From fb5eea97709f1c6f223602b94261da8e09e20469 Mon Sep 17 00:00:00 2001
From: John Hill <john.r.hill@stfc.ac.uk>
Date: Wed, 6 Aug 2014 16:28:05 +0100
Subject: [PATCH] Refs #10061 added files for loader
---
.../Framework/DataHandling/CMakeLists.txt | 8 +-
.../inc/MantidDataHandling/LoadFITS.h | 96 ++++++
.../Framework/DataHandling/src/LoadFITS.cpp | 294 ++++++++++++++++++
.../docs/source/algorithms/LoadFITS-v1.rst | 14 +
4 files changed, 409 insertions(+), 3 deletions(-)
create mode 100644 Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
create mode 100644 Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp
create mode 100644 Code/Mantid/docs/source/algorithms/LoadFITS-v1.rst
diff --git a/Code/Mantid/Framework/DataHandling/CMakeLists.txt b/Code/Mantid/Framework/DataHandling/CMakeLists.txt
index 8edcfd12003..5527225abe3 100644
--- a/Code/Mantid/Framework/DataHandling/CMakeLists.txt
+++ b/Code/Mantid/Framework/DataHandling/CMakeLists.txt
@@ -22,7 +22,7 @@ set ( SRC_FILES
src/Load.cpp
src/LoadAscii.cpp
src/LoadAscii2.cpp
- src/LoadBBY.cpp
+ src/LoadBBY.cpp
src/LoadCalFile.cpp
src/LoadCanSAS1D.cpp
src/LoadCanSAS1D2.cpp
@@ -34,6 +34,7 @@ set ( SRC_FILES
src/LoadEventNexus.cpp
src/LoadEventPreNexus.cpp
src/LoadEventPreNexus2.cpp
+ src/LoadFITS.cpp
src/LoadFullprofResolution.cpp
src/LoadGSASInstrumentFile.cpp
src/LoadGSS.cpp
@@ -163,7 +164,7 @@ set ( INC_FILES
inc/MantidDataHandling/Load.h
inc/MantidDataHandling/LoadAscii.h
inc/MantidDataHandling/LoadAscii2.h
- inc/MantidDataHandling/LoadBBY.h
+ inc/MantidDataHandling/LoadBBY.h
inc/MantidDataHandling/LoadCalFile.h
inc/MantidDataHandling/LoadCanSAS1D.h
inc/MantidDataHandling/LoadCanSAS1D2.h
@@ -175,6 +176,7 @@ set ( INC_FILES
inc/MantidDataHandling/LoadEventNexus.h
inc/MantidDataHandling/LoadEventPreNexus.h
inc/MantidDataHandling/LoadEventPreNexus2.h
+ inc/MantidDataHandling/LoadFITS.h
inc/MantidDataHandling/LoadFullprofResolution.h
inc/MantidDataHandling/LoadGSASInstrumentFile.h
inc/MantidDataHandling/LoadGSS.h
@@ -226,7 +228,7 @@ set ( INC_FILES
inc/MantidDataHandling/LoadSassena.h
inc/MantidDataHandling/LoadSpec.h
inc/MantidDataHandling/LoadSpice2D.h
- inc/MantidDataHandling/LoadTOFRawNexus.h
+ inc/MantidDataHandling/LoadTOFRawNexus.h
inc/MantidDataHandling/MaskDetectors.h
inc/MantidDataHandling/MaskDetectorsInShape.h
inc/MantidDataHandling/MergeLogs.h
diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
new file mode 100644
index 00000000000..06ee83f0b03
--- /dev/null
+++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h
@@ -0,0 +1,96 @@
+#ifndef MANTID_DATAHANDLING_LOADFITS_H_
+#define MANTID_DATAHANDLING_LOADFITS_H_
+
+#include "MantidAPI/IFileLoader.h"
+
+
+namespace Mantid
+{
+namespace DataHandling
+{
+ /** LoadFITS : Load FITS files to TableWorkspace(s)
+
+ Copyright © 2014 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+
+ 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 LoadFITS : public API::IFileLoader<Kernel::FileDescriptor>
+ {
+ public:
+ LoadFITS() {}
+ virtual ~LoadFITS() {}
+
+ /// Algorithm's name for identification overriding a virtual method
+ virtual const std::string name() const { return "LoadFITS" ;}
+
+ ///Summary of algorithms purpose
+ virtual const std::string summary() const {return "Load data from FITS files.";}
+
+ /// Algorithm's version for identification overriding a virtual method
+ virtual int version() const { return 1 ;}
+
+ /// Algorithm's category for identification overriding a virtual method
+ virtual const std::string category() const { return "DataHandling";}
+
+ /// Returns a confidence value that this algorithm can load a file
+ virtual int confidence(Kernel::FileDescriptor & descriptor) const;
+
+ private:
+ /// Initialisation code
+ void init();
+ /// Execution code
+ void exec();
+
+ ///// Implement abstract Algorithm methods
+ //void init();
+ ///// Implement abstract Algorithm methods
+ //void exec();
+
+ ///// Load file to a vector of strings
+ //void loadFile(std::string filename, std::vector<std::string>& lines);
