From a3d05d0c3ce74ed7b37f7ddf9c3c6f3f05079fd2 Mon Sep 17 00:00:00 2001 From: John Hill Date: Thu, 11 Sep 2014 12:05:35 +0100 Subject: [PATCH 01/52] Refs #10194 create files --- .../Framework/DataHandling/CMakeLists.txt | 2 + .../inc/MantidDataHandling/SaveNXTomo.h | 104 + .../Framework/DataHandling/src/SaveNXTomo.cpp | 307 +++ .../AutoTestData/UsageData/GEM_Definition.vtp | 2047 +++++++++++++++++ 4 files changed, 2460 insertions(+) create mode 100644 Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h create mode 100644 Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp create mode 100644 Test/AutoTestData/UsageData/GEM_Definition.vtp diff --git a/Code/Mantid/Framework/DataHandling/CMakeLists.txt b/Code/Mantid/Framework/DataHandling/CMakeLists.txt index 3351dfa21f25..22ab0e341303 100644 --- a/Code/Mantid/Framework/DataHandling/CMakeLists.txt +++ b/Code/Mantid/Framework/DataHandling/CMakeLists.txt @@ -127,6 +127,7 @@ set ( SRC_FILES src/SaveNXSPE.cpp src/SaveNexus.cpp src/SaveNexusProcessed.cpp + src/SaveNXTomo.cpp src/SaveParameterFile.cpp src/SavePAR.cpp src/SavePHX.cpp @@ -264,6 +265,7 @@ set ( INC_FILES inc/MantidDataHandling/SaveNXSPE.h inc/MantidDataHandling/SaveNexus.h inc/MantidDataHandling/SaveNexusProcessed.h + inc/MantidDataHandling/SaveNXTomo.h inc/MantidDataHandling/SaveParameterFile.h inc/MantidDataHandling/SavePAR.h inc/MantidDataHandling/SavePHX.h diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h new file mode 100644 index 000000000000..644ca2f8abdf --- /dev/null +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -0,0 +1,104 @@ +#ifndef MANTID_DATAHANDLING_SAVENXTOMO_H_ +#define MANTID_DATAHANDLING_SAVENXTOMO_H_ + +//--------------------------------------------------- +// Includes +//--------------------------------------------------- +//#include "MantidAPI/Algorithm.h" +//#include "MantidNexus/NexusClasses.h" +//#include "MantidAPI/MatrixWorkspace.h" +//#include "MantidAPI/Sample.h" +//#include "MantidDataObjects/Workspace2D.h" +//#include "MantidDataObjects/EventWorkspace.h" +//#include +//#include + +namespace Mantid +{ + namespace DataHandling + { + + /** + * Saves a workspace into a NeXus/HDF5 NXTomo file. + * + * Required properties: + *
    + *
  • InputWorkspace - The workspace to save.
    • + *
  • Filename - The filename for output
    • + *
+ * + * @author John R Hill, RAL + * @date 10/09/2014 + * + * 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 . + * + * File change history is stored at: + * Code Documentation is available at: + * + */ + + class DLLExport SaveNXTomo: public API::Algorithm + { + public: + /// Constructor + SaveNXTomo(); + /// Virtual dtor + virtual ~SaveNXTomo() + { + } + virtual const std::string name() const + { + return "SaveNXTomo"; + } + ///Summary of algorithms purpose + virtual const std::string summary() const {return "Writes a MatrixWorkspace to a file in the NXTomo format.";} + + /// Algorithm's version + virtual int version() const + { + return (1); + } + /// Algorithm's category for identification + virtual const std::string category() const + { + return "DataHandling\\Nexus;DataHandling\\Tomo;Diffraction"; + } + + private: + + /// Initialisation code + void init(); + ///Execution code + void exec(); + + ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change + //size_t nBins; + /// The filename of the output file + //std::string filename; + + // Some constants to be written for masked values. + /// Value for data if pixel is masked + //static const double MASK_FLAG; + /// Value for error if pixel is masked + //static const double MASK_ERROR; + /// file format version + //static const std::string NXSPE_VER; + }; + + } // namespace DataHandling +} // namespace Mantid + +#endif // MANTID_DATAHANDLING_SAVENXTOMO_H_ diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp new file mode 100644 index 000000000000..3a053edfa273 --- /dev/null +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -0,0 +1,307 @@ +#include "MantidDataHandling/SaveNXTomo.h" +#include "MantidAPI/FileProperty.h" +//#include "MantidKernel/ConfigService.h" +#include "MantidKernel/MantidVersion.h" +#include "MantidAPI/WorkspaceValidators.h" +//#include "MantidAPI/WorkspaceOpOverloads.h" +//#include "MantidGeometry/Instrument/Detector.h" +//#include "MantidGeometry/Instrument/ObjComponent.h" +//#include "MantidDataHandling/FindDetectorsPar.h" +// +//#include +//#include +//#include + +namespace Mantid +{ + namespace DataHandling + { + + // Register the algorithm into the algorithm factory + DECLARE_ALGORITHM(SaveNXTomo) + + using namespace Kernel; + using namespace API; + + SaveNXTomo::SaveNXTomo() : API::Algorithm() + { + } + + /** + * Initialise the algorithm + */ + void SaveNXTomo::init() + { + auto wsValidator = boost::make_shared() ; + wsValidator->add(boost::make_shared("DeltaE")); + wsValidator->add(); + wsValidator->add(); + + declareProperty(new WorkspaceProperty ("InputWorkspace", + "", Direction::Input, wsValidator), + "The name of the workspace to save."); + + declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), + "The name of the NXTomo file to write, as a full or relative path"); + } + + /** + * Execute the algorithm + */ + void SaveNXTomo::exec() + { + // Retrieve the input workspace + const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); + + // Do the full check for common binning + if (!WorkspaceHelpers::commonBoundaries(inputWS)) + { + g_log.error("The input workspace must have common bins"); + throw std::invalid_argument("The input workspace must have common bins"); + } + + // Number of spectra + const int nHist = static_cast(inputWS->getNumberHistograms()); + // Number of energy bins + this->nBins = inputWS->blocksize(); + + // Get a pointer to the sample + Geometry::IComponent_const_sptr sample = + inputWS->getInstrument()->getSample(); + + // Retrieve the filename from the properties + this->filename = getPropertyValue("Filename"); + + // Create the file. + ::NeXus::File nxFile(this->filename, NXACC_CREATE5); + + // Make the top level entry (and open it) + nxFile.makeGroup(inputWS->getName(), "NXentry", true); + + // Definition name and version + nxFile.writeData("definition", "NXSPE"); + nxFile.openData("definition"); + nxFile.putAttr("version", NXSPE_VER); + nxFile.closeData(); + + // Program name and version + nxFile.writeData("program_name", "mantid"); + nxFile.openData("program_name"); + nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); + nxFile.closeData(); + + // Create NXSPE_info + nxFile.makeGroup("NXSPE_info", "NXcollection", true); + + // Get the value out of the property first + double efixed = getProperty("Efixed"); + if ( isEmpty(efixed) ) efixed = MASK_FLAG; + // Now lets check to see if the workspace nows better. + // TODO: Check that this is the way round we want to do it. + const API::Run & run = inputWS->run(); + if (run.hasProperty("Ei")) + { + Kernel::Property* propEi = run.getProperty("Ei"); + efixed = boost::lexical_cast(propEi->value()); + } + nxFile.writeData("fixed_energy", efixed); + nxFile.openData("fixed_energy"); + nxFile.putAttr("units", "meV"); + nxFile.closeData(); + + double psi = getProperty("Psi"); + if ( isEmpty(psi) ) psi = MASK_FLAG; + nxFile.writeData("psi", psi); + nxFile.openData("psi"); + nxFile.putAttr("units", "degrees"); + nxFile.closeData(); + + bool kikfScaling = getProperty("KiOverKfScaling"); + if (kikfScaling) + { + nxFile.writeData("ki_over_kf_scaling", 1); + } + else + { + nxFile.writeData("ki_over_kf_scaling", 0); + } + + nxFile.closeGroup(); // NXSPE_info + + // NXinstrument + nxFile.makeGroup("instrument", "NXinstrument", true); + // Write the instrument name + nxFile.writeData("name", inputWS->getInstrument()->getName()); + // and the short name + nxFile.openData("name"); + // TODO: Get the instrument short name + nxFile.putAttr("short_name", inputWS->getInstrument()->getName()); + nxFile.closeData(); + + // NXfermi_chopper + nxFile.makeGroup("fermi", "NXfermi_chopper", true); + + nxFile.writeData("energy", efixed); + nxFile.closeGroup(); // NXfermi_chopper + + nxFile.closeGroup(); // NXinstrument + + // NXsample + nxFile.makeGroup("sample", "NXsample", true); + // TODO: Write sample info +// nxFile.writeData("rotation_angle", 0.0); +// nxFile.writeData("seblock", "NONE"); +// nxFile.writeData("temperature", 300.0); + + nxFile.closeGroup(); // NXsample + + // Make the NXdata group + nxFile.makeGroup("data", "NXdata", true); + + // Energy bins + // Get the Energy Axis (X) of the first spectra (they are all the same - checked above) + const MantidVec& X = inputWS->readX(0); + nxFile.writeData("energy", X); + nxFile.openData("energy"); + nxFile.putAttr("units", "meV"); + nxFile.closeData(); + + // let's create some blank arrays in the nexus file + + std::vector array_dims; + array_dims.push_back((int)nHist); + array_dims.push_back((int)nBins); + + nxFile.makeData("data", ::NeXus::FLOAT64, array_dims, false); + nxFile.makeData("error", ::NeXus::FLOAT64, array_dims, false); + + // Add the axes attributes to the data + nxFile.openData("data"); + nxFile.putAttr("signal", 1); + nxFile.putAttr("axes", "polar:energy"); + nxFile.closeData(); + + std::vector slab_start; + std::vector slab_size; + + // What size slabs are we going to write... + slab_size.push_back(1); + slab_size.push_back((int64_t)nBins); + + // And let's start at the beginning + slab_start.push_back(0); + slab_start.push_back(0); + + // define the data and error vectors for masked detectors + std::vector masked_data (nBins, MASK_FLAG); + std::vector masked_error (nBins, MASK_ERROR); + + // Create a progress reporting object + Progress progress(this,0,1,100); + const int progStep = (int)(ceil(nHist/100.0)); + Geometry::IDetector_const_sptr det; + // Loop over spectra + for (int i = 0; i < nHist; i++) + { + try{ // detector exist + det =inputWS->getDetector(i); + // Check that we aren't writing a monitor... + if (!det->isMonitor()) + { + Geometry::IDetector_const_sptr det = inputWS->getDetector(i); + + if (!det->isMasked()) + { + // no masking... + // Open the data + nxFile.openData("data"); + slab_start[0] = i; + nxFile.putSlab(const_cast (inputWS->readY(i)), + slab_start, slab_size); + // Close the data + nxFile.closeData(); + + // Open the error + nxFile.openData("error"); + //MantidVec& tmparr = const_cast(inputWS->dataE(i)); + //nxFile.putSlab((void*)(&(tmparr[0])), slab_start, slab_size); + nxFile.putSlab(const_cast (inputWS->readE(i)), + slab_start, slab_size); + // Close the error + nxFile.closeData(); + } + else + { + // Write a masked value... + // Open the data + nxFile.openData("data"); + slab_start[0] = i; + nxFile.putSlab(masked_data, slab_start, slab_size); + // Close the data + nxFile.closeData(); + + // Open the error + nxFile.openData("error"); + nxFile.putSlab(masked_error, slab_start, slab_size); + // Close the error + nxFile.closeData(); + } + } + }catch(Exception::NotFoundError&) + { + // Catch if no detector. Next line tests whether this happened - test placed + // outside here because Mac Intel compiler doesn't like 'continue' in a catch + // in an openmp block. + } + // If no detector found, skip onto the next spectrum + if ( !det ) continue; + + // make regular progress reports and check for canceling the algorithm + if ( i % progStep == 0 ) + { + progress.report(); + } + } + // execute the ChildAlgorithm to calculate the detector's parameters; + IAlgorithm_sptr spCalcDetPar = this->createChildAlgorithm("FindDetectorsPar", 0, 1, true, 1); + + spCalcDetPar->initialize(); + spCalcDetPar->setPropertyValue("InputWorkspace", inputWS->getName()); + std::string parFileName = this->getPropertyValue("ParFile"); + if(!(parFileName.empty()||parFileName=="not_used.par")){ + spCalcDetPar->setPropertyValue("ParFile",parFileName); + } + spCalcDetPar->execute(); + + // + FindDetectorsPar * pCalcDetPar = dynamic_cast(spCalcDetPar.get()); + if(!pCalcDetPar){ // "can not get pointer to FindDetectorsPar algorithm" + throw(std::bad_cast()); + } + const std::vector & azimuthal = pCalcDetPar->getAzimuthal(); + const std::vector & polar = pCalcDetPar->getPolar(); + const std::vector & azimuthal_width = pCalcDetPar->getAzimWidth(); + const std::vector & polar_width = pCalcDetPar->getPolarWidth(); + const std::vector & secondary_flightpath= pCalcDetPar->getFlightPath(); + + + // Write the Polar (2Theta) angles + nxFile.writeData("polar", polar); + + // Write the Azimuthal (phi) angles + nxFile.writeData("azimuthal", azimuthal); + + // Now the widths... + nxFile.writeData("polar_width", polar_width); + nxFile.writeData("azimuthal_width", azimuthal_width); + + // Secondary flight path + nxFile.writeData("distance", secondary_flightpath); + + nxFile.closeGroup(); // NXdata + + nxFile.closeGroup(); // Top level NXentry + } + + } // namespace DataHandling +} // namespace Mantid diff --git a/Test/AutoTestData/UsageData/GEM_Definition.vtp b/Test/AutoTestData/UsageData/GEM_Definition.vtp new file 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0.000787518 0.0588542 0.01 -0.00434413 0.117509 0.01 -0.0128776 0.175767 0 0.000787518 0.0588542 0 -0.00434413 0.117509 0 + + + 0 3 2 1 0 2 7 4 5 16 7 5 17 8 7 17 7 16 6 8 17 13 6 17 10 6 13 14 10 13 15 11 10 15 10 14 12 9 11 12 11 15 21 19 18 21 18 24 22 24 25 22 21 24 20 25 23 20 22 25 29 26 27 38 29 27 39 30 29 39 29 38 28 30 39 35 28 39 32 28 35 36 32 35 37 33 32 37 32 36 34 31 33 34 33 37 43 41 40 43 40 46 44 46 47 44 43 46 42 47 45 42 44 47 51 49 48 51 48 54 52 54 55 52 51 54 50 55 53 50 52 55 56 59 58 57 56 58 63 61 60 63 60 66 64 66 67 64 63 66 62 67 65 62 64 67 + 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 117 120 123 126 129 132 135 138 141 144 147 150 153 156 + + + + + + + + + + + + + + + + + + + + + + From 16547ade611a521a326530800f48f7a9aa6f311e Mon Sep 17 00:00:00 2001 From: John Hill Date: Wed, 24 Sep 2014 16:47:59 +0100 Subject: [PATCH 02/52] Refs #10194 basic implementation of nxtomo file saving alg --- .../inc/MantidDataHandling/SaveNXTomo.h | 51 ++-- .../Framework/DataHandling/src/SaveNXTomo.cpp | 229 +++++++++--------- 2 files changed, 137 insertions(+), 143 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 644ca2f8abdf..464f8d839495 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -4,12 +4,7 @@ //--------------------------------------------------- // Includes //--------------------------------------------------- -//#include "MantidAPI/Algorithm.h" //#include "MantidNexus/NexusClasses.h" -//#include "MantidAPI/MatrixWorkspace.h" -//#include "MantidAPI/Sample.h" -//#include "MantidDataObjects/Workspace2D.h" -//#include "MantidDataObjects/EventWorkspace.h" //#include //#include @@ -20,6 +15,7 @@ namespace Mantid /** * Saves a workspace into a NeXus/HDF5 NXTomo file. + * File format is defined here: http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html * * Required properties: *
    @@ -53,49 +49,44 @@ namespace Mantid class DLLExport SaveNXTomo: public API::Algorithm { public: - /// Constructor SaveNXTomo(); /// Virtual dtor - virtual ~SaveNXTomo() - { - } - virtual const std::string name() const - { - return "SaveNXTomo"; - } + virtual ~SaveNXTomo() {} + + /// Algorithm's name for identification overriding a virtual method + virtual const std::string name() const { return "SaveNXTomo"; } + ///Summary of algorithms purpose virtual const std::string summary() const {return "Writes a MatrixWorkspace to a file in the NXTomo format.";} /// Algorithm's version - virtual int version() const - { - return (1); - } + virtual int version() const { return (1); } + /// Algorithm's category for identification - virtual const std::string category() const - { - return "DataHandling\\Nexus;DataHandling\\Tomo;Diffraction"; - } + virtual const std::string category() const { return "DataHandling\\Nexus;DataHandling\\Tomo;Diffraction"; } - private: - + private: /// Initialisation code void init(); - ///Execution code + /// Execution code void exec(); + /// Save all data to file + + /// Save batch of images to the file + ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change - //size_t nBins; + size_t m_nBins; /// The filename of the output file - //std::string filename; + std::string m_filename; // Some constants to be written for masked values. /// Value for data if pixel is masked - //static const double MASK_FLAG; + static const double MASK_FLAG; /// Value for error if pixel is masked - //static const double MASK_ERROR; - /// file format version - //static const std::string NXSPE_VER; + static const double MASK_ERROR; + /// file format version + static const std::string NXTOMO_VER; }; } // namespace DataHandling diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 3a053edfa273..51c5f256d435 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -1,28 +1,24 @@ -#include "MantidDataHandling/SaveNXTomo.h" #include "MantidAPI/FileProperty.h" -//#include "MantidKernel/ConfigService.h" -#include "MantidKernel/MantidVersion.h" #include "MantidAPI/WorkspaceValidators.h" -//#include "MantidAPI/WorkspaceOpOverloads.h" -//#include "MantidGeometry/Instrument/Detector.h" -//#include "MantidGeometry/Instrument/ObjComponent.h" -//#include "MantidDataHandling/FindDetectorsPar.h" -// -//#include -//#include -//#include +#include "MantidDataHandling/FindDetectorsPar.h" +#include "MantidDataHandling/SaveNXTomo.h" +#include "MantidKernel/MantidVersion.h" +#include "MantidNexus/NexusClasses.h" namespace Mantid { namespace DataHandling - { - + { // Register the algorithm into the algorithm factory DECLARE_ALGORITHM(SaveNXTomo) using namespace Kernel; using namespace API; + const double SaveNXTomo::MASK_FLAG = std::numeric_limits::quiet_NaN(); + const double SaveNXTomo::MASK_ERROR = 0.0; + const std::string SaveNXTomo::NXTOMO_VER = "2.0"; + SaveNXTomo::SaveNXTomo() : API::Algorithm() { } @@ -33,7 +29,7 @@ namespace Mantid void SaveNXTomo::init() { auto wsValidator = boost::make_shared() ; - wsValidator->add(boost::make_shared("DeltaE")); + //wsValidator->add(boost::make_shared("DeltaE")); wsValidator->add(); wsValidator->add(); @@ -52,7 +48,13 @@ namespace Mantid { // Retrieve the input workspace const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); - + + const std::string workspaceID = inputWS->id(); + + if ((workspaceID.find("Workspace2D") == std::string::npos) && + (workspaceID.find("RebinnedOutput") == std::string::npos)) + throw Exception::NotImplementedError("SaveNexusProcessed passed invalid workspaces. Must be Workspace2D, EventWorkspace, ITableWorkspace, or OffsetsWorkspace."); + // Do the full check for common binning if (!WorkspaceHelpers::commonBoundaries(inputWS)) { @@ -63,98 +65,88 @@ namespace Mantid // Number of spectra const int nHist = static_cast(inputWS->getNumberHistograms()); // Number of energy bins - this->nBins = inputWS->blocksize(); + this->m_nBins = inputWS->blocksize(); // Get a pointer to the sample Geometry::IComponent_const_sptr sample = inputWS->getInstrument()->getSample(); // Retrieve the filename from the properties - this->filename = getPropertyValue("Filename"); + this->m_filename = getPropertyValue("Filename"); - // Create the file. - ::NeXus::File nxFile(this->filename, NXACC_CREATE5); + // Create some arrays for the nexus api to use + std::vector array_dims; + array_dims.push_back((int)nHist); + array_dims.push_back((int)m_nBins); + // Create the file. + ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); + // Make the top level entry (and open it) - nxFile.makeGroup(inputWS->getName(), "NXentry", true); + nxFile.makeGroup("entry1", "NXentry", true); + + // Make a sub-group for the entry to work with DAWN software (and open it) + nxFile.makeGroup("tomo_entry", "NXsubentry", true); + + // Title + nxFile.writeData("title", this->m_filename); + + // Start Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("start_time", ); + + // End Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("end_time", ); // Definition name and version - nxFile.writeData("definition", "NXSPE"); + nxFile.writeData("definition", "NXtomo"); nxFile.openData("definition"); - nxFile.putAttr("version", NXSPE_VER); + nxFile.putAttr("version", NXTOMO_VER); nxFile.closeData(); - // Program name and version + // Originating program name and version nxFile.writeData("program_name", "mantid"); nxFile.openData("program_name"); nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); - nxFile.closeData(); - - // Create NXSPE_info - nxFile.makeGroup("NXSPE_info", "NXcollection", true); - - // Get the value out of the property first - double efixed = getProperty("Efixed"); - if ( isEmpty(efixed) ) efixed = MASK_FLAG; - // Now lets check to see if the workspace nows better. - // TODO: Check that this is the way round we want to do it. - const API::Run & run = inputWS->run(); - if (run.hasProperty("Ei")) - { - Kernel::Property* propEi = run.getProperty("Ei"); - efixed = boost::lexical_cast(propEi->value()); - } - nxFile.writeData("fixed_energy", efixed); - nxFile.openData("fixed_energy"); - nxFile.putAttr("units", "meV"); - nxFile.closeData(); - - double psi = getProperty("Psi"); - if ( isEmpty(psi) ) psi = MASK_FLAG; - nxFile.writeData("psi", psi); - nxFile.openData("psi"); - nxFile.putAttr("units", "degrees"); - nxFile.closeData(); - - bool kikfScaling = getProperty("KiOverKfScaling"); - if (kikfScaling) - { - nxFile.writeData("ki_over_kf_scaling", 1); - } - else - { - nxFile.writeData("ki_over_kf_scaling", 0); - } - - nxFile.closeGroup(); // NXSPE_info + nxFile.closeData(); + // ****************************************** // NXinstrument nxFile.makeGroup("instrument", "NXinstrument", true); - // Write the instrument name + // Write the instrument name | could add short_name attribute to name nxFile.writeData("name", inputWS->getInstrument()->getName()); - // and the short name - nxFile.openData("name"); - // TODO: Get the instrument short name - nxFile.putAttr("short_name", inputWS->getInstrument()->getName()); - nxFile.closeData(); - - // NXfermi_chopper - nxFile.makeGroup("fermi", "NXfermi_chopper", true); - - nxFile.writeData("energy", efixed); - nxFile.closeGroup(); // NXfermi_chopper - + + // detector group - diamond example file contains {data,distance,image_key,x_pixel_size,y_pixel_size} Only adding image_key for now, 0 filled. + nxFile.makeGroup("detector", "NXdetector", true); + std::vector imageKey(array_dims[1],0); + nxFile.writeData("image_key", imageKey); + nxFile.closeGroup(); + + // source group // from diamond file contains {current,energy,name,probe,type} - probe = neutron | x-ray | electron + + nxFile.closeGroup(); // NXinstrument + // ****************************************** // NXsample nxFile.makeGroup("sample", "NXsample", true); // TODO: Write sample info -// nxFile.writeData("rotation_angle", 0.0); -// nxFile.writeData("seblock", "NONE"); -// nxFile.writeData("temperature", 300.0); - + // name + // nxFile.writeData("rotation_angle", 0.0); + // x_translation + // y_translation + // z_translation nxFile.closeGroup(); // NXsample + + // ****************************************** + // Make the NXmonitor group - Holds base beam intensity for each image + // If information is not present, set as 1 + std::vector intensity(array_dims[1],1); + nxFile.makeGroup("control", "NXmonitor", true); + nxFile.writeData("data", intensity); + nxFile.closeGroup(); // NXmonitor + + // ****************************************** // Make the NXdata group nxFile.makeGroup("data", "NXdata", true); @@ -164,37 +156,31 @@ namespace Mantid nxFile.writeData("energy", X); nxFile.openData("energy"); nxFile.putAttr("units", "meV"); - nxFile.closeData(); - - // let's create some blank arrays in the nexus file - - std::vector array_dims; - array_dims.push_back((int)nHist); - array_dims.push_back((int)nBins); + nxFile.closeData(); nxFile.makeData("data", ::NeXus::FLOAT64, array_dims, false); nxFile.makeData("error", ::NeXus::FLOAT64, array_dims, false); // Add the axes attributes to the data - nxFile.openData("data"); - nxFile.putAttr("signal", 1); - nxFile.putAttr("axes", "polar:energy"); - nxFile.closeData(); + //nxFile.openData("data"); + //nxFile.putAttr("signal", 1); + //nxFile.putAttr("axes", "polar:energy"); + //nxFile.closeData(); std::vector slab_start; std::vector slab_size; // What size slabs are we going to write... slab_size.push_back(1); - slab_size.push_back((int64_t)nBins); + slab_size.push_back((int64_t)m_nBins); // And let's start at the beginning slab_start.push_back(0); slab_start.push_back(0); // define the data and error vectors for masked detectors - std::vector masked_data (nBins, MASK_FLAG); - std::vector masked_error (nBins, MASK_ERROR); + std::vector masked_data (m_nBins, MASK_FLAG); + std::vector masked_error (m_nBins, MASK_ERROR); // Create a progress reporting object Progress progress(this,0,1,100); @@ -203,8 +189,9 @@ namespace Mantid // Loop over spectra for (int i = 0; i < nHist; i++) { - try{ // detector exist - det =inputWS->getDetector(i); + try + { // detector exist + det = inputWS->getDetector(i); // Check that we aren't writing a monitor... if (!det->isMonitor()) { @@ -247,7 +234,8 @@ namespace Mantid nxFile.closeData(); } } - }catch(Exception::NotFoundError&) + } + catch(Exception::NotFoundError&) { // Catch if no detector. Next line tests whether this happened - test placed // outside here because Mac Intel compiler doesn't like 'continue' in a catch @@ -263,7 +251,7 @@ namespace Mantid } } // execute the ChildAlgorithm to calculate the detector's parameters; - IAlgorithm_sptr spCalcDetPar = this->createChildAlgorithm("FindDetectorsPar", 0, 1, true, 1); + /* IAlgorithm_sptr spCalcDetPar = this->createChildAlgorithm("FindDetectorsPar", 0, 1, true, 1); spCalcDetPar->initialize(); spCalcDetPar->setPropertyValue("InputWorkspace", inputWS->getName()); @@ -271,37 +259,52 @@ namespace Mantid if(!(parFileName.empty()||parFileName=="not_used.par")){ spCalcDetPar->setPropertyValue("ParFile",parFileName); } - spCalcDetPar->execute(); + spCalcDetPar->execute();*/ // - FindDetectorsPar * pCalcDetPar = dynamic_cast(spCalcDetPar.get()); - if(!pCalcDetPar){ // "can not get pointer to FindDetectorsPar algorithm" - throw(std::bad_cast()); - } - const std::vector & azimuthal = pCalcDetPar->getAzimuthal(); + //FindDetectorsPar * pCalcDetPar = dynamic_cast(spCalcDetPar.get()); + //if(!pCalcDetPar){ // "can not get pointer to FindDetectorsPar algorithm" + // throw(std::bad_cast()); + //} + /* const std::vector & azimuthal = pCalcDetPar->getAzimuthal(); const std::vector & polar = pCalcDetPar->getPolar(); const std::vector & azimuthal_width = pCalcDetPar->getAzimWidth(); const std::vector & polar_width = pCalcDetPar->getPolarWidth(); - const std::vector & secondary_flightpath= pCalcDetPar->getFlightPath(); + const std::vector & secondary_flightpath= pCalcDetPar->getFlightPath();*/ - // Write the Polar (2Theta) angles - nxFile.writeData("polar", polar); + //// Write the Polar (2Theta) angles + //nxFile.writeData("polar", polar); - // Write the Azimuthal (phi) angles - nxFile.writeData("azimuthal", azimuthal); + //// Write the Azimuthal (phi) angles + //nxFile.writeData("azimuthal", azimuthal); - // Now the widths... - nxFile.writeData("polar_width", polar_width); - nxFile.writeData("azimuthal_width", azimuthal_width); + //// Now the widths... + //nxFile.writeData("polar_width", polar_width); + //nxFile.writeData("azimuthal_width", azimuthal_width); - // Secondary flight path - nxFile.writeData("distance", secondary_flightpath); + //// Secondary flight path + //nxFile.writeData("distance", secondary_flightpath); nxFile.closeGroup(); // NXdata + nxFile.closeGroup(); // tomo_entry sub-group + nxFile.closeGroup(); // Top level NXentry + + // Validate the file against the schema + } + //void someRoutineToAddDataToExisting() + //{ + // //TODO: + //} + } // namespace DataHandling } // namespace Mantid + + +// TODO: don't allow a multi-file +// Follow mtd conventions +// Add comments / function descriptions etc \ No newline at end of file From eec972f34e9be0bec19f1ff444b32aaaefe4b3e9 Mon Sep 17 00:00:00 2001 From: Dan Nixon Date: Wed, 8 Oct 2014 14:24:27 +0100 Subject: [PATCH 03/52] Modified existing MSGDiffRed algorith for Vesuvio Refs #10323 --- .../MSGDiffractionReduction.py | 7 +++++++ Code/Mantid/instrument/VESUVIO_Parameters.xml | 21 +++++++++++++++++++ .../Inelastic/IndirectDiffractionReduction.py | 17 +++++++++++++-- 3 files changed, 43 insertions(+), 2 deletions(-) diff --git a/Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSGDiffractionReduction.py b/Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSGDiffractionReduction.py index f85252698ceb..ed75174e90ee 100644 --- a/Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSGDiffractionReduction.py +++ b/Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSGDiffractionReduction.py @@ -19,6 +19,9 @@ def PyInit(self): self.declareProperty(name='SumFiles', defaultValue=False, doc='Enabled to sum spectra from each input file.') + self.declareProperty(name='IndividualGrouping', defaultValue=False, + doc='Do not group results into a single spectra.') + self.declareProperty(name='Instrument', defaultValue='IRIS', validator=StringListValidator(['IRIS', 'OSIRIS', 'TOSCA', 'VESUVIO']), doc='Instrument used for run') @@ -77,6 +80,7 @@ def PyExec(self): input_files = self.getProperty('InputFiles').value sum_files = self.getProperty('SumFiles').value + individual_grouping = self.getProperty('IndividualGrouping').value instrument_name = self.getPropertyValue('Instrument') mode = self.getPropertyValue('Mode') detector_range = self.getProperty('DetectorRange').value @@ -93,6 +97,9 @@ def PyExec(self): reducer.set_sum_files(sum_files) reducer.set_save_formats(save_formats) + if individual_grouping: + reducer.set_grouping_policy('Individual') + for in_file in input_files: reducer.append_data_file(in_file) diff --git a/Code/Mantid/instrument/VESUVIO_Parameters.xml b/Code/Mantid/instrument/VESUVIO_Parameters.xml index d1fcdc31ad6a..1ac00f2294d0 100644 --- a/Code/Mantid/instrument/VESUVIO_Parameters.xml +++ b/Code/Mantid/instrument/VESUVIO_Parameters.xml @@ -132,6 +132,27 @@ + + + + + + + + + + + + + + + + + + + + + diff --git a/Code/Mantid/scripts/Inelastic/IndirectDiffractionReduction.py b/Code/Mantid/scripts/Inelastic/IndirectDiffractionReduction.py index fafc71c22180..f41533106ec1 100644 --- a/Code/Mantid/scripts/Inelastic/IndirectDiffractionReduction.py +++ b/Code/Mantid/scripts/Inelastic/IndirectDiffractionReduction.py @@ -2,12 +2,14 @@ from msg_reducer import MSGReducer import inelastic_indirect_reduction_steps as steps + class MSGDiffractionReducer(MSGReducer): """Reducer for Diffraction on IRIS and TOSCA. """ def __init__(self): super(MSGDiffractionReducer, self).__init__() + self._grouping_policy = 'All' def _setup_steps(self): self.append_step(steps.IdentifyBadDetectors( @@ -36,11 +38,11 @@ def _setup_steps(self): self.append_step(steps.RebinToFirstSpectrum()) step = steps.Grouping() - step.set_grouping_policy("All") + step.set_grouping_policy(self._grouping_policy) self.append_step(step) # The "SaveItem" step saves the files in the requested formats. - if (len(self._save_formats) > 0): + if len(self._save_formats) > 0: step = steps.SaveItem() step.set_formats(self._save_formats) self.append_step(step) @@ -48,6 +50,17 @@ def _setup_steps(self): step = steps.Naming() self.append_step(step) + def set_grouping_policy(self, policy): + """ + Sets the grouping policy for the result data. + + @parm policy New grouping policy + """ + if not isinstance(policy, str): + raise ValueError('Grouping policy must be a string') + + self._grouping_policy = policy + def getStringProperty(workspace, property): """This function is used in the interface. From d756244389c7af7897b4e70ec131b6a77245c47c Mon Sep 17 00:00:00 2001 From: Dan Nixon Date: Thu, 9 Oct 2014 11:26:07 +0100 Subject: [PATCH 04/52] Corrected naming, do not sum when only one file given Refs #10323 --- .../IndirectDiffractionReduction.ui | 767 +++++++++--------- .../src/IndirectDiffractionReduction.cpp | 9 + Code/Mantid/instrument/VESUVIO_Parameters.xml | 4 + 3 files changed, 406 insertions(+), 374 deletions(-) diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.ui index 24ddd75627be..c439e8803cf6 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.ui +++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.ui @@ -7,437 +7,456 @@ 0 0 495 - 370 + 433 Indirect Diffraction - - - - - Instrument - - - - - - - 0 - 0 - - - - - TOF Indirect Geometry Spectroscopy - TOF Indirect Geometry Diffraction - - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - Reflection - - - - - - - - 0 - 0 - - - - - - - - - - - Input - - - - 6 + + + + + Instrument - - - - - - - 0 - 41 - - - - Run Numbers - - - true - - - + + + + + + 0 + 0 + + + + + TOF Indirect Geometry Spectroscopy + TOF Indirect Geometry Diffraction + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + Reflection + + + + + + + + 0 + 0 + + + + + + + + + + + Input + + + + 6 + + + + + + + + 0 + 41 + + + + Run Numbers + + + true + + + + + + + Sum Files + + + + + + + + + + + Spectra Min + + + + + + + + + + Spectra Max + + + + + + + + + + + + + + + + 0 + 0 + + + + 0 + + + + + 0 + 0 + + + + + 0 + - - - Sum Files + + + Calibration + + + 6 + + + + + + 0 + 0 + + + + Cal File + + + false + + + false + + + + .cal + + + + + + + + true + + + + 0 + 0 + + + + Vanadium Runs + + + true + + + + - - - - - - - Spectra Min - - - - - - + + + + + 0 + 0 + + + + + 0 + - - - Spectra Max + + + Rebin in D-Spacing (optional) + + + 6 + + + 6 + + + + + Start: + + + + + + + + + + color: rgb(170, 0, 0); + + + * + + + + + + + Width: + + + + + + + + + + color: rgb(170, 0, 0); + + + * + + + + + + + End: + + + + + + + + + + color: rgb(170, 0, 0); + + + * + + + + - - - - - - - - - - - - 0 - 0 - - - - 0 - - - - - 0 - 0 - + + + + + + + Options - - - 0 - + - - - Calibration + + + <html><head/><body><p>When enabled spectra are not grouped and the output workspace will contain one spectrum per detector.