec(); }
-} // CustomInterfaces
-} // MantidQt
\ No newline at end of file
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogSavu.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogSavu.cpp
deleted file mode 100644
index 2d3aa5a7749..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogSavu.cpp
+++ /dev/null
@@ -1,632 +0,0 @@
-#include "MantidAPI/AnalysisDataService.h"
-#include "MantidAPI/ITableWorkspace.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h"
-
-#include <boost/lexical_cast.hpp>
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogSavu.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoReconToolsUserSettings.h"
-
-#include <MantidAPI/TableRow.h>
-#include <MantidAPI/WorkspaceFactory.h>
-#include <Poco/String.h>
-#include <json/reader.h>
-#include <MantidAPI/NotebookWriter.h>
-#include <QFileDialog>
-#include <QMessageBox>
-#include <MantidAPI/AlgorithmManager.h>
-
-using namespace Mantid::API;
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-TomoToolConfigDialogSavu::TomoToolConfigDialogSavu(QWidget *parent)
- : QMainWindow(parent) {
- // TODO init the 545231453t54 variables
- m_availPlugins = Mantid::API::WorkspaceFactory::Instance().createTable();
- m_availPlugins->addColumns("str", "name", 4);
- m_currPlugins = Mantid::API::WorkspaceFactory::Instance().createTable();
- m_currPlugins->addColumns("str", "name", 4);
-}
-
-int TomoToolConfigDialogSavu::executeQt() {
- this->show();
- QEventLoop el;
- connect(this, SIGNAL(destroyed()), &el, SLOT(quit()));
- return el.exec();
-}
-
-void TomoToolConfigDialogSavu::initialiseDialog() {
- throw Mantid::Kernel::Exception::NotImplementedError(
- "SAVU interface not implemented");
-}
-void TomoToolConfigDialogSavu::setupMethodSelected() {
- throw Mantid::Kernel::Exception::NotImplementedError(
- "SAVU interface not implemented");
-}
-void TomoToolConfigDialogSavu::setupToolSettingsFromPaths() {
- throw Mantid::Kernel::Exception::NotImplementedError(
- "SAVU interface not implemented");
-}
-
-void TomoToolConfigDialogSavu::setupDialogUi() {
- m_savuUi.setupUi(this);
- initSavuWindow();
- this->setWindowModality(Qt::ApplicationModal);
-}
-
-void TomoToolConfigDialogSavu::initSavuWindow() {
- // geometry, etc. niceties
- // on the left (just plugin names) 1/2, right: 2/3
- QList<int> sizes{100, 200};
- m_savuUi.splitterPlugins->setSizes(std::move(sizes));
-
- // Setup Parameter editor tab
- loadAvailablePlugins();
- m_savuUi.treeCurrentPlugins->setHeaderHidden(true);
-
- // Connect slots
- // Lists/trees
- connect(m_savuUi.listAvailablePlugins, SIGNAL(itemSelectionChanged()), this,
- SLOT(availablePluginSelected()));
- connect(m_savuUi.treeCurrentPlugins, SIGNAL(itemSelectionChanged()), this,
- SLOT(currentPluginSelected()));
- connect(m_savuUi.treeCurrentPlugins, SIGNAL(itemExpanded(QTreeWidgetItem *)),
- this, SLOT(expandedItem(QTreeWidgetItem *)));
-
- // Buttons
- connect(m_savuUi.btnTransfer, SIGNAL(released()), this,
- SLOT(transferClicked()));
- connect(m_savuUi.btnMoveUp, SIGNAL(released()), this, SLOT(moveUpClicked()));
- connect(m_savuUi.btnMoveDown, SIGNAL(released()), this,
- SLOT(moveDownClicked()));
- connect(m_savuUi.btnRemove, SIGNAL(released()), this, SLOT(removeClicked()));
-}
-
-// TODO: what's in this file should become a class of its own,
-// 'SavuConfigDialog' or similar
-
-void TomoToolConfigDialogSavu::loadAvailablePlugins() {
- // TODO:: load actual plugins when we know them
- // creating a few relatively realistic choices for now (should crossh check
- // with the savu api when finalized).
- // - Should also verify the param string is valid json when setting
-
- // Create plugin table
- Mantid::API::TableRow row = m_availPlugins->appendRow();
- row << "savu.plugins.timeseries_field_corrections"
- << "{}"
- << "Time Series Field Corrections"
- << "Citation info";
-
- row = m_availPlugins->appendRow();
- row << "savu.plugins.median_filter"
- << "{\"kernel_size\":[1, 3, 3]}"
- << "Median Filter"
- << "Citation info";
-
- row = m_availPlugins->appendRow();
- row << "savu.plugins.vo_centering"
- << "{}"
- << "Vo Centering"
- << "Citation info";
-
- row = m_availPlugins->appendRow();
- row << "savu.plugins.simple_recon"
- << "{\"center_of_rotation\":86}"
- << "Simple Reconstruction"
- << "Citation info";
-
- row = m_availPlugins->appendRow();
- row << "savu.plugins.astra_recon"
- << "{\"center_of_rotation\":\"86\", "
- "\"reconsturction_type\":\"SIRT\", \"number_of_iterations\":5}"
- << "Simple Reconstruction"
- << "Citation info";
-
- // Update the UI
- refreshAvailablePluginListUI();
-}
-
-// Reloads the GUI list of available plugins from the data object ::
-// Populating only through this ensures correct indexing.
-void TomoToolConfigDialogSavu::refreshAvailablePluginListUI() {
- // Table WS structure, id/params/name/cite
- m_savuUi.listAvailablePlugins->clear();
- const size_t rowcount = m_availPlugins->rowCount();
- for (size_t i = 0; i < rowcount; ++i) {
- const QString str =
- QString::fromStdString(m_availPlugins->cell<std::string>(i, 2));
- m_savuUi.listAvailablePlugins->addItem(std::move(str));
- }
-}
-
-// Reloads the GUI list of current plugins from the data object ::
-// Populating only through this ensures correct indexing.
-void TomoToolConfigDialogSavu::refreshCurrentPluginListUI() {
- // Table WS structure, id/params/name/cite
- m_savuUi.treeCurrentPlugins->clear();
- createPluginTreeEntries(m_currPlugins);
-}
-
-// Updates the selected plugin info from Available plugins list.
-void TomoToolConfigDialogSavu::availablePluginSelected() {
- if (m_savuUi.listAvailablePlugins->selectedItems().count() != 0) {
- const size_t idx = static_cast<size_t>(
- m_savuUi.listAvailablePlugins->currentIndex().row());
- if (idx < m_availPlugins->rowCount()) {
- m_savuUi.availablePluginDesc->setText(
- tableWSRowToString(m_availPlugins, idx));
- }
- }
-}
-
-// Updates the selected plugin info from Current plugins list.
-void TomoToolConfigDialogSavu::currentPluginSelected() {
- if (m_savuUi.treeCurrentPlugins->selectedItems().count() != 0) {
- auto currItem = m_savuUi.treeCurrentPlugins->selectedItems()[0];
-
- while (currItem->parent() != NULL)
- currItem = currItem->parent();
-
- int topLevelIndex =
- m_savuUi.treeCurrentPlugins->indexOfTopLevelItem(currItem);
-
- m_savuUi.currentPluginDesc->setText(
- tableWSRowToString(m_currPlugins, topLevelIndex));
- }
-}
-
-class OwnTreeWidgetItem : public QTreeWidgetItem {
-public:
- OwnTreeWidgetItem(QTreeWidgetItem *parent,
- QTreeWidgetItem *logicalParent = NULL,
- const std::string &key = "")
- : QTreeWidgetItem(parent), m_rootParent(logicalParent), m_key(key) {}
-
- OwnTreeWidgetItem(QStringList list, QTreeWidgetItem *logicalParent = NULL,
- const std::string &key = "")
- : QTreeWidgetItem(list), m_rootParent(logicalParent), m_key(key) {}
-
- OwnTreeWidgetItem(QTreeWidgetItem *parent, QStringList list,
- QTreeWidgetItem *logicalParent = NULL,
- const std::string &key = "")
- : QTreeWidgetItem(parent, list), m_rootParent(logicalParent), m_key(key) {
- }
-
- QTreeWidgetItem *getRootParent() { return m_rootParent; }
-
- std::string getKey() { return m_key; }
-
-private:
- QTreeWidgetItem *m_rootParent;
- std::string m_key;
-};
-
-// On user editing a parameter tree item, update the data object to match.
-void TomoToolConfigDialogSavu::paramValModified(QTreeWidgetItem *item,
- int /*column*/) {
- OwnTreeWidgetItem *ownItem = dynamic_cast<OwnTreeWidgetItem *>(item);
- if (!ownItem)
- return;
-
- int topLevelIndex = -1;
- if (ownItem->getRootParent() != NULL) {
- topLevelIndex = m_savuUi.treeCurrentPlugins->indexOfTopLevelItem(
- ownItem->getRootParent());
- }
- if (-1 == topLevelIndex)
- return;
-
- // Recreate the json string from the nodes and write back
- std::string json = m_currPlugins->cell<std::string>(topLevelIndex, 1);
- // potential new line out, and trim spaces
- json.erase(std::remove(json.begin(), json.end(), '\n'), json.end());
- json.erase(std::remove(json.begin(), json.end(), '\r'), json.end());
- json = Poco::trimInPlace(json);
-
- ::Json::Reader r;
- ::Json::Value root;
- if (r.parse(json, root)) {
- // Look for the key and replace it
- root[ownItem->getKey()] = ownItem->text(0).toStdString();
- }
-
- m_currPlugins->cell<std::string>(topLevelIndex, 1) =
- ::Json::FastWriter().write(root);
- currentPluginSelected();
-}
-
-// When a top level item is expanded, also expand its child items - if tree
-// items
-void TomoToolConfigDialogSavu::expandedItem(QTreeWidgetItem *item) {
- if (item->parent() == NULL) {
- for (int i = 0; i < item->childCount(); ++i) {
- item->child(i)->setExpanded(true);
- }
- }
-}
-
-// Adds one plugin from the available plugins list into the list of
-// current plugins
-void TomoToolConfigDialogSavu::transferClicked() {
- if (0 == m_savuUi.listAvailablePlugins->selectedItems().count())
- return;
-
- const int idx = m_savuUi.listAvailablePlugins->currentIndex().row();
- const size_t columnCount = m_currPlugins->columnCount();
-
- Mantid::API::TableRow row = m_currPlugins->appendRow();
- for (size_t j = 0; j < columnCount; ++j) {
- row << m_availPlugins->cell<std::string>(idx, j);
- }
- createPluginTreeEntry(row);
-}
-
-void TomoToolConfigDialogSavu::moveUpClicked() {
- if (0 == m_savuUi.treeCurrentPlugins->selectedItems().count())
- return;
-
- const size_t idx =
- static_cast<size_t>(m_savuUi.treeCurrentPlugins->currentIndex().row());
- if (idx > 0 && idx < m_currPlugins->rowCount()) {
- // swap row, all columns
- const size_t columnCount = m_currPlugins->columnCount();
- for (size_t j = 0; j < columnCount; ++j) {
- const std::string swap = m_currPlugins->cell<std::string>(idx, j);
- m_currPlugins->cell<std::string>(idx, j) =
- m_currPlugins->cell<std::string>(idx - 1, j);
- m_currPlugins->cell<std::string>(idx - 1, j) = swap;
- }
- refreshCurrentPluginListUI();
- }
-}
-
-void TomoToolConfigDialogSavu::moveDownClicked() {
- // TODO: this can be done with the same function as above...
- if (0 == m_savuUi.treeCurrentPlugins->selectedItems().count())
- return;
-
- const size_t idx =
- static_cast<size_t>(m_savuUi.treeCurrentPlugins->currentIndex().row());
- if (idx < m_currPlugins->rowCount() - 1) {
- // swap all columns
-
- const size_t columnCount = m_currPlugins->columnCount();
- for (size_t j = 0; j < columnCount; ++j) {
- const std::string swap = m_currPlugins->cell<std::string>(idx, j);
- m_currPlugins->cell<std::string>(idx, j) =
- m_currPlugins->cell<std::string>(idx + 1, j);
- m_currPlugins->cell<std::string>(idx + 1, j) = swap;
- }
- refreshCurrentPluginListUI();
- }
-}
-
-void TomoToolConfigDialogSavu::removeClicked() {
- // Also clear ADS entries
- if (0 == m_savuUi.treeCurrentPlugins->selectedItems().count())
- return;
-
- const int idx = m_savuUi.treeCurrentPlugins->currentIndex().row();
- m_currPlugins->removeRow(idx);
-
- refreshCurrentPluginListUI();
-}
-
-void TomoToolConfigDialogSavu::menuOpenClicked() {
- QString s = QFileDialog::getOpenFileName(0, "Open file", QDir::currentPath(),
- "NeXus files (*.nxs);;All files (*)",
- new QString("NeXus files (*.nxs)"));
- std::string name = s.toStdString();
-
- if ("" == name)
- return;
-
- bool opening = true;
- if (m_currPlugins->rowCount() > 0) {
- QMessageBox::StandardButton reply = QMessageBox::question(
- this, "Open file confirmation",
- "Opening the configuration file will clear the current list."
- "\nWould you like to continue?",
- QMessageBox::Yes | QMessageBox::No);
- if (reply == QMessageBox::No) {
- opening = false;
- }
- }
-
- if (opening) {
- loadSavuTomoConfig(name, m_currPlugins);
-
- m_currentParamPath = name;
- refreshCurrentPluginListUI();
- }
-}
-
-/**
-* Load a savu tomo config file into the current plugin list, overwriting it.
-* Uses the algorithm LoadSavuTomoConfig
-*/
-void TomoToolConfigDialogSavu::loadSavuTomoConfig(
- std::string &filePath, Mantid::API::ITableWorkspace_sptr ¤tPlugins) {
- // try to load tomo reconstruction parametereization file
- auto alg = Mantid::API::AlgorithmManager::Instance().createUnmanaged(
- "LoadSavuTomoConfig");
- alg->initialize();
- alg->setPropertyValue("Filename", filePath);
- alg->setPropertyValue("OutputWorkspace", createUniqueNameHidden());
- try {
- alg->execute();
- } catch (std::runtime_error &e) {
- throw std::runtime_error(
- std::string("Error when trying to load tomographic reconstruction "
- "parameter file: ") +
- e.what());
- }
-
- // new processing plugins list
- try {
- currentPlugins = alg->getProperty("OutputWorkspace");
- } catch (std::exception &e) {
- userError("Could not load config file", "Failed to load the file "
- "with the following error: " +
- std::string(e.what()));
- }
-}
-void TomoToolConfigDialogSavu::menuSaveClicked() {
- if (m_currentParamPath.empty()) {
- menuSaveAsClicked();
- return;
- }
-
- if (0 == m_currPlugins->rowCount()) {
- // Alert that the plugin list is empty
- QMessageBox::information(this, tr("Unable to save file"),
- "The current plugin list is empty, please add one "
- "or more to the list.");
- } else {
- AnalysisDataService::Instance().add(createUniqueNameHidden(),
- m_currPlugins);
- std::string csvWorkspaceNames = m_currPlugins->getName();
-
- auto alg = Mantid::API::AlgorithmManager::Instance().createUnmanaged(
- "SaveTomoConfig");
- alg->initialize();
- alg->setPropertyValue("Filename", m_currentParamPath);
- alg->setPropertyValue("InputWorkspaces", csvWorkspaceNames);
- alg->execute();
-
- if (!alg->isExecuted()) {
- throw std::runtime_error("Error when trying to save config file");
- }
- }
-}
-size_t TomoToolConfigDialogSavu::g_nameSeqNo = 0;
-
-// Build a unique (and hidden) name for the table ws
-std::string TomoToolConfigDialogSavu::createUniqueNameHidden() {
- std::string name;
- do {
- // with __ prefix => hidden
- name = "__TomoConfigTableWS_Seq_" +
- boost::lexical_cast<std::string>(g_nameSeqNo++);
- } while (AnalysisDataService::Instance().doesExist(name));
-
- return name;
-}
-
-void TomoToolConfigDialogSavu::menuSaveAsClicked() {
- QString s = QFileDialog::getSaveFileName(0, "Save file", QDir::currentPath(),
- "NeXus files (*.nxs);;All files (*)",
- new QString("NeXus files (*.nxs)"));
- std::string name = s.toStdString();
- if ("" == name)
- return;
-
- m_currentParamPath = name;
- menuSaveClicked();
-}
-
-QString TomoToolConfigDialogSavu::tableWSRowToString(ITableWorkspace_sptr table,
- size_t i) {
- std::stringstream msg;
- msg << "ID: " << table->cell<std::string>(i, 0)
- << "\nParams: " << table->cell<std::string>(i, 1)
- << "\nName: " << table->cell<std::string>(i, 2)
- << "\nCite: " << table->cell<std::string>(i, 3);
- return QString::fromStdString(msg.str());
-}
-
-/**
-* Creates a treewidget item for a row of a table workspace.
-*
-* @param row Row from a table workspace with each row specfying a savu plugin
-*/
-void TomoToolConfigDialogSavu::createPluginTreeEntry(TableRow &row) {
- QStringList idStr, nameStr, citeStr, paramsStr;
- idStr.push_back(QString::fromStdString("ID: " + row.cell<std::string>(0)));
- nameStr.push_back(
- QString::fromStdString("Name: " + row.cell<std::string>(2)));
- citeStr.push_back(
- QString::fromStdString("Cite: " + row.cell<std::string>(3)));
- paramsStr.push_back(QString::fromStdString("Params:"));
-
- // Setup editable tree items
- QList<QTreeWidgetItem *> items;
- OwnTreeWidgetItem *pluginBaseItem = new OwnTreeWidgetItem(nameStr);
- OwnTreeWidgetItem *pluginParamsItem =
- new OwnTreeWidgetItem(pluginBaseItem, paramsStr, pluginBaseItem);
-
- // Add to the tree list. Adding now to build hierarchy for later setItemWidget
- // call
- items.push_back(new OwnTreeWidgetItem(pluginBaseItem, idStr, pluginBaseItem));
- items.push_back(
- new OwnTreeWidgetItem(pluginBaseItem, nameStr, pluginBaseItem));
- items.push_back(
- new OwnTreeWidgetItem(pluginBaseItem, citeStr, pluginBaseItem));
- items.push_back(pluginParamsItem);
-
- // Params will be a json string which needs splitting into child tree items
- // [key/value]
- ::Json::Value root;
- std::string paramString = row.cell<std::string>(1);
- ::Json::Reader r;
- if (r.parse(paramString, root)) {
- auto members = root.getMemberNames();
- for (auto it = members.begin(); it != members.end(); ++it) {
- OwnTreeWidgetItem *container =
- new OwnTreeWidgetItem(pluginParamsItem, pluginBaseItem);
-
- QWidget *w = new QWidget();
- w->setAutoFillBackground(true);
-
- QHBoxLayout *layout = new QHBoxLayout(w);
- layout->setMargin(1);
- QLabel *label1 = new QLabel(QString::fromStdString((*it) + ": "));
-
- QTreeWidget *paramContainerTree = new QTreeWidget(w);
- connect(paramContainerTree, SIGNAL(itemChanged(QTreeWidgetItem *, int)),
- this, SLOT(paramValModified(QTreeWidgetItem *, int)));
- paramContainerTree->setHeaderHidden(true);
- paramContainerTree->setIndentation(0);
-
- auto jsonVal = root.get(*it, "");
- std::string valStr = pluginParamValString(jsonVal, *it);
-
- QStringList paramVal(QString::fromStdString(valStr));
- OwnTreeWidgetItem *paramValueItem =
- new OwnTreeWidgetItem(paramVal, pluginBaseItem, *it);
- paramValueItem->setFlags(Qt::ItemIsEditable | Qt::ItemIsEnabled);
-
- paramContainerTree->addTopLevelItem(paramValueItem);
- QRect rect = paramContainerTree->visualItemRect(paramValueItem);
- paramContainerTree->setMaximumHeight(rect.height());
- paramContainerTree->setFrameShape(QFrame::NoFrame);
-
- layout->addWidget(label1);
- layout->addWidget(paramContainerTree);
-
- pluginParamsItem->addChild(container);
- m_savuUi.treeCurrentPlugins->setItemWidget(container, 0, w);
- }
- }
-
- pluginBaseItem->addChildren(items);
- m_savuUi.treeCurrentPlugins->addTopLevelItem(pluginBaseItem);
-}
-
-/**
-* This is a kind of .asString() method for arrays. It iterates
-* through the array elements and builds the string enclosed by [].
-*
-* @param jsonVal Value of a parameter that seems to be an array
-*(isArray()==true)
-* @param name Name of the parameter (to give informative messages)
-*
-* @return String with a parameter value(s), enclosed by [] and
-* separated by commas
-*/
-std::string
-TomoToolConfigDialogSavu::paramValStringFromArray(const Json::Value &jsonVal,
- const std::string &name) {
- std::string s;
- s = "[";
- for (Json::ArrayIndex i = 0; i < jsonVal.size(); ++i) {
- if (jsonVal[i].isArray()) {
- userWarning(
- "Could not recognize parameter value in list/array",
- "The value of parameter '" + name +
- "' could not be interpreted "
- "as a string. It does not seem to be well formed or supported. "
- "For example, parameter values given as lists of lists are not "
- "supported.");
- } else {
- try {
- s += jsonVal[i].asString() + " ,";
- } catch (std::exception &e) {
- userWarning(
- "Could not recognize value in list/array of values",
- "The " + boost::lexical_cast<std::string>(i) +
- "-th value of the list/array could not be interpreted "
- "as a text string. It will be empty in the list of current "
- "plugins. You can still edit it. Error details: " +
- std::string(e.what()));
- }
- }
- }
- // this could be s.back() with C++11
- s[s.length() - 1] = ']'; // and last comma becomes closing ]
- return s;
-}
-
-/**
-* Build a string with the value of a parameter in a json
-* string. Works for scalar and list/array values.
-*
-* @param jsonVal Value of a parameter that seems to be an array
-* @param name Name of the parameter (to give informative messages)
-*
-* @return String with a parameter value
-*/
-std::string
-TomoToolConfigDialogSavu::pluginParamValString(const Json::Value &jsonVal,
- const std::string &name) {
- std::string s;
- // string and numeric values can (normally) be converted to string but arrays
- // cannot
- if (!jsonVal.isArray()) {
- try {
- s = jsonVal.asString();
- } catch (std::exception &e) {
- userWarning(
- "Could not recognize parameter value",
- "The value of parameter '" + name +
- "' could not be interpreted "
- "as a string. It will be empty in the list of current plugins. "
- "You can still edit it. Error details: " +
- std::string(e.what()));
- }
- } else {
- s = paramValStringFromArray(jsonVal, name);
- }
- return s;
-}
-
-void TomoToolConfigDialogSavu::createPluginTreeEntries(
- Mantid::API::ITableWorkspace_sptr table) {
- for (size_t i = 0; i < table->rowCount(); ++i) {
- Mantid::API::TableRow r = table->getRow(i);
- createPluginTreeEntry(r);
- }
-}
-
-/** TODO move into a class, extract from here and QtView interface
-* Show an error (serious) message to the user (pop up)
-*
-* @param err Basic error title
-* @param description More detailed explanation, hints, additional
-* information, etc.
-*/
-void TomoToolConfigDialogSavu::userError(const std::string &err,
- const std::string &description) {
- QMessageBox::critical(this, QString::fromStdString(err),
- QString::fromStdString(description), QMessageBox::Ok,
- QMessageBox::Ok);
-}
-
-/**
-* Show a warning message to the user (pop up)
-*
-* @param err Basic error title
-* @param description More detailed explanation, hints, additional
-* information, etc.
-*/
-void TomoToolConfigDialogSavu::userWarning(const std::string &err,
- const std::string &description) {
- QMessageBox::warning(this, QString::fromStdString(err),
- QString::fromStdString(description), QMessageBox::Ok,
- QMessageBox::Ok);
-}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogTomoPy.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogTomoPy.cpp
deleted file mode 100644
index e20fafd4782..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomoToolConfigDialogTomoPy.cpp
+++ /dev/null
@@ -1,47 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogTomoPy.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h"
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string TomoToolConfigDialogTomoPy::DEFAULT_TOOL_NAME = "TomoPy";
-const std::string TomoToolConfigDialogTomoPy::DEFAULT_TOOL_METHOD = "gridrec";
-
-void TomoToolConfigDialogTomoPy::setupDialogUi() {
- m_tomoPyUi.setupUi(m_dialog);
- m_tomoPyUi.comboBox_method->clear();
-
- const auto &methods = getToolMethods();
- for (auto &method : methods) {
- m_tomoPyUi.comboBox_method->addItem(QString::fromStdString(method.second));
- }
-}
-
-void TomoToolConfigDialogTomoPy::initialiseDialog() { m_dialog = new QDialog; }
-
-void TomoToolConfigDialogTomoPy::setupToolSettingsFromPaths() {
- // TODO: for the output path, probably better to take the sample path,
- // then up one level
- m_toolSettings = std::make_shared<ToolConfigTomoPy>(
- m_runPath, m_pathOut + m_localOutNameAppendix, m_paths.pathDarks(),
- m_paths.pathOpenBeam(), m_paths.pathSamples());
-}
-void TomoToolConfigDialogTomoPy::setupMethodSelected() {
- // move to member/global variable and use more space OR keep here
- const auto &methods = getToolMethods();
-
- const int mi = m_tomoPyUi.comboBox_method->currentIndex();
- // TODO maybe comboBox_method->currentText?
- m_toolMethod = methods[mi].first;
-}
-
-/** Calls the execute of the QDialog
-*/
-int TomoToolConfigDialogTomoPy::executeQt() { return m_dialog->exec(); }
-
-std::vector<std::pair<std::string, std::string>>
-TomoToolConfigDialogTomoPy::getToolMethods() {
- return ToolConfigTomoPy::methods();
-}
-} // Custominterfaces
-} // MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
deleted file mode 100644
index 1ee58d8ace5..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
+++ /dev/null
@@ -1,1048 +0,0 @@
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidKernel/FacilityInfo.h"
-#include "MantidQtAPI/AlgorithmRunner.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyProcess.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyThread.h"
-
-#include <Poco/Path.h>
-
-#ifndef _WIN32
-// This is exclusively for kill/waitpid (interim solution, see below)
-#include <signal.h>
-#include <sys/wait.h>
-
-#endif
-
-using namespace Mantid::API;
-using namespace MantidQt::CustomInterfaces;
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-namespace {
-Mantid::Kernel::Logger g_log("TomographyGUI");
-}
-
-// names by which we know compute resourcess
-const std::string TomographyIfaceModel::g_SCARFName = "SCARF@STFC";
-const std::string TomographyIfaceModel::g_LocalResourceName = "Local";
-
-const std::string TomographyIfaceModel::g_mainReconstructionScript =
- "/Imaging/IMAT/tomo_reconstruct.py";
-
-const std::string TomographyIfaceModel::g_tomoScriptFolderPath = "/scripts";
-
-// names by which we know image/tomography reconstruction tools (3rd party)
-const std::string TomographyIfaceModel::g_TomoPyTool = "TomoPy";
-const std::string TomographyIfaceModel::g_AstraTool = "Astra";
-const std::string TomographyIfaceModel::g_CCPiTool = "CCPi CGLS";
-const std::string TomographyIfaceModel::g_SavuTool = "Savu";
-const std::string TomographyIfaceModel::g_customCmdTool = "Custom command";
-
-/**
- * Default constructor, but note that this currently relies on the
- * SCARF cluster (only in ISIS facility) as the only supported remote
- * compute resource.
- */
-TomographyIfaceModel::TomographyIfaceModel()
- : m_facility("ISIS"), m_experimentRef("RB000000"), m_loggedInUser(""),
- m_loggedInComp(""), m_computeResStatus(), m_reconTools(),
- m_reconToolsStatus(), m_jobsStatus(), m_prePostProcSettings(),
- m_imageStackPreParams(), m_statusMutex(NULL) {
-
- m_computeRes = {g_SCARFName, g_LocalResourceName};
-
- m_SCARFtools = {g_TomoPyTool, g_AstraTool, g_CCPiTool, g_SavuTool,
- g_customCmdTool};
-
- m_currentToolName = m_SCARFtools.front();
-
- m_statusMutex = new QMutex();
-}
-
-TomographyIfaceModel::~TomographyIfaceModel() {
- if (m_statusMutex)
- delete m_statusMutex;
-}
-
-void TomographyIfaceModel::cleanup() {
- const std::string user = loggedIn();
- if (!user.empty()) {
- doLogout(m_loggedInComp, user);
- m_loggedInUser = "";
- }
-}
-
-/**
- * Check that the selected compute resource is listed as supported and
- * usable for the remote manager (if it is not local). Local jobs are
- * not supported for the time being, so this currently raises an
- * exception if the local resource has been selected.
- *
- * This should never throw an exception if the
- * construction/initialization and setup steps went fine and the rest
- * of the code is kept consistent with those steps.
- *
- * @param res Name of the compute resource selected in the interface
- *
- * @return Name of a compute resource (which can be the 'Local' one)
- *
- * @throws std::runtime_error on inconsistent selection of compute
- * resource
- */
-std::string
-TomographyIfaceModel::validateCompResource(const std::string &res) const {
- if (res == g_LocalResourceName) {
- return g_LocalResourceName;
- }
-
- if (m_computeRes.size() <= 0) {
- throw std::runtime_error("No compute resource registered in the list "
- "of supported resources. This graphical interface "
- "is in an inconsistent status.");
- }
-
- const std::string supported = m_computeRes.front();
- if (supported.empty()) {
- throw std::runtime_error("The first compute resource registered in this "
- "interface has an empty name.");
- }
-
- if (res != supported) {
- throw std::runtime_error("The compute resource selected (" + res +
- ") is not the one in principle supported by this "
- "interface: " +
- supported);
- }
-
- return supported;
-}
-
-/**
- * Sets the compute resource that will be used to run reconstruction
- * or other types of jobs. It checks that the facility and compute
- * resource are fine (the one expected). Otherwise, shows an error
- * and not much can be done.
- */
-void TomographyIfaceModel::setupComputeResource() {
- // m_computeRes is initialized in the constructor and doesn't change
- m_computeResStatus.clear();
-
- if (!facilitySupported()) {
- const std::string facName =
- Mantid::Kernel::ConfigService::Instance().getFacility().name();
- throw std::runtime_error(
- "Failed to initialize because the facility is " + facName +
- " (and not " + m_facility +
- "). "
- "Facility not supported. This interface is designed "
- "to be used at " +
- m_facility +
- ". You will probably not be able to use it in a useful way "
- "because your facility is " +
- facName +
- ". If you have set that facility by mistake in your settings, "
- "please update it.");
- }
-
- // this implies a nearly empty / no functionality interface
- if (m_computeRes.size() < 1) {
- return;
- }
-
- // assume the present reality: just SCARF
- const std::string &required = m_computeRes.front();
- std::vector<std::string> res = Mantid::Kernel::ConfigService::Instance()
- .getFacility()
- .computeResources();
- if (res.end() == std::find(res.begin(), res.end(), required)) {
- throw std::runtime_error(
- "Required compute resource: '" + required +
- "' not found. "
- "This interface requires the " +
- required + " compute resource. Even though your current facility is " +
- "in principle supported, the compute resource was not found. "
- "In principle the compute resource should have been "
- "defined in the facilities file for you facility. "
- "Please check your settings.");
- }
- m_computeResStatus.push_back(true);
-
- // finally, put local as last compute resource, and enable it by default
- // TODO: as in validateCompResource() some basic sanity checks could
- // be done before enabling it, including availability of the
- // necessaryy external tools
- m_computeResStatus.push_back(true);
-}
-
-/**
- * Sets the tools that can be run once we know the compute resource
- * where they're going to run. This is very dependent on how the
- * facility and compute resource is adminstered and what the resource
- * provides.
- *
- * @param compRes compute resource for which the tools have to be set
- * up. If empty, the default resource is assumed
- */
-void TomographyIfaceModel::setupRunTool(const std::string &compRes) {
- m_reconToolsStatus.clear();
-
- // catch all the useable/relevant tools for the compute
- // resources. For the time being this is rather simple (just
- // SCARF) and will probably stay like this for a while.
- if (g_LocalResourceName == compRes ||
- ("ISIS" == m_facility && (compRes.empty() || g_SCARFName == compRes))) {
- m_reconTools = m_SCARFtools;
- } else {
- throw std::runtime_error("Cannot setup this interface for the facility: " +
- m_facility +
- ". There is no information about tools for it. ");
- }
- // others would/could come here
-
- for (size_t i = 0; i < m_reconTools.size(); i++) {
- // put CCPi but disable it, as it's not yet sorted out how it is
- // configured / run
- if (g_CCPiTool == m_reconTools[i] ||
- // also, we cannot run Savu at present, and CCPi is not available
- g_SavuTool == m_reconTools[i]) {
- m_reconToolsStatus.push_back(false);
- } else {
- m_reconToolsStatus.push_back(true);
- }
- }
-}
-
-bool TomographyIfaceModel::facilitySupported() {
- const Mantid::Kernel::FacilityInfo &fac =
- Mantid::Kernel::ConfigService::Instance().getFacility();
-
- return (fac.name() == m_facility);
-}
-
-/**
- * Ping the compute resource / server to check if it's alive and
- * responding.
- *
- * @return True if ping succeeded
- */
-bool TomographyIfaceModel::doPing(const std::string &compRes) {
- // This actually does more than a simple ping. Ping and check that a
- // transaction can be created succesfully
- try {
- auto alg = Mantid::API::AlgorithmManager::Instance().createUnmanaged(
- "StartRemoteTransaction");
- alg->initialize();
- alg->setProperty("ComputeResource", compRes);
- std::string tid;
- alg->execute();
- tid = alg->getPropertyValue("TransactionID");
- g_log.information() << "Pinged '" << compRes
- << "'succesfully. Checked that a transaction could "
- "be created, with ID: " << tid << '\n';
- } catch (std::runtime_error &e) {
- throw std::runtime_error("Error. Failed to ping and start a transaction on "
- "the remote resource." +
- std::string(e.what()));
- }
-
- return true;
-}
-
-/**
- * Log into remote compute resource.
- *
- * @param compRes Name of the compute resource where to login
- * @param user Username
- * @param pw Password/authentication credentials as a string
- */
-void TomographyIfaceModel::doLogin(const std::string &compRes,
- const std::string &user,
- const std::string &pw) {
- auto alg =
- Mantid::API::AlgorithmManager::Instance().createUnmanaged("Authenticate");
- try {
- alg->initialize();
- alg->setPropertyValue("UserName", user);
- alg->setPropertyValue("ComputeResource", compRes);
- alg->setPropertyValue("Password", pw);
- alg->execute();
- } catch (std::runtime_error &e) {
- throw std::runtime_error("Unexpected error when trying to log into the "
- "remote compute resource " +
- compRes + " with username " + user + ": " +
- e.what());
- }
-
- // Status: logged in
- if (alg->isExecuted()) {
- m_loggedInUser = user;
- m_loggedInComp = compRes;
- }
-}
-
-void TomographyIfaceModel::doLogout(const std::string &compRes,
- const std::string &username) {
- try {
- auto alg =
- Mantid::API::AlgorithmManager::Instance().createUnmanaged("Logout");
- alg->initialize();
- alg->setProperty("ComputeResource", compRes);
- alg->setProperty("UserName", username);
- alg->execute();
- } catch (std::runtime_error &e) {
- throw std::runtime_error(
- "Error when trying to log out from the remote compute resource " +
- compRes + " with username " + username + ": " + e.what());
- }
-
- m_loggedInUser = "";
-}
-
-void TomographyIfaceModel::doQueryJobStatus(const std::string &compRes,
- std::vector<std::string> &ids,
- std::vector<std::string> &names,
- std::vector<std::string> &status,
- std::vector<std::string> &cmds) {
- auto alg = Mantid::API::AlgorithmManager::Instance().createUnmanaged(
- "QueryAllRemoteJobs");
- try {
- alg->initialize();
- alg->setPropertyValue("ComputeResource", compRes);
- alg->execute();
- } catch (std::runtime_error &e) {
- throw std::runtime_error(
- "Error when trying to query the status of jobs in " + compRes + ": " +
- e.what());
- }
- ids = alg->getProperty("JobId");
- names = alg->getProperty("JobName");
- status = alg->getProperty("JobStatusString");
- cmds = alg->getProperty("CommandLine");
-}
-
-/**
- * Build the components of the command line to run on the remote or local
- * compute resource. Produces a (normally full) path to a runnable, and
- * the options (quite like $0 and $* in scripts).
- *
- * The local and remote command lines look a bit different:
- * - local also has the interpreter path at the front: python /scriptPath/
- * --params..
- * - remote only has the script path: /scriptPathOnRemote/ --params..
- *
- * @param local Is the resource local or remote
- * @param runnable Path to a runnable application (script, python module, etc.)
- * @param args A vector that contains all the arguments
- * @param allOpts The concatenated arguments in a single string
- */
-void TomographyIfaceModel::prepareSubmissionArguments(
- const bool local, std::string &runnable, std::vector<std::string> &args,
- std::string &allOpts) {
-
- const std::string tool = usingTool();
- const std::string cmd = m_currentToolSettings->toCommand();
-
- std::string longOpt;
- // this gets the runnable from the whole string
- splitCmdLine(cmd, runnable, longOpt);
-
- // this is discarded for all tools but the custom command
- std::string trailingCommands;
- if (local) {
- std::string execScriptPath;
- splitCmdLine(longOpt, execScriptPath, trailingCommands);
- args.emplace_back(execScriptPath);
- }
-
- if (tool == g_customCmdTool) {
- // if it's local we need to append the trailingCommands, as the
- // external interpreter and script path are already appended, the script
- // path has to be in a separate argument member otherwise running the
- // external interpreter fails if remote we just want to append all of the
- // options, the script path is already appended
- args.emplace_back(local ? trailingCommands : longOpt);
- allOpts = constructSingleStringFromVector(args);
- return;
- }
-
- // appends the additional options tool name, algorithm name, filters, etc
- makeTomoRecScriptOptions(local, args);
-
- checkIfToolIsSetupProperly(tool, cmd, args);
-
- // used for remote submission
- allOpts = constructSingleStringFromVector(args);
-
- logMsg("Running " + usingTool() + ", with binary: " + runnable +
- ", with parameters: " + allOpts);
-}
-
-/**
- * Build the command line options string in the way the tomorec
- * scripts (remote and local) expect it.
- *
- * @param local whether to adapt the options for a local run (as
- * opposed to a remote compute resource)
- * @param opts The vector of arguments in which the additional
- * arguments will be inserted
- * @return command options ready for the tomorec script
- */
-void TomographyIfaceModel::makeTomoRecScriptOptions(
- const bool local, std::vector<std::string> &opts) const {
- // options with all the info from filters and regions
- // 9 is the current number of arguments being added
- opts.reserve(9);
-
- const std::string currentTool = usingTool();
- const std::string toolNameArg = prepareToolNameForArgs(currentTool);
-
- const std::string toolArgument = "--tool=" + toolNameArg;
-
- opts.emplace_back(toolArgument);
-
- opts.emplace_back("--algorithm=" + m_currentToolMethod);
-
- // TODO fix proper iterations reading from the interface
- opts.emplace_back("--num-iter=5");
-
- filtersCfgToCmdOpts(m_prePostProcSettings, m_imageStackPreParams, local,
- opts);
-}
-
-/** Processes the tool name so that it is appropriate for the command line when
- * executed
- */
-std::string TomographyIfaceModel::prepareToolNameForArgs(
- const std::string &toolName) const {
-
- // the only processing we have for now is converting it to lower case
- std::string outputString = toolName; // copy over the string
- std::transform(toolName.cbegin(), toolName.cend(), outputString.begin(),
- ::tolower);
- return outputString;
-}
-
-std::string TomographyIfaceModel::constructSingleStringFromVector(
- const std::vector<std::string> args) const {
- std::string allOpts;
- for (const auto &arg : args) {
- allOpts += arg + " ";
- }
- return allOpts;
-}
-
-void TomographyIfaceModel::doRemoteRunReconstructionJob(
- const std::string &compRes, const std::string &runnable,
- const std::string &allOpts) {
- // with SCARF we use one (pseudo)-transaction for every submission
- auto transAlg = Mantid::API::AlgorithmManager::Instance().createUnmanaged(
- "StartRemoteTransaction");
- transAlg->initialize();
- transAlg->setProperty("ComputeResource", compRes);
- std::string tid;
- try {
- transAlg->execute();
- tid = transAlg->getPropertyValue("TransactionID");
- } catch (std::runtime_error &e) {
- throw std::runtime_error("Error when trying to start a transaction right "
- "before submitting a reconstruction job: " +
- std::string(e.what()));
- }
-
- auto submitAlg = Mantid::API::AlgorithmManager::Instance().createUnmanaged(
- "SubmitRemoteJob");
- submitAlg->initialize();
- submitAlg->setProperty("ComputeResource", compRes);
- submitAlg->setProperty("TaskName", "Mantid tomographic reconstruction job");
- submitAlg->setProperty("TransactionID", tid);
- submitAlg->setProperty("ScriptName", runnable);
- submitAlg->setProperty("ScriptParams", allOpts);
- try {
- submitAlg->execute();
- } catch (std::runtime_error &e) {
- throw std::runtime_error(
- "Error when trying to submit a reconstruction job: " +
- std::string(e.what()));
- }
-}
-
-/** Starts the local thread with the external reconstruction process
- * @param runnable Path to a runnable application (script, python module, etc.)
- * @param args A vector that contains all the arguments
- * @param allOpts The concatenated arguments in a single string
- * @param thread This thread will be started after the worker is set up with the
- * runnable and the arguments
- * @param worker The worker will only be set up with the runnable and arguments
- * @param workerName The process name with which it will be shown in the
- * reconstruction jobs. Default is "Mantid_Local"
- */
-void TomographyIfaceModel::doLocalRunReconstructionJob(
- const std::string &runnable, const std::vector<std::string> &args,
- const std::string &allOpts, TomographyThread &thread,
- TomographyProcess &worker, const std::string &workerName) {
-
- // Can only run one reconstruction at a time
- // Qt doesn't use exceptions so we can't make sure it ran here
- worker.setup(runnable, args, allOpts, workerName);
- thread.start();
-}
-
-void TomographyIfaceModel::addJobToStatus(const qint64 pid,
- const std::string &runnable,
- const std::string &allOpts,
- const std::string &workerName) {
- Mantid::API::IRemoteJobManager::RemoteJobInfo info;
- info.id = boost::lexical_cast<std::string>(pid);
- info.name = pid > 0 ? workerName : "none";
- info.status = pid > 0 ? "Starting" : "Exit";
- info.cmdLine = runnable + " " + allOpts;
- m_jobsStatusLocal.emplace_back(info);
- doRefreshJobsInfo(g_LocalResourceName);
-}
-
-void TomographyIfaceModel::doCancelJobs(const std::string &compRes,
- const std::vector<std::string> &ids) {
- for (size_t i = 0; i < ids.size(); i++) {
- const std::string id = ids[i];
- auto algJob = Mantid::API::AlgorithmManager::Instance().createUnmanaged(
- "AbortRemoteJob");
- algJob->initialize();
- algJob->setPropertyValue("ComputeResource", compRes);
- algJob->setPropertyValue("JobID", id);
- try {
- algJob->execute();
- } catch (std::runtime_error &e) {
- throw std::runtime_error(
- "Error when trying to cancel a reconstruction job: " +
- std::string(e.what()));
- }
- }
- // doesn't do StopRemoteTransaction. If there are multiple jobs per
- // transaction there could be others that are still running.
-}
-
-void TomographyIfaceModel::doRefreshJobsInfo(const std::string &compRes) {
-
- if (g_LocalResourceName == compRes) {
- refreshLocalJobsInfo();
- return;
- }
-
- // get the info from the server into data members. This operation is subject
- // to delays in the connection, etc.
- try {
- getJobStatusInfo(compRes);
- } catch (std::runtime_error &e) {
- g_log.warning() << "There was an issue while trying to retrieve job status "
- "information from the remote compute resource ("
- << compRes
- << "). Stopping periodic (automatic) status update to "
- "prevent more failures. You can start the automatic "
- "update mechanism again by logging in, as apparently "
- "there is some problem with the last session: "
- << e.what() << '\n';
- }
-}
-
-void TomographyIfaceModel::refreshLocalJobsInfo() {
- for (auto &job : m_jobsStatusLocal) {
- if ("Exit" == job.status || "Done" == job.status)
- continue;
-
- if (processIsRunning(boost::lexical_cast<int>(job.id))) {
- job.status = "Running";
- } else {
- job.status = "Done";
- }
- }
-}
-
-void TomographyIfaceModel::updateProcessInJobList(const qint64 pid,
- const int exitCode) {
- // cast to string from qint64 so we can compare
- const std::string processPID = std::to_string(pid);
- for (auto &job : m_jobsStatusLocal) {
- if (job.id == processPID && exitCode == 1) {
- job.status = "Exit";
- }
- }
-}
-
-void TomographyIfaceModel::getJobStatusInfo(const std::string &compRes) {
- if (m_loggedInUser.empty())
- return;
-
- std::vector<std::string> ids, names, status, cmds;
- doQueryJobStatus(compRes, ids, names, status, cmds);
-
- size_t jobMax = ids.size();
- if (ids.size() != names.size() || ids.size() != status.size() ||
- ids.size() != cmds.size()) {
- // this should not really happen
- jobMax = std::min(ids.size(), names.size());
- jobMax = std::min(jobMax, status.size());
- jobMax = std::min(jobMax, cmds.size());
- g_log.warning()
- << "Problem retrieving job status information. "
- "The response from the compute resource did not seem "
- "correct. The table of jobs may not be fully up to date.";
- }
-
- {
- QMutexLocker lockit(m_statusMutex);
- m_jobsStatus.clear();
- // TODO: udate when we update to remote algorithms v2 and more
- // info might become available from SCARF.
- // As SCARF doesn't provide all the info at the moment, the
- // IRemoteJobManager::RemoteJobInfo struct is for now used only
- // partially (cmds out). So this loop feels both incomplete and an
- // unecessary second step that could be avoided.
- for (size_t i = 0; i < ids.size(); ++i) {
- IRemoteJobManager::RemoteJobInfo ji;
- ji.id = ids[i];
- ji.name = names[i];
- ji.status = status[i];
- ji.cmdLine = cmds[i];
- m_jobsStatus.push_back(ji);
- }
- }
-}
-
-/**
- * Make sure that the data paths (sample, dark, open beam) make
- * sense. Otherwise, warn the user and log error.
- *
- * @throw std::runtime_error if the required fields are not set
- * properly
- */
-void TomographyIfaceModel::checkDataPathsSet() const {
- if (!m_pathsConfig.validate()) {
- const std::string detail =
- "Please define the paths to your dataset images. "
- "You have not defined some of the following paths: sample, "
- "dark, or open beam images. "
- "They are all required to run reconstruction jobs. Please "
- "define these paths in the settings of the interface. ";
- throw std::runtime_error(
- "Cannot run any reconstruction job without the "
- "paths to the sample, dark and open beam images. " +
- detail);
- }
-}
-
-/**
- * Whether a process (identified by pid) is running.
- *
- * This should use Poco::Process, but only more recent Poco versions
- * than what we currently support across platforms have the required
- * Poco::Process::isRunning. Allternatively, it could use QProcess,
- * but that would require Qt 5.
- *
- * @param pid ID of the process
- *
- * @return running status
- */
-bool TomographyIfaceModel::processIsRunning(qint64 pid) const {
-#ifdef _WIN32
- HANDLE handle = OpenProcess(PROCESS_ALL_ACCESS, FALSE, static_cast<int>(pid));
- DWORD code;
- BOOL rc = GetExitCodeProcess(handle, &code);
- CloseHandle(handle);
- return (rc && code == STILL_ACTIVE);
-#else
- // zombie/defunct processes
- while (waitpid(-1, 0, WNOHANG) > 0) {
- }
- return (0 == kill(static_cast<int>(pid), 0));
-#endif
- // return Poco::Process::isRunning(pid);
-}
-
-/**
- * This can produce a tool-specific warning that can be shown for
- * different tools when they are not fully setup (any required
- * parameter is missing).
- *
- * @param tool Name of the tool this warning applies to
- * @param cmd command/script/executable derived from the settings
- * @param args All the arguments for the run
- */
-bool TomographyIfaceModel::checkIfToolIsSetupProperly(
- const std::string &tool, const std::string &cmd,
- const std::vector<std::string> &args) const {
- if (tool.empty() || cmd.empty() || args.empty()) {
- const std::string detail =
- "Please define the settings of this tool. "
- "You have not defined any settings for this tool: " +
- tool +
- ". Before running it you need to define its settings "
- "(method, parameters, etc.). You can do so by clicking on the setup "
- "button.";
- throw std::runtime_error("Cannot run the tool " + tool +
- " without setting it up." + detail);
- }
- return true;
-}
-
-/**
- * Temporary helper to do an operation that shouldn't be needed any longer
- * when the code is reorganized to use the tool settings objects better.
- */
-void TomographyIfaceModel::splitCmdLine(const std::string &cmd,
- std::string &runnable,
- std::string &opts) const {
- if (cmd.empty())
- return;
-
- const auto pos = cmd.find(" ");
- if (std::string::npos == pos)
- return;
-
- runnable = cmd.substr(0, pos);
- opts = cmd.substr(pos + 1);
-}
-
-/**
-* Helper to get a FITS image into a workspace. Uses the LoadFITS
-* algorithm. If the algorithm throws, this method shows user (pop-up)
-* warning/error messages but does not throw.
-*
-* This method returns a workspace group which most probably you want
-* to delete after using the image to draw it.
-*
-* @param path Path to a FITS image
-*
-* @return Group Workspace containing a Matrix workspace with a FITS
-* image, one pixel per histogram, as loaded by LoadFITS (can be empty
-* if the load goes wrong and the workspace is not available from the
-* ADS).
-*/
-WorkspaceGroup_sptr
-TomographyIfaceModel::loadFITSImage(const std::string &path) {
- // get fits file into workspace and retrieve it from the ADS
- auto alg = AlgorithmManager::Instance().createUnmanaged("LoadFITS");
- alg->initialize();
- alg->setPropertyValue("Filename", path);
- std::string wsName = "__fits_ws_tomography_gui";
- alg->setProperty("OutputWorkspace", wsName);
- // this is way faster when loading into a MatrixWorkspace
- alg->setProperty("LoadAsRectImg", true);
- try {
- alg->execute();
- } catch (std::exception &e) {
- throw std::runtime_error(
- "Failed to load image. Could not load this file as a "
- "FITS image: " +
- std::string(e.what()));
- }
- if (!alg->isExecuted()) {
- throw std::runtime_error(
- "Failed to load image correctly. Note that even though "
- "the image file has been loaded it seems to contain errors.");
- }
- WorkspaceGroup_sptr wsg;
- MatrixWorkspace_sptr ws;
- try {
- wsg = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(wsName);
- ws = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
- wsg->getNames()[0]);
- } catch (std::exception &e) {
- throw std::runtime_error(
- "Could not load image contents. An unrecoverable error "
- "happened when trying to load the image contents. Cannot "
- "display it. Error details: " +
- std::string(e.what()));
- }
-
- // draw image from workspace
- if (wsg && ws &&
- Mantid::API::AnalysisDataService::Instance().doesExist(ws->getName())) {
- return wsg;
- } else {
- return WorkspaceGroup_sptr();
- }
-}
-
-void TomographyIfaceModel::logMsg(const std::string &msg) { g_log.notice(msg); }
-
-void TomographyIfaceModel::logErrMsg(const std::string &msg) {
- g_log.error(msg);
-}
-
-/**
- * Produces a comma separated list of coordinates as a string of real values
- *
- * @param coords Coordinates given as point 1 (x,y), point 2 (x,y)
- *
- * @returns A string like "x1, y1, x2, y2"
- */
-std::string boxCoordinatesToCSV(const ImageStackPreParams::Box2D &coords) {
- const std::string s_left = std::to_string(coords.second.X());
- const std::string s_top = std::to_string(coords.first.Y());
- const std::string s_right = std::to_string(coords.first.X());
- const std::string s_bottom = std::to_string(coords.second.Y());
-
- return s_left + ", " + s_top + ", " + s_right + ", " + s_bottom;
-}
-
-/**
- * Build options string to send them to the tomographic reconstruction
- * scripts command line.
- *
- * @param filters Settings for the pre-post processing steps/filters
- *
- * @param corRegions center and regions selected by the user (region
- * of intererst/analysis area and normalization or air region).
- *
- * @param local whether to adapt the options for a local run (as
- * opposed to a remote compute resource)
- *
- * @param opts array where to add the options (one element will be
- * added for every option).
- *
- * This doesn't belong here and should be moved to more appropriate
- * place when the settings settle.
- */
-void TomographyIfaceModel::filtersCfgToCmdOpts(
- const TomoReconFiltersSettings &filters,
- const ImageStackPreParams &corRegions, const bool local,
- std::vector<std::string> &opts) const {
-
- opts.emplace_back("--input-path=" + adaptInputPathForExecution(
- m_pathsConfig.pathSamples(), local));
-
- const std::string alg = getCurrentToolMethod();
-
- // check the general enable option and the dataset specific enable
- if (filters.prep.normalizeByFlats && m_pathsConfig.m_pathOpenBeamEnabled) {
- const std::string flat = m_pathsConfig.pathOpenBeam();
- if (!flat.empty())
- opts.emplace_back("--input-path-flat=" +
- adaptInputPathForExecution(flat, local));
- }
-
- if (filters.prep.normalizeByDarks && m_pathsConfig.m_pathDarkEnabled) {
- const std::string dark = m_pathsConfig.pathDarks();
- if (!dark.empty())
- opts.emplace_back("--input-path-dark=" +
- adaptInputPathForExecution(dark, local));
- }
-
- std::string openList;
- std::string closeList;
- // TODOMODL how to handle this? we still need to know what the resource is,
- // because local is windows and remote is linux
- if (local) {
- openList = "[";
- closeList = "]";
- } else {
- openList = "'[";
- closeList = "]'";
- }
- if ((corRegions.roi.first.X() > 0 || corRegions.roi.second.X() > 0) &&
- (corRegions.roi.first.Y() > 0 || corRegions.roi.second.Y() > 0)) {
- opts.emplace_back("--region-of-interest=" + openList +
- boxCoordinatesToCSV(corRegions.roi) + closeList);
- }
-
- if (filters.prep.normalizeByAirRegion) {
- if (0 != corRegions.normalizationRegion.first.X() ||
- 0 != corRegions.normalizationRegion.second.X())
- opts.emplace_back("--air-region=" + openList +
- boxCoordinatesToCSV(corRegions.normalizationRegion) +
- closeList);
- }
-
- const std::string outBase =
- buildOutReconstructionDir(m_pathsConfig.pathSamples(), local);
-
- // append a 'now' string
- auto now = Mantid::Kernel::DateAndTime::getCurrentTime();
- const std::string timeAppendix = now.toFormattedString("%Y%B%d_%H%M%S") +
- "_" + std::to_string(now.nanoseconds());
-
- // one name for this particular reconstruction, like:
- // out_reconstruction_TomoPy_gridrec_
- const std::string reconName =
- "reconstruction_" + m_currentToolName + "_" + alg + "_" + timeAppendix;
-
- const std::string outOpt = outBase + "/" + reconName;
-
- if (local) {
- // doesn't go through the shell so it should not have quotes
- opts.emplace_back("--output=" + adaptInputPathForExecution(outOpt, local));
- } else {
- opts.emplace_back("--output=\"" +
- adaptInputPathForExecution(outOpt, local) + "\"");
- }
-
- // TODO: will/should use m_systemSettings.m_outputPathCompPreProcessed to
- // set an option like --output-pre_processed. For now the pre_processed
- // files go inside the directory of the reconstructed files.
-
- opts.emplace_back("--median-filter-size=" +
- std::to_string(filters.prep.medianFilterWidth));
-
- // Filters:
-
- // TODO: (we'd require here IMAT specific headers to become available soon)
- // if (filters.prep.normalizeByProtonCharge)
-
- double cor = 0;
- cor = corRegions.cor.X();
- opts.emplace_back("--cor=" + std::to_string(cor));
-
- int rotationIdx = static_cast<int>(corRegions.rotation / 90);
- // filters.prep.rotation
- opts.emplace_back("--rotation=" + std::to_string(rotationIdx));
-
- // filters.prep.maxAngle
- opts.emplace_back("--max-angle=" + std::to_string(filters.prep.maxAngle));
-
- // prep.scaleDownFactor
- if (filters.prep.scaleDownFactor > 1)
- opts.emplace_back("--scale-down=" +
- std::to_string(filters.prep.scaleDownFactor));
-
- // postp.circMaskRadius
- opts.emplace_back("--circular-mask=" +
- std::to_string(filters.postp.circMaskRadius));
-
- // postp.cutOffLevel
- if (filters.postp.cutOffLevel > 0.0)
- opts.emplace_back("--cut-off=" + std::to_string(filters.postp.cutOffLevel));
-
- // TODO: this should take the several possible alternatives from the user
- // interface
- opts.emplace_back("--out-img-format=png");
-}
-
-/**
- * Converts paths to paths that will work for the reconstruction
- * scripts on the local or remote machine.
- *
- * @param path path to a directory (samples/flats/darks)
- * @param local adapt the path to local or remote execution
- *
- * @return path string ready to be used by the reconstruction scripts
- */
-std::string
-TomographyIfaceModel::adaptInputPathForExecution(const std::string &path,
- const bool local) const {
- if (local)
- return path;
-
- std::string result;
- // For example, request /media/scarf/data/RB0000/...
- // which needs to be translated into: /work/scarf/data/RB0000/...