+
+ ///// Get Histogram type
+ //std::string getHistogramType(const std::vector<std::string>& lines);
+
+ ///// Get Number of banks
+ //size_t getNumberOfBanks(const std::vector<std::string>& lines);
+
+ ///// Scan imported file for bank information
+ //void scanBanks(const std::vector<std::string>& lines, std::vector<size_t>& bankStartIndex );
+
+ ///// Parse bank in file to a map
+ //void parseBank(std::map<std::string, double>& parammap, const std::vector<std::string>& lines, size_t bankid, size_t startlineindex, int nProf);
+
+ ///// Find first INS line at or after lineIndex
+ //size_t findINSLine(const std::vector<std::string>& lines, size_t lineIndex);
+
+ ///// Generate output workspace
+ //DataObjects::TableWorkspace_sptr genTableWorkspace(std::map<size_t, std::map<std::string, double> > bankparammap);
+
+
+ };
+
+
+
+
+} // namespace DataHandling
+} // namespace Mantid
+
+#endif // MANTID_DATAHANDLING_LOADFITS_H_
diff --git a/Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp b/Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp
new file mode 100644
index 00000000000..2275a68b869
--- /dev/null
+++ b/Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp
@@ -0,0 +1,294 @@
+#include "MantidDataHandling/LoadFITS.h"
+
+#include "MantidDataObjects/EventWorkspace.h"
+#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/RegisterFileLoader.h"
+//#include "MantidAPI/WorkspaceValidators.h"
+//#include "MantidKernel/UnitFactory.h"
+//#include "MantidGeometry/Instrument.h"
+//#include "MantidGeometry/Instrument/RectangularDetector.h"
+//#include "MantidGeometry/Objects/ShapeFactory.h"
+//
+//#include "MantidNexus/NexusClasses.h"
+//
+//#include <boost/math/special_functions/fpclassify.hpp>
+//#include <Poco/File.h>
+//#include <iostream>
+//#include <fstream>
+//#include <iomanip>
+
+using namespace Mantid::DataHandling;
+using namespace Mantid::API;
+using namespace Mantid::Kernel;
+
+namespace Mantid
+{
+namespace DataHandling
+{
+ // Register the algorithm into the AlgorithmFactory
+ DECLARE_FILELOADER_ALGORITHM(LoadFITS);
+
+ int LoadFITS::confidence(Kernel::FileDescriptor & descriptor) const
+ {
+ return (descriptor.extension() == ".fits" || descriptor.extension() == ".fit") ? 80 : 0;
+ }
+
+ /**
+ * Execute the algorithm.
+ */
+ void LoadFITS::exec()
+ {
+ // Delete the output workspace name if it existed
+ std::string outName = getPropertyValue("OutputWorkspace");
+ if (AnalysisDataService::Instance().doesExist(outName))
+ AnalysisDataService::Instance().remove(outName);
+
+ // Get the name of the file.
+ std::string filenameBin = getPropertyValue("Filename");
+
+ size_t nBins = 1;
+ double tofMinBoundary = 5;
+ double tofMaxBoundary = 5;
+
+ //// 100 for "loading neutron counts", 100 for "creating neutron event lists", 100 for "loading neutron events"
+ //Progress prog(this, 0.0, 1.0, 100 + 100 + 100);
+ //prog.doReport("creating instrument");
+
+ // Create a workspace
+ DataObjects::EventWorkspace_sptr eventWS(new DataObjects::EventWorkspace());
+
+ eventWS->initialize(
+ nHist,
+ nBins + 1, // number of TOF bin boundaries
+ nBins);
+
+ // Set the units
+ eventWS->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
+ eventWS->setYUnit("Counts");
+
+ // ???
+ //eventWS->setYUnitLabel("Counts");
+
+ eventWS->setTitle("my title");
+ eventWS->mutableRun().addProperty("Filename", filenameBin);
+ //eventWS->mutableRun().addProperty("run_number", 1);
+ //eventWS->mutableRun().addProperty("run_start", "1991-01-01T00:00:00", true );
+ //eventWS->mutableRun().addProperty("duration", duration[0], units);
+
+ // Build instrument geometry
+
+ // Create a new instrument and set its name
+ std::string instrumentname = "BILBY";
+ Geometry::Instrument_sptr instrument(new Geometry::Instrument(instrumentname));
+ eventWS->setInstrument(instrument);
+
+ // Add dummy source and samplepos to instrument
+
+ // Create an instrument component wich will represent the sample position.