</p></body></html> + + + Use Individual Grouping - - - 6 - - - - - - 0 - 0 - - - - Cal File - - - false - - - false - - - - .cal - - - - - - - - true - - - - 0 - 0 - - - - Vanadium Runs - - - true - - - - - - - - 0 - 0 - + + + + + Output - + - 0 + 6 - - - Rebin in D-Spacing (optional) + + + Plot Type: - - - 6 + + + + + + + None - - 6 + + + + Spectra - - - - Start: - - - - - - - - - - color: rgb(170, 0, 0); - - - * - - - - - - - Width: - - - - - - - - - - color: rgb(170, 0, 0); - - - * - - - - - - - End: - - - - - - - - - - color: rgb(170, 0, 0); - - - * - - - - + - - - - - - Output - - - - 6 + + + + + Select which file formats the data should be saved in. + + Save Formats + + + + 6 + + + + + GSS + + + + + + + Nexus + + + + + + + ASCII (DAT) + + + + + + + + - + + + true + + + + 0 + 0 + + + + + 20 + 20 + + - Plot Type: + ? - - - - None - - - - - Spectra - - - + + + Qt::Horizontal + + + + 40 + 20 + + + - - - - - - - Select which file formats the data should be saved in. - - - Save Formats - - - - 6 - - + - GSS + Run - - - Nexus + + + Qt::Horizontal - + + + 40 + 20 + + + - + - ASCII (DAT) + Manage Directories - - - - - - - - true - - - - 0 - 0 - - - - - 20 - 20 - - - - ? - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - Run - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - Manage Directories - - - - - - + + diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp index 0c49bcf0c373..4250658fffdd 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp @@ -129,6 +129,8 @@ void IndirectDiffractionReduction::runGenericReduction(QString instName, QString if(!rebinStart.isEmpty() && !rebinWidth.isEmpty() && !rebinEnd.isEmpty()) rebin = rebinStart + "," + rebinWidth + "," + rebinEnd; + bool individualGrouping = m_uiForm.ckIndividualGrouping->isChecked(); + // Get detector range std::vector detRange; detRange.push_back(m_uiForm.set_leSpecMin->text().toLong()); @@ -138,6 +140,7 @@ void IndirectDiffractionReduction::runGenericReduction(QString instName, QString IAlgorithm_sptr msgDiffReduction = AlgorithmManager::Instance().create("MSGDiffractionReduction"); msgDiffReduction->initialize(); + // Get save formats std::vector saveFormats; if(m_uiForm.ckGSS->isChecked()) saveFormats.push_back("gss"); if(m_uiForm.ckNexus->isChecked()) saveFormats.push_back("nxs"); @@ -150,6 +153,7 @@ void IndirectDiffractionReduction::runGenericReduction(QString instName, QString msgDiffReduction->setProperty("InputFiles", m_uiForm.dem_rawFiles->getFilenames().join(",").toStdString()); msgDiffReduction->setProperty("DetectorRange", detRange); msgDiffReduction->setProperty("RebinParam", rebin.toStdString()); + msgDiffReduction->setProperty("IndividualGrouping", individualGrouping); msgDiffReduction->setProperty("SaveFormats", saveFormats); msgDiffReduction->setProperty("OutputWorkspaceGroup", "IndirectDiffraction_Workspaces"); @@ -530,6 +534,11 @@ void IndirectDiffractionReduction::runFilesFound() m_uiForm.pbRun->setText("Run"); else m_uiForm.pbRun->setText("Invalid Run"); + + // Disable sum files if only one file is given + int fileCount = m_uiForm.dem_rawFiles->getFilenames().size(); + if(fileCount < 2) + m_uiForm.dem_ckSumFiles->setChecked(false); } } diff --git a/Code/Mantid/instrument/VESUVIO_Parameters.xml b/Code/Mantid/instrument/VESUVIO_Parameters.xml index 1ac00f2294d0..9d2fbcaab635 100644 --- a/Code/Mantid/instrument/VESUVIO_Parameters.xml +++ b/Code/Mantid/instrument/VESUVIO_Parameters.xml @@ -153,6 +153,10 @@ + + + + From 53155ca651682bb3433aadea099d2fc079abbf70 Mon Sep 17 00:00:00 2001 From: Dan Nixon Date: Mon, 13 Oct 2014 16:17:13 +0100 Subject: [PATCH 05/52] Added more realistic monitor data to IPF Refs #10323 --- Code/Mantid/instrument/VESUVIO_Parameters.xml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/Code/Mantid/instrument/VESUVIO_Parameters.xml b/Code/Mantid/instrument/VESUVIO_Parameters.xml index 9d2fbcaab635..d45c5accb8c3 100644 --- a/Code/Mantid/instrument/VESUVIO_Parameters.xml +++ b/Code/Mantid/instrument/VESUVIO_Parameters.xml @@ -137,20 +137,23 @@ + + + - + - + - + - + From f841acf595c0a2ce5a2a420aae6fccc7552ce99b Mon Sep 17 00:00:00 2001 From: Dan Nixon Date: Mon, 13 Oct 2014 16:46:26 +0100 Subject: [PATCH 06/52] Added option to plot contour when using ind. groups Disable individual grouping for OSIRIS diffonly Refs #10323 --- .../IndirectDiffractionReduction.h | 1 + .../src/IndirectDiffractionReduction.cpp | 59 ++++++++++++++++++- 2 files changed, 58 insertions(+), 2 deletions(-) diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.h index 924729afa2e0..2631379786e7 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.h +++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.h @@ -38,6 +38,7 @@ public slots: void runFilesChanged(); void runFilesFinding(); void runFilesFound(); + void individualGroupingToggled(int state); private: virtual void initLayout(); diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp index 4250658fffdd..c14a5e509879 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp @@ -102,13 +102,22 @@ void IndirectDiffractionReduction::plotResults(bool error) QString instName = m_uiForm.cbInst->currentText(); QString mode = m_uiForm.cbReflection->currentText(); - QString pyInput = "from mantidplot import plotSpectrum\n"; - if(m_uiForm.cbPlotType->currentText() == "Spectra") + QString plotType = m_uiForm.cbPlotType->currentText(); + + QString pyInput = "from mantidplot import plotSpectrum, plot2D\n"; + + if(plotType == "Spectra" || plotType == "Both") { for(auto it = m_plotWorkspaces.begin(); it != m_plotWorkspaces.end(); ++it) pyInput += "plotSpectrum('" + *it + "', 0)\n"; } + if(plotType == "Contour" || plotType == "Both") + { + for(auto it = m_plotWorkspaces.begin(); it != m_plotWorkspaces.end(); ++it) + pyInput += "plot2D('" + *it + "')\n"; + } + runPythonCode(pyInput); } @@ -344,15 +353,26 @@ void IndirectDiffractionReduction::reflectionSelected(int) // Hide options that the current instrument config cannot process if(instrumentName == "OSIRIS" && reflection == "diffonly") { + // Disable individual grouping + m_uiForm.ckIndividualGrouping->setToolTip("OSIRIS cannot group detectors individually in diffonly mode"); + m_uiForm.ckIndividualGrouping->setEnabled(false); + m_uiForm.ckIndividualGrouping->setChecked(false); + + // Disable sum files m_uiForm.dem_ckSumFiles->setToolTip("OSIRIS cannot sum files in diffonly mode"); m_uiForm.dem_ckSumFiles->setEnabled(false); m_uiForm.dem_ckSumFiles->setChecked(false); } else { + // Re-enable sum files m_uiForm.dem_ckSumFiles->setToolTip(""); m_uiForm.dem_ckSumFiles->setEnabled(true); m_uiForm.dem_ckSumFiles->setChecked(true); + + // Re-enable individual grouping + m_uiForm.ckIndividualGrouping->setToolTip(""); + m_uiForm.ckIndividualGrouping->setEnabled(true); } } @@ -404,6 +424,9 @@ void IndirectDiffractionReduction::initLayout() m_uiForm.leRebinWidth->setValidator(m_valDbl); m_uiForm.leRebinEnd->setValidator(m_valDbl); + // Update the list of plot options when individual grouping is toggled + connect(m_uiForm.ckIndividualGrouping, SIGNAL(stateChanged(int)), this, SLOT(individualGroupingToggled(int))); + loadSettings(); // Update invalid rebinning markers @@ -541,5 +564,37 @@ void IndirectDiffractionReduction::runFilesFound() m_uiForm.dem_ckSumFiles->setChecked(false); } +/** + * Handles the user toggling the individual grouping check box. + * + * @param state The selection state of the check box + */ +void IndirectDiffractionReduction::individualGroupingToggled(int state) +{ + int itemCount = m_uiForm.cbPlotType->count(); + + switch(state) + { + case Qt::Unchecked: + if(itemCount == 4) + { + m_uiForm.cbPlotType->removeItem(3); + m_uiForm.cbPlotType->removeItem(2); + } + break; + + case Qt::Checked: + if(itemCount == 2) + { + m_uiForm.cbPlotType->insertItem(2, "Contour"); + m_uiForm.cbPlotType->insertItem(3, "Both"); + } + break; + + default: + return; + } +} + } } From 6fd48173055d72f77627ff3f9cfa1a7f54dd8df6 Mon Sep 17 00:00:00 2001 From: Owen Arnold Date: Tue, 14 Oct 2014 11:24:43 +0100 Subject: [PATCH 07/52] refs #10333. Work around NeXus bug. Fixed and enabled tests that Russell previously disabled. Extracted confidence functionality and exposed as a static public class member. Give good, but not excellent confidence for restricted partial string matches with NXSPE. Added extra tests for the confidence funtionality. --- .../inc/MantidDataHandling/LoadNXSPE.h | 3 + .../Framework/DataHandling/src/LoadNXSPE.cpp | 653 +++++++++--------- .../DataHandling/test/LoadNXSPETest.h | 22 +- Test/AutoTestData/NXSPEData.nxspe | Bin 0 -> 24600 bytes 4 files changed, 354 insertions(+), 324 deletions(-) create mode 100644 Test/AutoTestData/NXSPEData.nxspe diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNXSPE.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNXSPE.h index 73c12b72f787..2145b9733d06 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNXSPE.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadNXSPE.h @@ -57,6 +57,9 @@ namespace DataHandling /// Returns a confidence value that this algorithm can load a file virtual int confidence(Kernel::NexusDescriptor & descriptor) const; + /// Confidence in identifier. + static int identiferConfidence(const std::string& value); + private: /// Initialise the properties diff --git a/Code/Mantid/Framework/DataHandling/src/LoadNXSPE.cpp b/Code/Mantid/Framework/DataHandling/src/LoadNXSPE.cpp index c8605ec72e57..3c23bdb5de91 100644 --- a/Code/Mantid/Framework/DataHandling/src/LoadNXSPE.cpp +++ b/Code/Mantid/Framework/DataHandling/src/LoadNXSPE.cpp @@ -16,371 +16,396 @@ #include #include #include +#include namespace Mantid { -namespace DataHandling -{ - - DECLARE_NEXUS_FILELOADER_ALGORITHM(LoadNXSPE); + namespace DataHandling + { - using namespace Mantid::Kernel; - using namespace Mantid::API; + DECLARE_NEXUS_FILELOADER_ALGORITHM(LoadNXSPE); + using namespace Mantid::Kernel; + using namespace Mantid::API; - //---------------------------------------------------------------------------------------------- - /** Constructor - */ - LoadNXSPE::LoadNXSPE() - { - } - - //---------------------------------------------------------------------------------------------- - /** Destructor - */ - LoadNXSPE::~LoadNXSPE() - { - } + //---------------------------------------------------------------------------------------------- + /** Constructor + */ + LoadNXSPE::LoadNXSPE() + { + } + //---------------------------------------------------------------------------------------------- + /** Destructor + */ + LoadNXSPE::~LoadNXSPE() + { + } - //---------------------------------------------------------------------------------------------- + //---------------------------------------------------------------------------------------------- - /** - * Return the confidence with with this algorithm can load the file - * @param descriptor A descriptor for the file - * @returns An integer specifying the confidence level. 0 indicates it will not be used - */ - int LoadNXSPE::confidence(Kernel::NexusDescriptor & descriptor) const - { - int confidence(0); - typedef std::map string_map_t; - try + /** + * Calculate the confidence in the string value. This is used for file identification. + * @param value + * @return confidence 0 - 100% + */ + int LoadNXSPE::identiferConfidence(const std::string& value) { - ::NeXus::File file = ::NeXus::File(descriptor.filename()); - string_map_t entries = file.getEntries(); - for(string_map_t::const_iterator it = entries.begin(); it != entries.end(); ++it) + int confidence = 0; + if (value.compare("NXSPE") == 0) + { + confidence = 99; + } + else { - if (it->second == "NXentry") + boost::regex re("^NXSP", boost::regex::icase); + if (boost::regex_match(value, re)) { - file.openGroup(it->first, it->second); - file.openData("definition"); - if (file.getStrData().compare("NXSPE")==0) confidence =99; + confidence = 95; } } + return confidence; } - catch(::NeXus::Exception&) - { - } - return confidence; - } - //---------------------------------------------------------------------------------------------- - /** Initialize the algorithm's properties. - */ - void LoadNXSPE::init() - { - std::vector exts; - exts.push_back(".nxspe"); - exts.push_back(""); - declareProperty(new FileProperty("Filename", "", FileProperty::Load, exts), - "An NXSPE file"); - declareProperty(new WorkspaceProperty<>("OutputWorkspace", - "",Direction::Output), "The name of the workspace that will be created."); - } - - //---------------------------------------------------------------------------------------------- - /** Execute the algorithm. - */ - void LoadNXSPE::exec() - { - std::string filename = getProperty("Filename"); - //quicly check if it's really nxspe - try + /** + * Return the confidence with with this algorithm can load the file + * @param descriptor A descriptor for the file + * @returns An integer specifying the confidence level. 0 indicates it will not be used + */ + int LoadNXSPE::confidence(Kernel::NexusDescriptor & descriptor) const { - ::NeXus::File file(filename); - std::string mainEntry=(*(file.getEntries().begin())).first; - file.openGroup(mainEntry, "NXentry"); - file.openData("definition"); - if (file.getStrData().compare("NXSPE")) throw std::invalid_argument("Not NXSPE"); - file.close(); + int confidence(0); + typedef std::map string_map_t; + try + { + ::NeXus::File file = ::NeXus::File(descriptor.filename()); + string_map_t entries = file.getEntries(); + for (string_map_t::const_iterator it = entries.begin(); it != entries.end(); ++it) + { + if (it->second == "NXentry") + { + file.openGroup(it->first, it->second); + file.openData("definition"); + const std::string value = file.getStrData(); + confidence = identiferConfidence(value); + } + } + } catch (::NeXus::Exception&) + { + } + return confidence; } - catch(...) + + //---------------------------------------------------------------------------------------------- + /** Initialize the algorithm's properties. + */ + void LoadNXSPE::init() { - throw std::invalid_argument("Not NeXus or notNXSPE"); + std::vector exts; + exts.push_back(".nxspe"); + exts.push_back(""); + declareProperty(new FileProperty("Filename", "", FileProperty::Load, exts), "An NXSPE file"); + declareProperty(new WorkspaceProperty<>("OutputWorkspace", "", Direction::Output), + "The name of the workspace that will be created."); } - //Load the data - ::NeXus::File file(filename); + //---------------------------------------------------------------------------------------------- + /** Execute the algorithm. + */ + void LoadNXSPE::exec() + { + std::string filename = getProperty("Filename"); + //quicly check if it's really nxspe + try + { + ::NeXus::File file(filename); + std::string mainEntry = (*(file.getEntries().begin())).first; + file.openGroup(mainEntry, "NXentry"); + file.openData("definition"); + if (identiferConfidence(file.getStrData()) < 1) + { + throw std::invalid_argument("Not NXSPE"); + } + file.close(); + } + catch (...) + { + throw std::invalid_argument("Not NeXus or not NXSPE"); + } - std::string mainEntry=(*(file.getEntries().begin())).first; - file.openGroup(mainEntry, "NXentry"); + //Load the data + ::NeXus::File file(filename); - file.openGroup("NXSPE_info", "NXcollection"); - std::map entries=file.getEntries(); - std::vector temporary; - double fixed_energy,psi=0.; + std::string mainEntry = (*(file.getEntries().begin())).first; + file.openGroup(mainEntry, "NXentry"); - if (!entries.count("fixed_energy")) - { - throw std::invalid_argument("fixed_energy field was not found"); - } - file.openData("fixed_energy"); - file.getData(temporary); - fixed_energy=temporary.at(0); - file.closeData(); + file.openGroup("NXSPE_info", "NXcollection"); + std::map entries = file.getEntries(); + std::vector temporary; + double fixed_energy, psi = 0.; - if (entries.count("psi")) - { - file.openData("psi"); + if (!entries.count("fixed_energy")) + { + throw std::invalid_argument("fixed_energy field was not found"); + } + file.openData("fixed_energy"); file.getData(temporary); - psi=temporary.at(0); + fixed_energy = temporary.at(0); file.closeData(); - } - int kikfscaling=0; - if (entries.count("ki_over_kf_scaling")) - { - file.openData("ki_over_kf_scaling"); - std::vector temporaryint; - file.getData(temporaryint); - kikfscaling=temporaryint.at(0); - file.closeData(); - } - - file.closeGroup();//NXSPE_Info + if (entries.count("psi")) + { + file.openData("psi"); + file.getData(temporary); + psi = temporary.at(0); + file.closeData(); + } + int kikfscaling = 0; + if (entries.count("ki_over_kf_scaling")) + { + file.openData("ki_over_kf_scaling"); + std::vector temporaryint; + file.getData(temporaryint); + kikfscaling = temporaryint.at(0); + file.closeData(); + } - file.openGroup("data", "NXdata"); - entries=file.getEntries(); + file.closeGroup(); //NXSPE_Info - if (!entries.count("data")) - { - throw std::invalid_argument("data field was not found"); - } - file.openData("data"); - ::NeXus::Info info = file.getInfo(); - std::size_t numSpectra=static_cast(info.dims.at(0)); - std::size_t numBins=static_cast(info.dims.at(1)); - std::vector data; - file.getData(data); - file.closeData(); - - if (!entries.count("error")) - { - throw std::invalid_argument("error field was not found"); - } - file.openData("error"); - std::vector error; - file.getData(error); - file.closeData(); + file.openGroup("data", "NXdata"); + entries = file.getEntries(); - if (!entries.count("energy")) - { - throw std::invalid_argument("energy field was not found"); - } - file.openData("energy"); - std::vector energies; - file.getData(energies); - file.closeData(); + if (!entries.count("data")) + { + throw std::invalid_argument("data field was not found"); + } + file.openData("data"); + ::NeXus::Info info = file.getInfo(); + std::size_t numSpectra = static_cast(info.dims.at(0)); + std::size_t numBins = static_cast(info.dims.at(1)); + std::vector data; + file.getData(data); + file.closeData(); - if (!entries.count("azimuthal")) - { - throw std::invalid_argument("azimuthal field was not found"); - } - file.openData("azimuthal"); - std::vector azimuthal; - file.getData(azimuthal); - file.closeData(); + if (!entries.count("error")) + { + throw std::invalid_argument("error field was not found"); + } + file.openData("error"); + std::vector error; + file.getData(error); + file.closeData(); - if (!entries.count("azimuthal_width")) - { - throw std::invalid_argument("azimuthal_width field was not found"); - } - file.openData("azimuthal_width"); - std::vector azimuthal_width; - file.getData(azimuthal_width); - file.closeData(); + if (!entries.count("energy")) + { + throw std::invalid_argument("energy field was not found"); + } + file.openData("energy"); + std::vector energies; + file.getData(energies); + file.closeData(); - if (!entries.count("polar")) - { - throw std::invalid_argument("polar field was not found"); - } - file.openData("polar"); - std::vector polar; - file.getData(polar); - file.closeData(); + if (!entries.count("azimuthal")) + { + throw std::invalid_argument("azimuthal field was not found"); + } + file.openData("azimuthal"); + std::vector azimuthal; + file.getData(azimuthal); + file.closeData(); - if (!entries.count("polar_width")) - { - throw std::invalid_argument("polar_width field was not found"); - } - file.openData("polar_width"); - std::vector polar_width; - file.getData(polar_width); - file.closeData(); - - //distance might not have been saved in all NXSPE files - std::vector distance; - if (entries.count("distance")) - { - file.openData("distance"); - file.getData(distance); + if (!entries.count("azimuthal_width")) + { + throw std::invalid_argument("azimuthal_width field was not found"); + } + file.openData("azimuthal_width"); + std::vector azimuthal_width; + file.getData(azimuthal_width); file.closeData(); - } - file.closeGroup();//data group - file.closeGroup();//Main entry - file.close(); + if (!entries.count("polar")) + { + throw std::invalid_argument("polar field was not found"); + } + file.openData("polar"); + std::vector polar; + file.getData(polar); + file.closeData(); - //check if dimensions of the vectors are correct - if ((error.size()!=data.size())||(azimuthal.size()!=numSpectra)||(azimuthal_width.size()!=numSpectra)|| - (polar.size()!=numSpectra)||(polar_width.size()!=numSpectra)||((energies.size()!=numBins)&&(energies.size()!=numBins+1))) - { - throw std::invalid_argument("incompatible sizes of fields in the NXSPE file"); - } + if (!entries.count("polar_width")) + { + throw std::invalid_argument("polar_width field was not found"); + } + file.openData("polar_width"); + std::vector polar_width; + file.getData(polar_width); + file.closeData(); - MatrixWorkspace_sptr outputWS = boost::dynamic_pointer_cast - (WorkspaceFactory::Instance().create("Workspace2D",numSpectra,energies.size(),numBins)); - // Need to get hold of the parameter map - Geometry::ParameterMap& pmap = outputWS->instrumentParameters(); - outputWS->getAxis(0)->unit() = UnitFactory::Instance().create("DeltaE"); - std::vector::iterator itdata=data.begin(),iterror=error.begin(),itdataend,iterrorend; - API::Progress prog = API::Progress(this, 0.0, 0.9, numSpectra); - for (std::size_t i=0; idataX(i)=energies; - if (((*itdata)==std::numeric_limits::quiet_NaN())||(*itdata<=-1e10))//masked bin + //distance might not have been saved in all NXSPE files + std::vector distance; + if (entries.count("distance")) { - outputWS->dataY(i)=std::vector(numBins,0); - outputWS->dataE(i)=std::vector(numBins,0); - pmap.addBool(outputWS->getDetector(i).get(),"masked",true); + file.openData("distance"); + file.getData(distance); + file.closeData(); } - else + + file.closeGroup(); //data group + file.closeGroup(); //Main entry + file.close(); + + //check if dimensions of the vectors are correct + if ((error.size() != data.size()) || (azimuthal.size() != numSpectra) + || (azimuthal_width.size() != numSpectra) || (polar.size() != numSpectra) + || (polar_width.size() != numSpectra) + || ((energies.size() != numBins) && (energies.size() != numBins + 1))) { - outputWS->dataY(i)=std::vector(itdata,itdataend); - outputWS->dataE(i)=std::vector(iterror,iterrorend); + throw std::invalid_argument("incompatible sizes of fields in the NXSPE file"); } - itdata=(itdataend); - iterror=(iterrorend); - prog.report(); - } - //add logs - outputWS->mutableRun().addLogData(new PropertyWithValue("Ei", fixed_energy)); - outputWS->mutableRun().addLogData(new PropertyWithValue("psi", psi)); - outputWS->mutableRun().addLogData(new PropertyWithValue("ki_over_kf_scaling", kikfscaling==1?"true":"false")); - - //Set Goniometer - Geometry::Goniometer gm; - gm.pushAxis("psi",0,1,0,psi); - outputWS->mutableRun().setGoniometer(gm, true); - - //generate instrument - Geometry::Instrument_sptr instrument(new Geometry::Instrument("NXSPE")); - outputWS->setInstrument(instrument); - - Geometry::ObjComponent *source = new Geometry::ObjComponent("source"); - source->setPos(0.0,0.0,-10.0); - instrument->add(source); - instrument->markAsSource(source); - Geometry::ObjComponent *sample = new Geometry::ObjComponent("sample"); - instrument->add(sample); - instrument->markAsSamplePos(sample); - - Geometry::Object_const_sptr cuboid(createCuboid(0.1,0.1,0.1));//FIXME: memory hog on rendering. Also, make each detector separate size - for (std::size_t i=0;i( + WorkspaceFactory::Instance().create("Workspace2D", numSpectra, energies.size(), numBins)); + // Need to get hold of the parameter map + Geometry::ParameterMap& pmap = outputWS->instrumentParameters(); + outputWS->getAxis(0)->unit() = UnitFactory::Instance().create("DeltaE"); + std::vector::iterator itdata = data.begin(), iterror = error.begin(), itdataend, + iterrorend; + API::Progress prog = API::Progress(this, 0.0, 0.9, numSpectra); + for (std::size_t i = 0; i < numSpectra; ++i) { - r=distance.at(i); + itdataend = itdata + numBins; + iterrorend = iterror + numBins; + outputWS->dataX(i) = energies; + if (((*itdata) == std::numeric_limits::quiet_NaN()) || (*itdata <= -1e10)) //masked bin + { + outputWS->dataY(i) = std::vector(numBins, 0); + outputWS->dataE(i) = std::vector(numBins, 0); + pmap.addBool(outputWS->getDetector(i).get(), "masked", true); + } + else + { + outputWS->dataY(i) = std::vector(itdata, itdataend); + outputWS->dataE(i) = std::vector(iterror, iterrorend); + } + itdata = (itdataend); + iterror = (iterrorend); + prog.report(); } - Kernel::V3D pos; - pos.spherical(r,polar.at(i),azimuthal.at(i)); + //add logs + outputWS->mutableRun().addLogData(new PropertyWithValue("Ei", fixed_energy)); + outputWS->mutableRun().addLogData(new PropertyWithValue("psi", psi)); + outputWS->mutableRun().addLogData( + new PropertyWithValue("ki_over_kf_scaling", kikfscaling == 1 ? "true" : "false")); + + //Set Goniometer + Geometry::Goniometer gm; + gm.pushAxis("psi", 0, 1, 0, psi); + outputWS->mutableRun().setGoniometer(gm, true); + + //generate instrument + Geometry::Instrument_sptr instrument(new Geometry::Instrument("NXSPE")); + outputWS->setInstrument(instrument); + + Geometry::ObjComponent *source = new Geometry::ObjComponent("source"); + source->setPos(0.0, 0.0, -10.0); + instrument->add(source); + instrument->markAsSource(source); + Geometry::ObjComponent *sample = new Geometry::ObjComponent("sample"); + instrument->add(sample); + instrument->markAsSamplePos(sample); + + Geometry::Object_const_sptr cuboid(createCuboid(0.1, 0.1, 0.1)); //FIXME: memory hog on rendering. Also, make each detector separate size + for (std::size_t i = 0; i < numSpectra; ++i) + { + double r = 1.0; + if (!distance.empty()) + { + r = distance.at(i); + } - Geometry::Detector *det = new Geometry::Detector("pixel",static_cast(i+1),sample); - det->setPos(pos); - det->setShape(cuboid); - instrument->add(det); - instrument->markAsDetector(det); - } + Kernel::V3D pos; + pos.spherical(r, polar.at(i), azimuthal.at(i)); - setProperty("OutputWorkspace", outputWS); - } + Geometry::Detector *det = new Geometry::Detector("pixel", static_cast(i + 1), sample); + det->setPos(pos); + det->setShape(cuboid); + instrument->add(det); + instrument->markAsDetector(det); + } + setProperty("OutputWorkspace", outputWS); + } - Geometry::Object_sptr LoadNXSPE:: createCuboid(double dx,double dy, double dz) - { + Geometry::Object_sptr LoadNXSPE::createCuboid(double dx, double dy, double dz) + { + + dx = 0.5 * std::fabs(dx); + dy = 0.5 * std::fabs(dy); + dz = 0.5 * std::fabs(dz); + /* + std::stringstream planeName; + + planeName.str("px ");planeName<<-dx; + std::string C1=planeName.str(); + planeName.str("px ");planeName< CubeSurMap; + CubeSurMap[1]=new Geometry::Plane(); + CubeSurMap[2]=new Geometry::Plane(); + CubeSurMap[3]=new Geometry::Plane(); + CubeSurMap[4]=new Geometry::Plane(); + CubeSurMap[5]=new Geometry::Plane(); + CubeSurMap[6]=new Geometry::Plane(); + + CubeSurMap[1]->setSurface(C1); + CubeSurMap[2]->setSurface(C2); + CubeSurMap[3]->setSurface(C3); + CubeSurMap[4]->setSurface(C4); + CubeSurMap[5]->setSurface(C5); + CubeSurMap[6]->setSurface(C6); + CubeSurMap[1]->setName(1); + CubeSurMap[2]->setName(2); + CubeSurMap[3]->setName(3); + CubeSurMap[4]->setName(4); + CubeSurMap[5]->setName(5); + CubeSurMap[6]->setName(6); + + // Cube (id 68) + // using surface ids: 1-6 + std::string ObjCube="1 -2 3 -4 5 -6"; + + Geometry::Object_sptr retVal = Geometry::Object_sptr(new Geometry::Object); + retVal->setObject(68,ObjCube); + retVal->populate(CubeSurMap); + */ + std::string S41 = "so 0.01"; // Sphere at origin radius 0.01 + + // First create some surfaces + std::map SphSurMap; + SphSurMap[41] = new Geometry::Sphere(); + SphSurMap[41]->setSurface(S41); + SphSurMap[41]->setName(41); + + // A sphere + std::string ObjSphere = "-41"; + Geometry::Object_sptr retVal = Geometry::Object_sptr(new Geometry::Object); + retVal->setObject(41, ObjSphere); + retVal->populate(SphSurMap); + + return retVal; + } - dx=0.5*std::fabs(dx); - dy=0.5*std::fabs(dy); - dz=0.5*std::fabs(dz); - /* - std::stringstream planeName; - - planeName.str("px ");planeName<<-dx; - std::string C1=planeName.str(); - planeName.str("px ");planeName< CubeSurMap; - CubeSurMap[1]=new Geometry::Plane(); - CubeSurMap[2]=new Geometry::Plane(); - CubeSurMap[3]=new Geometry::Plane(); - CubeSurMap[4]=new Geometry::Plane(); - CubeSurMap[5]=new Geometry::Plane(); - CubeSurMap[6]=new Geometry::Plane(); - - CubeSurMap[1]->setSurface(C1); - CubeSurMap[2]->setSurface(C2); - CubeSurMap[3]->setSurface(C3); - CubeSurMap[4]->setSurface(C4); - CubeSurMap[5]->setSurface(C5); - CubeSurMap[6]->setSurface(C6); - CubeSurMap[1]->setName(1); - CubeSurMap[2]->setName(2); - CubeSurMap[3]->setName(3); - CubeSurMap[4]->setName(4); - CubeSurMap[5]->setName(5); - CubeSurMap[6]->setName(6); - - // Cube (id 68) - // using surface ids: 1-6 - std::string ObjCube="1 -2 3 -4 5 -6"; - - Geometry::Object_sptr retVal = Geometry::Object_sptr(new Geometry::Object); - retVal->setObject(68,ObjCube); - retVal->populate(CubeSurMap); -*/ - std::string S41="so 0.01"; // Sphere at origin radius 0.01 - - // First create some surfaces - std::map SphSurMap; - SphSurMap[41]=new Geometry::Sphere(); - SphSurMap[41]->setSurface(S41); - SphSurMap[41]->setName(41); - - // A sphere - std::string ObjSphere="-41" ; - Geometry::Object_sptr retVal = Geometry::Object_sptr(new Geometry::Object); - retVal->setObject(41,ObjSphere); - retVal->populate(SphSurMap); - - return retVal; - } - - -} // namespace Mantid + } // namespace Mantid } // namespace DataHandling diff --git a/Code/Mantid/Framework/DataHandling/test/LoadNXSPETest.h b/Code/Mantid/Framework/DataHandling/test/LoadNXSPETest.h index 01379b78eade..c08f14c79ae1 100644 --- a/Code/Mantid/Framework/DataHandling/test/LoadNXSPETest.h +++ b/Code/Mantid/Framework/DataHandling/test/LoadNXSPETest.h @@ -25,7 +25,7 @@ class LoadNXSPETest : public CxxTest::TestSuite TS_ASSERT( alg.isInitialized() ) } - void xtest_exec() + void test_exec() { // Name of the output workspace. std::string outWSName("LoadNXSPETest_OutputWS"); @@ -33,29 +33,31 @@ class LoadNXSPETest : public CxxTest::TestSuite LoadNXSPE alg; TS_ASSERT_THROWS_NOTHING( alg.initialize() ) TS_ASSERT( alg.isInitialized() ) - TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("Filename", "/home/andrei/Mantid/Test/Data/CNCS_7850.nxspe") ); + TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("Filename", "NXSPEData.nxspe") ); TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("OutputWorkspace", outWSName) ); TS_ASSERT_THROWS_NOTHING( alg.execute(); ); TS_ASSERT( alg.isExecuted() ); -// TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("Filename", "/home/andrei/Desktop/cncs.nxspe") ); - TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("Filename", "/home/andrei/Desktop/reduction.py") ); - TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("OutputWorkspace", outWSName) ); - TS_ASSERT_THROWS_NOTHING( alg.execute(); ); - TS_ASSERT( alg.isExecuted() ); // Retrieve the workspace from data service. Workspace_sptr ws; TS_ASSERT_THROWS_NOTHING( ws = AnalysisDataService::Instance().retrieveWS(outWSName) ); TS_ASSERT(ws); if (!ws) return; - // TODO: Check the results - - // Remove workspace from the data service. AnalysisDataService::Instance().remove(outWSName); } + void test_identifier_confidence() + { + const int high_confidence = LoadNXSPE::identiferConfidence("NXSPE"); + const int good_confidence = LoadNXSPE::identiferConfidence("NXSP"); + const int no_confidence = LoadNXSPE::identiferConfidence("NXS"); + + TS_ASSERT(high_confidence > good_confidence); + TS_ASSERT(good_confidence > no_confidence); + } + }; diff --git a/Test/AutoTestData/NXSPEData.nxspe b/Test/AutoTestData/NXSPEData.nxspe new file mode 100644 index 0000000000000000000000000000000000000000..b5c0fed5d77cf97740a12a5f3688becf54605d1e GIT binary patch literal 24600 zcmeHP4Oo;_7QQ2ih!|s8k(G?5g{UwC=%TEB7X<^+0pxE~Xl8_A7=;06h80<#q878B zN^Gr`bThNs)y+)PRr1LmwJbA#$P`#xvmc-05i52rb=}H6_dECUGc^3VD)n6+=X~ef zbMHO(z4xB){`ox`7c+IB?+{Atfm`#_TeO*h`#6BHw0v2g>EbupehkZ!))y zy}FRdkO^RdA3+3L+3T{kviH^&_J(P75o2}QvAXb7-S~;&x{2d-qqW+JT11Q0+e^m8 z-5-?jft`faCLQ^My8fux)Ar@XDWsPnApF55Zny9Yrco#m<96R&$kzuUZ5{{xaoie= z+4*KCcnl0|+_J7H#;xAql*bj1CMo*F7!}0w?n;WT!x*7o$@wa8kwT$Ahk$4wcf2~& zK5Qx=@YWl^89EjL-w$OxLPgNSs8lEr`ht2v3$kb7r~7igPoF-riVvh`4_+$G0JNWZ z^X6~^?*UB5+8CAUN3esjp27aan}FrdraE$_Ky@Ku@XLbevB+KSU+kye+$ut}gRul* zhk^4YH=|tmU3GA4y-3a*#-LpE`+ed8#ch5gxn$RE_#n!y=e*BQlw&IqqG3R_6XJN> z8a|#ye(vMDoh-T)CBIDz%yyS8M^3MHQOt)@W|Uij3x8|DnHQ*q(y(?{PQ%q zYUq-NK~Xd!9Kx1KbW~==p6`PwUHL48MbXr^_Qj$}`zO=IgE!v$*^n4IfbsKU>F*i8 zV=Bh`#vwmDo}OVDzA_E@iwVdl%%G)Af2E!_$OR@+;7SLtPNKOiOif1qn`GplnMnhe zfaX0Z$bXrF{IXPPW%}dOkpCo&GIM;Frc-8hW@rZTwHe4iU_k!vS#&vzKRk=ZL9rVb z&c^y{<{)Y9sPhoN7%}hO69!@;Vb`)hr!j zM*T7~@<+`WA2b*F#d9&fdM-V90K$lDjK^?2&Y=Tu>Bc)vf(v z5`B`@Cy~-aEd7RPY!}}tG@jMZ8bcX;L-)qgw?VC9_`Ot~nU=-Tdsu^>h{yJsn1FUw zPN(NUZO`{Ju-ueHlpB%|zkbOW|Mz6HKW8TD-I&60NF{~^mOFUaQb)# z@?#804{(}43wgiUNH=hrKZomQB0ZByS+x&r$in*P-^b&PC_iJwev@uOy3vI8_cbFf zS-f4gn(0dn&jE9>KG|~-uN`ygOnF>nQwHa~wruKP?Z1n+?*#~R{%4(j__XgS0C z4vRbviPnPSWwM2`WJPHf#52!AS+iA?a{VVPh#yhHHHko3F1C+Cf7v)(lb!EpjOxj} zk}Ux|&nrjrd1dQ`Lfd&I&ZK^BUO5Qz7xSR-kgyQ8_SR{&6GC(m5fM#w5i_SIL606h zt=}8@Jkr2(?`ZvQ;1fSidSsK5xc4C-*6*UfMDi+B@_r<0lxr)oi^IBz$%>pd zIcmPmSO{w@ib9wy)u0Po-8$;YJ{J{g!aQUVo9u&A(_=`1c)A3gju3Wzg?{U9sxi6Dr zu{tak*5fX3zY^z3VjyjSYKV!U46S}CPpX$0Kg$HLDB@qQ%i5l2vCZyuIpni3WArRtW-iJ%aK7YDlnXyl=hpt0(WG9Pl_!7O$Z_kezcq|(jdQOA zLovGB2)O%OHP5M%_al+9Sow%?+SA#T@VD;cy)*vSAB+-q=ne84z?hv^SX5+jfE@4n z2!)R4W!+u>OzG4-m5>qv;Z>pT=frU%u8JAGzEDs8wvKO`iMJ)rZ;8kIV~W4+^#^rVt(Vp?~91cg?|(MO2~Ukb1b=VPfP3;!9JFw(CRQ3G|dR*b7rH>o?D0|wVurq zB5tANz{M`6A?y_Mjh@;k(t8?j)%^Tl;L_20QX7IfMv9CT`l~`fjJHj^)_I)P&;0+w zAm%sj_g0$MW1jbS*(*hiE4=|nT1V?haVtnrFMe;R>-)M1d|ngO3Ly7=r{;S`S94$2 zr|DkNI(;j1+c09jx=%QcHX0~Ub9qUq2L&z`{;n>$eLdmdHDlY?3*ga@XxrD*@aW1J z?du7DSC!blUfX_!?XJS>XZ)71*t3N91<#J{8L-g(epac&9N^+|i_o^8At207KiI)= z+N^eSJ|XV=sA9Yb+C0wK4vG&km&lvI^0`CH^OK^&e6wSsSlzI3=e~ZpVt7cM!Gn;z z7HD0m#}O1uis$qmPW7BNa@!S(I4L+NI4}g1exURNr5`BcK=A{LA5i>&;s+Ezp!k8_ z=m)UXlwSn_1px&C1px&C1px&C1px&C1px&C1%Y2K0&UMj@uXUO&qSOD3)=njU?;zK zP{#gSSW|F655C&>DX$zJXZg9ff(JX(_fl1+VW&{=Ks*9wDR{7NWQp%1Rc7`EJkUl$ z#ElbikJ93B6gnVMzK;UbTxu&QcIC0FE^?6N#)Y;V7vBG9is!N%o6}{sXIr>>)BUkH zAyBA-KsOL5^SPtu$Xhj1*~a~AkBqO8Nad~53SK-Wkzv||BVIroCw>2!;iyDZ(!vXC zKa$A)`)5RcaYQ1~u@n9n0Cbi~^JC115*fUH+YD>9MEb1PKBhV>k))6Tt41D_Nb2Ud zMn!%g5pQeFrAhBgWZT^-$r0~KuW%L6 zlhyzI8sf=+%AQbfl1SB|Oz-C){ko`)wZq?l^zS}5WEJH9_+R^NQSFBR6#oy?)4^{` zM4ebTIRWg6*t)`L0{f1R`)RNh?A6Xlx^6DmAN2L$P(9S=&$VOU34;1PHF}}06zZ#f zA}b*s>Yww&@UKPz9%}#a?Pq~j4zJR00ldmTd|;Io@H@@EXwHu3Ei* zGTi3P+qYA&QTFS{k>`yRqqDcmnD>FK5ix2ciBhpC#r^fJga=`B4u8KGRQs z`eqW~Reh5xYxr9d$tx?}`6S?3QgS%$65v};kNji;yy?QQ-FL17y2A0$+11bvTdl`6 zk4Z$6mC^U;3ZRyODbKEz$nr6Fu8>}lNYS}(W6x}s$i8hE-r8-DZrQGLc{`vT)2%*F zLpi7ReQMtgndt~1NFHOuxDNZ z)K6>LQT`ItxBP~{<9~qqm%nk|kO6o+wZImt0etfOch{c)dS?5so0kKA%TJ$79uIh$ zUS2w(8fZY-G*=ejz2>=qO(%fXrxmVEg7!$-HmtTk#IHM@v1Bq(&38B6J&f@Q6=O4i z#znrdG#qH;_KO8pp!D%Iw?_jV@$aRHPN3ysLGQ%_&FdGqc+oK_b=vOrdn*FzwL(*_ zkUd>3r>pus#gjH}Zwwh8NELc*;h?$o-Sx{>22*0lxo!HfU`ihzXpDP4m}(Bq3fWQ{ zOh4WG>RKQrrjHUIzs literal 0 HcmV?d00001 From 40d7c14d9d5a6d626098c48a653cae8f4ed5a4eb Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 13:51:19 +0100 Subject: [PATCH 08/52] Refs #10194 faster save, output verified with DAWN software --- .../inc/MantidDataHandling/SaveNXTomo.h | 32 +- .../Framework/DataHandling/src/SaveNXTomo.cpp | 645 ++++++++++-------- 2 files changed, 377 insertions(+), 300 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 464f8d839495..13ccba3bb236 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -4,9 +4,10 @@ //--------------------------------------------------- // Includes //--------------------------------------------------- -//#include "MantidNexus/NexusClasses.h" -//#include -//#include +#include "vector" +#include "MantidGeometry/Instrument/RectangularDetector.h" + +using Mantid::Geometry::RectangularDetector; namespace Mantid { @@ -15,7 +16,7 @@ namespace Mantid /** * Saves a workspace into a NeXus/HDF5 NXTomo file. - * File format is defined here: http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html + * File format is defined here: http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html * * Required properties: *
