From fda84a9731aff3f1c7c809dbc0af81afd79b212a Mon Sep 17 00:00:00 2001
From: Simon Heybrock <simon.heybrock@esss.se>
Date: Thu, 22 Jun 2017 12:19:24 +0200
Subject: [PATCH] Re #0. Removed include of NeXusFile from V3D.h and
MatrixWorkspace.h.
---
Framework/API/inc/MantidAPI/MatrixWorkspace.h | 3 -
.../API/src/FileBackedExperimentInfo.cpp | 2 +-
Framework/API/src/FrameworkManager.cpp | 2 +
Framework/API/src/MatrixWorkspace.cpp | 116 -----------------
Framework/API/test/MatrixWorkspaceTest.h | 15 ---
.../MantidAlgorithms/DetectorEfficiencyCor.h | 2 +
.../src/ReflectometryReductionOne2.cpp | 1 +
.../MantidDataHandling/SaveNexusProcessed.h | 5 +
.../SaveToSNSHistogramNexus.h | 5 +-
.../DataHandling/src/LoadIDFFromNexus.cpp | 1 +
.../DataHandling/src/LoadMcStasNexus.cpp | 2 +-
Framework/DataHandling/src/LoadMuonNexus2.cpp | 2 +-
Framework/DataHandling/src/LoadNXSPE.cpp | 2 +-
Framework/DataHandling/src/LoadNXcanSAS.cpp | 1 +
Framework/DataHandling/src/SaveNXSPE.cpp | 1 +
Framework/DataHandling/src/SaveNXTomo.cpp | 2 +-
.../DataHandling/src/SaveNexusProcessed.cpp | 119 +++++++++++++++++-
Framework/DataHandling/test/CMakeLists.txt | 1 +
.../DataHandling/test/LoadDetectorInfoTest.h | 1 +
Framework/DataHandling/test/SaveNXTomoTest.h | 1 +
.../test/SaveNexusProcessedTest.h | 86 ++++++++++---
.../inc/MantidDataObjects/PeakColumn.h | 1 +
.../Crystal/MatrixVectorPairParser.h | 1 +
.../inc/MantidGeometry/Crystal/PointGroup.h | 1 +
.../Crystal/SymmetryElementFactory.h | 1 +
.../Geometry/inc/MantidGeometry/IComponent.h | 7 +-
.../inc/MantidGeometry/Surfaces/Line.h | 1 +
Framework/Geometry/src/Instrument.cpp | 1 +
.../Geometry/src/Instrument/ParameterMap.cpp | 1 +
Framework/Kernel/inc/MantidKernel/V3D.h | 6 +-
Framework/Kernel/src/V3D.cpp | 1 +
Framework/MDAlgorithms/src/LoadILLAscii.cpp | 1 +
32 files changed, 222 insertions(+), 170 deletions(-)
diff --git a/Framework/API/inc/MantidAPI/MatrixWorkspace.h b/Framework/API/inc/MantidAPI/MatrixWorkspace.h
index 55e11fd5fc0..d0065c7351b 100644
--- a/Framework/API/inc/MantidAPI/MatrixWorkspace.h
+++ b/Framework/API/inc/MantidAPI/MatrixWorkspace.h
@@ -455,9 +455,6 @@ public:
void saveInstrumentNexus(::NeXus::File *file) const;
void loadInstrumentNexus(::NeXus::File *file);
- void saveSpectraMapNexus(
- ::NeXus::File *file, const std::vector<int> &spec,
- const ::NeXus::NXcompression compression = ::NeXus::LZW) const;
//=====================================================================================
// MD Geometry methods
diff --git a/Framework/API/src/FileBackedExperimentInfo.cpp b/Framework/API/src/FileBackedExperimentInfo.cpp
index 69aa290c4c6..c0ae4a0a4b4 100644
--- a/Framework/API/src/FileBackedExperimentInfo.cpp
+++ b/Framework/API/src/FileBackedExperimentInfo.cpp
@@ -3,8 +3,8 @@
#include <sstream>
-#include <nexus/NeXusException.hpp>
#include <nexus/NeXusFile.hpp>
+#include <nexus/NeXusException.hpp>
namespace Mantid {
namespace API {
diff --git a/Framework/API/src/FrameworkManager.cpp b/Framework/API/src/FrameworkManager.cpp
index 0206b3c52f9..d9bb34fd738 100644
--- a/Framework/API/src/FrameworkManager.cpp
+++ b/Framework/API/src/FrameworkManager.cpp
@@ -11,6 +11,8 @@
#include "MantidKernel/PropertyManagerDataService.h"
#include "MantidKernel/UsageService.h"
+#include <nexus/NeXusFile.hpp>
+
#include <Poco/ActiveResult.h>
#include <clocale>
diff --git a/Framework/API/src/MatrixWorkspace.cpp b/Framework/API/src/MatrixWorkspace.cpp
index e9e2aa541c7..a5e36f6477a 100644
--- a/Framework/API/src/MatrixWorkspace.cpp
+++ b/Framework/API/src/MatrixWorkspace.cpp
@@ -29,7 +29,6 @@
using Mantid::Kernel::DateAndTime;
using Mantid::Kernel::TimeSeriesProperty;
-using NeXus::NXcompression;
using Mantid::Kernel::Strings::toString;
namespace Mantid {
@@ -1571,121 +1570,6 @@ signal_t MatrixWorkspace::getSignalWithMaskAtCoord(
return getSignalAtCoord(coords, normalization);
}
-/** Save the spectra detector map to an open NeXus file.