- if (std::string::npos !=
- path.find(m_systemSettings.m_local.m_remoteDriveOrMountPoint)) {
- result = path;
- boost::replace_all(result,
- m_systemSettings.m_local.m_remoteDriveOrMountPoint,
- m_systemSettings.m_remote.m_basePathTomoData);
- boost::replace_all(result, "\\", "/");
- } else {
- result = path;
- // Remote (to UNIX), assuming SCARF or similar
- boost::replace_all(result, "\\", "/");
- if (result.length() >= 2 && ':' == result[1]) {
- if (2 == result.length())
- result = ""; // don't accept '/'
- else
- result = result.substr(2);
- }
- }
-
- return result;
-}
-
-/**
- * Builds a base path for the output directory and files (which go in
- * a subdirectory usually called 'processed' next to the
- * samples/flats/darks directories).
- *
- * @param samplesDir full path to samples
- *
- * @return path to which an output directory name can be appended, to
- * output the reconstructed volume to.
- */
-std::string
-TomographyIfaceModel::buildOutReconstructionDir(const std::string &samplesDir,
- bool) const {
- // TODO: guessing from sample dir always at the moment.
- // We might want to distinguish local/remote runs at some point
- // (second parameter)
- // Remote runs would ideally use buildOutReconstructionDirFromSystemRoot()
- return buildOutReconstructionDirFromSamplesDir(samplesDir);
-}
-
-/**
- * This method enforces the proper
- * path following current IMAT rules, regardless of where the samples
- * path was located.
- *
- * @param samplesDir full path to sample images
- *
- * @param local whether to adapt the path rules options for a local
- * run (as opposed to a remote compute resource)
- *
- * @return path to which an output directory name can be appended, to
- * output the reconstructed volume to.
- */
-std::string TomographyIfaceModel::buildOutReconstructionDirFromSystemRoot(
- const std::string &samplesDir, bool local) const {
- // Like /work/imat/data/RB00XYZTUV/sampleA/processed/
- // Split in components like: /work/imat + / + data + / + RB00XYZTUV + / +
- // sampleA + / + processed
- std::string rootBase;
- if (local) {
- rootBase = m_systemSettings.m_local.m_basePathTomoData;
- } else {
- rootBase = m_systemSettings.m_remote.m_basePathTomoData;
- }
-
- // Guess sample name (example: 'sampleA') from the input data path
- Poco::Path pathToSample(samplesDir);
- pathToSample = pathToSample.parent();
- std::string sampleName = pathToSample.directory(pathToSample.depth() - 1);
- // safe fallback for pathological cases (samples in a root directory, etc.)
- if (sampleName.empty())
- sampleName = "sample";
-
- const std::string outBase = rootBase + "/" +
- m_systemSettings.m_pathComponents[0] + "/" +
- m_experimentRef + "/" + sampleName + "/" +
- m_systemSettings.m_outputPathCompReconst;
-
- return outBase;
-}
-
-/**
- * Builds a base path for the output directory and files by looking
- * for the parent of the samples directory. This method will work
- * regardless of whether the samples directory location follows the
- * proper IMAT conventions.
- *
- * @param samplesDir full path to samples
- *
- * @return path to which an output directory name can be appended, to
- * output the reconstructed volume to.
- */
-std::string TomographyIfaceModel::buildOutReconstructionDirFromSamplesDir(
- const std::string &samplesDir) const {
- // Guess sample name (example 'sampleA') from the input data/sample
- // images path
- Poco::Path path(samplesDir);
-
- path = path.parent();
- path.append(m_systemSettings.m_outputPathCompReconst);
-
- return path.toString();
-}
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfacePresenter.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomographyIfacePresenter.cpp
deleted file mode 100644
index b211188bc95..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfacePresenter.cpp
+++ /dev/null
@@ -1,929 +0,0 @@
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/TableRow.h"
-#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidKernel/FacilityInfo.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyProcess.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyThread.h"
-
-#include <boost/lexical_cast.hpp>
-
-#include <Poco/DirectoryIterator.h>
-#include <Poco/Path.h>
-
-#include <QFileInfo>
-#include <QMutex>
-#include <QString>
-#include <QThread>
-#include <QTimer>
-
-using namespace Mantid::API;
-using namespace MantidQt::CustomInterfaces;
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string TomographyIfacePresenter::g_defOutPathLocal =
-#ifdef _WIN32
- "D:/imat-data/";
-#else
- "~/imat/";
-#endif
-
-const std::string TomographyIfacePresenter::g_defOutPathRemote =
-#ifdef _WIN32
- "I:/imat/imat-data/";
-#else
- "~/imat-data/";
-#endif
-
-TomographyIfacePresenter::TomographyIfacePresenter(ITomographyIfaceView *view)
- : m_view(view), m_model(new TomographyIfaceModel()),
- m_statusMutex(new QMutex()), m_keepAliveTimer(nullptr) {
- if (!m_view) {
- throw std::runtime_error("Severe inconsistency found. Presenter created "
- "with an empty/null view (tomography interface). "
- "Cannot continue.");
- }
-}
-
-TomographyIfacePresenter::~TomographyIfacePresenter() {
- cleanup();
-
- if (m_keepAliveTimer)
- delete m_keepAliveTimer;
-
- if (m_statusMutex)
- delete m_statusMutex;
-}
-
-/**
- * Close open sessions, kill timers/threads etc., save settings, etc. for a
- * graceful window close/destruct
- */
-void TomographyIfacePresenter::cleanup() {
- killKeepAliveMechanism();
- m_model->cleanup();
-}
-
-void TomographyIfacePresenter::notify(
- ITomographyIfacePresenter::Notification notif) {
-
- switch (notif) {
-
- case ITomographyIfacePresenter::SystemSettingsUpdated:
- processSystemSettingsUpdated();
- break;
-
- case ITomographyIfacePresenter::SetupResourcesAndTools:
- processSetupResourcesAndTools();
- break;
-
- case ITomographyIfacePresenter::CompResourceChanged:
- processCompResourceChanged();
- break;
-
- case ITomographyIfacePresenter::ToolChanged:
- processToolChanged();
- break;
-
- case ITomographyIfacePresenter::TomoPathsChanged:
- processTomoPathsChanged();
- break;
-
- case ITomographyIfacePresenter::TomoPathsEditedByUser:
- processTomoPathsEditedByUser();
- break;
-
- case ITomographyIfacePresenter::LogInRequested:
- processLogin();
- break;
-
- case ITomographyIfacePresenter::LogOutRequested:
- processLogout();
- break;
-
- case ITomographyIfacePresenter::SetupReconTool:
- processSetupReconTool();
- break;
-
- case ITomographyIfacePresenter::RunReconstruct:
- processRunRecon();
- break;
-
- case ITomographyIfacePresenter::RunExternalProcess:
- processRunExternalProcess();
- break;
-
- case ITomographyIfacePresenter::RefreshJobs:
- processRefreshJobs();
- break;
-
- case ITomographyIfacePresenter::CancelJobFromTable:
- processCancelJobs();
- break;
-
- case ITomographyIfacePresenter::VisualizeJobFromTable:
- processVisualizeJobs();
- break;
-
- case ITomographyIfacePresenter::AggregateEnergyBands:
- processAggregateEnergyBands();
- break;
-
- case ITomographyIfacePresenter::LogMsg:
- processLogMsg();
- break;
-
- case ITomographyIfacePresenter::ShutDown:
- processShutDown();
- break;
- }
-}
-
-void TomographyIfacePresenter::processRunExternalProcess() {
- // TODO unify with processRunRecon()
- // read the cached variables in view
- const std::string &cachedExec = m_view->getCachedExecutable();
- const std::vector<std::string> &cachedArgs = m_view->getCachedArguments();
-
- std::string runnable;
- std::vector<std::string> args;
- std::string allOpts;
- // still prepare submission arguments to get the defaults
- const bool local = true;
- prepareSubmissionArguments(local, runnable, args, allOpts);
-
- // if custom external is provided, overwrite the default one
- runnable = !cachedExec.empty() ? cachedExec : runnable;
-
- // append the additional args for now
- for (const auto &arg : cachedArgs) {
- args.emplace_back(arg);
- allOpts += arg;
- }
-
- setupAndRunLocalExternalProcess(runnable, args, allOpts);
-}
-
-void TomographyIfacePresenter::setupAndRunLocalExternalProcess(
- const std::string &runnable, const std::vector<std::string> &args,
- const std::string &allOpts) {
-
- if (m_reconRunning) {
- const auto result = m_view->userConfirmation(
- "Reconstruction is RUNNING",
- "Are you sure you want to<br>cancel the running reconstruction?");
-
- if (!result) {
- // user clicked NO, so we don't terminate the running reconstruction and
- // simply return
- return;
- }
- }
-
- // this kills the previous thread forcefully
- m_workerThread.reset();
- auto *worker = new MantidQt::CustomInterfaces::TomographyProcess();
- m_workerThread = Mantid::Kernel::make_unique<TomographyThread>(this, worker);
-
- // Specific connections for this presenter
- // we do this so the thread can independently read the process' output and
- // only signal the presenter after it's done reading and has something to
- // share so it doesn't block the presenter
- connect(m_workerThread.get(), SIGNAL(stdOutReady(QString)), this,
- SLOT(readWorkerStdOut(QString)));
- connect(m_workerThread.get(), SIGNAL(stdErrReady(QString)), this,
- SLOT(readWorkerStdErr(QString)));
-
- // remove the user confirmation for running recon, if the recon has finished
- connect(m_workerThread.get(), SIGNAL(workerFinished(qint64, int)), this,
- SLOT(emitExternalProcessOutput(qint64, int)));
-
- connect(worker, SIGNAL(started()), this, SLOT(addProcessToJobList()));
- m_model->doLocalRunReconstructionJob(runnable, args, allOpts, *m_workerThread,
- *worker, "Auto COR");
-}
-
-void TomographyIfacePresenter::emitExternalProcessOutput(const qint64 pid,
- const int exitCode) {
- workerFinished(pid, exitCode);
- m_view->emitExternalProcessFinished(m_workerOutputCache);
-}
-
-void TomographyIfacePresenter::processSystemSettingsUpdated() {
- m_model->setSystemSettings(m_view->systemSettings());
-
- // update the tool information with the new system settings
- setupConfigDialogSettingsAndUpdateModel(m_configDialog.get());
-}
-
-void TomographyIfacePresenter::processSetupResourcesAndTools() {
- // first time update, even if not requested by user
- processSystemSettingsUpdated();
-
- try {
- m_model->setupComputeResource();
- if (m_model->computeResources().size() < 1) {
- m_view->userWarning("No remote compute resource could be set up!",
- "No remote compute resource has been set up. Please "
- "note that without a "
- "remote compute resource the functionality of this "
- "interface might be limited.");
- }
- m_model->setupRunTool("");
- processTomoPathsChanged();
-
- m_view->enableLoggedActions(!m_model->loggedIn().empty());
-
- m_view->setComputeResources(m_model->computeResources(),
- m_model->computeResourcesStatus());
- m_view->setReconstructionTools(m_model->reconTools(),
- m_model->reconToolsStatus());
- } catch (std::runtime_error &e) {
- const std::string msg =
- "Failed to initialize remote compute resource(s). This "
- "custom interface will not work. Error description: " +
- std::string(e.what());
-
- m_view->enableLoggedActions(false);
- // This would ideally be shown to the user as a "fatal error" pop-up, as
- // it is an unrecoverable error. But in facilities other than ISIS this
- // would block the builds (docs-qthelp).
- // m_view->userError("Fatal error", msg);
- m_model->logMsg(msg);
- }
-}
-
-void TomographyIfacePresenter::processCompResourceChanged() {
- const std::string comp = m_view->currentComputeResource();
-
- // TODOPRES find a better way to set up the run tool in model
- m_model->setupRunTool(comp);
-
- if (isLocalResourceSelected()) {
- m_view->enableLoggedActions(true);
- } else {
- const bool status = !m_model->loggedIn().empty();
- m_view->enableLoggedActions(status);
- }
-
- // this will udpate the tool after a resource change
- setupConfigDialogSettingsAndUpdateModel(m_configDialog.get());
-}
-
-/** Called when the event ToolChanged fires. It gets the name for the current
- * tabToolTip and first tries to create it (if valid tool name), and if that
- * succeeds then updates the tool's settings to hold the current path and
- * afterwards updates the model's information about the tool's current settings
- */
-void TomographyIfacePresenter::processToolChanged() {
- const std::string toolName = m_view->currentReconTool();
-
- // disallow reconstruct on tools that don't run yet: Savu and CCPi
- if (TomographyIfaceModel::g_CCPiTool == toolName) {
- m_view->enableRunReconstruct(false);
- m_view->enableConfigTool(false);
- } else if (TomographyIfaceModel::g_SavuTool == toolName) {
- // for now, show setup dialog, but cannot run
- m_view->enableRunReconstruct(false);
- m_view->enableConfigTool(true);
- } else {
- // No need to be logged in anymore when local is selected
- const bool runningLocally = isLocalResourceSelected();
- m_view->enableRunReconstruct(runningLocally ||
- !(m_model->loggedIn().empty()));
- m_view->enableConfigTool(true);
- }
-
- // return if empty string
- if ("" == toolName) {
- return;
- }
-
- createConfigDialogUsingToolName(toolName);
- // this will set the default settings for the dialog
- setupConfigDialogSettingsAndUpdateModel(m_configDialog.get());
-}
-
-void TomographyIfacePresenter::setupConfigDialogSettingsAndUpdateModel(
- TomoToolConfigDialogBase *dialog) {
-
- // this check prevents a crash on initialisation where Qt passes a tool name
- // of "" and then we have a nullptr dialogue
- if (dialog) {
- setupConfigDialogSettings(*dialog);
- updateModelAfterToolChanged(*dialog);
- }
-}
-
-/** Uses the static method in TomoToolConfigDialogBase to create the proper tool
- * from the provided name
- * @param toolName The string holding the tool's name
- */
-void TomographyIfacePresenter::createConfigDialogUsingToolName(
- const std::string &toolName) {
- // free the previous dialogue pointer if any
- m_configDialog.reset();
- m_configDialog = TomoToolConfigDialogBase::getToolDialogFor(toolName);
-}
-
-/** Depending on whether local or remote resource is selected, do setup
-* the tool's run path, the paths out, the reconstruction index and
-* the localOutNameAppendix
-*
-* @param dialog The dialog pointer that will be set up
-*/
-void TomographyIfacePresenter::setupConfigDialogSettings(
- TomoToolConfigDialogBase &dialog) {
-
- if (isLocalResourceSelected()) {
- setupConfigDialogSettingsForLocal(dialog);
- } else {
- setupConfigDialogSettingsForRemote(dialog);
- }
-}
-
-/** Configures the dialog settings for local reconstruction, this means settings
- * the run command, the pathOut and the name of the output folder
- *
- * @param dialog The raw dialog pointer that will be configured.
- */
-void TomographyIfacePresenter::setupConfigDialogSettingsForLocal(
- TomoToolConfigDialogBase &dialog) {
- const std::string run = m_model->getExeternalInterpreterPath() + " " +
- m_model->getCurrentLocalScriptsBasePath() +
- m_model->getTomoScriptLocationPath();
-
- const TomoPathsConfig paths = m_view->currentPathsConfig();
-
- const std::string pathOut = Poco::Path::expand(
- g_defOutPathLocal + "/" + m_model->getCurrentExperimentReference());
- static size_t reconIdx = 1;
- const std::string localOutNameAppendix =
- std::string("/processed/") + "reconstruction_" + std::to_string(reconIdx);
-
- dialog.setupDialog(run, paths, pathOut, localOutNameAppendix);
-}
-
-/** Configures the dialog settings for remote reconstruction, this means
- * settings
- * the run command, the pathOut and the name of the output folder
- *
- * Currently it does NOT take into account the remote, this is
- * something that might be needed in the future if more remote reconstruction
- * locations are added, as currently the only one is SCARF
- *
- * @param dialog The raw dialog pointer that will be configured.
- */
-void TomographyIfacePresenter::setupConfigDialogSettingsForRemote(
- TomoToolConfigDialogBase &dialog) {
- // set up all the information we need for the dialog
- const std::string run = m_model->getCurrentRemoteScriptsBasePath() +
- m_model->getTomoScriptFolderPath() +
- m_model->getTomoScriptLocationPath();
-
- const TomoPathsConfig paths = m_view->currentPathsConfig();
- const std::string pathOut = Poco::Path::expand(
- g_defOutPathLocal + "/" + m_model->getCurrentExperimentReference());
- static size_t reconIdx = 1;
- const std::string localOutNameAppendix =
- std::string("/processed/") + "reconstruction_" + std::to_string(reconIdx);
-
- dialog.setupDialog(run, paths, pathOut, localOutNameAppendix);
-}
-
-/** Updated the model's information about the current tool
- * The settings that are updated are:
- * - the current tool name
- * - the current tool method
- * - the current tool settings
- *
- * @param dialog The raw dialog pointer that will be configured.
- */
-void TomographyIfacePresenter::updateModelAfterToolChanged(
- const TomoToolConfigDialogBase &dialog) {
-
- // if passed an empty string don't remove the name
- updateModelCurrentToolName(dialog);
- updateModelCurrentToolMethod(dialog);
- updateModelCurrentToolSettings(dialog);
-}
-
-/** Sets the model's current tool name by getting the tool name from the
-* dialogue itself
-*/
-void TomographyIfacePresenter::updateModelCurrentToolName(
- const TomoToolConfigDialogBase &dialog) {
- m_model->usingTool(dialog.getSelectedToolName());
-}
-/** Sets the model's current tool method by coyping the
-* string over to the model, getting it from the dialogue itself
-*/
-void TomographyIfacePresenter::updateModelCurrentToolMethod(
- const TomoToolConfigDialogBase &dialog) {
- m_model->setCurrentToolMethod(dialog.getSelectedToolMethod());
-}
-
-/** Shares the pointer with the model's tool settings. We don't want a
-* unique_ptr, because the dialogs don't die after they are closed, they die if
-* the tool is changed or the whole interface is closed
-*/
-void TomographyIfacePresenter::updateModelCurrentToolSettings(
- const TomoToolConfigDialogBase &dialog) {
- m_model->setCurrentToolSettings(dialog.getSelectedToolSettings());
-}
-
-/**
- * Simply take the paths that the user has provided.
- */
-void TomographyIfacePresenter::processTomoPathsChanged() {
- m_model->setTomoPathsConfig(m_view->currentPathsConfig());
-}
-
-/**
-* Updates the model with the new path. In the process it also tries to
-* guess and find a new path for the flats and darks images from the
-* path to the sample images that the user has given. It would normally
-* look one level up in the directory tree to see if it can find
-* 'dark*' and 'flat*'.
-*/
-void TomographyIfacePresenter::processTomoPathsEditedByUser() {
- TomoPathsConfig cfg = m_view->currentPathsConfig();
- const std::string samples = cfg.pathSamples();
- if (samples.empty())
- return;
-
- try {
- findFlatsDarksFromSampleGivenByUser(cfg);
- } catch (std::exception &exc) {
- const std::string msg = "There was a problem while trying to guess the "
- "location of dark and flat images from this path "
- "to sample images: " +
- samples + ". Error details: " + exc.what();
- m_model->logMsg(msg);
- }
-
- m_model->setTomoPathsConfig(cfg);
- m_view->updatePathsConfig(cfg);
-}
-
-void TomographyIfacePresenter::findFlatsDarksFromSampleGivenByUser(
- TomoPathsConfig &cfg) {
- Poco::Path samplesPath(cfg.pathSamples());
- Poco::DirectoryIterator end;
- bool foundDark = false;
- bool foundFlat = false;
- for (Poco::DirectoryIterator it(samplesPath.parent()); it != end; ++it) {
- if (!it->isDirectory()) {
- continue;
- }
-
- const std::string name = it.name();
- const std::string flatsPrefix = "flat";
- const std::string darksPrefix = "dark";
-
- if (boost::iequals(name.substr(0, flatsPrefix.length()), flatsPrefix)) {
- cfg.updatePathOpenBeam(it->path(), cfg.m_pathOpenBeamEnabled);
- foundFlat = true;
- } else if (boost::iequals(name.substr(0, darksPrefix.length()),
- darksPrefix)) {
- cfg.updatePathDarks(it->path(), cfg.m_pathDarkEnabled);
- foundDark = true;
- }
- if (foundFlat && foundDark)
- break;
- }
-}
-
-void TomographyIfacePresenter::processLogin() {
- if (!m_model->facilitySupported()) {
- m_view->userError(
- "Fatal error",
- "Cannot do any login operation because the current facility is not "
- "supported by this interface. Please check the log messages for "
- "more "
- "details.");
- return;
- }
-
- if (!m_model->loggedIn().empty()) {
- m_view->userError(
- "Better to logout before logging in again",
- "You're currently logged in. Please, log out before logging in "
- "again if that's what you meant.");
- return;
- }
-
- std::string compRes = m_view->currentComputeResource();
- // if local is selected, just take the first remote resource
- if (isLocalResourceSelected()) {
- compRes = "SCARF@STFC";
- }
- try {
- const std::string user = m_view->getUsername();
- if (user.empty()) {
- m_view->userError(
- "Cannot log in",
- "To log in you need to specify a username (and a password).");
- return;
- }
-
- const std::string passw = m_view->getPassword();
- if (passw.empty()) {
- m_view->userError(
- "Cannot log in with an empty password",
- "Empty passwords are not allowed. Please provide a password).");
- return;
- }
-
- m_model->doLogin(compRes, user, passw);
- } catch (std::exception &e) {
- throw(std::string("Problem when logging in. Error description: ") +
- e.what());
- }
-
- bool loggedOK = !m_model->loggedIn().empty();
- m_view->updateLoginControls(loggedOK);
- m_view->enableLoggedActions(loggedOK);
-
- if (!loggedOK)
- return;
-
- try {
- m_model->doRefreshJobsInfo(compRes);
- } catch (std::exception &e) {
- throw(std::string("The login operation went apparently fine but an issue "
- "was found while trying to retrieve the status of the "
- "jobs currently running on the remote resource. Error "
- "description: ") +
- e.what());
- }
-
- startKeepAliveMechanism(m_view->keepAlivePeriod());
- // show table for the first time
- processRefreshJobs();
-}
-
-void TomographyIfacePresenter::processLogout() {
- if (m_model->loggedIn().empty()) {
- m_model->logMsg("Cannot log out: not logged into any resource.");
- return;
- }
-
- try {
- std::string compRes = m_view->currentComputeResource();
- // if local is selected, just take the first remote resource
- if (isLocalResourceSelected()) {
- compRes = "SCARF@STFC";
- }
- m_model->doLogout(compRes, m_view->getUsername());
- } catch (std::exception &e) {
- throw(std::string("Problem when logging out. Error description: ") +
- e.what());
- }
-
- m_view->updateLoginControls(false);
-}
-
-void TomographyIfacePresenter::processSetupReconTool() {
- const std::string ¤tReconTool = m_view->currentReconTool();
-
- // this check prevents a crash on initialisation where Qt passes a tool name
- // of "" and then we have a nullptr dialogue
- auto dialog = m_configDialog.get();
- if (dialog) {
- if (TomographyIfaceModel::g_CCPiTool != currentReconTool) {
- // give pointer to showToolConfig, so it can run the dialogue
- m_view->showToolConfig(*dialog);
- updateModelAfterToolChanged(*dialog);
- }
- }
-}
-
-void TomographyIfacePresenter::processRunRecon() {
- TomoPathsConfig paths = m_view->currentPathsConfig();
- if (paths.pathSamples().empty()) {
- m_view->userWarning("Sample images path not set!",
- "The path to the sample images "
- "is strictly required to start "
- "a reconstruction");
- return;
- }
-
- // we have to branch out to handle local and remote somewhere
- const bool local = isLocalResourceSelected();
-
- std::string runnable;
- std::vector<std::string> args;
- std::string allOpts;
-
- prepareSubmissionArguments(local, runnable, args, allOpts);
- try {
- if (local) {
- setupAndRunLocalReconstruction(runnable, args, allOpts);
-
- // start the refresh jobs timer if not running
- startKeepAliveMechanism(m_view->keepAlivePeriod());
- } else {
- // get the actual compute resource name
- const std::string computingResouce = m_view->currentComputeResource();
- m_model->doRemoteRunReconstructionJob(computingResouce, runnable,
- allOpts);
- }
- } catch (std::exception &e) {
- m_view->userWarning("Issue when trying to start a job", e.what());
- }
-
- processRefreshJobs();
-}
-
-bool TomographyIfacePresenter::userConfirmationToCancelRecon() {
- if (m_reconRunning) {
- const bool result = m_view->userConfirmation(
- "Reconstruction is RUNNING",
- "Are you sure you want to<br>cancel the running reconstruction?");
-
- if (!result) {
- // user clicked NO, so we don't terminate the running reconstruction and
- // simply return
- return false;
- }
- m_reconRunning = false;
- }
- return true;
-}
-
-void TomographyIfacePresenter::setupAndRunLocalReconstruction(
- const std::string &runnable, const std::vector<std::string> &args,
- const std::string &allOpts) {
-
- if (!userConfirmationToCancelRecon()) {
- // user didnt confirm
- return;
- }
-
- // this kills the previous thread forcefully
- m_workerThread.reset();
- auto *worker = new MantidQt::CustomInterfaces::TomographyProcess();
- m_workerThread = Mantid::Kernel::make_unique<TomographyThread>(this, worker);
-
- // Specific connections for this presenter
- // we do this so the thread can independently read the process' output and
- // only signal the presenter after it's done reading and has something to
- // share so it doesn't block the presenter
- connect(m_workerThread.get(), SIGNAL(stdOutReady(QString)), this,
- SLOT(readWorkerStdOut(QString)));
- connect(m_workerThread.get(), SIGNAL(stdErrReady(QString)), this,
- SLOT(readWorkerStdErr(QString)));
-
- // remove the user confirmation for running recon, if the recon has finished
- connect(m_workerThread.get(), SIGNAL(workerFinished(qint64, int)), this,
- SLOT(workerFinished(qint64, int)));
-
- connect(worker, SIGNAL(started()), this, SLOT(addProcessToJobList()));
-
- m_model->doLocalRunReconstructionJob(runnable, args, allOpts, *m_workerThread,
- *worker, "Reconstruction");
-}
-
-/** Simply reset the switch that tracks if a recon is running and
- * update the process job in the reconstruction list
- */
-void TomographyIfacePresenter::workerFinished(const qint64 pid,
- const int exitCode) {
- m_reconRunning = false;
- m_model->updateProcessInJobList(pid, exitCode);
- processRefreshJobs();
-}
-
-void TomographyIfacePresenter::reconProcessFailedToStart() {
- m_view->userError("Reconstruction failed to start",
- "The reconstruction process has encountered an error and "
- "has failed to start.");
-}
-
-void TomographyIfacePresenter::addProcessToJobList() {
- auto *worker = qobject_cast<TomographyProcess *>(sender());
- const qint64 pid = worker->getPID();
- const auto runnable = worker->getRunnable();
- const auto args = worker->getArgs();
- const auto workerName = worker->getName();
-
- m_workerThread->setProcessPID(pid);
-
- m_model->addJobToStatus(pid, runnable, args, workerName);
-
- // update here that the reconstruction is running
- m_reconRunning = true;
-
- processRefreshJobs();
-}
-
-void TomographyIfacePresenter::readWorkerStdOut(const QString &workerString) {
- m_workerOutputCache.append(workerString);
- m_model->logMsg(workerString.toStdString());
-}
-
-void TomographyIfacePresenter::readWorkerStdErr(const QString &workerString) {
- m_workerErrorCache.append(workerString);
- m_model->logErrMsg(workerString.toStdString());
-}
-
-bool TomographyIfacePresenter::isLocalResourceSelected() const {
- return m_model->localComputeResource() == m_view->currentComputeResource();
-}
-
-void TomographyIfacePresenter::processRefreshJobs() {
- m_model->doRefreshJobsInfo(m_view->currentComputeResource());
-
- {
- QMutexLocker lockit(m_statusMutex);
-
- m_view->updateJobsInfoDisplay(m_model->jobsStatus(),
- m_model->jobsStatusLocal());
- }
-}
-
-void TomographyIfacePresenter::processCancelJobs() {
- const std::string &resource = m_view->currentComputeResource();
- if (isLocalResourceSelected() && userConfirmationToCancelRecon()) {
- // if local and user confirmed
- m_workerThread.reset();
- } else {
- m_model->doCancelJobs(resource, m_view->processingJobsIDs());
- }
-}
-
-void TomographyIfacePresenter::processVisualizeJobs() {
- doVisualize(m_view->processingJobsIDs());
-}
-
-void TomographyIfacePresenter::doVisualize(
- const std::vector<std::string> &ids) {
- m_model->logMsg(" Visualizing results from job: " + ids.front());
- m_view->userWarning("Visualizing not implemented", "Visualizing of the data "
- "has not been implemented "
- "yet and is unsupported");
- // TODOPRES: open dialog, send to Paraview, etc.
-}
-
-void TomographyIfacePresenter::processLogMsg() {
- std::vector<std::string> msgs = m_view->logMsgs();
- for (size_t i = 0; i < msgs.size(); i++) {
- m_model->logMsg(msgs[i]);
- }
-}
-
-void TomographyIfacePresenter::processAggregateEnergyBands() {
- auto algParams = m_view->currentAggregateBandsParams();
-
- // check necessary parameters
- if (algParams.end() == algParams.find("InputPath") ||
- algParams.end() == algParams.find("OutputPath") ||
- algParams["InputPath"].empty() || algParams["OutputPath"].empty()) {
- m_view->userError("Invalid input properties",
- "You need to provide the input properties InputPath and "
- "OutputPath. Both are mandatory and should point to "
- "existing directories");
- return;
- }
-
- // check the paths are usable
- if (!usableEnergyBandsPaths(algParams))
- return;
-
- const std::string algName = "ImggAggregateWavelengths";
- auto alg = Mantid::API::AlgorithmManager::Instance().create(algName);
- try {
- alg->initialize();
- for (const auto ¶m : algParams) {
- alg->setPropertyValue(param.first, param.second);
- }
- } catch (std::runtime_error &rexc) {
- m_view->userError("Problem when initializing algorithm",
- "Could not initialize the algorithm " + algName +
- " with the options currently set. Error details: " +
- rexc.what());
- }
-
- // pass hot potato to the view which has the algorithm runner
- m_view->runAggregateBands(alg);
-
- m_model->logMsg(" The energy/wavelength bands are being aggregated in the "
- "background. You can check the log messages and the "
- "algorithms window to track its progress. ");
-}
-
-/**
- * Checks that the input/output directories exists and are readable
- *
- * @param algParams parameters to be passed to the bands aggregation
- * algorithm
- *
- * @return whether it is safe to use the path properties/options given
- */
-bool TomographyIfacePresenter::usableEnergyBandsPaths(
- const std::map<std::string, std::string> &algParams) {
- bool usable = false;
- try {
- const std::string name = algParams.at("InputPath");
- Poco::File inPath(name);
- if (!inPath.canRead() || !inPath.isDirectory()) {
- m_view->userError("Invalid input path",
- "The input path must be a readable directory: " + name);
- return usable;
- }
- } catch (Poco::FileNotFoundException &rexc) {
- m_view->userError("Invalid input path",
- "The input path must exist on disk. Details: " +
- std::string(rexc.what()));
- return usable;
- }
- try {
- const std::string name = algParams.at("OutputPath");
- Poco::File outPath(name);
- if (!outPath.canRead() || !outPath.isDirectory()) {
- m_view->userError("Invalid output path",
- "The output path must be a readable directory: " +
- name);
- return usable;
- }
- } catch (Poco::FileNotFoundException &rexc) {
- m_view->userError("Invalid output path",
- "The output path must exist on disk. Details: " +
- std::string(rexc.what()));
- return usable;
- }
-
- usable = true;
- return usable;
-}
-
-void TomographyIfacePresenter::processShutDown() {
- m_view->saveSettings();
- cleanup();
-}
-
-void TomographyIfacePresenter::startKeepAliveMechanism(int period) {
- if (period <= 0) {
- m_model->logMsg("Tomography GUI: not starting the keep-alive mechanism. "
- "You might be logged out by the remote compute resource "
- "after some minutes "
- "depending on system configuration.");
- return;
- }
-
- // timer is already running, so return
- if (m_keepAliveTimer) {
- return;
- }
-
- m_model->logMsg(
- "Tomography GUI: starting mechanism to periodically query the "
- "status of jobs. This will update the status of running jobs every " +
- boost::lexical_cast<std::string>(period) +
- " seconds. You can also update it at any moment by clicking "
- "on the refresh button. This periodic update mechanism is "
- "also expected to keep sessions on remote compute resources "
- "alive after logging in.");
-
- if (m_keepAliveTimer)
- delete m_keepAliveTimer;
- m_keepAliveTimer = new QTimer(this); // no-parent so it can be moveToThread
-
- m_keepAliveTimer->setInterval(1000 * period); // interval in ms
-
- // remove previous connections
- m_keepAliveTimer->disconnect();
-
- connect(m_keepAliveTimer, SIGNAL(timeout()), this,
- SLOT(processRefreshJobs()));
-
- m_keepAliveTimer->start();
-}
-
-void TomographyIfacePresenter::killKeepAliveMechanism() {
- if (m_keepAliveTimer)
- m_keepAliveTimer->stop();
-}
-
-void TomographyIfacePresenter::prepareSubmissionArguments(
- const bool local, std::string &runnable, std::vector<std::string> &args,
- std::string &allOpts) {
- // update the filters and ROI settings
- // pre-/post processing steps and filters
- m_model->setPrePostProcSettings(m_view->prePostProcSettings());
- // center of rotation and regions
- m_model->setImageStackPreParams(m_view->currentROIEtcParams());
-
- // we have to branch out to handle local and remote somewhere
- m_model->prepareSubmissionArguments(local, runnable, args, allOpts);
-}
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceViewQtGUI.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceViewQtGUI.cpp
deleted file mode 100644
index 3a0899615e3..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceViewQtGUI.cpp
+++ /dev/null
@@ -1,1894 +0,0 @@
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/AnalysisDataService.h"
-#include "MantidAPI/ITableWorkspace.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/Run.h"
-#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidQtAPI/AlgorithmInputHistory.h"
-
-#include "MantidQtAPI/HelpWindow.h"
-#include "MantidQtCustomInterfaces/Tomography/TomoSystemSettings.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfaceViewQtGUI.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h"
-
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-
-using namespace Mantid::API;
-using namespace MantidQt::CustomInterfaces;
-
-#include <boost/lexical_cast.hpp>
-
-#include <Poco/File.h>
-#include <Poco/Path.h>
-
-#include <QFileDialog>
-#include <QFileSystemModel>
-#include <QMessageBox>
-#include <QPainter>
-#include <QSettings>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-const std::string TomographyIfaceViewQtGUI::g_styleSheetOffline =
- "QPushButton { "
- "margin: 6px;"
- "border-color: #0c457e;"
- "border-style: outset;"
- "border-radius: 3px;"
- "border-width: 0px;"
- "color: black;"
- "background-color: rgb(180, 180, 180); "
- "}"
- "QPushButton:flat { "
- "background-color: rgb(180, 180, 180); "
- "}"
- "QPushButton:pressed { "
- "background-color: rgb(180, 180, 180) "
- "}";
-
-const std::string TomographyIfaceViewQtGUI::g_styleSheetOnline =
- "QPushButton { "
- "margin: 6px;"
- "border-color: #0c457e;"
- "border-style: outset;"
- "border-radius: 3px;"
- "border-width: 0px;"
- "color: black;"
- "background-color: rgb(140, 255, 140); "
- "}"
- "QPushButton:flat { background-color: rgb(120, 255, 120); "
- "}"
- "QPushButton:pressed { background-color: rgb(120, 255, 120); "
- "}";
-
-// For paths where Python third party tools are installed, if they're
-// not included in the system python path. For example you could have
-// put the AstraToolbox package in
-// C:/local/tomo-tools/astra/astra-1.6-python27-win-x64/astra-1.6
-// Leaving this empty implies that the tools must have been installed
-// in the system Python path. As an example, in the Anaconda python
-// distribution for windows it could be in:
-// c:/local/Anaconda/Lib/site-packages/
-std::vector<std::string> TomographyIfaceViewQtGUI::g_defAddPathPython;
-
-const std::string TomographyIfaceViewQtGUI::g_SCARFName = "SCARF@STFC";
-const std::string TomographyIfaceViewQtGUI::g_defOutPathLocal =
-#ifdef _WIN32
- "D:/imat-data/";
-#else
- "~/imat/";
-#endif
-
-// TODOVIEW: could use ConfigService::isNetworkDrive(const std::string &)
-const std::string TomographyIfaceViewQtGUI::g_defOutPathRemote =
-#ifdef _WIN32
- "I:/imat/imat-data/";
-#else
- "~/imat-data/";
-#endif
-
-const std::string TomographyIfaceViewQtGUI::g_defParaviewPath =
-#ifdef _WIN32
- "C:\\Program Files\\ParaView\\";
-#else
- "/usr/bin/";
-#endif
-
-const std::string TomographyIfaceViewQtGUI::g_defParaviewAppendPath =
-#ifdef _WIN32
- "bin\\paraview.exe";
-#else
- "paraview";
-#endif
-
-const std::string notAvailTool = "This tool is not available on this platform";
-
-const std::string TomographyIfaceViewQtGUI::g_defOctopusVisPath =
-#ifdef _WIN32
- "C:/Program Files/Octopus Imaging/Octopus Visualisation";
-#else
- notAvailTool;
-#endif
-
-const std::string TomographyIfaceViewQtGUI::g_defOctopusAppendPath =
-#ifdef _WIN32
- "octoviewer3d.exe";
-#else
- notAvailTool;
-#endif
-
-const std::string TomographyIfaceViewQtGUI::g_defProcessedSubpath = "processed";
-
-// phase or cycle component, like: phase_commissioning, cycle_15_4, cycle_16_1
-const std::string TomographyIfaceViewQtGUI::g_defPathComponentPhase =
- "phase_commissioning";
-
-const std::string TomographyIfaceViewQtGUI::g_defExperimentRef = "RB000000";
-
-const std::string TomographyIfaceViewQtGUI::g_defPathReconScripts =
-#ifdef _WIN32
- "C:/MantidInstall/scripts";
-#else
- QDir::currentPath().toStdString();
-#endif
-
-const std::string TomographyIfaceViewQtGUI::g_defPathReconOut =
-#ifdef _WIN32
- "D:/imat";
-#else
- "~/imat/";
-#endif
-
-// Add this class to the list of specialised dialogs in this namespace
-DECLARE_SUBWINDOW(TomographyIfaceViewQtGUI)
-
-/**
- * Default constructor, but note that this interface currently
- * relies on the SCARF cluster (only in ISIS facility) as the only
- * supported remote compute resource.
- *
- * @param parent Parent window (most likely the Mantid main app window).
- */
-TomographyIfaceViewQtGUI::TomographyIfaceViewQtGUI(QWidget *parent)
- : UserSubWindow(parent), ITomographyIfaceView(), m_tabROIWidget(nullptr),
- m_tabImggFormats(nullptr), m_processingJobsIDs(), m_currentComputeRes(""),
- m_currentReconTool("TomoPy"), m_imgPath(""), m_logMsgs(),
- m_systemSettings(), m_settings(),
- m_settingsGroup("CustomInterfaces/Tomography"),
- m_settingsSubGroupEnergy(m_settingsGroup + "/EnergyBands"),
- m_aggAlgRunner(), m_availPlugins(), m_currPlugins(), m_currentParamPath(),
- m_presenter(nullptr) {}
-
-TomographyIfaceViewQtGUI::~TomographyIfaceViewQtGUI() {}
-
-void TomographyIfaceViewQtGUI::initLayout() {
- // setup container ui
- m_ui.setupUi(this);
- // add tab contents and set up their ui's
- QWidget *tabRunW = new QWidget(m_ui.tabMain);
- m_uiTabRun.setupUi(tabRunW);
- m_ui.tabMain->addTab(tabRunW, QString("Run"));
-
- // this is a Qt widget, let Qt manage the pointer
- m_tabROIWidget = new TomographyROIViewQtWidget(m_ui.tabMain);
- m_ui.tabMain->addTab(m_tabROIWidget, QString("ROI etc."));
-
- QWidget *tabFiltersW = new QWidget();
- m_uiTabFilters.setupUi(tabFiltersW);
- m_ui.tabMain->addTab(tabFiltersW, QString("Filters"));
-
- QWidget *tabVizW = new QWidget();
- m_uiTabVisualize.setupUi(tabVizW);
- m_ui.tabMain->addTab(tabVizW, QString("Visualize"));
-
- // this is a Qt widget, let Qt manage the pointer
- QWidget *m_tabImggFormats = new ImggFormatsConvertViewQtWidget();
- m_ui.tabMain->addTab(m_tabImggFormats, QString("Convert"));
-
- QWidget *tabEBandsW = new QWidget();
- m_uiTabEnergy.setupUi(tabEBandsW);
- m_ui.tabMain->addTab(tabEBandsW, QString("Energy bands"));
-
- QWidget *tabSystemSettingsW = new QWidget();
- m_uiTabSystemSettings.setupUi(tabSystemSettingsW);
- m_ui.tabMain->addTab(tabSystemSettingsW, QString("System"));
-
- readSettings();
-
- // basic UI setup
- doSetupGeneralWidgets();
- doSetupSectionSystemSettings();
- doSetupSectionRun();
- doSetupSectionFilters();
- doSetupSectionRoi();
-
- // extra / experimental tabs:
- doSetupSectionVisualize();
- doSetupSectionEnergy();
-
- // presenter that knows how to handle a ITomographyIfaceView should take care
- // of all the logic
- // note the view needs to now the concrete presenter
- m_presenter.reset(new TomographyIfacePresenter(this));
-
- // it will know what compute resources and tools we have available:
- // This view doesn't even know the names of compute resources, etc.
- m_presenter->notify(ITomographyIfacePresenter::SetupResourcesAndTools);
-}
-
-void TomographyIfaceViewQtGUI::doSetupSectionRoi() {
- // connect the auto CoR button to run an external python process
- connect(m_tabROIWidget,
- SIGNAL(findCORClickedSignal(std::string, std::vector<std::string>)),
- this,
- SLOT(runExternalProcess(std::string, std::vector<std::string>)));
- connect(this, SIGNAL(externalProcessFinished(QString)), m_tabROIWidget,
- SLOT(readCoRFromProcessOutput(QString)));
-
- connect(m_tabROIWidget, SIGNAL(imageOrStackLoadedSignal(std::string)), this,
- SLOT(imageOrStackLoadedInRoi(std::string)));
-}
-
-void TomographyIfaceViewQtGUI::imageOrStackLoadedInRoi(
- const std::string &path) {
- m_pathsConfig.updatePathSamples(path);
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsEditedByUser);
-}
-
-void TomographyIfaceViewQtGUI::runExternalProcess(
- const std::string &exec, const std::vector<std::string> &args) {
- m_extExec = exec;
- m_extArgs = args;
- m_presenter->notify(ITomographyIfacePresenter::RunExternalProcess);
-}
-
-void TomographyIfaceViewQtGUI::doSetupGeneralWidgets() {
-
- connect(m_ui.pushButton_help, SIGNAL(released()), this, SLOT(openHelpWin()));
- // note connection to the parent window, otherwise you'd be left
- // with an empty frame window
- if (this->parent()) {
- connect(m_ui.pushButton_close, SIGNAL(released()), this->parent(),
- SLOT(close()));
- }
-}
-
-void TomographyIfaceViewQtGUI::doSetupSectionRun() {
- // geometry, etc. niceties
- // on the left (just plugin names) 1/2, right: 2/3
- QList<int> sizes;
- sizes.push_back(420);
- sizes.push_back(80);
- m_uiTabRun.splitter_run_main_vertical->setSizes(sizes);
-
- sizes[0] = 470;
- sizes[1] = 30;
- m_uiTabRun.splitter_image_resource->setSizes(sizes);
-
- sizes[0] = 400;
- sizes[1] = 100;
- m_uiTabRun.splitter_run_jobs->setSizes(sizes);
-
- updateCompResourceStatus(false);
-
- // enable by default, which will use default tools setups
- m_uiTabRun.pushButton_reconstruct->setEnabled(true);
- // setup always possible with local compute resource
- // m_uiTabRun.pushButton_run_tool_setup->setEnabled(false);
- m_uiTabRun.pushButton_run_tool_setup->setEnabled(true);
- m_uiTabRun.pushButton_run_job_cancel->setEnabled(false);
- m_uiTabRun.pushButton_run_job_visualize->setEnabled(false);
-
- // Button signals
- connect(m_uiTabRun.pushButton_reconstruct, SIGNAL(released()), this,
- SLOT(reconstructClicked()));
- connect(m_uiTabRun.pushButton_run_tool_setup, SIGNAL(released()), this,
- SLOT(toolSetupClicked()));
- connect(m_uiTabRun.pushButton_run_refresh, SIGNAL(released()), this,
- SLOT(jobTableRefreshClicked()));
- connect(m_uiTabRun.pushButton_run_job_visualize, SIGNAL(released()), this,
- SLOT(runVisualizeClicked()));
- connect(m_uiTabRun.pushButton_run_job_cancel, SIGNAL(released()), this,
- SLOT(jobCancelClicked()));
-
- // RB number changes
- connect(m_uiTabRun.lineEdit_experiment_reference, SIGNAL(editingFinished()),
- this, SLOT(updatedExperimentReference()));
-
- // update tools for a resource
- connect(m_uiTabRun.comboBox_run_compute_resource,
- SIGNAL(currentIndexChanged(int)), this,
- SLOT(compResourceIndexChanged(int)));
-
- connect(m_uiTabRun.comboBox_run_tool, SIGNAL(currentIndexChanged(int)), this,
- SLOT(runToolIndexChanged(int)));
-
- // populate setup values from defaults
- const TomoPathsConfig cfg = currentPathsConfig();
- m_uiTabRun.lineEdit_path_samples->setText(
- QString::fromStdString(cfg.pathSamples()));
- m_uiTabRun.lineEdit_path_flats->setText(
- QString::fromStdString(cfg.pathOpenBeam()));
- m_uiTabRun.checkBox_path_flats->setChecked(cfg.m_pathOpenBeamEnabled);
- m_uiTabRun.lineEdit_path_darks->setText(
- QString::fromStdString(cfg.pathDarks()));
- m_uiTabRun.checkBox_path_darks->setChecked(cfg.m_pathDarkEnabled);
-
- m_uiTabRun.lineEdit_SCARF_password->setText("");
- m_uiTabRun.pushButton_SCARF_login->setEnabled(true);
- m_uiTabRun.pushButton_SCARF_logout->setEnabled(false);
-
- // check boxes to enable search for dark and flat images
- connect(m_uiTabRun.checkBox_path_flats, SIGNAL(stateChanged(int)), this,
- SLOT(flatsPathCheckStatusChanged(int)));
- connect(m_uiTabRun.checkBox_path_darks, SIGNAL(stateChanged(int)), this,
- SLOT(darksPathCheckStatusChanged(int)));
-
- // 'browse' buttons for image paths
- connect(m_uiTabRun.pushButton_samples_dir, SIGNAL(released()), this,
- SLOT(samplesPathBrowseClicked()));
- connect(m_uiTabRun.pushButton_flats_dir, SIGNAL(released()), this,
- SLOT(flatsPathBrowseClicked()));
- connect(m_uiTabRun.pushButton_darks_dir, SIGNAL(released()), this,
- SLOT(darksPathBrowseClicked()));
-
- // also manage the edit fields when edited non-programmatically
- connect(m_uiTabRun.lineEdit_path_samples, SIGNAL(editingFinished()), this,
- SLOT(samplesPathEditedByUser()));
- connect(m_uiTabRun.lineEdit_path_flats, SIGNAL(editingFinished()), this,
- SLOT(flatsPathEditedByUser()));
-
- connect(m_uiTabRun.lineEdit_path_darks, SIGNAL(editingFinished()), this,
- SLOT(darksPathEditedByUser()));
-
- m_uiTabRun.lineEdit_path_samples->setText(
- QString::fromStdString(m_pathsConfig.pathSamples()));
- m_uiTabRun.lineEdit_path_flats->setText(
- QString::fromStdString(m_pathsConfig.pathOpenBeam()));
- m_uiTabRun.lineEdit_path_darks->setText(
- QString::fromStdString(m_pathsConfig.pathDarks()));
-
- // log in/out
- connect(m_uiTabRun.pushButton_SCARF_login, SIGNAL(released()), this,
- SLOT(SCARFLoginClicked()));
- connect(m_uiTabRun.pushButton_SCARF_logout, SIGNAL(released()), this,
- SLOT(SCARFLogoutClicked()));
-}
-
-void TomographyIfaceViewQtGUI::doSetupSectionFilters() {
- connect(m_uiTabFilters.pushButton_reset, SIGNAL(released()), this,
- SLOT(resetPrePostFilters()));
-}
-
-void TomographyIfaceViewQtGUI::doSetupSectionVisualize() {
- // TODOVIEW: take g_def values first time, when Qsettings are empty, then from
- // QSettings
- m_setupParaviewPath = g_defParaviewPath;
- m_setupProcessedSubpath = g_defProcessedSubpath;
- m_setupOctopusVisPath = g_defOctopusVisPath;
-
- m_uiTabVisualize.lineEdit_paraview_location->setText(
- QString::fromStdString(g_defParaviewPath));
-
- // make a file system model for the visualization browser
- QFileSystemModel *model = new QFileSystemModel;
- model->setRootPath(QDir::currentPath());
-
- // set the model for the visualization browser
- m_uiTabVisualize.treeView_files->setModel(model);
- m_uiTabVisualize.treeView_files->setSelectionMode(
- QTreeView::ExtendedSelection);
- m_uiTabVisualize.treeView_files->setSelectionBehavior(QTreeView::SelectRows);
-
- // display: current dir
- const QString startDir =
- QString::fromStdString(Poco::Path::expand(g_defOutPathLocal));
-
- // start at default local path when possible
- const QString path =
- QString::fromStdString(Poco::Path::expand(g_defOutPathLocal));
- if (!path.isEmpty()) {
- m_uiTabVisualize.treeView_files->setRootIndex(model->index(path));
- } else {
- m_uiTabVisualize.treeView_files->setRootIndex(
- model->index(QDir::currentPath()));
- }
-
- connect(m_uiTabVisualize.pushButton_paraview, SIGNAL(released()), this,
- SLOT(sendToParaviewClicked()));
-
- connect(m_uiTabVisualize.pushButton_octopus, SIGNAL(released()), this,
- SLOT(sendToOctopusVisClicked()));
-
- connect(m_uiTabVisualize.pushButton_browse_files, SIGNAL(released()), this,
- SLOT(browseFilesToVisualizeClicked()));
-
- connect(m_uiTabVisualize.pushButton_local_default_dir, SIGNAL(released()),
- this, SLOT(defaultDirLocalVisualizeClicked()));
- connect(m_uiTabVisualize.pushButton_remote_default_dir, SIGNAL(released()),
- this, SLOT(defaultDirRemoteVisualizeClicked()));
-
- connect(m_uiTabVisualize.pushButton_browse_paraview, SIGNAL(released()), this,
- SLOT(browseVisToolParaviewClicked()));
- connect(m_uiTabVisualize.pushButton_browse_octopus, SIGNAL(released()), this,
- SLOT(browseVisToolOctopusClicked()));
-}
-
-void TomographyIfaceViewQtGUI::doSetupSectionSystemSettings() {
- // All possible modifications to system settings
- connect(m_uiTabSystemSettings.lineEdit_path_comp_1st,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsEdited()));
- connect(m_uiTabSystemSettings.lineEdit_path_comp_input_samples,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsEdited()));
- connect(m_uiTabSystemSettings.lineEdit_path_comp_input_flats,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsEdited()));
- connect(m_uiTabSystemSettings.lineEdit_path_comp_input_darks,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsEdited()));
-
- connect(m_uiTabSystemSettings.lineEdit_path_comp_out_processed,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsEdited()));
- connect(m_uiTabSystemSettings.lineEdit_path_comp_out_preprocessed,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsEdited()));
-
- connect(m_uiTabSystemSettings.lineEdit_remote_base_path_data,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsEdited()));
- connect(m_uiTabSystemSettings.lineEdit_remote_scripts_base_dir,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsEdited()));
-
- connect(m_uiTabSystemSettings.lineEdit_on_local_data_drive_or_path,
- SIGNAL(textChanged(const QString &)), this,
- SLOT(systemSettingsEdited()));
- connect(m_uiTabSystemSettings.lineEdit_on_local_remote_data_drive_path,
- SIGNAL(textChanged(const QString &)), this,
- SLOT(systemSettingsEdited()));
-
- connect(m_uiTabSystemSettings.lineEdit_local_recon_scripts,
- SIGNAL(textChanged(const QString &)), this,
- SLOT(systemSettingsEdited()));
-
- // 'browse' buttons for local (data) settings:
- connect(m_uiTabSystemSettings.pushButton_on_local_data_drive_or_path,
- SIGNAL(released()), this, SLOT(browseLocalInOutDirClicked()));
- connect(m_uiTabSystemSettings.pushButton_on_local_remote_data_drive_path,
- SIGNAL(released()), this, SLOT(browseLocalRemoteDriveOrPath()));
-
- // reset setup of the remote
- connect(m_uiTabSystemSettings.pushButton_reset_scripts_base_dir_remote,
- SIGNAL(released()), this, SLOT(resetRemoteSetup()));
-
- // remote execution settings
- connect(m_uiTabSystemSettings.spinBox_remote_cores, SIGNAL(editingFinished()),
- this, SLOT(systemSettingsNumericEdited()));
- connect(m_uiTabSystemSettings.spinBox_remote_cores, SIGNAL(editingFinished()),
- this, SLOT(systemSettingsNumericEdited()));
-
- // remote local settings
- connect(m_uiTabSystemSettings.spinBox_local_processes,
- SIGNAL(editingFinished()), this, SLOT(systemSettingsNumericEdited()));
- connect(m_uiTabSystemSettings.spinBox_local_cores, SIGNAL(editingFinished()),
- this, SLOT(systemSettingsNumericEdited()));
-
- // 'browse' buttons for local (scripts) settings:
- connect(m_uiTabSystemSettings.pushButton_local_recon_scripts_dir,
- SIGNAL(released()), this, SLOT(browseLocalReconScriptsDirClicked()));
-
- connect(m_uiTabSystemSettings.pushButton_local_external_interpreter,
- SIGNAL(released()), this,
- SLOT(browseLocalExternalInterpreterClicked()));
-
- connect(m_uiTabSystemSettings.pushButton_reset_all, SIGNAL(released()), this,
- SLOT(resetSystemSettings()));
-}
-
-void TomographyIfaceViewQtGUI::resetRemoteSetup() {
- m_uiTabSystemSettings.lineEdit_remote_base_path_data->setText(
- QString::fromStdString(TomoSystemSettingsRemote::g_defBasePathTomoData));
- m_uiTabSystemSettings.lineEdit_remote_scripts_base_dir->setText(
- QString::fromStdString(
- TomoSystemSettingsRemote::g_defBasePathReconScripts));
- m_uiTabSystemSettings.spinBox_remote_nodes->setValue(1);
- m_uiTabSystemSettings.spinBox_remote_cores->setValue(8);
-}
-
-void TomographyIfaceViewQtGUI::setComputeResources(
- const std::vector<std::string> &resources,
- const std::vector<bool> &enabled) {
- // set up the compute resource
- QComboBox *cr = m_uiTabRun.comboBox_run_compute_resource;
- if (!cr || resources.size() != enabled.size())
- return;
-
- cr->clear();
-
- for (size_t ri = 0; ri < resources.size(); ri++) {
- cr->addItem(QString::fromStdString(resources[ri]));
-
- if (!enabled[ri]) {
- // trick to display the text in a disabled row
- QModelIndex idx = cr->model()->index(static_cast<int>(ri), 0);
- QVariant disabled(0);
- cr->model()->setData(idx, disabled, Qt::UserRole - 1);
- }
- }
-}
-
-void TomographyIfaceViewQtGUI::setReconstructionTools(
- const std::vector<std::string> &tools, const std::vector<bool> &enabled) {
-
- // set up the reconstruction tool
- QComboBox *rt = m_uiTabRun.comboBox_run_tool;
- if (!rt || tools.size() != enabled.size())
- return;
-
- rt->clear();
-
- for (size_t ti = 0; ti < tools.size(); ti++) {
- rt->addItem(QString::fromStdString(tools[ti]));
-
- if (!enabled[ti]) {
- // trick to display it in a disabled row
- QModelIndex idx = rt->model()->index(static_cast<int>(ti), 0);
- QVariant disabled(0);
- rt->model()->setData(idx, disabled, Qt::UserRole - 1);
- }
- }
-}
-
-/**
- * Enables/disables buttons that require the user to be logged into
- * the (remote) compute resource, for example: reconstruct (submit job),
- * cancel job, etc.
- */
-void TomographyIfaceViewQtGUI::enableLoggedActions(bool enable) {
- // TODOVIEW: this may not make sense anymore when/if the "Local" compute
- // resource is used in the future (except when none of the tools
- // supported are available/detected on "Local")
- std::vector<QPushButton *> buttons;
- buttons.push_back(m_uiTabRun.pushButton_run_refresh);
- buttons.push_back(m_uiTabRun.pushButton_run_job_cancel);
- // no visualization yet, need vsi etc. support
- // buttons.push_back(m_uiTabRun.pushButton_run_job_visualize);
- buttons.push_back(m_uiTabRun.pushButton_reconstruct);
-
- for (size_t i = 0; i < buttons.size(); ++i) {
- buttons[i]->setEnabled(enable);
- }
-
- if (!enable) {
- m_uiTabRun.pushButton_reconstruct->setToolTip(
- "Start reconstruction job. You need to be logged in to use this");
- } else {
- m_uiTabRun.pushButton_reconstruct->setToolTip("");
- }
-}
-
-/**
- * Handle display of the current status of the remote/local compute resource
- * that is selected by the user.