      @@ -53,7 +54,7 @@ namespace Mantid /// Virtual dtor virtual ~SaveNXTomo() {} - /// Algorithm's name for identification overriding a virtual method + /// Algorithm's name for identification overriding a virtual method virtual const std::string name() const { return "SaveNXTomo"; } ///Summary of algorithms purpose @@ -71,22 +72,31 @@ namespace Mantid /// Execution code void exec(); - /// Save all data to file + /// Save all data to file + + /// Save batch of images to the file + + /// Fetch all rectangular Detector objects defined for an instrument + std::vector getRectangularDetectors(Geometry::Instrument_const_sptr &instrument); + + /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument + void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); - /// Save batch of images to the file + // Number of rows to + size_t m_numberOfRows; ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change - size_t m_nBins; + //size_t m_nBins; /// The filename of the output file - std::string m_filename; + std::string m_filename; // Some constants to be written for masked values. /// Value for data if pixel is masked static const double MASK_FLAG; /// Value for error if pixel is masked static const double MASK_ERROR; - /// file format version - static const std::string NXTOMO_VER; + /// file format version + static const std::string NXTOMO_VER; }; } // namespace DataHandling diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 51c5f256d435..7b79819b9826 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -2,309 +2,376 @@ #include "MantidAPI/WorkspaceValidators.h" #include "MantidDataHandling/FindDetectorsPar.h" #include "MantidDataHandling/SaveNXTomo.h" +#include "MantidGeometry/IComponent.h" #include "MantidKernel/MantidVersion.h" #include "MantidNexus/NexusClasses.h" namespace Mantid { - namespace DataHandling - { - // Register the algorithm into the algorithm factory - DECLARE_ALGORITHM(SaveNXTomo) - - using namespace Kernel; - using namespace API; - - const double SaveNXTomo::MASK_FLAG = std::numeric_limits::quiet_NaN(); - const double SaveNXTomo::MASK_ERROR = 0.0; - const std::string SaveNXTomo::NXTOMO_VER = "2.0"; - - SaveNXTomo::SaveNXTomo() : API::Algorithm() - { - } - - /** - * Initialise the algorithm - */ - void SaveNXTomo::init() - { - auto wsValidator = boost::make_shared() ; - //wsValidator->add(boost::make_shared("DeltaE")); - wsValidator->add(); - wsValidator->add(); - - declareProperty(new WorkspaceProperty ("InputWorkspace", - "", Direction::Input, wsValidator), - "The name of the workspace to save."); - - declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), - "The name of the NXTomo file to write, as a full or relative path"); - } - - /** - * Execute the algorithm - */ - void SaveNXTomo::exec() - { - // Retrieve the input workspace - const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); - - const std::string workspaceID = inputWS->id(); - - if ((workspaceID.find("Workspace2D") == std::string::npos) && - (workspaceID.find("RebinnedOutput") == std::string::npos)) - throw Exception::NotImplementedError("SaveNexusProcessed passed invalid workspaces. Must be Workspace2D, EventWorkspace, ITableWorkspace, or OffsetsWorkspace."); + namespace DataHandling + { + // Register the algorithm into the algorithm factory + DECLARE_ALGORITHM(SaveNXTomo) + + using namespace Kernel; + using namespace API; + using Geometry::RectangularDetector; + + const double SaveNXTomo::MASK_FLAG = std::numeric_limits::quiet_NaN(); + const double SaveNXTomo::MASK_ERROR = 0.0; + const std::string SaveNXTomo::NXTOMO_VER = "2.0"; + + SaveNXTomo::SaveNXTomo() : API::Algorithm() + { + m_filename = ""; + m_numberOfRows = 32; + } + + /** + * Initialise the algorithm + */ + void SaveNXTomo::init() + { + auto wsValidator = boost::make_shared() ; + //wsValidator->add(boost::make_shared("DeltaE")); + wsValidator->add(); + wsValidator->add(); + + declareProperty(new WorkspaceProperty ("InputWorkspace", "", Direction::Input, wsValidator), + "The name of the workspace to save."); + + declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), + "The name of the NXTomo file to write, as a full or relative path"); + + declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), + "Please use an evenly divisible number smaller than the image height"); + } + + /** + * Execute the algorithm + */ + void SaveNXTomo::exec() + { + // Retrieve the input workspace + const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); + + m_numberOfRows = getProperty("Row chunk size"); + + const std::string workspaceID = inputWS->id(); + + if ((workspaceID.find("Workspace2D") == std::string::npos) && + (workspaceID.find("RebinnedOutput") == std::string::npos)) + throw Exception::NotImplementedError("SaveNXTomo passed invalid workspaces. Must be Workspace2D"); + + // Do the full check for common binning + if (!WorkspaceHelpers::commonBoundaries(inputWS)) + { + g_log.error("The input workspace must have common bins"); + throw std::invalid_argument("The input workspace must have common bins"); + } + + // Number of spectra + const int nHist = static_cast(inputWS->getNumberHistograms()); + // Number of energy bins + //this->m_nBins = inputWS->blocksize(); + + // Get a pointer to the sample + //Geometry::IComponent_const_sptr sample = + // inputWS->getInstrument()->getSample(); + + // Retrieve the filename from the properties + this->m_filename = getPropertyValue("Filename"); + + // Dimensions for axis in nxTomo file. + std::vector dims_array; + dims_array.push_back(inputWS->blocksize()); // Number of bins + + // Populate the array + getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument()), dims_array); + + // Create the file. + ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); + + // Make the top level entry (and open it) + nxFile.makeGroup("entry1", "NXentry", true); + + // Make a sub-group for the entry to work with DAWN software (and open it) + nxFile.makeGroup("tomo_entry", "NXsubentry", true); + + // Title + nxFile.writeData("title", this->m_filename); + + // Start Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("start_time", ); + + // End Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("end_time", ); + + // Definition name and version + nxFile.writeData("definition", "NXtomo"); + nxFile.openData("definition"); + nxFile.putAttr("version", NXTOMO_VER); + nxFile.closeData(); + + // Originating program name and version + nxFile.writeData("program_name", "mantid"); + nxFile.openData("program_name"); + nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); + nxFile.closeData(); + + // ****************************************** + // NXinstrument + nxFile.makeGroup("instrument", "NXinstrument", true); + // Write the instrument name | could add short_name attribute to name + nxFile.writeData("name", inputWS->getInstrument()->getName()); + + // detector group - diamond example file contains {data,distance,image_key,x_pixel_size,y_pixel_size} Only adding image_key for now, 0 filled. + nxFile.makeGroup("detector", "NXdetector", true); + std::vector imageKeys(dims_array[0],0); + nxFile.writeData("image_key", imageKeys); + // Create link to image_key + nxFile.openData("image_key"); + NXlink imageKeyLink = nxFile.getDataID(); + nxFile.closeData(); + nxFile.closeGroup(); + + // source group // from diamond file contains {current,energy,name,probe,type} - probe = [neutron | x-ray | electron] + + nxFile.closeGroup(); // NXinstrument + + // ****************************************** + // NXsample + nxFile.makeGroup("sample", "NXsample", true); + // TODO: Write sample info + // name + + std::vector rotationAngles(dims_array[0]); + // Initialise rotations - if unknown, fill with equal steps from 0 to 180 over all frames. + // TODO: collect and use actual rotation values + + double step = static_cast(180/dims_array[0]); + rotationAngles[0] = step; + + for(auto it = rotationAngles.begin()+1; it != rotationAngles.end(); ++it) + { + *it = (*(it-1)) + step; + } + + nxFile.writeData("rotation_angle", rotationAngles); + + // Create a link object for rotation_angle to use later + nxFile.openData("rotation_angle"); + NXlink rotationLink = nxFile.getDataID(); + nxFile.closeData(); + // x_translation + // y_translation + // z_translation + nxFile.closeGroup(); // NXsample + + // ****************************************** + // Make the NXmonitor group - Holds base beam intensity for each image + // If information is not present, set as 1 + + std::vector intensity(dims_array[0],1); + nxFile.makeGroup("control", "NXmonitor", true); + nxFile.writeData("data", intensity); + nxFile.closeGroup(); // NXmonitor + + nxFile.makeGroup("data", "NXdata", true); + + nxFile.makeLink(rotationLink); + + nxFile.makeData("data", ::NeXus::FLOAT64, dims_array, false); + nxFile.makeData("error", ::NeXus::FLOAT64, dims_array, false); + + std::vector slabStart; + std::vector slabSize; + + // What size slabs are we going to write + slabSize.push_back(dims_array[0]); + slabSize.push_back((int64_t)dims_array[1]); + slabSize.push_back((int64_t)m_numberOfRows); + + // Init start to first row + slabStart.push_back(0); + slabStart.push_back(0); + slabStart.push_back(0); + + // define the data and error vectors for masked detectors + std::vector masked_data (dims_array[0], MASK_FLAG); + std::vector masked_error (dims_array[0], MASK_ERROR); + + // Create a progress reporting object + Progress progress(this,0,1,100); + const int progStep = (int)(ceil(nHist/100.0)); + Geometry::IDetector_const_sptr det; - // Do the full check for common binning - if (!WorkspaceHelpers::commonBoundaries(inputWS)) - { - g_log.error("The input workspace must have common bins"); - throw std::invalid_argument("The input workspace must have common bins"); - } - - // Number of spectra - const int nHist = static_cast(inputWS->getNumberHistograms()); - // Number of energy bins - this->m_nBins = inputWS->blocksize(); - - // Get a pointer to the sample - Geometry::IComponent_const_sptr sample = - inputWS->getInstrument()->getSample(); - - // Retrieve the filename from the properties - this->m_filename = getPropertyValue("Filename"); - - // Create some arrays for the nexus api to use - std::vector array_dims; - array_dims.push_back((int)nHist); - array_dims.push_back((int)m_nBins); - - // Create the file. - ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); - - // Make the top level entry (and open it) - nxFile.makeGroup("entry1", "NXentry", true); + double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + double *errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - // Make a sub-group for the entry to work with DAWN software (and open it) - nxFile.makeGroup("tomo_entry", "NXsubentry", true); + int currY = 0; + int rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab - // Title - nxFile.writeData("title", this->m_filename); - - // Start Time; Format ISO8601 | unused but part of NXtomo schema - //nxFile.writeData("start_time", ); - - // End Time; Format ISO8601 | unused but part of NXtomo schema - //nxFile.writeData("end_time", ); - - // Definition name and version - nxFile.writeData("definition", "NXtomo"); - nxFile.openData("definition"); - nxFile.putAttr("version", NXTOMO_VER); - nxFile.closeData(); - - // Originating program name and version - nxFile.writeData("program_name", "mantid"); - nxFile.openData("program_name"); - nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); - nxFile.closeData(); - - // ****************************************** - // NXinstrument - nxFile.makeGroup("instrument", "NXinstrument", true); - // Write the instrument name | could add short_name attribute to name - nxFile.writeData("name", inputWS->getInstrument()->getName()); - - // detector group - diamond example file contains {data,distance,image_key,x_pixel_size,y_pixel_size} Only adding image_key for now, 0 filled. - nxFile.makeGroup("detector", "NXdetector", true); - std::vector imageKey(array_dims[1],0); - nxFile.writeData("image_key", imageKey); - nxFile.closeGroup(); - - // source group // from diamond file contains {current,energy,name,probe,type} - probe = neutron | x-ray | electron - - - nxFile.closeGroup(); // NXinstrument - - // ****************************************** - // NXsample - nxFile.makeGroup("sample", "NXsample", true); - // TODO: Write sample info - // name - // nxFile.writeData("rotation_angle", 0.0); - // x_translation - // y_translation - // z_translation - nxFile.closeGroup(); // NXsample - - // ****************************************** - // Make the NXmonitor group - Holds base beam intensity for each image - // If information is not present, set as 1 - - std::vector intensity(array_dims[1],1); - nxFile.makeGroup("control", "NXmonitor", true); - nxFile.writeData("data", intensity); - nxFile.closeGroup(); // NXmonitor - - // ****************************************** - // Make the NXdata group - nxFile.makeGroup("data", "NXdata", true); - - // Energy bins - // Get the Energy Axis (X) of the first spectra (they are all the same - checked above) - const MantidVec& X = inputWS->readX(0); - nxFile.writeData("energy", X); - nxFile.openData("energy"); - nxFile.putAttr("units", "meV"); - nxFile.closeData(); - - nxFile.makeData("data", ::NeXus::FLOAT64, array_dims, false); - nxFile.makeData("error", ::NeXus::FLOAT64, array_dims, false); - - // Add the axes attributes to the data - //nxFile.openData("data"); - //nxFile.putAttr("signal", 1); - //nxFile.putAttr("axes", "polar:energy"); - //nxFile.closeData(); - - std::vector slab_start; - std::vector slab_size; - - // What size slabs are we going to write... - slab_size.push_back(1); - slab_size.push_back((int64_t)m_nBins); - - // And let's start at the beginning - slab_start.push_back(0); - slab_start.push_back(0); - - // define the data and error vectors for masked detectors - std::vector masked_data (m_nBins, MASK_FLAG); - std::vector masked_error (m_nBins, MASK_ERROR); - - // Create a progress reporting object - Progress progress(this,0,1,100); - const int progStep = (int)(ceil(nHist/100.0)); - Geometry::IDetector_const_sptr det; - // Loop over spectra - for (int i = 0; i < nHist; i++) - { + // Loop over detectors + for (size_t i = 0; i < nHist; ++i) + { try - { // detector exist - det = inputWS->getDetector(i); - // Check that we aren't writing a monitor... - if (!det->isMonitor()) + { + // detector exist + //det = inputWS->getDetector(i); + // Check that we aren't writing a monitor + //if (!det->isMonitor()) + //{ + //Geometry::IDetector_const_sptr det = inputWS->getDetector(i); + + // Figure out where this pixel is supposed to be going and set the correct slab start. + const MantidVec *y = &inputWS->readY(i); + + if(i!=0 && (i)%dims_array[1] == 0){ // When this iteration matches end of a row + currY += 1; + } + size_t currX = (i) - (currY*dims_array[1]); + + const MantidVec & thisY = inputWS->readY(i); + // No masking - Set the data and error as is + for(int j=0; jisMasked()) + // { + dataArr[currInd] = thisY.at(j); + errorArr[currInd] = inputWS->readE(i).at(j); + //} + //else + //{ + // dataArr[currInd] = masked_data[j]; + // errorArr[currInd] = masked_error[j]; + //} + } + + // If end of the row has been reached, check for end of slab and write data/error + if(((i+1)%dims_array[2]) == 0) { - Geometry::IDetector_const_sptr det = inputWS->getDetector(i); - - if (!det->isMasked()) - { - // no masking... - // Open the data - nxFile.openData("data"); - slab_start[0] = i; - nxFile.putSlab(const_cast (inputWS->readY(i)), - slab_start, slab_size); - // Close the data - nxFile.closeData(); + rowIndForSlab += 1; - // Open the error - nxFile.openData("error"); - //MantidVec& tmparr = const_cast(inputWS->dataE(i)); - //nxFile.putSlab((void*)(&(tmparr[0])), slab_start, slab_size); - nxFile.putSlab(const_cast (inputWS->readE(i)), - slab_start, slab_size); - // Close the error + // if a slab has been collected. Put it into the file + if(rowIndForSlab >= m_numberOfRows) + { + slabStart[2] = currY-(rowIndForSlab-1); + + // Write Data + nxFile.openData("data"); + nxFile.putSlab(dataArr, slabStart, slabSize); nxFile.closeData(); - } - else - { - // Write a masked value... - // Open the data - nxFile.openData("data"); - slab_start[0] = i; - nxFile.putSlab(masked_data, slab_start, slab_size); - // Close the data - nxFile.closeData(); - - // Open the error - nxFile.openData("error"); - nxFile.putSlab(masked_error, slab_start, slab_size); - // Close the error + // Write Error + nxFile.openData("error"); + nxFile.putSlab(errorArr, slabStart, slabSize); nxFile.closeData(); + + // Reset slab index count + rowIndForSlab = 0; } - } - } - catch(Exception::NotFoundError&) - { - // Catch if no detector. Next line tests whether this happened - test placed - // outside here because Mac Intel compiler doesn't like 'continue' in a catch - // in an openmp block. - } - // If no detector found, skip onto the next spectrum - if ( !det ) continue; - - // make regular progress reports and check for canceling the algorithm - if ( i % progStep == 0 ) - { - progress.report(); - } - } - // execute the ChildAlgorithm to calculate the detector's parameters; - /* IAlgorithm_sptr spCalcDetPar = this->createChildAlgorithm("FindDetectorsPar", 0, 1, true, 1); - - spCalcDetPar->initialize(); - spCalcDetPar->setPropertyValue("InputWorkspace", inputWS->getName()); - std::string parFileName = this->getPropertyValue("ParFile"); - if(!(parFileName.empty()||parFileName=="not_used.par")){ - spCalcDetPar->setPropertyValue("ParFile",parFileName); - } - spCalcDetPar->execute();*/ - - // - //FindDetectorsPar * pCalcDetPar = dynamic_cast(spCalcDetPar.get()); - //if(!pCalcDetPar){ // "can not get pointer to FindDetectorsPar algorithm" - // throw(std::bad_cast()); - //} - /* const std::vector & azimuthal = pCalcDetPar->getAzimuthal(); - const std::vector & polar = pCalcDetPar->getPolar(); - const std::vector & azimuthal_width = pCalcDetPar->getAzimWidth(); - const std::vector & polar_width = pCalcDetPar->getPolarWidth(); - const std::vector & secondary_flightpath= pCalcDetPar->getFlightPath();*/ - - - //// Write the Polar (2Theta) angles - //nxFile.writeData("polar", polar); - - //// Write the Azimuthal (phi) angles - //nxFile.writeData("azimuthal", azimuthal); - - //// Now the widths... - //nxFile.writeData("polar_width", polar_width); - //nxFile.writeData("azimuthal_width", azimuthal_width); - - //// Secondary flight path - //nxFile.writeData("distance", secondary_flightpath); - - nxFile.closeGroup(); // NXdata - - nxFile.closeGroup(); // tomo_entry sub-group - - nxFile.closeGroup(); // Top level NXentry - - // Validate the file against the schema - - } - - //void someRoutineToAddDataToExisting() - //{ - // //TODO: - //} - - } // namespace DataHandling + } + } + catch(Exception::NotFoundError&) + { + /*Catch if no detector. Next line tests whether this happened - test placed + outside here because Mac Intel compiler doesn't like 'continue' in a catch + in an openmp block.*/ + } + // If no detector found, skip onto the next spectrum + if ( !det ) continue; + + // Make regular progress reports and check for canceling the algorithm + if ( i % progStep == 0 ) + { + progress.report(); + } + } + + // Create a link object for the data + nxFile.openData("data"); + NXlink dataLink = nxFile.getDataID(); + nxFile.closeData(); + + nxFile.closeGroup(); // Close Data group + + // Put a link to the data in instrument/detector + nxFile.openGroup("instrument","NXinstrument"); + nxFile.openGroup("detector","NXdetector"); + nxFile.makeLink(dataLink); + nxFile.closeGroup(); + nxFile.closeGroup(); + + + nxFile.closeGroup(); // tomo_entry sub-group + nxFile.closeGroup(); // Top level NXentry + + // Clean up memory + delete [] dataArr; + delete [] errorArr; + } + + /** + * Find all RectangularDetector objects in an instrument + * @param instrument instrument to search for detectors in + * @returns vector of all Rectangular Detectors + */ + std::vector SaveNXTomo::getRectangularDetectors(Geometry::Instrument_const_sptr &instrument) + { + std::vector> components; + instrument->getChildren(components,true); + + std::vector rectDetectors; + + for(auto it = components.begin(); it != components.end(); ++it) + { + // for all components, compare to RectangularDetector - if it is one, add it to detectors list. + const Geometry::IComponent* c = dynamic_cast(&(**it)); + + if(const RectangularDetector* r = dynamic_cast(c)) + { + rectDetectors.push_back(*(dynamic_cast(&(**it)))); + } + } + + return rectDetectors; + } + + /** + * Populates the dimensions vector with number of files, x and y sizes from a specified rectangular detector + * @param rectDetectors List of rectangular detectors to get axis sizes from + * @param dims_array vector which is populated with the different dimension values for the nxTomo file + * @param useDetectorIndex index of the detector to select from the list, default = 0 + * + * @throw runtime_error Thrown if there are no rectangular detectors + */ + void SaveNXTomo::getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) + { + // Add number of pixels in X and Y from instrument definition + // Throws if no rectangular detector is present. + + if(rectDetectors.size() != 0) + { + // Assume the first rect detector is the desired one. + dims_array.push_back(rectDetectors[useDetectorIndex].xpixels()); + dims_array.push_back(rectDetectors[useDetectorIndex].ypixels()); + } + else + { + // Incorrect workspace : requires the x/y pixel count from the instrument definition + g_log.error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); + throw std::runtime_error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); + } + } + + //void someRoutineToAddDataToExisting() + //{ + // //TODO: + //} + + } // namespace DataHandling } // namespace Mantid -// TODO: don't allow a multi-file -// Follow mtd conventions -// Add comments / function descriptions etc \ No newline at end of file From 5ccf1e5ec712d21726107ef76d04dfe507729e9b Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 15:06:33 +0100 Subject: [PATCH 09/52] Refs #10194 attempting to fix build error --- .../inc/MantidDataHandling/SaveNXTomo.h | 8 +- .../Framework/DataHandling/src/SaveNXTomo.cpp | 187 +++++++++--------- 2 files changed, 96 insertions(+), 99 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 13ccba3bb236..219aca172721 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -7,8 +7,6 @@ #include "vector" #include "MantidGeometry/Instrument/RectangularDetector.h" -using Mantid::Geometry::RectangularDetector; - namespace Mantid { namespace DataHandling @@ -77,12 +75,12 @@ namespace Mantid /// Save batch of images to the file /// Fetch all rectangular Detector objects defined for an instrument - std::vector getRectangularDetectors(Geometry::Instrument_const_sptr &instrument); + std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); + void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); - // Number of rows to + // Number of rows to size_t m_numberOfRows; ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 7b79819b9826..38d35ca0737b 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -24,7 +24,7 @@ namespace Mantid SaveNXTomo::SaveNXTomo() : API::Algorithm() { m_filename = ""; - m_numberOfRows = 32; + m_numberOfRows = 32; } /** @@ -38,13 +38,13 @@ namespace Mantid wsValidator->add(); declareProperty(new WorkspaceProperty ("InputWorkspace", "", Direction::Input, wsValidator), - "The name of the workspace to save."); + "The name of the workspace to save."); declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), "The name of the NXTomo file to write, as a full or relative path"); - declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), - "Please use an evenly divisible number smaller than the image height"); + declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), + "Please use an evenly divisible number smaller than the image height"); } /** @@ -55,7 +55,7 @@ namespace Mantid // Retrieve the input workspace const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); - m_numberOfRows = getProperty("Row chunk size"); + m_numberOfRows = getProperty("Row chunk size"); const std::string workspaceID = inputWS->id(); @@ -71,7 +71,7 @@ namespace Mantid } // Number of spectra - const int nHist = static_cast(inputWS->getNumberHistograms()); + const size_t nHist = inputWS->getNumberHistograms(); // Number of energy bins //this->m_nBins = inputWS->blocksize(); @@ -84,7 +84,7 @@ namespace Mantid // Dimensions for axis in nxTomo file. std::vector dims_array; - dims_array.push_back(inputWS->blocksize()); // Number of bins + dims_array.push_back(inputWS->blocksize()); // Number of bins // Populate the array getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument()), dims_array); @@ -188,9 +188,9 @@ namespace Mantid std::vector slabSize; // What size slabs are we going to write - slabSize.push_back(dims_array[0]); - slabSize.push_back((int64_t)dims_array[1]); - slabSize.push_back((int64_t)m_numberOfRows); + slabSize.push_back(dims_array[0]); + slabSize.push_back((int64_t)dims_array[1]); + slabSize.push_back((int64_t)m_numberOfRows); // Init start to first row slabStart.push_back(0); @@ -203,91 +203,90 @@ namespace Mantid // Create a progress reporting object Progress progress(this,0,1,100); - const int progStep = (int)(ceil(nHist/100.0)); + const size_t progStep = static_cast(ceil(nHist/100.0)); Geometry::IDetector_const_sptr det; - - double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - double *errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + + double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + double *errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - int currY = 0; - int rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab + int currY = 0; + size_t rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab // Loop over detectors for (size_t i = 0; i < nHist; ++i) { - try - { - // detector exist - //det = inputWS->getDetector(i); - // Check that we aren't writing a monitor - //if (!det->isMonitor()) - //{ - //Geometry::IDetector_const_sptr det = inputWS->getDetector(i); - - // Figure out where this pixel is supposed to be going and set the correct slab start. - const MantidVec *y = &inputWS->readY(i); - - if(i!=0 && (i)%dims_array[1] == 0){ // When this iteration matches end of a row - currY += 1; - } - size_t currX = (i) - (currY*dims_array[1]); - - const MantidVec & thisY = inputWS->readY(i); - // No masking - Set the data and error as is - for(int j=0; jisMasked()) - // { - dataArr[currInd] = thisY.at(j); - errorArr[currInd] = inputWS->readE(i).at(j); - //} - //else - //{ - // dataArr[currInd] = masked_data[j]; - // errorArr[currInd] = masked_error[j]; - //} - } + try + { + // detector exist + //det = inputWS->getDetector(i); + // Check that we aren't writing a monitor + //if (!det->isMonitor()) + //{ + //Geometry::IDetector_const_sptr det = inputWS->getDetector(i); + + // Figure out where this pixel is supposed to be going and set the correct slab start. + + if(i!=0 && (i)%dims_array[1] == 0){ // When this iteration matches end of a row + currY += 1; + } + size_t currX = (i) - (currY*dims_array[1]); + + const MantidVec & thisY = inputWS->readY(i); + // No masking - Set the data and error as is + for(int j=0; jisMasked()) + // { + dataArr[currInd] = thisY.at(j); + errorArr[currInd] = inputWS->readE(i).at(j); + //} + //else + //{ + // dataArr[currInd] = masked_data[j]; + // errorArr[currInd] = masked_error[j]; + //} + } - // If end of the row has been reached, check for end of slab and write data/error - if(((i+1)%dims_array[2]) == 0) - { - rowIndForSlab += 1; - - // if a slab has been collected. Put it into the file - if(rowIndForSlab >= m_numberOfRows) - { - slabStart[2] = currY-(rowIndForSlab-1); - - // Write Data - nxFile.openData("data"); - nxFile.putSlab(dataArr, slabStart, slabSize); - nxFile.closeData(); - // Write Error - nxFile.openData("error"); - nxFile.putSlab(errorArr, slabStart, slabSize); - nxFile.closeData(); - - // Reset slab index count - rowIndForSlab = 0; - } - } - } - catch(Exception::NotFoundError&) - { - /*Catch if no detector. Next line tests whether this happened - test placed - outside here because Mac Intel compiler doesn't like 'continue' in a catch - in an openmp block.*/ - } - // If no detector found, skip onto the next spectrum - if ( !det ) continue; - - // Make regular progress reports and check for canceling the algorithm - if ( i % progStep == 0 ) - { - progress.report(); - } + // If end of the row has been reached, check for end of slab and write data/error + if(((i+1)%dims_array[2]) == 0) + { + rowIndForSlab += 1; + + // if a slab has been collected. Put it into the file + if(rowIndForSlab >= m_numberOfRows) + { + slabStart[2] = currY-(rowIndForSlab-1); + + // Write Data + nxFile.openData("data"); + nxFile.putSlab(dataArr, slabStart, slabSize); + nxFile.closeData(); + // Write Error + nxFile.openData("error"); + nxFile.putSlab(errorArr, slabStart, slabSize); + nxFile.closeData(); + + // Reset slab index count + rowIndForSlab = 0; + } + } + } + catch(Exception::NotFoundError&) + { + /*Catch if no detector. Next line tests whether this happened - test placed + outside here because Mac Intel compiler doesn't like 'continue' in a catch + in an openmp block.