+ Geometry::ObjComponent *samplepos = new Geometry::ObjComponent("Sample",instrument.get());
+ instrument->add(samplepos);
+ instrument->markAsSamplePos(samplepos);
+ // Put the sample in the centre of the coordinate system
+ samplepos->setPos(0.0,0.0,0.0);
+
+ // Create a component to represent the source
+ Geometry::ObjComponent *source = new Geometry::ObjComponent("Source",instrument.get());
+ instrument->add(source);
+ instrument->markAsSource(source);
+
+ // Read in the L1 value and place the source at (0,0,-L1)
+ double l1 = 3949.1824;
+ source->setPos(0.0,0.0,-1.0*l1);
+
+ // Create a component for the detector.
+
+ size_t xPixelCount = HISTO_BINS_X / 6;
+ size_t yPixelCount = HISTO_BINS_Y;
+ size_t pixelCount = xPixelCount * yPixelCount;
+
+ // We assumed that these are the dimensions of the detector, and height is in y direction and width is in x direction
+ double width = 0.4; // meters
+ double height = 1.0;
+
+ // We assumed that individual pixels have the same size and shape of a cuboid with dimensions:
+ double pixel_width = width / static_cast<double>(xPixelCount);
+ double pixel_height = height / static_cast<double>(yPixelCount);
+
+ // Create size strings for shape creation
+ std::string pixel_width_str = boost::lexical_cast<std::string>(pixel_width / 2);
+ std::string pixel_height_str = boost::lexical_cast<std::string>(pixel_height / 2);
+ std::string pixel_depth_str = "0.00001"; // Set the depth of a pixel to a very small number
+
+ // Define shape of a pixel as an XML string. See http://www.mantidproject.org/HowToDefineGeometricShape for details
+ // on shapes in Mantid.
+ std::string detXML =
+ "<cuboid id=\"pixel\">"
+ "<left-front-bottom-point x=\"+"+pixel_width_str+"\" y=\"-"+pixel_height_str+"\" z=\"0\" />"
+ "<left-front-top-point x=\"+"+pixel_width_str+"\" y=\"-"+pixel_height_str+"\" z=\""+pixel_depth_str+"\" />"
+ "<left-back-bottom-point x=\"-"+pixel_width_str+"\" y=\"-"+pixel_height_str+"\" z=\"0\" />"
+ "<right-front-bottom-point x=\"+"+pixel_width_str+"\" y=\"+"+pixel_height_str+"\" z=\"0\" />"
+ "</cuboid>";
+
+ // Create a shape object which will be shared by all pixels.
+ Geometry::Object_sptr shape = Geometry::ShapeFactory().createShape(detXML);
+
+ double detectorZ = 5;
+ double angle = 10;
+
+ double curtZOffset = width / 2 * sin(angle * 3.14159265359 / 180);
+
+ if (!filenameHdf.empty()) {
+ NeXus::NXRoot root(filenameHdf);
+ NeXus::NXEntry entry = root.openFirstEntry();
+
+ }
+
+ // 6 detector banks are available
+
+ // curtain 1
+ AddDetectorBank(
+ instrument,
+ xPixelCount,
+ yPixelCount,
+ 0 * pixelCount,
+ shape,
+ width,
+ height,
+ Kernel::V3D(+(width + height) / 2, 0, detectorZ - curtZOffset),
+ Kernel::Quat( 0, Kernel::V3D(0, 0, 1)) * Kernel::Quat(angle, Kernel::V3D(0, 1, 0)));
+
+ // curtain 2
+ AddDetectorBank(
+ instrument,
+ xPixelCount,
+ yPixelCount,
+ 1 * pixelCount,
+ shape,
+ width,
+ height,
+ Kernel::V3D(-(width + height) / 2, 0, detectorZ - curtZOffset),
+ Kernel::Quat(180, Kernel::V3D(0, 0, 1)) * Kernel::Quat(angle, Kernel::V3D(0, 1, 0)));
+
+ // curtain 3
+ AddDetectorBank(
+ instrument,
+ xPixelCount,
+ yPixelCount,
+ 2 * pixelCount,
+ shape,
+ width,
+ height,
+ Kernel::V3D(0, +(width + height) / 2, detectorZ - curtZOffset),
+ Kernel::Quat( 90, Kernel::V3D(0, 0, 1)) * Kernel::Quat(angle, Kernel::V3D(0, 1, 0)));
+
+ // curtain 4
+ AddDetectorBank(
+ instrument,
+ xPixelCount,
+ yPixelCount,
+ 3 * pixelCount,
+ shape,