- *
- * @param online whether to show good/working/online status
- */
-void TomographyIfaceViewQtGUI::updateCompResourceStatus(bool online) {
- if (online) {
- m_uiTabRun.pushButton_remote_status->setText("Online");
- // push buttons won't work with something like:
- // m_uiTabRun.pushButton_remote_status->setBackground(QColor(120, 255,
- // 120));
- m_uiTabRun.pushButton_remote_status->setStyleSheet(
- QString::fromStdString(g_styleSheetOnline));
- } else {
- m_uiTabRun.pushButton_remote_status->setText("Offline");
- m_uiTabRun.pushButton_remote_status->setStyleSheet(
- QString::fromStdString(g_styleSheetOffline));
- }
-}
-
-#ifndef _MSC_VER
-QDataStream &operator>>(QDataStream &stream, size_t &num) {
- qint64 i;
- stream >> i;
- if (QDataStream::Ok == stream.status()) {
- num = i;
- }
- return stream;
-}
-#endif
-
-inline QDataStream &operator>>(QDataStream &stream, std::string &str) {
- QString s;
- stream >> s;
- str = s.toStdString();
- return stream;
-}
-
-/// deserialize the remote part of the system settings, from a QDataStream <=
-/// QByteArray
-QDataStream &operator>>(QDataStream &stream, TomoSystemSettingsRemote &ssr) {
- // clang-format off
- stream >> ssr.m_basePathTomoData
- >> ssr.m_basePathReconScripts
- >> ssr.m_nodes
- >> ssr.m_cores;
- // clang-format on
-
- return stream;
-}
-
-/// deserialize the local part of the system settings, from a QDataStream <=
-/// QByteArray
-QDataStream &operator>>(QDataStream &stream, TomoSystemSettingsLocal &ssl) {
- // clang-format off
- stream >> ssl.m_basePathTomoData
- >> ssl.m_remoteDriveOrMountPoint
- >> ssl.m_reconScriptsPath
- >> ssl.m_externalInterpreterPath
- >> ssl.m_processes
- >> ssl.m_cores;
- // clang-format on
-
- return stream;
-}
-
-/// deserialize system settings, from a QDataStream <= QByteArray
-QDataStream &operator>>(QDataStream &stream, TomoSystemSettings &ss) {
- stream >> ss.m_local >> ss.m_remote;
- for (size_t i = 0; i < ss.m_pathComponents.size(); i++) {
- stream >> ss.m_pathComponents[i];
- }
- // clang-format off
- stream >> ss.m_samplesDirPrefix
- >> ss.m_flatsDirPrefix
- >> ss.m_darksDirPrefix
- >> ss.m_outputPathCompPreProcessed
- >> ss.m_outputPathCompReconst;
- // clang-format on
-
- return stream;
-}
-
-/// deserialize a filters settings, from a QDataStream <= QByteArray
-QDataStream &operator>>(QDataStream &stream, TomoReconFiltersSettings &fs) {
- // clang-format off
- stream >> fs.prep.normalizeByAirRegion
- >> fs.prep.normalizeByProtonCharge
- >> fs.prep.normalizeByFlats
- >> fs.prep.normalizeByDarks
- >> fs.prep.medianFilterWidth
- >> fs.prep.rotation
- >> fs.prep.maxAngle
- >> fs.prep.scaleDownFactor
- >> fs.postp.circMaskRadius
- >> fs.postp.cutOffLevel
- >> fs.outputPreprocImages;
- // clang-format on
- fs.prep.rotation *= 90;
-
- return stream;
-}
-
-/// deserialize an input paths configuration
-QDataStream &operator>>(QDataStream &stream, TomoPathsConfig &cfg) {
- QString samples;
- QString ob;
- bool obEnabled;
- QString darks;
- bool darksEnabled;
- stream >> samples >> ob >> obEnabled >> darks >> darksEnabled;
- cfg.updatePathSamples(samples.toStdString());
- cfg.updatePathOpenBeam(ob.toStdString(), obEnabled);
- cfg.updatePathDarks(darks.toStdString(), darksEnabled);
-
- return stream;
-}
-
-/**
- * Load the settings for the tabs and widgets of the interface. This
- * relies on Qt settings functionality (QSettings class).
- *
- * This includes setting the default browsing directory to be the
- * default save directory.
- */
-void TomographyIfaceViewQtGUI::readSettings() {
- QSettings qs;
- qs.beginGroup(QString::fromStdString(m_settingsGroup));
-
- m_settings.SCARFBasePath =
- qs.value("SCARF-base-path",
- QString::fromStdString(m_settings.SCARFBasePath))
- .toString()
- .toStdString();
- // WARNING: it's critical to keep 'false' as default value, otherwise
- // tests and scripted runs may have issues. The CI builds could get stuck
- // when closing this interface.
- m_settings.onCloseAskForConfirmation =
- qs.value("on-close-ask-for-confirmation", false).toBool();
-
- m_settings.useKeepAlive =
- qs.value("use-keep-alive", m_settings.useKeepAlive).toInt();
-
- // User parameters for reconstructions
- m_setupExperimentRef = qs.value("experiment-reference",
- QString::fromStdString(g_defExperimentRef))
- .toString()
- .toStdString();
-
- m_uiTabRun.lineEdit_SCARF_username->setText(
- qs.value("SCARF-remote-username",
- QString::fromStdString(
- Mantid::Kernel::ConfigService::Instance().getUsername()))
- .toString());
-
- m_uiTabSystemSettings.lineEdit_remote_base_path_data->setText(
- QString::fromStdString(m_settings.SCARFBasePath));
- QByteArray rawSysSettings = qs.value("system-settings").toByteArray();
- QDataStream streamSys(rawSysSettings);
- TomoSystemSettings sysSettings;
- streamSys >> sysSettings;
- if (QDataStream::Ok == streamSys.status()) {
- updateSystemSettingsTabFields(sysSettings);
- } else {
- updateSystemSettingsTabFields(TomoSystemSettings());
- }
-
- // Get input paths (sample/dark/flats)
- QByteArray rawInputPaths =
- qs.value("input-paths-samples-flats-darks").toByteArray();
- QDataStream streamPaths(rawInputPaths);
- TomoPathsConfig inputPaths;
- streamPaths >> inputPaths;
- if (QDataStream::Ok == streamPaths.status()) {
- updatePathsConfig(inputPaths);
- } else {
- // factory defaults / blank/unknown paths
- updatePathsConfig(TomoPathsConfig());
- }
-
- // Get all the pre-/post-processing options from a stream
- QByteArray rawFiltersSettings = qs.value("filters-settings").toByteArray();
- QDataStream streamFilters(rawFiltersSettings);
- TomoReconFiltersSettings filtersSettings;
- streamFilters >> filtersSettings;
- if (QDataStream::Ok == streamFilters.status()) {
- setPrePostProcSettings(filtersSettings);
- } else {
- // something wrong in the settings previously saved => go back to factory
- // defaults
- setPrePostProcSettings(TomoReconFiltersSettings());
- }
-
- int pathSize = qs.beginReadArray("path-default-add-for-python");
- for (int i = 0; i < pathSize; ++i) {
- qs.setArrayIndex(i);
- m_defAddPathPython.push_back(
- qs.value("value", "").toString().toStdString());
- }
- if (0 == m_defAddPathPython.size())
- m_defAddPathPython = g_defAddPathPython;
- qs.endArray();
-
- // general GUI state
- m_ui.tabMain->setCurrentIndex(qs.value("selected-tab-index").toInt());
-
- restoreGeometry(qs.value("interface-win-geometry").toByteArray());
-
- readSettingsEnergy();
-
- qs.endGroup();
-}
-
-#ifndef _MSC_VER
-QDataStream &operator<<(QDataStream &stream, size_t const &num) {
- return stream << static_cast<qint64>(num);
-}
-#endif
-
-inline QDataStream &operator<<(QDataStream &stream, std::string const &str) {
- stream << QString::fromStdString(str);
- return stream;
-}
-
-/// serialize the local part of the system settings as a QDataStream =>
-/// QByteArray
-QDataStream &operator<<(QDataStream &stream,
- TomoSystemSettingsLocal const &ssl) {
- // clang-format off
- stream << ssl.m_basePathTomoData
- << ssl.m_remoteDriveOrMountPoint
- << ssl.m_reconScriptsPath
- << ssl.m_externalInterpreterPath
- << ssl.m_processes
- << ssl.m_cores;
- // clang-format on
-
- return stream;
-}
-
-/// serialize the remote part of the system settings as a QDataStream =>
-/// QByteArray
-QDataStream &operator<<(QDataStream &stream,
- TomoSystemSettingsRemote const &ssr) {
- // clang-format off
- stream << ssr.m_basePathTomoData
- << ssr.m_basePathReconScripts
- << ssr.m_nodes
- << ssr.m_cores;
- // clang-format on
-
- return stream;
-}
-
-/// serialize system settings as a QDataStream => QByteArray
-QDataStream &operator<<(QDataStream &stream, TomoSystemSettings const &ss) {
- // clang-format off
- stream << ss.m_local << ss.m_remote;
- for (const auto comp : ss.m_pathComponents) {
- stream << comp;
- }
- stream << ss.m_samplesDirPrefix
- << ss.m_flatsDirPrefix
- << ss.m_darksDirPrefix
- << ss.m_outputPathCompPreProcessed
- << ss.m_outputPathCompReconst;
- // clang-format on
-
- return stream;
-}
-
-/// serialize a filters settings, as a QDataStream => QByteArray
-QDataStream &operator<<(QDataStream &stream,
- TomoReconFiltersSettings const &fs) {
- // clang-format off
- stream << fs.prep.normalizeByAirRegion
- << fs.prep.normalizeByProtonCharge
- << fs.prep.normalizeByFlats
- << fs.prep.normalizeByDarks
- << fs.prep.medianFilterWidth
- << (fs.prep.rotation/90)
- << fs.prep.maxAngle
- << fs.prep.scaleDownFactor
- << fs.postp.circMaskRadius
- << fs.postp.cutOffLevel
- << fs.outputPreprocImages;
- // clang-format on
-
- return stream;
-}
-
-/// serialize an input paths config (samples/darks/flats)
-QDataStream &operator<<(QDataStream &stream, TomoPathsConfig const &cfg) {
- // clang-format off
- stream << QString::fromStdString(cfg.pathSamples())
- << QString::fromStdString(cfg.pathOpenBeam())
- << cfg.m_pathOpenBeamEnabled
- << QString::fromStdString(cfg.pathDarks())
- << cfg.m_pathDarkEnabled;
- // clang-format on
-
- return stream;
-}
-
-/**
- * Save persistent settings. Qt based.
- */
-void TomographyIfaceViewQtGUI::saveSettings() const {
- QSettings qs;
- qs.beginGroup(QString::fromStdString(m_settingsGroup));
-
- saveSettingsEnergy();
-
- qs.setValue("on-close-ask-for-confirmation",
- m_settings.onCloseAskForConfirmation);
- qs.setValue("use-keep-alive", m_settings.useKeepAlive);
-
- qs.setValue("experiment-reference",
- QString::fromStdString(m_setupExperimentRef));
-
- qs.setValue("SCARF-remote-username",
- m_uiTabRun.lineEdit_SCARF_username->text());
-
- // Save all the SystemSettings via a Qt stream
- QByteArray sysSettings;
- QDataStream streamSys(&sysSettings, QIODevice::WriteOnly);
- streamSys << systemSettings();
- qs.setValue("system-settings", sysSettings);
- QString s = m_uiTabSystemSettings.lineEdit_remote_base_path_data->text();
- qs.setValue("SCARF-base-path", s);
-
- // Save input data paths (samples/flats/darks, etc.)
- QByteArray pathsConfig;
- QDataStream streamPaths(&pathsConfig, QIODevice::WriteOnly);
- streamPaths << currentPathsConfig();
- qs.setValue("input-paths-samples-flats-darks", pathsConfig);
-
- // Save all the pre-/post-processing options through a stream
- QByteArray filtersSettings;
- QDataStream streamFilters(&filtersSettings, QIODevice::WriteOnly);
- streamFilters << grabPrePostProcSettings();
- qs.setValue("filters-settings", filtersSettings);
-
- // User parameters for reconstructions
- qs.setValue("RB-number", QString::fromStdString(m_setupExperimentRef));
-
- qs.beginWriteArray("path-default-add-for-python");
- for (size_t i = 0; i < m_defAddPathPython.size(); ++i) {
- qs.setArrayIndex(static_cast<int>(i));
- qs.setValue("value", QString::fromStdString(m_defAddPathPython[i]));
- }
- qs.endArray();
-
- // general GUI status
- qs.setValue("selected-tab-index", m_ui.tabMain->currentIndex());
-
- qs.setValue("interface-win-geometry", saveGeometry());
-
- qs.endGroup();
-}
-
-/// needs to at least update the 'tool' combo box
-void TomographyIfaceViewQtGUI::compResourceIndexChanged(int /* i */) {
- QComboBox *rt = m_uiTabRun.comboBox_run_compute_resource;
- if (!rt)
- return;
-
- m_currentComputeRes = rt->currentText().toStdString();
- m_presenter->notify(ITomographyIfacePresenter::CompResourceChanged);
-}
-
-void TomographyIfaceViewQtGUI::runToolIndexChanged(int /* i */) {
- QComboBox *rt = m_uiTabRun.comboBox_run_tool;
- m_currentReconTool = rt->currentText().toStdString();
- m_presenter->notify(ITomographyIfacePresenter::ToolChanged);
-}
-
-void TomographyIfaceViewQtGUI::enableConfigTool(bool on) {
- m_uiTabRun.pushButton_run_tool_setup->setEnabled(on);
-}
-
-void TomographyIfaceViewQtGUI::enableRunReconstruct(bool on) {
- m_uiTabRun.pushButton_reconstruct->setEnabled(on);
-}
-
-/**
- * Update or toggle on/off the log in/out control widgets (like
- * enabling/disabling push buttons, updating a display that tells the
- * user if we're logged in, etc.).
- *
- * @param loggedIn Status (true when logged in)
- */
-void TomographyIfaceViewQtGUI::updateLoginControls(bool loggedIn) {
- m_uiTabRun.pushButton_SCARF_login->setEnabled(!loggedIn);
- m_uiTabRun.pushButton_SCARF_logout->setEnabled(loggedIn);
-
- enableLoggedActions(loggedIn);
- updateCompResourceStatus(loggedIn);
-}
-
-/**
- * Slot for when the 'login' or similar button is clicked (released)
- */
-void TomographyIfaceViewQtGUI::SCARFLoginClicked() {
- m_presenter->notify(ITomographyIfacePresenter::LogInRequested);
-}
-
-/**
- * Slot for when the 'logout' or similar button is clicked (released)
- */
-void TomographyIfaceViewQtGUI::SCARFLogoutClicked() {
- m_presenter->notify(ITomographyIfacePresenter::LogOutRequested);
-}
-
-/**
- * Slot for when the user requests to open the tool specific setup dialog.
- */
-void TomographyIfaceViewQtGUI::toolSetupClicked() {
- QComboBox *rt = m_uiTabRun.comboBox_run_tool;
- if (!rt)
- return;
-
- m_presenter->notify(ITomographyIfacePresenter::SetupReconTool);
-}
-
-/**
- * Takes and displays a new configuration of paths to
- * sample/flats/dark input images.
- */
-void TomographyIfaceViewQtGUI::updatePathsConfig(const TomoPathsConfig &cfg) {
- m_uiTabRun.lineEdit_path_samples->setText(
- QString::fromStdString(cfg.pathSamples()));
- m_uiTabRun.lineEdit_path_flats->setText(
- QString::fromStdString(cfg.pathOpenBeam()));
- m_uiTabRun.checkBox_path_flats->setChecked(cfg.m_pathOpenBeamEnabled);
- m_uiTabRun.lineEdit_path_darks->setText(
- QString::fromStdString(cfg.pathDarks()));
- m_uiTabRun.checkBox_path_darks->setChecked(cfg.m_pathDarkEnabled);
- m_pathsConfig = cfg;
-}
-
-/**
- * Updates the view/forms with new system settings (local and remote,
- * including multiple paths and path components)
- */
-void TomographyIfaceViewQtGUI::updateSystemSettingsTabFields(
- const TomoSystemSettings &setts) {
- // paths and related
- m_uiTabSystemSettings.lineEdit_path_comp_1st->setText(
- QString::fromStdString(setts.m_pathComponents[0]));
- // Not modifyable at the moment: m_uiTabSystemSettings.lineEdit_path_comp_2nd;
- // Not modifyable at the moment: m_uiTabSystemSettings.lineEdit_path_comp_3rd;
- m_uiTabSystemSettings.lineEdit_path_comp_input_samples->setText(
- QString::fromStdString(setts.m_samplesDirPrefix));
-
- m_uiTabSystemSettings.lineEdit_path_comp_input_flats->setText(
- QString::fromStdString(setts.m_flatsDirPrefix));
-
- m_uiTabSystemSettings.lineEdit_path_comp_input_darks->setText(
- QString::fromStdString(setts.m_darksDirPrefix));
-
- m_uiTabSystemSettings.lineEdit_path_comp_out_preprocessed->setText(
- QString::fromStdString(setts.m_outputPathCompPreProcessed));
-
- m_uiTabSystemSettings.lineEdit_path_comp_out_processed->setText(
- QString::fromStdString(setts.m_outputPathCompReconst));
-
- m_uiTabSystemSettings.lineEdit_remote_base_path_data->setText(
- QString::fromStdString(setts.m_remote.m_basePathTomoData));
-
- m_uiTabSystemSettings.lineEdit_remote_scripts_base_dir->setText(
- QString::fromStdString(setts.m_remote.m_basePathReconScripts));
-
- m_uiTabSystemSettings.lineEdit_on_local_data_drive_or_path->setText(
- QString::fromStdString(setts.m_local.m_basePathTomoData));
-
- m_uiTabSystemSettings.lineEdit_on_local_remote_data_drive_path->setText(
- QString::fromStdString(setts.m_local.m_remoteDriveOrMountPoint));
-
- // scripts and processes
- m_uiTabSystemSettings.spinBox_remote_nodes->setValue(setts.m_remote.m_nodes);
- m_uiTabSystemSettings.spinBox_remote_cores->setValue(setts.m_remote.m_cores);
-
- m_uiTabSystemSettings.spinBox_local_processes->setValue(
- setts.m_local.m_processes);
- m_uiTabSystemSettings.spinBox_local_cores->setValue(setts.m_local.m_cores);
-
- m_uiTabSystemSettings.lineEdit_local_recon_scripts->setText(
- QString::fromStdString(setts.m_local.m_reconScriptsPath));
- m_uiTabSystemSettings.lineEdit_local_external_interpreter->setText(
- QString::fromStdString(setts.m_local.m_externalInterpreterPath));
-}
-
-/**
- * Displays and gets the results of a tool specific configuration dialog.
- *
- * @param dialog The pointer to the current dialog
- */
-void TomographyIfaceViewQtGUI::showToolConfig(
- TomoToolConfigDialogBase &dialog) {
-
- // execute also intiialises all the parts of the GUI
- dialog.initialiseGUIandExecute();
-}
-
-/**
- * Slot - when the user clicks the 'reconstruct data' or similar button.
- */
-void TomographyIfaceViewQtGUI::reconstructClicked() {
- m_presenter->notify(ITomographyIfacePresenter::RunReconstruct);
-}
-
-/**
- * Slot - when the user clicks the 'visualize job results' or similar button.
- */
-void TomographyIfaceViewQtGUI::runVisualizeClicked() {
- QTableWidget *tbl = m_uiTabRun.tableWidget_run_jobs;
- const int idCol = 2;
- QTableWidgetItem *hdr = tbl->horizontalHeaderItem(idCol);
- if ("ID" != hdr->text())
- throw std::runtime_error("Expected to get the Id of jobs from the "
- "second column of the table of jobs, but I "
- "found this at that column: " +
- hdr->text().toStdString());
-
- QModelIndexList idSel = tbl->selectionModel()->selectedRows();
- if (idSel.count() <= 0)
- return;
-
- const std::string id = tbl->item(idSel[0].row(), idCol)->text().toStdString();
- if (idSel.count() > 1) {
- m_processingJobsIDs.clear();
- m_processingJobsIDs.push_back(id);
- m_presenter->notify(ITomographyIfacePresenter::VisualizeJobFromTable);
- }
-}
-
-/**
- * Slot - when the user clicks the 'cancel job' or similar button.
- */
-void TomographyIfaceViewQtGUI::jobCancelClicked() {
- m_processingJobsIDs.clear();
- QTableWidget *tbl = m_uiTabRun.tableWidget_run_jobs;
- const int idCol = 2;
- QTableWidgetItem *hdr = tbl->horizontalHeaderItem(idCol);
- if ("ID" != hdr->text())
- throw std::runtime_error("Expected to get the Id of jobs from the "
- "second column of the table of jobs, but I "
- "found this at that column: " +
- hdr->text().toStdString());
-
- QModelIndexList idSel = tbl->selectionModel()->selectedRows();
- for (int i = 0; i < idSel.count(); ++i) {
- const std::string id =
- tbl->item(idSel[i].row(), idCol)->text().toStdString();
- m_processingJobsIDs.push_back(id);
- }
-
- m_presenter->notify(ITomographyIfacePresenter::CancelJobFromTable);
-}
-
-/**
- * Slot - when the user clicks the 'refresh job list/table' or similar button.
- */
-void TomographyIfaceViewQtGUI::jobTableRefreshClicked() {
- m_presenter->notify(ITomographyIfacePresenter::RefreshJobs);
-}
-
-/**
- * Update the job status and general info table/tree from the info
- * stored in this class' data members, which ideally should have
- * information from a recent query to the server.
- */
-void TomographyIfaceViewQtGUI::updateJobsInfoDisplay(
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &status,
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &
- localStatus) {
-
- QTableWidget *t = m_uiTabRun.tableWidget_run_jobs;
- bool sort = t->isSortingEnabled();
- t->setRowCount(static_cast<int>(status.size() + localStatus.size()));
-
- for (size_t i = 0; i < status.size(); ++i) {
- int ii = static_cast<int>(i);
- t->setItem(ii, 0,
- new QTableWidgetItem(QString::fromStdString(g_SCARFName)));
- t->setItem(ii, 1,
- new QTableWidgetItem(QString::fromStdString(status[i].name)));
- t->setItem(ii, 2,
- new QTableWidgetItem(QString::fromStdString(status[i].id)));
-
- t->setItem(ii, 3,
- new QTableWidgetItem(QString::fromStdString(status[i].status)));
-
- // beware "Exit" is called "Exited" on the web portal, but the REST
- // responses
- // call it "Exit"
- if (std::string::npos != status[i].status.find("Exit") ||
- std::string::npos != status[i].status.find("Suspend"))
- t->item(ii, 3)->setBackground(QColor(255, 120, 120)); // Qt::red
- else if (std::string::npos != status[i].status.find("Pending"))
- t->item(ii, 3)->setBackground(QColor(150, 150, 150)); // Qt::gray
- else if (std::string::npos != status[i].status.find("Running") ||
- std::string::npos != status[i].status.find("Active"))
- t->item(ii, 3)->setBackground(QColor(120, 120, 255)); // Qt::blue
- else if (std::string::npos != status[i].status.find("Finished") ||
- std::string::npos != status[i].status.find("Done"))
- t->item(ii, 3)->setBackground(QColor(120, 255, 120)); // Qt::green
-
- t->setItem(ii, 4,
- new QTableWidgetItem(QString::fromStdString(status[i].cmdLine)));
- }
-
- // Local processes
- for (size_t i = 0; i < localStatus.size(); ++i) {
-
- // This won't work well, at least on windows.
- // bool runs = Poco::isRunning(
- // boost::lexical_cast<Poco::Process::PID>(localStatus[i].id));
- // if (!runs)
- // m_localStatus[i].status = "Done";
-
- int ii = static_cast<int>(status.size() + i);
- t->setItem(ii, 0, new QTableWidgetItem(QString::fromStdString("local")));
- t->setItem(ii, 1, new QTableWidgetItem(
- QString::fromStdString(localStatus[i].name)));
- t->setItem(ii, 2,
- new QTableWidgetItem(QString::fromStdString(localStatus[i].id)));
-
- t->setItem(ii, 3, new QTableWidgetItem(
- QString::fromStdString(localStatus[i].status)));
-
- // beware "Exit" is called "Exited" on the web portal, but the
- // REST responses call it "Exit"
- if (std::string::npos != localStatus[i].status.find("Exit") ||
- std::string::npos != localStatus[i].status.find("Suspend"))
- t->item(ii, 3)->setBackground(QColor(255, 120, 120)); // Qt::red
- else if (std::string::npos != localStatus[i].status.find("Pending"))
- t->item(ii, 3)->setBackground(QColor(150, 150, 150)); // Qt::gray
- else if (std::string::npos != localStatus[i].status.find("Running") ||
- std::string::npos != localStatus[i].status.find("Active"))
- t->item(ii, 3)->setBackground(QColor(120, 120, 255)); // Qt::blue
- else if (std::string::npos != localStatus[i].status.find("Finished") ||
- std::string::npos != localStatus[i].status.find("Done"))
- t->item(ii, 3)->setBackground(QColor(120, 255, 120)); // Qt::green
-
- t->setItem(ii, 4, new QTableWidgetItem(
- QString::fromStdString(localStatus[i].cmdLine)));
- }
-
- t->setSortingEnabled(sort);
-}
-
-std::string TomographyIfaceViewQtGUI::getUsername() const {
- if (g_SCARFName ==
- m_uiTabRun.comboBox_run_compute_resource->currentText().toStdString())
- return m_uiTabRun.lineEdit_SCARF_username->text().toStdString();
- else
- return "invalid";
-}
-
-/**
- * Retrieve the username being used for the selected compute resource.
- *
- * @return Username ready to be used in remote queries
- */
-std::string TomographyIfaceViewQtGUI::getPassword() const {
- if (g_SCARFName ==
- m_uiTabRun.comboBox_run_compute_resource->currentText().toStdString())
- return m_uiTabRun.lineEdit_SCARF_password->text().toStdString();
- else
- return "none";
-}
-
-void TomographyIfaceViewQtGUI::flatsPathCheckStatusChanged(int status) {
- bool enable(0 != status);
-
- // grab new value and enable/disable related widgets
- m_pathsConfig.m_pathOpenBeamEnabled = enable;
- m_uiTabRun.lineEdit_path_flats->setEnabled(enable);
- m_uiTabRun.pushButton_flats_dir->setEnabled(enable);
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsChanged);
-}
-
-void TomographyIfaceViewQtGUI::darksPathCheckStatusChanged(int status) {
- bool enable(0 != status);
-
- m_pathsConfig.m_pathDarkEnabled = enable;
- m_uiTabRun.lineEdit_path_darks->setEnabled(enable);
- m_uiTabRun.pushButton_darks_dir->setEnabled(enable);
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsChanged);
-}
-
-void TomographyIfaceViewQtGUI::samplesPathBrowseClicked() {
- std::string str;
- processPathBrowseClick(m_uiTabRun.lineEdit_path_samples, str);
- if (!str.empty()) {
- m_pathsConfig.updatePathSamples(str);
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsEditedByUser);
- }
-}
-
-void TomographyIfaceViewQtGUI::flatsPathBrowseClicked() {
- std::string str;
- processPathBrowseClick(m_uiTabRun.lineEdit_path_flats, str);
- if (!str.empty()) {
- m_pathsConfig.updatePathOpenBeam(
- str, m_uiTabRun.checkBox_path_flats->isChecked());
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsChanged);
- }
-}
-
-void TomographyIfaceViewQtGUI::darksPathBrowseClicked() {
- std::string str;
- processPathBrowseClick(m_uiTabRun.lineEdit_path_darks, str);
- if (!str.empty()) {
- m_pathsConfig.updatePathDarks(str,
- m_uiTabRun.checkBox_path_darks->isChecked());
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsChanged);
- }
-}
-
-void TomographyIfaceViewQtGUI::samplesPathEditedByUser() {
- const std::string path =
- m_uiTabRun.lineEdit_path_samples->text().toStdString();
- m_pathsConfig.updatePathSamples(path);
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsEditedByUser);
-}
-
-void TomographyIfaceViewQtGUI::flatsPathEditedByUser() {
- const std::string path = m_uiTabRun.lineEdit_path_flats->text().toStdString();
- m_pathsConfig.updatePathOpenBeam(path,
- m_uiTabRun.checkBox_path_flats->isChecked());
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsChanged);
-}
-
-void TomographyIfaceViewQtGUI::darksPathEditedByUser() {
- const std::string path = m_uiTabRun.lineEdit_path_darks->text().toStdString();
- m_pathsConfig.updatePathDarks(path,
- m_uiTabRun.checkBox_path_flats->isChecked());
- m_presenter->notify(ITomographyIfacePresenter::TomoPathsChanged);
-}
-
-void TomographyIfaceViewQtGUI::browseLocalInOutDirClicked() {
- checkUserBrowseDir(
- m_uiTabSystemSettings.lineEdit_on_local_data_drive_or_path);
-}
-
-void TomographyIfaceViewQtGUI::browseLocalRemoteDriveOrPath() {
- checkUserBrowseDir(
- m_uiTabSystemSettings.lineEdit_on_local_remote_data_drive_path);
-}
-
-void TomographyIfaceViewQtGUI::browseLocalReconScriptsDirClicked() {
- checkUserBrowseDir(m_uiTabSystemSettings.lineEdit_local_recon_scripts,
- "Select location of scripts (scripts subdirectory/folder "
- "in the Mantid installation",
- false);
- systemSettingsEdited();
-}
-
-void TomographyIfaceViewQtGUI::browseLocalExternalInterpreterClicked() {
- checkUserBrowseFile(m_uiTabSystemSettings.lineEdit_local_external_interpreter,
- "Select interpreter executable", false);
- systemSettingsEdited();
-}
-
-/**
- * Get path from user and update a line edit and a variable.
- *
- * @param le a line edit where the path is shown.
- *
- * @param data variable where the path is stored (in addition to the line
- * edit object).
- */
-void TomographyIfaceViewQtGUI::processPathBrowseClick(QLineEdit *le,
- std::string &data) {
- QString algPrev =
- MantidQt::API::AlgorithmInputHistory::Instance().getPreviousDirectory();
- /*
- // This would remember every widget's old value, and not the last path
- QString prev;
- if (le->text().isEmpty()) {
- prev = algPrev;
- } else {
- prev = le->text();
- }
- */
- QString prev = algPrev;
-
- QString path(QFileDialog::getExistingDirectory(
- this, tr("Open directory/folder"), prev));
-
- if (!path.isEmpty()) {
- le->setText(path);
- data = path.toStdString();
-
- MantidQt::API::AlgorithmInputHistory::Instance().setPreviousDirectory(path);
- }
-}
-
-TomoReconFiltersSettings TomographyIfaceViewQtGUI::prePostProcSettings() const {
- return grabPrePostProcSettings();
-}
-
-TomoReconFiltersSettings
-TomographyIfaceViewQtGUI::grabPrePostProcSettings() const {
- TomoReconFiltersSettings opts;
-
- // pre-processing
- opts.prep.normalizeByAirRegion =
- m_uiTabFilters.checkBox_normalize_by_air_region->isChecked();
-
- // TODOVIEW
- // m_uiTabFilters.checkBox_normalize_by_proton_charge is disabled for now
- opts.prep.normalizeByProtonCharge = false;
-
- opts.prep.normalizeByFlats =
- m_uiTabFilters.checkBox_normalize_by_flats->isChecked();
-
- opts.prep.normalizeByDarks =
- m_uiTabFilters.checkBox_normalize_by_darks->isChecked();
-
- // TODOVIEW
- // m_uiTabFilters.checkBox_corrections_MCP_detector is disabled for now
-
- opts.prep.medianFilterWidth = static_cast<size_t>(
- m_uiTabFilters.spinBox_prep_median_filter_width->value());
-
- opts.prep.rotation =
- 90 * m_uiTabFilters.comboBox_prep_rotation->currentIndex();
-
- opts.prep.maxAngle = m_uiTabFilters.doubleSpinBox_prep_max_angle->value();
-
- opts.prep.scaleDownFactor =
- static_cast<size_t>(m_uiTabFilters.spinBox_prep_scale_factor->value());
-
- // post-processing
- opts.postp.circMaskRadius =
- m_uiTabFilters.doubleSpinBox_post_circ_mask->value();
-
- opts.postp.cutOffLevel = m_uiTabFilters.doubleSpinBox_post_cutoff->value();
-
- // outputs
- opts.outputPreprocImages =
- m_uiTabFilters.checkBox_out_preproc_images->isChecked();
-
- return opts;
-}
-
-void TomographyIfaceViewQtGUI::setPrePostProcSettings(
- const TomoReconFiltersSettings &opts) {
-
- // pre-processing
- m_uiTabFilters.checkBox_normalize_by_air_region->setChecked(
- opts.prep.normalizeByAirRegion);
-
- m_uiTabFilters.checkBox_normalize_by_proton_charge->setChecked(
- opts.prep.normalizeByProtonCharge);
-
- m_uiTabFilters.checkBox_normalize_by_flats->setChecked(
- opts.prep.normalizeByFlats);
-
- m_uiTabFilters.checkBox_normalize_by_darks->setChecked(
- opts.prep.normalizeByDarks);
-
- m_uiTabFilters.spinBox_prep_median_filter_width->setValue(
- static_cast<int>(opts.prep.medianFilterWidth));
-
- m_uiTabFilters.comboBox_prep_rotation->setCurrentIndex(
- static_cast<int>(opts.prep.rotation / 90));
-
- m_uiTabFilters.doubleSpinBox_prep_max_angle->setValue(opts.prep.maxAngle);
-
- m_uiTabFilters.spinBox_prep_scale_factor->setValue(
- static_cast<int>(opts.prep.scaleDownFactor));
-
- // post-processing
- m_uiTabFilters.doubleSpinBox_post_circ_mask->setValue(
- opts.postp.circMaskRadius);
-
- m_uiTabFilters.doubleSpinBox_post_cutoff->setValue(opts.postp.cutOffLevel);
-
- // outputs
- m_uiTabFilters.checkBox_out_preproc_images->setChecked(
- opts.outputPreprocImages);
-}
-
-TomoSystemSettings TomographyIfaceViewQtGUI::systemSettings() const {
- return grabSystemSettingsFromUser();
-}
-
-TomoSystemSettings
-TomographyIfaceViewQtGUI::grabSystemSettingsFromUser() const {
- TomoSystemSettings setts;
-
- // paths and related
- setts.m_pathComponents[0] =
- m_uiTabSystemSettings.lineEdit_path_comp_1st->text().toStdString();
- // Not modifiable at the moment:
- // m_uiTabSystemSettings.lineEdit_path_comp_2nd;
- // Not modifiable at the moment:
- // m_uiTabSystemSettings.lineEdit_path_comp_3rd;
- setts.m_samplesDirPrefix =
- m_uiTabSystemSettings.lineEdit_path_comp_input_samples->text()
- .toStdString();
- setts.m_flatsDirPrefix =
- m_uiTabSystemSettings.lineEdit_path_comp_input_flats->text()
- .toStdString();
- setts.m_darksDirPrefix =
- m_uiTabSystemSettings.lineEdit_path_comp_input_darks->text()
- .toStdString();
-
- setts.m_outputPathCompPreProcessed =
- m_uiTabSystemSettings.lineEdit_path_comp_out_preprocessed->text()
- .toStdString();
- setts.m_outputPathCompReconst =
- m_uiTabSystemSettings.lineEdit_path_comp_out_processed->text()
- .toStdString();
-
- setts.m_remote.m_basePathTomoData =
- m_uiTabSystemSettings.lineEdit_remote_base_path_data->text()
- .toStdString();
- setts.m_remote.m_basePathReconScripts =
- m_uiTabSystemSettings.lineEdit_remote_scripts_base_dir->text()
- .toStdString();
-
- setts.m_local.m_basePathTomoData =
- m_uiTabSystemSettings.lineEdit_on_local_data_drive_or_path->text()
- .toStdString();
- setts.m_local.m_remoteDriveOrMountPoint =
- m_uiTabSystemSettings.lineEdit_on_local_remote_data_drive_path->text()
- .toStdString();
-
- // scripts and processes
- setts.m_remote.m_nodes = m_uiTabSystemSettings.spinBox_remote_nodes->value();
- setts.m_remote.m_cores = m_uiTabSystemSettings.spinBox_remote_cores->value();
-
- setts.m_local.m_processes =
- m_uiTabSystemSettings.spinBox_local_processes->value();
- setts.m_local.m_cores = m_uiTabSystemSettings.spinBox_local_cores->value();
-
- setts.m_local.m_reconScriptsPath =
- m_uiTabSystemSettings.lineEdit_local_recon_scripts->text().toStdString();
-
- setts.m_local.m_externalInterpreterPath =
- m_uiTabSystemSettings.lineEdit_local_external_interpreter->text()
- .toStdString();
-
- setts.m_experimentReference =
- m_uiTabRun.lineEdit_experiment_reference->text().toStdString();
-
- return setts;
-}
-
-void TomographyIfaceViewQtGUI::sendToOctopusVisClicked() {
- sendToVisTool("Octopus Visualization 3D", m_setupOctopusVisPath,
- g_defOctopusAppendPath);
-}
-
-void TomographyIfaceViewQtGUI::sendToParaviewClicked() {
- sendToVisTool("ParaView", m_setupParaviewPath, g_defParaviewAppendPath);
-}
-
-/**
- * Start a third party tool as a process. TODOVIEW: This is a very early
- * experimental implementation that should be moved out of this view.
- *
- * @param toolName Human understandable name of the tool/program
- * @param pathString Path where the tool is installed
- * @param appendBin string to append to the path if required, example:
- * bin/tool.exe
- */
-void TomographyIfaceViewQtGUI::sendToVisTool(const std::string &toolName,
- const std::string &pathString,
- const std::string &appendBin) {
- // prepare external tool executable path
- Poco::Path tmpPath(pathString);
- if (!appendBin.empty()) {
- tmpPath.append(appendBin);
- }
- const std::string toolPath = tmpPath.toString();
-
- // get path to pass as parameter
- const QFileSystemModel *model = dynamic_cast<QFileSystemModel *>(
- m_uiTabVisualize.treeView_files->model());
- if (!model)
- return;
-
- const auto selection =
- m_uiTabVisualize.treeView_files->selectionModel()->selectedIndexes();
- // just take the first selected item/directory
- if (selection.empty())
- return;
- QString selPath = model->filePath(selection.first());
-
- // Execute
- std::vector<std::string> args;
- args.push_back(selPath.toStdString());
-
- sendLog("Executing visualization tool: " + toolName + ". Executing: '" +
- toolPath + "', with parameters: '" + args[0] + "'.");
- try {
- Mantid::Kernel::ConfigService::Instance().launchProcess(toolPath, args);
- } catch (std::runtime_error &rexc) {
- sendLog("The execution of " + toolName + "failed. details: " +
- std::string(rexc.what()));
- userWarning("Execution failed ",
- "Coult not execute the tool. Error details: " +
- std::string(rexc.what()));
- }
-}
-
-void TomographyIfaceViewQtGUI::browseFilesToVisualizeClicked() {
- // an alternative would be to start from the current selection, instead of
- // the
- // current root:
- const QFileSystemModel *model = dynamic_cast<QFileSystemModel *>(
- m_uiTabVisualize.treeView_files->model());
- if (!model)
- return;
-
- const QString currentPath = model->rootPath();
- QString path(QFileDialog::getExistingDirectory(
- this, tr("Select root directory/folder with processed data "
- "(reconstructions) under it"),
- currentPath));
-
- if (!path.isEmpty()) {
- m_uiTabVisualize.treeView_files->setRootIndex(model->index(path));
- }
-}
-
-// helper that should go to the presenter. Makes sure that the path is
-// effectively readable
-std::string TomographyIfaceViewQtGUI::checkDefaultVisualizeDir(
- const std::string &basePath, const std::string &appendComp) {
- Poco::Path location(Poco::Path::expand(basePath));
- location.append(appendComp);
- Poco::File locationDir(location);
-
- std::string path;
- if (locationDir.exists()) {
- path = location.toString();
- } else {
- userWarning(
- "Cannot open the path",
- "Cannot open " + location.toString() +
- ". Please check that it exists on your system and it is readable.");
- }
-
- return path;
-}
-
-void TomographyIfaceViewQtGUI::defaultDirLocalVisualizeClicked() {
- const QFileSystemModel *model = dynamic_cast<QFileSystemModel *>(
- m_uiTabVisualize.treeView_files->model());
- if (!model)
- return;
-
- // TODOVIEW: this should be moved to presenter?
- std::string checkedPath = checkDefaultVisualizeDir(
- m_uiTabSystemSettings.lineEdit_on_local_data_drive_or_path->text()
- .toStdString(),
- m_uiTabSystemSettings.lineEdit_path_comp_1st->text().toStdString());
-
- const QString path = QString::fromStdString(checkedPath);
- if (!path.isEmpty()) {
- m_uiTabVisualize.treeView_files->setRootIndex(model->index(path));
- }
-}
-
-void TomographyIfaceViewQtGUI::defaultDirRemoteVisualizeClicked() {
- const QFileSystemModel *model = dynamic_cast<QFileSystemModel *>(
- m_uiTabVisualize.treeView_files->model());
- if (!model)
- return;
-
- // TODOVIEW: this should be moved to presenter?
- std::string checkedPath = checkDefaultVisualizeDir(
- m_uiTabSystemSettings.lineEdit_on_local_remote_data_drive_path->text()
- .toStdString(),
- m_uiTabSystemSettings.lineEdit_path_comp_1st->text().toStdString());
-
- const QString path = QString::fromStdString(checkedPath);
- if (!path.isEmpty()) {
- m_uiTabVisualize.treeView_files->setRootIndex(model->index(path));
- }
-}
-
-void TomographyIfaceViewQtGUI::browseVisToolParaviewClicked() {
- m_setupParaviewPath =
- checkUserBrowseDir(m_uiTabVisualize.lineEdit_paraview_location);
-}
-
-void TomographyIfaceViewQtGUI::browseVisToolOctopusClicked() {
- m_setupOctopusVisPath =
- checkUserBrowseDir(m_uiTabVisualize.lineEdit_octopus_vis_location);
-}
-
-/**
- * Show the usual pop-up asking for a directory. Checks if the
- * directory is valid, and updates the "previous/last directory" for
- * the next browse directory.
- *
- * @param le line edit object on which the path is displayed.
- *
- * @param userMsg message to show in the pop-up window
- *
- * @param remember whether to remember this path for the next time
- * that a browse-directory button is used. Normally you would set it
- * to true for the data paths, but not for things like executable,
- * external tools, etc.
- *
- * @return the directory path as a string
- */
-std::string TomographyIfaceViewQtGUI::checkUserBrowseDir(
- QLineEdit *le, const std::string &userMsg, bool remember) {
-
- QString prev;
- if (le->text().isEmpty()) {
- prev =
- MantidQt::API::AlgorithmInputHistory::Instance().getPreviousDirectory();
- } else {
- prev = le->text();
- }
-
- QString path(
- QFileDialog::getExistingDirectory(this, tr(userMsg.c_str()), prev));
-
- if (!path.isEmpty()) {
- le->setText(path);
- if (remember) {
- MantidQt::API::AlgorithmInputHistory::Instance().setPreviousDirectory(
- path);
- }
- }
-
- return path.toStdString();
-}
-
-/**
- * Show the usual pop-up asking for an (existing) file. Checks if a
- * file is actually selected, and updates the "previous/last directory" for
- * the next browse file/directory.
- *
- * @param le line edit object on which the path is displayed.
- *
- * @param userMsg message to show in the pop-up window
- *
- * @param remember whether to remember this path for the next time
- * that a browse-file/directory button is used. Normally you would set
- * it to true for the data paths, but not for things like executable,
- * external tools, etc.
- *
- * @return the file path as a string
- */
-std::string TomographyIfaceViewQtGUI::checkUserBrowseFile(
- QLineEdit *le, const std::string &userMsg, bool remember) {
-
- QString prev;
- if (le->text().isEmpty()) {
- prev =
- MantidQt::API::AlgorithmInputHistory::Instance().getPreviousDirectory();
- } else {
- prev = le->text();
- }
-
- QString path(QFileDialog::getOpenFileName(this, tr(userMsg.c_str()), prev));
-
- if (!path.isEmpty()) {
- le->setText(path);
- if (remember) {
- MantidQt::API::AlgorithmInputHistory::Instance().setPreviousDirectory(
- path);
- }
- }
-
- return path.toStdString();
-}
-
-void TomographyIfaceViewQtGUI::resetPrePostFilters() {
- auto reply = QMessageBox::question(
- this, "Reset Confirmation", "Are you sure you want to <br><strong>RESET "
- "ALL</strong> Filter settings?<br>This "
- "action cannot be undone!",
- QMessageBox::Yes | QMessageBox::No);
- // default constructors with factory defaults
- if (reply == QMessageBox::Yes) {
- TomoReconFiltersSettings def;
- setPrePostProcSettings(def);
- }
-}
-
-void TomographyIfaceViewQtGUI::systemSettingsEdited() {
- m_presenter->notify(ITomographyIfacePresenter::SystemSettingsUpdated);
-}
-
-void TomographyIfaceViewQtGUI::systemSettingsNumericEdited() {
- m_presenter->notify(ITomographyIfacePresenter::SystemSettingsUpdated);
-}
-
-void TomographyIfaceViewQtGUI::resetSystemSettings() {
- const auto title = "Reset Confirmation";
- const auto body = "Are you sure you want to <br><strong>RESET "
- "ALL</strong> System settings?<br>This "
- "action cannot be undone!";
- // default constructors with factory defaults
- if (userConfirmation(title, body)) {
- // From factory defaults
- TomoSystemSettings defaults;
- updateSystemSettingsTabFields(defaults);
- }
-}
-
-/**
- * Prompts the user for confirmation with a yes/no dialogue.
- * The body can use HTML formatting.
- *
- * @param title The title that the message has
- * @param body The body that the message has. This CAN use HTML formatting
- */
-bool TomographyIfaceViewQtGUI::userConfirmation(const std::string &title,
- const std::string &body) {
- auto reply = QMessageBox::question(this, QString::fromStdString(title),
- QString::fromStdString(body),
- QMessageBox::Yes | QMessageBox::No);
- return reply == QMessageBox::Yes;
-}
-
-/**
-* Show a warning message to the user (pop up)
-*
-* @param err Basic error title
-* @param description More detailed explanation, hints, additional
-* information, etc.
-*/
-void TomographyIfaceViewQtGUI::userWarning(const std::string &err,
- const std::string &description) {
- QMessageBox::warning(this, QString::fromStdString(err),
- QString::fromStdString(description), QMessageBox::Ok,
- QMessageBox::Ok);
-}
-
-void TomographyIfaceViewQtGUI::updatedExperimentReference() {
- m_setupExperimentRef =
- m_uiTabRun.lineEdit_experiment_reference->text().toStdString();
- // Might have to change: m_uiTabSystemSettings.lineEdit_local_out_recon_dir
- // as
- // well
-}
-
-/**
- * To log a message without waiting.
- */
-void TomographyIfaceViewQtGUI::sendLog(const std::string &msg) {
- m_logMsgs.push_back(msg);
- m_presenter->notify(ITomographyIfacePresenter::LogMsg);
- m_logMsgs.clear();
-}
-
-/**
- * Show an error (serious) message to the user (pop up)
- *
- * @param err Basic error title
- * @param description More detailed explanation, hints, additional
- * information, etc.
- */
-void TomographyIfaceViewQtGUI::userError(const std::string &err,
- const std::string &description) {
- QMessageBox::critical(this, QString::fromStdString(err),
- QString::fromStdString(description), QMessageBox::Ok,
- QMessageBox::Ok);
-}
-
-void TomographyIfaceViewQtGUI::closeEvent(QCloseEvent *event) {
- int answer = QMessageBox::AcceptRole;
-
- bool ask = m_settings.onCloseAskForConfirmation;
- if (ask) {
- QMessageBox msgBox;
- msgBox.setWindowTitle("Close the tomographic reconstruction interface");
- // with something like this, we'd have layout issues:
- // msgBox.setStandardButtons(QMessageBox::No | QMessageBox::Yes);
- // msgBox.setDefaultButton(QMessageBox::Yes);
- msgBox.setIconPixmap(QPixmap(":/win/unknown.png"));
- QCheckBox confirmCheckBox("Always ask for confirmation", &msgBox);
- confirmCheckBox.setCheckState(Qt::Checked);
- msgBox.layout()->addItem(new QSpacerItem(0, 0, QSizePolicy::Expanding));
- msgBox.layout()->addWidget(&confirmCheckBox);
- QPushButton *bYes = msgBox.addButton("Yes", QMessageBox::YesRole);
- bYes->setIcon(style()->standardIcon(QStyle::SP_DialogYesButton));
- QPushButton *bNo = msgBox.addButton("No", QMessageBox::NoRole);
- bNo->setIcon(style()->standardIcon(QStyle::SP_DialogNoButton));
- msgBox.setDefaultButton(bNo);
- msgBox.setText("You are about to close this interface");
- msgBox.setInformativeText(
- "If you close this interface you will need to log in again "
- "and you might loose some of the current state. Jobs running on "
- "remote "
- "compute resources will remain unaffected though. Are you sure?");
-
- m_settings.onCloseAskForConfirmation = confirmCheckBox.isChecked();
- answer = msgBox.exec();
- }
-
- if (answer == QMessageBox::AcceptRole) {
- // TODOVIEW? cleanup();
- m_presenter->notify(ITomographyIfacePresenter::ShutDown);
- event->accept();
- } else {
- event->ignore();
- }
-}
-
-void TomographyIfaceViewQtGUI::openHelpWin() {
- MantidQt::API::HelpWindow::showCustomInterface(
- NULL, QString("Tomographic_Reconstruction"));
-}
-
-void TomographyIfaceViewQtGUI::emitExternalProcessFinished(const QString &str) {
- emit externalProcessFinished(str);
-}
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomographyROIPresenter.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomographyROIPresenter.cpp
deleted file mode 100644
index f7fc10bd615..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomographyROIPresenter.cpp
+++ /dev/null
@@ -1,603 +0,0 @@
-#include "MantidAPI/AlgorithmManager.h"
-#include "MantidAPI/AnalysisDataService.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidQtAPI/BatchAlgorithmRunner.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyROIView.h"
-#include "MantidQtCustomInterfaces/Tomography/ImageStackPreParams.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyProcess.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyThread.h"
-
-using namespace MantidQt::CustomInterfaces;
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-namespace {
-Mantid::Kernel::Logger g_log("ImageROI");
-}
-
-const std::string TomographyROIPresenter::g_wsgName =
- "__tomography_gui_stack_fits_viewer_sample_images";
-const std::string TomographyROIPresenter::g_wsgFlatsName =
- "__tomography_gui_stack_fits_viewer_flat_images";
-const std::string TomographyROIPresenter::g_wsgDarksName =
- "__tomography_gui_stack_fits_viewer_dark_images";
-
-bool TomographyROIPresenter::g_warnIfUnexpectedFileExtensions = false;
-
-TomographyROIPresenter::TomographyROIPresenter(ITomographyROIView *view)
- : m_playStatus(false), m_stackPath(), m_view(view),
- m_model(new ImageStackPreParams()) {
- if (!m_view) {
- throw std::runtime_error("Severe inconsistency found. Presenter created "
- "with an empty/null view (tomography interface). "
- "Cannot continue.");
- }
- m_algRunner =
- Mantid::Kernel::make_unique<MantidQt::API::BatchAlgorithmRunner>();
-}
-
-TomographyROIPresenter::~TomographyROIPresenter() { cleanup(); }
-
-void TomographyROIPresenter::cleanup() {}
-
-void TomographyROIPresenter::notify(Notification notif) {
-
- switch (notif) {
-
- case ITomographyROIPresenter::Init:
- processInit();
- break;
-
- case ITomographyROIPresenter::BrowseImage:
- processBrowseImage();
- break;
-
- case ITomographyROIPresenter::BrowseStack:
- processBrowseStack();
- break;
-
- case ITomographyROIPresenter::ChangeImageType:
- processChangeImageType();
- break;
-
- case ITomographyROIPresenter::ChangeRotation:
- processChangeRotation();
- break;
-
- case ITomographyROIPresenter::UpdateImgIndex:
- processUpdateImgIndex();
- break;
-
- case ITomographyROIPresenter::PlayStartStop:
- processPlayStartStop();
- break;
-
- case ITomographyROIPresenter::UpdateColorMap:
- processUpdateColorMap();
- break;
-
- case ITomographyROIPresenter::ColorRangeUpdated:
- processColorRangeUpdated();
- break;
-
- case ITomographyROIPresenter::SelectCoR:
- processSelectCoR();
- break;
-
- case ITomographyROIPresenter::SelectROI:
- processSelectROI();
- break;
-
- case ITomographyROIPresenter::SelectNormalization:
- processSelectNormalization();
- break;
-
- case ITomographyROIPresenter::FinishedCoR:
- processFinishedCoR();
- break;
-
- case ITomographyROIPresenter::FinishedROI:
- processFinishedROI();
- break;
-
- case ITomographyROIPresenter::FinishedNormalization:
- processFinishedNormalization();
- break;
-
- case ITomographyROIPresenter::ResetCoR:
- processResetCoR();
- break;
-
- case ITomographyROIPresenter::ResetROI:
- processResetROI();
- break;
-
- case ITomographyROIPresenter::ResetNormalization:
- processResetNormalization();
- break;
-
- case ITomographyROIPresenter::ShutDown:
- processShutDown();
- break;
- }
-}
-
-void TomographyROIPresenter::processInit() {
- ImageStackPreParams p;
- m_view->setParams(p);
-}
-
-void TomographyROIPresenter::processBrowseImage() {
- const std::string path = m_view->askImagePath();
-
- if (path.empty())
- return;
-
- m_stackPath = path;
- processLoadSingleImage();
- m_view->imageOrStackLoaded(trimFileNameFromPath(path));
-}
-
-void TomographyROIPresenter::processBrowseStack() {
- const std::string path = m_view->askImagePath("Open directory");
-
- if (path.empty())
- return;
-
- // we're loading at stack so we trim the filename
- const std::string trimmedPath = trimFileNameFromPath(path);
-
- m_stackPath = trimmedPath;
- processLoadStackOfImages();
- m_view->imageOrStackLoaded(trimmedPath);
-}
-
-/**
- * Validates the input stack of images (directories and files), and
- * shows warning/error messages as needed. The outocome of the
- * validation can be checkec via isValid() on the returned stack of
- * images object.
- *
- * @param path user provided path to the stack of images
- *
- * @return a stack of images built from the path passed, not
- * necessarily correct (check with isValid())
- */
-StackOfImagesDirs
-TomographyROIPresenter::checkInputStack(const std::string &path) {
- StackOfImagesDirs soid(path, true);
-
- const std::string soiPath = soid.sampleImagesDir();
- if (soiPath.empty()) {
- m_view->userWarning("Error trying to find a stack of images",
- "Could not find the sample images directory. The stack "
- "of images is expected as: \n\n" +
- soid.description());
- } else if (!soid.isValid()) {
- m_view->userWarning("Error while checking/validating the stack of images",
- "The stack of images could not be loaded correctly. " +
- soid.status());
- }
-
- return soid;
-}
-
-void TomographyROIPresenter::processLoadSingleImage() {
- try {
- auto &ads = Mantid::API::AnalysisDataService::Instance();
- if (ads.doesExist(g_wsgName)) {
- ads.remove(g_wsgName);
- }
- if (ads.doesExist(g_wsgFlatsName)) {
- ads.remove(g_wsgFlatsName);
- }
- if (ads.doesExist(g_wsgDarksName)) {
- ads.remove(g_wsgDarksName);
- }
- } catch (std::runtime_error &rexc) {
- g_log.warning("There was a problem while trying to remove apparently "
- "existing workspaces. Error details: " +
- std::string(rexc.what()));
- }
-
- loadFITSImage(m_stackPath, g_wsgName);
- setupAlgorithmRunnerAfterLoad();
-}
-
-void TomographyROIPresenter::processLoadStackOfImages() {
- StackOfImagesDirs soid("");
- try {
- soid = checkInputStack(m_stackPath);
- } catch (std::exception &e) {
- // Poco::FileNotFoundException: this should never happen, unless
- // the open dir dialog misbehaves unexpectedly, or in tests
- m_view->userWarning("Error trying to open directories/files",
- "The path selected via the dialog cannot be openend or "
- "there was a problem while trying to access it. This "
- "is an unexpected inconsistency. Error details: " +
- std::string(e.what()));
- }
-
- if (!soid.isValid())
- return;
-
- std::vector<std::string> imgs = soid.sampleFiles();
- if (0 >= imgs.size()) {
- m_view->userWarning(
- "Error while trying to find image/projection files in the stack "
- "directories",
- "Could not find any (image) file in the samples subdirectory: " +
- soid.sampleImagesDir());
- return;
- }
-
- loadFITSStack(soid, g_wsgName, g_wsgFlatsName, g_wsgDarksName);
- m_stackFlats = nullptr;
- m_stackDarks = nullptr;
- setupAlgorithmRunnerAfterLoad();
-}
-
-void TomographyROIPresenter::setupAlgorithmRunnerAfterLoad() {
- // reset any previous connections
- m_algRunner.get()->disconnect();
- connect(m_algRunner.get(), SIGNAL(batchComplete(bool)), this,
- SLOT(finishedLoadStack(bool)), Qt::QueuedConnection);
-
- m_view->enableActions(false);
- m_algRunner->executeBatchAsync();
-}
-
-void TomographyROIPresenter::finishedLoadStack(bool error) {
- if (error) {
- m_view->userWarning("Could not load the stack of images",
-
- "There was a failure while running the Mantid "
- "algorithms that tried to load the stack of images. "
- "Please check the error logs for details.");
- m_view->enableActions(true);
- return;
- }
-
- const auto &ads = Mantid::API::AnalysisDataService::Instance();
- try {
- m_stackSamples = ads.retrieveWS<Mantid::API::WorkspaceGroup>(g_wsgName);
- } catch (std::exception &e) {
- m_view->userWarning("Could not load the stack of sample images",
-
- "Could not produce a workspace group for the "
- "stack of sample images. Cannot "
- "display this stack. Please check the error log "
- "for further details. Error when trying to "
- "retrieve the sample images workspace: " +
- std::string(e.what()));
- m_view->enableActions(true);
- return;
- }
-
- // TODO: could be useful to do a check like this on wsg->size()?