*/ + } + // If no detector found, skip onto the next spectrum + if ( !det ) continue; + + // Make regular progress reports and check for canceling the algorithm + if ( i % progStep == 0 ) + { + progress.report(); + } } // Create a link object for the data @@ -308,9 +307,9 @@ namespace Mantid nxFile.closeGroup(); // tomo_entry sub-group nxFile.closeGroup(); // Top level NXentry - // Clean up memory - delete [] dataArr; - delete [] errorArr; + // Clean up memory + delete [] dataArr; + delete [] errorArr; } /** @@ -318,7 +317,7 @@ namespace Mantid * @param instrument instrument to search for detectors in * @returns vector of all Rectangular Detectors */ - std::vector SaveNXTomo::getRectangularDetectors(Geometry::Instrument_const_sptr &instrument) + std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) { std::vector> components; instrument->getChildren(components,true); @@ -329,8 +328,8 @@ namespace Mantid { // for all components, compare to RectangularDetector - if it is one, add it to detectors list. const Geometry::IComponent* c = dynamic_cast(&(**it)); - - if(const RectangularDetector* r = dynamic_cast(c)) + + if(dynamic_cast(c)) { rectDetectors.push_back(*(dynamic_cast(&(**it)))); } From f05ab53faa0bfe56ec2db7dca9a271c129829ba5 Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 15:48:16 +0100 Subject: [PATCH 10/52] Refs #10194 attempting to fix build error --- .../inc/MantidDataHandling/SaveNXTomo.h | 5 ++- .../Framework/DataHandling/src/SaveNXTomo.cpp | 38 +++++++++++++------ 2 files changed, 30 insertions(+), 13 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 219aca172721..92b1d63c4244 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -78,11 +78,14 @@ namespace Mantid std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); + void getDimensionsFromDetector(const std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); // Number of rows to size_t m_numberOfRows; + // Include error data in the written file + bool m_includeError; + ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change //size_t m_nBins; /// The filename of the output file diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 38d35ca0737b..c648698319e8 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -24,6 +24,7 @@ namespace Mantid SaveNXTomo::SaveNXTomo() : API::Algorithm() { m_filename = ""; + m_includeError = false; m_numberOfRows = 32; } @@ -45,6 +46,9 @@ namespace Mantid declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), "Please use an evenly divisible number smaller than the image height"); + + declareProperty(new PropertyWithValue("Include error", false, Kernel::Direction::Input), + "Write the error values to NXTomo file?"); } /** @@ -56,6 +60,7 @@ namespace Mantid const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); m_numberOfRows = getProperty("Row chunk size"); + m_includeError = getProperty("Include error"); const std::string workspaceID = inputWS->id(); @@ -182,7 +187,8 @@ namespace Mantid nxFile.makeLink(rotationLink); nxFile.makeData("data", ::NeXus::FLOAT64, dims_array, false); - nxFile.makeData("error", ::NeXus::FLOAT64, dims_array, false); + if(m_includeError) + nxFile.makeData("error", ::NeXus::FLOAT64, dims_array, false); std::vector slabStart; std::vector slabSize; @@ -199,15 +205,18 @@ namespace Mantid // define the data and error vectors for masked detectors std::vector masked_data (dims_array[0], MASK_FLAG); - std::vector masked_error (dims_array[0], MASK_ERROR); + if(m_includeError) + std::vector masked_error (dims_array[0], MASK_ERROR); // Create a progress reporting object Progress progress(this,0,1,100); - const size_t progStep = static_cast(ceil(nHist/100.0)); + const size_t progStep = static_cast(ceil(static_cast(nHist)/100.0)); Geometry::IDetector_const_sptr det; double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - double *errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + double *errorArr; + if(m_includeError) + errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; int currY = 0; size_t rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab @@ -240,12 +249,14 @@ namespace Mantid // if(!det->isMasked()) // { dataArr[currInd] = thisY.at(j); - errorArr[currInd] = inputWS->readE(i).at(j); + if(m_includeError) + errorArr[currInd] = inputWS->readE(i).at(j); //} //else //{ // dataArr[currInd] = masked_data[j]; - // errorArr[currInd] = masked_error[j]; + // if(m_includeError) + // errorArr[currInd] = masked_error[j]; //} } @@ -264,10 +275,12 @@ namespace Mantid nxFile.putSlab(dataArr, slabStart, slabSize); nxFile.closeData(); // Write Error - nxFile.openData("error"); - nxFile.putSlab(errorArr, slabStart, slabSize); - nxFile.closeData(); - + if(m_includeError) + { + nxFile.openData("error"); + nxFile.putSlab(errorArr, slabStart, slabSize); + nxFile.closeData(); + } // Reset slab index count rowIndForSlab = 0; } @@ -309,7 +322,8 @@ namespace Mantid // Clean up memory delete [] dataArr; - delete [] errorArr; + if(m_includeError) + delete [] errorArr; } /** @@ -346,7 +360,7 @@ namespace Mantid * * @throw runtime_error Thrown if there are no rectangular detectors */ - void SaveNXTomo::getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) + void SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) { // Add number of pixels in X and Y from instrument definition // Throws if no rectangular detector is present. From c86e82908c83165e9dceee47bea1f82ed3214a38 Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 17:05:33 +0100 Subject: [PATCH 11/52] Refs #10194 attempting to fix build error --- .../inc/MantidDataHandling/SaveNXTomo.h | 4 +-- .../Framework/DataHandling/src/SaveNXTomo.cpp | 29 ++++++++++--------- 2 files changed, 18 insertions(+), 15 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 92b1d63c4244..59e072ad7878 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -75,10 +75,10 @@ namespace Mantid /// Save batch of images to the file /// Fetch all rectangular Detector objects defined for an instrument - std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); + std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - void getDimensionsFromDetector(const std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); + void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); // Number of rows to size_t m_numberOfRows; diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index c648698319e8..a1d84c7666e2 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -136,7 +136,7 @@ namespace Mantid nxFile.writeData("image_key", imageKeys); // Create link to image_key nxFile.openData("image_key"); - NXlink imageKeyLink = nxFile.getDataID(); + //NXlink imageKeyLink = nxFile.getDataID(); nxFile.closeData(); nxFile.closeGroup(); @@ -206,7 +206,7 @@ namespace Mantid // define the data and error vectors for masked detectors std::vector masked_data (dims_array[0], MASK_FLAG); if(m_includeError) - std::vector masked_error (dims_array[0], MASK_ERROR); + std::vector masked_error (dims_array[0], MASK_ERROR); // Create a progress reporting object Progress progress(this,0,1,100); @@ -214,7 +214,7 @@ namespace Mantid Geometry::IDetector_const_sptr det; double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - double *errorArr; + double *errorArr = NULL; if(m_includeError) errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; @@ -256,15 +256,19 @@ namespace Mantid //{ // dataArr[currInd] = masked_data[j]; // if(m_includeError) - // errorArr[currInd] = masked_error[j]; + // errorArr[currInd] = masked_error[j]; //} } - // If end of the row has been reached, check for end of slab and write data/error + // If end of the row has been reached, check for end of slab (or end of row count) and write data/error if(((i+1)%dims_array[2]) == 0) { rowIndForSlab += 1; + // Check if we have collected all of the rows (prior to completing a slab) - if so, write the final section + // TODO:: + + // if a slab has been collected. Put it into the file if(rowIndForSlab >= m_numberOfRows) { @@ -322,8 +326,7 @@ namespace Mantid // Clean up memory delete [] dataArr; - if(m_includeError) - delete [] errorArr; + delete [] errorArr; } /** @@ -331,12 +334,12 @@ namespace Mantid * @param instrument instrument to search for detectors in * @returns vector of all Rectangular Detectors */ - std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) + std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) { std::vector> components; instrument->getChildren(components,true); - std::vector rectDetectors; + std::vector rectDetectors; for(auto it = components.begin(); it != components.end(); ++it) { @@ -345,7 +348,7 @@ namespace Mantid if(dynamic_cast(c)) { - rectDetectors.push_back(*(dynamic_cast(&(**it)))); + rectDetectors.push_back(dynamic_cast(&(**it))); } } @@ -360,7 +363,7 @@ namespace Mantid * * @throw runtime_error Thrown if there are no rectangular detectors */ - void SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) + void SaveNXTomo::getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) { // Add number of pixels in X and Y from instrument definition // Throws if no rectangular detector is present. @@ -368,8 +371,8 @@ namespace Mantid if(rectDetectors.size() != 0) { // Assume the first rect detector is the desired one. - dims_array.push_back(rectDetectors[useDetectorIndex].xpixels()); - dims_array.push_back(rectDetectors[useDetectorIndex].ypixels()); + dims_array.push_back(rectDetectors[useDetectorIndex]->xpixels()); + dims_array.push_back(rectDetectors[useDetectorIndex]->ypixels()); } else { From 5c40edf6c156083df9c238dc7ecc5bcca568f568 Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 17:59:18 +0100 Subject: [PATCH 12/52] Refs #10194 attempting to fix build error --- .../inc/MantidDataHandling/SaveNXTomo.h | 2 +- .../Framework/DataHandling/src/SaveNXTomo.cpp | 22 ++++++++++++------- 2 files changed, 15 insertions(+), 9 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 59e072ad7878..80e0cacbe038 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -78,7 +78,7 @@ namespace Mantid std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); + std::vector getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex = 0); // Number of rows to size_t m_numberOfRows; diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index a1d84c7666e2..c843331981be 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -89,10 +89,12 @@ namespace Mantid // Dimensions for axis in nxTomo file. std::vector dims_array; - dims_array.push_back(inputWS->blocksize()); // Number of bins + + // Populate the array + dims_array = getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument())); - // Populate the array - getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument()), dims_array); + // Insert number of bins at front + dims_array.insert(dims_array.begin(), inputWS->blocksize()); // Number of bins // Create the file. ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); @@ -358,21 +360,23 @@ namespace Mantid /** * Populates the dimensions vector with number of files, x and y sizes from a specified rectangular detector * @param rectDetectors List of rectangular detectors to get axis sizes from - * @param dims_array vector which is populated with the different dimension values for the nxTomo file * @param useDetectorIndex index of the detector to select from the list, default = 0 - * + * @returns vector of both axis dimensions for specified detector + * * @throw runtime_error Thrown if there are no rectangular detectors */ - void SaveNXTomo::getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) + std::vector SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex) { // Add number of pixels in X and Y from instrument definition // Throws if no rectangular detector is present. + std::vector dims; + if(rectDetectors.size() != 0) { // Assume the first rect detector is the desired one. - dims_array.push_back(rectDetectors[useDetectorIndex]->xpixels()); - dims_array.push_back(rectDetectors[useDetectorIndex]->ypixels()); + dims.push_back(rectDetectors[useDetectorIndex]->xpixels()); + dims.push_back(rectDetectors[useDetectorIndex]->ypixels()); } else { @@ -380,6 +384,8 @@ namespace Mantid g_log.error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); throw std::runtime_error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); } + + return dims; } //void someRoutineToAddDataToExisting() From 6a0670ef0a13d1c10eb1c1b8a0f96ad037da207d Mon Sep 17 00:00:00 2001 From: John Hill Date: Thu, 11 Sep 2014 12:05:35 +0100 Subject: [PATCH 13/52] Refs #10194 create files --- .../Framework/DataHandling/CMakeLists.txt | 2 + .../inc/MantidDataHandling/SaveNXTomo.h | 104 + .../Framework/DataHandling/src/SaveNXTomo.cpp | 307 +++ .../AutoTestData/UsageData/GEM_Definition.vtp | 2047 +++++++++++++++++ 4 files changed, 2460 insertions(+) create mode 100644 Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h create mode 100644 Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp create mode 100644 Test/AutoTestData/UsageData/GEM_Definition.vtp diff --git a/Code/Mantid/Framework/DataHandling/CMakeLists.txt b/Code/Mantid/Framework/DataHandling/CMakeLists.txt index e0a7349e7f16..72aa94c182d8 100644 --- a/Code/Mantid/Framework/DataHandling/CMakeLists.txt +++ b/Code/Mantid/Framework/DataHandling/CMakeLists.txt @@ -128,6 +128,7 @@ set ( SRC_FILES src/SaveNXSPE.cpp src/SaveNexus.cpp src/SaveNexusProcessed.cpp + src/SaveNXTomo.cpp src/SaveParameterFile.cpp src/SavePAR.cpp src/SavePHX.cpp @@ -266,6 +267,7 @@ set ( INC_FILES inc/MantidDataHandling/SaveNXSPE.h inc/MantidDataHandling/SaveNexus.h inc/MantidDataHandling/SaveNexusProcessed.h + inc/MantidDataHandling/SaveNXTomo.h inc/MantidDataHandling/SaveParameterFile.h inc/MantidDataHandling/SavePAR.h inc/MantidDataHandling/SavePHX.h diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h new file mode 100644 index 000000000000..644ca2f8abdf --- /dev/null +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -0,0 +1,104 @@ +#ifndef MANTID_DATAHANDLING_SAVENXTOMO_H_ +#define MANTID_DATAHANDLING_SAVENXTOMO_H_ + +//--------------------------------------------------- +// Includes +//--------------------------------------------------- +//#include "MantidAPI/Algorithm.h" +//#include "MantidNexus/NexusClasses.h" +//#include "MantidAPI/MatrixWorkspace.h" +//#include "MantidAPI/Sample.h" +//#include "MantidDataObjects/Workspace2D.h" +//#include "MantidDataObjects/EventWorkspace.h" +//#include +//#include + +namespace Mantid +{ + namespace DataHandling + { + + /** + * Saves a workspace into a NeXus/HDF5 NXTomo file. + * + * Required properties: + *
        + *
      • InputWorkspace - The workspace to save.
        • + *
      • Filename - The filename for output
        • + *
      + * + * @author John R Hill, RAL + * @date 10/09/2014 + * + * 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 . + * + * File change history is stored at: + * Code Documentation is available at: + * + */ + + class DLLExport SaveNXTomo: public API::Algorithm + { + public: + /// Constructor + SaveNXTomo(); + /// Virtual dtor + virtual ~SaveNXTomo() + { + } + virtual const std::string name() const + { + return "SaveNXTomo"; + } + ///Summary of algorithms purpose + virtual const std::string summary() const {return "Writes a MatrixWorkspace to a file in the NXTomo format.";} + + /// Algorithm's version + virtual int version() const + { + return (1); + } + /// Algorithm's category for identification + virtual const std::string category() const + { + return "DataHandling\\Nexus;DataHandling\\Tomo;Diffraction"; + } + + private: + + /// Initialisation code + void init(); + ///Execution code + void exec(); + + ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change + //size_t nBins; + /// The filename of the output file + //std::string filename; + + // Some constants to be written for masked values. + /// Value for data if pixel is masked + //static const double MASK_FLAG; + /// Value for error if pixel is masked + //static const double MASK_ERROR; + /// file format version + //static const std::string NXSPE_VER; + }; + + } // namespace DataHandling +} // namespace Mantid + +#endif // MANTID_DATAHANDLING_SAVENXTOMO_H_ diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp new file mode 100644 index 000000000000..3a053edfa273 --- /dev/null +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -0,0 +1,307 @@ +#include "MantidDataHandling/SaveNXTomo.h" +#include "MantidAPI/FileProperty.h" +//#include "MantidKernel/ConfigService.h" +#include "MantidKernel/MantidVersion.h" +#include "MantidAPI/WorkspaceValidators.h" +//#include "MantidAPI/WorkspaceOpOverloads.h" +//#include "MantidGeometry/Instrument/Detector.h" +//#include "MantidGeometry/Instrument/ObjComponent.h" +//#include "MantidDataHandling/FindDetectorsPar.h" +// +//#include +//#include +//#include + +namespace Mantid +{ + namespace DataHandling + { + + // Register the algorithm into the algorithm factory + DECLARE_ALGORITHM(SaveNXTomo) + + using namespace Kernel; + using namespace API; + + SaveNXTomo::SaveNXTomo() : API::Algorithm() + { + } + + /** + * Initialise the algorithm + */ + void SaveNXTomo::init() + { + auto wsValidator = boost::make_shared() ; + wsValidator->add(boost::make_shared("DeltaE")); + wsValidator->add(); + wsValidator->add(); + + declareProperty(new WorkspaceProperty ("InputWorkspace", + "", Direction::Input, wsValidator), + "The name of the workspace to save."); + + declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), + "The name of the NXTomo file to write, as a full or relative path"); + } + + /** + * Execute the algorithm + */ + void SaveNXTomo::exec() + { + // Retrieve the input workspace + const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); + + // Do the full check for common binning + if (!WorkspaceHelpers::commonBoundaries(inputWS)) + { + g_log.error("The input workspace must have common bins"); + throw std::invalid_argument("The input workspace must have common bins"); + } + + // Number of spectra + const int nHist = static_cast(inputWS->getNumberHistograms()); + // Number of energy bins + this->nBins = inputWS->blocksize(); + + // Get a pointer to the sample + Geometry::IComponent_const_sptr sample = + inputWS->getInstrument()->getSample(); + + // Retrieve the filename from the properties + this->filename = getPropertyValue("Filename"); + + // Create the file. + ::NeXus::File nxFile(this->filename, NXACC_CREATE5); + + // Make the top level entry (and open it) + nxFile.makeGroup(inputWS->getName(), "NXentry", true); + + // Definition name and version + nxFile.writeData("definition", "NXSPE"); + nxFile.openData("definition"); + nxFile.putAttr("version", NXSPE_VER); + nxFile.closeData(); + + // Program name and version + nxFile.writeData("program_name", "mantid"); + nxFile.openData("program_name"); + nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); + nxFile.closeData(); + + // Create NXSPE_info + nxFile.makeGroup("NXSPE_info", "NXcollection", true); + + // Get the value out of the property first + double efixed = getProperty("Efixed"); + if ( isEmpty(efixed) ) efixed = MASK_FLAG; + // Now lets check to see if the workspace nows better. + // TODO: Check that this is the way round we want to do it. + const API::Run & run = inputWS->run(); + if (run.hasProperty("Ei")) + { + Kernel::Property* propEi = run.getProperty("Ei"); + efixed = boost::lexical_cast(propEi->value()); + } + nxFile.writeData("fixed_energy", efixed); + nxFile.openData("fixed_energy"); + nxFile.putAttr("units", "meV"); + nxFile.closeData(); + + double psi = getProperty("Psi"); + if ( isEmpty(psi) ) psi = MASK_FLAG; + nxFile.writeData("psi", psi); + nxFile.openData("psi"); + nxFile.putAttr("units", "degrees"); + nxFile.closeData(); + + bool kikfScaling = getProperty("KiOverKfScaling"); + if (kikfScaling) + { + nxFile.writeData("ki_over_kf_scaling", 1); + } + else + { + nxFile.writeData("ki_over_kf_scaling", 0); + } + + nxFile.closeGroup(); // NXSPE_info + + // NXinstrument + nxFile.makeGroup("instrument", "NXinstrument", true); + // Write the instrument name + nxFile.writeData("name", inputWS->getInstrument()->getName()); + // and the short name + nxFile.openData("name"); + // TODO: Get the instrument short name + nxFile.putAttr("short_name", inputWS->getInstrument()->getName()); + nxFile.closeData(); + + // NXfermi_chopper + nxFile.makeGroup("fermi", "NXfermi_chopper", true); + + nxFile.writeData("energy", efixed); + nxFile.closeGroup(); // NXfermi_chopper + + nxFile.closeGroup(); // NXinstrument + + // NXsample + nxFile.makeGroup("sample", "NXsample", true); + // TODO: Write sample info +// nxFile.writeData("rotation_angle", 0.0); +// nxFile.writeData("seblock", "NONE"); +// nxFile.writeData("temperature", 300.0); + + nxFile.closeGroup(); // NXsample + + // Make the NXdata group + nxFile.makeGroup("data", "NXdata", true); + + // Energy bins + // Get the Energy Axis (X) of the first spectra (they are all the same - checked above) + const MantidVec& X = inputWS->readX(0); + nxFile.writeData("energy", X); + nxFile.openData("energy"); + nxFile.putAttr("units", "meV"); + nxFile.closeData(); + + // let's create some blank arrays in the nexus file + + std::vector array_dims; + array_dims.push_back((int)nHist); + array_dims.push_back((int)nBins); + + nxFile.makeData("data", ::NeXus::FLOAT64, array_dims, false); + nxFile.makeData("error", ::NeXus::FLOAT64, array_dims, false); + + // Add the axes attributes to the data + nxFile.openData("data"); + nxFile.putAttr("signal", 1); + nxFile.putAttr("axes", "polar:energy"); + nxFile.closeData(); + + std::vector slab_start; + std::vector slab_size; + + // What size slabs are we going to write... + slab_size.push_back(1); + slab_size.push_back((int64_t)nBins); + + // And let's start at the beginning + slab_start.push_back(0); + slab_start.push_back(0); + + // define the data and error vectors for masked detectors + std::vector masked_data (nBins, MASK_FLAG); + std::vector masked_error (nBins, MASK_ERROR); + + // Create a progress reporting object + Progress progress(this,0,1,100); + const int progStep = (int)(ceil(nHist/100.0)); + Geometry::IDetector_const_sptr det; + // Loop over spectra + for (int i = 0; i < nHist; i++) + { + try{ // detector exist + det =inputWS->getDetector(i); + // Check that we aren't writing a monitor... + if (!det->isMonitor()) + { + Geometry::IDetector_const_sptr det = inputWS->getDetector(i); + + if (!det->isMasked()) + { + // no masking... + // Open the data + nxFile.openData("data"); + slab_start[0] = i; + nxFile.putSlab(const_cast (inputWS->readY(i)), + slab_start, slab_size); + // Close the data + nxFile.closeData(); + + // Open the error + nxFile.openData("error"); + //MantidVec& tmparr = const_cast(inputWS->dataE(i)); + //nxFile.putSlab((void*)(&(tmparr[0])), slab_start, slab_size); + nxFile.putSlab(const_cast (inputWS->readE(i)), + slab_start, slab_size); + // Close the error + nxFile.closeData(); + } + else + { + // Write a masked value... + // Open the data + nxFile.openData("data"); + slab_start[0] = i; + nxFile.putSlab(masked_data, slab_start, slab_size); + // Close the data + nxFile.closeData(); + + // Open the error + nxFile.openData("error"); + nxFile.putSlab(masked_error, slab_start, slab_size); + // Close the error + nxFile.closeData(); + } + } + }catch(Exception::NotFoundError&) + { + // Catch if no detector. Next line tests whether this happened - test placed + // outside here because Mac Intel compiler doesn't like 'continue' in a catch + // in an openmp block. + } + // If no detector found, skip onto the next spectrum + if ( !det ) continue; + + // make regular progress reports and check for canceling the algorithm + if ( i % progStep == 0 ) + { + progress.report(); + } + } + // execute the ChildAlgorithm to calculate the detector's parameters; + IAlgorithm_sptr spCalcDetPar = this->createChildAlgorithm("FindDetectorsPar", 0, 1, true, 1); + + spCalcDetPar->initialize(); + spCalcDetPar->setPropertyValue("InputWorkspace", inputWS->getName()); + std::string parFileName = this->getPropertyValue("ParFile"); + if(!(parFileName.empty()||parFileName=="not_used.par")){ + spCalcDetPar->setPropertyValue("ParFile",parFileName); + } + spCalcDetPar->execute(); + + // + FindDetectorsPar * pCalcDetPar = dynamic_cast(spCalcDetPar.get()); + if(!pCalcDetPar){ // "can not get pointer to FindDetectorsPar algorithm" + throw(std::bad_cast()); + } + const std::vector & azimuthal = pCalcDetPar->getAzimuthal(); + const std::vector & polar = pCalcDetPar->getPolar(); + const std::vector & azimuthal_width = pCalcDetPar->getAzimWidth(); + const std::vector & polar_width = pCalcDetPar->getPolarWidth(); + const std::vector & secondary_flightpath= pCalcDetPar->getFlightPath(); + + + // Write the Polar (2Theta) angles + nxFile.writeData("polar", polar); + + // Write the Azimuthal (phi) angles + nxFile.writeData("azimuthal", azimuthal); + + // Now the widths... + nxFile.writeData("polar_width", polar_width); + nxFile.writeData("azimuthal_width", azimuthal_width); + + // Secondary flight path + nxFile.writeData("distance", secondary_flightpath); + + nxFile.closeGroup(); // NXdata + + nxFile.closeGroup(); // Top level NXentry + } + + } // namespace DataHandling +} // namespace Mantid diff --git a/Test/AutoTestData/UsageData/GEM_Definition.vtp b/Test/AutoTestData/UsageData/GEM_Definition.vtp new file 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0.000787518 0.0588542 0.01 -0.00434413 0.117509 0.01 -0.0128776 0.175767 0 0.000787518 0.0588542 0 -0.00434413 0.117509 0 + + + 0 3 2 1 0 2 7 4 5 16 7 5 17 8 7 17 7 16 6 8 17 13 6 17 10 6 13 14 10 13 15 11 10 15 10 14 12 9 11 12 11 15 21 19 18 21 18 24 22 24 25 22 21 24 20 25 23 20 22 25 29 26 27 38 29 27 39 30 29 39 29 38 28 30 39 35 28 39 32 28 35 36 32 35 37 33 32 37 32 36 34 31 33 34 33 37 43 41 40 43 40 46 44 46 47 44 43 46 42 47 45 42 44 47 51 49 48 51 48 54 52 54 55 52 51 54 50 55 53 50 52 55 56 59 58 57 56 58 63 61 60 63 60 66 64 66 67 64 63 66 62 67 65 62 64 67 + 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 117 120 123 126 129 132 135 138 141 144 147 150 153 156 + + + + + + + + + + + + + + + + + + + + + + From f1b69a795ee41c7b227386fc10bcfb1c4d2f562c Mon Sep 17 00:00:00 2001 From: John Hill Date: Wed, 24 Sep 2014 16:47:59 +0100 Subject: [PATCH 14/52] Refs #10194 basic implementation of nxtomo file saving alg --- .../inc/MantidDataHandling/SaveNXTomo.h | 51 ++-- .../Framework/DataHandling/src/SaveNXTomo.cpp | 229 +++++++++--------- 2 files changed, 137 insertions(+), 143 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 644ca2f8abdf..464f8d839495 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -4,12 +4,7 @@ //--------------------------------------------------- // Includes //--------------------------------------------------- -//#include "MantidAPI/Algorithm.h" //#include "MantidNexus/NexusClasses.h" -//#include "MantidAPI/MatrixWorkspace.h" -//#include "MantidAPI/Sample.h" -//#include "MantidDataObjects/Workspace2D.h" -//#include "MantidDataObjects/EventWorkspace.h" //#include //#include @@ -20,6 +15,7 @@ namespace Mantid /** * Saves a workspace into a NeXus/HDF5 NXTomo file. + * File format is defined here: http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html * * Required properties: *
        @@ -53,49 +49,44 @@ namespace Mantid class DLLExport SaveNXTomo: public API::Algorithm { public: - /// Constructor SaveNXTomo(); /// Virtual dtor - virtual ~SaveNXTomo() - { - } - virtual const std::string name() const - { - return "SaveNXTomo"; - } + virtual ~SaveNXTomo() {} + + /// Algorithm's name for identification overriding a virtual method + virtual const std::string name() const { return "SaveNXTomo"; } + ///Summary of algorithms purpose virtual const std::string summary() const {return "Writes a MatrixWorkspace to a file in the NXTomo format.";} /// Algorithm's version - virtual int version() const - { - return (1); - } + virtual int version() const { return (1); } + /// Algorithm's category for identification - virtual const std::string category() const - { - return "DataHandling\\Nexus;DataHandling\\Tomo;Diffraction"; - } + virtual const std::string category() const { return "DataHandling\\Nexus;DataHandling\\Tomo;Diffraction"; } - private: - + private: /// Initialisation code void init(); - ///Execution code + /// Execution code void exec(); + /// Save all data to file + + /// Save batch of images to the file + ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change - //size_t nBins; + size_t m_nBins; /// The filename of the output file - //std::string filename; + std::string m_filename; // Some constants to be written for masked values. /// Value for data if pixel is masked - //static const double MASK_FLAG; + static const double MASK_FLAG; /// Value for error if pixel is masked - //static const double MASK_ERROR; - /// file format version - //static const std::string NXSPE_VER; + static const double MASK_ERROR; + /// file format version + static const std::string NXTOMO_VER; }; } // namespace DataHandling diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 3a053edfa273..51c5f256d435 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -1,28 +1,24 @@ -#include "MantidDataHandling/SaveNXTomo.h" #include "MantidAPI/FileProperty.h" -//#include "MantidKernel/ConfigService.h" -#include "MantidKernel/MantidVersion.h" #include "MantidAPI/WorkspaceValidators.h" -//#include "MantidAPI/WorkspaceOpOverloads.h" -//#include "MantidGeometry/Instrument/Detector.h" -//#include "MantidGeometry/Instrument/ObjComponent.h" -//#include "MantidDataHandling/FindDetectorsPar.h" -// -//#include -//#include -//#include +#include "MantidDataHandling/FindDetectorsPar.h" +#include "MantidDataHandling/SaveNXTomo.h" +#include "MantidKernel/MantidVersion.h" +#include "MantidNexus/NexusClasses.h" namespace Mantid { namespace DataHandling - { - + { // Register the algorithm into the algorithm factory DECLARE_ALGORITHM(SaveNXTomo) using namespace Kernel; using namespace API; + const double SaveNXTomo::MASK_FLAG = std::numeric_limits::quiet_NaN(); + const double SaveNXTomo::MASK_ERROR = 0.0; + const std::string SaveNXTomo::NXTOMO_VER = "2.0"; + SaveNXTomo::SaveNXTomo() : API::Algorithm() { } @@ -33,7 +29,7 @@ namespace Mantid void SaveNXTomo::init() { auto wsValidator = boost::make_shared() ; - wsValidator->add(boost::make_shared("DeltaE")); + //wsValidator->add(boost::make_shared("DeltaE")); wsValidator->add(); wsValidator->add(); @@ -52,7 +48,13 @@ namespace Mantid { // Retrieve the input workspace const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); - + + const std::string workspaceID = inputWS->id(); + + if ((workspaceID.find("Workspace2D") == std::string::npos) && + (workspaceID.find("RebinnedOutput") == std::string::npos)) + throw Exception::NotImplementedError("SaveNexusProcessed passed invalid workspaces. Must be Workspace2D, EventWorkspace, ITableWorkspace, or OffsetsWorkspace."); + // Do the full check for common binning if (!WorkspaceHelpers::commonBoundaries(inputWS)) { @@ -63,98 +65,88 @@ namespace Mantid // Number of spectra const int nHist = static_cast(inputWS->getNumberHistograms()); // Number of energy bins - this->nBins = inputWS->blocksize(); + this->m_nBins = inputWS->blocksize(); // Get a pointer to the sample Geometry::IComponent_const_sptr sample = inputWS->getInstrument()->getSample(); // Retrieve the filename from the properties - this->filename = getPropertyValue("Filename"); + this->m_filename = getPropertyValue("Filename"); - // Create the file. - ::NeXus::File nxFile(this->filename, NXACC_CREATE5); + // Create some arrays for the nexus api to use + std::vector array_dims; + array_dims.push_back((int)nHist); + array_dims.push_back((int)m_nBins); + // Create the file. + ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); + // Make the top level entry (and open it) - nxFile.makeGroup(inputWS->getName(), "NXentry", true); + nxFile.makeGroup("entry1", "NXentry", true); + + // Make a sub-group for the entry to work with DAWN software (and open it) + nxFile.makeGroup("tomo_entry", "NXsubentry", true); + + // Title + nxFile.writeData("title", this->m_filename); + + // Start Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("start_time", ); + + // End Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("end_time", ); // Definition name and version - nxFile.writeData("definition", "NXSPE"); + nxFile.writeData("definition", "NXtomo"); nxFile.openData("definition"); - nxFile.putAttr("version", NXSPE_VER); + nxFile.putAttr("version", NXTOMO_VER); nxFile.closeData(); - // Program name and version + // Originating program name and version nxFile.writeData("program_name", "mantid"); nxFile.openData("program_name"); nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); - nxFile.closeData(); - - // Create NXSPE_info - nxFile.makeGroup("NXSPE_info", "NXcollection", true); - - // Get the value out of the property first - double efixed = getProperty("Efixed"); - if ( isEmpty(efixed) ) efixed = MASK_FLAG; - // Now lets check to see if the workspace nows better. - // TODO: Check that this is the way round we want to do it. - const API::Run & run = inputWS->run(); - if (run.hasProperty("Ei")) - { - Kernel::Property* propEi = run.getProperty("Ei"); - efixed = boost::lexical_cast(propEi->value()); - } - nxFile.writeData("fixed_energy", efixed); - nxFile.openData("fixed_energy"); - nxFile.putAttr("units", "meV"); - nxFile.closeData(); - - double psi = getProperty("Psi"); - if ( isEmpty(psi) ) psi = MASK_FLAG; - nxFile.writeData("psi", psi); - nxFile.openData("psi"); - nxFile.putAttr("units", "degrees"); - nxFile.closeData(); - - bool kikfScaling = getProperty("KiOverKfScaling"); - if (kikfScaling) - { - nxFile.writeData("ki_over_kf_scaling", 1); - } - else - { - nxFile.writeData("ki_over_kf_scaling", 0); - } - - nxFile.closeGroup(); // NXSPE_info + nxFile.closeData(); + // ****************************************** // NXinstrument nxFile.makeGroup("instrument", "NXinstrument", true); - // Write the instrument name + // Write the instrument name | could add short_name attribute to name nxFile.writeData("name", inputWS->getInstrument()->getName()); - // and the short name - nxFile.openData("name"); - // TODO: Get the instrument short name - nxFile.putAttr("short_name", inputWS->getInstrument()->getName()); - nxFile.closeData(); - - // NXfermi_chopper - nxFile.makeGroup("fermi", "NXfermi_chopper", true); - - nxFile.writeData("energy", efixed); - nxFile.closeGroup(); // NXfermi_chopper - + + // detector group - diamond example file contains {data,distance,image_key,x_pixel_size,y_pixel_size} Only adding image_key for now, 0 filled. + nxFile.makeGroup("detector", "NXdetector", true); + std::vector imageKey(array_dims[1],0); + nxFile.writeData("image_key", imageKey); + nxFile.closeGroup(); + + // source group // from diamond file contains {current,energy,name,probe,type} - probe = neutron | x-ray | electron + + nxFile.closeGroup(); // NXinstrument + // ****************************************** // NXsample nxFile.makeGroup("sample", "NXsample", true); // TODO: Write sample info -// nxFile.writeData("rotation_angle", 0.0); -// nxFile.writeData("seblock", "NONE"); -// nxFile.writeData("temperature", 300.0); - + // name + // nxFile.writeData("rotation_angle", 0.0); + // x_translation + // y_translation + // z_translation nxFile.closeGroup(); // NXsample + + // ****************************************** + // Make the NXmonitor group - Holds base beam intensity for each image + // If information is not present, set as 1 + std::vector intensity(array_dims[1],1); + nxFile.makeGroup("control", "NXmonitor", true); + nxFile.writeData("data", intensity); + nxFile.closeGroup(); // NXmonitor + + // ****************************************** // Make the NXdata group nxFile.makeGroup("data", "NXdata", true); @@ -164,37 +156,31 @@ namespace Mantid nxFile.writeData("energy", X); nxFile.openData("energy"); nxFile.putAttr("units", "meV"); - nxFile.closeData(); - - // let's create some blank arrays in the nexus file - - std::vector array_dims; - array_dims.push_back((int)nHist); - array_dims.push_back((int)nBins); + nxFile.closeData(); nxFile.makeData("data", ::NeXus::FLOAT64, array_dims, false); nxFile.makeData("error", ::NeXus::FLOAT64, array_dims, false); // Add the axes attributes to the data - nxFile.openData("data"); - nxFile.putAttr("signal", 1); - nxFile.putAttr("axes", "polar:energy"); - nxFile.closeData(); + //nxFile.openData("data"); + //nxFile.putAttr("signal", 1); + //nxFile.putAttr("axes", "polar:energy"); + //nxFile.closeData(); std::vector slab_start; std::vector slab_size; // What size slabs are we going to write... slab_size.push_back(1); - slab_size.push_back((int64_t)nBins); + slab_size.push_back((int64_t)m_nBins); // And let's start at the beginning slab_start.push_back(0); slab_start.push_back(0); // define the data and error vectors for masked detectors - std::vector masked_data (nBins, MASK_FLAG); - std::vector masked_error (nBins, MASK_ERROR); + std::vector masked_data (m_nBins, MASK_FLAG); + std::vector masked_error (m_nBins, MASK_ERROR); // Create a progress reporting object Progress progress(this,0,1,100); @@ -203,8 +189,9 @@ namespace Mantid // Loop over spectra for (int i = 0; i < nHist; i++) { - try{ // detector exist - det =inputWS->getDetector(i); + try + { // detector exist + det = inputWS->getDetector(i); // Check that we aren't writing a monitor... if (!det->isMonitor()) { @@ -247,7 +234,8 @@ namespace Mantid nxFile.closeData(); } } - }catch(Exception::NotFoundError&) + } + catch(Exception::NotFoundError&) { // Catch if no detector. Next line tests whether this happened - test placed // outside here because Mac Intel compiler doesn't like 'continue' in a catch @@ -263,7 +251,7 @@ namespace Mantid } } // execute the ChildAlgorithm to calculate the detector's parameters; - IAlgorithm_sptr spCalcDetPar = this->createChildAlgorithm("FindDetectorsPar", 0, 1, true, 1); + /* IAlgorithm_sptr spCalcDetPar = this->createChildAlgorithm("FindDetectorsPar", 0, 1, true, 1); spCalcDetPar->initialize(); spCalcDetPar->setPropertyValue("InputWorkspace", inputWS->getName()); @@ -271,37 +259,52 @@ namespace Mantid if(!