-* @param file :: open NeXus file
-* @param spec :: list of the Workspace Indices to save.
-* @param compression :: NXcompression int to indicate how to compress
-*/
-void MatrixWorkspace::saveSpectraMapNexus(
- ::NeXus::File *file, const std::vector<int> &spec,
- const ::NeXus::NXcompression compression) const {
- // Count the total number of detectors
- std::size_t nDetectors = 0;
- for (auto index : spec) {
- nDetectors +=
- this->getSpectrum(static_cast<size_t>(index)).getDetectorIDs().size();
- }
-
- if (nDetectors < 1) {
- // No data in spectraMap to write
- g_log.warning("No spectramap data to write");
- return;
- }
-
- // Start the detector group
- file->makeGroup("detector", "NXdetector", 1);
- file->putAttr("version", 1);
-
- int numberSpec = int(spec.size());
- // allocate space for the Nexus Muon format of spctra-detector mapping
- std::vector<int32_t> detector_index(
- numberSpec + 1, 0); // allow for writing one more than required
- std::vector<int32_t> detector_count(numberSpec, 0);
- std::vector<int32_t> detector_list(nDetectors, 0);
- std::vector<int32_t> spectra(numberSpec, 0);
- std::vector<double> detPos(nDetectors * 3);
- detector_index[0] = 0;
- int id = 0;
-
- int ndet = 0;
- // get data from map into Nexus Muon format
- for (int i = 0; i < numberSpec; i++) {
- // Workspace index
- int si = spec[i];
- // Spectrum there
- const auto &spectrum = this->getSpectrum(si);
- spectra[i] = int32_t(spectrum.getSpectrumNo());
-
- // The detectors in this spectrum
- const auto &detectorgroup = spectrum.getDetectorIDs();
- const int ndet1 = static_cast<int>(detectorgroup.size());
-
- detector_index[i + 1] = int32_t(
- detector_index[i] +
- ndet1); // points to start of detector list for the next spectrum
- detector_count[i] = int32_t(ndet1);
- ndet += ndet1;
-
- std::set<detid_t>::const_iterator it;
- for (it = detectorgroup.begin(); it != detectorgroup.end(); ++it) {
- detector_list[id++] = int32_t(*it);
- }
- }
- // Cut the extra entry at the end of detector_index
- detector_index.resize(numberSpec);
-
- // write data as Nexus sections detector{index,count,list}
- std::vector<int> dims(1, numberSpec);
- file->writeCompData("detector_index", detector_index, dims, compression,
- dims);
- file->writeCompData("detector_count", detector_count, dims, compression,
- dims);
- dims[0] = ndet;
- file->writeCompData("detector_list", detector_list, dims, compression, dims);
- dims[0] = numberSpec;
- file->writeCompData("spectra", spectra, dims, compression, dims);
-
- // Get all the positions
- try {
- Geometry::Instrument_const_sptr inst = this->getInstrument();
- Geometry::IComponent_const_sptr sample = inst->getSample();
- if (sample) {
- Kernel::V3D sample_pos = sample->getPos();
- for (int i = 0; i < ndet; i++) {
- double R, Theta, Phi;
- try {
- Geometry::IDetector_const_sptr det =
- inst->getDetector(detector_list[i]);
- Kernel::V3D pos = det->getPos() - sample_pos;
- pos.getSpherical(R, Theta, Phi);
- R = det->getDistance(*sample);
- Theta = this->detectorTwoTheta(*det) * rad2deg;
- } catch (...) {
- R = 0.;
- Theta = 0.;
- Phi = 0.;
- }
- // Need to get R & Theta through these methods to be correct for grouped
- // detectors
- detPos[3 * i] = R;
- detPos[3 * i + 1] = Theta;
- detPos[3 * i + 2] = Phi;
- }
- } else
- for (int i = 0; i < 3 * ndet; i++)
- detPos[i] = 0.;
-
- dims[0] = ndet;
- dims.push_back(3);
- dims[1] = 3;
- file->writeCompData("detector_positions", detPos, dims, compression, dims);
- } catch (...) {
- g_log.error("Unknown error caught when saving detector positions.");
- }
-
- file->closeGroup();
-}
-
/*
MDMasking for a Matrix Workspace has not been implemented.