- // if (wsg &&
- // Mantid::API::AnalysisDataService::Instance().doesExist(wsg->name()) &&
- // wsg->size() > 0 && imgs.size() >= wsg->size()) {
- // return wsg;
- // } else {
- // return Mantid::API::WorkspaceGroup_sptr();
- // }
-
- try {
- m_stackSamples = ads.retrieveWS<Mantid::API::WorkspaceGroup>(g_wsgName);
- Mantid::API::MatrixWorkspace_sptr ws =
- ads.retrieveWS<Mantid::API::MatrixWorkspace>(
- m_stackSamples->getNames()[0]);
- } catch (std::exception &exc) {
- m_view->userWarning(
- "Failed to load contents for at least the first sample image",
- "Could not load image contents for the first image file. "
- "An unrecoverable error happened when trying to load the "
- "image contents. Cannot display it. Error details: " +
- std::string(exc.what()));
- m_view->enableActions(true);
- return;
- }
-
- size_t imgCount = m_stackSamples->size();
- if (0 == imgCount) {
- m_view->userWarning(
- "Failed to load any FITS images - directory structure issue",
- "Even though a directory apparently holding a stack of images was "
- "found, "
- "it was not possible to load any image file correctly from: " +
- m_stackPath);
- m_view->enableActions(true);
- return;
- }
-
- // check flats and darks
- try {
- if (ads.doesExist(g_wsgFlatsName)) {
- m_stackFlats =
- ads.retrieveWS<Mantid::API::WorkspaceGroup>(g_wsgFlatsName);
- }
- } catch (std::runtime_error &exc) {
- m_view->userWarning("Failed to load the stack of flat (open beam) images",
- "Could not produce a workspace group for the "
- "stack of flat images. Cannot "
- "display the flat images of this stack. "
- "Please check the error log "
- "for further details. Error when trying to "
- "retrieve the flat images workspace:" +
- std::string(exc.what()));
- }
-
- try {
- if (ads.doesExist(g_wsgDarksName)) {
- m_stackDarks =
- ads.retrieveWS<Mantid::API::WorkspaceGroup>(g_wsgDarksName);
- }
- } catch (std::runtime_error &exc) {
- m_view->userWarning(
- "Failed to load the stack of dark images",
- "Could not produce a workspace group for the "
- "stack of dark images. Cannot "
- "display the dark images of this stack. Please check the error log "
- "for further details. Error when trying to "
- "retrieve the dark images workspace:" +
- std::string(exc.what()));
- }
-
- m_view->showStack(m_stackSamples, m_stackFlats, m_stackDarks);
- m_view->enableActions(true);
-}
-
-void TomographyROIPresenter::processChangeImageType() {
- m_view->updateImageType(m_view->currentImageTypeStack());
-}
-
-void TomographyROIPresenter::processChangeRotation() {
- m_view->updateRotationAngle(m_view->currentRotationAngle());
-}
-
-void TomographyROIPresenter::processUpdateImgIndex() {
- m_view->updateImgWithIndex(m_view->currentImgIndex());
-}
-
-void TomographyROIPresenter::processPlayStartStop() {
- auto wsg = m_view->currentImageTypeStack();
- if (!wsg)
- return;
-
- if (wsg->size() <= 1) {
- m_view->userWarning(
- "Cannot \"play\" a single image",
- "The stack currently loaded has a single image. Cannot play it.");
- return;
- }
-
- if (m_playStatus) {
- m_view->playStop();
- m_playStatus = false;
- m_view->enableActions(true);
- } else {
- m_view->enableActions(false);
- m_playStatus = true;
- m_view->playStart();
- }
-}
-
-void TomographyROIPresenter::processUpdateColorMap() {
- std::string filename = m_view->askColorMapFile();
- if (filename.empty())
- return;
-
- m_view->updateColorMap(filename);
-}
-
-void TomographyROIPresenter::processColorRangeUpdated() {
- m_view->updateImgWithIndex(m_view->currentImgIndex());
-}
-
-void TomographyROIPresenter::processSelectCoR() {
- m_view->changeSelectionState(ITomographyROIView::SelectCoR);
-}
-
-void TomographyROIPresenter::processSelectROI() {
- m_view->changeSelectionState(ITomographyROIView::SelectROIFirst);
-}
-
-void TomographyROIPresenter::processSelectNormalization() {
- m_view->changeSelectionState(ITomographyROIView::SelectNormAreaFirst);
-}
-
-void TomographyROIPresenter::processFinishedCoR() {
- m_view->changeSelectionState(ITomographyROIView::SelectNone);
-}
-
-void TomographyROIPresenter::processFinishedROI() {
- m_view->changeSelectionState(ITomographyROIView::SelectNone);
-}
-
-void TomographyROIPresenter::processFinishedNormalization() {
- m_view->changeSelectionState(ITomographyROIView::SelectNone);
-}
-
-void TomographyROIPresenter::processResetCoR() {
- m_view->resetCoR();
- m_view->changeSelectionState(ITomographyROIView::SelectNone);
-}
-
-void TomographyROIPresenter::processResetROI() {
- m_view->resetROI();
- m_view->changeSelectionState(ITomographyROIView::SelectNone);
-}
-
-void TomographyROIPresenter::processResetNormalization() {
- m_view->resetNormArea();
- m_view->changeSelectionState(ITomographyROIView::SelectNone);
-}
-
-void TomographyROIPresenter::processShutDown() { m_view->saveSettings(); }
-
-void TomographyROIPresenter::loadFITSStack(const StackOfImagesDirs &soid,
- const std::string &wsgName,
- const std::string &wsgFlatsName,
- const std::string &wsgDarksName) {
- const std::vector<std::string> &imgs = soid.sampleFiles();
- if (imgs.empty())
- return;
-
- loadFITSList(imgs, wsgName);
-
- auto flats = soid.flatFiles();
- m_stackFlats = nullptr;
- loadFITSList(flats, wsgFlatsName);
-
- auto darks = soid.darkFiles();
- m_stackDarks = nullptr;
- loadFITSList(darks, wsgDarksName);
-}
-
-void TomographyROIPresenter::loadFITSList(const std::vector<std::string> &imgs,
- const std::string &wsName) {
-
- auto &ads = Mantid::API::AnalysisDataService::Instance();
- try {
- if (ads.doesExist(wsName)) {
- ads.remove(wsName);
- }
- } catch (std::runtime_error &exc) {
- m_view->userError(
- "Error accessing the analysis data service",
- "There was an error while accessing the Mantid analysis data service "
- "to check for the presence of (and remove if present) workspace '" +
- wsName + "'. This is a severe inconsistency . Error details:: " +
- std::string(exc.what()));
- }
-
- // This would be the alternative that loads images one by one (one
- // algorithm run per image file)
- // for (size_t i = 0; i < imgs.size(); ++i) {
- // loadFITSImage(imgs[i], wsName);
- // }
-
- // Load all requested/supported image files using a list with their names
- try {
- const std::string allPaths = filterImagePathsForFITSStack(imgs);
- if (allPaths.empty()) {
- return;
- }
- loadFITSImage(allPaths, wsName);
- } catch (std::runtime_error &exc) {
- m_view->userWarning("Error trying to start the loading of FITS file(s)",
- "There was an error which prevented the file(s) from "
- "being loaded. Details: " +
- std::string(exc.what()));
- }
-}
-
-/**
- * Produces a string with paths separated by commas. Takes the patsh from the
- * input paths string but selects only the ones that look consistent with the
- * supported format / extension.
- *
- * @param paths of the supposedly image files
- *
- * @return string with comma separated value (paths) ready to be passed as
- *input
- * to LoadFITS or similar algorithms
- */
-std::string TomographyROIPresenter::filterImagePathsForFITSStack(
- const std::vector<std::string> &paths) {
- std::string allPaths = "";
-
- // Let's take only the ones that we can effectively load
- const std::string expectedShort = "fit";
- const std::string expectedLong = "fits";
- const std::string summedSkipStr = "_SummedImg.";
- std::vector<std::string> unexpectedFiles, summedFiles;
- for (const auto &pathStr : paths) {
- const std::string extShort = pathStr.substr(pathStr.size() - 3);
- const std::string extLong = pathStr.substr(pathStr.size() - 4);
- // exception / sum images generated by some detectors
- if (std::string::npos != pathStr.find(summedSkipStr)) {
- summedFiles.push_back(pathStr);
- } else if (extShort != expectedShort && extLong != expectedLong) {
- unexpectedFiles.push_back(pathStr);
- } else {
- if (allPaths.empty()) {
- allPaths = pathStr;
- } else {
- allPaths.append(", " + pathStr);
- }
- }
- }
-
- // If needed, give a warning once, at the end
- if (!unexpectedFiles.empty()) {
- std::string filesStrMsg = "";
- for (auto path : unexpectedFiles) {
- filesStrMsg += path + "\n";
- }
-
- const std::string msg =
- "Found files with unrecognized or unsupported extension in this "
- "stack ( " +
- m_stackPath + "). Expected files with extension '" + expectedShort +
- "' or '" + expectedLong +
- "' the following file(s) were found (and not loaded):" + filesStrMsg;
-
- if (g_warnIfUnexpectedFileExtensions) {
- m_view->userWarning("Files with invalid/unrecognized extension found in "
- "the stack of images",
- msg);
- }
- g_log.warning(msg);
- }
- if (!summedFiles.empty()) {
- std::string filesStrMsg = "";
- for (auto path : summedFiles) {
- filesStrMsg += path + "\n";
- }
-
- const std::string msg =
- "Found file(s) that look like summed images (have '" + summedSkipStr +
- "' in their name) in this "
- "stack ( " +
- m_stackPath + "). Ignoring them under the assumption that these are "
- "note original images. Please make sure that this is "
- "correct. The files ignored are: " +
- filesStrMsg;
-
- if (g_warnIfUnexpectedFileExtensions) {
- m_view->userWarning("Files that presumably are summed images have been "
- "found in the stack of images",
- msg);
- }
- g_log.warning(msg);
- }
-
- return allPaths;
-}
-
-void TomographyROIPresenter::loadFITSImage(const std::string &path,
- const std::string &wsName) {
- // get fits file into workspace and retrieve it from the ADS
- auto alg = Mantid::API::AlgorithmManager::Instance().create("LoadFITS");
- try {
- alg->initialize();
- alg->setPropertyValue("Filename", path);
- alg->setProperty("OutputWorkspace", wsName);
- // this is way faster when loading into a MatrixWorkspace
- alg->setProperty("LoadAsRectImg", true);
- } catch (std::exception &e) {
- throw std::runtime_error("Failed to initialize the mantid algorithm to "
- "load images. Error description: " +
- std::string(e.what()));
- }
-
- m_algRunner->addAlgorithm(alg);
-}
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomographyROIViewQtWidget.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomographyROIViewQtWidget.cpp
deleted file mode 100644
index 91d90683a34..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/TomographyROIViewQtWidget.cpp
+++ /dev/null
@@ -1,1366 +0,0 @@
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/Run.h"
-#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidQtAPI/AlgorithmInputHistory.h"
-#include "MantidQtAPI/AlgorithmRunner.h"
-#include "MantidQtAPI/MantidColorMap.h"
-
-#include "MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyROIViewQtWidget.h"
-
-using namespace Mantid::API;
-using namespace MantidQt::CustomInterfaces;
-
-#include <QCloseEvent>
-#include <QDir>
-#include <QFileDialog>
-#include <QMessageBox>
-#include <QPainter>
-#include <QSettings>
-#include <QTimer>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-// this would be more like a CustomWidget if it's eventually moved there
-const std::string TomographyROIViewQtWidget::m_settingsGroup =
- "CustomInterfaces/TomographyROIView";
-
-TomographyROIViewQtWidget::TomographyROIViewQtWidget(QWidget *parent)
- : QWidget(parent), ITomographyROIView(), m_colorMapFilename(),
- m_imgWidth(0), m_imgHeight(0), m_selectionState(SelectNone),
- m_presenter(NULL) {
- initLayout();
-
- // using an event filter. might be worth refactoring into a specific
- // QLabel + selection of ROI+NormArea+CoR class
- // not using Qwt Pickers to avoid Qwt version issues..
- m_ui.label_img->installEventFilter(this);
-}
-
-TomographyROIViewQtWidget::~TomographyROIViewQtWidget() {
- m_presenter->notify(TomographyROIPresenter::ShutDown);
-}
-
-void TomographyROIViewQtWidget::setParams(ImageStackPreParams ¶ms) {
- m_params = params;
- setParamWidgets(m_params);
-}
-
-void TomographyROIViewQtWidget::initLayout() {
- // setup container ui
- m_ui.setupUi(this);
-
- QList<int> sizes;
- sizes.push_back(1000);
- sizes.push_back(200);
- // between image and right panel
- m_ui.splitter_main_horiz->setSizes(sizes);
-
- sizes.clear();
- sizes.push_back(200);
- sizes.push_back(50);
- // between color bar and coordinates panel
- m_ui.splitter_right_horiz->setSizes(sizes);
-
- m_ui.comboBox_image_type->setCurrentIndex(0);
- m_ui.comboBox_rotation->setCurrentIndex(0);
-
- sizes.clear();
- sizes.push_back(10);
- sizes.push_back(1000);
- m_ui.splitter_img_vertical->setSizes(sizes);
- m_ui.horizontalScrollBar_img_stack->setEnabled(false);
- m_ui.lineEdit_img_seq->setText("---");
- m_ui.label_img_name->setText("none");
-
- enableParamWidgets(false);
- m_ui.colorBarWidget->setEnabled(false);
-
- m_ui.colorBarWidget->setViewRange(1, 65536);
- m_ui.colorBarWidget->setAutoScale(true);
- m_ui.colorBarWidget->setCheckBoxMode(
- MantidWidgets::ColorBarWidget::ADD_AUTOSCALE_ON_LOAD);
- m_ui.colorBarWidget->setAutoScaleTooltipText(
- "This flag signals that the color scale range\n"
- "will be set automatically to the current slice range\n"
- "when an image is loaded. Note that auto\n"
- "scaling will be applied when an image is loaded\n"
- "for the very first time.");
-
- readSettings();
-
- setupConnections();
-
- initParamWidgets(1, 1);
- grabCoRFromWidgets();
- grabROIFromWidgets();
- grabNormAreaFromWidgets();
-
- // presenter that knows how to handle a ITomographyROIView should take care
- // of all the logic. Note the view needs to now the concrete presenter here
- m_presenter.reset(new TomographyROIPresenter(this));
-
- // it will know what compute resources and tools we have available:
- // This view doesn't even know the names of compute resources, etc.
- m_presenter->notify(TomographyROIPresenter::Init);
-}
-
-void TomographyROIViewQtWidget::setupConnections() {
-
- // 'browse' buttons
- connect(m_ui.pushButton_browse_img, SIGNAL(released()), this,
- SLOT(browseImageClicked()));
-
- connect(m_ui.pushButton_browse_stack, SIGNAL(released()), this,
- SLOT(browseStackClicked()));
-
- connect(m_ui.pushButton_cor, SIGNAL(released()), this, SLOT(corClicked()));
- connect(m_ui.pushButton_cor_reset, SIGNAL(released()), this,
- SLOT(corResetClicked()));
-
- connect(m_ui.pushButton_roi, SIGNAL(released()), this, SLOT(roiClicked()));
- connect(m_ui.pushButton_roi_reset, SIGNAL(released()), this,
- SLOT(roiResetClicked()));
-
- connect(m_ui.pushButton_norm_area, SIGNAL(released()), this,
- SLOT(normAreaClicked()));
- connect(m_ui.pushButton_norm_area_reset, SIGNAL(released()), this,
- SLOT(normAreaResetClicked()));
-
- // "Play" the stack for quick visualization of input images
- connect(m_ui.pushButton_play, SIGNAL(released()), this, SLOT(playClicked()));
-
- // Clicking Auto COR
- connect(m_ui.pushButton_center_find, SIGNAL(released()), this,
- SLOT(findCORClicked()));
-
- // image sequence scroll/slide:
- connect(m_ui.horizontalScrollBar_img_stack, SIGNAL(valueChanged(int)), this,
- SLOT(updateFromImagesSlider(int)));
-
- // changing CoR tool
- connect(m_ui.comboBox_center_method, SIGNAL(currentIndexChanged(int)), this,
- SLOT(autoCoRToolChanged(int)));
-
- // image rotation
- connect(m_ui.comboBox_rotation, SIGNAL(currentIndexChanged(int)), this,
- SLOT(rotationUpdated(int)));
-
- // image type
- connect(m_ui.comboBox_image_type, SIGNAL(currentIndexChanged(int)), this,
- SLOT(imageTypeUpdated(int)));
-
- // parameter (points) widgets
- connect(m_ui.spinBox_cor_x, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedCoR(int)));
- connect(m_ui.spinBox_cor_y, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedCoR(int)));
-
- connect(m_ui.spinBox_roi_right, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedROI(int)));
- connect(m_ui.spinBox_roi_top, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedROI(int)));
- connect(m_ui.spinBox_roi_left, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedROI(int)));
- connect(m_ui.spinBox_roi_bottom, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedROI(int)));
-
- connect(m_ui.spinBox_norm_right, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedNormArea(int)));
- connect(m_ui.spinBox_norm_top, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedNormArea(int)));
- connect(m_ui.spinBox_norm_left, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedNormArea(int)));
- connect(m_ui.spinBox_norm_bottom, SIGNAL(valueChanged(int)), this,
- SLOT(valueUpdatedNormArea(int)));
-
- // colors
- connect(m_ui.colorBarWidget, SIGNAL(colorBarDoubleClicked()), this,
- SLOT(loadColorMapRequest()));
-
- connect(m_ui.colorBarWidget, SIGNAL(changedColorRange(double, double, bool)),
- this, SLOT(colorRangeChanged()));
-}
-
-void TomographyROIViewQtWidget::readSettings() {
- QSettings qs;
- qs.beginGroup(QString::fromStdString(m_settingsGroup));
-
- // Color bar widget settings
- // The factory default would be "Gray.map"
- const auto mapsDir = QString::fromStdString(
- Mantid::Kernel::ConfigService::Instance().getString(
- "colormaps.directory"));
- const auto defMapFile =
- QFileInfo(mapsDir).absoluteDir().filePath("Gamma1.map");
- const auto filepath = qs.value("colorbar-file", defMapFile).toString();
- m_ui.colorBarWidget->getColorMap().loadMap(filepath);
- m_ui.colorBarWidget->updateColorMap();
-
- m_ui.colorBarWidget->setScale(qs.value("colorbar-scale-type", 0).toInt());
- m_ui.colorBarWidget->setExponent(
- qs.value("colorbar-power-exponent", 2.0).toDouble());
- m_ui.colorBarWidget->setAutoScale(
- qs.value("colorbar-autoscale", false).toBool());
- // ColorBarWidget doesn't support setting "AutoColorScaleforCurrentSlice"
- // qsetting: "colorbar-autoscale-current-slice"
-
- restoreGeometry(qs.value("interface-win-geometry").toByteArray());
- qs.endGroup();
-}
-
-void TomographyROIViewQtWidget::saveSettings() const {
- QSettings qs;
- qs.beginGroup(QString::fromStdString(m_settingsGroup));
-
- // Color bar widget settings
- qs.setValue("colorbar-file",
- m_ui.colorBarWidget->getColorMap().getFilePath());
- qs.setValue("colorbar-scale-type", m_ui.colorBarWidget->getScale());
- qs.setValue("colorbar-power-exponent", m_ui.colorBarWidget->getExponent());
- qs.setValue("colorbar-autoscale", m_ui.colorBarWidget->getAutoScale());
- qs.setValue("colorbar-autoscale-current-slice",
- m_ui.colorBarWidget->getAutoScaleforCurrentSlice());
-
- qs.setValue("interface-win-geometry", saveGeometry());
- qs.endGroup();
-}
-
-ImageStackPreParams TomographyROIViewQtWidget::userSelection() const {
- return m_params;
-}
-
-void TomographyROIViewQtWidget::changeSelectionState(
- const ITomographyROIView::SelectionState &state) {
- m_selectionState = state;
-}
-
-void TomographyROIViewQtWidget::showStack(const std::string & /*path*/) {
- // TODO:
- // a) load as proper stack of images workspace - this can only be done when
- // we have a first working version of the "lean MD workspace". This method
- // would then load into one workspace of such type.
- // b) load as workspace group - this is done in the overloaded method below
-
- // enableParamWidgets(true);
-}
-
-void TomographyROIViewQtWidget::showStack(
- const Mantid::API::WorkspaceGroup_sptr &wsg,
- const Mantid::API::WorkspaceGroup_sptr &wsgFlats,
- const Mantid::API::WorkspaceGroup_sptr &wsgDarks) {
- if (0 == wsg->size())
- return;
-
- m_stackSamples = wsg;
- m_stackFlats = wsgFlats;
- m_stackDarks = wsgDarks;
-
- resetWidgetsOnNewStack();
-
- size_t width = 0, height = 0;
- try {
- MatrixWorkspace_sptr ws =
- boost::dynamic_pointer_cast<MatrixWorkspace>(wsg->getItem(0));
- if (!ws)
- return;
- width = ws->blocksize();
- height = ws->getNumberHistograms();
- } catch (std::exception &e) {
- QMessageBox::warning(this, "Cannot load image information",
- "There was a problem while "
- " trying to find the size of the image: " +
- QString::fromStdString(e.what()));
- }
-
- showProjection(m_stackSamples, 0);
- initParamWidgets(width, height);
- refreshImage();
- enableParamWidgets(true);
- enableImageTypes(wsg && wsg->size() > 0, wsgFlats && wsgFlats->size() > 0,
- wsgDarks && wsgDarks->size() > 0);
-}
-
-void TomographyROIViewQtWidget::showProjection(
- const Mantid::API::WorkspaceGroup_sptr &wsg, size_t idx) {
-
- m_params.rotation = 0;
- m_ui.comboBox_rotation->setCurrentIndex(0);
- showProjectionImage(wsg, idx, 0);
-
- // give name, set up scroll/slider
- std::string name;
- try {
- MatrixWorkspace_sptr ws =
- boost::dynamic_pointer_cast<MatrixWorkspace>(wsg->getItem(idx));
- if (!ws)
- return;
- name = ws->run().getLogData("run_title")->value();
- } catch (std::exception &e) {
- QMessageBox::warning(this, "Cannot load image information",
- "There was a problem while "
- " trying to find the name of the image: " +
- QString::fromStdString(e.what()));
- }
- m_ui.label_img_name->setText(QString::fromStdString(name));
-
- const size_t numPics = wsg->size();
- m_ui.lineEdit_img_seq->setText(
- QString::fromStdString("1/" + boost::lexical_cast<std::string>(numPics)));
- m_ui.horizontalScrollBar_img_stack->setValue(static_cast<int>(idx));
-}
-
-void TomographyROIViewQtWidget::userWarning(const std::string &err,
- const std::string &description) {
- QMessageBox::warning(this, QString::fromStdString(err),
- QString::fromStdString(description), QMessageBox::Ok,
- QMessageBox::Ok);
-}
-
-void TomographyROIViewQtWidget::userError(const std::string &err,
- const std::string &description) {
- QMessageBox::critical(this, QString::fromStdString(err),
- QString::fromStdString(description), QMessageBox::Ok,
- QMessageBox::Ok);
-}
-
-void TomographyROIViewQtWidget::enableActions(bool enable) {
- m_ui.pushButton_browse_img->setEnabled(enable);
- m_ui.pushButton_browse_stack->setEnabled(enable);
- m_ui.pushButton_play->setEnabled(enable);
- m_ui.pushButton_center_find->setEnabled(enable);
-
- m_ui.colorBarWidget->setEnabled(enable);
-
- m_ui.comboBox_center_method->setEnabled(enable);
- m_ui.comboBox_image_type->setEnabled(enable);
- m_ui.comboBox_rotation->setEnabled(enable);
- m_ui.groupBox_cor->setEnabled(enable);
- m_ui.groupBox_roi->setEnabled(enable);
- m_ui.groupBox_norm->setEnabled(enable);
-}
-
-std::string TomographyROIViewQtWidget::askImagePath(
- const std::string &windowTitle = "Open image") {
- // only FITS is supported right now
- QString fitsStr = QString("Supported formats: FITS"
- "(*.fits *.fit);;"
- "FITS, Flexible Image Transport System images "
- "(*.fits *.fit);;");
- QString prevPath =
- MantidQt::API::AlgorithmInputHistory::Instance().getPreviousDirectory();
- QString filepath(QFileDialog::getOpenFileName(this, tr(windowTitle.c_str()),
- prevPath, fitsStr));
- if (!filepath.isEmpty()) {
- MantidQt::API::AlgorithmInputHistory::Instance().setPreviousDirectory(
- filepath);
- }
-
- return filepath.toStdString();
-}
-
-void TomographyROIViewQtWidget::enableImageTypes(bool enableSamples,
- bool enableFlats,
- bool enableDarks) {
- QComboBox *itypes = m_ui.comboBox_image_type;
- if (!itypes || 3 != itypes->count())
- return;
-
- std::vector<bool> enable = {enableSamples, enableFlats, enableDarks};
- for (size_t idx = 0; idx < enable.size(); idx++) {
- QVariant var;
- if (!enable[idx]) {
- var = 0;
- } else {
- var = 1 | 32;
- }
- // trick to display a combobox entry as a disabled/enabled row
- QModelIndex modelIdx = itypes->model()->index(static_cast<int>(idx), 0);
- itypes->model()->setData(modelIdx, var, Qt::UserRole - 1);
- }
-}
-
-void TomographyROIViewQtWidget::resetCoR() {
- int midx =
- (m_ui.spinBox_cor_x->minimum() + m_ui.spinBox_cor_x->maximum()) / 2;
- m_ui.spinBox_cor_x->setValue(midx);
- int midy =
- (m_ui.spinBox_cor_y->minimum() + m_ui.spinBox_cor_y->maximum()) / 2;
- m_ui.spinBox_cor_y->setValue(midy);
-}
-
-void TomographyROIViewQtWidget::resetROI() {
- m_ui.spinBox_roi_left->setValue(0);
- m_ui.spinBox_roi_top->setValue(0);
- m_ui.spinBox_roi_right->setValue(m_ui.spinBox_roi_right->maximum());
- m_ui.spinBox_roi_bottom->setValue(m_ui.spinBox_roi_bottom->maximum());
-}
-
-void TomographyROIViewQtWidget::resetNormArea() {
- m_ui.spinBox_norm_right->setValue(0);
- m_ui.spinBox_norm_top->setValue(0);
- m_ui.spinBox_norm_left->setValue(0);
- m_ui.spinBox_norm_bottom->setValue(0);
-}
-
-void TomographyROIViewQtWidget::resetWidgetsOnNewStack() {
- m_ui.horizontalScrollBar_img_stack->setEnabled(true);
- m_ui.horizontalScrollBar_img_stack->setMinimum(0);
- m_ui.horizontalScrollBar_img_stack->setMaximum(
- static_cast<int>(m_stackSamples->size() - 1));
- m_ui.comboBox_rotation->setCurrentIndex(0);
-}
-
-void TomographyROIViewQtWidget::valueUpdatedCoR(int) {
- grabCoRFromWidgets();
- refreshImage();
-}
-
-void TomographyROIViewQtWidget::valueUpdatedROI(int) {
- grabROIFromWidgets();
- refreshImage();
-}
-
-void TomographyROIViewQtWidget::valueUpdatedNormArea(int) {
- grabNormAreaFromWidgets();
- refreshImage();
-}
-
-/**
- * Parameter values from spin box widgets => coordinate parameters
- * data member
- */
-void TomographyROIViewQtWidget::grabCoRFromWidgets() {
- m_params.cor = Mantid::Kernel::V2D(m_ui.spinBox_cor_x->value(),
- m_ui.spinBox_cor_y->value());
-}
-
-void TomographyROIViewQtWidget::grabROIFromWidgets() {
- m_params.roi =
- std::make_pair(Mantid::Kernel::V2D(m_ui.spinBox_roi_right->value(),
- m_ui.spinBox_roi_top->value()),
- Mantid::Kernel::V2D(m_ui.spinBox_roi_left->value(),
- m_ui.spinBox_roi_bottom->value()));
-}
-
-void TomographyROIViewQtWidget::grabNormAreaFromWidgets() {
- m_params.normalizationRegion =
- std::make_pair(Mantid::Kernel::V2D(m_ui.spinBox_norm_right->value(),
- m_ui.spinBox_norm_top->value()),
- Mantid::Kernel::V2D(m_ui.spinBox_norm_left->value(),
- m_ui.spinBox_norm_bottom->value()));
-}
-
-/**
- * Updates the image view with the current image index and selection
- * of parameters (ROI, normalization area, CoR). This needs to be used
- * for every event that modifies the current image and/or selection of
- * parameters.
- */
-void TomographyROIViewQtWidget::refreshImage() {
-
- const QPixmap *pp = m_ui.label_img->pixmap();
- if (!pp)
- return;
-
- m_ui.label_img->setMaximumWidth(static_cast<int>(m_imgWidth));
- m_ui.label_img->setMaximumHeight(static_cast<int>(m_imgHeight));
-
- QPixmap toDisplay(*m_basePixmap.get());
- QPainter painter(&toDisplay);
-
- drawCenterCrossSymbol(painter, m_params.cor);
-
- drawBoxROI(painter, m_params.roi.first, m_params.roi.second);
-
- drawBoxNormalizationRegion(painter, m_params.normalizationRegion.first,
- m_params.normalizationRegion.second);
-
- m_ui.label_img->setPixmap(toDisplay);
-}
-
-void TomographyROIViewQtWidget::refreshCoR() {
- const QPixmap *pp = m_ui.label_img->pixmap();
- if (!pp)
- return;
-
- grabCoRFromWidgets();
-
- QPixmap toDisplay(*m_basePixmap.get());
- QPainter painter(&toDisplay);
- drawCenterCrossSymbol(painter, m_params.cor);
-
- m_ui.label_img->setPixmap(toDisplay);
-}
-
-void TomographyROIViewQtWidget::refreshROI() {
- const QPixmap *pp = m_ui.label_img->pixmap();
- if (!pp)
- return;
-
- grabROIFromWidgets();
- // TODO: display proper symbol
-
- // QPixmap const *pm = m_ui.label_img->pixmap();
- QPixmap toDisplay(*m_basePixmap.get());
- QPainter painter(&toDisplay);
- drawBoxROI(painter, m_params.roi.first, m_params.roi.second);
-
- m_ui.label_img->setPixmap(toDisplay);
-}
-
-void TomographyROIViewQtWidget::refreshNormArea() {
- // TODO: display proper symbol
- const QPixmap *pp = m_ui.label_img->pixmap();
- if (!pp)
- return;
-
- grabNormAreaFromWidgets();
-
- // QPixmap const *pm = m_ui.label_img->pixmap();
- QPixmap toDisplay(*m_basePixmap.get());
- QPainter painter(&toDisplay);
-
- drawBoxNormalizationRegion(painter, m_params.normalizationRegion.first,
- m_params.normalizationRegion.second);
-
- m_ui.label_img->setPixmap(toDisplay);
-}
-
-void TomographyROIViewQtWidget::drawCenterCrossSymbol(
- QPainter &painter, const Mantid::Kernel::V2D ¢er) const {
- // TODO: display settings / nicer symbol?
-
- QPen penCoR(Qt::red);
- painter.setPen(penCoR);
- painter.drawLine(
- static_cast<int>(center.X() - 5), static_cast<int>(center.Y()),
- static_cast<int>(center.X() + 5), static_cast<int>(center.Y()));
- painter.drawLine(
- static_cast<int>(center.X()), static_cast<int>(center.Y() - 5),
- static_cast<int>(center.X()), static_cast<int>(center.Y() + 5));
-}
-
-void TomographyROIViewQtWidget::drawBoxROI(
- QPainter &painter, const Mantid::Kernel::V2D &first,
- const Mantid::Kernel::V2D &second) const {
- QPen penROI(Qt::green);
- painter.setPen(penROI);
- painter.drawRect(static_cast<int>(first.X()), static_cast<int>(first.Y()),
- static_cast<int>(second.X() - first.X()),
- static_cast<int>(second.Y() - first.Y()));
-}
-
-void TomographyROIViewQtWidget::drawBoxNormalizationRegion(
- QPainter &painter, const Mantid::Kernel::V2D &first,
- const Mantid::Kernel::V2D &second) const {
- QPen penNA(Qt::yellow);
- painter.setPen(penNA);
- painter.drawRect(static_cast<int>(first.X()), static_cast<int>(first.Y()),
- static_cast<int>(second.X() - first.X()),
- static_cast<int>(second.Y() - first.Y()));
-}
-
-void TomographyROIViewQtWidget::enableParamWidgets(bool enable) {
- m_ui.comboBox_image_type->setEnabled(enable);
- m_ui.comboBox_rotation->setEnabled(enable);
-
- m_ui.groupBox_cor->setEnabled(enable);
- m_ui.groupBox_roi->setEnabled(enable);
- m_ui.groupBox_norm->setEnabled(enable);
-}
-
-void TomographyROIViewQtWidget::initParamWidgets(size_t maxWidth,
- size_t maxHeight) {
- m_imgWidth = static_cast<int>(maxWidth);
- m_imgHeight = static_cast<int>(maxHeight);
-
- m_ui.spinBox_cor_x->setMinimum(0);
- m_ui.spinBox_cor_x->setMaximum(m_imgWidth - 1);
- m_ui.spinBox_cor_y->setMinimum(0);
- m_ui.spinBox_cor_y->setMaximum(m_imgHeight - 1);
- resetCoR();
-
- m_ui.spinBox_roi_right->setMinimum(0);
- m_ui.spinBox_roi_right->setMaximum(m_imgWidth - 1);
- m_ui.spinBox_roi_top->setMinimum(0);
- m_ui.spinBox_roi_top->setMaximum(m_imgHeight - 1);
-
- m_ui.spinBox_roi_left->setMinimum(0);
- m_ui.spinBox_roi_left->setMaximum(m_imgWidth - 1);
- m_ui.spinBox_roi_bottom->setMinimum(0);
- m_ui.spinBox_roi_bottom->setMaximum(m_imgHeight - 1);
-
- resetROI();
-
- m_ui.spinBox_norm_right->setMinimum(0);
- m_ui.spinBox_norm_right->setMaximum(m_imgWidth - 1);
- m_ui.spinBox_norm_top->setMinimum(0);
- m_ui.spinBox_norm_top->setMaximum(m_imgHeight - 1);
-
- m_ui.spinBox_norm_left->setMinimum(0);
- m_ui.spinBox_norm_left->setMaximum(m_imgWidth - 1);
- m_ui.spinBox_norm_bottom->setMinimum(0);
- m_ui.spinBox_norm_bottom->setMaximum(m_imgHeight - 1);
-
- resetNormArea();
-}
-
-void TomographyROIViewQtWidget::setParamWidgets(ImageStackPreParams ¶ms) {
- if (params.rotation > 0 && params.rotation <= 360) {
- m_ui.comboBox_rotation->setCurrentIndex(
- static_cast<int>(params.rotation / 90.0f) % 4);
- } else {
- m_ui.comboBox_rotation->setCurrentIndex(0);
- }
-
- m_ui.spinBox_cor_x->setValue(static_cast<int>(params.cor.X()));
- m_ui.spinBox_cor_y->setValue(static_cast<int>(params.cor.Y()));
-
- m_ui.spinBox_roi_right->setValue(static_cast<int>(params.roi.first.X()));
- m_ui.spinBox_roi_top->setValue(static_cast<int>(params.roi.first.Y()));
-
- m_ui.spinBox_roi_left->setValue(static_cast<int>(params.roi.second.X()));
- m_ui.spinBox_roi_bottom->setValue(static_cast<int>(params.roi.second.Y()));
-
- m_ui.spinBox_norm_right->setValue(
- static_cast<int>(params.normalizationRegion.first.X()));
- m_ui.spinBox_norm_top->setValue(
- static_cast<int>(params.normalizationRegion.first.Y()));
-
- m_ui.spinBox_norm_left->setValue(
- static_cast<int>(params.normalizationRegion.second.X()));
- m_ui.spinBox_norm_bottom->setValue(
- static_cast<int>(params.normalizationRegion.second.Y()));
-}
-
-void TomographyROIViewQtWidget::corClicked() {
- m_presenter->notify(ITomographyROIPresenter::SelectCoR);
-}
-
-void TomographyROIViewQtWidget::corResetClicked() {
- m_presenter->notify(ITomographyROIPresenter::ResetCoR);
- refreshImage();
-}
-
-void TomographyROIViewQtWidget::roiClicked() {
- m_presenter->notify(ITomographyROIPresenter::SelectROI);
-}
-
-void TomographyROIViewQtWidget::roiResetClicked() {
- m_presenter->notify(ITomographyROIPresenter::ResetROI);
- refreshImage();
-}
-
-void TomographyROIViewQtWidget::normAreaClicked() {
- m_presenter->notify(ITomographyROIPresenter::SelectNormalization);
-}
-
-void TomographyROIViewQtWidget::normAreaResetClicked() {
- m_presenter->notify(ITomographyROIPresenter::ResetNormalization);
- refreshImage();
-}
-
-void TomographyROIViewQtWidget::playClicked() {
- m_presenter->notify(ITomographyROIPresenter::PlayStartStop);
-}
-
-void TomographyROIViewQtWidget::playStart() {
- m_ui.pushButton_play->setText("Stop");
- // start timer
- m_playTimer = Mantid::Kernel::make_unique<QTimer>(this);
- connect(m_playTimer.get(), SIGNAL(timeout()), this, SLOT(updatePlay()));
- m_playTimer->start(133);
- m_ui.pushButton_play->setEnabled(true);
-}
-
-void TomographyROIViewQtWidget::playStop() {
- // stop timer
- m_playTimer->stop();
- m_ui.pushButton_play->setText("Play");
-}
-
-void TomographyROIViewQtWidget::updatePlay() {
- // TODO: maybe change to sample? Not obvious what would be users'
- // preference
- int val = m_ui.horizontalScrollBar_img_stack->value();
- ++val;
- if (m_ui.horizontalScrollBar_img_stack->maximum() <= val) {
- val = m_ui.horizontalScrollBar_img_stack->minimum();
- }
- m_ui.horizontalScrollBar_img_stack->setValue(val);
- showProjectionImage(m_stackSamples, val, currentRotationAngle());
-}
-
-void TomographyROIViewQtWidget::browseStackClicked() {
- m_presenter->notify(ITomographyROIPresenter::BrowseStack);
-}
-
-void TomographyROIViewQtWidget::browseImageClicked() {
- m_presenter->notify(ITomographyROIPresenter::BrowseImage);
-}
-
-void TomographyROIViewQtWidget::updateFromImagesSlider(int /* current */) {
- m_presenter->notify(ITomographyROIPresenter::UpdateImgIndex);
-}
-
-void TomographyROIViewQtWidget::imageTypeUpdated(int /* idx */) {
- m_presenter->notify(TomographyROIPresenter::ChangeImageType);
-}
-
-void TomographyROIViewQtWidget::rotationUpdated(int /* idx */) {
- m_params.rotation =
- static_cast<float>(m_ui.comboBox_rotation->currentIndex()) * 90.0f;
- m_presenter->notify(TomographyROIPresenter::ChangeRotation);
-}
-
-void TomographyROIViewQtWidget::autoCoRToolChanged(int /* idx */) {
- // todo notify presenter that the tool is changed, however for now we only
- // have one tool -> tomopy
-}
-
-size_t TomographyROIViewQtWidget::currentImgIndex() const {
- return m_ui.horizontalScrollBar_img_stack->value();
-}
-
-void TomographyROIViewQtWidget::updateImgWithIndex(size_t idx) {
- int max = m_ui.horizontalScrollBar_img_stack->maximum();
- int current = m_ui.horizontalScrollBar_img_stack->value();
-
- m_ui.lineEdit_img_seq->setText(
- QString::fromStdString(boost::lexical_cast<std::string>(current + 1) +
- "/" + boost::lexical_cast<std::string>(max + 1)));
-
- showProjectionImage(currentImageTypeStack(), idx, currentRotationAngle());
-}
-
-void TomographyROIViewQtWidget::showProjectionImage(
- const Mantid::API::WorkspaceGroup_sptr &wsg, size_t idx,
- float rotationAngle) {
-
- size_t width, height;
- std::string imgName;
- Mantid::API::MatrixWorkspace_sptr ws;
- try {
- checkNewProjectionImage(wsg, idx, width, height, ws, imgName);
- } catch (std::runtime_error &rexc) {
- QMessageBox::critical(this, "Cannot load image",
- "There was a problem while trying to "
- "find essential parameters of the image. Details: " +
- QString::fromStdString(rexc.what()));
- return;
- }
-
- m_ui.label_img_name->setText(QString::fromStdString(imgName));
- // load / transfer image into a QImage, handling the rotation, width height
- // consistently
- QPixmap pixmap = transferWSImageToQPixmap(ws, width, height, rotationAngle);
-
- m_ui.label_img->setPixmap(pixmap);
- m_ui.label_img->show();
- m_basePixmap.reset(new QPixmap(pixmap));
-
- refreshImage();
-}
-
-/**
- * Paint an image from a workspace (MatrixWorkspace) into a
- * QPixmap. The QPixmap can then be display by for example setting
- * it into a QLabel widget.
- *
- * @param ws image workspace
- *
- * @param width width of the image in pixels
- *
- * @param height height of the image in pixels
- *
- * @param rotationAngle rotate the image by this angle with respect to the
- * original image in the workspace when displaying it
- */
-QPixmap TomographyROIViewQtWidget::transferWSImageToQPixmap(
- const MatrixWorkspace_sptr ws, size_t width, size_t height,
- float rotationAngle) {
-
- QImage rawImg(QSize(static_cast<int>(width), static_cast<int>(height)),
- QImage::Format_RGB32);
-
- double minVal = std::numeric_limits<double>::max(),
- maxVal = std::numeric_limits<double>::min();
- // find min and max to scale pixel values, whether from user-given
- // range, or auto-range
- if (!m_ui.colorBarWidget->getAutoScale()) {
- minVal = m_ui.colorBarWidget->getMinimum();
- maxVal = m_ui.colorBarWidget->getMaximum();
- } else {
-
- getPixelMinMax(ws, minVal, maxVal);
- if (maxVal <= minVal) {
- QMessageBox::warning(
- this, "Empty image!",
- "The image could be loaded but it contains "
- "effectively no information, all pixels have the same value.");
- // black picture
- QPixmap pix(static_cast<int>(width), static_cast<int>(height));
- pix.fill(QColor(0, 0, 0));
- return pix;
- }
- m_ui.colorBarWidget->setViewRange(minVal, maxVal);
- }
- const double max_min = maxVal - minVal;
- const double scaleFactor = 255.0 / max_min;
-
- // normal Qt rgb values
- QwtDoubleInterval rgbInterval(0.0, 255.0);
- const QVector<QRgb> colorTable =
- m_ui.colorBarWidget->getColorMap().colorTable(rgbInterval);
- rawImg.setColorTable(colorTable);
-
- for (size_t yi = 0; yi < width; ++yi) {
- const auto &yvec = ws->readY(yi);
- for (size_t xi = 0; xi < width; ++xi) {
- const double &v = yvec[xi];
- const int scaled = static_cast<int>(scaleFactor * (v - minVal));
- // You would use this for a trivial mapping of valus to colors:
- // Coloring the range min-max in gray scale. But setColorTable()
- // is used to apply different color maps from files QRgb vRgb =
- // qRgb(scaled, scaled, scaled);
- // rawImg.setPixel(static_cast<int>(rotX), static_cast<int>(rotY),
- // scaled);
- size_t rotX = 0, rotY = 0;
- if (0 == rotationAngle) {
- rotX = xi;
- rotY = yi;
- } else if (90 == rotationAngle) {
- rotX = height - (yi + 1);
- rotY = xi;
- } else if (180 == rotationAngle) {
- rotX = width - (xi + 1);
- rotY = height - (yi + 1);
- } else if (270 == rotationAngle) {
- rotX = yi;
- rotY = width - (xi + 1);
- }
-
- const auto rgb =
- m_ui.colorBarWidget->getColorMap().rgb(rgbInterval, scaled);
- rawImg.setPixel(static_cast<int>(rotX), static_cast<int>(rotY), rgb);
- // This would be faster, using the look-up color table, but for unknown
- // reasons MantidColorMap::colorTable forces linear scale.
- // rawImg.setPixel(static_cast<int>(rotX), static_cast<int>(rotY),
- // colorTable[scaled]);
- }
- }
-
- // paint image direct from QImage object
- QPixmap pix = QPixmap::fromImage(rawImg);
- // Alternative, drawing with a painter:
- // QPixmap pix(static_cast<int>(width), static_cast<int>(height));
- // QPainter painter;
- // painter.begin(&pix);
- // painter.drawImage(0, 0, rawImg);
- // painter.end();
-
- return pix;
-}
-
-/**
- * Finds several parameters from an image in a stack (given the group
- * of images and an index), checking for errors. This is meant to be
- * used whenever a new image is going to be shown (for example when
- * using the slider to go through a stack).
- *
- * @param wsg the group of images
- * @param idx index of the image
- * @param width width or number of columns (in pixels)
- * @param height height or number of rows (in pixels)
- * @param imgWS image workspace corresponding to the index given
- * @param imgName name of the image (normally derived from the
- * original filename)
- *
- * @throws runtime_error when unrecoverable errors are found (no
- * data, issue with dimensions, etc.).
- */
-void TomographyROIViewQtWidget::checkNewProjectionImage(
- const Mantid::API::WorkspaceGroup_sptr &wsg, size_t idx, size_t &width,
- size_t &height, Mantid::API::MatrixWorkspace_sptr &imgWS,
- std::string &imgName) {
- try {
- imgWS = boost::dynamic_pointer_cast<MatrixWorkspace>(wsg->getItem(idx));
- if (!imgWS)
- return;
- } catch (std::exception &exc) {
- throw std::runtime_error("Could not find the image data: " +
- std::string(exc.what()));
- }
-
- try {
- getCheckedDimensions(imgWS, width, height);
- } catch (std::runtime_error &rexc) {
- throw std::runtime_error("Could not find the width of the image: " +
- std::string(rexc.what()));
- }
-
- try {
- imgName = imgWS->run().getLogData("run_title")->value();
- } catch (std::exception &e) {
- QMessageBox::warning(
- this, "Cannot load image information",
- "There was a problem while "
- " trying to find the name (run_title log entry) of the image: " +
- QString::fromStdString(e.what()));
- }
-}
-
-/**
- * Gets the width and height of an image MatrixWorkspace.
- *
- * @param ws image workspace
- *
- * @param width width of the image in pixels (bins)
- *
- * @param height height of the image in pixels (histograms)
- *
- * @throws runtime_error if there are problems when retrieving the
- * width/height or if they are inconsistent.
- */
-void TomographyROIViewQtWidget::getCheckedDimensions(
- const MatrixWorkspace_sptr ws, size_t &width, size_t &height) {
- const size_t MAXDIM = 2048 * 32;
- const std::string widthLogName = "Axis1";
- try {
- width = boost::lexical_cast<size_t>(
- ws->run().getLogData(widthLogName)->value());
- // TODO: add a settings option for this (like max mem allocation for
- // images)?
- if (width >= MAXDIM)
- width = MAXDIM;
- } catch (std::exception &exc) {
- throw std::runtime_error(
- "Could not find the width of the image from the run log data (entry: " +
- widthLogName + "). Error: " + exc.what());
- }
-
- const std::string heightLogName = "Axis2";
- try {
- height = boost::lexical_cast<size_t>(
- ws->run().getLogData(heightLogName)->value());
- if (height >= MAXDIM)
- height = MAXDIM;
- } catch (std::exception &exc) {
- throw std::runtime_error("could not find the height of the image from the "
- "run log data (entry: " +
- heightLogName + "). Error: " + exc.what());
- }
-
- // images are loaded as 1 histogram == 1 row (1 bin per image column):
- size_t histos = ws->getNumberHistograms();
- size_t bins = ws->blocksize();
- if (height != histos || width != bins) {
- throw std::runtime_error(
- "Image dimensions do not match in the input image workspace. "
- "Could not load the expected "
- "number of rows and columns. The width and height found in the run log "
- "data of the input files is: " +
- std::to_string(width) + ", " + std::to_string(height) +
- ", but the number of bins, histograms in "
- "the workspace loaded is: " +
- std::to_string(histos) + ", " + std::to_string(bins) + ".");
- }
-}
-
-void TomographyROIViewQtWidget::getPixelMinMax(MatrixWorkspace_sptr ws,
- double &min, double &max) {
- for (size_t i = 0; i < ws->getNumberHistograms(); ++i) {
- for (size_t j = 0; j < ws->blocksize(); ++j) {
- const double &v = ws->readY(i)[j];
- if (v < min)
- min = v;
- if (v > max)
- max = v;
- }
- }
-}
-
-float TomographyROIViewQtWidget::currentRotationAngle() const {
- return m_params.rotation;
-}
-
-void TomographyROIViewQtWidget::updateRotationAngle(float angle) {
- if (angle < 0 || (0 != static_cast<int>(angle) % 90))
- return;
-
- m_params.rotation = angle;
- m_ui.comboBox_rotation->setCurrentIndex(
- static_cast<int>((static_cast<int>(angle) / 90) % 4));
-
- showProjectionImage(currentImageTypeStack(), currentImgIndex(),
- currentRotationAngle());
-}
-
-void TomographyROIViewQtWidget::updateImageType(
- const Mantid::API::WorkspaceGroup_sptr wsg) {
- if (!wsg || 0 == wsg->size())
- return;
-
- const int newIdx = 0;
- m_ui.horizontalScrollBar_img_stack->setEnabled(true);
- m_ui.horizontalScrollBar_img_stack->setMinimum(0);
- m_ui.horizontalScrollBar_img_stack->setValue(newIdx);
- m_ui.horizontalScrollBar_img_stack->setMaximum(
- static_cast<int>(wsg->size() - 1));
-
- const size_t numPics = wsg->size();
- m_ui.lineEdit_img_seq->setText(
- QString::fromStdString("1/" + boost::lexical_cast<std::string>(numPics)));
-
- showProjectionImage(wsg, currentImgIndex(), currentRotationAngle());
-}
-
-Mantid::API::WorkspaceGroup_sptr
-TomographyROIViewQtWidget::currentImageTypeStack() const {
- int type = m_ui.comboBox_image_type->currentIndex();
-
- if (1 == type) {
- return m_stackFlats;
- } else if (2 == type) {
- return m_stackDarks;
- } else {
- return m_stackSamples;
- }
-}
-
-/**
- * Qt events filter for the mouse click and click&drag events that are
- * used to select points and rectangles. Part of the logic of the
- * selection is handled here. The test on the presenter can only test
- * the begin and end of the selection. For full testability (including
- * the mouse interaction), this method should be implemented fully in
- * terms of notifications to the presenter. This would require a bunch
- * of new notifications in ITomographyROIPresenter, and making at least all
- * the mouseUpdateCoR, mouseUpdateROICorners12, mouseXXX methods
- * public in this view interface. This can be considered at a later
- * stage.
- *
- * @param obj object concerned by the event
- * @param event event received (mouse click, release, move, etc.)
- **/
-bool TomographyROIViewQtWidget::eventFilter(QObject *obj, QEvent *event) {
- // quick ignore
- if (ITomographyROIView::SelectNone == m_selectionState)
- return false;
-
- if (m_ui.label_img == obj) {
-
- QPoint p = m_ui.label_img->mapFromGlobal(QCursor::pos());
- int x = p.x();
- int y = p.y();
- // ignore potential clicks outside of the image
- if (x >= m_imgWidth || y >= m_imgHeight || x < 0 || y < 0)
- return false;
-
- auto type = event->type();
- if (type == QEvent::MouseButtonPress) {
-
- if (ITomographyROIView::SelectCoR == m_selectionState) {
- mouseUpdateCoR(x, y);
- } else if (ITomographyROIView::SelectROIFirst == m_selectionState) {
- mouseUpdateROICornersStartSelection(x, y);
- } else if (ITomographyROIView::SelectNormAreaFirst == m_selectionState) {
- mouseUpdateNormAreaCornersStartSelection(x, y);
- }
-
- } else if (type == QEvent::MouseMove) {
-
- if (ITomographyROIView::SelectROISecond == m_selectionState) {
- mouseUpdateROICornerContinuedSelection(x, y);
- } else if (ITomographyROIView::SelectNormAreaSecond == m_selectionState) {
- mouseUpdateNormAreaCornerContinuedSelection(x, y);
- }
- } else if (type == QEvent::MouseButtonRelease) {
-
- if (ITomographyROIView::SelectROISecond == m_selectionState) {
- mouseFinishROI(x, y);
- } else if (ITomographyROIView::SelectNormAreaSecond == m_selectionState) {
- mouseFinishNormArea(x, y);
- }
- }
- }
- // pass on the event up to the parent class
- return false;
-}
-
-/**
- * Parameter values from mouse position (at a relevant event like
- * first click, or last release) => spin box widgets, AND coordinate
- * parameters data member. This grabs the Center of Rotation (CoR)
- *
- * @param x position on x axis (local to the image)
- * @param y position on y axis (local to the image)
- */
-void TomographyROIViewQtWidget::grabCoRFromMousePoint(const int x,
- const int y) {
- // m_params.cor = Mantid::Kernel::V2D(x, y);
- m_ui.spinBox_cor_x->setValue(x);
- m_ui.spinBox_cor_y->setValue(y);
-}
-
-void TomographyROIViewQtWidget::grabROICorner1FromMousePoint(const int x,
- const int y) {
- // this is re-used for Norm Region selection as you cannot be selecting both
- // at the same time
- m_startOfRectangle.right = x;
- m_startOfRectangle.top = y;
-
- m_ui.spinBox_roi_right->setValue(x);
- m_ui.spinBox_roi_top->setValue(y);
-}
-
-void TomographyROIViewQtWidget::grabROICorner2FromMousePoint(const int x,
- const int y) {
- updateValuesForSpinBoxes(x, y, m_startOfRectangle, m_ui.spinBox_roi_left,
- m_ui.spinBox_roi_top, m_ui.spinBox_roi_right,
- m_ui.spinBox_roi_bottom);
-}
-
-void TomographyROIViewQtWidget::grabNormAreaCorner1FromMousePoint(const int x,
- const int y) {
- // this is re-used for Norm Region selection as you cannot be selecting both
- // at the same time
- m_startOfRectangle.right = x;
- m_startOfRectangle.top = y;
-
- m_ui.spinBox_norm_right->setValue(x);
- m_ui.spinBox_norm_top->setValue(y);
-}
-
-void TomographyROIViewQtWidget::grabNormAreaCorner2FromMousePoint(const int x,
- const int y) {
-
- updateValuesForSpinBoxes(x, y, m_startOfRectangle, m_ui.spinBox_norm_left,
- m_ui.spinBox_norm_top, m_ui.spinBox_norm_right,
- m_ui.spinBox_norm_bottom);
-}
-
-void TomographyROIViewQtWidget::updateValuesForSpinBoxes(
- const int x, const int y, const RectangleXY startPositions,
- QSpinBox *spinLeft, QSpinBox *spinTop, QSpinBox *spinRight,
- QSpinBox *spinBottom) {
-
- // put at the top so that it has chance to fire before a setValue event
- spinLeft->blockSignals(true);
- spinTop->blockSignals(true);
- spinRight->blockSignals(true);
- spinBottom->blockSignals(true);
-
- int left = x;
- int right = startPositions.right;
- int bottom = y;
- int top = startPositions.top;
-
- // left side is over the right one
- if (left > right) {
- std::swap(left, right);
- }
-
- if (top > bottom) {
- std::swap(top, bottom);
- }
-
- spinLeft->setValue(left);
- spinTop->setValue(top);
- spinRight->setValue(right);
- spinBottom->setValue(bottom);
-
- spinLeft->blockSignals(false);
- spinTop->blockSignals(false);
- spinRight->blockSignals(false);
- spinBottom->blockSignals(false);
-}
-
-/**
- * This is an update and implicity a finish, as there's only one
- * update for the CoR (single point-click). The coordinates count as
- * usual in Qt widgets. Top-left is (0,0).
- *
- * @param x position on x axis (local to the image)
- * @param y position on y axis (local to the image)
- */
-void TomographyROIViewQtWidget::mouseUpdateCoR(const int x, const int y) {
- grabCoRFromMousePoint(x, y);
- refreshImage();
-
- m_presenter->notify(ITomographyROIPresenter::FinishedCoR);
-}
-
-/**
- * Start of ROI selection (or first click after pushing "select
- * ROI". The rectangle starts as a point from the mouse click.
- *
- * @param x position on x axis (local to the image)
- * @param y position on y axis (local to the image)
- */
-void TomographyROIViewQtWidget::mouseUpdateROICornersStartSelection(
- const int x, const int y) {
- grabROICorner1FromMousePoint(x, y);
- grabROICorner2FromMousePoint(x, y);
- refreshImage();
- m_selectionState = ITomographyROIView::SelectROISecond;
-}
-
-/**
- * Change the rectangle while pressing the mouse button. The first
- * corner stays at the first click, now only the second corner changes
- * to the new mouse position. On release of the mouse button we'll get
- * to mouseFinishROICorner2() and end the selection of the ROI.