(parFileName.empty()||parFileName=="not_used.par")){ spCalcDetPar->setPropertyValue("ParFile",parFileName); } - spCalcDetPar->execute(); + spCalcDetPar->execute();*/ // - FindDetectorsPar * pCalcDetPar = dynamic_cast(spCalcDetPar.get()); - if(!pCalcDetPar){ // "can not get pointer to FindDetectorsPar algorithm" - throw(std::bad_cast()); - } - const std::vector & azimuthal = pCalcDetPar->getAzimuthal(); + //FindDetectorsPar * pCalcDetPar = dynamic_cast(spCalcDetPar.get()); + //if(!pCalcDetPar){ // "can not get pointer to FindDetectorsPar algorithm" + // throw(std::bad_cast()); + //} + /* const std::vector & azimuthal = pCalcDetPar->getAzimuthal(); const std::vector & polar = pCalcDetPar->getPolar(); const std::vector & azimuthal_width = pCalcDetPar->getAzimWidth(); const std::vector & polar_width = pCalcDetPar->getPolarWidth(); - const std::vector & secondary_flightpath= pCalcDetPar->getFlightPath(); + const std::vector & secondary_flightpath= pCalcDetPar->getFlightPath();*/ - // Write the Polar (2Theta) angles - nxFile.writeData("polar", polar); + //// Write the Polar (2Theta) angles + //nxFile.writeData("polar", polar); - // Write the Azimuthal (phi) angles - nxFile.writeData("azimuthal", azimuthal); + //// Write the Azimuthal (phi) angles + //nxFile.writeData("azimuthal", azimuthal); - // Now the widths... - nxFile.writeData("polar_width", polar_width); - nxFile.writeData("azimuthal_width", azimuthal_width); + //// Now the widths... + //nxFile.writeData("polar_width", polar_width); + //nxFile.writeData("azimuthal_width", azimuthal_width); - // Secondary flight path - nxFile.writeData("distance", secondary_flightpath); + //// Secondary flight path + //nxFile.writeData("distance", secondary_flightpath); nxFile.closeGroup(); // NXdata + nxFile.closeGroup(); // tomo_entry sub-group + nxFile.closeGroup(); // Top level NXentry + + // Validate the file against the schema + } + //void someRoutineToAddDataToExisting() + //{ + // //TODO: + //} + } // namespace DataHandling } // namespace Mantid + + +// TODO: don't allow a multi-file +// Follow mtd conventions +// Add comments / function descriptions etc \ No newline at end of file From 9a271c65600de7d616078324d88afe14ec7fa6e8 Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 13:51:19 +0100 Subject: [PATCH 15/52] Refs #10194 faster save, output verified with DAWN software --- .../inc/MantidDataHandling/SaveNXTomo.h | 32 +- .../Framework/DataHandling/src/SaveNXTomo.cpp | 645 ++++++++++-------- 2 files changed, 377 insertions(+), 300 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 464f8d839495..13ccba3bb236 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -4,9 +4,10 @@ //--------------------------------------------------- // Includes //--------------------------------------------------- -//#include "MantidNexus/NexusClasses.h" -//#include -//#include +#include "vector" +#include "MantidGeometry/Instrument/RectangularDetector.h" + +using Mantid::Geometry::RectangularDetector; namespace Mantid { @@ -15,7 +16,7 @@ namespace Mantid /** * Saves a workspace into a NeXus/HDF5 NXTomo file. - * File format is defined here: http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html + * File format is defined here: http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html * * Required properties: *
          @@ -53,7 +54,7 @@ namespace Mantid /// Virtual dtor virtual ~SaveNXTomo() {} - /// Algorithm's name for identification overriding a virtual method + /// Algorithm's name for identification overriding a virtual method virtual const std::string name() const { return "SaveNXTomo"; } ///Summary of algorithms purpose @@ -71,22 +72,31 @@ namespace Mantid /// Execution code void exec(); - /// Save all data to file + /// Save all data to file + + /// Save batch of images to the file + + /// Fetch all rectangular Detector objects defined for an instrument + std::vector getRectangularDetectors(Geometry::Instrument_const_sptr &instrument); + + /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument + void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); - /// Save batch of images to the file + // Number of rows to + size_t m_numberOfRows; ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change - size_t m_nBins; + //size_t m_nBins; /// The filename of the output file - std::string m_filename; + std::string m_filename; // Some constants to be written for masked values. /// Value for data if pixel is masked static const double MASK_FLAG; /// Value for error if pixel is masked static const double MASK_ERROR; - /// file format version - static const std::string NXTOMO_VER; + /// file format version + static const std::string NXTOMO_VER; }; } // namespace DataHandling diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 51c5f256d435..7b79819b9826 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -2,309 +2,376 @@ #include "MantidAPI/WorkspaceValidators.h" #include "MantidDataHandling/FindDetectorsPar.h" #include "MantidDataHandling/SaveNXTomo.h" +#include "MantidGeometry/IComponent.h" #include "MantidKernel/MantidVersion.h" #include "MantidNexus/NexusClasses.h" namespace Mantid { - namespace DataHandling - { - // Register the algorithm into the algorithm factory - DECLARE_ALGORITHM(SaveNXTomo) - - using namespace Kernel; - using namespace API; - - const double SaveNXTomo::MASK_FLAG = std::numeric_limits::quiet_NaN(); - const double SaveNXTomo::MASK_ERROR = 0.0; - const std::string SaveNXTomo::NXTOMO_VER = "2.0"; - - SaveNXTomo::SaveNXTomo() : API::Algorithm() - { - } - - /** - * Initialise the algorithm - */ - void SaveNXTomo::init() - { - auto wsValidator = boost::make_shared() ; - //wsValidator->add(boost::make_shared("DeltaE")); - wsValidator->add(); - wsValidator->add(); - - declareProperty(new WorkspaceProperty ("InputWorkspace", - "", Direction::Input, wsValidator), - "The name of the workspace to save."); - - declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), - "The name of the NXTomo file to write, as a full or relative path"); - } - - /** - * Execute the algorithm - */ - void SaveNXTomo::exec() - { - // Retrieve the input workspace - const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); - - const std::string workspaceID = inputWS->id(); - - if ((workspaceID.find("Workspace2D") == std::string::npos) && - (workspaceID.find("RebinnedOutput") == std::string::npos)) - throw Exception::NotImplementedError("SaveNexusProcessed passed invalid workspaces. Must be Workspace2D, EventWorkspace, ITableWorkspace, or OffsetsWorkspace."); + namespace DataHandling + { + // Register the algorithm into the algorithm factory + DECLARE_ALGORITHM(SaveNXTomo) + + using namespace Kernel; + using namespace API; + using Geometry::RectangularDetector; + + const double SaveNXTomo::MASK_FLAG = std::numeric_limits::quiet_NaN(); + const double SaveNXTomo::MASK_ERROR = 0.0; + const std::string SaveNXTomo::NXTOMO_VER = "2.0"; + + SaveNXTomo::SaveNXTomo() : API::Algorithm() + { + m_filename = ""; + m_numberOfRows = 32; + } + + /** + * Initialise the algorithm + */ + void SaveNXTomo::init() + { + auto wsValidator = boost::make_shared() ; + //wsValidator->add(boost::make_shared("DeltaE")); + wsValidator->add(); + wsValidator->add(); + + declareProperty(new WorkspaceProperty ("InputWorkspace", "", Direction::Input, wsValidator), + "The name of the workspace to save."); + + declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), + "The name of the NXTomo file to write, as a full or relative path"); + + declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), + "Please use an evenly divisible number smaller than the image height"); + } + + /** + * Execute the algorithm + */ + void SaveNXTomo::exec() + { + // Retrieve the input workspace + const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); + + m_numberOfRows = getProperty("Row chunk size"); + + const std::string workspaceID = inputWS->id(); + + if ((workspaceID.find("Workspace2D") == std::string::npos) && + (workspaceID.find("RebinnedOutput") == std::string::npos)) + throw Exception::NotImplementedError("SaveNXTomo passed invalid workspaces. Must be Workspace2D"); + + // Do the full check for common binning + if (!WorkspaceHelpers::commonBoundaries(inputWS)) + { + g_log.error("The input workspace must have common bins"); + throw std::invalid_argument("The input workspace must have common bins"); + } + + // Number of spectra + const int nHist = static_cast(inputWS->getNumberHistograms()); + // Number of energy bins + //this->m_nBins = inputWS->blocksize(); + + // Get a pointer to the sample + //Geometry::IComponent_const_sptr sample = + // inputWS->getInstrument()->getSample(); + + // Retrieve the filename from the properties + this->m_filename = getPropertyValue("Filename"); + + // Dimensions for axis in nxTomo file. + std::vector dims_array; + dims_array.push_back(inputWS->blocksize()); // Number of bins + + // Populate the array + getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument()), dims_array); + + // Create the file. + ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); + + // Make the top level entry (and open it) + nxFile.makeGroup("entry1", "NXentry", true); + + // Make a sub-group for the entry to work with DAWN software (and open it) + nxFile.makeGroup("tomo_entry", "NXsubentry", true); + + // Title + nxFile.writeData("title", this->m_filename); + + // Start Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("start_time", ); + + // End Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("end_time", ); + + // Definition name and version + nxFile.writeData("definition", "NXtomo"); + nxFile.openData("definition"); + nxFile.putAttr("version", NXTOMO_VER); + nxFile.closeData(); + + // Originating program name and version + nxFile.writeData("program_name", "mantid"); + nxFile.openData("program_name"); + nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); + nxFile.closeData(); + + // ****************************************** + // NXinstrument + nxFile.makeGroup("instrument", "NXinstrument", true); + // Write the instrument name | could add short_name attribute to name + nxFile.writeData("name", inputWS->getInstrument()->getName()); + + // detector group - diamond example file contains {data,distance,image_key,x_pixel_size,y_pixel_size} Only adding image_key for now, 0 filled. + nxFile.makeGroup("detector", "NXdetector", true); + std::vector imageKeys(dims_array[0],0); + nxFile.writeData("image_key", imageKeys); + // Create link to image_key + nxFile.openData("image_key"); + NXlink imageKeyLink = nxFile.getDataID(); + nxFile.closeData(); + nxFile.closeGroup(); + + // source group // from diamond file contains {current,energy,name,probe,type} - probe = [neutron | x-ray | electron] + + nxFile.closeGroup(); // NXinstrument + + // ****************************************** + // NXsample + nxFile.makeGroup("sample", "NXsample", true); + // TODO: Write sample info + // name + + std::vector rotationAngles(dims_array[0]); + // Initialise rotations - if unknown, fill with equal steps from 0 to 180 over all frames. + // TODO: collect and use actual rotation values + + double step = static_cast(180/dims_array[0]); + rotationAngles[0] = step; + + for(auto it = rotationAngles.begin()+1; it != rotationAngles.end(); ++it) + { + *it = (*(it-1)) + step; + } + + nxFile.writeData("rotation_angle", rotationAngles); + + // Create a link object for rotation_angle to use later + nxFile.openData("rotation_angle"); + NXlink rotationLink = nxFile.getDataID(); + nxFile.closeData(); + // x_translation + // y_translation + // z_translation + nxFile.closeGroup(); // NXsample + + // ****************************************** + // Make the NXmonitor group - Holds base beam intensity for each image + // If information is not present, set as 1 + + std::vector intensity(dims_array[0],1); + nxFile.makeGroup("control", "NXmonitor", true); + nxFile.writeData("data", intensity); + nxFile.closeGroup(); // NXmonitor + + nxFile.makeGroup("data", "NXdata", true); + + nxFile.makeLink(rotationLink); + + nxFile.makeData("data", ::NeXus::FLOAT64, dims_array, false); + nxFile.makeData("error", ::NeXus::FLOAT64, dims_array, false); + + std::vector slabStart; + std::vector slabSize; + + // What size slabs are we going to write + slabSize.push_back(dims_array[0]); + slabSize.push_back((int64_t)dims_array[1]); + slabSize.push_back((int64_t)m_numberOfRows); + + // Init start to first row + slabStart.push_back(0); + slabStart.push_back(0); + slabStart.push_back(0); + + // define the data and error vectors for masked detectors + std::vector masked_data (dims_array[0], MASK_FLAG); + std::vector masked_error (dims_array[0], MASK_ERROR); + + // Create a progress reporting object + Progress progress(this,0,1,100); + const int progStep = (int)(ceil(nHist/100.0)); + Geometry::IDetector_const_sptr det; - // Do the full check for common binning - if (!WorkspaceHelpers::commonBoundaries(inputWS)) - { - g_log.error("The input workspace must have common bins"); - throw std::invalid_argument("The input workspace must have common bins"); - } - - // Number of spectra - const int nHist = static_cast(inputWS->getNumberHistograms()); - // Number of energy bins - this->m_nBins = inputWS->blocksize(); - - // Get a pointer to the sample - Geometry::IComponent_const_sptr sample = - inputWS->getInstrument()->getSample(); - - // Retrieve the filename from the properties - this->m_filename = getPropertyValue("Filename"); - - // Create some arrays for the nexus api to use - std::vector array_dims; - array_dims.push_back((int)nHist); - array_dims.push_back((int)m_nBins); - - // Create the file. - ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); - - // Make the top level entry (and open it) - nxFile.makeGroup("entry1", "NXentry", true); + double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + double *errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - // Make a sub-group for the entry to work with DAWN software (and open it) - nxFile.makeGroup("tomo_entry", "NXsubentry", true); + int currY = 0; + int rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab - // Title - nxFile.writeData("title", this->m_filename); - - // Start Time; Format ISO8601 | unused but part of NXtomo schema - //nxFile.writeData("start_time", ); - - // End Time; Format ISO8601 | unused but part of NXtomo schema - //nxFile.writeData("end_time", ); - - // Definition name and version - nxFile.writeData("definition", "NXtomo"); - nxFile.openData("definition"); - nxFile.putAttr("version", NXTOMO_VER); - nxFile.closeData(); - - // Originating program name and version - nxFile.writeData("program_name", "mantid"); - nxFile.openData("program_name"); - nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); - nxFile.closeData(); - - // ****************************************** - // NXinstrument - nxFile.makeGroup("instrument", "NXinstrument", true); - // Write the instrument name | could add short_name attribute to name - nxFile.writeData("name", inputWS->getInstrument()->getName()); - - // detector group - diamond example file contains {data,distance,image_key,x_pixel_size,y_pixel_size} Only adding image_key for now, 0 filled. - nxFile.makeGroup("detector", "NXdetector", true); - std::vector imageKey(array_dims[1],0); - nxFile.writeData("image_key", imageKey); - nxFile.closeGroup(); - - // source group // from diamond file contains {current,energy,name,probe,type} - probe = neutron | x-ray | electron - - - nxFile.closeGroup(); // NXinstrument - - // ****************************************** - // NXsample - nxFile.makeGroup("sample", "NXsample", true); - // TODO: Write sample info - // name - // nxFile.writeData("rotation_angle", 0.0); - // x_translation - // y_translation - // z_translation - nxFile.closeGroup(); // NXsample - - // ****************************************** - // Make the NXmonitor group - Holds base beam intensity for each image - // If information is not present, set as 1 - - std::vector intensity(array_dims[1],1); - nxFile.makeGroup("control", "NXmonitor", true); - nxFile.writeData("data", intensity); - nxFile.closeGroup(); // NXmonitor - - // ****************************************** - // Make the NXdata group - nxFile.makeGroup("data", "NXdata", true); - - // Energy bins - // Get the Energy Axis (X) of the first spectra (they are all the same - checked above) - const MantidVec& X = inputWS->readX(0); - nxFile.writeData("energy", X); - nxFile.openData("energy"); - nxFile.putAttr("units", "meV"); - nxFile.closeData(); - - nxFile.makeData("data", ::NeXus::FLOAT64, array_dims, false); - nxFile.makeData("error", ::NeXus::FLOAT64, array_dims, false); - - // Add the axes attributes to the data - //nxFile.openData("data"); - //nxFile.putAttr("signal", 1); - //nxFile.putAttr("axes", "polar:energy"); - //nxFile.closeData(); - - std::vector slab_start; - std::vector slab_size; - - // What size slabs are we going to write... - slab_size.push_back(1); - slab_size.push_back((int64_t)m_nBins); - - // And let's start at the beginning - slab_start.push_back(0); - slab_start.push_back(0); - - // define the data and error vectors for masked detectors - std::vector masked_data (m_nBins, MASK_FLAG); - std::vector masked_error (m_nBins, MASK_ERROR); - - // Create a progress reporting object - Progress progress(this,0,1,100); - const int progStep = (int)(ceil(nHist/100.0)); - Geometry::IDetector_const_sptr det; - // Loop over spectra - for (int i = 0; i < nHist; i++) - { + // Loop over detectors + for (size_t i = 0; i < nHist; ++i) + { try - { // detector exist - det = inputWS->getDetector(i); - // Check that we aren't writing a monitor... - if (!det->isMonitor()) + { + // detector exist + //det = inputWS->getDetector(i); + // Check that we aren't writing a monitor + //if (!det->isMonitor()) + //{ + //Geometry::IDetector_const_sptr det = inputWS->getDetector(i); + + // Figure out where this pixel is supposed to be going and set the correct slab start. + const MantidVec *y = &inputWS->readY(i); + + if(i!=0 && (i)%dims_array[1] == 0){ // When this iteration matches end of a row + currY += 1; + } + size_t currX = (i) - (currY*dims_array[1]); + + const MantidVec & thisY = inputWS->readY(i); + // No masking - Set the data and error as is + for(int j=0; jisMasked()) + // { + dataArr[currInd] = thisY.at(j); + errorArr[currInd] = inputWS->readE(i).at(j); + //} + //else + //{ + // dataArr[currInd] = masked_data[j]; + // errorArr[currInd] = masked_error[j]; + //} + } + + // If end of the row has been reached, check for end of slab and write data/error + if(((i+1)%dims_array[2]) == 0) { - Geometry::IDetector_const_sptr det = inputWS->getDetector(i); - - if (!det->isMasked()) - { - // no masking... - // Open the data - nxFile.openData("data"); - slab_start[0] = i; - nxFile.putSlab(const_cast (inputWS->readY(i)), - slab_start, slab_size); - // Close the data - nxFile.closeData(); + rowIndForSlab += 1; - // Open the error - nxFile.openData("error"); - //MantidVec& tmparr = const_cast(inputWS->dataE(i)); - //nxFile.putSlab((void*)(&(tmparr[0])), slab_start, slab_size); - nxFile.putSlab(const_cast (inputWS->readE(i)), - slab_start, slab_size); - // Close the error + // if a slab has been collected. Put it into the file + if(rowIndForSlab >= m_numberOfRows) + { + slabStart[2] = currY-(rowIndForSlab-1); + + // Write Data + nxFile.openData("data"); + nxFile.putSlab(dataArr, slabStart, slabSize); nxFile.closeData(); - } - else - { - // Write a masked value... - // Open the data - nxFile.openData("data"); - slab_start[0] = i; - nxFile.putSlab(masked_data, slab_start, slab_size); - // Close the data - nxFile.closeData(); - - // Open the error - nxFile.openData("error"); - nxFile.putSlab(masked_error, slab_start, slab_size); - // Close the error + // Write Error + nxFile.openData("error"); + nxFile.putSlab(errorArr, slabStart, slabSize); nxFile.closeData(); + + // Reset slab index count + rowIndForSlab = 0; } - } - } - catch(Exception::NotFoundError&) - { - // Catch if no detector. Next line tests whether this happened - test placed - // outside here because Mac Intel compiler doesn't like 'continue' in a catch - // in an openmp block. - } - // If no detector found, skip onto the next spectrum - if ( !det ) continue; - - // make regular progress reports and check for canceling the algorithm - if ( i % progStep == 0 ) - { - progress.report(); - } - } - // execute the ChildAlgorithm to calculate the detector's parameters; - /* IAlgorithm_sptr spCalcDetPar = this->createChildAlgorithm("FindDetectorsPar", 0, 1, true, 1); - - spCalcDetPar->initialize(); - spCalcDetPar->setPropertyValue("InputWorkspace", inputWS->getName()); - std::string parFileName = this->getPropertyValue("ParFile"); - if(!(parFileName.empty()||parFileName=="not_used.par")){ - spCalcDetPar->setPropertyValue("ParFile",parFileName); - } - spCalcDetPar->execute();*/ - - // - //FindDetectorsPar * pCalcDetPar = dynamic_cast(spCalcDetPar.get()); - //if(!pCalcDetPar){ // "can not get pointer to FindDetectorsPar algorithm" - // throw(std::bad_cast()); - //} - /* const std::vector & azimuthal = pCalcDetPar->getAzimuthal(); - const std::vector & polar = pCalcDetPar->getPolar(); - const std::vector & azimuthal_width = pCalcDetPar->getAzimWidth(); - const std::vector & polar_width = pCalcDetPar->getPolarWidth(); - const std::vector & secondary_flightpath= pCalcDetPar->getFlightPath();*/ - - - //// Write the Polar (2Theta) angles - //nxFile.writeData("polar", polar); - - //// Write the Azimuthal (phi) angles - //nxFile.writeData("azimuthal", azimuthal); - - //// Now the widths... - //nxFile.writeData("polar_width", polar_width); - //nxFile.writeData("azimuthal_width", azimuthal_width); - - //// Secondary flight path - //nxFile.writeData("distance", secondary_flightpath); - - nxFile.closeGroup(); // NXdata - - nxFile.closeGroup(); // tomo_entry sub-group - - nxFile.closeGroup(); // Top level NXentry - - // Validate the file against the schema - - } - - //void someRoutineToAddDataToExisting() - //{ - // //TODO: - //} - - } // namespace DataHandling + } + } + catch(Exception::NotFoundError&) + { + /*Catch if no detector. Next line tests whether this happened - test placed + outside here because Mac Intel compiler doesn't like 'continue' in a catch + in an openmp block.*/ + } + // If no detector found, skip onto the next spectrum + if ( !det ) continue; + + // Make regular progress reports and check for canceling the algorithm + if ( i % progStep == 0 ) + { + progress.report(); + } + } + + // Create a link object for the data + nxFile.openData("data"); + NXlink dataLink = nxFile.getDataID(); + nxFile.closeData(); + + nxFile.closeGroup(); // Close Data group + + // Put a link to the data in instrument/detector + nxFile.openGroup("instrument","NXinstrument"); + nxFile.openGroup("detector","NXdetector"); + nxFile.makeLink(dataLink); + nxFile.closeGroup(); + nxFile.closeGroup(); + + + nxFile.closeGroup(); // tomo_entry sub-group + nxFile.closeGroup(); // Top level NXentry + + // Clean up memory + delete [] dataArr; + delete [] errorArr; + } + + /** + * Find all RectangularDetector objects in an instrument + * @param instrument instrument to search for detectors in + * @returns vector of all Rectangular Detectors + */ + std::vector SaveNXTomo::getRectangularDetectors(Geometry::Instrument_const_sptr &instrument) + { + std::vector> components; + instrument->getChildren(components,true); + + std::vector rectDetectors; + + for(auto it = components.begin(); it != components.end(); ++it) + { + // for all components, compare to RectangularDetector - if it is one, add it to detectors list. + const Geometry::IComponent* c = dynamic_cast(&(**it)); + + if(const RectangularDetector* r = dynamic_cast(c)) + { + rectDetectors.push_back(*(dynamic_cast(&(**it)))); + } + } + + return rectDetectors; + } + + /** + * Populates the dimensions vector with number of files, x and y sizes from a specified rectangular detector + * @param rectDetectors List of rectangular detectors to get axis sizes from + * @param dims_array vector which is populated with the different dimension values for the nxTomo file + * @param useDetectorIndex index of the detector to select from the list, default = 0 + * + * @throw runtime_error Thrown if there are no rectangular detectors + */ + void SaveNXTomo::getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) + { + // Add number of pixels in X and Y from instrument definition + // Throws if no rectangular detector is present. + + if(rectDetectors.size() != 0) + { + // Assume the first rect detector is the desired one. + dims_array.push_back(rectDetectors[useDetectorIndex].xpixels()); + dims_array.push_back(rectDetectors[useDetectorIndex].ypixels()); + } + else + { + // Incorrect workspace : requires the x/y pixel count from the instrument definition + g_log.error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); + throw std::runtime_error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); + } + } + + //void someRoutineToAddDataToExisting() + //{ + // //TODO: + //} + + } // namespace DataHandling } // namespace Mantid -// TODO: don't allow a multi-file -// Follow mtd conventions -// Add comments / function descriptions etc \ No newline at end of file From 4fc0666d294fe2383654b4b4a65315d044635c1a Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 15:06:33 +0100 Subject: [PATCH 16/52] Refs #10194 attempting to fix build error --- .../inc/MantidDataHandling/SaveNXTomo.h | 8 +- .../Framework/DataHandling/src/SaveNXTomo.cpp | 187 +++++++++--------- 2 files changed, 96 insertions(+), 99 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 13ccba3bb236..219aca172721 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -7,8 +7,6 @@ #include "vector" #include "MantidGeometry/Instrument/RectangularDetector.h" -using Mantid::Geometry::RectangularDetector; - namespace Mantid { namespace DataHandling @@ -77,12 +75,12 @@ namespace Mantid /// Save batch of images to the file /// Fetch all rectangular Detector objects defined for an instrument - std::vector getRectangularDetectors(Geometry::Instrument_const_sptr &instrument); + std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); + void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); - // Number of rows to + // Number of rows to size_t m_numberOfRows; ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 7b79819b9826..38d35ca0737b 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -24,7 +24,7 @@ namespace Mantid SaveNXTomo::SaveNXTomo() : API::Algorithm() { m_filename = ""; - m_numberOfRows = 32; + m_numberOfRows = 32; } /** @@ -38,13 +38,13 @@ namespace Mantid wsValidator->add(); declareProperty(new WorkspaceProperty ("InputWorkspace", "", Direction::Input, wsValidator), - "The name of the workspace to save."); + "The name of the workspace to save."); declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), "The name of the NXTomo file to write, as a full or relative path"); - declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), - "Please use an evenly divisible number smaller than the image height"); + declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), + "Please use an evenly divisible number smaller than the image height"); } /** @@ -55,7 +55,7 @@ namespace Mantid // Retrieve the input workspace const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); - m_numberOfRows = getProperty("Row chunk size"); + m_numberOfRows = getProperty("Row chunk size"); const std::string workspaceID = inputWS->id(); @@ -71,7 +71,7 @@ namespace Mantid } // Number of spectra - const int nHist = static_cast(inputWS->getNumberHistograms()); + const size_t nHist = inputWS->getNumberHistograms(); // Number of energy bins //this->m_nBins = inputWS->blocksize(); @@ -84,7 +84,7 @@ namespace Mantid // Dimensions for axis in nxTomo file. std::vector dims_array; - dims_array.push_back(inputWS->blocksize()); // Number of bins + dims_array.push_back(inputWS->blocksize()); // Number of bins // Populate the array getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument()), dims_array); @@ -188,9 +188,9 @@ namespace Mantid std::vector slabSize; // What size slabs are we going to write - slabSize.push_back(dims_array[0]); - slabSize.push_back((int64_t)dims_array[1]); - slabSize.push_back((int64_t)m_numberOfRows); + slabSize.push_back(dims_array[0]); + slabSize.push_back((int64_t)dims_array[1]); + slabSize.push_back((int64_t)m_numberOfRows); // Init start to first row slabStart.push_back(0); @@ -203,91 +203,90 @@ namespace Mantid // Create a progress reporting object Progress progress(this,0,1,100); - const int progStep = (int)(ceil(nHist/100.0)); + const size_t progStep = static_cast(ceil(nHist/100.0)); Geometry::IDetector_const_sptr det; - - double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - double *errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + + double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + double *errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - int currY = 0; - int rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab + int currY = 0; + size_t rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab // Loop over detectors for (size_t i = 0; i < nHist; ++i) { - try - { - // detector exist - //det = inputWS->getDetector(i); - // Check that we aren't writing a monitor - //if (!det->isMonitor()) - //{ - //Geometry::IDetector_const_sptr det = inputWS->getDetector(i); - - // Figure out where this pixel is supposed to be going and set the correct slab start. - const MantidVec *y = &inputWS->readY(i); - - if(i!=0 && (i)%dims_array[1] == 0){ // When this iteration matches end of a row - currY += 1; - } - size_t currX = (i) - (currY*dims_array[1]); - - const MantidVec & thisY = inputWS->readY(i); - // No masking - Set the data and error as is - for(int j=0; jisMasked()) - // { - dataArr[currInd] = thisY.at(j); - errorArr[currInd] = inputWS->readE(i).at(j); - //} - //else - //{ - // dataArr[currInd] = masked_data[j]; - // errorArr[currInd] = masked_error[j]; - //} - } + try + { + // detector exist + //det = inputWS->getDetector(i); + // Check that we aren't writing a monitor + //if (!det->isMonitor()) + //{ + //Geometry::IDetector_const_sptr det = inputWS->getDetector(i); + + // Figure out where this pixel is supposed to be going and set the correct slab start. + + if(i!=0 && (i)%dims_array[1] == 0){ // When this iteration matches end of a row + currY += 1; + } + size_t currX = (i) - (currY*dims_array[1]); + + const MantidVec & thisY = inputWS->readY(i); + // No masking - Set the data and error as is + for(int j=0; jisMasked()) + // { + dataArr[currInd] = thisY.at(j); + errorArr[currInd] = inputWS->readE(i).at(j); + //} + //else + //{ + // dataArr[currInd] = masked_data[j]; + // errorArr[currInd] = masked_error[j]; + //} + } - // If end of the row has been reached, check for end of slab and write data/error - if(((i+1)%dims_array[2]) == 0) - { - rowIndForSlab += 1; - - // if a slab has been collected. Put it into the file - if(rowIndForSlab >= m_numberOfRows) - { - slabStart[2] = currY-(rowIndForSlab-1); - - // Write Data - nxFile.openData("data"); - nxFile.putSlab(dataArr, slabStart, slabSize); - nxFile.closeData(); - // Write Error - nxFile.openData("error"); - nxFile.putSlab(errorArr, slabStart, slabSize); - nxFile.closeData(); - - // Reset slab index count - rowIndForSlab = 0; - } - } - } - catch(Exception::NotFoundError&) - { - /*Catch if no detector. Next line tests whether this happened - test placed - outside here because Mac Intel compiler doesn't like 'continue' in a catch - in an openmp block.