@param :
diff --git a/Framework/API/test/MatrixWorkspaceTest.h b/Framework/API/test/MatrixWorkspaceTest.h
index 3b984074a19..00b73f8761a 100644
--- a/Framework/API/test/MatrixWorkspaceTest.h
+++ b/Framework/API/test/MatrixWorkspaceTest.h
@@ -803,21 +803,6 @@ public:
TS_ASSERT_THROWS(wkspace.binIndexOf(0.), std::out_of_range);
}
- void test_nexus_spectraMap() {
- NexusTestHelper th(true);
- th.createFile("MatrixWorkspaceTest.nxs");
- auto ws = makeWorkspaceWithDetectors(100, 50);
- std::vector<int> spec;
- for (int i = 0; i < 100; i++) {
- // Give some funny numbers, so it is not the default
- ws->getSpectrum(size_t(i)).setSpectrumNo(i * 11);
- ws->getSpectrum(size_t(i)).setDetectorID(99 - i);
- spec.push_back(i);
- }
- // Save that to the NXS file
- TS_ASSERT_THROWS_NOTHING(ws->saveSpectraMapNexus(th.file, spec););
- }
-
void test_hasGroupedDetectors() {
auto ws = makeWorkspaceWithDetectors(5, 1);
TS_ASSERT_EQUALS(ws->hasGroupedDetectors(), false);
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/DetectorEfficiencyCor.h b/Framework/Algorithms/inc/MantidAlgorithms/DetectorEfficiencyCor.h
index 9bdfd7a2db4..32fb36d812f 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/DetectorEfficiencyCor.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/DetectorEfficiencyCor.h
@@ -6,6 +6,8 @@
#include "MantidKernel/V3D.h"
#include "MantidGeometry/IDetector.h"
+#include <list>
+
namespace Mantid {
namespace Algorithms {
/**
diff --git a/Framework/Algorithms/src/ReflectometryReductionOne2.cpp b/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
index ad729a1c504..7725eb4f199 100644
--- a/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
+++ b/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
@@ -8,6 +8,7 @@
#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/StringTokenizer.h"
#include "MantidKernel/Unit.h"
+#include "MantidGeometry/IDetector.h"
#include <algorithm>
#include <boost/lexical_cast.hpp>
diff --git a/Framework/DataHandling/inc/MantidDataHandling/SaveNexusProcessed.h b/Framework/DataHandling/inc/MantidDataHandling/SaveNexusProcessed.h
index 0c9139a92c8..00519e38145 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/SaveNexusProcessed.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/SaveNexusProcessed.h
@@ -66,6 +66,11 @@ public:
/// Algorithm's category for identification overriding a virtual method
const std::string category() const override { return "DataHandling\\Nexus"; }
+ void saveSpectraMapNexus(
+ const API::MatrixWorkspace &ws, ::NeXus::File *file,
+ const std::vector<int> &spec,
+ const ::NeXus::NXcompression compression = ::NeXus::LZW) const;
+
protected:
/// Override process groups
bool processGroups() override;
diff --git a/Framework/DataHandling/inc/MantidDataHandling/SaveToSNSHistogramNexus.h b/Framework/DataHandling/inc/MantidDataHandling/SaveToSNSHistogramNexus.h
index e8dc0396f6f..dc53024f175 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/SaveToSNSHistogramNexus.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/SaveToSNSHistogramNexus.h
@@ -1,9 +1,6 @@
#ifndef MANTID_DATAHANDLING_SAVESNSNEXUS_H_
#define MANTID_DATAHANDLING_SAVESNSNEXUS_H_
-//----------------------------------------------------------------------
-// Includes
-//----------------------------------------------------------------------
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/MatrixWorkspace_fwd.h"
#include "MantidAPI/Progress.h"
@@ -12,8 +9,8 @@
#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include <climits>
-#include <nexus/NeXusException.hpp>
#include <nexus/NeXusFile.hpp>
+#include <nexus/NeXusException.hpp>
namespace Mantid {
namespace DataHandling {
diff --git a/Framework/DataHandling/src/LoadIDFFromNexus.cpp b/Framework/DataHandling/src/LoadIDFFromNexus.cpp
index ab9e7484b49..f68ae54eb58 100644
--- a/Framework/DataHandling/src/LoadIDFFromNexus.cpp
+++ b/Framework/DataHandling/src/LoadIDFFromNexus.cpp
@@ -12,6 +12,7 @@
#include <Poco/DOM/NodeIterator.h>
#include <Poco/File.h>
#include <Poco/Path.h>
+#include <nexus/NeXusFile.hpp>
using Poco::XML::DOMParser;
using Poco::XML::Document;
diff --git a/Framework/DataHandling/src/LoadMcStasNexus.cpp b/Framework/DataHandling/src/LoadMcStasNexus.cpp
index cb42ae556e7..ec1aebbaf44 100644
--- a/Framework/DataHandling/src/LoadMcStasNexus.cpp
+++ b/Framework/DataHandling/src/LoadMcStasNexus.cpp