- *
- * @param x position on x axis (local to the image)
- * @param y position on y axis (local to the image)
- */
-void TomographyROIViewQtWidget::mouseUpdateROICornerContinuedSelection(
- const int x, const int y) {
- grabROICorner2FromMousePoint(x, y);
- grabROIFromWidgets();
- refreshImage();
-}
-
-/**
- * End of ROI selection (or mouse button release after clicking once
- * and move, all after pushing "select ROI". The second corner of the
- * rectangle is set at the current position.
- *
- * @param x position on x axis (local to the image)
- * @param y position on y axis (local to the image)
- */
-void TomographyROIViewQtWidget::mouseFinishROI(const int x, const int y) {
- grabROICorner2FromMousePoint(x, y);
- refreshImage();
- m_presenter->notify(ITomographyROIPresenter::FinishedROI);
-}
-
-void TomographyROIViewQtWidget::mouseUpdateNormAreaCornersStartSelection(
- const int x, const int y) {
- grabNormAreaCorner1FromMousePoint(x, y);
- grabNormAreaCorner2FromMousePoint(x, y);
- refreshImage();
- m_selectionState = ITomographyROIView::SelectNormAreaSecond;
-}
-
-void TomographyROIViewQtWidget::mouseUpdateNormAreaCornerContinuedSelection(
- const int x, const int y) {
- grabNormAreaCorner2FromMousePoint(x, y);
- grabNormAreaFromWidgets();
- refreshImage();
-}
-
-void TomographyROIViewQtWidget::mouseFinishNormArea(const int x, const int y) {
- grabNormAreaCorner2FromMousePoint(x, y);
- refreshImage();
- m_presenter->notify(ITomographyROIPresenter::FinishedNormalization);
-}
-
-/**
- * Slot for the signal emitted by the color bar widget when the user
- * requests a new color map.
- */
-void TomographyROIViewQtWidget::loadColorMapRequest() {
- m_presenter->notify(ITomographyROIPresenter::UpdateColorMap);
-}
-
-std::string TomographyROIViewQtWidget::askColorMapFile() {
- QString filename = MantidColorMap::loadMapDialog(
- QString::fromStdString(m_colorMapFilename), this);
- return filename.toStdString();
-}
-
-void TomographyROIViewQtWidget::updateColorMap(const std::string &filename) {
- // Load from file
- m_ui.colorBarWidget->getColorMap().loadMap(QString::fromStdString(filename));
- m_ui.colorBarWidget->updateColorMap();
-
- // if (!m_colorMapFilename.empty())
- // updateColorMap(m_colorMapFilename);
- m_ui.colorBarWidget->setViewRange(1, 65536);
-
- m_presenter->notify(ITomographyROIPresenter::ColorRangeUpdated);
-}
-
-/**
- * Slot for the signal emitted by the color bar widget when there's an
- * update in the values
- */
-void TomographyROIViewQtWidget::colorRangeChanged() {
- // the presenter should handle the image display update
- m_presenter->notify(ITomographyROIPresenter::ColorRangeUpdated);
-}
-
-void TomographyROIViewQtWidget::closeEvent(QCloseEvent *event) {
- m_presenter->notify(ITomographyROIPresenter::ShutDown);
- event->accept();
-}
-
-void TomographyROIViewQtWidget::readCoRFromProcessOutput(const QString &str) {
- if (str.isEmpty()) {
- // the process string is empty, it is likely the process crashed or was
- // unable to execute properly
- return;
- }
-
- // The COR will be printed on the last line of the output, and will be the
- // only
- // output on the line, the way we read it here, is to just the last line,
- // starting from the back and going until the first new line.
- // Cropping that out will be the COR that the script found.
- // ........ other strings above ........
- // 145
- const std::string output = str.toStdString();
-
- // -- to not be on the null character
- auto back_iterator = --(output.cend());
- std::string cor_number;
- for (; back_iterator != output.cbegin(); --back_iterator) {
- if (*back_iterator == '\n') {
- // found the last new line
- cor_number = std::string(back_iterator + 1, output.cend());
- break;
- }
- }
- int centreOfRotationValue = 0;
- try {
- centreOfRotationValue = std::stoi(cor_number);
- } catch (std::invalid_argument &) {
- // output centreOfRotationValue cannot be converted, do not change anything
- // and just return
- // silently
- return;
- }
- m_ui.spinBox_cor_x->setValue(centreOfRotationValue);
- // middle of image is ((bottom - top) / 2)
- // center is (top location + middle)
- int imageCentre =
- m_ui.spinBox_roi_top->value() +
- ((m_ui.spinBox_roi_bottom->value() - m_ui.spinBox_roi_top->value()) / 2);
-
- m_ui.spinBox_cor_y->setValue(imageCentre);
-
- // refresh all coordinate variables
- grabCoRFromWidgets();
- grabROIFromWidgets();
- grabNormAreaFromWidgets();
- // redraw the image with the rectangles
- refreshImage();
-}
-
-// TomographyROIViewQtWidget Signals
-void TomographyROIViewQtWidget::findCORClicked() {
- // this will run a --find-cor, empty executable path string signifies that
- // the default external interpretor will be used
- emit(findCORClickedSignal("", {"--find-cor"}));
-}
-
-void TomographyROIViewQtWidget::imageOrStackLoaded(const std::string &path) {
- emit(imageOrStackLoadedSignal(path));
-}
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/ToolConfig.cpp b/MantidQt/CustomInterfaces/src/Tomography/ToolConfig.cpp
deleted file mode 100644
index 5ef6a0785a7..00000000000
--- a/MantidQt/CustomInterfaces/src/Tomography/ToolConfig.cpp
+++ /dev/null
@@ -1,85 +0,0 @@
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigAstraToolbox.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigCustom.h"
-#include "MantidQtCustomInterfaces/Tomography/ToolConfigTomoPy.h"
-
-#include <boost/lexical_cast.hpp>
-
-namespace MantidQt {
-namespace CustomInterfaces {
-
-// pairs of name-in-the-tool, human-readable-name
-const std::vector<
- std::pair<std::string, std::string>> ToolConfigTomoPy::g_tomopyMethods = {
- std::make_pair("gridrec", "gridrec: Fourier grid reconstruction "
- "algorithm (Dowd, 19999; Rivers, 2006)"),
- std::make_pair("sirt",
- "sirt: Simultaneous algebraic reconstruction technique"),
-
- std::make_pair("art",
- "art: Algebraic reconstruction technique (Kak, 1998)"),
- std::make_pair("bart", "bart: Block algebraic reconstruction technique."),
- std::make_pair("fbp", "fbp: Filtered back-projection algorithm"),
- std::make_pair("mlem", "mlem: Maximum-likelihood expectation maximization "
- "algorithm (Dempster, 1977)"),
- std::make_pair("osem", "osem: Ordered-subset expectation maximization "
- "algorithm (Hudson, 1994)"),
- std::make_pair("ospml_hybrid",
- "ospml_hybrid: Ordered-subset penalized maximum "
- "likelihood algorithm with weighted "
- "linear and quadratic penalties"),
- std::make_pair("ospml_quad", "ospml_quad: Ordered-subset penalized maximum "
- "likelihood algorithm with quadratic "
- "penalties"),
- std::make_pair("pml_hybrid",
- "pml_hybrid: Penalized maximum likelihood algorithm "
- "with weighted linear and quadratic "
- "penalties (Chang, 2004)"),
- std::make_pair("pml_quad", "pml_quad: Penalized maximum likelihood "
- "algorithm with quadratic penalty"),
-};
-
-ToolConfigTomoPy::ToolConfigTomoPy()
- : TomoRecToolConfig(""), m_pathOut(""), m_pathDark(""), m_pathOpen(""),
- m_pathSample("") {}
-
-ToolConfigTomoPy::ToolConfigTomoPy(const std::string &runnable,
- const std::string &pathOut,
- const std::string &pathDark,
- const std::string &pathOpen,
- const std::string &pathSample)
- : TomoRecToolConfig(runnable), m_pathOut(pathOut), m_pathDark(pathDark),
- m_pathOpen(pathOpen), m_pathSample(pathSample) {}
-
-std::string ToolConfigTomoPy::makeCmdLineOptions() const {
- return "--input-path=" + m_pathSample + " --output-path=" + m_pathOut;
-}
-
-ToolConfigAstraToolbox::ToolConfigAstraToolbox()
- : TomoRecToolConfig(""), m_pathOut(""), m_pathDark(""), m_pathOpen(""),
- m_pathSample("") {}
-
-ToolConfigAstraToolbox::ToolConfigAstraToolbox(const std::string &runnable,
- const std::string &pathOut,
- const std::string &pathDark,
- const std::string &pathOpen,
- const std::string &pathSample)
- : TomoRecToolConfig(runnable), m_pathOut(pathOut), m_pathDark(pathDark),
- m_pathOpen(pathOpen), m_pathSample(pathSample) {}
-
-std::string ToolConfigAstraToolbox::makeCmdLineOptions() const {
- return " --input-path=" + m_pathSample + " --output-path=" + m_pathOut;
-}
-
-const std::vector<std::pair<
- std::string, std::string>> ToolConfigAstraToolbox::g_astraMethods = {
- std::make_pair("FBP3D_CUDA", "FBP 3D: Filtered Back-Propagation"),
- std::make_pair(
- "SIRT3D_CUDA",
- "SIRT 3D: Simultaneous Iterative Reconstruction Technique algorithm"),
- std::make_pair("CGLS3D_CUDA",
- "CGLS 3D: Conjugate gradient least square algorithm"),
- std::make_pair("FDK_CUDA", "FDK 3D: Feldkamp-Davis-Kress algorithm for "
- "3D circular cone beam data sets")};
-
-} // namespace CustomInterfaces
-} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/test/ImggFormatsConvertPresenterTest.h b/MantidQt/CustomInterfaces/test/ImggFormatsConvertPresenterTest.h
deleted file mode 100644
index fa5c6eaf5cc..00000000000
--- a/MantidQt/CustomInterfaces/test/ImggFormatsConvertPresenterTest.h
+++ /dev/null
@@ -1,108 +0,0 @@
-#ifndef MANTID_CUSTOMINTERFACES_IMGGFORMATSCONVERTPRESENTERTEST_H
-#define MANTID_CUSTOMINTERFACES_IMGGFORMATSCONVERTPRESENTERTEST_H
-
-#include "MantidAPI/FrameworkManager.h"
-#include "MantidQtCustomInterfaces/Tomography/ImggFormatsConvertPresenter.h"
-
-#include <cxxtest/TestSuite.h>
-#include "ImggFormatsConvertViewMock.h"
-
-using namespace MantidQt::CustomInterfaces;
-using testing::TypedEq;
-using testing::Return;
-
-class ImggFormatsConvertPresenterTest : public CxxTest::TestSuite {
-
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static ImggFormatsConvertPresenterTest *createSuite() {
- return new ImggFormatsConvertPresenterTest();
- }
-
- static void destroySuite(ImggFormatsConvertPresenterTest *suite) {
- delete suite;
- }
-
- ImggFormatsConvertPresenterTest() {
- Mantid::API::FrameworkManager::Instance(); // make sure framework is
- // initialized
- }
-
- void setUp() override {
- m_view.reset(new testing::NiceMock<ImggFormatsConvertViewMock>());
- m_presenter.reset(
- new MantidQt::CustomInterfaces::ImggFormatsConvertPresenter(
- m_view.get()));
- }
-
- void tearDown() override {
- TS_ASSERT(testing::Mock::VerifyAndClearExpectations(m_view.get()));
- }
-
- void test_init() {
- testing::NiceMock<ImggFormatsConvertViewMock> mockView;
- MantidQt::CustomInterfaces::ImggFormatsConvertPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, setFormats(testing::_, testing::_, testing::_))
- .Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(IImggFormatsConvertPresenter::Init);
- TSM_ASSERT("Mock view not used as expected. Some EXPECT_CALL conditions "
- "were not satisfied",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_convertFails() {
- testing::NiceMock<ImggFormatsConvertViewMock> mockView;
- MantidQt::CustomInterfaces::ImggFormatsConvertPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, inputPath()).Times(1).WillRepeatedly(Return(""));
- EXPECT_CALL(mockView, outputPath()).Times(1).WillRepeatedly(Return(""));
- EXPECT_CALL(mockView, maxSearchDepth()).Times(1).WillRepeatedly(Return(3));
- // should not get there
- EXPECT_CALL(mockView, inputFormatName()).Times(0);
- EXPECT_CALL(mockView, outputFormatName()).Times(0);
-
- // empty paths should produce an error
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(1);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(IImggFormatsConvertPresenter::Convert);
- TSM_ASSERT("Mock view not used as expected. Some EXPECT_CALL conditions "
- "were not satisfied",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_shutDown() {
- testing::NiceMock<ImggFormatsConvertViewMock> mockView;
- MantidQt::CustomInterfaces::ImggFormatsConvertPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, saveSettings()).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(IImggFormatsConvertPresenter::ShutDown);
- TSM_ASSERT("Mock view not used as expected. Some EXPECT_CALL conditions "
- "were not satisfied",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
-private:
- std::unique_ptr<testing::NiceMock<ImggFormatsConvertViewMock>> m_view;
-
- std::unique_ptr<MantidQt::CustomInterfaces::ImggFormatsConvertPresenter>
- m_presenter;
- // To have one FITS, etc.
- Mantid::API::MatrixWorkspace_sptr m_ws;
- static std::string g_scarfName;
- static std::string g_ccpi;
-};
-
-#endif // MANTID_CUSTOMINTERFACES_IMGGFORMATSCONVERTPRESENTERTEST_H
diff --git a/MantidQt/CustomInterfaces/test/ImggFormatsConvertViewMock.h b/MantidQt/CustomInterfaces/test/ImggFormatsConvertViewMock.h
deleted file mode 100644
index 497be107528..00000000000
--- a/MantidQt/CustomInterfaces/test/ImggFormatsConvertViewMock.h
+++ /dev/null
@@ -1,74 +0,0 @@
-#ifndef MANTID_CUSTOMINTERFACES_IMGGFORMATSCONVERTVIEWMOCK_H
-#define MANTID_CUSTOMINTERFACES_IMGGFORMATSCONVERTVIEWMOCK_H
-
-#include "MantidAPI/MatrixWorkspace_fwd.h"
-#include "MantidKernel/WarningSuppressions.h"
-#include "MantidQtCustomInterfaces/Tomography/IImggFormatsConvertView.h"
-
-#include <gmock/gmock.h>
-
-GCC_DIAG_OFF_SUGGEST_OVERRIDE
-
-// This is a simple mock for the tomo interface view when using SCARF.
-class ImggFormatsConvertViewMock
- : public MantidQt::CustomInterfaces::IImggFormatsConvertView {
-public:
- // void userWarning(const std::string &warn, const std::string &description)
- MOCK_METHOD2(userWarning,
- void(const std::string &warn, const std::string &description));
-
- // void userError(const std::string &err, const std::string &description)
- MOCK_METHOD2(userError,
- void(const std::string &err, const std::string &description));
-
- // void setFormats(const std::vector<std::string> &fmts,
- // std::vector<bool> &enableLoad, std::vector<bool> &enableSave)
- MOCK_METHOD3(setFormats, void(const std::vector<std::string> &fmts,
- const std::vector<bool> &enableLoad,
- const std::vector<bool> &enableSave));
-
- // std::string inputPath() const
- MOCK_CONST_METHOD0(inputPath, std::string());
-
- // std::string inputFormatName() const
- MOCK_CONST_METHOD0(inputFormatName, std::string());
-
- // std::string outputPath() const
- MOCK_CONST_METHOD0(outputPath, std::string());
-
- // std::string outputFormatName() const
- MOCK_CONST_METHOD0(outputFormatName, std::string());
-
- // bool compressHint() const
- MOCK_CONST_METHOD0(compressHint, bool());
-
- // void convert(const std::string &inputName, const std::string
- // &inputFormat, const std::string &outputName, const std::string
- // &outputFormat) const
- MOCK_CONST_METHOD4(convert, void(const std::string &inputName,
- const std::string &inputFormat,
- const std::string &outputName,
- const std::string &outputFormat));
-
- // void writeImg(MatrixWorkspace_sptr inWks, const std::string
- // &outputName, const std::string &outFormat) const
-
- MOCK_CONST_METHOD3(writeImg, void(Mantid::API::MatrixWorkspace_sptr inWks,
- const std::string &outputName,
- const std::string &outFormat));
-
- // MatrixWorkspace_sptr loadImg(const std::string &inputName, const
- // std::string &inputFormat) const
- MOCK_CONST_METHOD2(
- loadImg, Mantid::API::MatrixWorkspace_sptr(const std::string &outputName,
- const std::string &outFormat));
-
- // size_t maxSearchDepth() const
- MOCK_CONST_METHOD0(maxSearchDepth, size_t());
-
- // void saveSettings() const
- MOCK_CONST_METHOD0(saveSettings, void());
-};
-
-GCC_DIAG_ON_SUGGEST_OVERRIDE
-#endif // MANTID_CUSTOMINTERFACES_IMGGFORMATSCONVERTVIEWMOCK_H
diff --git a/MantidQt/CustomInterfaces/test/StackOfImagesDirsTest.h b/MantidQt/CustomInterfaces/test/StackOfImagesDirsTest.h
deleted file mode 100644
index 803eaece6bb..00000000000
--- a/MantidQt/CustomInterfaces/test/StackOfImagesDirsTest.h
+++ /dev/null
@@ -1,111 +0,0 @@
-#ifndef MANTID_CUSTOMINTERFACES_STACKOFIMAGESDIRSTEST_H
-#define MANTID_CUSTOMINTERFACES_STACKOFIMAGESDIRSTEST_H
-
-#include "MantidAPI/FrameworkManager.h"
-#include "MantidQtCustomInterfaces/Tomography/StackOfImagesDirs.h"
-
-#include <boost/scoped_ptr.hpp>
-
-#include <cxxtest/TestSuite.h>
-
-using namespace MantidQt::CustomInterfaces;
-
-class StackOfImagesDirsTest : public CxxTest::TestSuite {
-
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static StackOfImagesDirsTest *createSuite() {
- return new StackOfImagesDirsTest();
- }
-
- static void destroySuite(StackOfImagesDirsTest *suite) { delete suite; }
-
- StackOfImagesDirsTest() {
- Mantid::API::FrameworkManager::Instance(); // make sure the framework is
- // initialized
- }
-
- void setUp() override {
- // just to test more dynamic allocation
- m_soid.reset(new StackOfImagesDirs(""));
- }
-
- void tearDown() override {}
-
- void test_construct() {
- StackOfImagesDirs obj("");
-
- TSM_ASSERT("A stack just constructed with an empty path string should not "
- "be valid",
- !obj.isValid());
- }
-
- void test_description() {
- StackOfImagesDirs obj("");
-
- TS_ASSERT_THROWS_NOTHING(obj.description());
- TSM_ASSERT("A description string should be produced",
- "" != obj.description());
- }
-
- void test_status() {
- StackOfImagesDirs obj("");
-
- TS_ASSERT_THROWS_NOTHING(obj.description());
- TSM_ASSERT("A status string should be produced", "" != obj.status());
- }
-
- void test_sampleImagesDir() {
- StackOfImagesDirs obj("");
-
- TS_ASSERT_THROWS_NOTHING(obj.description());
- TSM_ASSERT("The sample images directory of an empty stack should be empty",
- "" == obj.sampleImagesDir());
- }
-
- void test_flatImagesDir() {
- StackOfImagesDirs obj("");
-
- TS_ASSERT_THROWS_NOTHING(obj.description());
- TSM_ASSERT("The flat images directory of an empty stack should be empty",
- "" == obj.flatImagesDir());
- }
-
- void test_darkImagesDir() {
- StackOfImagesDirs obj("");
-
- TS_ASSERT_THROWS_NOTHING(obj.description());
- TSM_ASSERT("The dark images directory of an empty stack should be empty",
- "" == obj.flatImagesDir());
- }
-
- void test_sampleFiles() {
- StackOfImagesDirs obj("");
-
- TS_ASSERT_THROWS_NOTHING(obj.description());
- TSM_ASSERT("There should not be any sample files in an empty stack",
- 0 == obj.sampleImagesDir().size());
- }
-
- void test_flatFiles() {
- StackOfImagesDirs obj("");
-
- TS_ASSERT_THROWS_NOTHING(obj.description());
- TSM_ASSERT("There should not be any flat image files in an empty stack",
- 0 == obj.flatImagesDir().size());
- }
-
- void test_darkFiles() {
- StackOfImagesDirs obj("");
-
- TS_ASSERT_THROWS_NOTHING(obj.description());
- TSM_ASSERT("There should not be any dark image files in an empty stack",
- 0 == obj.darkImagesDir().size());
- }
-
-private:
- boost::scoped_ptr<StackOfImagesDirs> m_soid;
-};
-
-#endif /* MANTID_CUSTOMINTERFACES_STACKOFIMAGESDIRSTEST_H */
diff --git a/MantidQt/CustomInterfaces/test/TomographyIfaceModelTest.h b/MantidQt/CustomInterfaces/test/TomographyIfaceModelTest.h
deleted file mode 100644
index 8abf9d97d95..00000000000
--- a/MantidQt/CustomInterfaces/test/TomographyIfaceModelTest.h
+++ /dev/null
@@ -1,406 +0,0 @@
-#ifndef MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEMODELTEST_H
-#define MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEMODELTEST_H
-
-#include "MantidAPI/FrameworkManager.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidKernel/FacilityInfo.h"
-
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfaceModel.h"
-
-#include "MantidQtCustomInterfaces/Tomography/TomoToolConfigDialogBase.h"
-
-#include <cxxtest/TestSuite.h>
-
-using namespace Mantid::API;
-using namespace MantidQt::CustomInterfaces;
-
-class TomographyIfaceModelTest : public CxxTest::TestSuite {
-
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static TomographyIfaceModelTest *createSuite() {
- return new TomographyIfaceModelTest();
- }
-
- static void destroySuite(TomographyIfaceModelTest *suite) { delete suite; }
-
- TomographyIfaceModelTest() {
- Mantid::API::FrameworkManager::Instance(); // make sure framework is
- // initialized
- }
-
- void test_noInit() {
- auto model = Mantid::Kernel::make_unique<TomographyIfaceModel>();
-
- TSM_ASSERT_EQUALS("Unexpected number of compute resources",
- model->computeResources().size(), 2);
-
- TSM_ASSERT_EQUALS("Unexpected number of compute resources (status)",
- model->computeResourcesStatus().size(), 0);
-
- TSM_ASSERT_EQUALS("Unexpected default tool", model->usingTool(), "TomoPy");
-
- TSM_ASSERT_EQUALS("Unexpected name for local machine",
- model->localComputeResource(), "Local");
- }
-
- void test_setupComputeResource() {
- auto model = Mantid::Kernel::make_unique<TomographyIfaceModel>();
-
- model->setupComputeResource();
-
- TSM_ASSERT_EQUALS("Unexpected number of compute resources",
- model->computeResources().size(), 2);
-
- auto status = model->computeResourcesStatus();
- TSM_ASSERT_EQUALS("Unexpected number of compute resources (status)",
- status.size(), 2);
- TSM_ASSERT("Unexpected status for first compute resource ", status[0]);
- TSM_ASSERT("Unexpected status for second compute resource ", status[1]);
-
- TSM_ASSERT_THROWS_NOTHING("Problem in cleanup", model->cleanup());
- }
-
- void test_setupToolsDefaults() {
- TomographyIfaceModel model;
-
- model.setupRunTool("Local");
-
- TSM_ASSERT_EQUALS("Unexpected number of reconstruction tools",
- model.reconTools().size(), 5);
-
- const auto status = model.reconToolsStatus();
-
- const std::vector<bool> expected = {true, true, false, false, true};
- TSM_ASSERT_EQUALS("Unexpected number of reconstruction tools (status)",
- status.size(), 5);
- for (size_t idx = 0; idx < status.size(); ++idx) {
- TSM_ASSERT("Unexpected status for tool number " + std::to_string(idx + 1),
- status[idx] == expected[idx]);
- }
- }
-
- void test_facilities() {
- TomographyIfaceModel model;
-
- // save original facility
- const Mantid::Kernel::FacilityInfo &prevFac =
- Mantid::Kernel::ConfigService::Instance().getFacility();
-
- Mantid::Kernel::ConfigService::Instance().setFacility("ISIS");
- auto isSupported = model.facilitySupported();
- TSM_ASSERT("This facility should be supported", isSupported);
-
- const std::vector<std::string> otherFacilities = {"SNS", "HFIR", "ILL",
- "ANSTO", "TEST_LIVE"};
- for (const auto &facility : otherFacilities) {
- Mantid::Kernel::ConfigService::Instance().setFacility(facility);
- TSM_ASSERT("This facility should not be supported",
- !model.facilitySupported());
- }
-
- // restore facility
- Mantid::Kernel::ConfigService::Instance().setFacility(prevFac.name());
- }
-
- void test_jobsStatus() {
- TomographyIfaceModel model;
-
- model.setupComputeResource();
- model.setupRunTool("Local");
-
- TSM_ASSERT_THROWS_NOTHING("Problem with experiment number",
- model.setExperimentReference("RB0001234"));
-
- auto sts = model.jobsStatus();
- TSM_ASSERT_EQUALS("Unexpected number of jobs", sts.size(), 0);
-
- auto localSts = model.jobsStatusLocal();
- TSM_ASSERT_EQUALS("Unexpected number of jobs (local)", localSts.size(), 0);
-
- model.refreshLocalJobsInfo();
- localSts = model.jobsStatusLocal();
- TSM_ASSERT_EQUALS("Unexpected number of jobs (local), after refreshing",
- localSts.size(), 0);
-
- model.doRefreshJobsInfo("phony");
- sts = model.jobsStatus();
- TSM_ASSERT_EQUALS("Unexpected number of jobs, after refreshing", sts.size(),
- 0);
- }
-
- void test_pingFail() {
- TomographyIfaceModel model;
-
- TSM_ASSERT_THROWS("Exception not thrown as expected - ping local",
- model.doPing("Local"), std::invalid_argument);
- }
-
- void test_loginFail() {
- TomographyIfaceModel model;
-
- TSM_ASSERT_EQUALS("Should not be logged in", model.loggedIn(), "");
-
- TSM_ASSERT_THROWS("Exception not thrown as expected - login local",
- model.doLogin("Local", "foo_user", "password"),
- std::invalid_argument);
- }
-
- void test_logoutFail() {
- TomographyIfaceModel model;
-
- TSM_ASSERT_THROWS("Exception not thrown as expected - logout local",
- model.doLogout("Local", "foo_user"),
- std::invalid_argument);
- }
-
- void test_queryFail() {
- TomographyIfaceModel model;
-
- std::vector<std::string> ids;
- std::vector<std::string> names;
- std::vector<std::string> status;
- std::vector<std::string> cmds;
- TSM_ASSERT_THROWS("Exception not thrown as expected - ping local",
- model.doQueryJobStatus("Local", ids, names, status, cmds),
- std::invalid_argument);
- TS_ASSERT_EQUALS(ids.size(), 0);
- TS_ASSERT_EQUALS(names.size(), 0);
- TS_ASSERT_EQUALS(status.size(), 0);
- TS_ASSERT_EQUALS(cmds.size(), 0);
- }
-
- void test_cancelFail() {
- TomographyIfaceModel model;
-
- TSM_ASSERT_EQUALS("Should not be logged in", model.loggedIn(), "");
-
- const std::vector<std::string> ids = {"none", "inexistent"};
- TSM_ASSERT_THROWS("Exception not thrown as expected - login local",
- model.doCancelJobs("Local", ids), std::invalid_argument);
- }
-
- void test_loadFITSFail() {
- TomographyIfaceModel model;
-
- TSM_ASSERT_THROWS("Exception not thrown as expected - load FITS",
- model.loadFITSImage("/i_dont_exist.nope"),
- std::invalid_argument);
- }
-
- // this currently just transforms the names to lower case
- void test_prepareToolNameForArgs() {
-
- TestableTomographyIfaceModel model;
-
- const std::string exp1 = model.prepareToolNameForArgs("TomoPy");
- const std::string exp2 = model.prepareToolNameForArgs("Astra");
- const std::string exp3 = model.prepareToolNameForArgs("Savu");
- const std::string exp4 = model.prepareToolNameForArgs("Custom Command");
-
- TS_ASSERT_EQUALS(exp1, "tomopy");
- TS_ASSERT_EQUALS(exp2, "astra");
- TS_ASSERT_EQUALS(exp3, "savu");
- TS_ASSERT_EQUALS(exp4, "custom command");
- // although custom command never reaches that function
- }
-
- void test_makeRemoteRunnableWithOptionsCustom() {
- std::string inputRunnable = "/scriptPath/";
- // the custom one just processes a single member
- std::vector<std::string> inputArgsVector{
- "--some params --some other params"};
-
- TestableTomographyIfaceModel model;
-
- std::string inputArgsString =
- model.constructSingleStringFromVector(inputArgsVector);
-
- std::shared_ptr<TomoRecToolConfig> d = std::shared_ptr<TomoRecToolConfig>(
- new ToolConfigCustom(inputRunnable, inputArgsString));
-
- model.usingTool(TestableTomographyIfaceModel::g_customCmdTool);
- model.setCurrentToolMethod("gridrec");
-
- model.setCurrentToolSettings(d);
-
- const bool local = false;
-
- std::string actualRunnable;
- std::string allOpts;
- std::vector<std::string> actualArgsVector;
- model.prepareSubmissionArguments(local, actualRunnable, actualArgsVector,
- allOpts);
-
- std::string expectedRunnable = "/scriptPath/";
- // the space at the end is necessary, because of how
- // constructSingleStringFromVector works
- std::vector<std::string> expectedArgsVector{
- "--some params --some other params "};
- doTestExpectedRunnableAndArguments(expectedRunnable, actualRunnable,
- expectedArgsVector, actualArgsVector);
- }
-
- void test_makeLocalRunnableWithOptionsCustom() {
- std::string inputRunnable = "python /scriptPath/";
- // the custom one just processes a single member
- std::vector<std::string> inputArgsVector{
- "--some params --some other params"};
-
- TestableTomographyIfaceModel model;
-
- std::string inputArgsString =
- model.constructSingleStringFromVector(inputArgsVector);
-
- std::shared_ptr<TomoRecToolConfig> d = std::shared_ptr<TomoRecToolConfig>(
- new ToolConfigCustom(inputRunnable, inputArgsString));
-
- model.usingTool(TestableTomographyIfaceModel::g_customCmdTool);
- model.setCurrentToolMethod("gridrec");
-
- model.setCurrentToolSettings(d);
-
- const bool local = true;
-
- std::string actualRunnable;
- std::string allOpts;
-
- std::vector<std::string> actualArgsVector;
- model.prepareSubmissionArguments(local, actualRunnable, actualArgsVector,
- allOpts);
-
- std::string expectedRunnable = "python";
- // the space at the end is necessary, because of how
- // constructSingleStringFromVector works
- std::vector<std::string> expectedArgsVector{
- "/scriptPath/", "--some params --some other params "};
- doTestExpectedRunnableAndArguments(expectedRunnable, actualRunnable,
- expectedArgsVector, actualArgsVector);
- }
-
- void test_makeRemoteRunnableWithOptions() {
- std::string expectedRunnable =
- "/work/imat/phase_commissioning/scripts/Imaging/"
- "IMAT/tomo_reconstruct.py";
- TomoPathsConfig pathConfig;
-
- const std::string pathOut = "/work/imat";
- static size_t reconIdx = 1;
- const std::string localOutNameAppendix = std::string("/processed/") +
- "reconstruction_" +
- std::to_string(reconIdx);
-
- std::shared_ptr<TomoRecToolConfig> d = std::shared_ptr<TomoRecToolConfig>(
- new ToolConfigTomoPy(expectedRunnable, pathOut + localOutNameAppendix,
- pathConfig.pathDarks(), pathConfig.pathOpenBeam(),
- pathConfig.pathSamples()));
-
- TestableTomographyIfaceModel model;
-
- model.usingTool(TestableTomographyIfaceModel::g_TomoPyTool);
- model.setCurrentToolMethod("gridrec");
-
- model.setCurrentToolSettings(d);
-
- const bool local = false;
-
- std::string allOpts;
- std::string actualRunnable;
- std::vector<std::string> actualArgsVector;
- model.prepareSubmissionArguments(local, actualRunnable, actualArgsVector,
- allOpts);
-
- std::vector<std::string> expectedArgsVector{
- "--tool=tomopy", "--algorithm=gridrec", "--num-iter=5",
- "--input-path=" + pathConfig.pathSamples(),
- "--input-path-flat=" + pathConfig.pathOpenBeam(),
- "--input-path-dark=" + pathConfig.pathDarks(),
- "--output=\"/work/imat/phase_commissioning/processed/"
- "reconstruction_TomoPy_gridrec_2016October20_113701_413275000",
- "--median-filter-size=3", "--cor=0.000000", "--rotation=0",
- "--max-angle=360.000000", "--circular-mask=0.940000",
- "--out-img-format=png"};
- doTestExpectedRunnableAndArguments(expectedRunnable, actualRunnable,
- expectedArgsVector, actualArgsVector);
- }
-
- void test_makeLocalRunnableWithOptions() {
- std::string inputRunnable = "python "
- "/work/imat/phase_commissioning/scripts/"
- "Imaging/IMAT/tomo_reconstruct.py";
-
- TomoPathsConfig pathConfig;
- const std::string pathOut = "~/imat/RB000XXX";
- static size_t reconIdx = 1;
- const std::string localOutNameAppendix = std::string("/processed/") +
- "reconstruction_" +
- std::to_string(reconIdx);
-
- std::shared_ptr<TomoRecToolConfig> d = std::shared_ptr<TomoRecToolConfig>(
- new ToolConfigTomoPy(inputRunnable, pathOut + localOutNameAppendix,
- pathConfig.pathDarks(), pathConfig.pathOpenBeam(),
- pathConfig.pathSamples()));
-
- TestableTomographyIfaceModel model;
-
- model.usingTool(TestableTomographyIfaceModel::g_TomoPyTool);
- model.setCurrentToolMethod("gridrec");
-
- model.setCurrentToolSettings(d);
-
- const bool local = true;
-
- // should be just the externalInterpretor path
- std::string actualRunnable;
- std::string allOpts;
- std::vector<std::string> actualArgsVector;
- model.prepareSubmissionArguments(local, actualRunnable, actualArgsVector,
- allOpts);
-
- std::string expectedRunnable = "python";
- std::vector<std::string> expectedArgsVector{
- "/work/imat/phase_commissioning/scripts/Imaging/IMAT/"
- "tomo_reconstruct.py",
- "--tool=tomopy", "--algorithm=gridrec", "--num-iter=5",
- "--input-path=/work/imat/phase_commissioning/data",
- "--input-path-flat=/work/imat/phase_commissioning/flat",
- "--input-path-dark=/work/imat/phase_commissioning/dark",
- "--output=/work/imat/phase_commissioning/processed/"
- "reconstruction_TomoPy_gridrec_2016October20_113701_413275000",
- "--median-filter-size=3", "--cor=0.000000", "--rotation=0",
- "--max-angle=360.000000", "--circular-mask=0.940000",
- "--out-img-format=png"};
-
- doTestExpectedRunnableAndArguments(expectedRunnable, actualRunnable,
- expectedArgsVector, actualArgsVector);
- }
-
-private:
- // inner class to access the model's protected functions
- class TestableTomographyIfaceModel : public TomographyIfaceModel {
- friend class TomographyIfaceModelTest;
- TestableTomographyIfaceModel() : TomographyIfaceModel() {}
- };
-
- void doTestExpectedRunnableAndArguments(
- const std::string &expectedRunnable, const std::string &actualRunnable,
- const std::vector<std::string> &expectedArguments,
- const std::vector<std::string> &actualArguments) {
- TSM_ASSERT_EQUALS("Local interpreter executable not properly separated",
- actualRunnable, expectedRunnable);
- TSM_ASSERT_EQUALS("Invalid argument size", expectedArguments.size(),
- actualArguments.size());
-
- for (size_t i = 0; i < expectedArguments.size(); ++i) {
- // this is the --output one that varies depending on time, so just skip
- if (expectedArguments[i].substr(0, 8) == "--output") {
- continue;
- }
- TS_ASSERT_EQUALS(expectedArguments[i], actualArguments[i]);
- }
- }
-};
-
-#endif // MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEMODELTEST_H
diff --git a/MantidQt/CustomInterfaces/test/TomographyIfacePresenterTest.h b/MantidQt/CustomInterfaces/test/TomographyIfacePresenterTest.h
deleted file mode 100644
index 5af4eff11e6..00000000000
--- a/MantidQt/CustomInterfaces/test/TomographyIfacePresenterTest.h
+++ /dev/null
@@ -1,732 +0,0 @@
-#ifndef MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEPRESENTERTEST_H
-#define MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEPRESENTERTEST_H
-
-#include "MantidAPI/FrameworkManager.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyIfacePresenter.h"
-
-#include "TomographyViewMock.h"
-#include <cxxtest/TestSuite.h>
-
-using namespace MantidQt::CustomInterfaces;
-using testing::TypedEq;
-using testing::Return;
-
-class TomographyIfacePresenterTest : public CxxTest::TestSuite {
-
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static TomographyIfacePresenterTest *createSuite() {
- return new TomographyIfacePresenterTest();
- }
-
- static void destroySuite(TomographyIfacePresenterTest *suite) {
- delete suite;
- }
-
- TomographyIfacePresenterTest() {
- // make sure the framework is initialized
- Mantid::API::FrameworkManager::Instance();
- }
-
- void setUp() override {
- m_view.reset(new testing::NiceMock<MockTomographyIfaceView>());
- m_presenter.reset(
- new MantidQt::CustomInterfaces::TomographyIfacePresenter(m_view.get()));
- }
-
- void tearDown() override {
- TS_ASSERT(testing::Mock::VerifyAndClearExpectations(m_view.get()));
- }
-
- void test_setupSystemSettings() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- // system settings should be self-contained - no need for any of these:
- EXPECT_CALL(mockView, currentPathsConfig()).Times(0);
- EXPECT_CALL(mockView, enableLoggedActions(false)).Times(0);
- EXPECT_CALL(mockView, setComputeResources(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, setReconstructionTools(testing::_, testing::_))
- .Times(0);
-
- EXPECT_CALL(mockView, systemSettings())
- .Times(1)
- .WillOnce(Return(TomoSystemSettings()));
-
- // No errors/warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::SystemSettingsUpdated);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_setupGood() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- // needs the basic paths at a very minimum
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
-
- EXPECT_CALL(mockView, systemSettings())
- .Times(1)
- .WillOnce(Return(TomoSystemSettings()));
- EXPECT_CALL(mockView, enableLoggedActions(false)).Times(1);
- EXPECT_CALL(mockView, setComputeResources(testing::_, testing::_)).Times(1);
- EXPECT_CALL(mockView, setReconstructionTools(testing::_, testing::_))
- .Times(1);
-
- // No errors/warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::SetupResourcesAndTools);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_setupWithWrongTool() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, systemSettings())
- .Times(1)
- .WillOnce(Return(TomoSystemSettings()));
- EXPECT_CALL(mockView, enableLoggedActions(false)).Times(1);
- EXPECT_CALL(mockView, setComputeResources(testing::_, testing::_)).Times(1);
- EXPECT_CALL(mockView, setReconstructionTools(testing::_, testing::_))
- .Times(1);
-
- // but this should be called once at setup time
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
-
- // One error, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::SetupResourcesAndTools);
-
- // needs one tool at a very minimum
- EXPECT_CALL(mockView, currentReconTool()).Times(1).WillOnce(Return(g_ccpi));
- // and basic tools settings
- EXPECT_CALL(mockView, currentPathsConfig()).Times(0);
-
- // tool config not available
- EXPECT_CALL(mockView, showToolConfig(testing::_)).Times(0);
- // this also implies that a second call to reconToolsSettings doesn't occur
-
- pres.notify(ITomographyIfacePresenter::SetupReconTool);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- // setup reconstruction tool now in preseter, have a unit test
- void test_setupReconToolGood() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, systemSettings()).Times(0);
- // needs the basic paths at a very minimum
- EXPECT_CALL(mockView, currentReconTool())
- .Times(2)
- .WillRepeatedly(Return("TomoPy"));
- // and basic tools settings
- TomoPathsConfig toolPaths;
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(toolPaths));
-
- EXPECT_CALL(mockView, showToolConfig(testing::_)).Times(1);
-
- // No errors/warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::ToolChanged);
- pres.notify(ITomographyIfacePresenter::SetupReconTool);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_valuesAtInit() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, systemSettings())
- .Times(1)
- .WillOnce(Return(TomoSystemSettings()));
- // needs basic paths config - using defaults
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::SetupResourcesAndTools);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_logOut_notIn() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- // would need compute resource and username if logged in
- EXPECT_CALL(mockView, getUsername()).Times(0);
- EXPECT_CALL(mockView, updateLoginControls(testing::_)).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::LogOutRequested);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_changeTool() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- std::vector<std::string> tools{"Astra", "TomoPy"};
-
- TomoPathsConfig toolPaths;
- for (const auto &tool : tools) {
- // expect the current paths config will be read only once
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(toolPaths));
-
- // expect the current reconstruction tool will be called only once
- EXPECT_CALL(mockView, currentReconTool()).Times(1).WillOnce(Return(tool));
-
- EXPECT_CALL(mockView, enableRunReconstruct(testing::_)).Times(1);
- EXPECT_CALL(mockView, enableConfigTool(testing::_)).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::ToolChanged);
- }
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_changeResource() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, currentReconTool()).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::CompResourceChanged);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_changePathsWithBrowseEmpty() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, updatePathsConfig(testing::_)).Times(0);
- EXPECT_CALL(mockView, experimentReference()).Times(0);
-
- // needs some basic paths config - using defaults from constructor
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::TomoPathsChanged);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_changePathsWithBrowseNonEmpty() {
- for (bool enableFlatDark : {true, false}) {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- TomoPathsConfig cfg;
- cfg.updatePathSamples("/nowhere/foo_samples");
- cfg.updatePathOpenBeam("/nonexistent/bla_ob", enableFlatDark);
- cfg.updatePathDarks("/missing_place/bla_dark", enableFlatDark);
- mockView.updatePathsConfig(cfg);
-
- EXPECT_CALL(mockView, updatePathsConfig(testing::_)).Times(0);
- EXPECT_CALL(mockView, experimentReference()).Times(0);
-
- // needs some basic paths config - using test / inexistent paths
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(cfg));
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::TomoPathsChanged);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
- }
-
- void test_changePathsEditingByHandEmpty() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, updatePathsConfig(testing::_)).Times(1);
- EXPECT_CALL(mockView, experimentReference()).Times(0);
-
- // needs some basic paths config - using defaults from constructor
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::TomoPathsEditedByUser);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_changePathsEditingByHand() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, experimentReference()).Times(0);
-
- // give only the samples path
- TomoPathsConfig cfg;
- cfg.updatePathSamples("/nowhere/foo_samples");
- mockView.updatePathsConfig(cfg);
-
- EXPECT_CALL(mockView, updatePathsConfig(testing::_)).Times(1);
-
- // needs some basic paths config - using defaults from constructor
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::TomoPathsEditedByUser);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_loginFails() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- // 1 Error, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(1);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::LogInRequested);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_runFails() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, systemSettings())
- .Times(1)
- .WillOnce(Return(TomoSystemSettings()));
-
- // needs basic paths config - using defaults
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- // EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
- pres.notify(ITomographyIfacePresenter::SetupResourcesAndTools);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_log() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- std::vector<std::string> msgs;
- msgs.emplace_back("foo log");
- msgs.emplace_back("baz log");
-
- EXPECT_CALL(mockView, logMsgs()).Times(1).WillOnce(Return(msgs));
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::LogMsg);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_refreshJobsNotIn() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, updateJobsInfoDisplay(testing::_, testing::_))
- .Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::RefreshJobs);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_cancelJobNotIn() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, updateJobsInfoDisplay(testing::_, testing::_))
- .Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::RefreshJobs);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_systemSettingsDefs() {
- TomoSystemSettings sets;
-
- const std::string msg = "Global tomography system settings default values "
- "should be as expected";
-
- TSM_ASSERT_EQUALS(msg + " (number of path components for image data)",
- sets.m_pathComponents.size(), 4);
-
- TSM_ASSERT_EQUALS(msg + " (prefix for sample images dir)",
- sets.m_samplesDirPrefix, "data");
-
- TSM_ASSERT_EQUALS(msg + " (prefix for flat/open beam images dir)",
- sets.m_flatsDirPrefix, "flat");
-
- TSM_ASSERT_EQUALS(msg + " (prefix for dark images dir)",
- sets.m_darksDirPrefix, "dark");
-
- TSM_ASSERT_EQUALS(
- msg + " (path component in the output for pre-processed images)",
- sets.m_outputPathCompPreProcessed, "pre_processed");
-
- TSM_ASSERT_EQUALS(msg + " (path component in the output for "
- "processed/reconstructed images/volumes)",
- sets.m_outputPathCompReconst, "processed");
- }
-
- void test_systemSettingsDefsLocal() {
- TomoSystemSettings sets;
-
- const std::string msg =
- "Local system settings default values should be as expected";
-
- // Normally this would be 3 for Win32 (example: D:\) and
- // >=5 otherwise
- const std::string path = sets.m_local.m_basePathTomoData;
- TSM_ASSERT_LESS_THAN_EQUALS(
- msg + " (base path for tomography data too short)", 3, path.length());
- }
-
- void test_systemSettingsDefsRemote() {
- TomoSystemSettings sets;
-
- const std::string msg =
- "Remote system settings default values should be as expected";
-
- TSM_ASSERT_EQUALS(msg + " (base path for tomography data)",
- sets.m_remote.m_basePathTomoData, "/work/imat");
-
- TSM_ASSERT_EQUALS(msg + " (base path for reconstruction scripts)",
- sets.m_remote.m_basePathReconScripts,
- "/work/imat/phase_commissioning");
- }
-
- void test_filtersSettings() {
- TomoReconFiltersSettings def;
-
- // When the presenter uses these settings for job submission there
- // the test should be extended with something like this:
- // EXPECT_CALL(mockView, prePostProcSettings()).Times(1).WillOnce(
- // Return("TomoPy"));
-
- TSM_ASSERT_EQUALS("Pre-processing filter settings default values should be "
- "as expected (normalization by air region)",
- def.prep.normalizeByAirRegion, true);
-
- TSM_ASSERT_EQUALS("Pre-processing settings default values should be as "
- "expected (proton-charge normalization)",
- def.prep.normalizeByProtonCharge, false);
-
- TSM_ASSERT_EQUALS("Pre-processing filter settings default values should be "
- "as expected (normalization by flat images)",
- def.prep.normalizeByFlats, true);
-
- TSM_ASSERT_EQUALS("Pre-processing filter settings default values should be "
- "as expected (normalization by dark images)",
- def.prep.normalizeByDarks, true);
-
- TSM_ASSERT_EQUALS("Pre-processing settings default values should be as "
- "expected (median filter width)",
- def.prep.medianFilterWidth, 3);
-
- TSM_ASSERT_EQUALS("Pre-processing settings default values should be as "
- "expected (rotation)",
- def.prep.rotation, 0);
-
- TSM_ASSERT_EQUALS("Pre-processing settings default values should be as "
- "expected (maximum angle)",
- def.prep.maxAngle, 360.0);
-
- TSM_ASSERT_LESS_THAN_EQUALS(
- "Pre-processing settings default values should be as "
- "expected (scale down)",
- def.prep.scaleDownFactor, 1);
-
- TSM_ASSERT_DELTA("Post-processing settings default values should be as "
- "expected (circular mask)",
- def.postp.circMaskRadius, 0.94, 1e-5);
-
- TSM_ASSERT_EQUALS("Post-processing settings default values should be as "
- "expected (cut-off)",
- def.postp.cutOffLevel, 0.0);
-
- TSM_ASSERT_EQUALS("Output settings default values should be as expected",
- def.outputPreprocImages, true);
- }
-
- void test_aggregateBandsFailsMissingPaths() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- // Empty params, missing the required ones for sure
- EXPECT_CALL(mockView, currentAggregateBandsParams())
- .Times(1)
- .WillOnce(Return(std::map<std::string, std::string>()));
-
- // Error
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(1);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::AggregateEnergyBands);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_aggregateBandsFailsWrongPaths() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- std::map<std::string, std::string> params;
- params["InputPath"] = "I_cannot_be_found_fail_";
- params["OutputPath"] = "fail_for_sure_i_m_not_found";
- params["UniformBands"] = "2";
- params["OutPrefixBands"] = "band_prefix_";
- params["InuptImageFormat"] = "FITS";
- params["OutputImageFormat"] = "FITS";
-
- // Will contain wrong values in the required paths
- EXPECT_CALL(mockView, currentAggregateBandsParams())
- .Times(1)
- .WillOnce(Return(params));
-
- // Error
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(1);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::AggregateEnergyBands);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- // disabled as this is I/O intensive and uses the algorithm runner (Qt)
- void disabled_test_aggregateBandsRuns() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- std::map<std::string, std::string> params;
- params["InputPath"] = "here_some_valid_input_images_path_";
- params["OutputPath"] = "here_some_valid_existing_output_path";
- params["UniformBands"] = "1";
- params["OutPrefixBands"] = "band_prefix_";
- params["InputImageFormat"] = "FITS";
- params["OutputImageFormat"] = "FITS";
-
- EXPECT_CALL(mockView, runAggregateBands(testing::_)).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::AggregateEnergyBands);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_sillySessionRemote() {
- // the user does a few silly things...
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, systemSettings()).Times(0);
-
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
-
- // user changes some paths
- pres.notify(ITomographyIfacePresenter::TomoPathsChanged);
- EXPECT_CALL(mockView, currentComputeResource())
- .WillRepeatedly(Return(g_scarfName));
-
- // user changes the compute resource
- pres.notify(ITomographyIfacePresenter::CompResourceChanged);
-
- EXPECT_CALL(mockView, currentReconTool())
- .Times(2)
- .WillRepeatedly(Return("TomoPy"));
-
- // and basic tools settings
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(TomoPathsConfig()));
-
- // the tool changed event sets up the tool's paths
- pres.notify(ITomographyIfacePresenter::ToolChanged);
- // user opens dialog and sets up a reconstruction tool
- pres.notify(ITomographyIfacePresenter::SetupReconTool);
-
- TomoPathsConfig pathsCfg;
- EXPECT_CALL(mockView, currentPathsConfig())
- .Times(1)
- .WillOnce(Return(pathsCfg));
-
- ImageStackPreParams roiEtc;
- EXPECT_CALL(mockView, currentROIEtcParams())
- .Times(1)
- .WillOnce(Return(roiEtc));
-
- TomoReconFiltersSettings filters;
- EXPECT_CALL(mockView, prePostProcSettings())
- .Times(1)
- .WillOnce(Return(filters));
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
-
- // we get one warning from trying to submit a job to remote
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(1);
-
- // finally, user tries to run a reconstruction job
- pres.notify(ITomographyIfacePresenter::RunReconstruct);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
- void test_shutDown() {
- testing::NiceMock<MockTomographyIfaceView> mockView;
- MantidQt::CustomInterfaces::TomographyIfacePresenter pres(&mockView);
-
- EXPECT_CALL(mockView, saveSettings()).Times(1);
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyIfacePresenter::ShutDown);
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView))
- }
-
-private:
- // boost::shared_ptr
- boost::scoped_ptr<testing::NiceMock<MockTomographyIfaceView>> m_view;
- // MockTomographyIfaceModel *m_model;
- boost::scoped_ptr<MantidQt::CustomInterfaces::TomographyIfacePresenter>
- m_presenter;
- // To have one FITS, etc.