*/ - } - // If no detector found, skip onto the next spectrum - if ( !det ) continue; - - // Make regular progress reports and check for canceling the algorithm - if ( i % progStep == 0 ) - { - progress.report(); - } + // If end of the row has been reached, check for end of slab and write data/error + if(((i+1)%dims_array[2]) == 0) + { + rowIndForSlab += 1; + + // if a slab has been collected. Put it into the file + if(rowIndForSlab >= m_numberOfRows) + { + slabStart[2] = currY-(rowIndForSlab-1); + + // Write Data + nxFile.openData("data"); + nxFile.putSlab(dataArr, slabStart, slabSize); + nxFile.closeData(); + // Write Error + nxFile.openData("error"); + nxFile.putSlab(errorArr, slabStart, slabSize); + nxFile.closeData(); + + // Reset slab index count + rowIndForSlab = 0; + } + } + } + catch(Exception::NotFoundError&) + { + /*Catch if no detector. Next line tests whether this happened - test placed + outside here because Mac Intel compiler doesn't like 'continue' in a catch + in an openmp block.*/ + } + // If no detector found, skip onto the next spectrum + if ( !det ) continue; + + // Make regular progress reports and check for canceling the algorithm + if ( i % progStep == 0 ) + { + progress.report(); + } } // Create a link object for the data @@ -308,9 +307,9 @@ namespace Mantid nxFile.closeGroup(); // tomo_entry sub-group nxFile.closeGroup(); // Top level NXentry - // Clean up memory - delete [] dataArr; - delete [] errorArr; + // Clean up memory + delete [] dataArr; + delete [] errorArr; } /** @@ -318,7 +317,7 @@ namespace Mantid * @param instrument instrument to search for detectors in * @returns vector of all Rectangular Detectors */ - std::vector SaveNXTomo::getRectangularDetectors(Geometry::Instrument_const_sptr &instrument) + std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) { std::vector> components; instrument->getChildren(components,true); @@ -329,8 +328,8 @@ namespace Mantid { // for all components, compare to RectangularDetector - if it is one, add it to detectors list. const Geometry::IComponent* c = dynamic_cast(&(**it)); - - if(const RectangularDetector* r = dynamic_cast(c)) + + if(dynamic_cast(c)) { rectDetectors.push_back(*(dynamic_cast(&(**it)))); } From 1dc316fa694c60cace60ab6a1c183e5e802fa0e0 Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 15:48:16 +0100 Subject: [PATCH 17/52] Refs #10194 attempting to fix build error --- .../inc/MantidDataHandling/SaveNXTomo.h | 5 ++- .../Framework/DataHandling/src/SaveNXTomo.cpp | 38 +++++++++++++------ 2 files changed, 30 insertions(+), 13 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 219aca172721..92b1d63c4244 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -78,11 +78,14 @@ namespace Mantid std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); + void getDimensionsFromDetector(const std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); // Number of rows to size_t m_numberOfRows; + // Include error data in the written file + bool m_includeError; + ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change //size_t m_nBins; /// The filename of the output file diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 38d35ca0737b..c648698319e8 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -24,6 +24,7 @@ namespace Mantid SaveNXTomo::SaveNXTomo() : API::Algorithm() { m_filename = ""; + m_includeError = false; m_numberOfRows = 32; } @@ -45,6 +46,9 @@ namespace Mantid declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), "Please use an evenly divisible number smaller than the image height"); + + declareProperty(new PropertyWithValue("Include error", false, Kernel::Direction::Input), + "Write the error values to NXTomo file?"); } /** @@ -56,6 +60,7 @@ namespace Mantid const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); m_numberOfRows = getProperty("Row chunk size"); + m_includeError = getProperty("Include error"); const std::string workspaceID = inputWS->id(); @@ -182,7 +187,8 @@ namespace Mantid nxFile.makeLink(rotationLink); nxFile.makeData("data", ::NeXus::FLOAT64, dims_array, false); - nxFile.makeData("error", ::NeXus::FLOAT64, dims_array, false); + if(m_includeError) + nxFile.makeData("error", ::NeXus::FLOAT64, dims_array, false); std::vector slabStart; std::vector slabSize; @@ -199,15 +205,18 @@ namespace Mantid // define the data and error vectors for masked detectors std::vector masked_data (dims_array[0], MASK_FLAG); - std::vector masked_error (dims_array[0], MASK_ERROR); + if(m_includeError) + std::vector masked_error (dims_array[0], MASK_ERROR); // Create a progress reporting object Progress progress(this,0,1,100); - const size_t progStep = static_cast(ceil(nHist/100.0)); + const size_t progStep = static_cast(ceil(static_cast(nHist)/100.0)); Geometry::IDetector_const_sptr det; double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - double *errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + double *errorArr; + if(m_includeError) + errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; int currY = 0; size_t rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab @@ -240,12 +249,14 @@ namespace Mantid // if(!det->isMasked()) // { dataArr[currInd] = thisY.at(j); - errorArr[currInd] = inputWS->readE(i).at(j); + if(m_includeError) + errorArr[currInd] = inputWS->readE(i).at(j); //} //else //{ // dataArr[currInd] = masked_data[j]; - // errorArr[currInd] = masked_error[j]; + // if(m_includeError) + // errorArr[currInd] = masked_error[j]; //} } @@ -264,10 +275,12 @@ namespace Mantid nxFile.putSlab(dataArr, slabStart, slabSize); nxFile.closeData(); // Write Error - nxFile.openData("error"); - nxFile.putSlab(errorArr, slabStart, slabSize); - nxFile.closeData(); - + if(m_includeError) + { + nxFile.openData("error"); + nxFile.putSlab(errorArr, slabStart, slabSize); + nxFile.closeData(); + } // Reset slab index count rowIndForSlab = 0; } @@ -309,7 +322,8 @@ namespace Mantid // Clean up memory delete [] dataArr; - delete [] errorArr; + if(m_includeError) + delete [] errorArr; } /** @@ -346,7 +360,7 @@ namespace Mantid * * @throw runtime_error Thrown if there are no rectangular detectors */ - void SaveNXTomo::getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) + void SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) { // Add number of pixels in X and Y from instrument definition // Throws if no rectangular detector is present. From c0fd0586d2eafb99c42701e7e3ddf218f8e9a868 Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 17:05:33 +0100 Subject: [PATCH 18/52] Refs #10194 attempting to fix build error --- .../inc/MantidDataHandling/SaveNXTomo.h | 4 +-- .../Framework/DataHandling/src/SaveNXTomo.cpp | 29 ++++++++++--------- 2 files changed, 18 insertions(+), 15 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 92b1d63c4244..59e072ad7878 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -75,10 +75,10 @@ namespace Mantid /// Save batch of images to the file /// Fetch all rectangular Detector objects defined for an instrument - std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); + std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - void getDimensionsFromDetector(const std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); + void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); // Number of rows to size_t m_numberOfRows; diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index c648698319e8..a1d84c7666e2 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -136,7 +136,7 @@ namespace Mantid nxFile.writeData("image_key", imageKeys); // Create link to image_key nxFile.openData("image_key"); - NXlink imageKeyLink = nxFile.getDataID(); + //NXlink imageKeyLink = nxFile.getDataID(); nxFile.closeData(); nxFile.closeGroup(); @@ -206,7 +206,7 @@ namespace Mantid // define the data and error vectors for masked detectors std::vector masked_data (dims_array[0], MASK_FLAG); if(m_includeError) - std::vector masked_error (dims_array[0], MASK_ERROR); + std::vector masked_error (dims_array[0], MASK_ERROR); // Create a progress reporting object Progress progress(this,0,1,100); @@ -214,7 +214,7 @@ namespace Mantid Geometry::IDetector_const_sptr det; double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - double *errorArr; + double *errorArr = NULL; if(m_includeError) errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; @@ -256,15 +256,19 @@ namespace Mantid //{ // dataArr[currInd] = masked_data[j]; // if(m_includeError) - // errorArr[currInd] = masked_error[j]; + // errorArr[currInd] = masked_error[j]; //} } - // If end of the row has been reached, check for end of slab and write data/error + // If end of the row has been reached, check for end of slab (or end of row count) and write data/error if(((i+1)%dims_array[2]) == 0) { rowIndForSlab += 1; + // Check if we have collected all of the rows (prior to completing a slab) - if so, write the final section + // TODO:: + + // if a slab has been collected. Put it into the file if(rowIndForSlab >= m_numberOfRows) { @@ -322,8 +326,7 @@ namespace Mantid // Clean up memory delete [] dataArr; - if(m_includeError) - delete [] errorArr; + delete [] errorArr; } /** @@ -331,12 +334,12 @@ namespace Mantid * @param instrument instrument to search for detectors in * @returns vector of all Rectangular Detectors */ - std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) + std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) { std::vector> components; instrument->getChildren(components,true); - std::vector rectDetectors; + std::vector rectDetectors; for(auto it = components.begin(); it != components.end(); ++it) { @@ -345,7 +348,7 @@ namespace Mantid if(dynamic_cast(c)) { - rectDetectors.push_back(*(dynamic_cast(&(**it)))); + rectDetectors.push_back(dynamic_cast(&(**it))); } } @@ -360,7 +363,7 @@ namespace Mantid * * @throw runtime_error Thrown if there are no rectangular detectors */ - void SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) + void SaveNXTomo::getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) { // Add number of pixels in X and Y from instrument definition // Throws if no rectangular detector is present. @@ -368,8 +371,8 @@ namespace Mantid if(rectDetectors.size() != 0) { // Assume the first rect detector is the desired one. - dims_array.push_back(rectDetectors[useDetectorIndex].xpixels()); - dims_array.push_back(rectDetectors[useDetectorIndex].ypixels()); + dims_array.push_back(rectDetectors[useDetectorIndex]->xpixels()); + dims_array.push_back(rectDetectors[useDetectorIndex]->ypixels()); } else { From 8e79090c0b59997b756c35c427a9563b324f01a0 Mon Sep 17 00:00:00 2001 From: John Hill Date: Tue, 14 Oct 2014 17:59:18 +0100 Subject: [PATCH 19/52] Refs #10194 attempting to fix build error --- .../inc/MantidDataHandling/SaveNXTomo.h | 2 +- .../Framework/DataHandling/src/SaveNXTomo.cpp | 22 ++++++++++++------- 2 files changed, 15 insertions(+), 9 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 59e072ad7878..80e0cacbe038 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -78,7 +78,7 @@ namespace Mantid std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - void getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex = 0); + std::vector getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex = 0); // Number of rows to size_t m_numberOfRows; diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index a1d84c7666e2..c843331981be 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -89,10 +89,12 @@ namespace Mantid // Dimensions for axis in nxTomo file. std::vector dims_array; - dims_array.push_back(inputWS->blocksize()); // Number of bins + + // Populate the array + dims_array = getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument())); - // Populate the array - getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument()), dims_array); + // Insert number of bins at front + dims_array.insert(dims_array.begin(), inputWS->blocksize()); // Number of bins // Create the file. ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); @@ -358,21 +360,23 @@ namespace Mantid /** * Populates the dimensions vector with number of files, x and y sizes from a specified rectangular detector * @param rectDetectors List of rectangular detectors to get axis sizes from - * @param dims_array vector which is populated with the different dimension values for the nxTomo file * @param useDetectorIndex index of the detector to select from the list, default = 0 - * + * @returns vector of both axis dimensions for specified detector + * * @throw runtime_error Thrown if there are no rectangular detectors */ - void SaveNXTomo::getDimensionsFromDetector(std::vector &rectDetectors, std::vector &dims_array, size_t useDetectorIndex) + std::vector SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex) { // Add number of pixels in X and Y from instrument definition // Throws if no rectangular detector is present. + std::vector dims; + if(rectDetectors.size() != 0) { // Assume the first rect detector is the desired one. - dims_array.push_back(rectDetectors[useDetectorIndex]->xpixels()); - dims_array.push_back(rectDetectors[useDetectorIndex]->ypixels()); + dims.push_back(rectDetectors[useDetectorIndex]->xpixels()); + dims.push_back(rectDetectors[useDetectorIndex]->ypixels()); } else { @@ -380,6 +384,8 @@ namespace Mantid g_log.error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); throw std::runtime_error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); } + + return dims; } //void someRoutineToAddDataToExisting() From d2d639c41a71a85b62b4655e1eb504265e7a34ab Mon Sep 17 00:00:00 2001 From: Alex Buts Date: Wed, 15 Oct 2014 13:17:11 +0100 Subject: [PATCH 20/52] refs #10351 This should do it --- Code/Mantid/scripts/Inelastic/dgreduce.py | 30 ++++++++++++----------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/Code/Mantid/scripts/Inelastic/dgreduce.py b/Code/Mantid/scripts/Inelastic/dgreduce.py index fed605942091..b89d69c8b542 100644 --- a/Code/Mantid/scripts/Inelastic/dgreduce.py +++ b/Code/Mantid/scripts/Inelastic/dgreduce.py @@ -45,7 +45,7 @@ def setup(instname=None,reload=False): def help(keyword=None) : """function returns help on reduction parameters. - Returns the list of the parameters availible if provided without arguments + Returns the list of the parameters available if provided without arguments or the description and the default value for the key requested """ if Reducer == None: @@ -54,7 +54,7 @@ def help(keyword=None) : Reducer.help(keyword) -def arb_units(wb_run,sample_run,ei_guess,rebin,map_file='default',monovan_run=None,**kwargs): +def arb_units(wb_run,sample_run,ei_guess,rebin,map_file='default',monovan_run=None,second_wb=None,**kwargs): """ One step conversion of run into workspace containing information about energy transfer Usage: >>arb_units(wb_run,sample_run,ei_guess,rebin) @@ -190,7 +190,10 @@ def arb_units(wb_run,sample_run,ei_guess,rebin,map_file='default',monovan_run=No wb_for_monovanadium = kwargs['wb_for_monovanadium'] del kwargs['wb_for_monovanadium'] else: - wb_for_monovanadium = wb_run; + if second_wb is None: + wb_for_monovanadium = wb_run; + else: + wb_for_monovanadium = second_wb; @@ -256,7 +259,7 @@ def arb_units(wb_run,sample_run,ei_guess,rebin,map_file='default',monovan_run=No #this sums the runs together before passing the summed file to the rest of the reduction #this circumvents the inbuilt method of summing which fails to sum the files for diag - #the D.E.C. tries to be too clever so we have to fool it into thinking the raw file is already exists as a workpsace + #the D.E.C. tries to be too clever so we have to fool it into thinking the raw file is already exists as a workspace sumfilename=Reducer.instr_name+str(sample_run[0])+'.raw' sample_run =sum_files(Reducer.instr_name,sumfilename, sample_run) common.apply_calibration(Reducer.instr_name,sample_run,Reducer.det_cal_file) @@ -291,7 +294,7 @@ def arb_units(wb_run,sample_run,ei_guess,rebin,map_file='default',monovan_run=No if not masks_done: print '########### Run diagnose for sample run ##############################' masking = Reducer.diagnose(wb_run,sample = mask_run, - second_white = None,print_results=True) + second_white=None,print_results=True) header = "Diag Processed workspace with {0:d} spectra and masked {1:d} bad spectra" @@ -412,7 +415,7 @@ def abs_units(wb_for_run,sample_run,monovan_run,wb_for_monovanadium,samp_rmm,sam variation -The number of medians the ratio of the first/second white beam can deviate from the average by (default=1.1) bleed_test - If true then the CreatePSDBleedMask algorithm is run - bleed_maxrate - If the bleed test is on then this is the maximum framerate allowed in a tube + bleed_maxrate - If the bleed test is on then this is the maximum frame rate allowed in a tube bleed_pixels - If the bleed test is on then this is the number of pixels ignored within the bleed test diagnostic print_results - If True then the results are printed to the screen @@ -438,11 +441,10 @@ def abs_units(wb_for_run,sample_run,monovan_run,wb_for_monovanadium,samp_rmm,sam abs_units_van_range=[-40,40] integral range for absolute vanadium data - mono_correction_factor=float User specified correction factor for absolute units normalisation + mono_correction_factor=float User specified correction factor for absolute units normalization """ kwargs['monovan_mapfile'] = monovan_mapfile - kwargs['wb_for_monovanadium']= wb_for_monovanadium kwargs['sample_mass'] = samp_mass kwargs['sample_rmm'] = samp_rmm @@ -462,7 +464,7 @@ def abs_units(wb_for_run,sample_run,monovan_run,wb_for_monovanadium,samp_rmm,sam results_name = wksp_out - wksp_out = arb_units(wb_for_run,sample_run,ei_guess,rebin,map_file,monovan_run,**kwargs) + wksp_out = arb_units(wb_for_run,sample_run,ei_guess,rebin,map_file,monovan_run,wb_for_monovanadium,**kwargs) if results_name != wksp_out.getName(): @@ -522,7 +524,7 @@ def apply_absolute_normalization(Reducer,deltaE_wkspace_sample,monovan_run,ei_gu def process_legacy_parameters(**kwargs) : """ The method to deal with old parameters which have logi c different from default and easy to process using - subprogram. All other parameters just copiet to output + subprogram. All other parameters just copied to output """ params = dict(); for key,value in kwargs.iteritems(): @@ -568,7 +570,7 @@ def get_abs_normalization_factor(Reducer,deltaE_wkspaceName,ei_monovan) : are different and accounted for by dividing each MV value by corresponding WBV value, the signal on a detector has poison distribution and the error for a detector is the square root of correspondent signal on a detector. - Error for WBV considered negligebly small wrt the error on MV + Error for WBV considered negligibly small wrt. the error on MV """ van_mass=Reducer.van_mass; @@ -627,7 +629,7 @@ def get_abs_normalization_factor(Reducer,deltaE_wkspaceName,ei_monovan) : weight = err_sq/signal signal3_sum += err_sq weight3_sum += weight - # Guess which estimatnes value sum(n_i^2/Sigma_i^2)/sum(n_i/Sigma_i^2) TGP suggestion from 12-2012 + # Guess which estimates value sum(n_i^2/Sigma_i^2)/sum(n_i/Sigma_i^2) TGP suggestion from 12-2012 signal4_sum += signal*signal/err_sq weight4_sum += signal/err_sq @@ -638,7 +640,7 @@ def get_abs_normalization_factor(Reducer,deltaE_wkspaceName,ei_monovan) : #---------------- Loop finished if( weight1_sum==0.0 or weight2_sum == 0.0 or weight3_sum == 0.0 or weight4_sum == 0.0) : - print "WB integral has been calculated incorrectrly, look at van_int workspace in the input workspace: ",deltaE_wkspaceName + print "WB integral has been calculated incorrectly, look at van_int workspace in the input workspace: ",deltaE_wkspaceName raise IOError(" divided by 0 weight") integral_monovanLibISIS=signal1_sum / weight1_sum @@ -693,7 +695,7 @@ def get_abs_normalization_factor(Reducer,deltaE_wkspaceName,ei_monovan) : def sum_files(inst_name, accumulator, files): """ Custom sum for multiple runs - Left for compartibility as internal summation had some unspecified problems. + Left for compatibility as internal summation had some unspecified problems. Will go in a future """ accum_name = accumulator From 7450a0f59198821516d50c343eca702c0a019d87 Mon Sep 17 00:00:00 2001 From: Alex Buts Date: Wed, 15 Oct 2014 13:54:38 +0100 Subject: [PATCH 21/52] REFS #10351 a bit more needs to change --- Code/Mantid/scripts/Inelastic/dgreduce.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Code/Mantid/scripts/Inelastic/dgreduce.py b/Code/Mantid/scripts/Inelastic/dgreduce.py index b89d69c8b542..df35acd037bc 100644 --- a/Code/Mantid/scripts/Inelastic/dgreduce.py +++ b/Code/Mantid/scripts/Inelastic/dgreduce.py @@ -332,7 +332,7 @@ def arb_units(wb_run,sample_run,ei_guess,rebin,map_file='default',monovan_run=No # calculate absolute units integral and apply it to the workspace if monovan_run != None or Reducer.mono_correction_factor != None : - deltaE_wkspace_sample = apply_absolute_normalization(Reducer,deltaE_wkspace_sample,monovan_run,ei_guess,wb_run) + deltaE_wkspace_sample = apply_absolute_normalization(Reducer,deltaE_wkspace_sample,monovan_run,ei_guess,wb_for_monovanadium) # Hack for multirep #if isinstance(monovan_run,int): # filename = common.find_file(monovan_run) From bc8a9775c0dc477c8ede7f0c3625c52c8b8c7b35 Mon Sep 17 00:00:00 2001 From: John Hill Date: Wed, 15 Oct 2014 16:50:32 +0100 Subject: [PATCH 22/52] Refs #10194 fixing property name for system test --- Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index c843331981be..99bab4ece30a 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -44,10 +44,10 @@ namespace Mantid declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), "The name of the NXTomo file to write, as a full or relative path"); - declareProperty(new PropertyWithValue("Row chunk size", 32, Kernel::Direction::Input), + declareProperty(new PropertyWithValue("RowChunkSize", 32, Kernel::Direction::Input), "Please use an evenly divisible number smaller than the image height"); - declareProperty(new PropertyWithValue("Include error", false, Kernel::Direction::Input), + declareProperty(new PropertyWithValue("IncludeError", false, Kernel::Direction::Input), "Write the error values to NXTomo file?"); } From 664d2da2bb5f0334802fdff2671b4959ddd1d3e9 Mon Sep 17 00:00:00 2001 From: Federico Montesino Pouzols Date: Thu, 16 Oct 2014 17:46:46 +0100 Subject: [PATCH 23/52] recent files menu added into the main app menu, re #10335 --- .../MantidPlot/src/ApplicationWindow.cpp | 100 ++++++++++++++---- .../Mantid/MantidPlot/src/ApplicationWindow.h | 19 +++- 2 files changed, 96 insertions(+), 23 deletions(-) diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp index 9bef2715e1ac..45b97f127fc0 100644 --- a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp +++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp @@ -551,7 +551,8 @@ void ApplicationWindow::init(bool factorySettings, const QStringList& args) connect(lv, SIGNAL(itemRenamed(Q3ListViewItem *, int, const QString &)), this, SLOT(renameWindow(Q3ListViewItem *, int, const QString &))); - connect(recent, SIGNAL(activated(int)), this, SLOT(openRecentProject(int))); + connect(recentProjectsMenu, SIGNAL(activated(int)), this, SLOT(openRecentProject(int))); + connect(recentFilesMenu, SIGNAL(activated(int)), this, SLOT(openRecentFile(int))); //apply user settings updateAppFonts(); @@ -1155,6 +1156,7 @@ void ApplicationWindow::insertTranslatedStrings() formatToolBar->setWindowTitle(tr("Format")); fileMenu->changeItem(recentMenuID, tr("&Recent Projects")); + fileMenu->changeItem(recentFilesMenuID, tr("R&ecent Files")); translateActionsStrings(); customMenu(activeWindow()); @@ -1166,8 +1168,9 @@ void ApplicationWindow::initMainMenu() fileMenu->setObjectName("fileMenu"); connect(fileMenu, SIGNAL(aboutToShow()), this, SLOT(fileMenuAboutToShow())); - recent = new QMenu(this); newMenu = new QMenu(this); + recentProjectsMenu = new QMenu(this); + recentFilesMenu = new QMenu(this); newMenu->setObjectName("newMenu"); exportPlotMenu = new QMenu(this); exportPlotMenu->setObjectName("exportPlotMenu"); @@ -4461,9 +4464,31 @@ ApplicationWindow* ApplicationWindow::open(const QString& fn, bool factorySettin return app; } +void ApplicationWindow::openRecentFile(int index) +{ + QString fn = recentFilesMenu->text(index); + int pos = fn.find(" ",0); + fn = fn.right(fn.length()-pos-1); + + QFile f(fn); + if (!f.exists()){ + QMessageBox::critical(this, tr("MantidPlot - File Open Error"),//Mantid + tr("The file: %1

          does not exist anymore!" + "

          It will be removed from the list.").arg(fn)); + + recentFiles.remove(fn); + updateRecentFilesList(fn); + return; + } + + loadDataFileByName(fn); + updateRecentFilesList(fn); + saveSettings(); // save new list of recent files +} + void ApplicationWindow::openRecentProject(int index) { - QString fn = recent->text(index); + QString fn = recentProjectsMenu->text(index); int pos = fn.find(" ",0); fn = fn.right(fn.length()-pos-1); @@ -4502,6 +4527,7 @@ void ApplicationWindow::openRecentProject(int index) } } + ApplicationWindow* ApplicationWindow::openProject(const QString& fn, bool factorySettings, bool newProject) { ApplicationWindow *app = this; @@ -5039,6 +5065,7 @@ void ApplicationWindow::readSettings() show_windows_policy = (ShowWindowsPolicy)settings.value("/ShowWindowsPolicy", ApplicationWindow::ActiveFolder).toInt(); recentProjects = settings.value("/RecentProjects").toStringList(); + recentFiles = settings.value("/RecentFiles").toStringList(); //Follows an ugly hack added by Ion in order to fix Qt4 porting issues //(only needed on Windows due to a Qt bug?) #ifdef Q_OS_WIN @@ -5049,9 +5076,18 @@ void ApplicationWindow::readSettings() if (s.remove(QRegExp("\\s")).isEmpty()) recentProjects = QStringList(); } + + if (!recentFiles.isEmpty() && recentFiles[0].contains("^e")) + recentFiles = recentFiles[0].split("^e", QString::SkipEmptyParts); + else if (recentFiles.count() == 1){ + QString s = recentFiles[0]; + if (s.remove(QRegExp("\\s")).isEmpty()) + recentFiles = QStringList(); + } #endif updateRecentProjectsList(); + updateRecentFilesList(); changeAppStyle(settings.value("/Style", appStyle).toString()); autoSave = settings.value("/AutoSave", false).toBool(); @@ -5513,6 +5549,7 @@ void ApplicationWindow::saveSettings() settings.setValue("/Language", appLanguage); settings.setValue("/ShowWindowsPolicy", show_windows_policy); settings.setValue("/RecentProjects", recentProjects); + settings.setValue("/RecentFiles", recentFiles); settings.setValue("/Style", appStyle); settings.setValue("/AutoSave", autoSave); settings.setValue("/AutoSaveTime", autoSaveTime); @@ -6209,7 +6246,7 @@ void ApplicationWindow::savetoNexusFile() savedatainNexusFormat(wsName,fileName.toStdString()); MantidQt::API::AlgorithmInputHistory::Instance().setPreviousDirectory(QFileInfo(fileName).absoluteDir().path()); - + updateRecentFilesList(fileName); } } @@ -6218,18 +6255,27 @@ void ApplicationWindow::loadDataFile() // Ask user for file QString fn = QFileDialog::getOpenFileName( 0, tr("Mantidplot - Open file to load"), AlgorithmInputHistory::Instance().getPreviousDirectory()); if(fn != "") { - QFileInfo fnInfo(fn); - AlgorithmInputHistory::Instance().setPreviousDirectory(fnInfo.absoluteDir().path()); - if( fnInfo.suffix() == "py") - { // We have a python file, just load it into script window - loadScript( fn, true ); - } - else if(mantidUI) - { // Run Load algorithm on file - QHash params; - params["Filename"] = fn; - mantidUI->showAlgorithmDialog(QString("Load"),params); - } + loadDataFileByName(fn); + } + updateRecentFilesList(fn); + saveSettings(); // save new list of recent files +} + +void ApplicationWindow::loadDataFileByName(QString fn) +{ + QFileInfo fnInfo(fn); + AlgorithmInputHistory::Instance().setPreviousDirectory(fnInfo.absoluteDir().path()); + if( fnInfo.suffix() == "py") + { + // We have a python file, just load it into script window + loadScript( fn, true ); + } + else if(mantidUI) + { + // Run Load algorithm on file + QHash params; + params["Filename"] = fn; + mantidUI->showAlgorithmDialog(QString("Load"),params); } } @@ -9280,7 +9326,9 @@ void ApplicationWindow::fileMenuAboutToShow() openMenu->addAction(actionOpenProj); openMenu->addAction(actionLoadFile); - recentMenuID = fileMenu->insertItem(tr("&Recent Projects"), recent); + recentMenuID = fileMenu->insertItem(tr("&Recent Projects"), recentProjectsMenu); + + recentFilesMenuID = fileMenu->insertItem(tr("R&ecent Files"), recentFilesMenu); fileMenu->insertSeparator(); fileMenu->addAction(actionManageDirs); @@ -14438,10 +14486,24 @@ void ApplicationWindow::updateRecentProjectsList() while ((int)recentProjects.size() > MaxRecentProjects) recentProjects.pop_back(); - recent->clear(); + recentProjectsMenu->clear(); for (int i = 0; i<(int)recentProjects.size(); i++ ) - recent->insertItem("&" + QString::number(i+1) + " " + recentProjects[i]); + recentProjectsMenu->insertItem("&" + QString::number(i+1) + " " + recentProjects[i]); +} + +void ApplicationWindow::updateRecentFilesList(QString fname) +{ + if (!fname.isEmpty()) { + recentFiles.remove(fname); + recentFiles.push_front(fname); + } + while ((int)recentFiles.size() > MaxRecentFiles) + recentFiles.pop_back(); + + recentFilesMenu->clear(); + for (int i = 0; i<(int)recentFiles.size(); i++ ) + recentFilesMenu->insertItem("&" + QString::number(i+1) + " " + recentFiles[i]); } void ApplicationWindow::translateCurveHor() diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.h b/Code/Mantid/MantidPlot/src/ApplicationWindow.h index 5de461c6140a..1b3ea9c2f2e3 100644 --- a/Code/Mantid/MantidPlot/src/ApplicationWindow.h +++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.h @@ -213,8 +213,13 @@ public slots: ApplicationWindow* open(const QString& fn, bool factorySettings = false, bool newProject = true); ApplicationWindow* openProject(const QString& fn, bool factorySettings = false, bool newProject = true); ApplicationWindow* importOPJ(const QString& fn, bool factorySettings = false, bool newProject = true); - /// Load mantid data files using generic load algorithm + /// Load mantid data files using generic load algorithm, opening user dialog void loadDataFile(); + /// Load mantid data files (generic load algorithm) + void loadDataFileByName(QString fn); + /// Open from the list of recent files + void openRecentFile(int index); + /** * \brief Create a new project from a data file. * @@ -619,6 +624,7 @@ public slots: Graph3D* openSurfacePlot(ApplicationWindow* app, const QStringList &lst); Graph* openGraph(ApplicationWindow* app, MultiLayer *plot, const QStringList &list); void openRecentProject(int index); + //@} //! \name Table Tools @@ -852,8 +858,12 @@ public slots: void custom3DGrids(int grids); //@} + //! Updates the recent projects list and menu (but doesn't insert anything) void updateRecentProjectsList(); + //! Inserts file name in the list of recent files (if fname not empty) and updates the "recent files" menu + void updateRecentFilesList(QString fname=""); + //! connected to the done(bool) signal of the http object //void receivedVersionFile(bool error); //! called when the user presses the actionCheckUpdates @@ -1279,6 +1289,7 @@ public slots: //! Describes which windows are shown when the folder becomes the current folder ShowWindowsPolicy show_windows_policy; enum {MaxRecentProjects = 10}; + enum {MaxRecentFiles = MaxRecentProjects}; //! File version code used when opening project files (= maj * 100 + min * 10 + patch) int d_file_version; @@ -1327,9 +1338,9 @@ public slots: QColor tableBkgdColor, tableTextColor, tableHeaderColor; QString projectname, columnSeparator, helpFilePath, appLanguage; QString configFilePath, fitPluginsPath, fitModelsPath, asciiDirPath, imagesDirPath, scriptsDirPath; - int ignoredLines, savingTimerId, plot3DResolution, recentMenuID; + int ignoredLines, savingTimerId, plot3DResolution, recentMenuID, recentFilesMenuID; bool renameColumns, strip_spaces, simplify_spaces; - QStringList recentProjects; + QStringList recentProjects, recentFiles; bool saved, showPlot3DProjection, showPlot3DLegend, orthogonal3DPlots, autoscale3DPlots; QStringList plot3DColors, locales; QStringList functions; //user-defined functions; @@ -1413,7 +1424,7 @@ public slots: QWidget* catalogSearch; - QMenu *windowsMenu, *foldersMenu, *view, *graph, *fileMenu, *format, *edit, *recent, *interfaceMenu; + QMenu *windowsMenu, *foldersMenu, *view, *graph, *fileMenu, *format, *edit, *recentProjectsMenu, *recentFilesMenu, *interfaceMenu; QMenu *help, *plot2DMenu, *analysisMenu, *multiPeakMenu, *icat; QMenu *matrixMenu, *plot3DMenu, *plotDataMenu, *tablesDepend, *scriptingMenu; From c8ee45c5625d9517ad484c77eb604c91445ce7fa Mon Sep 17 00:00:00 2001 From: Federico Montesino Pouzols Date: Thu, 16 Oct 2014 18:02:20 +0100 Subject: [PATCH 24/52] a bit shorter lines, re #10335 --- Code/Mantid/MantidPlot/src/ApplicationWindow.h | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.h b/Code/Mantid/MantidPlot/src/ApplicationWindow.h index 1b3ea9c2f2e3..c27bf6582ac3 100644 --- a/Code/Mantid/MantidPlot/src/ApplicationWindow.h +++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.h @@ -1424,7 +1424,8 @@ public slots: QWidget* catalogSearch; - QMenu *windowsMenu, *foldersMenu, *view, *graph, *fileMenu, *format, *edit, *recentProjectsMenu, *recentFilesMenu, *interfaceMenu; + QMenu *windowsMenu, *foldersMenu, *view, *graph, *fileMenu, *format, *edit; + QMenu *recentProjectsMenu, *recentFilesMenu, *interfaceMenu; QMenu *help, *plot2DMenu, *analysisMenu, *multiPeakMenu, *icat; QMenu *matrixMenu, *plot3DMenu, *plotDataMenu, *tablesDepend, *scriptingMenu; From fe546e5affcf34d3a8f4fd23cdc966d3575d9668 Mon Sep 17 00:00:00 2001 From: Raquel Alvarez Banos Date: Fri, 17 Oct 2014 09:15:19 +0100 Subject: [PATCH 25/52] partial spectra loading in LoadEventNexus Re #3878 --- .../inc/MantidDataHandling/LoadEventNexus.h | 10 ++ .../DataHandling/src/LoadEventNexus.cpp | 107 +++++++++++++++++- .../inc/MantidDataObjects/EventWorkspace.h | 2 + .../DataObjects/src/EventWorkspace.cpp | 23 ++++ 4 files changed, 140 insertions(+), 2 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadEventNexus.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadEventNexus.h index 1fb267994473..2fc947dc03c0 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadEventNexus.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadEventNexus.h @@ -142,6 +142,13 @@ namespace DataHandling /// Filter by a maximum time-of-flight double filter_tof_max; + /// Spectra list to load + std::vector m_specList; + /// Minimum spectrum to load + int32_t m_specMin; + /// Maximum spectrum to load + int32_t m_specMax; + /// Filter by start time Kernel::DateAndTime filter_time_start; /// Filter by stop time @@ -245,6 +252,9 @@ namespace DataHandling void filterDuringPause(API::MatrixWorkspace_sptr workspace); + // Validate the optional spectra input properties and initialize m_specList + void createSpectraList(int32_t min, int32_t max); + public: /// name of top level NXentry to use std::string m_top_entry_name; diff --git a/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp b/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp index ef501b221f70..39b6893d61d4 100644 --- a/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp +++ b/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp @@ -168,6 +168,13 @@ namespace DataHandling if (alg->precount) { + + if ( alg->m_specMin !=EMPTY_INT() && alg->m_specMax !=EMPTY_INT() ) + { + m_min_id = alg->m_specMin; + m_max_id = alg->m_specMax; + } + std::vector counts(m_max_id-m_min_id+1, 0); for (size_t i=0; i < numEvents; i++) { @@ -1108,6 +1115,14 @@ namespace DataHandling setPropertyGroup("FilterMonByTimeStart", grp4); setPropertyGroup("FilterMonByTimeStop", grp4); + declareProperty("SpectrumMin",(int32_t)EMPTY_INT(), mustBePositive, + "The number of the first spectrum to read."); + declareProperty("SpectrumMax",(int32_t)EMPTY_INT(), mustBePositive, + "The number of the last spectrum to read."); + declareProperty(new ArrayProperty("SpectrumList"), + "A comma-separated list of individual spectra to read."); + + declareProperty( new PropertyWithValue("MetaDataOnly", false, Direction::Input), "If true, only the meta data and sample logs will be loaded."); @@ -2097,6 +2112,10 @@ void LoadEventNexus::createSpectraMapping(const std::string &nxsfile, const bool monitorsOnly, const std::vector &bankNames) { bool spectramap = false; + m_specMin = getProperty("SpectrumMin"); + m_specMax = getProperty("SpectrumMax"); + m_specList = getProperty("SpectrumList"); + // set up the if( !monitorsOnly && !bankNames.empty() ) { @@ -2137,8 +2156,10 @@ void LoadEventNexus::createSpectraMapping(const std::string &nxsfile, if( !spectramap ) { g_log.debug() << "No custom spectra mapping found, continuing with default 1:1 mapping of spectrum:detectorID\n"; - // The default 1:1 will suffice but exclude the monitors as they are always in a separate workspace - WS->padSpectra(); + auto specList= WS->getInstrument()->getDetectorIDs(true); + createSpectraList(*std::min_element(specList.begin(),specList.end()),*std::max_element(specList.begin(),specList.end())); + // The default 1:1 will suffice but exclude the monitors as they are always in a separate workspace + WS->padSpectra(m_specList); g_log.debug() << "Populated 1:1 spectra map for the whole instrument \n"; } } @@ -2296,6 +2317,26 @@ bool LoadEventNexus::loadSpectraMapping(const std::string& filename, const bool else { g_log.debug() << "Loading only detector spectra from " << filename << "\n"; + + // If optional spectra are provided, if so, m_specList is initialized. spec is used if necessary + createSpectraList(*std::min_element(spec.begin(),spec.end()), *std::max_element(spec.begin(),spec.end())); + + if ( !m_specList.empty() ) { + int i=0; + std::vector spec_temp, udet_temp; + for(auto it=spec.begin(); it!=spec.end(); it++) + { + if ( find(m_specList.begin(),m_specList.end(),*it)!= m_specList.end() ) // spec element *it is not in spec_list + { + spec_temp.push_back( *it ); + udet_temp.push_back( udet.at(i) ); + } + i++; + } + spec=spec_temp; + udet=udet_temp; + } + SpectrumDetectorMapping mapping(spec,udet, monitors); WS->resizeTo(mapping.getMapping().size()); // Make sure spectrum numbers are correct @@ -2691,6 +2732,68 @@ boost::shared_ptr LoadEventNexus::runLoadNexusLogs(const std::st return out; } +/** +* Check the validity of the optional spectrum range/list provided and identify if partial data should be loaded. +* +* @param min :: The minimum spectrum number read from file +* @param max :: The maximum spectrum number read from file +*/ + +void LoadEventNexus::createSpectraList(int32_t min, int32_t max){ + + // check if range [SpectrumMin, SpectrumMax] was supplied + if( m_specMin != EMPTY_INT() || m_specMax != EMPTY_INT() ) + { + if ( m_specMax == EMPTY_INT() ) + { + m_specMax = max; + } + if ( m_specMin == EMPTY_INT() ) + { + m_specMin = min; + } + + if ( m_specMax > max ) + { + throw std::invalid_argument("Inconsistent range property: SpectrumMax is larger than maximum spectrum found in file."); + } + + // Sanity checks for min/max + if ( m_specMin > m_specMax ) + { + throw std::invalid_argument("Inconsistent range property: SpectrumMin is larger than SpectrumMax."); + } + + // Populate spec_list + for (int32_t i=m_specMin; i<=m_specMax; i++) + m_specList.push_back(i); + } + else{ + // Check if SpectrumList was supplied + + if ( !m_specList.empty() ) + { + // Check no negative/zero numbers have been passed + std::vector::iterator itr = std::find_if(m_specList.begin(), m_specList.end(), std::bind2nd(std::less(), 1)); + if( itr != m_specList.end() ) + { + throw std::invalid_argument("Negative/Zero SpectraList property encountered."); + } + + // Check range and set m_specMax to maximum value in m_specList + if ( (m_specMax=*std::max_element(m_specList.begin(),m_specList.end())) > *std::max_element(m_specList.begin(),m_specList.end()) ) + { + throw std::invalid_argument("Inconsistent range property: SpectrumMax is larger than number of spectra."); + } + + // Set m_specMin to minimum value in m_specList + m_specMin=*std::min_element(m_specList.begin(),m_specList.end()); + } + + } + + +} } // namespace DataHandling } // namespace Mantid diff --git a/Code/Mantid/Framework/DataObjects/inc/MantidDataObjects/EventWorkspace.h b/Code/Mantid/Framework/DataObjects/inc/MantidDataObjects/EventWorkspace.h index 50ff948b4a36..01ed2e99ef0f 100644 --- a/Code/Mantid/Framework/DataObjects/inc/MantidDataObjects/EventWorkspace.h +++ b/Code/Mantid/Framework/DataObjects/inc/MantidDataObjects/EventWorkspace.h @@ -152,6 +152,8 @@ class DLLExport EventWorkspace : public API::IEventWorkspace void resizeTo(const std::size_t numSpectra); // Pad pixels in the workspace using the loaded spectra. Requires a non-empty spectra-detector map void padSpectra(); + // Pad pixels in the workspace using specList. Requires a non-empty vector + void padSpectra(const std::vector & specList); // Remove pixels in the workspace that do not contain events. void deleteEmptyLists(); diff --git a/Code/Mantid/Framework/DataObjects/src/EventWorkspace.cpp b/Code/Mantid/Framework/DataObjects/src/EventWorkspace.cpp index 222e78fd56b6..5027c8a023a5 100644 --- a/Code/Mantid/Framework/DataObjects/src/EventWorkspace.cpp +++ b/Code/Mantid/Framework/DataObjects/src/EventWorkspace.cpp @@ -615,6 +615,29 @@ namespace Mantid } } + /** Expands the workspace to a number of spectra corresponding to the number of + * pixels/detectors contained in specList. + * All events lists will be empty after calling this method. + */ + void EventWorkspace::padSpectra(const std::vector & specList) + { + if (specList.empty()) + { + padSpectra(); + } + else + { + resizeTo(specList.size()); + for (size_t i = 0; i < specList.size(); ++i) + { + // specList ranges from 1, ..., N + // detector ranges from 0, ..., N-1 + getSpectrum(i)->setDetectorID(specList[i]-1); + getSpectrum(i)->setSpectrumNo(specList[i]); + } + } + } + void EventWorkspace::deleteEmptyLists() { // figure out how much data to copy From d752c06a0ef063f76eeb3f2566f5d6ef280b5d6c Mon Sep 17 00:00:00 2001 From: Raquel Alvarez Banos Date: Fri, 17 Oct 2014 09:15:24 +0100 Subject: [PATCH 26/52] test partial spectra loading in LoadEventNexus Re #3878 --- .../DataHandling/test/LoadEventNexusTest.h | 35 ++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h b/Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h index 9739246443c0..b6141c3fd555 100644 --- a/Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h +++ b/Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h @@ -218,7 +218,40 @@ class LoadEventNexusTest : public CxxTest::TestSuite TSM_ASSERT("The min TOF in the workspace should be equal to or greater than the filtered cut-off", min >= filterStart); } - void test_Load_And_CompressEvents() + void test_partial_spectra_loading() + { + const std::string wsName = "test_partial_spectra_loading"; + const int specMin = 200; + const int specMax = 2000; + std::vector specList; + specList.push_back(13); + specList.push_back(16); + specList.push_back(21); + specList.push_back(28); + + LoadEventNexus ld; + ld.initialize(); + ld.setPropertyValue("OutputWorkspace", wsName); + ld.setPropertyValue("Filename","CNCS_7860_event.nxs"); + //ld.setProperty("SpectrumMin", specMin); + //ld.setProperty("SpectrumMax", specMax); + ld.setProperty("SpectrumList", specList); + ld.setProperty("LoadLogs", false); // Time-saver + + TS_ASSERT( ld.execute() ); + + auto outWs = AnalysisDataService::Instance().retrieveWS(wsName); + +// TSM_ASSERT("The number of spectra in the workspace should be equal to the spectra filtered", outWs->getNumberHistograms()==specMax-specMin+1); + TSM_ASSERT("The number of spectra in the workspace should be equal to the spectra filtered", outWs->getNumberHistograms()==specList.size()); + TSM_ASSERT("Some spectra were not found in the workspace", outWs->getSpectrum(0)->getSpectrumNo()==13); + TSM_ASSERT("Some spectra were not found in the workspace", outWs->getSpectrum(1)->getSpectrumNo()==16); + TSM_ASSERT("Some spectra were not found in the workspace", outWs->getSpectrum(2)->getSpectrumNo()==21); + TSM_ASSERT("Some spectra were not found in the workspace", outWs->getSpectrum(3)->getSpectrumNo()==28); + + } + + void test_Load_And_CompressEvents() { Mantid::API::FrameworkManager::Instance(); LoadEventNexus ld; From d206e01224d3099b36652d81e8b9f870cfc9ecc4 Mon Sep 17 00:00:00 2001 From: Raquel Alvarez Banos Date: Fri, 17 Oct 2014 09:41:57 +0100 Subject: [PATCH 27/52] formatting LoadEventNexus Re #3878 --- Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp b/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp index 39b6893d61d4..f4a0e0795d1c 100644 --- a/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp +++ b/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp @@ -165,7 +165,6 @@ namespace DataHandling // ---- Pre-counting events per pixel ID ---- auto & outputWS = *(alg->WS); - if (alg->precount) { From 0cf537dc76342ee15e81acf57f498ab06e186e8b Mon Sep 17 00:00:00 2001 From: Raquel Alvarez Banos Date: Fri, 17 Oct 2014 10:01:06 +0100 Subject: [PATCH 28/52] new formatting LoadEventNexus Re #3878 --- Code/Mantid/Framework/DataHandling/src/LoadNexusMonitors.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/Code/Mantid/Framework/DataHandling/src/LoadNexusMonitors.cpp b/Code/Mantid/Framework/DataHandling/src/LoadNexusMonitors.cpp index 7418eaf89e6a..80918d270b23 100644 --- a/Code/Mantid/Framework/DataHandling/src/LoadNexusMonitors.cpp +++ b/Code/Mantid/Framework/DataHandling/src/LoadNexusMonitors.cpp @@ -460,6 +460,7 @@ void LoadNexusMonitors::runLoadLogs(const std::string filename, API::MatrixWorks { // do the actual work API::IAlgorithm_sptr loadLogs = createChildAlgorithm("LoadNexusLogs"); + // Now execute the Child Algorithm. Catch and log any error, but don't stop. try { From 3a687602baf2ec6d371716949b79749fdf492d3f Mon Sep 17 00:00:00 2001 From: Pete Peterson Date: Fri, 17 Oct 2014 15:08:44 -0400 Subject: [PATCH 29/52] Re #10386. Adding name method to class_maker.py --- Code/Mantid/Build/class_maker.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Code/Mantid/Build/class_maker.py b/Code/Mantid/Build/class_maker.py index a129c029385f..4e30ae21084f 100755 --- a/Code/Mantid/Build/class_maker.py +++ b/Code/Mantid/Build/class_maker.py @@ -129,6 +129,8 @@ def write_source(subproject, classname, filename, args): algorithm_source = """ //---------------------------------------------------------------------------------------------- + /// Algorithms name for identification. @see Algorithm::name + const std::string %s::name() const { return "%s"; } /// Algorithm's version for identification. @see Algorithm::version int %s::version() const { return 1;}; @@ -156,7 +158,7 @@ def write_source(subproject, classname, filename, args): // TODO Auto-generated execute stub } -""" % (classname, classname, classname, classname, classname) +""" % (classname, classname, classname, classname, classname, classname, classname) if not args.alg: algorithm_top = "" From dbd38823eaa36629b53387cef82683e40a08bfd9 Mon Sep 17 00:00:00 2001 From: Raquel Alvarez Banos Date: Mon, 20 Oct 2014 09:25:22 +0100 Subject: [PATCH 30/52] LoadEventNexusTest Linux compiler warnings fixed Re #3878 --- Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h | 5 ----- 1 file changed, 5 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h b/Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h index b6141c3fd555..18b9221ff970 100644 --- a/Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h +++ b/Code/Mantid/Framework/DataHandling/test/LoadEventNexusTest.h @@ -221,8 +221,6 @@ class LoadEventNexusTest : public CxxTest::TestSuite void test_partial_spectra_loading() { const std::string wsName = "test_partial_spectra_loading"; - const int specMin = 200; - const int specMax = 2000; std::vector specList; specList.push_back(13); specList.push_back(16); @@ -233,8 +231,6 @@ class LoadEventNexusTest : public CxxTest::TestSuite ld.initialize(); ld.setPropertyValue("OutputWorkspace", wsName); ld.setPropertyValue("Filename","CNCS_7860_event.nxs"); - //ld.setProperty("SpectrumMin", specMin); - //ld.setProperty("SpectrumMax", specMax); ld.setProperty("SpectrumList", specList); ld.setProperty("LoadLogs", false); // Time-saver @@ -242,7 +238,6 @@ class LoadEventNexusTest : public CxxTest::TestSuite auto outWs = AnalysisDataService::Instance().retrieveWS(wsName); -// TSM_ASSERT("The number of spectra in the workspace should be equal to the spectra filtered", outWs->getNumberHistograms()==specMax-specMin+1); TSM_ASSERT("The number of spectra in the workspace should be equal to the spectra filtered", outWs->getNumberHistograms()==specList.size()); TSM_ASSERT("Some spectra were not found in the workspace", outWs->getSpectrum(0)->getSpectrumNo()==13); TSM_ASSERT("Some spectra were not found in the workspace", outWs->getSpectrum(1)->getSpectrumNo()==16); From 642f35743a21a5f467725895c8863c6e9a581262 Mon Sep 17 00:00:00 2001 From: Federico Montesino Pouzols Date: Mon, 20 Oct 2014 14:34:42 +0100 Subject: [PATCH 31/52] updateRecentFiles when loading new files removed from here, re #10335 also improved some error messages --- Code/Mantid/MantidPlot/src/ApplicationWindow.cpp | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp index 45b97f127fc0..ad8a24640adb 100644 --- a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp +++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp @@ -4474,15 +4474,14 @@ void ApplicationWindow::openRecentFile(int index) if (!f.exists()){ QMessageBox::critical(this, tr("MantidPlot - File Open Error"),//Mantid tr("The file: %1

          does not exist anymore!" - "

          It will be removed from the list.").arg(fn)); + "

          It will be removed from the list of recent files.").arg(fn)); recentFiles.remove(fn); - updateRecentFilesList(fn); + updateRecentFilesList(); return; } loadDataFileByName(fn); - updateRecentFilesList(fn); saveSettings(); // save new list of recent files } @@ -4496,7 +4495,7 @@ void ApplicationWindow::openRecentProject(int index) if (!f.exists()){ QMessageBox::critical(this, tr("MantidPlot - File Open Error"),//Mantid tr("The file: %1

          does not exist anymore!" - "

          It will be removed from the list.").arg(fn)); + "

          It will be removed from the list of recent projects.").arg(fn)); recentProjects.remove(fn); updateRecentProjectsList(); @@ -6257,7 +6256,6 @@ void ApplicationWindow::loadDataFile() if(fn != "") { loadDataFileByName(fn); } - updateRecentFilesList(fn); saveSettings(); // save new list of recent files } From ffd6edb88d22b5e294eeb42dae0017fc42f59510 Mon Sep 17 00:00:00 2001 From: John Hill Date: Mon, 20 Oct 2014 15:36:54 +0100 Subject: [PATCH 32/52] Refs #10194 corrected property --- .../inc/MantidDataHandling/SaveNXTomo.h | 176 ++--- .../Framework/DataHandling/src/SaveNXTomo.cpp | 735 +++++++++--------- 2 files changed, 456 insertions(+), 455 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 80e0cacbe038..2058f5dcdddb 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -9,98 +9,98 @@ namespace Mantid { - namespace DataHandling - { - - /** - * Saves a workspace into a NeXus/HDF5 NXTomo file. - * File format is defined here: http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html - * - * Required properties: - *

            - *
          • InputWorkspace - The workspace to save.
            • - *
          • Filename - The filename for output
            • - *
          - * - * @author John R Hill, RAL - * @date 10/09/2014 - * - * 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 . - * - * File change history is stored at: - * Code Documentation is available at: - * - */ - - class DLLExport SaveNXTomo: public API::Algorithm - { - public: - SaveNXTomo(); - /// Virtual dtor - virtual ~SaveNXTomo() {} - - /// Algorithm's name for identification overriding a virtual method - virtual const std::string name() const { return "SaveNXTomo"; } - - ///Summary of algorithms purpose - virtual const std::string summary() const {return "Writes a MatrixWorkspace to a file in the NXTomo format.";} - - /// Algorithm's version - virtual int version() const { return (1); } - - /// Algorithm's category for identification - virtual const std::string category() const { return "DataHandling\\Nexus;DataHandling\\Tomo;Diffraction"; } - - private: - /// Initialisation code - void init(); - /// Execution code - void exec(); - - /// Save all data to file - - /// Save batch of images to the file - - /// Fetch all rectangular Detector objects defined for an instrument - std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); - - /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - std::vector getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex = 0); - - // Number of rows to - size_t m_numberOfRows; + namespace DataHandling + { + + /** + * Saves a workspace into a NeXus/HDF5 NXTomo file. + * File format is defined here: http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html + * + * Required properties: + *
            + *
          • InputWorkspace - The workspace to save.
            • + *
          • Filename - The filename for output
            • + *
          + * + * @author John R Hill, RAL + * @date 10/09/2014 + * + * 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 . + * + * File change history is stored at: + * Code Documentation is available at: + * + */ + + class DLLExport SaveNXTomo: public API::Algorithm + { + public: + SaveNXTomo(); + /// Virtual dtor + virtual ~SaveNXTomo() {} + + /// Algorithm's name for identification overriding a virtual method + virtual const std::string name() const { return "SaveNXTomo"; } + + ///Summary of algorithms purpose + virtual const std::string summary() const {return "Writes a MatrixWorkspace to a file in the NXTomo format.";} + + /// Algorithm's version + virtual int version() const { return (1); } + + /// Algorithm's category for identification + virtual const std::string category() const { return "DataHandling\\Nexus;DataHandling\\Tomo;Diffraction"; } + + private: + /// Initialisation code + void init(); + /// Execution code + void exec(); + + /// Save all data to file + + /// Save batch of images to the file + + /// Fetch all rectangular Detector objects defined for an instrument + std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); + + /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument + std::vector getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex = 0); + + // Number of rows to + size_t m_numberOfRows; // Include error data in the written file bool m_includeError; - ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change - //size_t m_nBins; - /// The filename of the output file - std::string m_filename; - - // Some constants to be written for masked values. - /// Value for data if pixel is masked - static const double MASK_FLAG; - /// Value for error if pixel is masked - static const double MASK_ERROR; - /// file format version - static const std::string NXTOMO_VER; - }; - - } // namespace DataHandling + ///the number of bins in each histogram, as the histogram must have common bins this shouldn't change + //size_t m_nBins; + /// The filename of the output file + std::string m_filename; + + // Some constants to be written for masked values. + /// Value for data if pixel is masked + static const double MASK_FLAG; + /// Value for error if pixel is masked + static const double MASK_ERROR; + /// file format version + static const std::string NXTOMO_VER; + }; + + } // namespace DataHandling } // namespace Mantid #endif // MANTID_DATAHANDLING_SAVENXTOMO_H_ diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index 99bab4ece30a..a1e25e8002ab 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -8,392 +8,393 @@ namespace Mantid { - namespace DataHandling - { - // Register the algorithm into the algorithm factory - DECLARE_ALGORITHM(SaveNXTomo) - - using namespace Kernel; - using namespace API; - using Geometry::RectangularDetector; - - const double SaveNXTomo::MASK_FLAG = std::numeric_limits::quiet_NaN(); - const double SaveNXTomo::MASK_ERROR = 0.0; - const std::string SaveNXTomo::NXTOMO_VER = "2.0"; - - SaveNXTomo::SaveNXTomo() : API::Algorithm() - { - m_filename = ""; - m_includeError = false; - m_numberOfRows = 32; - } - - /** - * Initialise the algorithm - */ - void SaveNXTomo::init() - { - auto wsValidator = boost::make_shared() ; - //wsValidator->add(boost::make_shared("DeltaE")); - wsValidator->add(); - wsValidator->add(); - - declareProperty(new WorkspaceProperty ("InputWorkspace", "", Direction::Input, wsValidator), - "The name of the workspace to save."); - - declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), - "The name of the NXTomo file to write, as a full or relative path"); - - declareProperty(new PropertyWithValue("RowChunkSize", 32, Kernel::Direction::Input), - "Please use an evenly divisible number smaller than the image height"); - - declareProperty(new PropertyWithValue("IncludeError", false, Kernel::Direction::Input), - "Write the error values to NXTomo file?"); - } - - /** - * Execute the algorithm - */ - void SaveNXTomo::exec() - { - // Retrieve the input workspace - const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); - - m_numberOfRows = getProperty("Row chunk size"); - m_includeError = getProperty("Include error"); - - const std::string workspaceID = inputWS->id(); - - if ((workspaceID.find("Workspace2D") == std::string::npos) && - (workspaceID.find("RebinnedOutput") == std::string::npos)) - throw Exception::NotImplementedError("SaveNXTomo passed invalid workspaces. Must be Workspace2D"); - - // Do the full check for common binning - if (!WorkspaceHelpers::commonBoundaries(inputWS)) - { - g_log.error("The input workspace must have common bins"); - throw std::invalid_argument("The input workspace must have common bins"); - } - - // Number of spectra - const size_t nHist = inputWS->getNumberHistograms(); - // Number of energy bins - //this->m_nBins = inputWS->blocksize(); - - // Get a pointer to the sample - //Geometry::IComponent_const_sptr sample = - // inputWS->getInstrument()->getSample(); - - // Retrieve the filename from the properties - this->m_filename = getPropertyValue("Filename"); - - // Dimensions for axis in nxTomo file. - std::vector dims_array; + namespace DataHandling + { + // Register the algorithm into the algorithm factory + DECLARE_ALGORITHM(SaveNXTomo) + + using namespace Kernel; + using namespace API; + using Geometry::RectangularDetector; + + const double SaveNXTomo::MASK_FLAG = std::numeric_limits::quiet_NaN(); + const double SaveNXTomo::MASK_ERROR = 0.0; + const std::string SaveNXTomo::NXTOMO_VER = "2.0"; + + SaveNXTomo::SaveNXTomo() : API::Algorithm() + { + m_filename = ""; + m_includeError = false; + m_numberOfRows = 32; + } + + /** + * Initialise the algorithm + */ + void SaveNXTomo::init() + { + auto wsValidator = boost::make_shared() ; + //wsValidator->add(boost::make_shared("DeltaE")); + wsValidator->add(); + wsValidator->add(); + + declareProperty(new WorkspaceProperty ("InputWorkspace", "", Direction::Input, wsValidator), + "The name of the workspace to save."); + + declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, std::vector(1,".nxs")), + "The name of the NXTomo file to write, as a full or relative path"); + + declareProperty(new PropertyWithValue("RowChunkSize", 32, Kernel::Direction::Input), + "Please use an evenly divisible number smaller than the image height"); + + declareProperty(new PropertyWithValue("IncludeError", false, Kernel::Direction::Input), + "Write the error values to NXTomo file?"); + } + + /** + * Execute the algorithm + */ + void SaveNXTomo::exec() + { + // Retrieve the input workspace + const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace"); + + m_numberOfRows = getProperty("RowChunkSize"); + m_includeError = getProperty("IncludeError"); + + const std::string workspaceID = inputWS->id(); + + if ((workspaceID.find("Workspace2D") == std::string::npos) && + (workspaceID.find("RebinnedOutput") == std::string::npos)) + throw Exception::NotImplementedError("SaveNXTomo passed invalid workspaces. Must be Workspace2D"); + + // Do the full check for common binning + if (!WorkspaceHelpers::commonBoundaries(inputWS)) + { + g_log.error("The input workspace must have common bins"); + throw std::invalid_argument("The input workspace must have common bins"); + } + + // Number of spectra + const size_t nHist = inputWS->getNumberHistograms(); + // Number of energy bins + //this->m_nBins = inputWS->blocksize(); + + // Get a pointer to the sample + //Geometry::IComponent_const_sptr sample = + // inputWS->getInstrument()->getSample(); + + // Retrieve the filename from the properties + this->m_filename = getPropertyValue("Filename"); + + // Dimensions for axis in nxTomo file. + std::vector dims_array; // Populate the array dims_array = getDimensionsFromDetector(getRectangularDetectors(inputWS->getInstrument())); // Insert number of bins at front - dims_array.insert(dims_array.begin(), inputWS->blocksize()); // Number of bins - - // Create the file. - ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); - - // Make the top level entry (and open it) - nxFile.makeGroup("entry1", "NXentry", true); - - // Make a sub-group for the entry to work with DAWN software (and open it) - nxFile.makeGroup("tomo_entry", "NXsubentry", true); - - // Title - nxFile.writeData("title", this->m_filename); - - // Start Time; Format ISO8601 | unused but part of NXtomo schema - //nxFile.writeData("start_time", ); - - // End Time; Format ISO8601 | unused but part of NXtomo schema - //nxFile.writeData("end_time", ); - - // Definition name and version - nxFile.writeData("definition", "NXtomo"); - nxFile.openData("definition"); - nxFile.putAttr("version", NXTOMO_VER); - nxFile.closeData(); - - // Originating program name and version - nxFile.writeData("program_name", "mantid"); - nxFile.openData("program_name"); - nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); - nxFile.closeData(); - - // ****************************************** - // NXinstrument - nxFile.makeGroup("instrument", "NXinstrument", true); - // Write the instrument name | could add short_name attribute to name - nxFile.writeData("name", inputWS->getInstrument()->getName()); - - // detector group - diamond example file contains {data,distance,image_key,x_pixel_size,y_pixel_size} Only adding image_key for now, 0 filled. - nxFile.makeGroup("detector", "NXdetector", true); - std::vector imageKeys(dims_array[0],0); - nxFile.writeData("image_key", imageKeys); - // Create link to image_key - nxFile.openData("image_key"); - //NXlink imageKeyLink = nxFile.getDataID(); - nxFile.closeData(); - nxFile.closeGroup(); - - // source group // from diamond file contains {current,energy,name,probe,type} - probe = [neutron | x-ray | electron] - - nxFile.closeGroup(); // NXinstrument - - // ****************************************** - // NXsample - nxFile.makeGroup("sample", "NXsample", true); - // TODO: Write sample info - // name - - std::vector rotationAngles(dims_array[0]); - // Initialise rotations - if unknown, fill with equal steps from 0 to 180 over all frames. - // TODO: collect and use actual rotation values - - double step = static_cast(180/dims_array[0]); - rotationAngles[0] = step; - - for(auto it = rotationAngles.begin()+1; it != rotationAngles.end(); ++it) - { - *it = (*(it-1)) + step; - } - - nxFile.writeData("rotation_angle", rotationAngles); - - // Create a link object for rotation_angle to use later - nxFile.openData("rotation_angle"); - NXlink rotationLink = nxFile.getDataID(); - nxFile.closeData(); - // x_translation - // y_translation - // z_translation - nxFile.closeGroup(); // NXsample - - // ****************************************** - // Make the NXmonitor group - Holds base beam intensity for each image - // If information is not present, set as 1 - - std::vector intensity(dims_array[0],1); - nxFile.makeGroup("control", "NXmonitor", true); - nxFile.writeData("data", intensity); - nxFile.closeGroup(); // NXmonitor - - nxFile.makeGroup("data", "NXdata", true); - - nxFile.makeLink(rotationLink); - - nxFile.makeData("data", ::NeXus::FLOAT64, dims_array, false); - if(m_includeError) - nxFile.makeData("error", ::NeXus::FLOAT64, dims_array, false); - - std::vector slabStart; - std::vector slabSize; - - // What size slabs are we going to write - slabSize.push_back(dims_array[0]); - slabSize.push_back((int64_t)dims_array[1]); - slabSize.push_back((int64_t)m_numberOfRows); - - // Init start to first row - slabStart.push_back(0); - slabStart.push_back(0); - slabStart.push_back(0); - - // define the data and error vectors for masked detectors - std::vector masked_data (dims_array[0], MASK_FLAG); - if(m_includeError) - std::vector masked_error (dims_array[0], MASK_ERROR); - - // Create a progress reporting object - Progress progress(this,0,1,100); - const size_t progStep = static_cast(ceil(static_cast(nHist)/100.0)); - Geometry::IDetector_const_sptr det; - - double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - double *errorArr = NULL; - if(m_includeError) - errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; - - int currY = 0; - size_t rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab - - // Loop over detectors - for (size_t i = 0; i < nHist; ++i) - { - try - { - // detector exist - //det = inputWS->getDetector(i); - // Check that we aren't writing a monitor - //if (!det->isMonitor()) - //{ - //Geometry::IDetector_const_sptr det = inputWS->getDetector(i); - - // Figure out where this pixel is supposed to be going and set the correct slab start. - - if(i!=0 && (i)%dims_array[1] == 0){ // When this iteration matches end of a row - currY += 1; - } - size_t currX = (i) - (currY*dims_array[1]); - - const MantidVec & thisY = inputWS->readY(i); - // No masking - Set the data and error as is - for(int j=0; jisMasked()) - // { - dataArr[currInd] = thisY.at(j); - if(m_includeError) - errorArr[currInd] = inputWS->readE(i).at(j); - //} - //else - //{ - // dataArr[currInd] = masked_data[j]; - // if(m_includeError) + dims_array.insert(dims_array.begin(), inputWS->blocksize()); // Number of bins + + // Create the file. + ::NeXus::File nxFile(this->m_filename, NXACC_CREATE5); + + // Make the top level entry (and open it) + nxFile.makeGroup("entry1", "NXentry", true); + + // Make a sub-group for the entry to work with DAWN software (and open it) + nxFile.makeGroup("tomo_entry", "NXsubentry", true); + + // Title + nxFile.writeData("title", this->m_filename); + + // Start Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("start_time", ); + + // End Time; Format ISO8601 | unused but part of NXtomo schema + //nxFile.writeData("end_time", ); + + // Definition name and version + nxFile.writeData("definition", "NXtomo"); + nxFile.openData("definition"); + nxFile.putAttr("version", NXTOMO_VER); + nxFile.closeData(); + + // Originating program name and version + nxFile.writeData("program_name", "mantid"); + nxFile.openData("program_name"); + nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version()); + nxFile.closeData(); + + // ****************************************** + // NXinstrument + nxFile.makeGroup("instrument", "NXinstrument", true); + // Write the instrument name | could add short_name attribute to name + nxFile.writeData("name", inputWS->getInstrument()->getName()); + + // detector group - diamond example file contains {data,distance,image_key,x_pixel_size,y_pixel_size} Only adding image_key for now, 0 filled. + nxFile.makeGroup("detector", "NXdetector", true); + std::vector imageKeys(dims_array[0],0); + nxFile.writeData("image_key", imageKeys); + // Create link to image_key + nxFile.openData("image_key"); + //NXlink imageKeyLink = nxFile.getDataID(); + nxFile.closeData(); + nxFile.closeGroup(); + + // source group // from diamond file contains {current,energy,name,probe,type} - probe = [neutron | x-ray | electron] + + nxFile.closeGroup(); // NXinstrument + + // ****************************************** + // NXsample + nxFile.makeGroup("sample", "NXsample", true); + // TODO: Write sample info + // name + + std::vector rotationAngles(dims_array[0]); + // Initialise rotations - if unknown, fill with equal steps from 0 to 180 over all frames. + // TODO: collect and use actual rotation values + + double step = static_cast(180/dims_array[0]); + rotationAngles[0] = step; + + for(auto it = rotationAngles.begin()+1; it != rotationAngles.end(); ++it) + { + *it = (*(it-1)) + step; + } + + nxFile.writeData("rotation_angle", rotationAngles); + + // Create a link object for rotation_angle to use later + nxFile.openData("rotation_angle"); + NXlink rotationLink = nxFile.getDataID(); + nxFile.closeData(); + // x_translation + // y_translation + // z_translation + nxFile.closeGroup(); // NXsample + + // ****************************************** + // Make the NXmonitor group - Holds base beam intensity for each image + // If information is not present, set as 1 + + std::vector intensity(dims_array[0],1); + nxFile.makeGroup("control", "NXmonitor", true); + nxFile.writeData("data", intensity); + nxFile.closeGroup(); // NXmonitor + + nxFile.makeGroup("data", "NXdata", true); + + nxFile.makeLink(rotationLink); + + nxFile.makeData("data", ::NeXus::FLOAT64, dims_array, false); + if(m_includeError) + nxFile.makeData("error", ::NeXus::FLOAT64, dims_array, false); + + std::vector slabStart; + std::vector slabSize; + + // What size slabs are we going to write + slabSize.push_back(dims_array[0]); + slabSize.push_back((int64_t)dims_array[1]); + slabSize.push_back((int64_t)m_numberOfRows); + + // Init start to first row + slabStart.push_back(0); + slabStart.push_back(0); + slabStart.push_back(0); + + // define the data and error vectors for masked detectors + std::vector masked_data (dims_array[0], MASK_FLAG); + if(m_includeError) + std::vector masked_error (dims_array[0], MASK_ERROR); + + // Create a progress reporting object + Progress progress(this,0,1,100); + const size_t progStep = static_cast(ceil(static_cast(nHist)/100.0)); + Geometry::IDetector_const_sptr det; + + double *dataArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + double *errorArr = NULL; + if(m_includeError) + errorArr = new double[dims_array[0]*dims_array[2]*m_numberOfRows]; + + int currY = 0; + size_t rowIndForSlab = 0; // as we're creating slabs of multiple rows, this says which y index we're at in current slab + + // Loop over detectors + for (size_t i = 0; i < nHist; ++i) + { + try + { + // detector exist + //det = inputWS->getDetector(i); + // Check that we aren't writing a monitor + //if (!det->isMonitor()) + //{ + //Geometry::IDetector_const_sptr det = inputWS->getDetector(i); + + // Figure out where this pixel is supposed to be going and set the correct slab start. + + if(i!