@@ -6,8 +6,8 @@
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidKernel/Unit.h"
-#include <nexus/NeXusException.hpp>
#include <nexus/NeXusFile.hpp>
+#include <nexus/NeXusException.hpp>
#include <boost/algorithm/string.hpp>
diff --git a/Framework/DataHandling/src/LoadMuonNexus2.cpp b/Framework/DataHandling/src/LoadMuonNexus2.cpp
index 608162ee272..0d649146403 100644
--- a/Framework/DataHandling/src/LoadMuonNexus2.cpp
+++ b/Framework/DataHandling/src/LoadMuonNexus2.cpp
@@ -16,8 +16,8 @@
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/UnitLabelTypes.h"
#include "MantidNexus/NexusClasses.h"
-#include <nexus/NeXusException.hpp>
#include <nexus/NeXusFile.hpp>
+#include <nexus/NeXusException.hpp>
#include <Poco/Path.h>
#include <boost/lexical_cast.hpp>
diff --git a/Framework/DataHandling/src/LoadNXSPE.cpp b/Framework/DataHandling/src/LoadNXSPE.cpp
index 9f5e0dcfddd..43eb55b4b9a 100644
--- a/Framework/DataHandling/src/LoadNXSPE.cpp
+++ b/Framework/DataHandling/src/LoadNXSPE.cpp
@@ -11,8 +11,8 @@
#include "MantidKernel/UnitFactory.h"
#include "MantidNexus/NexusClasses.h"
-#include <nexus/NeXusException.hpp>
#include <nexus/NeXusFile.hpp>
+#include <nexus/NeXusException.hpp>
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/Detector.h"
diff --git a/Framework/DataHandling/src/LoadNXcanSAS.cpp b/Framework/DataHandling/src/LoadNXcanSAS.cpp
index 191c24c271a..54bf55f6623 100644
--- a/Framework/DataHandling/src/LoadNXcanSAS.cpp
+++ b/Framework/DataHandling/src/LoadNXcanSAS.cpp
@@ -20,6 +20,7 @@
#include <H5Cpp.h>
#include <Poco/DirectoryIterator.h>
#include <Poco/Path.h>
+#include <nexus/NeXusFile.hpp>
#include <type_traits>
using namespace Mantid::Kernel;
diff --git a/Framework/DataHandling/src/SaveNXSPE.cpp b/Framework/DataHandling/src/SaveNXSPE.cpp
index 1a4f80f53a3..b76d875c136 100644
--- a/Framework/DataHandling/src/SaveNXSPE.cpp
+++ b/Framework/DataHandling/src/SaveNXSPE.cpp
@@ -16,6 +16,7 @@
#include <Poco/File.h>
#include <Poco/Path.h>
+#include <nexus/NeXusFile.hpp>
#include <boost/scoped_array.hpp>
#include <limits>
diff --git a/Framework/DataHandling/src/SaveNXTomo.cpp b/Framework/DataHandling/src/SaveNXTomo.cpp
index 2cdb0e63512..3b82c5aa249 100644
--- a/Framework/DataHandling/src/SaveNXTomo.cpp
+++ b/Framework/DataHandling/src/SaveNXTomo.cpp
@@ -14,8 +14,8 @@
#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/MantidVersion.h"
-#include <nexus/NeXusException.hpp>
#include <nexus/NeXusFile.hpp>
+#include <nexus/NeXusException.hpp>
namespace Mantid {
namespace DataHandling {
diff --git a/Framework/DataHandling/src/SaveNexusProcessed.cpp b/Framework/DataHandling/src/SaveNexusProcessed.cpp
index 154d8a8a20b..7908617397a 100644
--- a/Framework/DataHandling/src/SaveNexusProcessed.cpp
+++ b/Framework/DataHandling/src/SaveNexusProcessed.cpp
@@ -10,6 +10,7 @@
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/OffsetsWorkspace.h"
#include "MantidDataObjects/PeaksWorkspace.h"
+#include "MantidGeometry/Crystal/AngleUnits.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidNexus/NexusFileIO.h"
@@ -261,7 +262,7 @@ void SaveNexusProcessed::doExec(Workspace_sptr inputWorkspace,
}
cppFile->openGroup("instrument", "NXinstrument");
- matrixWorkspace->saveSpectraMapNexus(cppFile, spec, ::NeXus::LZW);
+ saveSpectraMapNexus(*matrixWorkspace, cppFile, spec, ::NeXus::LZW);
cppFile->closeGroup();
} // finish matrix workspace specifics
@@ -523,5 +524,121 @@ bool SaveNexusProcessed::processGroups() {
return true;
}
+/** Save the spectra detector map to an open NeXus file.
+* @param file :: open NeXus file
+* @param spec :: list of the Workspace Indices to save.
+* @param compression :: NXcompression int to indicate how to compress
+*/
+void SaveNexusProcessed::saveSpectraMapNexus(
+ const MatrixWorkspace &ws, ::NeXus::File *file,
+ const std::vector<int> &spec,
+ const ::NeXus::NXcompression compression) const {
+ // Count the total number of detectors
+ std::size_t nDetectors = 0;
+ for (auto index : spec) {
+ nDetectors +=
+ ws.getSpectrum(static_cast<size_t>(index)).getDetectorIDs().size();
+ }
+
+ if (nDetectors < 1) {
+ // No data in spectraMap to write
+ g_log.warning("No spectramap data to write");
+ return;
+ }
+
+ // Start the detector group
+ file->makeGroup("detector", "NXdetector", 1);
+ file->putAttr("version", 1);
+