- Mantid::API::MatrixWorkspace_sptr m_ws;
- static std::string g_scarfName;
- static std::string g_ccpi;
-};
-
-std::string TomographyIfacePresenterTest::g_scarfName = "SCARF@STFC";
-std::string TomographyIfacePresenterTest::g_ccpi = "CCPi CGLS";
-
-#endif // MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEPRESENTERTEST_H
diff --git a/MantidQt/CustomInterfaces/test/TomographyROIPresenterTest.h b/MantidQt/CustomInterfaces/test/TomographyROIPresenterTest.h
deleted file mode 100644
index a79981a47c5..00000000000
--- a/MantidQt/CustomInterfaces/test/TomographyROIPresenterTest.h
+++ /dev/null
@@ -1,679 +0,0 @@
-#ifndef MANTID_CUSTOMINTERFACES_TOMOGRAPHYROIPRESENTERTEST_H
-#define MANTID_CUSTOMINTERFACES_TOMOGRAPHYROIPRESENTERTEST_H
-
-#include "MantidAPI/FrameworkManager.h"
-#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidQtCustomInterfaces/Tomography/TomographyROIPresenter.h"
-#include "MantidTestHelpers/FakeObjects.h"
-
-#include <cxxtest/TestSuite.h>
-
-#include <Poco/File.h>
-
-#include "TomographyROIViewMock.h"
-
-using namespace MantidQt::CustomInterfaces;
-using testing::TypedEq;
-using testing::Return;
-
-class TomographyROIPresenterTest : public CxxTest::TestSuite {
-
-public:
- // This pair of boilerplate methods prevent the suite being created statically
- // This means the constructor isn't called when running other tests
- static TomographyROIPresenterTest *createSuite() {
- return new TomographyROIPresenterTest();
- }
-
- static void destroySuite(TomographyROIPresenterTest *suite) { delete suite; }
-
- TomographyROIPresenterTest() {
- Mantid::API::FrameworkManager::Instance(); // make sure the framework is
- // initialized
- }
-
- void setUp() override {
- m_view.reset(new testing::NiceMock<MockTomographyROIView>());
- m_presenter.reset(
- new MantidQt::CustomInterfaces::TomographyROIPresenter(m_view.get()));
- }
-
- void tearDown() override {
- TS_ASSERT(testing::Mock::VerifyAndClearExpectations(m_view.get()));
- }
-
- void test_initOK() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, setParams(testing::_)).Times(1);
-
- EXPECT_CALL(mockView, resetCoR()).Times(0);
- EXPECT_CALL(mockView, resetROI()).Times(0);
- EXPECT_CALL(mockView, resetNormArea()).Times(0);
- EXPECT_CALL(mockView, resetWidgetsOnNewStack()).Times(0);
- EXPECT_CALL(mockView, currentRotationAngle()).Times(0);
- EXPECT_CALL(mockView, updateRotationAngle(testing::_)).Times(0);
-
- // No errors/warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(TomographyROIPresenter::Init);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_initWithWrongParams() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, setParams(testing::_)).Times(1);
-
- EXPECT_CALL(mockView, resetWidgetsOnNewStack()).Times(0);
-
- // One error, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(TomographyROIPresenter::Init);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_browseSingleImg_EmptyPath() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, askImagePath(testing::_)).Times(1);
-
- // No error, no warning, just ignore
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- // because the path is wrong this should not happen
- EXPECT_CALL(mockView, resetWidgetsOnNewStack()).Times(0);
-
- // should not get there because there's no stack/img - it's just ignored:
- EXPECT_CALL(mockView, showStack(testing::An<const std::string &>()))
- .Times(0);
- EXPECT_CALL(
- mockView,
- showStack(testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>()))
- .Times(0);
- EXPECT_CALL(mockView, updateImgWithIndex(testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::BrowseImage);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_browseStack_EmptyPath() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, askImagePath(testing::_))
- .Times(1)
- .WillOnce(Return(""));
-
- // No error, no warnings, just ignored
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- // because the path is wrong this should not happen
- EXPECT_CALL(mockView, resetWidgetsOnNewStack()).Times(0);
-
- // should not get there:
- EXPECT_CALL(mockView, showStack(testing::An<const std::string &>()))
- .Times(0);
- EXPECT_CALL(
- mockView,
- showStack(testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>()))
- .Times(0);
- EXPECT_CALL(mockView, updateImgWithIndex(testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::BrowseStack);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_browseStack_WrongPath() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, askImagePath(testing::_))
- .Times(1)
- .WillOnce(Return("dont_look_for_me_i_dont_exist"));
-
- // A warning
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(1);
-
- // because the path is wrong this should not happen
- EXPECT_CALL(mockView, resetWidgetsOnNewStack()).Times(0);
-
- // should not get there because there's no stack/img
- EXPECT_CALL(mockView, showStack(testing::An<const std::string &>()))
- .Times(0);
- EXPECT_CALL(
- mockView,
- showStack(testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>()))
- .Times(0);
- EXPECT_CALL(mockView, updateImgWithIndex(testing::_)).Times(0);
-
- // this exception is currently handled, and a warning given
- // TSM_ASSERT_THROWS("There should be an exception if there is an unexpected
- // "
- // "error with the images path",
- // pres.notify(ITomographyROIPresenter::BrowseImgOrStack),
- // Poco::FileNotFoundException);
- pres.notify(ITomographyROIPresenter::BrowseStack);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_changeImageType() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- Mantid::API::WorkspaceGroup_sptr stack;
- EXPECT_CALL(mockView, currentImageTypeStack())
- .Times(1)
- .WillOnce(Return(stack));
- EXPECT_CALL(mockView, updateImageType(stack)).Times(1);
-
- // should not mix up with the img index
- EXPECT_CALL(mockView, currentImgIndex()).Times(0);
- EXPECT_CALL(mockView, updateImgWithIndex(testing::_)).Times(0);
-
- // Change without issues
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::ChangeImageType);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_changeRotation() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, currentRotationAngle()).Times(1).WillOnce(Return(0));
- EXPECT_CALL(mockView, updateRotationAngle(0.0f)).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::ChangeRotation);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_updateImgIndex() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- int idx = 0;
- EXPECT_CALL(mockView, currentImgIndex()).Times(1).WillOnce(Return(idx));
-
- EXPECT_CALL(mockView, updateImgWithIndex(idx)).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::UpdateImgIndex);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- // when the user clicks on 'play', with no images
- void test_playStartEmpty() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, currentImgIndex()).Times(0);
-
- Mantid::API::WorkspaceGroup_sptr emptyStack;
- EXPECT_CALL(mockView, currentImageTypeStack())
- .Times(1)
- .WillOnce(Return(emptyStack));
-
- EXPECT_CALL(mockView, enableActions(false)).Times(0);
- EXPECT_CALL(mockView, playStart()).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::PlayStartStop);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- // try to play a single image => a warning will pop up
- void test_playStartSingleImage() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- auto stack = boost::make_shared<Mantid::API::WorkspaceGroup>();
- auto img = boost::make_shared<WorkspaceTester>();
- stack->addWorkspace(img);
-
- EXPECT_CALL(mockView, currentImgIndex()).Times(0);
-
- EXPECT_CALL(mockView, currentImageTypeStack())
- .Times(1)
- .WillOnce(Return(stack));
-
- // for a single image, there should be a warning message, and we
- // should not even try to play
- EXPECT_CALL(mockView, enableActions(false)).Times(0);
- EXPECT_CALL(mockView, playStart()).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(1);
-
- pres.notify(ITomographyROIPresenter::PlayStartStop);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- // when the user clicks on 'play' with a reasonable stack of images
- void test_playOK() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- auto stack = boost::make_shared<Mantid::API::WorkspaceGroup>();
- auto img = boost::make_shared<WorkspaceTester>();
- auto img2 = boost::make_shared<WorkspaceTester>();
- stack->addWorkspace(img);
- stack->addWorkspace(img2);
-
- EXPECT_CALL(mockView, currentImageTypeStack())
- .Times(1)
- .WillOnce(Return(stack));
-
- EXPECT_CALL(mockView, currentImgIndex()).Times(0);
-
- EXPECT_CALL(mockView, enableActions(testing::_)).Times(1);
- EXPECT_CALL(mockView, playStart()).Times(1);
- EXPECT_CALL(mockView, playStop()).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- // start to play
- pres.notify(ITomographyROIPresenter::PlayStartStop);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- // when the user clicks on 'play', then 'stop', with a reasonable stack of
- // images
- void test_playStartStop() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- auto stack = boost::make_shared<Mantid::API::WorkspaceGroup>();
- auto img = boost::make_shared<WorkspaceTester>();
- auto img2 = boost::make_shared<WorkspaceTester>();
- stack->addWorkspace(img);
- stack->addWorkspace(img2);
-
- EXPECT_CALL(mockView, currentImageTypeStack())
- .Times(2)
- .WillRepeatedly(Return(stack));
-
- EXPECT_CALL(mockView, currentImgIndex()).Times(0);
-
- EXPECT_CALL(mockView, enableActions(testing::_)).Times(2);
- EXPECT_CALL(mockView, playStart()).Times(1);
- EXPECT_CALL(mockView, playStop()).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- // start first
- pres.notify(ITomographyROIPresenter::PlayStartStop);
- // then stop
- pres.notify(ITomographyROIPresenter::PlayStartStop);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_updateColorMapEmpty() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, askColorMapFile()).Times(1).WillOnce(Return(""));
-
- // Should not get there
- EXPECT_CALL(mockView, updateColorMap(testing::_)).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::UpdateColorMap);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_updateColorMapOK() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- const std::string filename = "test_inexistent_colormap.map";
- EXPECT_CALL(mockView, askColorMapFile())
- .Times(1)
- .WillOnce(Return(filename));
-
- EXPECT_CALL(mockView, updateColorMap(filename)).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::UpdateColorMap);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_changeColorRange() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, askColorMapFile()).Times(0);
-
- size_t img_idx = 0;
- EXPECT_CALL(mockView, currentImgIndex()).Times(1).WillOnce(Return(img_idx));
- EXPECT_CALL(mockView, updateImgWithIndex(img_idx)).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::ColorRangeUpdated);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_selectCoR() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, changeSelectionState(ITomographyROIView::SelectCoR))
- .Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::SelectCoR);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_resetCoR() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, resetCoR()).Times(1);
- EXPECT_CALL(mockView, changeSelectionState(ITomographyROIView::SelectNone))
- .Times(1);
-
- // just a few calls that should not happen
- EXPECT_CALL(mockView, resetROI()).Times(0);
- EXPECT_CALL(mockView, showStack(testing::An<const std::string &>()))
- .Times(0);
- EXPECT_CALL(
- mockView,
- showStack(testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>()))
- .Times(0);
- EXPECT_CALL(mockView, updateImgWithIndex(testing::_)).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::ResetCoR);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_selectROI() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, changeSelectionState(
- ITomographyROIView::SelectROIFirst)).Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::SelectROI);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_finishROI() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, changeSelectionState(ITomographyROIView::SelectNone))
- .Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::FinishedROI);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_resetROI() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, resetROI()).Times(1);
- EXPECT_CALL(mockView, changeSelectionState(ITomographyROIView::SelectNone))
- .Times(1);
-
- // just a few calls that should not happen
- EXPECT_CALL(mockView, resetCoR()).Times(0);
- EXPECT_CALL(mockView, showStack(testing::An<const std::string &>()))
- .Times(0);
- EXPECT_CALL(
- mockView,
- showStack(testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>()))
- .Times(0);
- EXPECT_CALL(mockView, updateImgWithIndex(testing::_)).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::ResetROI);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_selectNormalization() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView,
- changeSelectionState(ITomographyROIView::SelectNormAreaFirst))
- .Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::SelectNormalization);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_finishNormalization() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, changeSelectionState(ITomographyROIView::SelectNone))
- .Times(1);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::FinishedNormalization);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_resetNormalization() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, resetNormArea()).Times(1);
- EXPECT_CALL(mockView, changeSelectionState(ITomographyROIView::SelectNone))
- .Times(1);
-
- // just a few calls that should not happen
- EXPECT_CALL(mockView, resetCoR()).Times(0);
- EXPECT_CALL(mockView, resetROI()).Times(0);
- EXPECT_CALL(mockView, showStack(testing::An<const std::string &>()))
- .Times(0);
- EXPECT_CALL(
- mockView,
- showStack(testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>(),
- testing::An<const Mantid::API::WorkspaceGroup_sptr &>()))
- .Times(0);
- EXPECT_CALL(mockView, updateImgWithIndex(testing::_)).Times(0);
-
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(ITomographyROIPresenter::ResetNormalization);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
- void test_shutDown() {
- testing::NiceMock<MockTomographyROIView> mockView;
- MantidQt::CustomInterfaces::TomographyROIPresenter pres(&mockView);
-
- EXPECT_CALL(mockView, saveSettings()).Times(1);
- // No errors, no warnings
- EXPECT_CALL(mockView, userError(testing::_, testing::_)).Times(0);
- EXPECT_CALL(mockView, userWarning(testing::_, testing::_)).Times(0);
-
- pres.notify(TomographyROIPresenter::ShutDown);
-
- TSM_ASSERT(
- "Mock not used as expected. Some EXPECT_CALL conditions were not "
- "satisfied.",
- testing::Mock::VerifyAndClearExpectations(&mockView));
- }
-
-private:
- // boost::shared_ptr
- boost::scoped_ptr<testing::NiceMock<MockTomographyROIView>> m_view;
- boost::scoped_ptr<MantidQt::CustomInterfaces::TomographyROIPresenter>
- m_presenter;
-
- // To have one FITS, etc.
- Mantid::API::MatrixWorkspace_sptr m_ws;
-};
-
-#endif // MANTID_CUSTOMINTERFACES_TOMOGRAPHYROIPRESENTERTEST_H
diff --git a/MantidQt/CustomInterfaces/test/TomographyROIViewMock.h b/MantidQt/CustomInterfaces/test/TomographyROIViewMock.h
deleted file mode 100644
index c818e6ee7aa..00000000000
--- a/MantidQt/CustomInterfaces/test/TomographyROIViewMock.h
+++ /dev/null
@@ -1,112 +0,0 @@
-#ifndef MANTID_CUSTOMINTERFACES_TOMOGRAPHYROIVIEWMOCK_H
-#define MANTID_CUSTOMINTERFACES_TOMOGRAPHYROIVIEWMOCK_H
-
-#include "MantidKernel/WarningSuppressions.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h"
-
-#include <gmock/gmock.h>
-
-GCC_DIAG_OFF_SUGGEST_OVERRIDE
-
-class MockTomographyROIView
- : public MantidQt::CustomInterfaces::ITomographyROIView {
-public:
- // void initParams(ImageStackPreParams ¶ms)
- MOCK_METHOD1(setParams,
- void(MantidQt::CustomInterfaces::ImageStackPreParams &));
-
- // ImageStackPreParams userSelection() const;
- MOCK_CONST_METHOD0(userSelection,
- MantidQt::CustomInterfaces::ImageStackPreParams());
-
- // SelectionState selectionState() const;
- MOCK_CONST_METHOD0(selectionState, SelectionState());
-
- // void changeSelectionState(const SelectionState state);
- MOCK_METHOD1(changeSelectionState,
- void(const ITomographyROIView::SelectionState &));
-
- // void showStack(const std::string &path);
- MOCK_METHOD1(showStack, void(const std::string &));
-
- // void showStack(Mantid::API::WorkspaceGroup_sptr &ws,
- // Mantid::API::WorkspaceGroup_sptr &wsgFlats,
- // Mantid::API::WorkspaceGroup_sptr &wsgDarks);
- MOCK_METHOD3(showStack, void(const Mantid::API::WorkspaceGroup_sptr &,
- const Mantid::API::WorkspaceGroup_sptr &,
- const Mantid::API::WorkspaceGroup_sptr &));
-
- // const Mantid::API::WorkspaceGroup_sptr stackSamples() const;
- MOCK_CONST_METHOD0(stackSamples, const Mantid::API::WorkspaceGroup_sptr());
-
- // void showProjection(const Mantid::API::WorkspaceGroup_sptr &wsg, size_t
- // idx);
- MOCK_METHOD2(showProjection,
- void(const Mantid::API::WorkspaceGroup_sptr &wsg, size_t idx));
-
- // void userWarning(const std::string &warn, const std::string &description)
- MOCK_METHOD2(userWarning,
- void(const std::string &warn, const std::string &description));
-
- // void userError(const std::string &err, const std::string &description)
- MOCK_METHOD2(userError,
- void(const std::string &err, const std::string &description));
-
- // void enableActions(bool enable)
- MOCK_METHOD1(enableActions, void(bool));
-
- // Mantid::API::WorkspaceGroup_sptr currentImageTypeStack() const
- MOCK_CONST_METHOD0(currentImageTypeStack, Mantid::API::WorkspaceGroup_sptr());
-
- // void updateImageType(const Mantid::API::WorkspaceGroup_sptr wsg)
- MOCK_METHOD1(updateImageType,
- void(const Mantid::API::WorkspaceGroup_sptr wsg));
-
- // size_t currentImgIndex() const;
- MOCK_CONST_METHOD0(currentImgIndex, size_t());
-
- // void updateImgWithIndex(size_t idx)
- MOCK_METHOD1(updateImgWithIndex, void(size_t));
-
- // void playStart( idx)
- MOCK_METHOD0(playStart, void());
-
- // void playStop()
- MOCK_METHOD0(playStop, void());
-
- // float currentRotationAngle() const
- MOCK_CONST_METHOD0(currentRotationAngle, float());
-
- // void updateRotationAngle(float angle)
- MOCK_METHOD1(updateRotationAngle, void(float));
-
- // std::string askImgOrStackPath();
- MOCK_METHOD1(askImagePath, std::string(const std::string &));
-
- // std::string askColorMapFile();
- MOCK_METHOD0(askColorMapFile, std::string());
-
- MOCK_METHOD1(imageOrStackLoaded, void(const std::string &));
-
- // void updateColorMap(const std::string &filename);
- MOCK_METHOD1(updateColorMap, void(const std::string &));
-
- // void saveSettings() const {}
- MOCK_CONST_METHOD0(saveSettings, void());
-
- // void resetCoR()
- MOCK_METHOD0(resetCoR, void());
-
- // void resetROI()
- MOCK_METHOD0(resetROI, void());
-
- // void resetNormArea()
- MOCK_METHOD0(resetNormArea, void());
-
- // void resetNormArea()
- MOCK_METHOD0(resetWidgetsOnNewStack, void());
-};
-
-GCC_DIAG_ON_SUGGEST_OVERRIDE
-
-#endif // MANTID_CUSTOMINTERFACES_TOMOGRAPHYROIVIEWMOCK_H
diff --git a/MantidQt/CustomInterfaces/test/TomographyViewMock.h b/MantidQt/CustomInterfaces/test/TomographyViewMock.h
deleted file mode 100644
index 542dbfed903..00000000000
--- a/MantidQt/CustomInterfaces/test/TomographyViewMock.h
+++ /dev/null
@@ -1,139 +0,0 @@
-#ifndef MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEVIEWMOCK_H
-#define MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEVIEWMOCK_H
-
-#include "MantidKernel/WarningSuppressions.h"
-#include "MantidQtCustomInterfaces/Tomography/ITomographyIfaceView.h"
-
-#include <QString>
-
-#include <gmock/gmock.h>
-
-GCC_DIAG_OFF_SUGGEST_OVERRIDE
-
-// This is a simple mock for the tomo interface view when using SCARF.
-class MockTomographyIfaceView
- : public MantidQt::CustomInterfaces::ITomographyIfaceView {
-public:
- // void userWarning(const std::string &warn, const std::string &description)
- // {}
- MOCK_METHOD2(userWarning,
- void(const std::string &warn, const std::string &description));
-
- // void userError(const std::string &err, const std::string &description) {}
- MOCK_METHOD2(userError,
- void(const std::string &err, const std::string &description));
-
- // std::vector<std::string> logMsgs() const {}
- MOCK_CONST_METHOD0(logMsgs, std::vector<std::string>());
-
- // void setComputeResources(const std::vector<std::string> &resources,
- // const std::vector<bool> &enabled) {}
- MOCK_METHOD2(setComputeResources,
- void(const std::vector<std::string> &resources,
- const std::vector<bool> &enabled));
-
- // void setReconstructionTools(const std::vector<std::string> &tools,
- // const std::vector<bool> &enabled) {}
- MOCK_METHOD2(setReconstructionTools,
- void(const std::vector<std::string> &tools,
- const std::vector<bool> &enabled));
-
- // void saveSettings() const {}
- MOCK_CONST_METHOD0(saveSettings, void());
-
- // std::string getPassword() const {}
- MOCK_CONST_METHOD0(getUsername, std::string());
-
- // std::string experimentReference() const {}
- MOCK_CONST_METHOD0(experimentReference, std::string());
-
- // std::string getPassword() const {}
- MOCK_CONST_METHOD0(getPassword, std::string());
-
- // std::vector<std::string> processingJobsIDs() const {}
- MOCK_CONST_METHOD0(processingJobsIDs, std::vector<std::string>());
-
- // std::string currentComputeResource() const {}
- MOCK_CONST_METHOD0(currentComputeResource, std::string());
-
- // std::string currentReconTool() const {}
- MOCK_CONST_METHOD0(currentReconTool, std::string());
-
- // void updateLoginControls(bool loggedIn) {}
- MOCK_METHOD1(updateLoginControls, void(bool loggedIn));
-
- // void enableLoggedActions(bool enable) {}
- MOCK_METHOD1(enableLoggedActions, void(bool enable));
-
- // void enableConfigTool(bool on) {}
- MOCK_METHOD1(enableConfigTool, void(bool on));
-
- // void enableRunReconstruct(bool on) {}
- MOCK_METHOD1(enableRunReconstruct, void(bool on));
-
- // TomoPathsConfig currentPathsConfig() const {}
- MOCK_CONST_METHOD0(currentPathsConfig,
- MantidQt::CustomInterfaces::TomoPathsConfig());
-
- // void updatePathsConfig(const TomoPathsConfig &cfg)
- MOCK_METHOD1(updatePathsConfig,
- void(const MantidQt::CustomInterfaces::TomoPathsConfig &cfg));
-
- // ImageStackPreParams currentROIEtcParams() const = 0;
- MOCK_CONST_METHOD0(currentROIEtcParams,
- MantidQt::CustomInterfaces::ImageStackPreParams());
-
- // void showToolConfig(const std::string &name) {}
- MOCK_METHOD1(
- showToolConfig,
- void(MantidQt::CustomInterfaces::TomoToolConfigDialogBase &dialog));
-
- // virtual void updateJobsInfoDisplay( const
- // std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo>
- // &status, const
- // std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &
- // localStatus) = 0;
- MOCK_METHOD2(
- updateJobsInfoDisplay,
- void(const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &
- status,
- const std::vector<Mantid::API::IRemoteJobManager::RemoteJobInfo> &
- localStatus));
-
- // TomoSystemSettings systemSettings() const
- MOCK_CONST_METHOD0(systemSettings,
- MantidQt::CustomInterfaces::TomoSystemSettings());
-
- // MantidQt::CustomInterfaces::TomoReconToolsUserSettings
- // prePostProcSettings() const
- MOCK_CONST_METHOD0(prePostProcSettings,
- MantidQt::CustomInterfaces::TomoReconFiltersSettings());
-
- // virtual std::map<std::string, std::string>
- // currentAggregateBandsParams() const
- typedef std::map<std::string, std::string>
- workaroundForMSVCIssueWithVariadicMacros;
- MOCK_CONST_METHOD0(currentAggregateBandsParams,
- workaroundForMSVCIssueWithVariadicMacros());
-
- // virtual void runAggregateBands(Mantid::API::IAlgorithm_sptr alg)
- MOCK_METHOD1(runAggregateBands, void(Mantid::API::IAlgorithm_sptr alg));
-
- // virtual bool userConfirmation(const std::string &title, const std::string
- // &body)
- MOCK_METHOD2(userConfirmation,
- bool(const std::string &title, const std::string &body));
-
- // virtual std::string getCachedExecutable() const = 0;
- MOCK_CONST_METHOD0(getCachedExecutable, std::string());
-
- // virtual std::vector<std::string> getCachedArguments() const = 0;
- MOCK_CONST_METHOD0(getCachedArguments, std::vector<std::string>());
-
- // virtual void externalProcessFinished(const QString &str) = 0;
- MOCK_METHOD1(emitExternalProcessFinished, void(const QString &str));
-};
-
-GCC_DIAG_ON_SUGGEST_OVERRIDE
-
-#endif // MANTID_CUSTOMINTERFACES_TOMOGRAPHYIFACEVIEWMOCK_H
diff --git a/docs/source/algorithms/ImggAggregateWavelengths-v1.rst b/docs/source/algorithms/ImggAggregateWavelengths-v1.rst
deleted file mode 100644
index 834b945dde7..00000000000
--- a/docs/source/algorithms/ImggAggregateWavelengths-v1.rst
+++ /dev/null
@@ -1,163 +0,0 @@
-
-.. algorithm::
-
-.. summary::
-
-.. alias::
-
-.. properties::
-
-Description
------------
-
-.. warning::
-
- This algorithm is experimental and it is at the moment being
- developed for a specific instrument (IMAT at ISIS). It might be
- changed significantly, renamed, or even removed without a
- notification, should instrument scientists decide to do so.
-
-.. warning::
-
- The property **ToFRanges** requires specific headers in the input
- (FITS) files and it is not enabled. At the moment, trying to use
- this property will produce an error.
-
-This algorithm aggregates images from multiple energy bands or
-wavelengths into one or more output wavelength bands. The algorithm
-applies to energy selective imaging data. It aggregates images by
-summing up counts, and assumes that the image pixel values represent
-neutron counts.
-
-Given an input path (directory) and an output path (directory) the
-algorithm will combine images from the input path and write the result
-into the output path. Two different uses are considered: neutron
-radiography (single projection angle) and tomography (multiple
-projection angles). The image format supported is FITS (using the
-algorithm :ref:`algm-LoadFITS`).
-
-The algorithm produces its main outputs as files on disk. It also
-outputs two values: the number of projections (or angles) processed
-successfully (which will be always one for neutron radiography), and
-the number of wavelength bands aggregated. One and only one of the
-options **UniformBands**, **IndexRanges** or **ToFRanges** must be
-specified. This defines the number of output bands and how the input
-bands are aggregated or combined into the output bands.
-
-For the sake of simplicity let us explain first the files that the
-algorithm produces when a single output band is generated. This single
-output band could correspond to the aggregation of all or a subset of
-the input bands. This is the case when the property UniformBands is
-set to 1, or the properties **IndexRanges** or **ToFRanges** are set
-to a single range (and not multiple ranges separated by commas).
-
-For neutron radiography data the input path points to a set of image
-files where every file is assumed to correspond to a different
-wavelength or energy band. The algorithm will produce an image in the
-output path by combining the energy bands selected (as specified in
-the algorithm options, and using all the input images as default).
-
-For neutron tomography data the input path points to a set of
-subdirectories, one per projection angle, and each of them containing
-image files. It is assumed that each of the directories corresponds to
-a projection angle. The algorithm will produce as many images in the
-output path as subdirectories are found in the input path a single
-image in the output path by combining the energy bands selected,
-separately for every input subdirectory, i.e., projection angle
-(selecting the bands as specified in the algorithm options, and using
-all the input bands as default). The images are written in a
-subdirectory that is named depending on the type of aggregation
-used. For the uniform bands (**UniformBands** property) the
-subdirectory will be named **bands_uniform_idx_<start>_to_<end>**,
-where **<start>** and **<end>** are the limits of the range(s). When
-the index ranges option (**IndexRanges**) is used the names of the
-output subdirectory will be named
-**bands_index_idx_<start>_to_<end>**. And when the time of flight
-range option (**ToFRanges**) is used the names will be
-**bands_tof_idx_<start>_to_<end>**. The initial prefix
-(bands_uniform, bands_index, bands_tof) can be mofified via the
-input properties **OutputSubdirsPrefixUniformBands**,
-**OutputSubdirsPrefixIndexBands**, **OutputSubdirsPrefixToFBands**,
-respectively.
-
-The output images are created as described above when there is a
-single output band or stack of images. When multiple output ranges are
-specified the outputs are produced similarly but every range will be
-generated in a separate subdirectory created under the output path
-given to the algorithm. For example the algorithm would produce
-subdirectories named bands_by_index_idx_0_99,
-bands_by_index_idx_50_149, and bands_by_index_idx_99_149, or
-bands_uniform_idx_0_49, bands_uniform_idx_50_99.
-
-A relevant consideration is how to use the range options to generate
-multiple output stacks of images. This is very important for
-performance reasons and concerns how to use the properties
-**IndexRanges** and **ToFRanges**. The comma separated list of ranges
-enables the user to generate multiple output stacks of images in one
-call to this algorithm. The same result can be obtained by calling the
-algorithm repeatedly with the different individual ranges, one at a
-time. This second alternative would be significantly slower though,
-and it is discouraged to use that approach in scripts. That is because
-the algorithm would need to read through the input images for every
-individual call. This can make a big different in terms of run time,
-given that this algorithm is meant to process large sets of images
-which can take of the order of tens of minutes or hours to read and/or
-write depending on the disk resources available.
-
-
-As the algorithm tries to find images and subdirectories with images
-from the input path, to decide whether to process the data as a single
-projection (radiography) or multiple projections (tomography), there
-can be ambiguities. When an input path is given that contains both
-image files and subdirectories with image files, the algorithm
-processes the image files and does not try to process the
-subdirectories. That is, it is assumed that the input path given
-contains data for a single projection, and that the subdirectories do
-not necessarily contain images for different projections (tomography
-data).
-
-Usage
------
-
-**Example - ImggAggregateWavelengthsSingleProjection**
-
-.. code-block:: python
-
- # Create an image combining all energy bands
- projections, bands = ImggAggregateWavelengths(InputPath='D:\Data\RB000000\SampleA\',
- OutputPath='D:\Data\RB000000\SampleA_all_wavelenghts'
- UniformBands=1)
-
- if 1 != projections:
- print "An error happened. Expected to process one projection but processed: {0}".format(projections)
- # Print some details
- print "Wrote a projection image combining {1} wavelength bands".format(bands)
-
-Output:
-
-.. code-block:: none
-
- Wrote a projection image combining 2000 wavelength bands
-
-**Example - ImggAggregateWavelengthsTomography**
-
-.. code-block:: python
-
- # Create a stack of images that can be used in tomographic reconstruction
- angles, bands = ImggAggregateWavelengths(InputPath='D:\Data\RB000000\SampleA\',
- OutputPath='D:\Data\RB000000\SampleA\all_wavelenghts',
- UniformBands=1)
-
- # Print some details
- print "Wrote {0} projection images, each combining {1} wavelength bands".format(angles, bands)
-
-Output:
-
-.. code-block:: none
-
- Wrote 144 projection images, each combining 2000 wavelength bands
-
-.. categories::
-
-.. sourcelink::
-
diff --git a/docs/source/algorithms/ImggTomographicReconstruction-v1.rst b/docs/source/algorithms/ImggTomographicReconstruction-v1.rst
deleted file mode 100644
index 709b0f076e9..00000000000
--- a/docs/source/algorithms/ImggTomographicReconstruction-v1.rst
+++ /dev/null
@@ -1,125 +0,0 @@
-
-.. algorithm::
-
-.. summary::
-
-.. alias::
-
-.. properties::
-
-Description
------------
-
-.. warning:: This is an early, experimental version of the algorithm.
-
-The input and output workspaces are workspace groups where every
-element is an image workspace. In the input workspace every image is a
-2D projection from a different angle whereas in the output workspace
-every image is a slice of a reconstructed 3D volume. The input
-workspace must have one image workspace per projection from a
-tomography imaging experiment. The output workspace will have one
-image workspace for every slice of the output reconstructed volume.
-
-The following method is supported: FBP (following the TomoPy
-implementation [TomoPy2014]).
-
-The implementation of TomoPy methods are based on the TomoPy source
-code available from https://github.com/tomopy/tomopy/, which is:
-
-::
-
- Copyright 2015. UChicago Argonne, LLC. This software was produced
- under U.S. Government contract DE-AC02-06CH11357 for Argonne National
- Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
- U.S. Department of Energy. The U.S. Government has rights to use,
- reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR
- UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
- ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is
- modified to produce derivative works, such modified software should
- be clearly marked, so as not to confuse it with the version available
- from ANL.
-
- Additionally, redistribution and use in source and binary forms, with
- or without modification, are permitted provided that the following
- conditions are met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in
- the documentation and/or other materials provided with the
- distribution.
-
- * Neither the name of UChicago Argonne, LLC, Argonne National
- Laboratory, ANL, the U.S. Government, nor the names of its
- contributors may be used to endorse or promote products derived
- from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago
- Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGE.
-
-References:
-
-.. [TomoPy2014] Gursoy D, De Carlo F, Xiao X,
- Jacobsen C. (2014). TomoPy: a framework for the analysis of
- synchrotron tomographic data. J. Synchrotron Rad. 21. 1188-1193
- doi:10.1107/S1600577514013939
-
-
-Usage
------
-
-**Example - ReconstructProjections**
-
-.. testcode:: ReconstructProjections
-
- # Note: you would load FITS images like this:
- # wsg = LoadFITS(Filename='FITS_small_01.fits', LoadAsRectImg=1, OutputWorkspace='projections')
- wsg_name = 'projections'
- # Produce 16 projections with 32x32 pixels
- projections = []
- unit_label=UnitFactory.create('Label')
- unit_label.setLabel('width','cm')
- for proj in range(0, 8):
- wks_name = 'wks_proj_' + str(proj)
- wks = CreateSampleWorkspace(NumBanks=32, BankPixelWidth=1, XMin=0, XMax=32, BinWidth=1, OutputWorkspace=wks_name)
- wks.getAxis(0).setUnit('Label')
- projections.append(wks)
- wsg_proj = GroupWorkspaces(projections, OutputWorkspace=wsg_name)
- wsg_reconstructed = ImggTomographicReconstruction(InputWorkspace=wsg_proj, CenterOfRotation=15)
- rows = wsg_reconstructed.getItem(0).getNumberHistograms()
- columns = wsg_reconstructed.getItem(0).blocksize()
- print ("The output reconstruction has {0} slices of {1} by {2} pixels".
- format(wsg_reconstructed.size(), rows, columns))
- slice_idx = 2
- coord_x = 8
- coord_y = 15
- print ("Value of pixel at coordinate ({0},{1}) in slice {2}: {3:.1f}".
- format(coord_x, coord_y, slice_idx,
- wsg_reconstructed.getItem(2).readY(coord_y)[coord_x]))
-
-.. testcleanup:: ReconstructProjections
-
- DeleteWorkspace(wsg_name)
-
-Output:
-
-.. testoutput:: ReconstructProjections
-
- The output reconstruction has 32 slices of 32 by 32 pixels
- Value of pixel at coordinate (8,15) in slice 2: 2.4
-
-.. categories::
-
-.. sourcelink::
diff --git a/docs/source/algorithms/LoadSavuTomoConfig-v1.rst b/docs/source/algorithms/LoadSavuTomoConfig-v1.rst
deleted file mode 100644
index 3ba9bc8ffb7..00000000000
--- a/docs/source/algorithms/LoadSavuTomoConfig-v1.rst
+++ /dev/null
@@ -1,76 +0,0 @@
-.. algorithm::
-
-.. summary::
-
-.. alias::
-
-.. properties::
-
-Description
------------
-
-This algorithm reads a tomographic reconstruction parameterization
-(configuration) file and stores the configuration in a `TableWorkspace
-<http://www.mantidproject.org/TableWorkspace>`_. The file is expected
-to follow the format used in the savu tomography reconstruction
-pipeline `<https://github.com/DiamondLightSource/Savu>`__. These files
-specify a sequence of plugins to be used for tomographic
-reconstruction. For each plugin four fields are given in this order:
-id, parameters, name, and cite. All fields are character strings. The
-parameters field is formatted as a JSON string of name,value
-pairs. The workspace produced has one row for every plugin found in
-the input file, and four columns of string type.
-
-This algorithm is used by the IMAT tomography reconstruction interface
-(GUI) to load and display configurations that can then be edited and
-saved.
-
-Usage
------
-
-**Example**
-
-.. testcode:: LoadSavuTomoConfig
-
- tws = LoadSavuTomoConfig("savu_test_data_process03.nxs", OutputWorkspace='savu_tomo_config')
- print "Number of columns: %d" % tws.columnCount()
- print "Number of rows / processing plugins: %d" % tws.rowCount()
- print "Cell 0,0: %s" % tws.cell(0,0)
- print "Cell 0,1: %s" % tws.cell(0,1)
- print "Cell 0,2: %s" % tws.cell(0,2)
- print "Cell 0,3: %s" % tws.cell(0,3)
- print "Cell 1,0: %s" % tws.cell(1,0)
- print "Cell 1,1: %s" % tws.cell(1,1)
- print "Cell 1,2: %s" % tws.cell(1,2)
- print "Cell 1,3: %s" % tws.cell(1,3)
- print "Cell 2,0: %s" % tws.cell(2,0)
- print "Cell 2,1: %s" % tws.cell(2,1)
- print "Cell 2,2: %s" % tws.cell(2,2)
- print "Cell 2,3: %s" % tws.cell(2,3)
-
-.. testcleanup:: LoadSavuTomoConfig
-
- DeleteWorkspace(tws)
-
-Output:
-
-.. testoutput:: LoadSavuTomoConfig
-
- Number of columns: 4
- Number of rows / processing plugins: 3
- Cell 0,0: savu.plugins.timeseries_field_corrections
- Cell 0,1: {}
- Cell 0,2: Timeseries Field Corrections
- Cell 0,3: Not available
- Cell 1,0: savu.plugins.median_filter
- Cell 1,1: {"kernel_size": [1, 3, 3]}
- Cell 1,2: Median Filter
- Cell 1,3: Not available
- Cell 2,0: savu.plugins.simple_recon
- Cell 2,1: {"center_of_rotation": 86}
- Cell 2,2: Simple Reconstruction
- Cell 2,3: Not available
-
-.. categories::
-
-.. sourcelink::
diff --git a/docs/source/algorithms/SCARFTomoReconstruction-v1.rst b/docs/source/algorithms/SCARFTomoReconstruction-v1.rst
deleted file mode 100644
index 5dc8c313a62..00000000000
--- a/docs/source/algorithms/SCARFTomoReconstruction-v1.rst
+++ /dev/null
@@ -1,89 +0,0 @@
-.. algorithm::
-
-.. summary::
-
-.. alias::
-
-.. properties::
-
-Description
------------
-
-Algorithm to control jobs running on the SCARF computer cluster at
-RAL, STFC (see http://www.scarf.rl.ac.uk/ for more information). This
-algorithm can be used to log in and out from the cluster, and to
-initiate, query the status of, or cancel a job. It has been introduced
-to control tomographic reconstruction jobs but in principle it can be
-used for any other task.
-
-In a typical use case or session you would use the algorithm a first
-time to login (for which you need to select the 'LogIn' action and set
-the username and password fields). After this step you can use the
-algorithm again several times, to submit jobs (setting the action
-'SubmitJob'), query the status of the jobs running on the computer
-cluster (setting the action to 'JobStatus' or 'JobStatusByID'), cancel
-jobs (setting the action 'CancelJob') and log out from the cluster
-(action 'LogOut'). You can also upload and download files. After
-logging out, subsequent submit or status queries will fail with an
-informative message. Note that the server will log out users every
-undetermined amount of time, which depends on server settings.
-
-In principle, in a simple use case, the same username will be used in
-all the calls to this algorithm. This means that you type in the
-username only the first time that you use this algorithm, as it will
-be remembered and filled in automatically in the next calls. But note
-that it is possible to change the username passed to the algorithm
-every time you call the algorithm. This means that you can use this
-algorithm to control jobs for multiple users simultaneously from the
-same instance of Mantid. You can use for example use the username
-associated to a particular project or instrument, and in parallel your
-personal username for different jobs (which can be useful to
-distinguish quick tests, calibration of parameters, etc.). For this to
-work, you of course need to perform a 'LogIn' action for every
-username that is used in submit or query status actions.
-
-The 'JobStatus' and 'JobStatusByID' actions produce an output several
-output properties with status and general information about the jobs,
-as retrieved from the compute resource/server.
-
-The algorithm relies on a web service provided by the SCARF computer
-cluster in order to control jobs on the cluster. If you use this
-algorithm from its dialog (for example starting it from the algorithm
-explorer in Mantid) the password will not be shown on the screen. This
-algorithm can be used interactively. In such case, it is absolutely
-not recommended to call it from scripts or the Python script
-interpreter window, as you will be passing passwords as plain text.
-
-The alternative ways to monitor and control your jobs are via shell
-login and via the web platform at https://portal.scarf.rl.ac.uk/.
-
-This algorithm is used by other components of Mantid, in particular
-the custom graphical interface for tomography (IMAT instrument).
-
-Usage
------
-
-**Example**
-
-.. testcode:: SCARFTomoReconstruction
-
- try:
- SCARFTomoReconstruction(UserName='foouser', Action='Login')
- except ValueError:
- print "ValueError, as expected, because no Password= parameter given"
-
- try:
- SCARFTomoReconstruction(UserName='foouser', Action='Submit')
- except ValueError:
- print "ValueError, as expected, as it was not previously logged on"
-
-Output:
-
-.. testoutput:: SCARFTomoReconstruction
-
- ValueError, as expected, because no Password= parameter given
- ValueError, as expected, as it was not previously logged on
-
-.. categories::
-
-.. sourcelink::
diff --git a/docs/source/algorithms/SaveSavuTomoConfig-v1.rst b/docs/source/algorithms/SaveSavuTomoConfig-v1.rst
deleted file mode 100644
index ddedb427278..00000000000
--- a/docs/source/algorithms/SaveSavuTomoConfig-v1.rst
+++ /dev/null
@@ -1,66 +0,0 @@
-.. algorithm::
-
-.. summary::
-
-.. alias::
-
-.. properties::
-
-Description
------------
-
-This algorithm writes a file with tomographic reconstruction
-parameterization (configuration) file using the format of the savu
-tomography reconstruction pipeline
-(`<https://github.com/DiamondLightSource/Savu>`__). The parameters are
-taken from a list of `TableWorkspace
-<http://www.mantidproject.org/TableWorkspace>`_ workspaces. The data
-in every workspace is expected to have four columns, with each row
-specifying one plugin. For every plugin four character string
-attributes (four columns) must be given, in this order: id, parameters
-(JSON string of name-value pairs), name, and cite (citation
-information about plugin documentation and authors).
-
-This algorithm is used by the IMAT tomography reconstruction interface
-(GUI) to save configuration files that can then be used to run
-tomography reconstruction jobs using the savu pipeline.
-
-Usage
------
-
-**Example**
-
-.. testcode:: SaveSavuTomoConfig
-
- import os.path
- tws_name = 'saveSavuTomoTest'
- tws = CreateEmptyTableWorkspace(OutputWorkspace=tws_name)
- tws.addColumn('str', 'ID')
- tws.addColumn('str', 'Parameters')
- tws.addColumn('str', 'Name')
- tws.addColumn('str', 'Cite')
- tws.addRow(['savu.id1', '{"param11": val1', 'plugin name1', 'cite info1'])
- tws.addRow(['savu.id2', '{"param21": val2', 'plugin name2', 'cite info2'])
- print "Columns: %d" % tws.columnCount()
- print "Rows: %d" % tws.rowCount()
- out_fname = 'saveSavuTomoTest.nxs'
- SaveSavuTomoConfig(Filename=out_fname, InputWorkspaces='saveSavuTomoTest')
- res = os.path.isfile(out_fname)
- print "Save result: ", res
-
-.. testcleanup:: SaveSavuTomoConfig
-
- DeleteWorkspace(tws)
- os.remove(out_fname)
-
-Output:
-
-.. testoutput:: SaveSavuTomoConfig
-
- Columns: 4
- Rows: 2
- Save result: True
-
-.. categories::
-
-.. sourcelink::
diff --git a/docs/source/interfaces/Tomographic_Reconstruction.rst b/docs/source/interfaces/Tomographic_Reconstruction.rst
deleted file mode 100644
index 3fa4756f6d2..00000000000
--- a/docs/source/interfaces/Tomographic_Reconstruction.rst
+++ /dev/null
@@ -1,497 +0,0 @@
-Tomographic Reconstruction
-==========================
-
-.. contents:: Table of Contents
- :local:
-
-Overview
---------
-
-This interface aims at integrating and simplifying the following tasks
-related to tomographic reconstruction and imaging with neutrons. While
-much of its functionality is being developed in a generic way, it is
-presently being tested and trialed for the IMAT instrument at ISIS.
-
-.. interface:: Tomographic Reconstruction
- :align: center
- :width: 600
-
-An important feature of this interface is the capability to submit
-jobs to a remote compute resource (a compute cluster for
-example). Currently remote jobs are run on the `SCARF cluster
-<http://www.scarf.rl.ac.uk/>`_, administered by the Scientific
-Computing Department of STFC. You can also use this cluster via remote
-login and through its `web portal
-<https://portal.scarf.rl.ac.uk/>`_. This resource is available for
-ISIS users.
-
-.. warning:: This interface is undergoing heavy works. The tabs are
- subject to changes and reorganization. New functionality is being added
- and the pre-post-processing and reconstruction workflow is being
- modified based on feedback from initial test data.
-
-Interface at a glance
----------------------
-
-By default the interface shows the *Run* tab, where you can visualize
-images, submit reconstruction jobs, see and control the status of the
-jobs submitted recently.
-
-.. figure:: /images/tomo_tab1_submission_reconstruction_jobs.png
- :align: right
- :scale: 50%
-
-In the *Setup* tab you can set the details of the remote and/or local
-compute resources. Importantly, here is where you can set you username
-and password to log into the remote compute resource. To be able to
-run jobs remotely you first need to log into the remote compute
-resource. Once you log in, an automatic mechanism will periodically
-query the status of jobs (for example every minute). You can also
-update it at any time by clicking on the refresh button.
-
-In the *Setup* tab you also have to set the folders/directories where the
-input data for reconstruction jobs is found. This information is
-required every time you start analyzing a new dataset. The required
-fields are:
-
-Samples directory
- Directory containing the sample images
-
-Open beam directory
- Where to find the open beam (flat/white) image(s)
-
-Dark field directory
- Where to find the dark image(s)
-
-.. figure:: /images/tomo_tab2_setup_authentication.png
- :align: center
- :scale: 60%
-
-**NB**: This interface is under heavy development. Several practical
-details lack polishing and/or are missing. This implies that there may
-be usability issues at times and some steps may not be as intuitive or
-simple as they could. Please, do not hesitate to provide suggestions
-and feedback.
-
-The next sections provide further details that might be needed to
-fully understand the process of generating tomographic reconstructions
-with this interface.
-
-Tools
------
-
-At the moment two reconstruction tools are being set up and trialed on
-SCARF and some ISIS machines:
-
-* `TomoPy
- <https://www1.aps.anl.gov/Science/Scientific-Software/TomoPy>`_
-
-* `Astra Toolbox <http://visielab.uantwerpen.be/astra-toolbox>`_ found from
- `here <http://sourceforge.net/p/astra-toolbox/wiki/Home/>`_.
-
-References for the Astra Toolbox:
-
-* W. van Aarle, W J. Palenstijn, J. De
- Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers,
- "The ASTRA Toolbox: a platform for advanced algorithm development in
- electron tomography", Ultramicroscopy, Vol. 147, p. 35–47, (2015)
-
-* W J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance
- improvements for iterative electron tomography reconstruction using
- graphics processing units (GPUs)", Journal of structural biology,
- vol. 176, issue 2, pp. 250-253, 2011
-
-References for TomoPy:
-
-* Gursoy D, De Carlo F, Xiao X, Jacobsen C. (2014). TomoPy: a
- framework for the analysis of synchrotron tomographic
- data. J. Synchrotron Rad. 21. 1188-1193
- doi:10.1107/S1600577514013939
-
-In the near future it is expected that support will be added for
-`Savu: Tomography Reconstruction Pipeline
-<https://github.com/DiamondLightSource/Savu>`_, developed at the
-Diamond Light Source.
-
-References for Savu:
-
-* Atwood R C, Bodey A J, Price S W T, Basham M and Drakopoulos M
- 2015 A high-throughput system for high-quality tomographic reconstruction of
- large datasets at diamond light source Philosophical Transactions A 373 20140398
-
-Data formats
-------------
-
-In principle, users do not need to deal with specificities of
-different file formats. That is the aim of this interface, but as it
-is currently being developed, and for reference a brief list of
-relevant file and data formats is given here:
-
-* FITS: `Flexible Image Transport System format
- <http://en.wikipedia.org/wiki/FITS>`__ used to store images in
- files. You can see the details on how FITS images can be loaded into
- Mantid in the documentation of the algorithm :ref:`LoadFITS <algm-LoadFITS>`.
-
-* TIFF: `Tagged Image File Format
- <http://en.wikipedia.org/wiki/Tagged_Image_File_Format>`__ images
- used as FITS for image or slice files. This format is presently not
- supported in the Mantid data analysis framework but it is used in
- the tomographic reconstruction interface.
-
-* Diamond Light Source (DLS) NXTomo: a specific NeXus format used by
- some of the tools that this interface supports or will support. See
- next sections for details.
-
-These formats are used in different processing steps and parts of this
-interface. For example, you can visualize FITS and TIFF images in the
-**Run** tab and also in the **ROI etc.** tab. As another example, the
-reconstruction tools typically need as inputs at least a stack of
-images which can be in different formats, including a set of FITS or
-TIFF files, or a single DLS NXTomo file. Other third party tools use
-files in these formats as inputs, outputs or both.
-
-Data locations
---------------
-
-This is dependent on the facility and instrument.
-
-.. warning:: This is work in progress. At ISIS, in principle data will
- be replicated in the ISIS archive, the IMAT disk space on
- the cluster SCARF (remote compute resource), and possibly
- an IMAT analysis machine.
-
-The path to the files of a particular tomographic reconstruction
-consists of several components. An example path would be (on a Windows
-system where the input/output data is on the drive "D"):
-
-* D:/data/RB987654321/experiment_foo/
-
-where:
-
-* *data* is the root or base path for all tomography data. This folder
- or directory is synchronized (at least partially) between the remote
- compute resource and the (local) instrument analysis machine.
-
-* *RB987654321* is the experiment reference number (or so-called RB number) which usually starts with the prefix "RB".
-
-* *experiment_foo* is a name given by the user to the particular
- experiment the data comes from. This is specified in free form.
-
-* inside the path there will normally be at least three folders or subdirectories for the sample, flat, and dark images:
-
- - data
- - flat
- - dark
-
-
-As the files are mirrored on the remote computer cluster, if a network
-drive has been added (or mapped) in the local system, for example
-using the drive "S:", then the following path would contain a similar
-tree of image files:
-
-* D:/data/RB987654321/experiment_foo/
-
-The equivalent on a non-Windows system would be for example:
-
-* /media/scarf/data/RB987654321/experiment_foo/
-
-These and related parameters can be inspected and modified in the
-**System** tab. Their default values are
-set for the current setup of the IMAT analysis machine. The "Reset
-all" button resets all these settings to their factory defaults. Note
-that the **Reset all** button currently requires **no confirmation**.
-The **System** tab of the interface is currently a work in
-progress and it may change significantly as required during
-commissioning of IMAT.
-
-The tab *Visualization* has simple push buttons to browse the files
-available from the local and remote locations, as well as any other
-directory or folder selected by the user. The data for the different
-experiments can be found under these locations.
-
-Running jobs remotely
----------------------
-
-To be able to run jobs on a remote compute resource (cluster, supercomputer, etc.)
-
-* Log into the resource (in **Setup**)
-* Then in **Run** select the compute resource and setup one
- reconstruction tool
-* Use the *Reconstruct* button in the **Run** tab of the interface
-
-You can monitor the status of the jobs currently running (and recently
-run) on remote compute resources in the same tab.
-
-Setting common parameters for the reconstruction jobs
------------------------------------------------------
-
-Before any reconstruction job is started several pre-/post-processing
-options would normally need to be fine tuned for the sample data to be
-processed correctly. The region of interest and the "air" region (or
-region for normalization) can be set visually in the *ROI etc* tab. All
-other pre- and post-processing settings are defined in the *Filters* tab.
-
-Regions
-~~~~~~~
-
-Several parameters can be set in the **ROI etc.** tab. These
-parameters will be used for all the reconstruction jobs, regardless of
-the tool and/or reconstruction method used.
-
-* Region of interest (ROI) for the analysis
-* Area for normalization (open beam, not blocked by sample)
-* Center of rotation, for tomographic reconstruction
-
-.. figure:: /images/tomo_tab3_ROI_etc.png
- :align: center
- :scale: 60%
-
-Stacks of images can be opened by using the browse button located at
-the top of the interface. You can point the interface to a folder
-(directory) containing directories for sample, dark, and flat images,
-or alternatively to a folder containing images. The interface will
-pick all the files recognized as images.
-
-At any stage during the process of selecting the regions it is also
-possible to see how the selections fit different images by sliding
-through the images of the stack (using the slider or scroll bar).
-
-The angle of the image can be changed by changing the Rotate(clockwise)
-option. This will affect how the image is displayed locally and reconstructed.
-
-The center of rotation can be selected interactively by clicking on
-the select button and then clicking on an image pixel. To select the
-regions of interest or the area of normalization, just click on the
-respective "Select" button and then click and drag with the mouse to
-select a rectangle. The precise coordinates of the center and regions
-can be set via the boxes of the right panel as well.
-
-Once you have selected or set one of the regions, or the center, they
-can be selected again by pushing the respective "Select" buttons
-and/or editing their coordinates manually.
-
-There is also the option to change the ColorMap that is used to show
-the images ONLY **locally**. This can be done by **double** clicking
-the ColorBar on the side and selecting a different ColorMap file.
-The changes are only local and will NOT affect the reconstruction.
-
-The default values, set in principle when a new stack of images is
-loaded, are as follows. The rotate angle is set to 0 degrees,
-the region of interest is set to cover all the images. The region
-of normalization is not set (empty), and the center of rotation is
-set to the center of the image. The option to find the center of
-rotation automatically is disabled at present.
-
-While selecting a region, if the mouse is moved outside of the images,
-it is possible to continue the selection of the region (second corner)
-by clicking again inside the image. Alternatively, any selection can
-be reset at any point by using the "Reset" buttons.
-
-When loading a stack of images, note that when the images are loaded
-from the folder(s) (directorie(s)) any files with unrecognized
-extension or type (for example .txt) will be ignored. Normally a
-warning about this will be shown in the Mantid logs. Image files with
-the string **_SummedImg** at the end of their names will be skipped as
-well, as this is a convention used by some detectors/control software
-to generate summed images.
-
-Pre-/post-processing
-~~~~~~~~~~~~~~~~~~~~
-
-The **Filters** tab can be used to set up the pre- and post-processing
-steps. These are applied regardless of the particular tomographic
-reconstruction tool and algorithm used when running reconstruction
-jobs. Pre-processing filters are applied on the raw input images
-before the reconstruction algorithm is run. Post-processing steps are
-applied on the reconstructed volume produced by the algorithm.
-
-.. figure:: /images/tomo_tab4_pre_post_proc_filters.png
- :align: center
- :scale: 60%
-
-Among other options, normalization by flat and/or dark images can be
-enabled here. Note that this setting is global and will be effective
-for any input dataset. In the **Setup** tab it is possible to
-enable or disable them specifically for the dataset being processed.
-
-The tab also shows options to define what outputs should be produced
-in addition to the reconstructed volume.
-
-The settings are remembered between sessions. It is possible to reset
-all the settings to their original defaults by clicking on the reset
-button.
-
-Results from reconstruction jobs
---------------------------------
-
-The results are written into the output paths selected in the
-interface (in the *Setup* tab). For every reconstructed
-volume a sequence of images (slices along the vertical axis) are
-written. In addition, two complementary outputs are generated in the
-same location:
-
-* A *readme* file with detailed information on the reconstruction and
- settings (0.README_reconstruction.txt), including paths, algorithms,
- filters and parameters used.
-
-* A compressed package file that contains the scripts and subpackages
- used for the reconstruction job, for reproducibility and to make it
- easier to track down potential issues. This file is written as
- 0.reconstruction_scripts.zip
-
-Running jobs locally
---------------------
-
-You can run local reconstructions as well, however that requires properly setting up the:
-
-* External python interpretor path, for example:
-
- - `C:/Anaconda/python.exe for Windows`
- - `~/Anaconda2/bin/python for Linux`
-
-* PYTHONPATH environment variable should contain the Python directories
- that have the installed plugins for the supported tools
-
-* (Optional) Scripts directory
- - By default this will be properly setup from the Mantid installation
-
-Visualization
--------------
-
-.. warning:: The interface is being extended to have integration with
- third party tools for 3D visualization and segmentation.
- This is work in progress.
-
-The **Visualization** tab can be used to browse the local and remote
-locations where results are stored. It is also possible to open these
-results in third party visualization applications. **NB**: ParaView is
-currently supported and additional tools are being integrated.
-
-.. figure:: /images/tomo_tab5_send_to_viz.png
- :align: center
- :scale: 60%
-
-Energy bands
-------------
-
-.. warning:: The interface is being extended to provide different methods
- of combining energy bands from energy selective experiments.
- This is work in progress.
-
-Here it is possible to aggregate stacks of images normally acquired as
-energy/wavelength selective data. This interface is based on the
-algorithm :ref:`ImggAggregateWavelengths <algm-ImggAggregateWavelengths>` which
-supports different ways of aggregating the input images. In the
-simplest case, a number of output bands can be produced by aggregating
-the input bands split into uniform segments. This is called "uniform
-bands". When the number of uniform bands is one, all the wavelengths
-are aggregated into a single output stack. It is also possible to
-specify a list of boundaries or ranges of image indices. For example
-if an input dataset consists of 1000 images per projection angle (here
-indexed from 0 to 999), three partially (50%) overlapping output bands
-could by produced by specifying the ranges as "0-499, 250-749,
-500-999". In principle it is also possible to aggregate images by time
-of flight ranges, based on specific extension headers that must be
-included in the input (FITS) images. This option is disabled at the
-moment. Please refer to the documentation of :ref:`ImggAggregateWavelengths
-<algm-ImggAggregateWavelengths>` for lower level details on how the
-algorithm processes the input directories and files.
-
-.. figure:: /images/tomo_tab7_energy_bands.png
- :align: center
- :scale: 60%
-
-Convert image formats
----------------------
-
-.. figure:: /images/tomo_tab6_formats_convert.png
- :align: center
- :scale: 60%
-
-This interface provides a simple way of converting stacks of images
-between diferent formats. This is for convenience and interoperability
-with third party tools that for example may not be able to load FITS
-images but require them in TIFF format. All the images found under the
-input path (directory) will be converted from the input format
-selected into the output format. The output images will be created
-under the output path (directory) with the same tree structure as the
-input images.
-
-The conversion process will look for images recursively inside the
-input directory. That is, it will process all its subdirectories and
-the subdirectories of these up to a given maximum depth. To limit the
-search depth. The usual default value is 3 which is sufficient for
-stacks of images and sets of stacks of images from a series of samples
-for an experiment, following the conventions for IMAT tomography
-data. If higher depth values than the default are used we recommend to
-take extreme care, making sure the input path given makes sense. This
-process can be lengthy and demanding in terms of disk space when
-processing more than one or a small number of experiments (RB
-reference numbers), and especially so for wavelength dependent
-experiments.
-
-System
-------
-
-.. figure:: /images/tomo_tab8_system_options.png
- :align: center
- :scale: 60%
-
-In the System tab you can specify the input folder names
-for the sample, flat, and dark images, and also the names of the output folders.
-The base paths for the SCARF file system can also be set here. Two options
-are included. The first one specifies where the Tomography data is found in the
-cluster, and the second specifies where the reconstruction tools and scripts
-can be found.
-The path can be changed to point to your own specific data and scripts on the
-SCARF cluster, so it could be helpful to create different directories for
-different scripts rather than changing the default script located in the default
-directory.
-
-Example
--------
-
-TODO: there should be a worked out example using a small data set.
-
-TomoPy
-------
-
-TODO: how to use it. Hints.
-
-Astra Toolbox
--------------
-
-TODO: how to use it. Hints.
-
-MuhRec
-------
-
-TODO: how to use it. Hints.
-
-Savu
-----
-
-TODO: how to use it. Hints.
-
-Savu uses a specific file format developed by the Diamond Light
-Source, the DLS NXTomo. A few examples can be found from `the savu
-repository on GitHub
-<https://github.com/DiamondLightSource/Savu/tree/master/test_data>`__.
-
-Pipeline configuration
-~~~~~~~~~~~~~~~~~~~~~~
-
-A Savu reconstruction pipeline is defined by a list of processing
-steps (or plugins) and their parameters. In the Savu setup dialog this
-list is built on the right panel (current configuration) by adding and
-sorting available plugins available from the tree shown on the left
-panel. From the file menu, different savu configurations can be saved for
-later use and loaded from previously saved files.
-
-.. Leave this out for now. Not used at the moment.
- .. interface:: Tomographic Reconstruction
- :widget: savuConfigCentralWidget
- :align: right
-
-
-.. categories:: Interfaces Diffraction
diff --git a/scripts/Imaging/IMAT/__init__.py b/scripts/Imaging/IMAT/__init__.py
deleted file mode 100644
index 763e55451a6..00000000000
--- a/scripts/Imaging/IMAT/__init__.py
+++ /dev/null
@@ -1,23 +0,0 @@
-from __future__ import (absolute_import, division, print_function)
-# Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-"""
-3D Tomographic reconstruction being devepeloped for the IMAT instrument
-"""
diff --git a/scripts/Imaging/IMAT/agg_energy_bands.py b/scripts/Imaging/IMAT/agg_energy_bands.py
deleted file mode 100644
index 44b39f203c8..00000000000
--- a/scripts/Imaging/IMAT/agg_energy_bands.py
+++ /dev/null
@@ -1,87 +0,0 @@
-"""
-Command line tool to aggregate multiple bands from energy selective imaging experiments.
-This simply provides a command line interface to prep.energy_bands_aggregator
-
-To print usage details:
-ipython agg_energy_bands.py --help
-
-Usage example:
-ipython -- agg_energy_bands.py --input-path=~/test/LARMOR/test_few_angles/ --output-path=out_stack_test
-
-ipython -- agg_energy_bands.py --input-path=~/test/LARMOR/test_few_angles/ --output-path=out_stack_test --energy-bands=100,299 --format=png
-
-"""
-# Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-
-import IMAT.prep.energy_bands_aggregator as eba
-import argparse
-
-
-def _indices_to_tuple(indices):
- """
- See if we have energy band indices. Turn something like '100,200' to a tuple (100,200)
-
- @param indices :: indices given by the user
-
- Returns:: a tuple with the min and max indices
- """
- tidx = None
- if indices:
- idxlist = indices.split(',')
- if 2 != len(indices) or not isinstance(indices[0], int) or not isinstance(indices[1], int):
- tidx = (int(idxlist[0]), int(idxlist[1]))
- else:
- raise ValueError("Wrong energy band indices given: {0}. "
- "I expect two integers separated by a comma".format(
- indices))
- return tidx
-
-
-def agg_cli():
- """
- Provides a command line interface to the EnergyBandsAggregator
- """
- arg_parser = argparse.ArgumentParser()
- eb_agg = eba.EnergyBandsAggregator()
-
- arg_parser.add_argument("-i","--input-path", required=True, help="Input directory")
- arg_parser.add_argument("-o","--output-path", help="Where to write the output stack of (aggregated) images. "
- "If left empty a default '{0}' in the current working directory.".
- format(eb_agg.default_out_path))
- arg_parser.add_argument("-b","--energy-bands", help="Energy band indices to aggregate into the outputs. "
- "Must be given as two integer values separated by comma. "
- "The indices start from 0. By default all bands are included.")
- arg_parser.add_argument("-t","--agg-type", help="Type of aggregation. Supported: {0} ".
- format(eb_agg.supported_aggs))
-
- arg_parser.add_argument("-f","--format", help="Format of output files. Supported: {0}. Default: {1}.".