+ width,
+ height,
+ Kernel::V3D(0, -(width + height) / 2, detectorZ - curtZOffset),
+ Kernel::Quat(-90, Kernel::V3D(0, 0, 1)) * Kernel::Quat(angle, Kernel::V3D(0, 1, 0)));
+
+ // back 1
+ AddDetectorBank(
+ instrument,
+ xPixelCount,
+ yPixelCount,
+ 4 * pixelCount,
+ shape,
+ width,
+ height,
+ Kernel::V3D(-width / 2 - 0.05, 0, detectorZ),
+ Kernel::Quat(180, Kernel::V3D(0, 0, 1)));
+
+ // back 2
+ AddDetectorBank(
+ instrument,
+ xPixelCount,
+ yPixelCount,
+ 5 * pixelCount,
+ shape,
+ width,
+ height,
+ Kernel::V3D(+width / 2 + 0.05, 0, detectorZ),
+ Kernel::Quat( 0, Kernel::V3D(0, 0, 1)));
+
+ // load events
+
+ size_t numberHistograms = eventWS->getNumberHistograms();
+
+ std::vector<EventVector_pt> eventVectors(numberHistograms, NULL);
+ std::vector<size_t> eventCounts(numberHistograms, 0);
+ std::vector<detid_t> detIDs = instrument->getDetectorIDs();
+
+ // count total events per pixel to reserve necessary memory
+ LoadFile_Counts(prog, filenameBin, HISTO_BINS_X, HISTO_BINS_Y, tofMinBoundary, tofMaxBoundary, eventCounts);
+
+ // for progress notifications
+ size_t progCount = 100;
+ size_t progStep = numberHistograms / progCount;
+ size_t progNext = progStep;
+
+ auto progMsg = "creating neutron event lists";
+ prog.doReport(progMsg);
+ for (size_t i = 0; i != numberHistograms; ++i) {
+ DataObjects::EventList& eventList = eventWS->getEventList(i);
+
+ eventList.setSortOrder(DataObjects::PULSETIME_SORT); // why not PULSETIME[TOF]_SORT ?
+ eventList.reserve(eventCounts[i]);
+ eventList.setDetectorID(detIDs[i]);
+ eventList.setSpectrumNo(detIDs[i]);
+
+ DataObjects::getEventsFrom(eventList, eventVectors[i]);
+
+ if ((progNext <= i) && (progCount != 0)) {
+ prog.report(progMsg);
+ progNext += progStep;
+ progCount--;
+ }
+ }
+ if (progCount != 0)
+ prog.reportIncrement(progCount, progMsg);
+
+ double shortest_tof(0.0), longest_tof(0.0);
+ LoadFile_Events(prog, filenameBin, HISTO_BINS_X, HISTO_BINS_Y, tofMinBoundary, tofMaxBoundary, eventVectors, shortest_tof, longest_tof);
+
+ cow_ptr<MantidVec> axis;
+ MantidVec& xRef = axis.access();
+ xRef.resize(2, 0.0);
+ if (longest_tof != 0.0) {
+ xRef[0] = std::max(0.0, shortest_tof - 1); // just to make sure the bins hold it all
+ xRef[1] = longest_tof + 1;
+ }
+ eventWS->setAllX(axis);
+
+ setProperty("OutputWorkspace", eventWS);
+ }
+
+ /**
+ * Initialise the algorithm. Declare properties which can be set before execution (input) or
+ * read from after the execution (output).
+ */
+ void LoadFITS::init()
+ {
+ // Specify file extensions which can be associated with a BBY file.
+ std::vector<std::string> exts;
+
+ // Declare the Filename algorithm property. Mandatory. Sets the path to the file to load.
+ exts.clear();
+ exts.push_back(".fit");
+ declareProperty(
+ new API::FileProperty("Filename", "", API::FileProperty::Load, exts),
+ "The input filename of the stored data");
+
+ declareProperty(
+ new API::WorkspaceProperty<API::IEventWorkspace>("OutputWorkspace", "", Kernel::Direction::Output));
+ }
+
+
+}
+}
\ No newline at end of file
diff --git a/Code/Mantid/docs/source/algorithms/LoadFITS-v1.rst b/Code/Mantid/docs/source/algorithms/LoadFITS-v1.rst
new file mode 100644
index 00000000000..557447bc10f
--- /dev/null
+++ b/Code/Mantid/docs/source/algorithms/LoadFITS-v1.rst
@@ -0,0 +1,14 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+Load data from FITS files
+
+.. categories::
--
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