+ int numberSpec = int(spec.size());
+ // allocate space for the Nexus Muon format of spctra-detector mapping
+ std::vector<int32_t> detector_index(
+ numberSpec + 1, 0); // allow for writing one more than required
+ std::vector<int32_t> detector_count(numberSpec, 0);
+ std::vector<int32_t> detector_list(nDetectors, 0);
+ std::vector<int32_t> spectra(numberSpec, 0);
+ std::vector<double> detPos(nDetectors * 3);
+ detector_index[0] = 0;
+ int id = 0;
+
+ int ndet = 0;
+ // get data from map into Nexus Muon format
+ for (int i = 0; i < numberSpec; i++) {
+ // Workspace index
+ int si = spec[i];
+ // Spectrum there
+ const auto &spectrum = ws.getSpectrum(si);
+ spectra[i] = int32_t(spectrum.getSpectrumNo());
+
+ // The detectors in this spectrum
+ const auto &detectorgroup = spectrum.getDetectorIDs();
+ const int ndet1 = static_cast<int>(detectorgroup.size());
+
+ detector_index[i + 1] = int32_t(
+ detector_index[i] +
+ ndet1); // points to start of detector list for the next spectrum
+ detector_count[i] = int32_t(ndet1);
+ ndet += ndet1;
+
+ std::set<detid_t>::const_iterator it;
+ for (it = detectorgroup.begin(); it != detectorgroup.end(); ++it) {
+ detector_list[id++] = int32_t(*it);
+ }
+ }
+ // Cut the extra entry at the end of detector_index
+ detector_index.resize(numberSpec);
+
+ // write data as Nexus sections detector{index,count,list}
+ std::vector<int> dims(1, numberSpec);
+ file->writeCompData("detector_index", detector_index, dims, compression,
+ dims);
+ file->writeCompData("detector_count", detector_count, dims, compression,
+ dims);
+ dims[0] = ndet;
+ file->writeCompData("detector_list", detector_list, dims, compression, dims);
+ dims[0] = numberSpec;
+ file->writeCompData("spectra", spectra, dims, compression, dims);
+
+ // Get all the positions
+ try {
+ Geometry::Instrument_const_sptr inst = ws.getInstrument();
+ Geometry::IComponent_const_sptr sample = inst->getSample();
+ if (sample) {
+ Kernel::V3D sample_pos = sample->getPos();
+ for (int i = 0; i < ndet; i++) {
+ double R, Theta, Phi;
+ try {
+ Geometry::IDetector_const_sptr det =
+ inst->getDetector(detector_list[i]);
+ Kernel::V3D pos = det->getPos() - sample_pos;
+ pos.getSpherical(R, Theta, Phi);
+ R = det->getDistance(*sample);
+ Theta = ws.detectorTwoTheta(*det) * Geometry::rad2deg;
+ } catch (...) {
+ R = 0.;
+ Theta = 0.;
+ Phi = 0.;
+ }
+ // Need to get R & Theta through these methods to be correct for grouped
+ // detectors
+ detPos[3 * i] = R;
+ detPos[3 * i + 1] = Theta;
+ detPos[3 * i + 2] = Phi;
+ }
+ } else
+ for (int i = 0; i < 3 * ndet; i++)
+ detPos[i] = 0.;
+
+ dims[0] = ndet;
+ dims.push_back(3);
+ dims[1] = 3;
+ file->writeCompData("detector_positions", detPos, dims, compression, dims);
+ } catch (...) {
+ g_log.error("Unknown error caught when saving detector positions.");
+ }
+
+ file->closeGroup();
+}
+
} // namespace DataHandling
} // namespace Mantid
diff --git a/Framework/DataHandling/test/CMakeLists.txt b/Framework/DataHandling/test/CMakeLists.txt
index 76b892c2683..0cfd3daaa25 100644
--- a/Framework/DataHandling/test/CMakeLists.txt
+++ b/Framework/DataHandling/test/CMakeLists.txt
@@ -11,6 +11,7 @@ if ( CXXTEST_FOUND )
../../TestHelpers/src/StartFrameworkManager.cpp
../../TestHelpers/src/TearDownWorld.cpp
../../TestHelpers/src/WorkspaceCreationHelper.cpp
+ ../../TestHelpers/src/NexusTestHelper.cpp
NXcanSASTestHelper.cpp
)
diff --git a/Framework/DataHandling/test/LoadDetectorInfoTest.h b/Framework/DataHandling/test/LoadDetectorInfoTest.h
index c41a65134db..31be49186dd 100644
--- a/Framework/DataHandling/test/LoadDetectorInfoTest.h
+++ b/Framework/DataHandling/test/LoadDetectorInfoTest.h
@@ -17,6 +17,7 @@
#include "MantidKernel/UnitFactory.h"
#include <Poco/File.h>
+#include <nexus/NeXusFile.hpp>
#include <boost/lexical_cast.hpp>
#include <vector>
diff --git a/Framework/DataHandling/test/SaveNXTomoTest.h b/Framework/DataHandling/test/SaveNXTomoTest.h
index d96d7e9fb57..c2632ae035c 100644
--- a/Framework/DataHandling/test/SaveNXTomoTest.h
+++ b/Framework/DataHandling/test/SaveNXTomoTest.h
@@ -8,6 +8,7 @@
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidTestHelpers/WorkspaceCreationHelper.h"
#include <Poco/File.h>
+#include <nexus/NeXusFile.hpp>
using namespace Mantid::API;
using namespace Mantid::Kernel;
diff --git a/Framework/DataHandling/test/SaveNexusProcessedTest.h b/Framework/DataHandling/test/SaveNexusProcessedTest.h