- format(eb_agg.supported_out_formats,
- eb_agg.default_out_format))
-
- args = arg_parser.parse_args()
- tidx = _indices_to_tuple(args.energy_bands)
-
- eb_agg.agg_angles(args.input_path, args.output_path, band_indices=tidx, agg_method=args.agg_type,
- out_format=args.format)
-
-
-if __name__=='__main__':
- agg_cli()
diff --git a/scripts/Imaging/IMAT/prep/__init__.py b/scripts/Imaging/IMAT/prep/__init__.py
deleted file mode 100644
index b1f7f578082..00000000000
--- a/scripts/Imaging/IMAT/prep/__init__.py
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright © 2014-2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-"""
-Pre-processing operations and filters that are applied on stacks of images
-or individual images.
-"""
-
-ERR_MSG = ("Inconsistency found. Could not import {0} which "
- "should be available in this package. Details: {1}")
-
-try:
- from . import filters
-except ImportError as exc:
- raise ImportError(ERR_MSG.format('filters', exc))
-
-try:
- from . import filters_adv
-except ImportError as exc:
- raise ImportError(ERR_MSG.format('filters_adv', exc))
diff --git a/scripts/Imaging/IMAT/prep/energy_bands_aggregator.py b/scripts/Imaging/IMAT/prep/energy_bands_aggregator.py
deleted file mode 100644
index a1f0a96a0db..00000000000
--- a/scripts/Imaging/IMAT/prep/energy_bands_aggregator.py
+++ /dev/null
@@ -1,365 +0,0 @@
-# Copyright © 2014-2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-
-import glob
-import os
-import re
-import sys
-import time
-
-try:
- from skimage import io as skio
-except ImportError:
- raise ImportError("Cannot find the package 'skimage.io' which is required to read/write image files in "
- "TIFF and other formats")
-
-try:
- from skimage import exposure
-except ImportError:
- raise ImportError("Unable to import package skimage.exposure which is required to write output image "
- "files with correct range of values")
-
-# Ideally, use freeimage plugin. That provides good support for tiff, png, and more
-# Backup solution: tifffile required for tiff format; skimage provides basic png, etc. support.
-try:
- skio.use_plugin('freeimage')
-except RuntimeError:
- FREEIMG_ERR_MSG = "Could not find the plugin 'freeimage' in skimage."
- # Because tifffile is going to be imported later on (in skio.imsave()) - check that it can be imported
- if not __package__:
- try:
- # it is unused here - it will be used by the tiff skio plugin
- #pylint: disable=unused-import
- import tifffile
- _USING_PLUGIN_TIFFFILE = True
- except ImportError:
- raise ImportError("Cannot find the package 'tifffile' which is required to read/write TIFF image "
- "files." + FREEIMG_ERR_MSG)
- else:
- try:
- #pylint: disable=no-name-in-module
- from . import tifffile
- _USING_PLUGIN_TIFFFILE = True
- except ImportError:
- try:
- import tifffile # noqa
- _USING_PLUGIN_TIFFFILE = True
- except ImportError:
- raise ImportError("Cannot find the package 'tifffile' in the system or together with this "
- "module. It is required to read/write TIFF image files. " + FREEIMG_ERR_MSG)
-
-
-try:
- import pyfits
-except ImportError:
- # In Anaconda python, the pyfits package is in a different place, and this is what you frequently
- # find on windows.
- try:
- import astropy.io.fits as pyfits
- except ImportError:
- raise ImportError("Cannot find the package 'pyfits' which is required to read/write FITS image files")
-
-try:
- import numpy as np
-except ImportError:
- raise ImportError("Cannot find the package 'numpy' which is required to calculate aggregated images")
-
-# alternative for when other plugins are not available. It can be distributed
-# and copied on remote machines where there are no other options
-_USING_PLUGIN_TIFFFILE = False
-
-#pylint: disable=too-many-instance-attributes
-
-
-class EnergyBandsAggregator(object):
- """
- Combines energy bands, producing stacks of images with one image per projection angle from
- energy-banded stacks of images (in which there can be thousands of images per projection angle).
-
- Usage example:
- eb_agg = Energy_Bands_Aggregator()
- eb_agg.agg_angles("~/test/LARMOR/test_few_angles/", "output_stack_all_bands")
-
- where the input directory (first argument) is expected to have several directories like 'angle0',
- 'angle1'... 'angle100', etc.
- """
-
- default_out_path = None
- supported_aggs = None
- supported_out_formats = None
- default_out_format = None
-
- def __init__(self, out_format='tiff', out_type='uint16'):
- """
- @param out_format :: format for the output image files. The list of supported format
- is given in in the attribute supported_out_formats. Default: tiff
-
- @param out_type :: pixel type for the output image files. Default: 2 bytes integer
- """
- # a default output path name for when the user doesn't provide any
- self.default_out_path = 'out_agg_stack'
- # types of aggregation across energy bands
- self.supported_aggs = ['sum', 'average']
- # format of the output images.
- self.supported_out_formats = ['tiff', 'png']
- # because tiff is the most common choice of third party tools
- self.default_out_format = 'tiff'
- # the default one
- self._out_format = out_format
-
- # plain sum by default
- self._default_agg_method = self.supported_aggs[0]
- # default pixel type of output files. Only this one supported for now.
- self._default_output_type = out_type
- # to handle the image index when doing incremental calculations
- self.__img_idx = 1
-
- def _write_image(self, img_data, filename, img_format=None, dtype=None):
- """
- Output image data to a file, in a given image format.
- Assumes that the output directory exists (must be checked before).
-
- @param img_data :: image data in the usual numpy representation
- @param filename :: file name, including directory and extension
- @param img_format :: image file format
- @param dtype :: can be used to force a pixel type, otherwise the type
- of the input data is used
-
- Returns :: name of the file saved
- """
- if not img_format:
- img_format = self.default_out_format
- filename = filename + '.' + img_format
-
- if dtype and img_data.dtype != dtype:
- img_data = np.array(img_data, dtype=dtype)
-
- if img_format == 'tiff' and _USING_PLUGIN_TIFFFILE:
- img_data = exposure.rescale_intensity(img_data, out_range='uint16')
- skio.imsave(filename, img_data, plugin='tifffile')
- else:
- img_data = exposure.rescale_intensity(img_data, out_range='uint16')
- skio.imsave(filename, img_data)
-
- return filename
-
- def _make_dirs_if_needed(self, dirname):
- """
- Makes sure that the directory needed to save the file exists, or creates it
-
- @param dirname :: (output) directory to check
- """
- absname = os.path.abspath(dirname)
- if not os.path.exists(absname):
- os.makedirs(absname)
-
- def _alphanum_key_split(self, path_str):
- """
- From a string to a list of alphabetic and numeric elements. Intended to
- be used for sequence number/natural sorting. In list.sort() the
- key can be a list, so here we split the alpha/numeric fields into
- a list. For example (in the final order after sort() would be applied):
-
- "angle4" -> ["angle", 4]
- "angle31" -> ["angle", 31]
- "angle42" -> ["angle", 42]
- "angle101" -> ["angle", 101]
-
- Several variants compared here:
- https://dave.st.germa.in/blog/2007/12/11/exception-handling-slow/
- """
- ALPHA_NUM_SPLIT_RE = re.compile('([0-9]+)')
- return [ int(c) if c.isdigit() else c for c in ALPHA_NUM_SPLIT_RE.split(path_str) ]
-
- def _agg_img(self, acc, img_data, agg_method=None, index=1):
- """
- Adds in data coming from a new image/hdu. Expects a numpy array of shape (N1, N2) where
- N1 and N2 are the number of rows and columns of the images.
-
- @param acc :: aggregated value accumulated so far
- @param img_data :: new image to add in
- @param agg_method :: whether to sum, average, etc. See options supported.
- @param index :: image index used when calculating incremental statistics like the average
-
- Returns :: result from aggregating (sum, average, etc.) the new image
- """
- if agg_method is None:
- agg_method = self._default_agg_method
-
- if 'sum' == agg_method:
- acc = np.add(acc, img_data)
- elif 'average' == agg_method:
- acc = np.add((index-1)*acc/index, img_data/index)
-
- return acc
-
- #pylint: disable=too-many-arguments
- def agg_indiv_angle(self, path_proj, band_indices=None, imgExt='fits', agg_method=None,
- verbose=True, too_verbose=False):
- """
- Aggregates (sum, average, etc.) all the energy bands selected for one projection angle and
- returns it. The aggregation is done sequentially through the potentially thousands of energy
- band images available for one projection angle. This requires memory for just two images at once.
- It aggregates between given minimum and maximum indices.
-
- @param path_proj :: path to the angle/projection subdirectory (ex.: '~/test/IMAT/test1/angle10').
-
- @param band_indices :: a typle with minimum and maximum indices of the energy bands/images
- to aggregate. Empty implies all bands. Their validity must have been checked before/elsewhere.
-
- @param imgExt :: extension of image files. Only fits supported for now as this is the format
- that we get from the intrument/cameras.
-
- @param agg_method :: whether to sum, average, etc. See options supported.
-
- Returns :: an aggregated image as a 2-dimensional numpy array with size number of image
- rows x columns.
- """
- img_files = glob.glob(os.path.join(path_proj, "*[0-9]." + imgExt))
- if len(img_files) <= 0:
- raise RuntimeError("No image files found in " + path_proj)
-
- imgs = pyfits.open(img_files[0])
- if len(imgs) < 1:
- raise RuntimeError(
- "Could not load at least one image from path: {0}".format(path_proj))
-
- data_dtype = imgs[0].data.dtype
- # from fits files we usually get this, just change it to uint16
- if '>i2' == data_dtype:
- data_dtype = np.uint16
- accum = np.zeros((imgs[0].shape[0], imgs[0].shape[1]), dtype=data_dtype)
-
- # filter, keep only the files between min and max indices given
- if band_indices:
- img_files = [f for idx,f in enumerate(img_files) if
- idx >= band_indices[0] and idx <= band_indices[1] ]
-
- for ifile in img_files:
- if too_verbose:
- sys.stdout.write('.')
-
- hdu = None
- try:
- hdu = pyfits.open(ifile)
- except IOError as exc:
- print "Got I/O exception trying to open and load {0}: {1}. Ignoring and going on.".format(
- ifile, str(exc))
- continue
-
- accum = self._agg_img(accum, hdu[0].data, agg_method=agg_method)
-
- if too_verbose:
- sys.stdout.write('\n')
-
- if verbose:
- print "Aggregated {0} images. Stats of result image. "\
- "Max : {1}, min: {2}, per-pixel-avg: {3:.3f}, all-sum: {4}".format(
- len(img_files), np.amax(accum), np.amin(accum), np.average(accum), np.sum(accum))
-
- return accum
-
- def _check_inputs_to_agg_angles(self, in_path, output_path, out_format, band_indices):
- """ Checks relevant user inputs"""
- if not in_path:
- raise ValueError("The input path cannot be empty")
-
- if output_path is None:
- output_path = self.default_out_path
-
- if out_format:
- self._out_format = out_format
- if not isinstance(self._out_format, str) or self._out_format not in self.supported_out_formats:
- raise ValueError("Only the following output formats are supported: {0}. Format requested: {1}".
- format(self.supported_out_formats, self._out_format))
-
- if band_indices:
- if 2 != len(band_indices) or not isinstance(band_indices[0], int) or\
- not isinstance(band_indices[1], int):
- raise ValueError("Wrong min-max energy band indices given: {0}".format(band_indices))
- if band_indices[0] > band_indices[1]:
- raise ValueError("The minimum energy band index must be lower than the maximum index")
-
- #pylint: disable=too-many-arguments
- def agg_angles(self, in_path, output_path=None, band_indices=None,
- agg_method='sum', out_format=None, angle_subdir_prefix='angle',
- verbose=True, too_verbose=False, out_files_name_prefix='angle_agg_', zero_pad=6):
- """
- Aggregate a stack, processing all the angles (projections) found. Produces an output stack with
- one single image per projection into an output directory. Does not store all the images in
- memory, only one at a time.
-
- @param in_path :: path to the multi-energy-band (energy selective) stack of images. It is
- expected to have several directories with the prefix 'angle' and additional alphanumeric
- characters (example: 'angle0', 'angle1', etc.)
-
- @param band_indices :: a typle with minimum and maximum indices of the energy bands/images
- to aggregate. Empty implies all bands. This method checks the validity of the values (if) given.
-
- @param output_path :: where to write the output image files
-
- @param angle_subdir_prefix :: prefix for the individual angle subdirectories. For example,
- 'angle', as used for IMAT data. Directories that do not match this are ignored.
-
- @param verbose :: write progress info and additional messages to the standard output
-
- @param too_verbose :: write more detailed progress information, for testing purposes
-
- @param zero_pad :: width (number of digits) to pad the index number to, in the output file
- names
- """
- self._check_inputs_to_agg_angles(in_path, output_path, out_format, band_indices)
-
- # in case they use '~' or similar
- in_path = os.path.expanduser(in_path)
-
- # This is the big loop through every angle's of the order of 1000s individual energy bands
- if verbose:
- print "Looking for projection angles in {0}".format(in_path)
-
- angle_subdirs = glob.glob(os.path.join(in_path, "{0}*".format(angle_subdir_prefix)))
- angle_subdirs.sort(key=self._alphanum_key_split)
-
- print "Found {0} projection (angle) subdirectories.".format(len(angle_subdirs))
-
- # Prepare output directory
- self._make_dirs_if_needed(output_path)
-
- start = time.time()
- for idx, adir in enumerate(angle_subdirs):
- print "Processing projection angle subdirectory: {0}".format(adir)
-
- # produce aggregated image
- img_data = self.agg_indiv_angle(adir, band_indices, agg_method=agg_method,
- verbose=verbose, too_verbose=too_verbose)
-
- # write into output image
- if self._default_output_type != img_data.dtype:
- img_data = img_data.astype(self._default_output_type)
-
- out_name = os.path.join(output_path, out_files_name_prefix + str(idx).zfill(zero_pad))
-
- out_name = self._write_image(img_data=img_data, filename=out_name,
- img_format=self._out_format, dtype=img_data.dtype)
-
- if verbose:
- print "Output image written in: {0}".format(out_name)
- tnow = time.time()
- print "Time elapsed: {0:.3f}".format(tnow - start)
diff --git a/scripts/Imaging/IMAT/prep/filters.py b/scripts/Imaging/IMAT/prep/filters.py
deleted file mode 100644
index cb6c7eed719..00000000000
--- a/scripts/Imaging/IMAT/prep/filters.py
+++ /dev/null
@@ -1,208 +0,0 @@
-# Copyright © 2014-2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-
-import numpy as np
-
-
-def scale_down(data_vol, block_size, method='average'):
- """
- Downscale to for example shrink 1Kx1K images to 512x512
-
- @param data_vol :: 3d volume to downscale
- @param block_size :: make block_size X block_size blocks to downscale
- @param method :: either 'average' (default) or 'sum' to calculate average or sum of blocks
-
- Returns :: downscaled volume, with the dimensions implied by block_size, and the
- same data type as the input data volume.
- """
- if not isinstance(data_vol, np.ndarray) or 3 != len(data_vol.shape):
- raise ValueError(
- "Wrong data volume when trying to crop (expected a 3d numpy array): {0}".
- format(data_vol))
- if block_size > data_vol.shape[1] or block_size > data_vol.shape[2]:
- raise ValueError(
- "Block size too large when trying to crop data volume. Block size: {0}, "
- "data dimensions: {1}".format(block_size, data_vol.shape))
-
- if 0 != np.mod(data_vol.shape[1], block_size) or 0 != np.mod(
- data_vol.shape[2], block_size):
- raise ValueError(
- "The block size ({0}) must be an exact integer divisor of the sizes of the "
- "x and y dimensions ({1} and {2} of the input data volume".format(
- data_vol.shape[2], data_vol.shape[1], block_size))
-
- supported_methods = ['average', 'sum']
- if method.lower() not in supported_methods:
- raise ValueError(
- "The method to combine pixels in blocks must be one of {0}. Got unknown "
- "value: {1}".format(supported_methods, method))
-
- rescaled_vol = np.zeros(
- (data_vol.shape[0], data_vol.shape[1] // block_size,
- data_vol.shape[2] // block_size),
- dtype=data_vol.dtype)
- # for block averages in every slice/image along the vertical/z axis
- tmp_shape = rescaled_vol.shape[1], block_size, rescaled_vol.shape[
- 2], block_size
- for vert_slice in range(len(rescaled_vol)):
- vsl = data_vol[vert_slice, :, :]
- if 'average' == method:
- rescaled_vol[vert_slice, :, :] = vsl.reshape(tmp_shape).mean(
- -1).mean(1)
- elif 'sum' == method:
- rescaled_vol[vert_slice, :, :] = vsl.reshape(tmp_shape).mean(
- -1).mean(1)
-
- return rescaled_vol
-
-
-def crop_vol(data_vol, coords):
- """
- Crops a data volume by a rectangle defined by two corner
- coordinates. Crops along the z axis (outermost numpy array index)
-
- @param data_vol :: 3D data volume
- @param coords :: coordinates of the corners that define a rectangle box (crop to this
- box, as when cropping to the regions of interest).
- Returns :: cropped data volume
- """
- # if nothing is provided make the user aware
- if not isinstance(coords, list) or 4 != len(coords):
- raise ValueError(
- "Wrong coordinates object when trying to crop: {0}".format(coords))
- elif not isinstance(data_vol, np.ndarray) or 3 != len(data_vol.shape):
- raise ValueError("Wrong data volume when trying to crop: {0}".format(
- data_vol))
- # move into named variables for ease of use
- left = coords[0]
- top = coords[1]
- right = coords[2]
- bottom = coords[3]
-
- cropped_data = None
- if not any(coords) or top > bottom or left > right:
- # skip if for example: 0, 0, 0, 0 (empty selection)
- print(" ! No coordinates given, not cropping the images")
- return data_vol
- elif not all(isinstance(crd, int) for crd in coords):
- raise ValueError(
- "Cannot use non-integer coordinates to crop images. Got "
- "these coordinates: {0}".format(coords))
- else:
- cropped_data = data_vol[:, top:bottom, left:right]
-
- return cropped_data
-
-
-def remove_stripes_ring_artifacts(data_vol, method='wavelet-fourier'):
- """
- Removal of stripes in sinograms / ring artifacts in reconstructed
- volume.
-
- This is an unimplemented stub at the moment.
- As first step it should implement one methods: the combined wavelet-Fourier method
- (Muench et al. 2009, Opt Express, 17(10), 8567-91), as implemented also in tomopy.
-
- @param data_vol :: stack of projection images as 3d data (dimensions z, y, x), with
- z different projections angles, and y and x the rows and columns of individual images.
-
- @param method :: 'wf': Wavelet-Fourier based method
-
- Returns :: filtered data hopefully without stripes which should dramatically decrease
- ring artifacts after reconstruction and the effect of these on post-processing tasks
- such as segmentation of the reconstructed 3d data volume.
- """
- supported_methods = ['wavelet-fourier']
-
- if not isinstance(data_vol, np.ndarray) or 3 != len(data_vol.shape):
- raise ValueError(
- "Wrong data volume when trying to filter stripes/ring artifacts: {0}".
- format(data_vol))
-
- if method.lower() not in supported_methods:
- raise ValueError(
- "The method to remove stripes and ring artifacts must be one of {0}. "
- "Got unknown value: {1}".format(supported_methods, method))
-
- try:
- import tomopy
- stripped_vol = tomopy.prep.stripe.remove_stripe_fw(data_vol)
- except ImportError:
- stripped_vol = remove_sino_stripes_rings_wf(data_vol)
-
- return stripped_vol
-
-
-def remove_sino_stripes_rings_wf(data_vol, wv_levels=None):
- if not wv_levels:
- max_len = np.max(data_vol.shape)
- wv_levels = int(np.ceil(np.log2(max_len)))
-
- from . import filters_adv
- return filters_adv.remove_sino_stripes_rings_wf(data_vol, wv_levels)
-
-
-def circular_mask(data_vol, ratio=1.0, mask_out_val=0.0):
- """
- Applies a circular mask on a 3D volume. The mask is applied along the z axis (first
- dimension of the numpy shape)
-
- @param data_vol :: 3D data volume
- @param ratio :: radius of the mask relative to the radius of the smallest from the
- x and y dimensions/edges
- @param mask_out_val :: value to use when masking out pixels outside of the mask radius
-
- Returns :: masked volume
- """
- if not isinstance(data_vol, np.ndarray) or 3 != len(data_vol.shape):
- raise ValueError(
- "Wrong data volume when trying to apply a circular mask: {0}".
- format(data_vol))
-
- edge_z, edge_y, edge_x = data_vol.shape
- mask_in = _calc_mask(edge_y, edge_x, ratio)
- for idx in range(edge_z):
- data_vol[idx, ~mask_in] = mask_out_val
-
- return data_vol
-
-
-def _calc_mask(ydim, xdim, ratio):
- """
- Prepare a mask object.
-
- @param ydim :: size/length of the y dimension (image rows)
- @param xdim :: size/length of the x dimension (innermost, image columns)
- @param ratio :: ratio in [0,1] relative to the smaller dimension
-
- Returns :: mask as a numpy array of boolean values (in/out-side mask)
- """
- radius_y = ydim / 2.0
- radius_x = xdim / 2.0
- if ydim < xdim:
- small_radius2 = radius_y * radius_y
- else:
- small_radius2 = radius_x * radius_x
-
- y_mask, x_mask = np.ogrid[0.5 - radius_y:0.5 + radius_y, 0.5 - radius_x:0.5
- + radius_x]
-
- small_radius2 *= ratio * ratio
- return (y_mask * y_mask + x_mask * x_mask) < (small_radius2)
diff --git a/scripts/Imaging/IMAT/prep/filters_adv.py b/scripts/Imaging/IMAT/prep/filters_adv.py
deleted file mode 100644
index 54c6bff5f1c..00000000000
--- a/scripts/Imaging/IMAT/prep/filters_adv.py
+++ /dev/null
@@ -1,135 +0,0 @@
-# Copyright © 2014-2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-
-import numpy as np
-
-# The code of the 'Wavelet-Fourier' stripe removal method is heavily based on
-# the implementation of this method in tomopy
-# The original code from Tomopy is:
-# #########################################################################
-# Copyright (c) 2015, UChicago Argonne, LLC. All rights reserved. #
-# #
-# Copyright 2015. UChicago Argonne, LLC. This software was produced #
-# under U.S. Government contract DE-AC02-06CH11357 for Argonne National #
-# Laboratory (ANL), which is operated by UChicago Argonne, LLC for the #
-# U.S. Department of Energy. The U.S. Government has rights to use, #
-# reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR #
-# UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR #
-# ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is #
-# modified to produce derivative works, such modified software should #
-# be clearly marked, so as not to confuse it with the version available #
-# from ANL. #
-# #
-# Additionally, redistribution and use in source and binary forms, with #
-# or without modification, are permitted provided that the following #
-# conditions are met: #
-# #
-# * Redistributions of source code must retain the above copyright #
-# notice, this list of conditions and the following disclaimer. #
-# #
-# * Redistributions in binary form must reproduce the above copyright #
-# notice, this list of conditions and the following disclaimer in #
-# the documentation and/or other materials provided with the #
-# distribution. #
-# #
-# * Neither the name of UChicago Argonne, LLC, Argonne National #
-# Laboratory, ANL, the U.S. Government, nor the names of its #
-# contributors may be used to endorse or promote products derived #
-# from this software without specific prior written permission. #
-# #
-# THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS #
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT #
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS #
-# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago #
-# Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, #
-# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, #
-# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; #
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER #
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT #
-# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN #
-# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
-# POSSIBILITY OF SUCH DAMAGE. #
-# #########################################################################
-
-
-def remove_sino_stripes_rings_wf(data_vol, wv_levels, wavelet_name='db5', sigma=2, pad=True):
- """
- Removes horizontal stripes in sinograms (reducing ring artifacts in the reconstructed volume).
- Implements a combined Wavelet-Fourier filter (wf) as described in:
-
- Muench B, Trtrik P, Marone F, and Stampanoni M. 2009. Optics Express, 17(10):8567-8591.
- Stripe and ring artifact removal with combined wavelet-fourier filtering. 2009.
-
- This implementation is heavily based on the implementation from tomopy. This is not parallel
- at the moment.
- """
- try:
- import pywt
- except ImportError as exc:
- raise ImportError("Could not import the package pywt. Details: {0}".format(exc))
-
- dimx = data_vol.shape[0]
- n_x = dimx
- if pad:
- n_x = dimx + dimx / 8
- xshift = int((n_x - dimx) / 2.)
-
- for sino_idx in range(0, data_vol.shape[1]):
- sli = np.zeros((n_x, data_vol.shape[2]), dtype='float32')
- sli[xshift:dimx + xshift] = data_vol[:, sino_idx, :]
-
- # Wavelet decomposition
- c_H, c_V, c_D = [], [], []
- for _ in range(wv_levels):
- sli, (cHt, cVt, cDt) = pywt.dwt2(sli, wavelet_name)
- c_H.append(cHt)
- c_V.append(cVt)
- c_D.append(cDt)
-
- c_V = ft_horizontal_bands(c_V, wv_levels, sigma)
-
- # Wavelet reconstruction
- for nlvl in range(wv_levels)[::-1]:
- sli = sli[0:c_H[nlvl].shape[0], 0:c_H[nlvl].shape[1]]
- sli = pywt.idwt2((sli, (c_H[nlvl], c_V[nlvl], c_D[nlvl])),
- wavelet_name)
- data_vol[:, sino_idx, :] = sli[xshift:dimx + xshift, 0:data_vol.shape[2]]
-
- return data_vol
-
-
-def ft_horizontal_bands(c_V, wv_levels, sigma):
- """
- Fourier transform of horizontal frequency bands
- """
- for nlvl in range(wv_levels):
- # FT
- fcV = np.fft.fftshift(np.fft.fft(c_V[nlvl], axis=0))
- m_y, m_x = fcV.shape
-
- # Damping of ring artifact information
- y_hat = (np.arange(-m_y, m_y, 2, dtype='float32') + 1) / 2
- damp = 1 - np.exp(-np.power(y_hat, 2) / (2 * np.power(sigma, 2)))
- fcV = np.multiply(fcV, np.transpose(np.tile(damp, (m_x, 1))))
-
- # Inverse FT
- c_V[nlvl] = np.real(np.fft.ifft(np.fft.ifftshift(fcV), axis=0))
-
- return c_V
diff --git a/scripts/Imaging/IMAT/tomo_reconstruct.py b/scripts/Imaging/IMAT/tomo_reconstruct.py
deleted file mode 100644
index 5cf75e478cb..00000000000
--- a/scripts/Imaging/IMAT/tomo_reconstruct.py
+++ /dev/null
@@ -1,411 +0,0 @@
-from __future__ import (absolute_import, division, print_function)
-# Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-"""
-Do a tomographic reconstruction, including:
-- Pre-processing of input raw images,
-- 3d volume reconstruction using a third party tomographic reconstruction tool
-- Post-processing of reconstructed volume
-- Saving reconstruction results (and pre-processing results, and self-save this script and subpackages)
-
-This command line script and the classes and packages that it uses are prepared so that
-they can be run from Mantid, locally (as a process) or remotely (through the tomographic reconstruction
-GUI remote job submission, or the remote algorithms).
-
-Example command lines:
-
-ipython -- tomo_reconstruct.py --help
-
-ipython -- scripts/Imaging/IMAT/tomo_reconstruct.py\
- --input-path=../tomography-tests/stack_larmor_metals_summed_all_bands/ --output-path=test_REMOVE_ME\
- --tool tomopy --algorithm gridrec --cor 123 --max-angle 360 --in-img-format=tiff\
- --region-of-interest='[5, 252, 507, 507]' --rotation=-1
-
-ipython -- scripts/Imaging/IMAT/tomo_reconstruct.py\
- --input-path=../tomography-tests/stack_larmor_metals_summed_all_bands/ --output-path=test_REMOVE_ME\
- --tool tomopy --algorithm sirt --num-iter 10 --cor 123 --max-angle 360 --in-img-format=tiff\
- --out-img-format png --region-of-interest='[5, 252, 507, 507]' --rotation=-1
-
-ipython -- scripts/Imaging/IMAT/tomo_reconstruct.py\
- --input-path=../tomography-tests/stack_larmor_metals_summed_all_bands/ --output-path=test_REMOVE_ME\
- --tool astra --algorithm FP3D_CUDA --num-iter 10 --cor 123 --max-angle 360 --in-img-format=tiff\
- --region-of-interest='[5, 252, 507, 507]' --rotation=-1
-"""
-
-# find first the package/subpackages in the path of this file.
-import sys
-import os
-from os import path
-# So insert in the path the directory that contains this file
-sys.path.insert(0, os.path.split(path.dirname(__file__))[0]) # noqa
-
-from tomorec import reconstruction_command as tomocmd
-import tomorec.configs as tomocfg
-
-
-def setup_cmd_options():
- """
- Build an argument parser
-
- Returns :: Python ArgumentParser set up and ready to parse command line arguments
- """
-
- import argparse
-
- parser = argparse.ArgumentParser(
- description='Run tomographic reconstruction via third party tools')
-
- grp_req = parser.add_argument_group('Mandatory/required options')
-
- grp_req.add_argument(
- "-i", "--input-path", required=True, type=str, help="Input directory")
-
- grp_req.add_argument(
- "-o",
- "--output-path",
- required=True,
- type=str,
- help="Where to write the output slice images (reconstructed volume)")
-
- grp_req.add_argument(
- "-c",
- "--cor",
- required=False,
- type=float,
- help="Provide a pre-calculated centre of rotation. If one is not provided it will be automatically calculated"
- )
-
- grp_req.add_argument(
- "-f",
- "--find-cor",
- action='store_true',
- required=False,
- help="Find the center of rotation (in pixels). rotation around y axis is assumed"
- )
-
- grp_recon = parser.add_argument_group('Reconstruction options')
-
- grp_recon.add_argument(
- "-t",
- "--tool",
- required=False,
- type=str,
- help="Tomographic reconstruction tool to use")
-
- grp_recon.add_argument(
- "-a",
- "--algorithm",
- required=False,
- type=str,
- help="Reconstruction algorithm (tool dependent)")
-
- grp_recon.add_argument(
- "-n",
- "--num-iter",
- required=False,
- type=int,
- help="Number of iterations (only valid for iterative methods "
- "(example: SIRT, ART, etc.).")
-
- grp_recon.add_argument(
- "--max-angle",
- required=False,
- type=float,
- help="Maximum angle (of the last projection), assuming first angle=0, and "
- "uniform angle increment for every projection (note: this "
- "is overriden by the angles found in the input FITS headers)")
-
- grp_pre = parser.add_argument_group(
- 'Pre-processing of input raw images/projections')
-
- grp_pre.add_argument(
- "--input-path-flat",
- required=False,
- default=None,
- type=str,
- help="Input directory for flat images")
-
- grp_pre.add_argument(
- "--input-path-dark",
- required=False,
- default=None,
- type=str,
- help="Input directory for flat images")
-
- img_formats = ['tiff', 'fits', 'tif', 'fit', 'png']
- grp_pre.add_argument(
- "--in-img-format",
- required=False,
- default='fits',
- type=str,
- help="Format/file extension expected for the input images. Supported: {0}".
- format(img_formats))
-
- grp_pre.add_argument(
- "--out-img-format",
- required=False,
- default='tiff',
- type=str,
- help="Format/file extension expected for the input images. Supported: {0}".
- format(img_formats))
-
- grp_pre.add_argument(
- "--region-of-interest",
- required=False,
- type=str,
- help="Region of interest (crop original "
- "images to these coordinates, given as comma separated values: x1,y1,x2,y2. If not "
- "given, the whole images are used.")
-
- grp_pre.add_argument(
- "--air-region",
- required=False,
- type=str,
- help="Air region /region for normalization. "
- "If not provided, the normalization against beam intensity fluctuations in this "
- "region will not be performed")
-
- grp_pre.add_argument(
- "--median-filter-size",
- type=int,
- required=False,
- help="Size/width of the median filter (pre-processing")
-
- grp_pre.add_argument(
- "--remove-stripes",
- default='wf',
- required=False,
- type=str,
- help="Methods supported: 'wf' (Wavelet-Fourier)")
-
- grp_pre.add_argument(
- "--rotation",
- required=False,
- type=int,
- help="Rotate images by 90 degrees a number of "
- "times. The rotation is clockwise unless a negative number is given which indicates "
- "rotation counterclocwise")
-
- grp_pre.add_argument(
- "--scale-down",
- required=False,
- type=int,
- help="Scale down factor, to reduce the size of "
- "the images for faster (lower-resolution) reconstruction. For example a factor of 2 "
- "reduces 1kx1k images to 512x512 images (combining blocks of 2x2 pixels into a single "
- "pixel. The output pixels are calculated as the average of the input pixel blocks."
- )
-
- grp_pre.add_argument(
- "--mcp-corrections",
- default='yes',
- required=False,
- type=str,
- help="Perform corrections specific to images taken with the MCP detector"
- )
-
- grp_post = parser.add_argument_group(
- 'Post-processing of the reconstructed volume')
-
- grp_post.add_argument(
- "--circular-mask",
- required=False,
- type=float,
- default=0.94,
- help="Radius of the circular mask to apply on the reconstructed volume. "
- "It is given in [0,1] relative to the size of the smaller dimension/edge "
- "of the slices. Empty or zero implies no masking.")
-
- grp_post.add_argument(
- "--cut-off",
- required=False,
- type=float,
- help="Cut off level (percentage) for reconstructed "
- "volume. pixels below this percentage with respect to maximum intensity in the stack "
- "will be set to the minimum value.")
-
- grp_post.add_argument(
- "--out-median-filter",
- required=False,
- type=float,
- help="Apply median filter (2d) on reconstructed volume with the given window size."
- )
-
- parser.add_argument(
- "-v",
- "--verbose",
- action="count",
- default=1,
- help="Verbosity level. Default: 1. "
- "User zero to supress outputs.")
-
- return parser
-
-
-def grab_preproc_options(args):
- """
- Get pre-proc options from the command line (through an argument parser)
-
- @param parser :: arguments parser already, set up with pre-processing options
-
- Returns:: a pre-processing config object set up according to the user inputs in the command line
- """
- import ast
-
- pre_config = tomocfg.PreProcConfig()
- pre_config.input_dir = args.input_path
- pre_config.input_dir_flat = args.input_path_flat
- pre_config.input_dir_dark = args.input_path_dark
-
- if args.in_img_format:
- pre_config.in_img_format = args.in_img_format
-
- if args.out_img_format:
- pre_config.out_img_format = args.out_img_format
-
- if args.max_angle:
- pre_config.max_angle = float(args.max_angle)
-
- if args.rotation:
- pre_config.rotation = int(args.rotation)
-
- if args.air_region:
- coords = ast.literal_eval(args.air_region)
- pre_config.normalize_air_region = [int(val) for val in coords]
-
- if args.air_region:
- coords = ast.literal_eval(args.air_region)
- pre_config.normalize_air_region = [int(val) for val in coords]
-
- if args.region_of_interest:
- roi_coords = ast.literal_eval(args.region_of_interest)
- pre_config.crop_coords = [int(val) for val in roi_coords]
-
- if 'yes' == args.mcp_corrections:
- pre_config.mcp_corrections = True
-
- if args.median_filter_size:
- if isinstance(args.median_filter_size,
- str) and not args.median_filter_size.isdigit():
- raise RuntimeError(
- "The median filter size/width must be an integer")
- pre_config.median_filter_size = args.median_filter_size
-
- if 'wf' == args.remove_stripes:
- pre_config.stripe_removal_method = 'wavelet-fourier'
-
- if args.cor:
- pre_config.cor = int(args.cor)
-
- return pre_config
-
-
-def grab_tool_alg_options(args):
- """
- Get tool and algorithm options from the command line (through an argument parser)
-
- @param parser :: arguments parsed already, set up with algorithm/tool options
-
- Returns:: an algorithm config object set up according to the user inputs in the command line
- """
- config = tomocfg.ToolAlgorithmConfig()
- config.tool = args.tool
- config.algorithm = args.algorithm
-
- if args.num_iter:
- if isinstance(args.num_iter, str) and not args.num_iter.isdigit():
- raise RuntimeError("The number of iterations must be an integer")
- config.num_iter = int(args.num_iter)
-
- return config
-
-
-def grab_postproc_options(args):
- """
- Get post-processing (on the reconstructed volume) options from the command line
- (through an argument parser)
-
- @param parser :: arguments parsed already, set up with post-processing options
-
- Returns:: a post-processing object set up according to the user inputs in the command line
- """
- config = tomocfg.PostProcConfig()
- config.output_dir = args.output_path
-
- if args.circular_mask:
- config.circular_mask = float(args.circular_mask)
-
- if args.cut_off:
- config.cut_off_level = float(args.cut_off)
-
- if args.out_median_filter:
- config.median_filter_size = float(args.out_median_filter)
-
- return config
-
-
-def main_tomo_rec():
- # several dependencies (numpy, scipy) are too out-of-date in standard Python 2.6
- # distributions, as found for example on rhel6
-
- vers = sys.version_info
- if vers < (2, 7, 0):
- raise RuntimeError(
- "Not running this test as it requires Python >= 2.7. Version found: {0}".
- format(vers))
-
- import inspect
-
- import IMAT.tomorec.io as tomoio
-
- arg_parser = setup_cmd_options()
- args = arg_parser.parse_args()
-
- # Grab and check pre-processing options + algorithm setup + post-processing options
- preproc_config = grab_preproc_options(args)
- alg_config = grab_tool_alg_options(args)
- postproc_config = grab_postproc_options(args)
-
- cmd_line = " ".join(sys.argv)
- cfg = tomocfg.ReconstructionConfig(preproc_config, alg_config,
- postproc_config)
-
- # Does all the real work
- cmd = tomocmd.ReconstructionCommand()
- # start the whole execution timer
- cmd.tomo_total_timer()
-
- if (args.find_cor):
- cmd.tomo_print(" >>> Finding COR <<<")
- cmd.find_center(cfg)
- else:
- # Save myself early. Save command this command line script and all packages/subpackages
- tomoio.self_save_zipped_scripts(
- args.output_path,
- os.path.abspath(inspect.getsourcefile(lambda: 0)))
- cmd.tomo_print(" >>> Running reconstruction <<<")
- cmd.do_recon(cfg, cmd_line=cmd_line)
-
- # end the whole execution timer
- cmd.tomo_total_timer()
-
-
-if __name__ == '__main__':
- main_tomo_rec()
diff --git a/scripts/Imaging/IMAT/tomorec/__init__.py b/scripts/Imaging/IMAT/tomorec/__init__.py
deleted file mode 100644
index ca06e379c16..00000000000
--- a/scripts/Imaging/IMAT/tomorec/__init__.py
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright © 2014-2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-"""
-A collection of scripts for neutron imaging. Includes
-pre-processing/preparation steps, reconstruction via third party
-tools, and post-processing steps, in addition to input/output and
-format conversion routines.
-
-"""
-
-IMPORT_ERR_MSG = ("Inconsistency found. Could not import {0} which should be "
- "available in this package. Details/reason: {1}")
-try:
- import io
-except ImportError as exc:
- raise ImportError(
- IMPORT_ERR_MSG.format("'io' (input/output routines)", exc))
-
-try:
- import configs
-except ImportError as exc:
- raise ImportError(
- IMPORT_ERR_MSG.format("'configs' (tomographic reconstruction "
- "configuration definitions)", exc))
-
-try:
- import tool_imports
-except ImportError as exc:
- raise ImportError(
- IMPORT_ERR_MSG.format("'tool_imports' (for third party "
- "tools such as Tomopy and Astra)", exc))
-try:
- import reconstruction_command
-except ImportError as exc:
- raise ImportError(
- IMPORT_ERR_MSG.format("'reconstruction_command' (tomographic "
- "reconstruction command)", exc))
diff --git a/scripts/Imaging/IMAT/tomorec/configs.py b/scripts/Imaging/IMAT/tomorec/configs.py
deleted file mode 100644
index 8f3cc189c75..00000000000
--- a/scripts/Imaging/IMAT/tomorec/configs.py
+++ /dev/null
@@ -1,195 +0,0 @@
-# Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-"""
-Classes to handle a tomographic reconstruction configuration, including
-pre-processing, reconstruction, and post-processing
-"""
-
-import os
-
-#pylint: disable=too-few-public-methods
-
-
-class ToolAlgorithmConfig(object):
- """
- Reconstruction algorithm specific configuration. Required for any reconstruction:
- a tool that implements the method/algorithm,
- the algorithm name,
- (only for the iterative algorithms) the number of iterations
- (only for some algorithms) a regularization/smoothing parameter
- """
-
- DEF_TOOL = 'tomopy'
- DEF_ALGORITHM = 'gridrec'
-
- def __init__(self):
- self.tool = self.DEF_TOOL
- self.algorithm = self.DEF_ALGORITHM
- self.num_iter = None
- self.regularization = None
-
- def __str__(self):
- mystr = "Tool: {0}\n".format(self.tool)
- mystr += "Algorithm: {0}\n".format(self.algorithm)
- if self.num_iter:
- mystr += "Number of algorith iterations: {0}\n".format(
- self.num_iter)
- else:
- mystr += "(Algorithm iterations: not defined)\n"
- if self.regularization:
- mystr += "Regularization parameter: {0}\n".format(
- self.regularization)
- else:
- mystr += "(Regularization parameter: not defined)\n"
-
- return mystr
-
-
-#pylint: disable=too-many-instance-attributes
-class PreProcConfig(object):
- """
- All pre-processing options required to run a tomographic reconstruction.
-
- Options like the stripe removal, MCP correction, or even the median filter would
- better be handled as plugins. For the time being we just have a panel with a fixed
- set of options to enable/disable/configure
- """
-
- DEF_NUM_ITER = 5
-
- def __init__(self):
- # defaults that look sensible for the MCP detector:
- # median_filter=3, rotate=-1, crop=[0, 252, 0, 512], MCP correction: on
- self.input_dir = None
- self.input_dir_flat = None
- self.input_dir_dark = None
- self.in_img_format = 'tiff'
- self.out_img_format = 'tiff'
- self.max_angle = 360
- # Rotation 90 degrees clockwise (positive) or counterclockwise (negative)
- # Example: -1 => (-90 degrees == 90 degrees counterclockwise)
- self.rotation = -1
- self.normalize_flat_dark = True
- # list with coordinates of the region for normalization / "air" / not blocked by any object
- self.normalize_air_region = None
- self.normalize_proton_charge = False
- # region of interest
- self.crop_coords = None
- self.cut_off_level = 0
- self.mcp_corrections = True
- self.scale_down = 0
- self.median_filter_size = 3
- self.line_projection = True
- self.stripe_removal_method = 'wavelet-fourier'
- # Center of rotation
- self.cor = None
- self.save_preproc_imgs = True
-
- def __str__(self):
-
- mystr = "Input path (relative): {0}\n".format(self.input_dir)
- if self.input_dir:
- mystr += "Input path (absolute): {0}\n".format(
- os.path.abspath(self.input_dir))
- else:
- mystr += "Input path (absolute): {0}\n".format(
- 'cannot find because the input '
- 'path has not been set')
- mystr += "Input path for flat (open beam) images (relative): {0}\n".format(
- self.input_dir_flat)
- mystr += "Input path for dark images (relative): {0}\n".format(
- self.input_dir_dark)
- mystr += "Input image format: {0}\n".format(self.in_img_format)
- mystr += "Output image format: {0}\n".format(self.out_img_format)
- mystr += "Maximum angle:: {0}\n".format(self.max_angle)
- mystr += "Center of rotation: {0}\n".format(self.cor)
- mystr += "Region of interest (crop coordinates): {0}\n".format(
- self.crop_coords)
- mystr += "Normalize by flat/dark images: {0}\n".format(
- self.normalize_flat_dark)
- mystr += "Normalize by air region: {0}\n".format(
- self.normalize_air_region)
- mystr += "Normalize by proton charge: {0}\n".format(
- self.normalize_proton_charge)
- mystr += "Cut-off on normalized images: {0}\n".format(
- self.cut_off_level)
- mystr += "Corrections for MCP detector: {0}\n".format(
- self.mcp_corrections)
- mystr += "Scale down factor for images: {0}\n".format(self.scale_down)
- mystr += "Median filter width: {0}\n".format(self.median_filter_size)
- mystr += "Rotation: {0}\n".format(self.rotation)
- mystr += "Line projection (line integral/log re-scale): {0}\n".format(
- 1)
- mystr += "Sinogram stripes removal: {0}".format(
- self.stripe_removal_method)
-
- return mystr
-
-
-class PostProcConfig(object):
- """
- All pre-processing options required to run a tomographic reconstruction
- """
-
- def __init__(self):
- """
- Builds a default post-processing configuration with a sensible choice of parameters
- """
- self.output_dir = None
- self.circular_mask = 0.94
- self.cut_off_level = 0
- self.gaussian_filter_par = 0
- self.median_filter_size = 0
- self.median_filter3d_size = 0
-
- def __str__(self):
-
- mystr = "Output path (relative): {0}\n".format(self.output_dir)
- if self.output_dir:
- mystr += "Output path (absolute): {0}\n".format(
- os.path.abspath(self.output_dir))
- else:
- mystr += "Output path (absolute): {0}\n".format(
- 'cannot find because the input '
- 'path has not been set')
- mystr += "Circular mask: {0}\n".format(self.circular_mask)
- mystr += "Cut-off on reconstructed volume: {0}\n".format(
- self.cut_off_level)
- mystr += "Gaussian filter: {0}\n".format(self.gaussian_filter_par)
- mystr += "Median filter size:: {0}\n".format(self.median_filter_size)
- mystr += "Median filter (3d) size:: {0}\n".format(
- self.median_filter3d_size)
-
- return mystr
-
-
-class ReconstructionConfig(object):
- """
- Full configuration (pre-proc + tool/algorithm + post-proc.
- """
-
- def __init__(self, preproc_cfg, alg_cfg, postproc_cfg):
- self.preproc_cfg = preproc_cfg
- self.alg_cfg = alg_cfg
- self.postproc_cfg = postproc_cfg
-
- def __str__(self):
- return str(self.preproc_cfg) + str(self.alg_cfg) + str(
- self.postproc_cfg)
diff --git a/scripts/Imaging/IMAT/tomorec/io.py b/scripts/Imaging/IMAT/tomorec/io.py
deleted file mode 100644
index 29c8fa057c6..00000000000
--- a/scripts/Imaging/IMAT/tomorec/io.py
+++ /dev/null
@@ -1,578 +0,0 @@
-from __future__ import (absolute_import, division, print_function)
-# Copyright © 2014-2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-"""
-Input/output functionality for stacks of images. For example: load
-a stack of images in different formats (.tif, FITS). Includes handling
-of paths, sample, flat, and dark images, file name prefixes, etc.
-
-"""
-
-import glob
-import os
-import re
-
-import numpy as np
-
-
-def _import_pyfits():
- """
- To import pyfits optionally only when it is/can be used
- """
- try:
- import pyfits
- except ImportError:
- # In Anaconda python, the pyfits package is in a different place, and this is what you frequently
- # find on windows.
- try:
- import astropy.io.fits as pyfits
- except ImportError:
- raise ImportError(
- "Cannot find the package 'pyfits' which is required to read/write FITS image files"
- )
-
- return pyfits
-
-
-def _import_skimage_io():
- """
- To import skimage io only when it is/can be used
- """
- try:
- from skimage import io as skio
- skio.use_plugin('freeimage')
- except ImportError as exc:
- raise ImportError(
- "Could not find the package skimage, its subpackage "
- "io and the pluging freeimage which are required to support "
- "several image formats. Error details: {0}".format(exc))
- return skio
-
-
-def make_dirs_if_needed(dirname):
- """
- Makes sure that the directory needed (for example to save a file)
- exists, otherwise creates it.
-
- @param dirname :: (output) directory to check
-
- """
- absname = os.path.abspath(dirname)
- if not os.path.exists(absname):
- os.makedirs(absname)
-
-
-#pylint: disable=too-many-arguments
-
-
-def write_image(img_data,
- min_pix,
- max_pix,
- filename,
- img_format=None,
- dtype=None,
- rescale_intensity=False):
- """
- Output image data, given as a numpy array, to a file, in a given image format.
- Assumes that the output directory exists (must be checked before). The pixel
- values are rescaled in the range [min_pix, max_pix] which would normally be set
- to the minimum/maximum values found in a stack of images.
-
- @param img_data :: image data in the usual numpy representation
-
- @param min_pix :: minimum reference value to rescale data (may be local to an
- image or global for a stack of images)
- @param max_pix :: maximum reference value to rescale data (may be local to an
- image or global for a stack of images)
-
- @param filename :: file name, including directory and extension
- @param img_format :: image file format
- @param dtype :: can be used to force a pixel type, otherwise the type
- of the input data is used
-
- Returns:: name of the file saved
- """
- if not img_format:
- img_format = 'png'
- filename = filename + '.' + img_format
-
- # The special case dtype = 'uint8' could be handled with bytescale:
- # img_data = scipy.misc.bytescale(img_data)
-
- # from bigger to smaller type, example: float32 => uint16
- if dtype and img_data.dtype != dtype:
- old_img_data = img_data
- img_data = np.zeros(old_img_data.shape, dtype='float32')
- pix_range = max_pix - float(min_pix)
- scale_factor = (np.iinfo(dtype).max - np.iinfo(dtype).min) / pix_range
-
- too_verbose = False
- if too_verbose:
- print("pix min: {0}, max: {1}, scale_factor: {2}".format(
- min_pix, max_pix, scale_factor))
- img_data = scale_factor * (old_img_data - min_pix)
- img_data = img_data.astype(dtype=dtype)
-
- # this rescale intensity would ignore the range of other images in the stack
- # in addition, it clips if the original values are below/above the destination type limits
- if rescale_intensity:
- try:
- from skimage import exposure
- except ImportError as exc:
- raise ImportError(
- "Could not find the exposure package (in skimage) "
- "Error details: {0}".format(exc))
- img_data = exposure.rescale_intensity(
- img_data, out_range=dtype) #'uint16')
-
- skio = _import_skimage_io()
- # Without this plugin tiff files don't seem to be generated correctly for some
- # bit depths (especially relevant for uint16), but you still need to load the
- # freeimage plugin with use_plugin!
- _USING_PLUGIN_TIFFFILE = True
- if img_format == 'tiff' and _USING_PLUGIN_TIFFFILE:
- # compression option intentionally not used: compress=6, 3rd party tools have
- # issues loading compressed tiff files)
- skio.imsave(filename, img_data, plugin='tifffile')
- else:
- skio.imsave(filename, img_data, plugin='freeimage')
-
- return filename
-
-
-def avg_image_files(path,
- base_path,
- file_prefix=None,
- file_extension=None,
- agg_method='average'):
- """
- Reads files from a directory, assuming they are images from a
- stack, and calculates the average image.
-
- @param base_path :: path that can be used as base path if the path to the images
- to average is relative (for example a dark images path relative to the samples
- path)
- """
- path = None
- if os.path.isabs(base_path):
- path = base_path
- else:
- os.path.join(base_path, path)
-
- path = os.path.expanduser(path)
-
- img_files = glob.glob(
- os.path.join(path, "{0}*.{1}".format(file_prefix, file_extension)))
-
- if len(img_files) <= 0:
- raise RuntimeError("No image files found in " + path)
-
- pyfits = _import_pyfits()
-
- imgs = pyfits.open(img_files[0])
- if len(imgs) < 1:
- raise RuntimeError("Could not load at least one image from path: {0}".
- format(base_path))
-
- data_dtype = imgs[0].data.dtype
- # from fits files we usually get this, just change it to uint16
- if '>i2' == data_dtype:
- data_dtype = np.uint16
-
- accum = np.zeros((imgs[0].shape[0], imgs[0].shape[1]), dtype=data_dtype)
-
- for ifile in img_files:
- hdu = None
- try:
- hdu = pyfits.open(ifile)
- except IOError as exc:
- print(
- "Got I/O exception trying to open and load {0}: {1}. Ignoring and going on.".
- format(ifile, str(exc)))
- continue
-
- accum = _agg_img(accum, hdu[0].data, agg_method=agg_method)
-
- return accum
-
-
-def _agg_img(acc, img_data, agg_method=None, index=1):
- """
- Adds in (with average, median, etc.) data coming from a new
- image/hdu. Expects a numpy array of shape (N1, N2) where N1 and N2
- are the number of rows and columns of the images.
-
- @param acc :: aggregated value accumulated so far
- @param img_data :: new image to add in
- @param agg_method :: whether to sum, average, etc. See options supported.
- @param index :: image index used when calculating incremental statistics like the average
-
- Returns :: result from aggregating (sum, average, etc.) the new image
-
- """
- if agg_method is None:
- agg_method = 'sum'
-
- if 'sum' == agg_method:
- acc = np.add(acc, img_data)
- elif 'average' == agg_method:
- acc = np.add((index - 1) * acc / index, img_data / index)
-
- return acc
-
-
-def _alphanum_key_split(path_str):
- """
- From a string to a list of alphabetic and numeric elements. Intended to
- be used for sequence number/natural sorting. In list.sort() the
- key can be a list, so here we split the alpha/numeric fields into
- a list. For example (in the final order after sort() would be applied):
-
- "angle4" -> ["angle", 4]
- "angle31" -> ["angle", 31]
- "angle42" -> ["angle", 42]
- "angle101" -> ["angle", 101]
-
- Several variants compared here:
- https://dave.st.germa.in/blog/2007/12/11/exception-handling-slow/
- """
- ALPHA_NUM_SPLIT_RE = re.compile('([0-9]+)')
- return [
- int(c) if c.isdigit() else c
- for c in ALPHA_NUM_SPLIT_RE.split(path_str)
- ]
-
-
-def _read_img(filename, file_extension=None):
- """
- Read one image and return it as a 2d numpy array
-
- @param filename :: name of the image file, can be relative or absolute path
- @param file_extension :: extension and effectively format to use ('tiff', 'fits')
- """
- if file_extension in ['fits', 'fit']:
- pyfits = _import_pyfits()
- imgs = pyfits.open(filename)
- if len(imgs) < 1:
- raise RuntimeError(
- "Could not load at least one FITS image/table file from: {0}".
- format(filename))
-
- # Input fits files always contain a single image
- img_arr = imgs[0].data
-
- elif file_extension in ['tiff', 'tif', 'png']:
- skio = _import_skimage_io()
- img_arr = skio.imread(filename)
-
- else:
- raise ValueError(
- "Don't know how to load a file with this extension: {0}".format(
- file_extension))
-
- return img_arr
-
-
-def _read_listed_files(files, slice_img_shape, file_extension, dtype):
- """
- Read several images in a row into a 3d numpy array. Useful when reading all the sample
- images, or all the flat or dark images.
-
- @param files :: list of image file paths given as strings
- @param slice_img_shape :: shape of every image
- @param file_extension :: file name extension if fixed (to set the expected image format)
- @param dtype :: data type for the output numpy array
-
- Returns:: a 3d data volume with the size of the first (outermost) dimension equal
- to the number of files, and the sizes of the second and third dimensions equal to
- the sizes given in the input slice_img_shape
- """
- data = np.zeros(
- (len(files), slice_img_shape[0], slice_img_shape[1]), dtype=dtype)
- for idx, in_file in enumerate(files):
- try:
- data[idx, :, :] = _read_img(in_file, file_extension)
- except IOError as exc:
- raise RuntimeError("Could not load file {0}. Error details: {2}".
- format(in_file, str(exc)))
-
- return data
-
-
-def get_flat_dark_stack(field_path, field_prefix, file_prefix, file_extension,
- img_shape, data_dtype):
- """
- Load the images of the flat/dark/other field and calculate an average of them.
-
- @param field_path :: path to the images
- @param field_prefix :: prefix for the images of the flat/dark/other field images (filter).
- example: OB, DARK, WHITE, etc.
-
- @param file_extension :: extension string to look for file names
- @param img_shape :: shape that every image should have
- @param data_dtype :: output data type
-
- Returns :: numpy array with an average (pixel-by-pixel) of the flat/dark/other field images
- """
- avg = None
- if field_prefix:
- if not file_prefix:
- file_prefix = ''
- files_match = glob.glob(
- os.path.join(field_path, "{0}*.{1}".format(field_prefix,
- file_extension)))
- if len(files_match) <= 0:
- print(
- "Could not find any flat field / open beam image files in: {0}".
- format(field_prefix))
- else:
- imgs_stack = _read_listed_files(files_match, img_shape,
- file_extension, data_dtype)
- avg = np.mean(imgs_stack, axis=0)
-
- return avg
-
-
-# This could become a command class. There's already many parameters and it's
-# likely that there will be more.
-
-
-def read_stack_of_images(sample_path,
- flat_field_path=None,
- dark_field_path=None,
- file_extension='tiff',
- file_prefix=None,
- flat_field_prefix=None,
- dark_field_prefix=None,
- verbose=True):
- """
- Reads a stack of images into memory, assuming dark and flat images
- are in separate directories.
-
- If several files are found in the same directory (for example you
- give image0001.fits and there's also image0002.fits,
- image0003.fits) these will also be loaded as the usual convention
- in ImageJ and related imaging tools, using the last digits to sort
- the images in the stack.
-
- @param sample_path :: path to sample images. Can be a file or directory
-
- @param flat_field_path :: (optional) path to open beam / white image(s).
- Can be a file or directory
-
- @param dark_field_path :: (optional) path to dark field image(s).
- Can be a file or directory
-
- @param file_extension :: file extension (typically 'tiff', 'tif', 'fits',
- or 'fit' (not including the dot)
-
- @param file_prefix :: prefix for the image files (example: IMAT00), to filter
- files that may be in the same directories but should not be loaded
-
- @param flat_field_prefix :: prefix for the flat field image files
-
- @param dark_field_prefix :: prefix for the dark field image files
-
- @param verbose :: verbose (some) output
-
- Returns :: 3 numpy arrays: input data volume (3d), average of flatt images (2d),
- average of dark images(2d)
- """
- SUPPORTED_EXTS = ['tiff', 'tif', 'fits', 'fit', 'png']
-
- if file_extension not in SUPPORTED_EXTS:
- raise ValueError(
- "File extension not supported: {0}. Supported extensions: {1}".
- format(file_extension, SUPPORTED_EXTS))
-
- sample_path = os.path.expanduser(sample_path)
-
- print(" * Loading stack of images from {0}".format(sample_path))
-
- if not file_prefix:
- file_prefix = ''
- files_match = glob.glob(
- os.path.join(sample_path, "{0}*.{1}".format(file_prefix,
- file_extension)))
- if len(files_match) <= 0:
- raise RuntimeError(
- "Could not find any image files in {0}, with prefix: {1}, extension: {2}".
- format(sample_path, file_prefix, file_extension))
-
- files_match.sort(key=_alphanum_key_split)
-
- print(" * Found {0} image files in {1}".format(
- len(files_match), sample_path))
-
- # It is assumed that all images have the same size and properties as the first.
- try:
- first_img = _read_img(files_match[0], file_extension)
- except RuntimeError as exc:
- raise RuntimeError(
- "Could not load at least one image file from: {0}. Details: {1}".
- format(sample_path, str(exc)))
-
- data_dtype = first_img.dtype
- # usual type in fits with 16-bit pixel depth
- if '>i2' == data_dtype:
- data_dtype = np.uint16
-
- img_shape = first_img.shape
- sample_data = _read_listed_files(files_match, img_shape, file_extension,
- data_dtype)
-
- flat_avg = get_flat_dark_stack(flat_field_path, flat_field_prefix,
- flat_field_prefix, file_extension,
- img_shape, data_dtype)
-
- dark_avg = get_flat_dark_stack(dark_field_path, flat_field_prefix,
- dark_field_prefix, file_extension,
- img_shape, data_dtype)
-
- return sample_data, flat_avg, dark_avg
-
-
-def save_recon_as_vertical_slices(recon_data,
- output_dir,
- img_format='tiff',
- name_prefix='out_recon_slice',
- zero_fill=6):
- """
- Save reconstructed volume (3d) into a series of slices along the Z axis (outermost numpy dimension)
-
- @param data :: data as images/slices stores in numpy array
- @param output_dir :: where to save the files
- @param name_prefix :: prefix for the names of the images - an index is appended to this prefix
- @param zero_fill :: number of zeros to pad the image/slice index number
- """
- make_dirs_if_needed(output_dir)
- min_pix = np.amin(recon_data)
- max_pix = np.amax(recon_data)
- for idx in range(0, recon_data.shape[0]):
- write_image(
- recon_data[idx, :, :],
- min_pix,
- max_pix,
- os.path.join(output_dir, name_prefix + str(idx).zfill(zero_fill)),
- img_format=img_format,
- dtype='uint16')
-
-
-def save_recon_as_horizontal_slices(recon_data,
- out_horiz_dir,
- img_format='tiff',
- name_prefix='out_recon_horiz_slice',
- zero_fill=6):
- """
- Save reconstructed volume (3d) into a series of slices along the Y axis (second numpy dimension)
-
- @param data :: data as images/slices stores in numpy array
- @param output_dir :: where to save the files
- @param name_prefix :: prefix for the names of the images throughout the horizontal axis
- @param zero_fill :: number of zeros to pad the image/slice index number. This index is appended to
- the prefix
- """
- make_dirs_if_needed(out_horiz_dir)
- for idx in range(0, recon_data.shape[1]):
- write_image(
- recon_data[:, idx, :],
- np.amin(recon_data),
- np.amax(recon_data),
- os.path.join(out_horiz_dir,
- name_prefix + str(idx).zfill(zero_fill)),
- img_format=img_format,
- dtype='uint16')
-
-
-def save_recon_netcdf(recon_data, output_dir, filename='tomo_recon_vol.nc'):
- """
- A netCDF, for compatibility/easier interoperation with other tools
-
- @param recon_data :: reconstructed data volume. A sequence of images will be saved from this
- @param output_dir :: where the outputs are being saved
- @param filename :: name for the NetCDF file
- """
- try:
- from scipy.io import netcdf_file
- except ImportError as exc:
- print(" WARNING: could not save NetCDF file. Import error: {0}".format(
- exc))
-
- xsize = recon_data.shape[0]
- ysize = recon_data.shape[1]
- zsize = recon_data.shape[2]
-
- nc_path = os.path.join(output_dir, filename)
- ncfile = netcdf_file(nc_path, 'w')
- ncfile.createDimension('x', xsize)
- ncfile.createDimension('y', ysize)
- ncfile.createDimension('z', zsize)
- print(" Creating netCDF volume data variable")
- dtype = 'int16'
- data = ncfile.createVariable('data', np.dtype(dtype).char, ('x', 'y', 'z'))
- print(" Data shape: {0}".format(data.shape))
- print(" Loading/assigning data...")
-
- # handle differences in pixel type
- save_data = recon_data
- if recon_data.dtype != dtype:
- save_data = np.zeros(recon_data.shape, dtype='float32')
- max_vol = np.amax(recon_data)
- min_vol = np.amin(recon_data)
- vol_range = max_vol - min_vol
- scale_factor = (np.iinfo(dtype).max - np.iinfo(dtype).min) / vol_range
- save_data = scale_factor * (recon_data - min_vol)
- save_data = save_data.astype(dtype=dtype)
-
- data[:, :, :] = save_data[0:xsize, 0:ysize, 0:zsize]
- print(" Closing netCDF file: {0}".format(nc_path))
- ncfile.close()
-
-
-def self_save_zipped_scripts(output_path, this_path):
- """
- Self-save a python file and its subpackages.
-
- @param output_path :: path where to save
- @param this_path :: full path to 'this' file, the file that wants to self-save itself.
- """
-
- def _zipdir(path, ziph):
- # ziph is zipfile handle
- for root, _, files in os.walk(path):
- for indiv_file in files:
- # Write all files, with the exception of the pyc's
- exclude_extensions = ['pyc']
- if not indiv_file.endswith(tuple(exclude_extensions)):
- ziph.write(os.path.join(root, indiv_file))
-
- scripts_path = os.path.dirname(this_path)
-
- make_dirs_if_needed(output_path)
- print("Saving myself (reconstruction scripts) from: {0} in: {1}".format(
- scripts_path, os.path.abspath(output_path)))
- import zipfile
- # os.path.join(output_path, ... )
- RECON_SCRIPTS_PKG_NAME = '0.reconstruction_scripts.zip'
- with zipfile.ZipFile(
- os.path.join(output_path, RECON_SCRIPTS_PKG_NAME), 'w',
- zipfile.ZIP_DEFLATED) as zip_scripts:
- # To write just this file: zipscr.write(this_path)
- _zipdir(scripts_path, zip_scripts)
diff --git a/scripts/Imaging/IMAT/tomorec/reconstruction_command.py b/scripts/Imaging/IMAT/tomorec/reconstruction_command.py
deleted file mode 100644
index 1bf9de103df..00000000000
--- a/scripts/Imaging/IMAT/tomorec/reconstruction_command.py
+++ /dev/null
@@ -1,1365 +0,0 @@
-from __future__ import (absolute_import, division, print_function)
-# Copyright © 2014,2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-
-import os
-import time
-import numpy as np
-
-# For 3d median filter
-try:
- import scipy
- print(
- scipy.__file__,
- "< this is the directory of where scipy was imported from. If this is a Mantid "
- "directory, then the scipy that fails to import here is older and/or missing ndimage than "
- "the one I have locally")
-except ImportError:
- raise ImportError(
- "Could not find the package scipy which is required for image pre-/post-processing"
- )
-
-try:
- # for some reason ndimage is not found here. reason unknown?
- import scipy.ndimage
- print(
- scipy.ndimage.__file__,
- "< this is the directory of where scipy was imported from. If this is a Mantid "
- "directory, then the scipy that fails to import here is older and/or missing ndimage than "
- "the one I have locally")
-except ImportError:
- raise ImportError(
- "Could not find the subpackage scipy.ndimage, required for image pre-/post-processing"
- )
-
-from . import io as tomoio
-from . import configs as tomocfg
-
-
-class ReconstructionCommand(object):
- """
- Run a tomographic reconstruction command, which can be a local process or a job on a
- remote machine/scheduler. This class provides functionality to pre-process a raw dataset,
- run a reconstruction (from pre-processed data to reconstructed volume), and post-process
- a reconstructed volume.
- """
-
- def __init__(self):
- self._PREPROC_IMGS_SUBDIR_NAME = 'pre_processed'
- self._OUT_README_FNAME = '0.README_reconstruction.txt'
- self._OUT_SLICES_FILENAME_PREFIX = 'out_recon_slice'
- self._OUT_HORIZ_SLICES_SUBDIR = 'out_recon_horiz_slice'
-
- self.preproc_cfg = tomocfg.PreProcConfig()
- self.alg_cfg = tomocfg.ToolAlgorithmConfig
- self.postproc_cfg = tomocfg.PostProcConfig()
-
- self._timer_running = False
- self._whole_exec_timer = False
-
- # whether to crop before applying normalization steps. If True, the air region cannot be
- # outside of the region of interest. Leaving as False by default, and not exposing this option.
- self.__class__.crop_before_normaliz = False
-
- def _debug_print_memory_usage_linux(self, message=""):
- try:
- # Windows doesn't seem to have resouce package, so this will silently fail
- import resource
- print(" >> Memory usage",
- resource.getrusage(resource.RUSAGE_SELF).ru_maxrss, "KB, ",
- int(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) /
- 1024, "MB", message)
- except Exception:
- pass
-
- def tomo_print(self, message, priority=1):
- """
- TODO currently the priority parameter is ignored
- Verbosity levels:
- 0 -> debug, print everything
- 1 -> information, print information about progress
- 2 -> print only major progress information, i.e data loaded, recon started, recon finished
-
- Print only messages that have priority >= config verbosity level
-
- :param message: Message to be printed
- :param priority: Importance level depending on which messages will be printed
- :return:
- """
-
- # should be moved in the configs somewhere
- temp_verbosity = 0
- if priority >= temp_verbosity:
- print(message)
-
- def tomo_print_timed_start(self, message, priority=1):
- """
- On every second call this will terminate and print the timer
- TODO currently the priority parameter is ignored
-
- Verbosity levels:
- 0 -> debug, print everything
- 1 -> information, print information about progress
- 2 -> print only major progress information, i.e data loaded, recon started, recon finished
-
- Print only messages that have priority >= config verbosity level
-
- :param message: Message to be printed
- :param priority: Importance level depending on which messages will be printed
- :return:
- """
-
- import time
-
- # should be moved in the configs somewhere
- temp_verbosity = 1
- print_string = ""
-
- if not self._timer_running:
- self._timer_running = True
- self._timer_start = time.time()
- print_string = message
-
- if priority >= temp_verbosity:
- print(print_string)
-
- def tomo_print_timed_stop(self, message, priority=1):
- """
- On every second call this will terminate and print the timer. This will append ". " to the string
- TODO currently the priority parameter is ignored
-
- Verbosity levels:
- 0 -> debug, print everything
- 1 -> information, print information about progress
- 2 -> print only major progress information, i.e data loaded, recon started, recon finished
-
- Print only messages that have priority >= config verbosity level
-
- :param message: Message to be printed
- :param priority: Importance level depending on which messages will be printed
- :return:
- """
-
- import time
-
- # should be moved in the configs somewhere
- temp_verbosity = 1
- print_string = ""
-
- if self._timer_running:
- self._timer_running = False
- timer_string = str(time.time() - self._timer_start)
- print_string = message + " Elapsed time: " + timer_string + " sec"
-
- if priority >= temp_verbosity:
- print(print_string)
-
- def tomo_total_timer(self, message="Total execution time was "):
- """
- This will ONLY be used to time the WHOLE execution time.
- The first call to this will be in tomo_reconstruct.py and it will start it.abs
- The last call will be at the end of find_center or do_recon.
- """
- import time
-
- if not self._whole_exec_timer:
- # change type from bool to timer
- self._whole_exec_timer = time.time()
- else:
- # change from timer to string
- self._whole_exec_timer = str(time.time() - self._whole_exec_timer)
- print(message + self._whole_exec_timer + " sec")
-
- def _check_paths_integrity(self, cfg):
- if not cfg or not isinstance(cfg, tomocfg.ReconstructionConfig):
- raise ValueError(
- "Cannot run a reconstruction without a valid configuration")
-
- if not cfg.preproc_cfg.input_dir:
- raise ValueError(
- "Cannot run a reconstruction without setting the input path")
-
- if not cfg.postproc_cfg.output_dir:
- raise ValueError(
- "Cannot run a reconstruction without setting the output path")
-
- def do_recon(self, cfg, cmd_line=None):
- """
- Run a reconstruction using a particular tool, algorithm and setup
-
- @param preproc_cfg :: configuration (pre-processing + tool+algorithm + post-processing)
-
- @param cmd_line :: command line text if running from the CLI. When provided it will
- be written in the output readme file(s) for reference.
- """
- self._check_paths_integrity(cfg)
-
- if not cfg or not isinstance(cfg, tomocfg.ReconstructionConfig):
- raise ValueError(
- "Cannot run a reconstruction without a valid configuration")
-
- if not cfg.preproc_cfg.input_dir:
- raise ValueError(
- "Cannot run a reconstruction without setting the input path")
-
- if not cfg.postproc_cfg.output_dir:
- raise ValueError(
- "Cannot run a reconstruction without setting the output path")
-
- # First step import the tool
- self.tomo_print_timed_start(" * Importing tool " + cfg.alg_cfg.tool)
- # import tool
- import tomorec.tool_imports as tti
- reconstruction_tool = tti.import_tomo_tool(cfg.alg_cfg.tool)
-
- self.tomo_print_timed_stop(" * Tool loaded.")
-
- # ----------------------------------------------------------------
-
- self.tomo_print_timed_start(" * Generating reconstruction script...")
- readme_fullpath = os.path.join(cfg.postproc_cfg.output_dir,
- self._OUT_README_FNAME)
- tstart = self.gen_readme_summary_begin(readme_fullpath, cfg, cmd_line)
- self.tomo_print_timed_stop(" * Finished generating script.")
-
- # ----------------------------------------------------------------
-
- self.tomo_print_timed_start(" * Loading data...")
- data, white, dark = self.read_in_stack(
- cfg.preproc_cfg.input_dir, cfg.preproc_cfg.in_img_format,
- cfg.preproc_cfg.input_dir_flat, cfg.preproc_cfg.input_dir_dark)
- self.tomo_print_timed_stop(
- " * Data loaded. Shape of raw data: {0}, dtype: {1}.".format(
- data.shape, data.dtype))
-
- # ----------------------------------------------------------------
-
- preproc_data = self.apply_all_preproc(data, cfg.preproc_cfg, white,
- dark)
-
- # ----------------------------------------------------------------
-
- # Save pre-proc images, print inside
- self.save_preproc_images(cfg.postproc_cfg.output_dir, preproc_data,
- cfg.preproc_cfg)
-
- # ----------------------------------------------------------------
-
- # Reconstruction
- # for file readme summary
- t_recon_start = time.time()
- recon_data = self.run_reconstruct_3d(preproc_data, cfg.preproc_cfg,
- cfg.alg_cfg, reconstruction_tool)
- t_recon_end = time.time()
-
- # ----------------------------------------------------------------
-
- # Post-processing
- self.apply_postproc_filters(recon_data, cfg.postproc_cfg)
-
- # Save output from the reconstruction
- self.save_recon_output(recon_data, cfg)
-
- # turned off for now, as it can't be opened from ParaView so it's a waste
- save_netcdf_vol = False
- if save_netcdf_vol:
- self.tomo_print_timed_start(
- " * Saving reconstructed volume as NetCDF...")
- tomoio.save_recon_netcdf(recon_data, cfg.postproc_cfg.output_dir)
- self.tomo_print_timed_stop(
- " * Finished saving reconstructed volume as NetCDF.")
-
- self.gen_readme_summary_end(readme_fullpath,
- (data, preproc_data, recon_data), tstart,
- t_recon_end - t_recon_start)
-
- def gen_readme_summary_begin(self, filename, cfg, cmd_line):
- """
- To write configuration, settings, etc. early on. As early as possible, before any failure
- can happen.
-
- @param filename :: name of the readme/final report file
- @param cfg :: full reconstruction configuration
- @param cmd_line :: command line originally used to run this reconstruction, when running
- from the command line
-
- Returns :: time now (begin of run) in number of seconds since epoch (time() time)
- """
- tstart = time.time()
-
- # generate file with dos/windows line end for windoze users' convenience
- with open(filename, 'w') as oreadme:
- file_hdr = (
- 'Tomographic reconstruction. Summary of inputs, settings and outputs.\n'
- 'Time now (run begin): ' + time.ctime(tstart) + '\n')
- oreadme.write(file_hdr)
-
- alg_hdr = ("\n"
- "--------------------------\n"
- "Tool/Algorithm\n"
- "--------------------------\n")
- oreadme.write(alg_hdr)
- oreadme.write(str(cfg.alg_cfg))
- oreadme.write("\n")
-
- preproc_hdr = ("\n"
- "--------------------------\n"
- "Pre-processing parameters\n"
- "--------------------------\n")
- oreadme.write(preproc_hdr)
- oreadme.write(str(cfg.preproc_cfg))
- oreadme.write("\n")
-
- postproc_hdr = ("\n"
- "--------------------------\n"
- "Post-processing parameters\n"
- "--------------------------\n")
- oreadme.write(postproc_hdr)
- oreadme.write(str(cfg.postproc_cfg))
- oreadme.write("\n")
-
- cmd_hdr = ("\n"
- "--------------------------\n"
- "Command line\n"
- "--------------------------\n")
- oreadme.write(cmd_hdr)
- oreadme.write(cmd_line)
- oreadme.write("\n")
-
- return tstart
-
- def gen_readme_summary_end(self, filename, data_stages, tstart,
- t_recon_elapsed):
- """
- Write last part of report in the output readme/report file. This should be used whenever a
- reconstruction runs correctly.
-
- @param filename :: name of the readme/final report file
- @param data_stages :: tuple with data in three stages (raw, pre-processed, reconstructed)
- @param tstart :: time at the beginning of the job/reconstruction, when the first part of the
- readme file was written
- @param t_recon_elapsed :: reconstruction time
- """
- # append to a readme/report that should have been pre-filled with the initial configuration
- with open(filename, 'a') as oreadme:
-
- run_hdr = ("\n"
- "--------------------------\n"
- "Run/job details:\n"
- "--------------------------\n")
- oreadme.write(run_hdr)
- (raw_data, preproc_data, recon_data) = data_stages
-
- oreadme.write("Dimensions of raw input sample data: {0}\n".format(
- raw_data.shape))
- oreadme.write("Dimensions of pre-processed sample data: {0}\n".
- format(preproc_data.shape))
- oreadme.write("Dimensions of reconstructed volume: {0}\n".format(
- recon_data.shape))
-
- oreadme.write("Raw input pixel type: {0}\n".format(raw_data.dtype))
- oreadme.write("Output pixel type: {0}\n".format('uint16'))
- oreadme.write("Time elapsed in reconstruction: {0:.3f}s\r\n".
- format(t_recon_elapsed))
- tend = time.time()
- oreadme.write("Total time elapsed: {0:.3f}s\r\n".format(tend -
- tstart))
- oreadme.write('Time now (run end): ' + time.ctime(tend))
-
- def apply_all_preproc(self, data, preproc_cfg, white, dark):
- """
- Do all the pre-processing. This does all that is needed between a)
- loading the input data, and b) starting a reconstruction
- run/job. From raw inputs to pre-proc data that is ready to go for
- reconstruction.
-
- @param data :: raw data (sample projection images)
- @param preproc_cfg :: pre-processing configuration
- @param white :: white / flat / open-beam image for normalization in some of the first
- pre-processing steps
- @param dark :: dark image for normalization
-
- Returns :: pre-processed data.
-
- """
- self._check_data_stack(data)
-
- self.tomo_print(" * Beginning pre-processing with pixel data type: " +
- str(data.dtype))
- preproc_data = self.apply_prep_filters(data, preproc_cfg, white, dark)
- preproc_data = self.apply_line_projection(preproc_data, preproc_cfg)
- preproc_data = self.apply_final_preproc_corrections(preproc_data,
- preproc_cfg)
-
- return preproc_data
-
- def apply_prep_filters(self, data, cfg, white, dark):
- """
- Apply the normal initial pre-processing filters, including simple
- operations as selecting/cropping to the region-of-interest,
- normalization, etc. If the images need to be rotated this is
- done as a first step (so all intermediate pre-processed
- results will be rotated as required).
-
- @param data :: projection images data, as 3d numpy array, with images along outermost (z)
- dimension
-
- @param cfg :: pre-processing configuration
- @param white :: white/flat/open-beam image for normalization
- @param dark :: dark image for normalization
-
- Returns :: process/filtered data (sizes can change (cropped) and data can be rotated)
-
- """
- self._check_data_stack(data)
-
- if 'float64' == data.dtype:
- # this is done because tomoio.write has problems with float64 to int16
- data = data.astype(dtype='float32')
- # print with top priority
- self.tomo_print(
- " * Note: pixel data type changed to: " + data.dtype,
- priority=2)
-
- data, white, dark = self.rotate_stack(data, cfg, white, dark)
-
- if self.crop_before_normaliz:
- data = self.crop_coords(data, cfg)
-
- data = self.normalize_flat_dark(data, cfg, white, dark)
- data = self.normalize_air_region(data, cfg)
-
- if not self.crop_before_normaliz:
- data = self.crop_coords(data, cfg)
-
- data = self.apply_cut_off_and_others(data, cfg)
-
- return data
-
- def apply_line_projection(self, imgs_angles, preproc_cfg):
- """
- Transform pixel values as $- ln (Is/I0)$, where $Is$ is the pixel (intensity) value and $I0$ is a
- reference value (pixel/intensity value for open beam, or maximum in the stack or the image).
-
- This produces a projection image, $ p(s) = -ln\\frac{I(s)}{I(0)} $,
- with $ I(s) = I(0) e^{-\\int_0^s \\mu(x)dx} $
- where:
- $p(s)$ represents the sum of the density of objects along a line (pixel) of the beam
- I(0) initital intensity of netron beam (white images)
- I(s) neutron count measured by detector/camera
-
- The integral is the density along the path through objects.
- This is required for example when pixels have neutron count values.
-
- @param imgs_angles :: stack of images (angular projections) as 3d numpy array. Every image will be
- processed independently, using as reference intensity the maximum pixel value found across all the
- images.
-
- @param preproc_cfg :: pre-processing configuration set up for a reconstruction
-
- Returns :: projected data volume (image stack)
- """
- self._check_data_stack(imgs_angles)
-
- if not preproc_cfg.line_projection:
- self.tomo_print(
- " * Note: NOT applying line projection.", priority=2)
- return imgs_angles
-
- self.tomo_print_timed_start(
- " * Starting to apply line projection on {0} images...".format(
- imgs_angles.shape[0]))
- imgs_angles = imgs_angles.astype('float32')
- for idx in range(0, imgs_angles.shape[0]):
- max_img = np.amax(imgs_angles[idx, :, :])
- to_log = np.true_divide(imgs_angles[idx, :, :], max_img)
- if False:
- print(
- " Initial image max: {0}. Transformed to log scale, min: {1}, max: {2}.".
- format(max_img, np.amin(to_log), np.amax(to_log)))
- imgs_angles[idx, :, :] = -np.log(to_log + 1e-6)
-
- self.tomo_print_timed_start(
- " * Finished applying line projection on {0} images. ".format(
- imgs_angles.shape[0]))
-
- return imgs_angles
-
- def apply_final_preproc_corrections(self, preproc_data, cfg):
- """
- Apply additional, optional, pre-processing steps/filters.
-
- @param preproc_data :: input data as a 3d volume (projection images)
- @param cfg :: pre-processing configuration
-
- Returns :: filtered data (stack of images)
- """
- self._check_data_stack(preproc_data)
-
- import tomorec.tool_imports as tti
- tomopy = tti.import_tomo_tool(cfg.alg_cfg.tool)
-
- # Remove stripes in sinograms / ring artefacts in reconstructed volume
- if cfg.stripe_removal_method:
- import prep as iprep
- if 'wavelet-fourier' == cfg.stripe_removal_method.lower():
- self.tomo_print_timed_start(
- " * Starting removal of stripes/ring artifacts using the method '{0}'...".
- format(cfg.stripe_removal_method))
-
- #preproc_data = tomopy.prep.stripe.remove_stripe_fw(preproc_data)
- preproc_data = iprep.filters.remove_stripes_ring_artifacts(
- preproc_data, 'wavelet-fourier')
-
- self.tomo_print_timed_start(
- " * Finished removal of stripes/ring artifacts.")
-
- elif 'titarenko' == cfg.stripe_removal_method.lower():
- self.tomo_print_timed_start(
- " * Starting removal of stripes/ring artifacts, using the method '{0}'...".
- format(cfg.stripe_removal_method))
-
- preproc_data = tomopy.prep.stripe.remove_stripe_ti(
- preproc_data)
-
- self.tomo_print_timed_stop(
- " * Finished removal of stripes/ring artifacts.")
- else:
- self.tomo_print(
- " * WARNING: stripe removal method '{0}' is unknown. Not applying it.".
- format(cfg.stripe_removal_method),
- priority=2)
- else:
- self.tomo_print(
- " * Note: NOT applying stripe removal.", priority=2)
-
- # Experimental options, disabled and not present in the config objects for now
- # These and related algorithms needs more evaluation/benchmarking
- if False:
- self.tomo_print_timed_start(" * Starting adjust range...")
- preproc_data = tomopy.misc.corr.adjust_range(preproc_data)
- self.tomo_print_timed_stop(" * Finished adjusting range.")
-
- if False:
- self.tomo_print_timed_start(
- " * Starting background normalisation...")
-
- preproc_data = tomopy.prep.normalize.normalize_bg(
- preproc_data, air=5)
- self.tomo_print_timed_stop(" * Finished background normalisation.")
-
- return preproc_data
-
- def normalize_air_region(self, data, pre_cfg):
- """
- TODO move to filters.py
- Normalize by beam intensity. This is not directly about proton
- charg - not using the proton charge field as usually found in
- experiment/nexus files. This uses an area of normalization, if
- provided in the pre-processing configuration. TODO: much
- of this method should be moved into filters.
-
- @param data :: stack of images as a 3d numpy array
- @param pre_cfg :: pre-processing configuration
-
- Returns :: filtered data (stack of images)
-
- """
- self._check_data_stack(data)
-
- if not pre_cfg or not isinstance(pre_cfg, tomocfg.PreProcConfig):
- raise ValueError(
- "Cannot normalize by air region without a valid pre-processing configuration"
- )
-
- if pre_cfg.normalize_air_region:
- if not isinstance(pre_cfg.normalize_air_region, list) or\
- 4 != len(pre_cfg.normalize_air_region):
- raise ValueError(
- "Wrong air region coordinates when trying to use them to normalize images: {0}".
- format(pre_cfg.normalize_air_region))
-
- if not all(
- isinstance(crd, int)
- for crd in pre_cfg.normalize_air_region):
- raise ValueError(
- "Cannot use non-integer coordinates to use the normalization region "
- "(air region). Got these coordinates: {0}".format(
- pre_cfg.normalize_air_region))
-
- right = pre_cfg.normalize_air_region[2] # why do we add 1?
- top = pre_cfg.normalize_air_region[1]
- left = pre_cfg.normalize_air_region[0]
- bottom = pre_cfg.normalize_air_region[3]
-
- # skip if for example: 0, 0, 0, 0 (empty selection)
- if top >= bottom or left >= right:
- self.tomo_print(
- " * NOTE: NOT applying Normalise by Air Region. Reason: Empty Selection"
- )
- return data
-
- self.tomo_print_timed_start(
- " * Starting normalization by air region. Statistics of values in the air region..."
- )
- air_sums = []
- for idx in range(0, data.shape[0]):
- air_data_sum = data[idx, top:bottom, left:right].sum()
- air_sums.append(air_data_sum)
-
- air_sums = np.true_divide(air_sums, np.amax(air_sums))
-
- self.tomo_print(
- " Air region sums (relative to maximum): " + air_sums,
- priority=0)
-
- for idx in range(0, data.shape[0]):
- data[idx, :, :] = np.true_divide(data[idx, :, :],
- air_sums[idx])
-
- avg = np.average(air_sums)
- self.tomo_print_timed_stop(
- " * Finished normalization by air region. Statistics of values in the air region, "
- "average: {0}, max ratio: {1}, min ratio: {2}.".format(
- avg, np.max(air_sums) / avg, np.min(air_sums) / avg))
-
- else:
- self.tomo_print(
- " * Note: NOT normalizing by air region", priority=2)
-
- return data
-
- def crop_coords(self, data, cfg):
- """
- Crop stack of images to a region (region of interest or similar), image by image
-
- @param data :: stack of images as a 3d numpy array
- @param cfg :: pre-processing configuration
-
- Returns :: filtered data (stack of images)
- """
- self._check_data_stack(data)
-
- # list with first-x, first-y, second-x, second-y
- if cfg.crop_coords:
- try:
- self.tomo_print_timed_start(
- " * Starting image cropping step, with pixel data type: {0}, coordinates: {1}. ...".
- format(data.dtype, cfg.crop_coords))
- import prep as iprep
- data = iprep.filters.crop_vol(data, cfg.crop_coords)
- self.tomo_print_timed_stop(
- " * Finished image cropping step, with pixel data type: {0}, coordinates: {1}. "
- "Resulting shape: {2}.".format(data.dtype, cfg.crop_coords,
- data.shape))
-
- except ValueError as exc:
- print(
- "Error in crop (region of interest) parameter (expecting a list with four integers. "
- "Got: {0}. Error details: ".format(cfg.crop_coords), exc)
- else:
- self.tomo_print(
- " * Note: NOT applying cropping to region of interest.",
- priority=2)
-
- return data
-
- def normalize_flat_dark(self, data, cfg, norm_flat_img, norm_dark_img):
- """
- Normalize by flat and dark images
-
- @param data :: image stack as a 3d numpy array
- @param cfg :: pre-processing configuration
- @param norm_flat_img :: flat (open beam) image to use in normalization
- @param norm_dark_img :: dark image to use in normalization
-
- Returns :: filtered data (stack of images)
- """
- self._check_data_stack(data)
-
- if not cfg or not isinstance(cfg, tomocfg.PreProcConfig):
- raise ValueError(
- "Cannot normalize by flat/dark images without a valid pre-processing "
- "configuration")
-
- if not cfg.normalize_flat_dark:
- self.tomo_print(
- " * Note: NOT applying normalization by flat/dark images.",
- priority=2)
- return data
-
- if isinstance(norm_flat_img, np.ndarray):
- if 2 != len(norm_flat_img.
- shape) or norm_flat_img.shape != data.shape[1:]:
- raise ValueError(
- "Incorrect shape of the flat image ({0}) which should match the "
- "shape of the sample images ({1})".format(
- norm_flat_img.shape, data[0].shape))
- self.tomo_print_timed_start(
- " * Starting normalization by flat/dark images with pixel data type: {0}...".
- format(data.dtype))
- norm_divide = None
- if norm_dark_img:
- norm_divide = norm_flat_img - norm_dark_img
- else:
- norm_divide = norm_flat_img
-
- if self.crop_before_normaliz and cfg.crop_coords:
- norm_divide = norm_divide[:, cfg.crop_coords[
- 1]:cfg.crop_coords[3] + 1, cfg.crop_coords[0]:
- cfg.crop_coords[2] + 1]
- # prevent divide-by-zero issues
- norm_divide[norm_divide == 0] = 1e-6
-
- if not norm_dark_img:
- norm_dark_img = 0
- for idx in range(0, data.shape[0]):
- data[idx, :, :] = np.true_divide(
- data[idx, :, :] - norm_dark_img, norm_divide)
- # true_divide produces float64, we assume that precision not needed (definitely not
- # for 16-bit depth output images as we usually have).
- self.tomo_print_timed_stop(
- " * Finished normalization by flat/dark images with pixel data type: {0}.".
- format(data.dtype))
- else:
- self.tomo_print(
- " * Note: cannot apply normalization by flat/dark images because no valid flat image has been "
- "provided in the inputs. Flat image given: {0}".format(
- norm_flat_img),
- priority=2)
-
- return data
-
- def apply_cut_off_and_others(self, data, cfg):
- """
- Applies several pre-processing steps meant to be applied before
- the line projection transformation and final pre-processing on
- it. This includes at the moment: cut-off, and median
- filter. TODO: MCP corrections, scaling down, others.
-
- Returns :: filtered data (stack of images)
-
- """
- self._check_data_stack(data)
-
- if not cfg or not isinstance(cfg, tomocfg.PreProcConfig):
- raise ValueError(
- "Cannot apply cut-off without a valid pre-processing configuration"
- )
-
- # Apply cut-off for the normalization?
- if cfg.cut_off_level and cfg.cut_off_level:
- self.tomo_print_timed_start(
- "* Applying cut-off with level: {0}".format(cfg.cut_off_level))
- dmin = np.amin(data)
- dmax = np.amax(data)
- rel_cut_off = dmin + cfg.cut_off_level * (dmax - dmin)
- data[data < rel_cut_off] = dmin
- self.tomo_print_timed_stop(
- " * Finished cut-off step, with pixel data type: {0}.".format(
- data.dtype))
- else:
- self.tomo_print(" * Note: NOT applying cut-off.", priority=2)
-
- if cfg.mcp_corrections:
- self.tomo_print(
- " * MCP corrections not implemented in this version",
- priority=2)
-
- if cfg.scale_down:
- self.tomo_print(
- " * Scale down not implemented in this version", priority=2)
-
- if cfg.median_filter_size and cfg.median_filter_size > 1:
- self.tomo_print_timed_start(
- " * Starting noise filter / median, with pixel data type: {0}, filter size/width: {1}.".
- format(data.dtype, cfg.median_filter_size))
- for idx in range(0, data.shape[0]):
- data[idx] = scipy.ndimage.median_filter(
- data[idx], cfg.median_filter_size, mode='mirror')
- #, mode='nearest')
- self.tomo_print_timed_stop(
- " * Finished noise filter / median, with pixel data type: {0}, filter size/width: {1}.".
- format(data.dtype, cfg.median_filter_size))
- else:
- self.tomo_print(
- " * Note: NOT applying noise filter /median.", priority=2)
-
- return data
-
- def rotate_stack(self, data, cfg, white=None, dark=None):
- """
- Rotates a stack (sample, white and dark images).
- This funciton is usually used on the whole picture, which is a square.
- If the picture is cropped first, the ROI coordinates
- have to be adjusted separately to be pointing at the NON ROTATED image!
-
- @param data :: stack of sample images
- @param cfg :: pre-processing configuration
- @param white :: stack of white images
- @param white :: stack of dark images
-
- Returns :: rotated images
- """
- if not cfg or not isinstance(cfg, tomocfg.PreProcConfig):
- raise ValueError(
- "Cannot rotate images without a valid pre-processing configuration"
- )
-
- if not cfg.rotation or cfg.rotation < 0:
- self.tomo_print(
- " * Note: NOT rotating the input images.", priority=2)
- return data, white, dark
-
- self.tomo_print_timed_start(
- " * Starting rotation step ({0} degrees clockwise), with pixel data type: {1}...".
- format(cfg.rotation * 90, data.dtype))
-
- data = self._rotate_imgs(data, cfg)
- if white:
- white = self._rotate_imgs(white, cfg)
- if dark:
- dark = self._rotate_imgs(dark, cfg)
-
- self.tomo_print_timed_stop(
- " * Finished rotation step ({0} degrees clockwise), with pixel data type: {1}.".
- format(cfg.rotation * 90, data.dtype))
-
- return (data, white, dark)
-
- def _rotate_imgs(self, data, cfg):
- """
- Rotate every image of a stack
-
- @param data :: image stack as a 3d numpy array
- @param cfg :: pre-processing configuration
-
- Returns :: rotated data (stack of images)
- """
-
- self._check_data_stack(data)
- self._debug_print_memory_usage_linux("before rotation.")
-
- for idx in range(0, data.shape[0]):
- # rot90 rotates counterclockwise; cfg.rotation rotates clockwise
- counterclock_rotations = 4 - cfg.rotation
- data[idx, :, :] = np.rot90(data[idx, :, :], counterclock_rotations)
-
- self._debug_print_memory_usage_linux("after rotation.")
-
- return data
-
- def run_reconstruct_3d(self,
- proj_data,
- preproc_cfg,
- alg_cfg,
- reconstruction_tool=None):
- """
- A 3D reconstruction
-
- @param proj_data :: Input projected images
- @param tool :: reconstruction tool to call/use
-
- Returns :: reconstructed volume
- """
- self._check_data_stack(proj_data)
-
- num_proj = proj_data.shape[0]
- inc = float(preproc_cfg.max_angle) / (num_proj - 1)
-
- proj_angles = np.arange(0, num_proj * inc, inc)
- # For tomopy
- proj_angles = np.radians(proj_angles)
-
- if 'astra' == alg_cfg.tool:
- # run_reconstruct_3d_astra(proj_data, algorithm, cor, proj_angles=proj_angles)
- return self.run_reconstruct_3d_astra_simple(
- proj_data, proj_angles, alg_cfg, preproc_cfg.cor,
- reconstruction_tool)
-
- self.tomo_print(" * Using center of rotation: {0}".format(
- preproc_cfg.cor))
- if 'tomopy' == alg_cfg.tool and 'gridrec' != alg_cfg.algorithm and 'fbp' != alg_cfg.algorithm:
- if not alg_cfg.num_iter:
- reconstruction_tool.cfg_num_iter = tomocfg.PreProcConfig.DEF_NUM_ITER
- # For ref, some typical run times with 4 cores:
- # 'bart' with num_iter=20 => 467.640s ~= 7.8m
- # 'sirt' with num_iter=30 => 698.119 ~= 11.63
- self.tomo_print_timed_start(
- " * Starting iterative method with TomoPy. Algorithm: {0}, "
- "number of iterations: {1}...".format(alg_cfg.algorithm,
- alg_cfg.num_iter))
- rec = reconstruction_tool.recon(
- tomo=proj_data,
- theta=proj_angles,
- center=preproc_cfg.cor,
- algorithm=alg_cfg.algorithm,
- num_iter=alg_cfg.num_iter) #, filter_name='parzen')
-
- else:
- self.tomo_print_timed_start(
- " * Starting non-iterative reconstruction algorithm with TomoPy. "
- "Algorithm: {0}...".format(alg_cfg.algorithm))
- rec = reconstruction_tool.recon(
- tomo=proj_data,
- theta=proj_angles,
- center=preproc_cfg.cor,
- algorithm=alg_cfg.algorithm)
-
- self.tomo_print_timed_stop(
- " * Reconstructed 3D volume. Shape: {0}, and pixel data type: {1}.".
- format(rec.shape, rec.dtype))
-
- return rec
-
- # def astra_reconstruct3d(self, sinogram, angles, depth, alg_cfg):
- # """
- # Run a reconstruction with astra
-
- # @param sinogram :: sinogram data
- # @param angles :: angles of the image projections
- # @param depth :: number of rows in images/sinograms
- # @param alg_cfg :: tool/algorithm configuration
- # """
- # # Some of these have issues depending on the GPU setup
- # algs_avail = "[FP3D_CUDA], [BP3D_CUDA]], [FDK_CUDA], [SIRT3D_CUDA], [CGLS3D_CUDA]"
-
- # if alg_cfg.algorithm.upper() not in algs_avail:
- # raise ValueError(
- # "Invalid algorithm requested for the Astra package: {0}. "
- # "Supported algorithms: {1}".format(alg_cfg.algorithm,
- # algs_avail))
- # det_rows = sinogram.shape[0]
- # det_cols = sinogram.shape[2]
-
- # vol_geom = astra.create_vol_geom(sinograms.shape[0], depth,
- # sinogram.shape[2])
- # proj_geom = astra.create_proj_geom('parallel3d', 1.0, 1.0, det_cols,
- # det_rows, np.deg2rad(angles))
-
- # sinogram_id = astra.data3d.create("-sino", proj_geom, sinogram)
- # # Create a data object for the reconstruction
- # rec_id = astra.data3d.create('-vol', vol_geom)
-
- # cfg = astra.astra_dict(alg_cfg.algorithm)
- # cfg['ReconstructionDataId'] = rec_id
- # cfg['ProjectionDataId'] = sinogram_id
-
- # # Create the algorithm object from the configuration structure
- # alg_id = astra.algorithm.create(cfg)
- # # This will have a runtime in the order of 10 seconds.
- # astra.algorithm.run(alg_id, alg_cfg.num_iter)
- # # This could be used to check the norm of the difference between the projection data
- # # and the forward projection of the reconstruction.
- # # if "CUDA" in cfg_alg.algorithm and "FBP" not cfg_alg.algorithm:
- # # self.norm_diff += astra.algorithm.get_res_norm(alg_id)**2
- # # print math.sqrt(self.norm_diff)
-
- # # Get the result
- # rec = astra.data3d.get(rec_id)
-
- # astra.algorithm.delete(alg_id)
- # astra.data3d.delete(rec_id)
- # astra.data3d.delete(sinogram_id)
-
- # return rec
-
- # def run_reconstruct_3d_astra(self, proj_data, proj_angles, alg_cfg):
- # """
- # Run a reconstruction with astra, approach based on swpapping axes
-
- # @param proj_data :: projection images
- # @param proj_angles :: angles corresponding to the projection images
- # @param alg_cfg :: tool/algorithm configuration
- # """
-
- # def get_max_frames(algorithm):
- # frames = 8 if "3D" in algorithm else 1
- # return frames
-
- # nSinos = get_max_frames(alg_cfg.algorithm)
- # iterations = alg_cfg.num_iter
- # print(" astra recon - doing {0} iterations".format(iterations))
-
- # swaps outermost dimensions so it is sinogram layout
- # sinogram = proj_data
- # sinogram = np.swapaxes(sinogram, 0, 1)
-
- # Needs to be figured out better
- #ctr = cor
- #width = sinogram.shape[1]
- #pad = 50
-
- #sino = np.nan_to_num(1./sinogram)
-
- # pad the array so that the centre of rotation is in the middle
- #alen = ctr
- #blen = width - ctr
- #mid = width / 2.0
-
- #if ctr > mid:
- #plow = pad
- #phigh = (alen - blen) + pad
- #else:
- #plow = (blen - alen) + pad
- #phigh = pad
-
- #logdata = np.log(sino+1)
-
- # sinogram = np.tile(sinogram.reshape((1, ) + sinogram.shape), (8, 1, 1))
-
- # rec = self.astra_reconstruct3d(
- # sinogram, proj_angles, depth=nSinos, alg_cfg=alg_cfg)
-
- # return rec
-
- def run_reconstruct_3d_astra_simple(self,
- proj_data,
- proj_angles,
- alg_cfg,
- cor=None,
- reconstruction_tool=None):
- """
- Run a reconstruction with astra, simple handling of projected data/images
-
- @param proj_data :: projection images
- @param alg_cfg :: tool/algorithm configuration
- @param cor :: center of rotation
- @param proj_angles :: angles corresponding to the projection images
- """
- import tomorec.tool_imports as tti
- astra = tti.import_tomo_tool('astra')
- sinograms = proj_data
-
- sinograms = np.swapaxes(sinograms, 0, 1)
-
- plow = (proj_data.shape[2] - cor * 2)
- phigh = 0
-
- # minval = np.amin(sinograms)
- sinograms = np.pad(sinograms, ((0, 0), (0, 0), (plow, phigh)),
- mode='reflect')
-
- proj_geom = astra.create_proj_geom('parallel3d', .0, 1.0,
- proj_data.shape[1],
- sinograms.shape[2], proj_angles)
- sinogram_id = astra.data3d.create('-sino', proj_geom, sinograms)
-
- vol_geom = astra.create_vol_geom(
- proj_data.shape[1], sinograms.shape[2], proj_data.shape[1])
- recon_id = astra.data3d.create('-vol', vol_geom)
- alg_cfg = astra.astra_dict(alg_cfg.algorithm)
- alg_cfg['ReconstructionDataId'] = recon_id
- alg_cfg['ProjectionDataId'] = sinogram_id
- alg_id = astra.algorithm.create(alg_cfg)
-
- number_of_iters = 100
- astra.algorithm.run(alg_id, number_of_iters)
- recon = astra.data3d.get(recon_id)
-
- astra.algorithm.delete(alg_id)
- astra.data3d.delete(recon_id)
- astra.data3d.delete(sinogram_id)
-
- return recon
-
- def apply_postproc_filters(self, recon_data, cfg):
- """
- Apply all post-processing steps/filters/transformations on a reconstructed volume
-
- @param cfg :: post-processing configuration
-
- Returns :: filtered data (reconstructed 3d volume)
- """
- import prep as iprep
-
- if cfg.circular_mask:
- self.tomo_print_timed_start(
- " * Applying circular mask on reconstructed volume...")
- recon_data = iprep.filters.circular_mask(
- recon_data, ratio=cfg.circular_mask)
- self.tomo_print_timed_stop(
- " * Finished applying circular mask on reconstructed volume")
- else:
- self.tomo_print(
- " * Note: NOT applied circular mask on reconstructed volume",
- priority=2)
-
- if cfg.cut_off_level and cfg.cut_off_level > 0.0:
- self.tomo_print_timed_start(
- " * Starting to apply cut-off: {0}".format(cfg.cut_off))
- dmin = np.amin(recon_data)
- dmax = np.amax(recon_data)
- rel_cut_off = dmin + cfg.cut_off * (dmax - dmin)
- recon_data[recon_data < rel_cut_off] = dmin
- self.tomo_print_timed_stop(" * Finished applying cut-off.")
-
- if cfg.gaussian_filter_par:
- self.tomo_print(" * Gaussian filter not implemented", priority=2)
-
- if cfg.median_filter_size and cfg.median_filter_size > 1:
- self.tomo_print_timed_start(
- " * Applying median_filter on reconstructed volume, with filtersize: {0}".
- format(cfg.median_filter_size))
-
- recon_data = scipy.ndimage.median_filter(recon_data,
- cfg.median_filter_size)
-
- self.tomo_print_timed_stop(
- " * Finished applying median_filter on reconstructed volume, with filtersize: {0}".
- format(cfg.median_filter_size))
- else:
- self.tomo_print(
- " * Note: NOT applied median_filter on reconstructed volume",
- priority=2)
-
- if cfg.median_filter3d_size and cfg.median_filter3d_size > 1:
- kernel_size = 3
-
- self.tomo_print_timed_start(
- " * Applying N-dimensional median filter on reconstructed volume, with filter size: {0} ".
- format(kernel_size))
-
- # Note this can be extremely slow
- recon_data = scipy.signal.medfilt(
- recon_data, kernel_size=kernel_size)
-
- self.tomo_print_timed_stop(
- " * Finished applying N-dimensional median filter on reconstructed volume, with filter size: {0} ".
- format(kernel_size))
- else:
- self.tomo_print(
- " * Note: NOT applied N-dimensional median filter on reconstructed volume"
- )
-
- def read_in_stack(self,
- sample_path,
- img_format,
- flat_field_path=None,
- dark_field_path=None):
- """
- Loads a stack, including sample, white and dark images.
-
- @param sample_path :: path to sample images
-
- @param img_format :: image format to expect/use (as a filename extension)
-
- @param flat_field_path :: (optional) path to open beam / white image(s).
- Can be a file or directory
-
- @param dark_field_path :: (optional) path to dark field image(s).
- Can be a file or directory
-
- Returns :: stack of images as a 3-elements tuple: numpy array with sample images, white image,
- and dark image.
- """
- # Note, not giving prefix. It will load all the files found.
- # Example prefixes are prefix = 'tomo_', prefix = 'LARMOR00', prefix = 'angle_agg'
-
- sample, white, dark = tomoio.read_stack_of_images(
- sample_path,
- flat_field_path=flat_field_path,
- dark_field_path=dark_field_path,
- file_extension=img_format)
-
- if not isinstance(sample, np.ndarray) or not sample.shape \
- or not isinstance(sample.shape, tuple) or 3 != len(sample.shape):
- raise RuntimeError(
- "Error reading sample images. Could not produce a 3-dimensional array "
- "of data from the sample images. Got: {0}".format(sample))
-
- return (sample, white, dark)
-
- def save_recon_output(self, recon_data, cfg, save_horiz_slices=False):
- """
- Save output reconstructed volume in different forms.
-
- @param recon_data :: reconstructed data volume. A sequence of images will be saved from this
- @param cfg :: configuration of the reconstruction, including output paths and formats
- @param save_horiz_slices :: Save images along the horizontal axis in addition to the vertical
- slices saved by defult. Useful for testing
- some tools
- """
- # slices along the vertical (z) axis
- # output_dir = 'output_recon_tomopy'
- output_dir = cfg.postproc_cfg.output_dir
- out_recon_dir = os.path.join(output_dir, 'reconstructed')
- self.tomo_print_timed_start(
- " * Starting saving slices of the reconstructed volume in: {0}...".
- format(out_recon_dir))
- tomoio.save_recon_as_vertical_slices(
- recon_data,
- out_recon_dir,
- name_prefix=self._OUT_SLICES_FILENAME_PREFIX,
- img_format=cfg.preproc_cfg.out_img_format)
-
- # Sideways slices:
- save_horiz_slices = False
- if save_horiz_slices:
- out_horiz_dir = os.path.join(output_dir, 'horiz_slices')
- print("* Saving horizontal slices in: {0}".format(out_horiz_dir))
- tomoio.save_recon_as_horizontal_slices(
- recon_data,
- out_horiz_dir,
- name_prefix=self._OUT_HORIZ_SLICES_SUBDIR,
- img_format=cfg.preproc_cfg.out_img_format)
-
- self.tomo_print_timed_stop(
- " * Finished saving slices of the reconstructed volume in: {0}".
- format(out_recon_dir))
-
- def save_preproc_images(self,
- output_dir,
- preproc_data,
- preproc_cfg,
- out_dtype='uint16'):
- """
- Save (pre-processed) images from a data array to image files.
-
- @param output_dir :: where results are being saved, including the pre-proc images/slices
- @param preproc_data :: data volume with pre-processed images
- @param preproc_cfg :: pre-processing configuration set up for a reconstruction
- @param out_dtype :: dtype used for the pixel type/depth in the output image files
- """
-
- min_pix = np.amin(preproc_data)
- max_pix = np.amax(preproc_data)
- # DEBUG message
- # print(" with min_pix: {0}, max_pix: {1}".format(min_pix, max_pix))
- if preproc_cfg.save_preproc_imgs:
- preproc_dir = os.path.join(output_dir,
- self._PREPROC_IMGS_SUBDIR_NAME)
- self.tomo_print_timed_start(
- " * Saving all pre-processed images (preproc_data) into {0} dtype: {1}".
- format(preproc_dir, preproc_data.dtype))
- tomoio.make_dirs_if_needed(preproc_dir)
- for idx in range(0, preproc_data.shape[0]):
- # rescale_intensity has issues with float64=>int16
- tomoio.write_image(
- preproc_data[idx, :, :],
- min_pix,
- max_pix,
- os.path.join(preproc_dir,
- 'out_preproc_proj_image' + str(idx).zfill(6)),
- img_format=preproc_cfg.out_img_format,
- dtype=out_dtype)
- self.tomo_print_timed_stop(
- " * Saving pre-processed images finished.")
- else:
- self.tomo_print(" * NOTE: NOT saving pre-processed images...")
-
- def _check_data_stack(self, data):
- if not isinstance(data, np.ndarray):
- raise ValueError(
- "Invalid stack of images data. It is not a numpy array: {0}".
- format(data))
-
- if 3 != len(data.shape):
- raise ValueError(
- "Invalid stack of images data. It does not have 3 dimensions. Shape: {0}".
- format(data.shape))
-
- def find_center(self, cfg):
- self._check_paths_integrity(cfg)
-
- self.tomo_print_timed_start(" * Importing tool " + cfg.alg_cfg.tool)
- # import tool
- import tomorec.tool_imports as tti
- tomopy = tti.import_tomo_tool(cfg.alg_cfg.tool)
- self.tomo_print_timed_stop(" * Tool loaded.")
-
- self.tomo_print_timed_start(" * Loading data...")
- # load in data
- sample, white, dark = self.read_in_stack(
- cfg.preproc_cfg.input_dir, cfg.preproc_cfg.in_img_format,
- cfg.preproc_cfg.input_dir_flat, cfg.preproc_cfg.input_dir_dark)
- self.tomo_print_timed_stop(
- " * Data loaded. Shape of raw data: {0}, dtype: {1}.".format(
- sample.shape, sample.dtype))
-
- # rotate
- sample, white, dark = self.rotate_stack(sample, cfg.preproc_cfg)
-
- # crop the ROI, this is done first, so beware of what the correct ROI coordinates are
- sample = self.crop_coords(sample, cfg.preproc_cfg)
-
- # sanity check
- self.tomo_print(" * Sanity check on data", 0)
- self._check_data_stack(sample)
-
- num_projections = sample.shape[0]
- inc = float(cfg.preproc_cfg.max_angle) / (num_projections - 1)
-
- self.tomo_print(" * Calculating projection angles")
- proj_angles = np.arange(0, num_projections * inc, inc)
- # For tomopy
- self.tomo_print(" * Calculating radians for TomoPy")
- proj_angles = np.radians(proj_angles)
-
- size = int(num_projections)
-
- # depending on the number of COR projections it will select different slice indices
- cor_num_checked_projections = 6
- cor_proj_slice_indices = []
- cor_slice_index = 0
-
- if cor_num_checked_projections < 2:
- # this will give us the middle slice
- cor_slice_index = int(size / 2)
- cor_proj_slice_indices.append(cor_slice_index)
- else:
- for c in range(cor_num_checked_projections):
- cor_slice_index += int(size / cor_num_checked_projections)
- cor_proj_slice_indices.append(cor_slice_index)
-
- calculated_cors = []
-
- self.tomo_print_timed_start(
- " * Starting COR calculation for " +
- str(cor_num_checked_projections) + " out of " +
- str(sample.shape[0]) + " projections", 2)
-
- cropCoords = cfg.preproc_cfg.crop_coords[0]
- imageWidth = sample.shape[2]
-
- # if crop corrds match with the image width then the full image was selected
- pixelsFromLeftSide = cropCoords if cropCoords - imageWidth <= 1 else 0
-
- for slice_idx in cor_proj_slice_indices:
- tomopy_cor = tomopy.find_center(
- tomo=sample, theta=proj_angles, ind=slice_idx, emission=False)
- print(" ** COR for slice", str(slice_idx), ".. REL to CROP ",
- str(tomopy_cor), ".. REL to FULL ",
- str(tomopy_cor + pixelsFromLeftSide))
- calculated_cors.append(tomopy_cor)
-
- self.tomo_print_timed_stop(" * Finished COR calculation.", 2)
-
- averageCORrelativeToCrop = sum(calculated_cors) / len(calculated_cors)
- averageCORrelativeToFullImage = sum(calculated_cors) / len(
- calculated_cors) + pixelsFromLeftSide
-
- # we add the pixels cut off from the left, to reflect the full image in Mantid
- self.tomo_print(" * Printing average COR in relation to cropped image "
- + str(cfg.preproc_cfg.crop_coords) + ":", 2)
- print(str(round(averageCORrelativeToCrop)))
- self.tomo_print(" * Printing average COR in relation to FULL image:",
- 2)
- print(str(round(averageCORrelativeToFullImage)))
diff --git a/scripts/Imaging/IMAT/tomorec/tool_imports.py b/scripts/Imaging/IMAT/tomorec/tool_imports.py
deleted file mode 100644
index 066d8c266ab..00000000000
--- a/scripts/Imaging/IMAT/tomorec/tool_imports.py
+++ /dev/null
@@ -1,69 +0,0 @@
-from __future__ import (absolute_import, division, print_function)
-# Copyright © 2014-2015 ISIS Rutherford Appleton Laboratory, NScD
-# Oak Ridge National Laboratory & European Spallation Source
-#
-# This file is part of Mantid.
-# Mantid is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# Mantid is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# File change history is stored at: <https://github.com/mantidproject/mantid>.
-# Code Documentation is available at: <http://doxygen.mantidproject.org>
-
-
-def _import_tool_tomopy():
- try:
- import tomopy
- import tomopy.prep
- import tomopy.recon
- import tomopy.misc
- import tomopy.io
-
- except ImportError as exc:
- raise ImportError("Could not import the tomopy package and its subpackages. Details: {0}".
- format(exc))
-
- return tomopy
-
-
-def _import_tool_astra():
- # current astra distributions install here, so check there by default
- ASTRA_LOCAL_PATH = '/usr/local/python/'
- import sys
- sys.path.append(ASTRA_LOCAL_PATH)
- try:
- import astra
- except ImportError as exc:
- raise ImportError("Cannot find and import the astra toolbox package: {0}".
- format(exc))
-
- MIN_ASTRA_VERSION = 106
- vers = astra.astra.version()
- if isinstance(vers, int) and vers >= MIN_ASTRA_VERSION:
- print("Imported astra successfully. Version: {0}".format(astra.astra.version()))
- else:
- raise RuntimeError("Could not find the required version of astra. Found version: {0}".format(vers))
-
- print("Astra using cuda: {0}". format(astra.astra.use_cuda()))
- return astra
-
-
-def import_tomo_tool(tool):
- if not tool or not isinstance(tool, str):
- raise ValueError("The name of a reconstruction tool is required as a string. Got: {0}".
- format(tool))
- if 'tomopy' == tool:
- return _import_tool_tomopy()
- elif 'astra' == tool:
- return _import_tool_astra()
- else:
- raise ValueError("Internal inconsistency. Tried to import unknown tool: {0}".format(tool))
--
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