index b0e10668043..3e0a7673695 100644
--- a/Framework/DataHandling/test/SaveNexusProcessedTest.h
+++ b/Framework/DataHandling/test/SaveNexusProcessedTest.h
@@ -24,6 +24,10 @@
#include "MantidKernel/Unit.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidDataHandling/LoadRaw3.h"
+#include "MantidGeometry/Instrument.h"
+#include "MantidTestHelpers/FakeObjects.h"
+#include "MantidTestHelpers/ComponentCreationHelper.h"
+#include "MantidTestHelpers/NexusTestHelper.h"
#include "MantidTestHelpers/WorkspaceCreationHelper.h"
#include <Poco/File.h>
#include <Poco/Path.h>
@@ -38,6 +42,7 @@ using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::DataHandling;
using namespace Mantid::DataObjects;
+using namespace Mantid::Geometry;
using namespace Mantid::NeXus;
using Mantid::HistogramData::HistogramDx;
@@ -84,7 +89,7 @@ public:
outputFile = doExec(outputFile, useXErrors);
// Assert XError correctness
- NeXus::File savedNexus(outputFile);
+ ::NeXus::File savedNexus(outputFile);
savedNexus.openGroup("mantid_workspace_1", "NXentry");
savedNexus.openGroup("workspace", "NXdata");
@@ -462,7 +467,7 @@ public:
outputFileName = alg.getPropertyValue("Filename");
try {
- NeXus::File savedNexus(outputFileName);
+ ::NeXus::File savedNexus(outputFileName);
savedNexus.openGroup("mantid_workspace_1", "NXentry");
savedNexus.openGroup("table_workspace", "NXdata");
@@ -471,7 +476,7 @@ public:
savedNexus.openData("column_1");
- NeXus::Info columnInfo1 = savedNexus.getInfo();
+ ::NeXus::Info columnInfo1 = savedNexus.getInfo();
TS_ASSERT_EQUALS(columnInfo1.dims.size(), 2);
TS_ASSERT_EQUALS(columnInfo1.dims[0], 3);
TS_ASSERT_EQUALS(columnInfo1.dims[1], 4);
@@ -487,7 +492,7 @@ public:
TS_ASSERT_EQUALS(data1[8], 4);
TS_ASSERT_EQUALS(data1[11], 7);
- std::vector<NeXus::AttrInfo> attrInfos1 = savedNexus.getAttrInfos();
+ std::vector<::NeXus::AttrInfo> attrInfos1 = savedNexus.getAttrInfos();
TS_ASSERT_EQUALS(attrInfos1.size(), 6);
if (attrInfos1.size() == 6) {
@@ -509,7 +514,7 @@ public:
savedNexus.openData("column_2");
- NeXus::Info columnInfo2 = savedNexus.getInfo();
+ ::NeXus::Info columnInfo2 = savedNexus.getInfo();
TS_ASSERT_EQUALS(columnInfo2.dims.size(), 2);
TS_ASSERT_EQUALS(columnInfo2.dims[0], 3);
TS_ASSERT_EQUALS(columnInfo2.dims[1], 2);
@@ -523,7 +528,7 @@ public:
TS_ASSERT_EQUALS(data2[3], 2.5);
TS_ASSERT_EQUALS(data2[5], 0.0);
- std::vector<NeXus::AttrInfo> attrInfos2 = savedNexus.getAttrInfos();
+ std::vector<::NeXus::AttrInfo> attrInfos2 = savedNexus.getAttrInfos();
TS_ASSERT_EQUALS(attrInfos2.size(), 6);
if (attrInfos2.size() == 6) {
@@ -633,7 +638,7 @@ public:
// Get full output file path
outputFileName = alg.getPropertyValue("Filename");
- NeXus::File savedNexus(outputFileName);
+ ::NeXus::File savedNexus(outputFileName);
savedNexus.openGroup("mantid_workspace_1", "NXentry");
savedNexus.openGroup("table_workspace", "NXdata");
@@ -697,13 +702,13 @@ public:
{
savedNexus.openData("column_9");
- NeXus::Info columnInfo = savedNexus.getInfo();
+ ::NeXus::Info columnInfo = savedNexus.getInfo();
TS_ASSERT_EQUALS(columnInfo.dims.size(), 2);
TS_ASSERT_EQUALS(columnInfo.dims[0], 3);
TS_ASSERT_EQUALS(columnInfo.dims[1], 9);
TS_ASSERT_EQUALS(columnInfo.type, NX_CHAR);
- std::vector<NeXus::AttrInfo> attrInfos = savedNexus.getAttrInfos();
+ std::vector<::NeXus::AttrInfo> attrInfos = savedNexus.getAttrInfos();
TS_ASSERT_EQUALS(attrInfos.size(), 3);
if (attrInfos.size() == 3) {
@@ -767,7 +772,7 @@ public:
// Get full output file path
outputFileName = alg.getPropertyValue("Filename");
- NeXus::File savedNexus(outputFileName);
+ ::NeXus::File savedNexus(outputFileName);
savedNexus.openGroup("mantid_workspace_1", "NXentry");
savedNexus.openGroup("table_workspace", "NXdata");
@@ -782,13 +787,13 @@ public:
{
savedNexus.openData("column_2");
- NeXus::Info columnInfo = savedNexus.getInfo();
+ ::NeXus::Info columnInfo = savedNexus.getInfo();
TS_ASSERT_EQUALS(columnInfo.dims.size(), 2);
TS_ASSERT_EQUALS(columnInfo.dims[0], 3);
TS_ASSERT_EQUALS(columnInfo.dims[1], 1);
TS_ASSERT_EQUALS(columnInfo.type, NX_CHAR);
- std::vector<NeXus::AttrInfo> attrInfos = savedNexus.getAttrInfos();
+ std::vector<::NeXus::AttrInfo> attrInfos = savedNexus.getAttrInfos();
TS_ASSERT_EQUALS(attrInfos.size(), 3);
if (attrInfos.size() == 3) {
@@ -856,16 +861,31 @@ public:
AnalysisDataService::Instance().remove("testSpace");
}
+ void test_nexus_spectraMap() {
+ NexusTestHelper th(true);
+ th.createFile("MatrixWorkspaceTest.nxs");
+ auto ws = makeWorkspaceWithDetectors(100, 50);
+ std::vector<int> spec;
+ for (int i = 0; i < 100; i++) {
+ // Give some funny numbers, so it is not the default
+ ws->getSpectrum(size_t(i)).setSpectrumNo(i * 11);
+ ws->getSpectrum(size_t(i)).setDetectorID(99 - i);
+ spec.push_back(i);
+ }
+ SaveNexusProcessed alg;
+ TS_ASSERT_THROWS_NOTHING(alg.saveSpectraMapNexus(*ws, th.file, spec););
+ }
+
private:
- void doTestColumnInfo(NeXus::File &file, int type,
+ void doTestColumnInfo(::NeXus::File &file, int type,
const std::string &interpret_as,
const std::string &name) {
- NeXus::Info columnInfo = file.getInfo();
+ ::NeXus::Info columnInfo = file.getInfo();
TSM_ASSERT_EQUALS(name, columnInfo.dims.size(), 1);
TSM_ASSERT_EQUALS(name, columnInfo.dims[0], 3);
TSM_ASSERT_EQUALS(name, columnInfo.type, type);
- std::vector<NeXus::AttrInfo> attrInfos = file.getAttrInfos();
+ std::vector<::NeXus::AttrInfo> attrInfos = file.getAttrInfos();
TSM_ASSERT_EQUALS(name, attrInfos.size(), 3);
if (attrInfos.size() == 3) {
@@ -880,16 +900,16 @@ private:
}
}
- void doTestColumnInfo2(NeXus::File &file, int type,
+ void doTestColumnInfo2(::NeXus::File &file, int type,
const std::string &interpret_as,
const std::string &name, int dim1) {
- NeXus::Info columnInfo = file.getInfo();
+ ::NeXus::Info columnInfo = file.getInfo();
TSM_ASSERT_EQUALS(name, columnInfo.dims.size(), 2);
TSM_ASSERT_EQUALS(name, columnInfo.dims[0], 3);
TSM_ASSERT_EQUALS(name, columnInfo.dims[1], dim1);
TSM_ASSERT_EQUALS(name, columnInfo.type, type);
- std::vector<NeXus::AttrInfo> attrInfos = file.getAttrInfos();
+ std::vector<::NeXus::AttrInfo> attrInfos = file.getAttrInfos();
TSM_ASSERT_EQUALS(name, attrInfos.size(), 6);
if (attrInfos.size() == 6) {
@@ -905,7 +925,7 @@ private:
}
template <typename T>
- void doTestColumnData(const std::string &name, NeXus::File &file,
+ void doTestColumnData(const std::string &name, ::NeXus::File &file,
const T expectedData[], size_t len = 3) {
std::vector<T> data;
file.getData(data);
@@ -977,6 +997,34 @@ private:
return outputFile;
}
+ /** Create a workspace with numSpectra, with
+ * each spectrum having one detector, at id = workspace index.
+ * @param numSpectra
+ * @return
+ */
+ boost::shared_ptr<MatrixWorkspace>
+ makeWorkspaceWithDetectors(size_t numSpectra, size_t numBins) const {
+ boost::shared_ptr<MatrixWorkspace> ws2 =
+ boost::make_shared<WorkspaceTester>();
+ ws2->initialize(numSpectra, numBins, numBins);
+
+ auto inst = boost::make_shared<Instrument>("TestInstrument");
+ // We get a 1:1 map by default so the detector ID should match the spectrum
+ // number
+ for (size_t i = 0; i < ws2->getNumberHistograms(); ++i) {
+ // Create a detector for each spectra
+ Detector *det =
+ new Detector("pixel", static_cast<detid_t>(i), inst.get());
+ det->setShape(
+ ComponentCreationHelper::createSphere(0.01, V3D(0, 0, 0), "1"));
+ inst->add(det);
+ inst->markAsDetector(det);
+ ws2->getSpectrum(i).addDetectorID(static_cast<detid_t>(i));
+ }
+ ws2->setInstrument(inst);
+ return ws2;
+ }
+
std::string outputFile;
std::string entryName;
std::string dataName;
diff --git a/Framework/DataObjects/inc/MantidDataObjects/PeakColumn.h b/Framework/DataObjects/inc/MantidDataObjects/PeakColumn.h
index 3079799086a..33fd493ebb0 100644
--- a/Framework/DataObjects/inc/MantidDataObjects/PeakColumn.h
+++ b/Framework/DataObjects/inc/MantidDataObjects/PeakColumn.h
@@ -5,6 +5,7 @@
#include "MantidDataObjects/Peak.h"
#include <boost/variant.hpp>
+#include <list>
namespace Mantid {
namespace DataObjects {
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/MatrixVectorPairParser.h b/Framework/Geometry/inc/MantidGeometry/Crystal/MatrixVectorPairParser.h
index abb01237fd5..6b18d347000 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/MatrixVectorPairParser.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/MatrixVectorPairParser.h
@@ -7,6 +7,7 @@
#include "MantidKernel/Exception.h"
#include <functional>
+#include <map>
#include <boost/spirit/include/qi.hpp>
namespace Mantid {
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/PointGroup.h b/Framework/Geometry/inc/MantidGeometry/Crystal/PointGroup.h
index 2032ca0603b..0de5373f0a9 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/PointGroup.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/PointGroup.h
@@ -10,6 +10,7 @@
#include <vector>
#include <string>
#include <set>
+#include <map>
#include "MantidGeometry/Crystal/SymmetryOperation.h"
#include "MantidGeometry/Crystal/Group.h"
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/SymmetryElementFactory.h b/Framework/Geometry/inc/MantidGeometry/Crystal/SymmetryElementFactory.h
index 30dd5b1603e..b0e3c5c1195 100644
--- a/Framework/Geometry/inc/MantidGeometry/Crystal/SymmetryElementFactory.h
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/SymmetryElementFactory.h
@@ -8,6 +8,7 @@
#include "MantidKernel/RegistrationHelper.h"
#include <boost/make_shared.hpp>
+#include <map>
#include <unordered_set>
namespace Mantid {
diff --git a/Framework/Geometry/inc/MantidGeometry/IComponent.h b/Framework/Geometry/inc/MantidGeometry/IComponent.h
index 0c00673b5bc..7da1732bd2b 100644
--- a/Framework/Geometry/inc/MantidGeometry/IComponent.h
+++ b/Framework/Geometry/inc/MantidGeometry/IComponent.h
@@ -1,12 +1,10 @@
#ifndef MANTID_GEOMETRY_ICOMPONENT_H_
#define MANTID_GEOMETRY_ICOMPONENT_H_
-//----------------------------------------------------------------------
-// Includes
-//----------------------------------------------------------------------
#include "MantidGeometry/DllConfig.h"
#include "MantidKernel/V3D.h"
+#include <map>
#include <string>
#include <vector>
#include <set>
@@ -22,9 +20,6 @@ class Quat;
}
namespace Geometry {
-//---------------------------------------------------------
-// Forward declarations
-//---------------------------------------------------------
class IComponent;
class BoundingBox;
class ParameterMap;
diff --git a/Framework/Geometry/inc/MantidGeometry/Surfaces/Line.h b/Framework/Geometry/inc/MantidGeometry/Surfaces/Line.h
index dd57786c636..e22c9417180 100644
--- a/Framework/Geometry/inc/MantidGeometry/Surfaces/Line.h
+++ b/Framework/Geometry/inc/MantidGeometry/Surfaces/Line.h
@@ -4,6 +4,7 @@
#include "MantidGeometry/DllConfig.h"
#include "MantidKernel/V3D.h"
#include <complex>
+#include <list>
namespace Mantid {
diff --git a/Framework/Geometry/src/Instrument.cpp b/Framework/Geometry/src/Instrument.cpp
index 963aea28060..712e7f331fe 100644
--- a/Framework/Geometry/src/Instrument.cpp
+++ b/Framework/Geometry/src/Instrument.cpp
@@ -12,6 +12,7 @@
#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/make_unique.h"
+#include <nexus/NeXusFile.hpp>
#include <boost/make_shared.hpp>
#include <queue>
diff --git a/Framework/Geometry/src/Instrument/ParameterMap.cpp b/Framework/Geometry/src/Instrument/ParameterMap.cpp
index 64b6b0e49cd..50bcb188e01 100644
--- a/Framework/Geometry/src/Instrument/ParameterMap.cpp
+++ b/Framework/Geometry/src/Instrument/ParameterMap.cpp
@@ -7,6 +7,7 @@
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/ParameterFactory.h"
#include <cstring>
+#include <nexus/NeXusFile.hpp>
#include <boost/algorithm/string.hpp>
#ifdef _WIN32
diff --git a/Framework/Kernel/inc/MantidKernel/V3D.h b/Framework/Kernel/inc/MantidKernel/V3D.h
index 938c88d012b..36547602a3c 100644
--- a/Framework/Kernel/inc/MantidKernel/V3D.h
+++ b/Framework/Kernel/inc/MantidKernel/V3D.h
@@ -2,9 +2,13 @@
#define MANTID_KERNEL_V3D_H_
#include <cmath>
+#include <iosfwd>
#include <vector>
#include "MantidKernel/DllConfig.h"
-#include <nexus/NeXusFile.hpp>
+
+namespace NeXus {
+class File;
+}
namespace Mantid {
namespace Kernel {
diff --git a/Framework/Kernel/src/V3D.cpp b/Framework/Kernel/src/V3D.cpp
index a3f5c4f8cec..1a95a402e68 100644
--- a/Framework/Kernel/src/V3D.cpp
+++ b/Framework/Kernel/src/V3D.cpp
@@ -9,6 +9,7 @@
#include "MantidKernel/Exception.h"
#include "MantidKernel/Quat.h"
#include <boost/math/common_factor.hpp>
+#include <nexus/NeXusFile.hpp>
namespace Mantid {
namespace Kernel {
diff --git a/Framework/MDAlgorithms/src/LoadILLAscii.cpp b/Framework/MDAlgorithms/src/LoadILLAscii.cpp
index 572e7af1de8..a33d44958c8 100644
--- a/Framework/MDAlgorithms/src/LoadILLAscii.cpp
+++ b/Framework/MDAlgorithms/src/LoadILLAscii.cpp
@@ -21,6 +21,7 @@
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidMDAlgorithms/LoadILLAsciiHelper.h"
+#include "MantidGeometry/IDetector.h"
#include <Poco/TemporaryFile.h>
#include <boost/shared_ptr.hpp>
--
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