=0 && (i)%dims_array[1] == 0){ // When this iteration matches end of a row + currY += 1; + } + size_t currX = (i) - (currY*dims_array[1]); + + const MantidVec & thisY = inputWS->readY(i); + // No masking - Set the data and error as is + for(int j=0; jisMasked()) + // { + dataArr[currInd] = thisY.at(j); + if(m_includeError) + errorArr[currInd] = inputWS->readE(i).at(j); + //} + //else + //{ + // dataArr[currInd] = masked_data[j]; + // if(m_includeError) // errorArr[currInd] = masked_error[j]; - //} - } - - // If end of the row has been reached, check for end of slab (or end of row count) and write data/error - if(((i+1)%dims_array[2]) == 0) - { - rowIndForSlab += 1; + //} + } + + // If end of the row has been reached, check for end of slab (or end of row count) and write data/error + if(((i+1)%dims_array[2]) == 0) + { + rowIndForSlab += 1; // Check if we have collected all of the rows (prior to completing a slab) - if so, write the final section // TODO:: - // if a slab has been collected. Put it into the file - if(rowIndForSlab >= m_numberOfRows) - { - slabStart[2] = currY-(rowIndForSlab-1); - - // Write Data - nxFile.openData("data"); - nxFile.putSlab(dataArr, slabStart, slabSize); - nxFile.closeData(); - // Write Error - if(m_includeError) - { - nxFile.openData("error"); - nxFile.putSlab(errorArr, slabStart, slabSize); - nxFile.closeData(); - } - // Reset slab index count - rowIndForSlab = 0; - } - } - } - catch(Exception::NotFoundError&) - { - /*Catch if no detector. Next line tests whether this happened - test placed - outside here because Mac Intel compiler doesn't like 'continue' in a catch - in an openmp block.*/ - } - // If no detector found, skip onto the next spectrum - if ( !det ) continue; - - // Make regular progress reports and check for canceling the algorithm - if ( i % progStep == 0 ) - { - progress.report(); - } - } - - // Create a link object for the data - nxFile.openData("data"); - NXlink dataLink = nxFile.getDataID(); - nxFile.closeData(); - - nxFile.closeGroup(); // Close Data group - - // Put a link to the data in instrument/detector - nxFile.openGroup("instrument","NXinstrument"); - nxFile.openGroup("detector","NXdetector"); - nxFile.makeLink(dataLink); - nxFile.closeGroup(); - nxFile.closeGroup(); - - - nxFile.closeGroup(); // tomo_entry sub-group - nxFile.closeGroup(); // Top level NXentry - - // Clean up memory - delete [] dataArr; - delete [] errorArr; - } - - /** - * Find all RectangularDetector objects in an instrument - * @param instrument instrument to search for detectors in - * @returns vector of all Rectangular Detectors - */ - std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) - { - std::vector> components; - instrument->getChildren(components,true); - - std::vector rectDetectors; - - for(auto it = components.begin(); it != components.end(); ++it) - { - // for all components, compare to RectangularDetector - if it is one, add it to detectors list. - const Geometry::IComponent* c = dynamic_cast(&(**it)); - - if(dynamic_cast(c)) - { - rectDetectors.push_back(dynamic_cast(&(**it))); - } - } - - return rectDetectors; - } - - /** - * Populates the dimensions vector with number of files, x and y sizes from a specified rectangular detector - * @param rectDetectors List of rectangular detectors to get axis sizes from - * @param useDetectorIndex index of the detector to select from the list, default = 0 - * @returns vector of both axis dimensions for specified detector + // if a slab has been collected. Put it into the file + if(rowIndForSlab >= m_numberOfRows) + { + slabStart[2] = currY-(rowIndForSlab-1); + + // Write Data + nxFile.openData("data"); + nxFile.putSlab(dataArr, slabStart, slabSize); + nxFile.closeData(); + // Write Error + if(m_includeError) + { + nxFile.openData("error"); + nxFile.putSlab(errorArr, slabStart, slabSize); + nxFile.closeData(); + } + // Reset slab index count + rowIndForSlab = 0; + } + } + } + catch(Exception::NotFoundError&) + { + /*Catch if no detector. Next line tests whether this happened - test placed + outside here because Mac Intel compiler doesn't like 'continue' in a catch + in an openmp block.*/ + } + // If no detector found, skip onto the next spectrum + if ( !det ) continue; + + // Make regular progress reports and check for canceling the algorithm + if ( i % progStep == 0 ) + { + progress.report(); + } + } + + // Create a link object for the data + nxFile.openData("data"); + NXlink dataLink = nxFile.getDataID(); + nxFile.closeData(); + + nxFile.closeGroup(); // Close Data group + + // Put a link to the data in instrument/detector + nxFile.openGroup("instrument","NXinstrument"); + nxFile.openGroup("detector","NXdetector"); + nxFile.makeLink(dataLink); + nxFile.closeGroup(); + nxFile.closeGroup(); + + + nxFile.closeGroup(); // tomo_entry sub-group + nxFile.closeGroup(); // Top level NXentry + + // Clean up memory + delete [] dataArr; + delete [] errorArr; + } + + /** + * Find all RectangularDetector objects in an instrument + * @param instrument instrument to search for detectors in + * @returns vector of all Rectangular Detectors + */ + std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) + { + std::vector> components; + instrument->getChildren(components,true); + + std::vector rectDetectors; + + for(auto it = components.begin(); it != components.end(); ++it) + { + // for all components, compare to RectangularDetector - if it is one, add it to detectors list. + const Geometry::IComponent* c = dynamic_cast(&(**it)); + + if(dynamic_cast(c)) + { + RectangularDetector rd = *(dynamic_cast(&(**it))); + rectDetectors.push_back(rd); + } + } + + return rectDetectors; + } + + /** + * Populates the dimensions vector with number of files, x and y sizes from a specified rectangular detector + * @param rectDetectors List of rectangular detectors to get axis sizes from + * @param useDetectorIndex index of the detector to select from the list, default = 0 + * @returns vector of both axis dimensions for specified detector * - * @throw runtime_error Thrown if there are no rectangular detectors - */ - std::vector SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex) - { - // Add number of pixels in X and Y from instrument definition - // Throws if no rectangular detector is present. + * @throw runtime_error Thrown if there are no rectangular detectors + */ + std::vector SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex) + { + // Add number of pixels in X and Y from instrument definition + // Throws if no rectangular detector is present. std::vector dims; - if(rectDetectors.size() != 0) - { - // Assume the first rect detector is the desired one. - dims.push_back(rectDetectors[useDetectorIndex]->xpixels()); - dims.push_back(rectDetectors[useDetectorIndex]->ypixels()); - } - else - { - // Incorrect workspace : requires the x/y pixel count from the instrument definition - g_log.error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); - throw std::runtime_error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); - } + if(rectDetectors.size() != 0) + { + // Assume the first rect detector is the desired one. + dims.push_back(rectDetectors[useDetectorIndex].xpixels()); + dims.push_back(rectDetectors[useDetectorIndex].ypixels()); + } + else + { + // Incorrect workspace : requires the x/y pixel count from the instrument definition + g_log.error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); + throw std::runtime_error("Unable to retrieve x and y pixel count from an instrument definition associated with this workspace."); + } return dims; - } + } - //void someRoutineToAddDataToExisting() - //{ - // //TODO: - //} + //void someRoutineToAddDataToExisting() + //{ + // //TODO: + //} - } // namespace DataHandling + } // namespace DataHandling } // namespace Mantid From 1225561e7bed336575ad17244263183d86c909f6 Mon Sep 17 00:00:00 2001 From: Federico Montesino Pouzols Date: Mon, 20 Oct 2014 15:57:05 +0100 Subject: [PATCH 33/52] update recent files list from LoadDialog's accept, re #10335 --- .../MantidPlot/src/ApplicationWindow.cpp | 2 +- .../Mantid/MantidPlot/src/Mantid/MantidUI.cpp | 32 +++++++++++++++++++ Code/Mantid/MantidPlot/src/Mantid/MantidUI.h | 4 +++ 3 files changed, 37 insertions(+), 1 deletion(-) diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp index ad8a24640adb..6635bae88c2b 100644 --- a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp +++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp @@ -4473,7 +4473,7 @@ void ApplicationWindow::openRecentFile(int index) QFile f(fn); if (!f.exists()){ QMessageBox::critical(this, tr("MantidPlot - File Open Error"),//Mantid - tr("The file: %1

          does not exist anymore!" + tr("The file: %1

          is not there anymore!" "

          It will be removed from the list of recent files.").arg(fn)); recentFiles.remove(fn); diff --git a/Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp b/Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp index d1dec3bfc58f..1df23c94c340 100644 --- a/Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp +++ b/Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp @@ -1354,6 +1354,14 @@ void MantidUI::showAlgorithmDialog(const QString & algName, int version) Mantid::API::IAlgorithm_sptr alg = this->createAlgorithm(algName, version); if( !alg ) return; MantidQt::API::AlgorithmDialog* dlg = createAlgorithmDialog(alg); + + if (algName == "Load") + { + // when loading files, we'll need to update the list of recent files + // hook up MantidUI::fileDialogAccept() to the LoadDialog dialog accepted() signal + connect(dlg, SIGNAL(accepted()), this, SLOT(loadFileDialogAccept())); + } + dlg->show(); dlg->raise(); dlg->activateWindow(); @@ -1380,6 +1388,14 @@ void MantidUI::showAlgorithmDialog(QString algName, QHash param alg->setPropertyValue(it.key().toStdString(),it.value().toStdString()); } MantidQt::API::AlgorithmDialog* dlg = createAlgorithmDialog(alg); + + if (algName == "Load") + { + // when loading files, we'll need to update the list of recent files + // hook up MantidUI::fileDialogAccept() to the LoadDialog dialog accepted() signal + connect(dlg, SIGNAL(accepted()), this, SLOT(loadFileDialogAccept())); + } + dlg->show(); dlg->raise(); dlg->activateWindow(); @@ -1748,6 +1764,22 @@ bool MantidUI::executeAlgorithmAsync(Mantid::API::IAlgorithm_sptr alg, const boo } } +/** +* Slot to update the recent files list (from main appWindow) when accepting LoadDialog dialogs +* @param dlg :: alg. dialog (in practice of subclass LoadDialog) that has been ok-clicked/accepted +*/ +void MantidUI::loadFileDialogAccept() +{ + QObject* sender = QObject::sender(); + MantidQt::API::AlgorithmDialog* dlg = reinterpret_cast(sender); + if (!dlg) + return; // should never happen + + QString fn = MantidQt::API::AlgorithmInputHistory::Instance().previousInput("Load", "Filename"); + appWindow()->updateRecentFilesList(fn); + // recent files list updated. After this point, the Qt signal handler will go to LoadDialog::accept() +} + void MantidUI::handleLoadDAEFinishedNotification(const Poco::AutoPtr& pNf) { std::string wsNAme = pNf->algorithm()->getProperty("OutputWorkspace"); diff --git a/Code/Mantid/MantidPlot/src/Mantid/MantidUI.h b/Code/Mantid/MantidPlot/src/Mantid/MantidUI.h index 5f7f9194029f..7b55d0b50767 100644 --- a/Code/Mantid/MantidPlot/src/Mantid/MantidUI.h +++ b/Code/Mantid/MantidPlot/src/Mantid/MantidUI.h @@ -440,6 +440,10 @@ class MantidUI:public QObject void memoryImage2(); #endif +private slots: + + // slot for file open dialogs created from the main app menu, or the workspaces dock window + void loadFileDialogAccept(); private: From c32f2d711aa7d645c08a0b3a04957bfdbc82b0be Mon Sep 17 00:00:00 2001 From: Federico Montesino Pouzols Date: Mon, 20 Oct 2014 16:15:38 +0100 Subject: [PATCH 34/52] small doxygen doc fix, re #10335 --- Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp b/Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp index 1df23c94c340..1dbd431e8603 100644 --- a/Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp +++ b/Code/Mantid/MantidPlot/src/Mantid/MantidUI.cpp @@ -1766,7 +1766,6 @@ bool MantidUI::executeAlgorithmAsync(Mantid::API::IAlgorithm_sptr alg, const boo /** * Slot to update the recent files list (from main appWindow) when accepting LoadDialog dialogs -* @param dlg :: alg. dialog (in practice of subclass LoadDialog) that has been ok-clicked/accepted */ void MantidUI::loadFileDialogAccept() { From e0374a67f46cc05ff73d96c56ef0b9255fa32ef7 Mon Sep 17 00:00:00 2001 From: John Hill Date: Mon, 20 Oct 2014 16:40:44 +0100 Subject: [PATCH 35/52] Refs #10194 attempting to fix build --- .../inc/MantidDataHandling/SaveNXTomo.h | 4 ++-- .../Framework/DataHandling/src/SaveNXTomo.cpp | 20 +++++++++---------- 2 files changed, 11 insertions(+), 13 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h index 2058f5dcdddb..cf83e7184b31 100644 --- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h +++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h @@ -75,10 +75,10 @@ namespace Mantid /// Save batch of images to the file /// Fetch all rectangular Detector objects defined for an instrument - std::vector getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); + std::vector> getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument); /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument - std::vector getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex = 0); + std::vector getDimensionsFromDetector(const std::vector> &rectDetectors, size_t useDetectorIndex = 0); // Number of rows to size_t m_numberOfRows; diff --git a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp index a1e25e8002ab..836047e6fb05 100644 --- a/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp +++ b/Code/Mantid/Framework/DataHandling/src/SaveNXTomo.cpp @@ -336,23 +336,21 @@ namespace Mantid * @param instrument instrument to search for detectors in * @returns vector of all Rectangular Detectors */ - std::vector SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) + std::vector> SaveNXTomo::getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument) { std::vector> components; instrument->getChildren(components,true); - std::vector rectDetectors; + std::vector> rectDetectors; for(auto it = components.begin(); it != components.end(); ++it) { // for all components, compare to RectangularDetector - if it is one, add it to detectors list. - const Geometry::IComponent* c = dynamic_cast(&(**it)); - - if(dynamic_cast(c)) + auto ptr = boost::dynamic_pointer_cast(*it); + if(ptr != NULL) { - RectangularDetector rd = *(dynamic_cast(&(**it))); - rectDetectors.push_back(rd); - } + rectDetectors.push_back(ptr); + } } return rectDetectors; @@ -366,7 +364,7 @@ namespace Mantid * * @throw runtime_error Thrown if there are no rectangular detectors */ - std::vector SaveNXTomo::getDimensionsFromDetector(const std::vector &rectDetectors, size_t useDetectorIndex) + std::vector SaveNXTomo::getDimensionsFromDetector(const std::vector> &rectDetectors, size_t useDetectorIndex) { // Add number of pixels in X and Y from instrument definition // Throws if no rectangular detector is present. @@ -376,8 +374,8 @@ namespace Mantid if(rectDetectors.size() != 0) { // Assume the first rect detector is the desired one. - dims.push_back(rectDetectors[useDetectorIndex].xpixels()); - dims.push_back(rectDetectors[useDetectorIndex].ypixels()); + dims.push_back(rectDetectors[useDetectorIndex]->xpixels()); + dims.push_back(rectDetectors[useDetectorIndex]->ypixels()); } else { From 3634da56d01c61f3cb9c4d74f5ffaf0b601fff72 Mon Sep 17 00:00:00 2001 From: Raquel Alvarez Banos Date: Tue, 21 Oct 2014 11:34:44 +0100 Subject: [PATCH 36/52] ConvertToMatrixWorkspace not working Re #8261 --- .../MantidPlot/src/ApplicationWindow.cpp | 24 ++++++++++++------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp index 9bef2715e1ac..8ac0a1563442 100644 --- a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp +++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp @@ -3502,14 +3502,22 @@ void ApplicationWindow::convertTableToWorkspace() void ApplicationWindow::convertTableToMatrixWorkspace() { Table* t = dynamic_cast(activeWindow(TableWindow)); - if (!t) return; - if(auto *mt = dynamic_cast(t)) - { - mt = convertTableToTableWorkspace(t); - QHash params; - params["InputWorkspace"] = QString::fromStdString(mt->getWorkspaceName()); - mantidUI->showAlgorithmDialog(QString("ConvertTableToMatrixWorkspace"),params); - } + if (!t) return; + + // dynamic_cast is successful when converting MantidTable to MatrixWorkspace + auto *mt = dynamic_cast(t); + + if (!mt){ + // if dynamic_cast is unsuccessful, create MantidTable from which to create MatrixWorkspace + mt = convertTableToTableWorkspace(t); + } + + if (mt){ + QHash params; + params["InputWorkspace"] = QString::fromStdString(mt->getWorkspaceName()); + mantidUI->showAlgorithmDialog(QString("ConvertTableToMatrixWorkspace"),params); + } + } /** From 1d4c7ede38a705337df11d208c4019f4fae85d20 Mon Sep 17 00:00:00 2001 From: Dan Nixon Date: Tue, 21 Oct 2014 12:08:49 +0100 Subject: [PATCH 37/52] Swapped IndirectResolution to use IIR Refs #10399 --- .../WorkflowAlgorithms/IndirectResolution.py | 30 +++++++------------ 1 file changed, 10 insertions(+), 20 deletions(-) diff --git a/Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectResolution.py b/Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectResolution.py index 7836213dd39e..d521ad91d69e 100644 --- a/Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectResolution.py +++ b/Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectResolution.py @@ -52,26 +52,16 @@ def PyExec(self): StartTime('IndirectResolution') self._setup() - # TODO: Replace with InelasticIndirectReduction algorithm - reducer = inelastic_indirect_reducer.IndirectReducer() - reducer.set_instrument_name(self._instrument) - reducer.set_detector_range(int(self._detector_range[0]) - 1, int(self._detector_range[1]) - 1) - for in_file in self._input_files: - reducer.append_data_file(in_file) - parfile = config['instrumentDefinition.directory'] - parfile += self._instrument + "_" + self._analyser + "_" + self._reflection + "_Parameters.xml" - reducer.set_parameter_file(parfile) - reducer.set_grouping_policy('All') - reducer.set_sum_files(True) - - try: - reducer.reduce() - except Exception, ex: - logger.error('IndirectResolution failed with error: ' + str(ex)) - EndTime('IndirectResolution') - return - - icon_ws = reducer.get_result_workspaces()[0] + InelasticIndirectReduction(Instrument=self._instrument, + Analyser=self._analyser, + Reflection=self._reflection, + Grouping='All', + SumFiles=True, + InputFiles=self._input_files, + DetectorRange=self._detector_range, + OutputWorkspaceGroup='__icon_ws_group') + + icon_ws = mtd['__icon_ws_group'].getItem(0).getName() if self._out_ws == "": self._out_ws = getWSprefix(icon_ws) + 'res' From 1ecf8470095ab84e2080f40b87a925a5302dcf69 Mon Sep 17 00:00:00 2001 From: Raquel Alvarez Banos Date: Tue, 21 Oct 2014 16:03:13 +0100 Subject: [PATCH 38/52] vector too long error fixed Re #3878 --- .../DataHandling/src/LoadEventNexus.cpp | 83 +++++++++++-------- 1 file changed, 48 insertions(+), 35 deletions(-) diff --git a/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp b/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp index d50256c070fd..9bb12b2449b7 100644 --- a/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp +++ b/Code/Mantid/Framework/DataHandling/src/LoadEventNexus.cpp @@ -1114,15 +1114,14 @@ namespace Mantid setPropertyGroup("FilterMonByTimeStart", grp4); setPropertyGroup("FilterMonByTimeStop", grp4); - declareProperty("SpectrumMin",(int32_t)EMPTY_INT(), mustBePositive, + declareProperty("SpectrumMin",(int32_t)EMPTY_INT(), mustBePositive, "The number of the first spectrum to read."); declareProperty("SpectrumMax",(int32_t)EMPTY_INT(), mustBePositive, "The number of the last spectrum to read."); declareProperty(new ArrayProperty("SpectrumList"), "A comma-separated list of individual spectra to read."); - - declareProperty( + declareProperty( new PropertyWithValue("MetaDataOnly", false, Direction::Input), "If true, only the meta data and sample logs will be loaded."); @@ -2352,44 +2351,44 @@ namespace Mantid } else { - g_log.debug() << "Loading only detector spectra from " << filename << "\n"; - - // If optional spectra are provided, if so, m_specList is initialized. spec is used if necessary - createSpectraList(*std::min_element(spec.begin(),spec.end()), *std::max_element(spec.begin(),spec.end())); + g_log.debug() << "Loading only detector spectra from " << filename << "\n"; + + // If optional spectra are provided, if so, m_specList is initialized. spec is used if necessary + createSpectraList(*std::min_element(spec.begin(),spec.end()), *std::max_element(spec.begin(),spec.end())); + + if ( !m_specList.empty() ) { + int i=0; + std::vector spec_temp, udet_temp; + for(auto it=spec.begin(); it!=spec.end(); it++) + { + if ( find(m_specList.begin(),m_specList.end(),*it)!= m_specList.end() ) // spec element *it is not in spec_list + { + spec_temp.push_back( *it ); + udet_temp.push_back( udet.at(i) ); + } + i++; + } + spec=spec_temp; + udet=udet_temp; + } - if ( !m_specList.empty() ) { - int i=0; - std::vector spec_temp, udet_temp; - for(auto it=spec.begin(); it!=spec.end(); it++) - { - if ( find(m_specList.begin(),m_specList.end(),*it)!= m_specList.end() ) // spec element *it is not in spec_list + SpectrumDetectorMapping mapping(spec,udet, monitors); + WS->resizeTo(mapping.getMapping().size()); + // Make sure spectrum numbers are correct + auto uniqueSpectra = mapping.getSpectrumNumbers(); + auto itend = uniqueSpectra.end(); + size_t counter = 0; + for(auto it = uniqueSpectra.begin(); it != itend; ++it) { - spec_temp.push_back( *it ); - udet_temp.push_back( udet.at(i) ); + WS->getSpectrum(counter)->setSpectrumNo(*it); + ++counter; } - i++; + // Fill detectors based on this mapping + WS->updateSpectraUsing(mapping); } - spec=spec_temp; - udet=udet_temp; + return true; } - SpectrumDetectorMapping mapping(spec,udet, monitors); - WS->resizeTo(mapping.getMapping().size()); - // Make sure spectrum numbers are correct - auto uniqueSpectra = mapping.getSpectrumNumbers(); - auto itend = uniqueSpectra.end(); - size_t counter = 0; - for(auto it = uniqueSpectra.begin(); it != itend; ++it) - { - WS->getSpectrum(counter)->setSpectrumNo(*it); - ++counter; - } - // Fill detectors based on this mapping - WS->updateSpectraUsing(mapping); - } - return true; - } - /** * Set the filters on TOF. * @param monitors :: If true check the monitor properties else use the standard ones @@ -2828,6 +2827,20 @@ void LoadEventNexus::createSpectraList(int32_t min, int32_t max){ } + if ( !m_specList.empty() ) { + + // Check that spectra supplied by user do not correspond to monitors + auto nmonitors = WS->getInstrument()->getMonitors().size(); + + for( size_t i = 0; i < nmonitors; ++i ) + { + if ( std::find(m_specList.begin(),m_specList.end(),i+1)!= m_specList.end() ) + { + throw std::invalid_argument("Inconsistent range property: some of the selected spectra correspond to monitors."); + } + } + + } } From 153e0963f059c3c90b9cfbca6e1ceb191ca8a94f Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Tue, 21 Oct 2014 16:53:20 +0100 Subject: [PATCH 39/52] Refs #10348 Align options column to the left --- .../Mantid/MantidQt/CustomInterfaces/src/QReflTableModel.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/QReflTableModel.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/QReflTableModel.cpp index afd0cee4c9ca..960261203cb7 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/QReflTableModel.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/QReflTableModel.cpp @@ -137,7 +137,10 @@ namespace MantidQt { if (role == Qt::TextAlignmentRole) { - return Qt::AlignRight; + if(index.column() == COL_OPTIONS) + return Qt::AlignLeft; + else + return Qt::AlignRight; } else if( role != Qt::DisplayRole && role != Qt::EditRole) { From e82ebfdcd648aaa478ae6563d6cc3bed795c1ec2 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Mon, 20 Oct 2014 15:53:43 +0100 Subject: [PATCH 40/52] Refs #10348 Delegate options column --- .../ReflOptionsDelegate.h | 25 +++++++++++++++++++ .../CustomInterfaces/src/QtReflMainView.cpp | 4 +++ 2 files changed, 29 insertions(+) create mode 100644 Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h new file mode 100644 index 000000000000..b0be6536fdd6 --- /dev/null +++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h @@ -0,0 +1,25 @@ +#ifndef MANTID_CUSTOMINTERFACES_REFLOPTIONSDELEGATE_H +#define MANTID_CUSTOMINTERFACES_REFLOPTIONSDELEGATE_H + +#include + +namespace MantidQt +{ + namespace CustomInterfaces + { + class ReflOptionsDelegate : public QStyledItemDelegate + { + public: + ReflOptionsDelegate() {}; + virtual ~ReflOptionsDelegate() {}; + virtual QWidget* createEditor(QWidget* parent, const QStyleOptionViewItem& option, const QModelIndex& index) const + { + Q_UNUSED(option); + Q_UNUSED(index); + return new QLineEdit(parent); + } + }; + } +} + +#endif /* MANTID_CUSTOMINTERFACES_REFLOPTIONSDELEGATE_H */ diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp index 9d16ea5a4f21..a882bf64c978 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp @@ -1,6 +1,7 @@ #include "MantidQtCustomInterfaces/QtReflMainView.h" #include "MantidQtCustomInterfaces/QReflTableModel.h" #include "MantidQtCustomInterfaces/ReflMainViewPresenter.h" +#include "MantidQtCustomInterfaces/ReflOptionsDelegate.h" #include "MantidAPI/ITableWorkspace.h" #include "MantidKernel/ConfigService.h" #include @@ -56,6 +57,9 @@ namespace MantidQt connect(ui.actionProcess, SIGNAL(triggered()), this, SLOT(actionProcess())); connect(ui.actionGroupRows, SIGNAL(triggered()), this, SLOT(actionGroupRows())); + QAbstractItemDelegate* delegate = new ReflOptionsDelegate(); + ui.viewTable->setItemDelegateForColumn(ReflMainViewPresenter::COL_OPTIONS, delegate); + //Finally, create a presenter to do the thinking for us m_presenter = boost::shared_ptr(new ReflMainViewPresenter(this)); } From ba3032e4d1ac8abe35ea94692515ca671b137ed3 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Tue, 21 Oct 2014 17:00:52 +0100 Subject: [PATCH 41/52] Refs #10348 Stub HintingLineEdit --- .../ReflOptionsDelegate.h | 13 +++++++- .../MantidQt/MantidWidgets/CMakeLists.txt | 2 ++ .../MantidQtMantidWidgets/HintingLineEdit.h | 33 +++++++++++++++++++ .../MantidWidgets/src/HintingLineEdit.cpp | 29 ++++++++++++++++ 4 files changed, 76 insertions(+), 1 deletion(-) create mode 100644 Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h create mode 100644 Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h index b0be6536fdd6..3e6867fb1932 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h +++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h @@ -3,6 +3,10 @@ #include +#include "MantidQtMantidWidgets/HintingLineEdit.h" + +using namespace MantidQt::MantidWidgets; + namespace MantidQt { namespace CustomInterfaces @@ -16,7 +20,14 @@ namespace MantidQt { Q_UNUSED(option); Q_UNUSED(index); - return new QLineEdit(parent); + + std::map hints; + //Create hints + + auto editor = new HintingLineEdit(parent, hints); + editor->setFrame(false); + + return editor; } }; } diff --git a/Code/Mantid/MantidQt/MantidWidgets/CMakeLists.txt b/Code/Mantid/MantidQt/MantidWidgets/CMakeLists.txt index 64ebe528e242..bde84dac1206 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/CMakeLists.txt +++ b/Code/Mantid/MantidQt/MantidWidgets/CMakeLists.txt @@ -12,6 +12,7 @@ set ( SRC_FILES src/FitPropertyBrowser.cpp src/FormulaDialogEditor.cpp src/FunctionBrowser.cpp + src/HintingLineEdit.cpp src/InstrumentSelector.cpp src/MantidHelpWindow.cpp src/MWDiag.cpp @@ -53,6 +54,7 @@ set ( MOC_FILES inc/MantidQtMantidWidgets/FindDialog.h inc/MantidQtMantidWidgets/FitPropertyBrowser.h inc/MantidQtMantidWidgets/FunctionBrowser.h + inc/MantidQtMantidWidgets/HintingLineEdit.h inc/MantidQtMantidWidgets/CatalogSearch.h inc/MantidQtMantidWidgets/CatalogSelector.h inc/MantidQtMantidWidgets/InstrumentSelector.h diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h new file mode 100644 index 000000000000..1c193f08d3c0 --- /dev/null +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h @@ -0,0 +1,33 @@ +#ifndef MANTID_MANTIDWIDGETS_HINTINGLINEEDIT_H_ +#define MANTID_MANTIDWIDGETS_HINTINGLINEEDIT_H_ + +#include "MantidKernel/System.h" +#include "MantidAPI/AlgorithmFactory.h" +#include "WidgetDllOption.h" + +#include +#include +#include + +//------------------------------------------------------------------------------ +// Forward declaration +//------------------------------------------------------------------------------ +namespace MantidQt +{ + namespace MantidWidgets + { + class EXPORT_OPT_MANTIDQT_MANTIDWIDGETS HintingLineEdit : public QLineEdit + { + Q_OBJECT + public: + HintingLineEdit(QWidget *parent, const std::map &hints); + virtual ~HintingLineEdit(); + protected: + std::map m_hints; + public slots: + void showHint(const QString& keyword); + }; + } //namespace MantidWidgets +} //namepsace MantidQt + +#endif /* MANTID_MANTIDWIDGETS_HINTINGLINEEDIT_H_ */ diff --git a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp new file mode 100644 index 000000000000..6a166fedeae2 --- /dev/null +++ b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp @@ -0,0 +1,29 @@ +#include "MantidQtMantidWidgets/HintingLineEdit.h" + +#include + +namespace MantidQt +{ + namespace MantidWidgets + { + + HintingLineEdit::HintingLineEdit(QWidget *parent, const std::map &hints) : QLineEdit(parent), m_hints(hints) + { + connect(this, SIGNAL(textEdited(const QString&)), this, SLOT(showHint(const QString&))); + } + + HintingLineEdit::~HintingLineEdit() + { + } + + void HintingLineEdit::showHint(const QString& keyword) + { + //Get the current word from the cursor position + + //If we're typing the key, auto complete and show matching keys + + //If we're typing the value, show the detailed description for this key + QToolTip::showText(mapToGlobal(QPoint(0, 5)), "You have entered:\n" + keyword); + } + } //namespace MantidWidgets +} //namepsace MantidQt From d6137c24a68fda4d4d1e9aabe191b45bfafb573c Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Wed, 22 Oct 2014 10:39:51 +0100 Subject: [PATCH 42/52] Refs #10348 Use properties for hints --- .../inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h index 3e6867fb1932..2d344b80099f 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h +++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h @@ -3,8 +3,11 @@ #include +#include "MantidAPI/AlgorithmManager.h" #include "MantidQtMantidWidgets/HintingLineEdit.h" +using namespace Mantid::API; +using namespace Mantid::Kernel; using namespace MantidQt::MantidWidgets; namespace MantidQt @@ -22,7 +25,12 @@ namespace MantidQt Q_UNUSED(index); std::map hints; + //Create hints + IAlgorithm_sptr algReflOne = AlgorithmManager::Instance().create("ReflectometryReductionOneAuto"); + auto properties = algReflOne->getProperties(); + for(auto it = properties.begin(); it != properties.end(); ++it) + hints[(*it)->name()] = (*it)->briefDocumentation(); auto editor = new HintingLineEdit(parent, hints); editor->setFrame(false); From 89f3a413c6efd8c0191c62616c1a70e27a7a6d19 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Wed, 22 Oct 2014 10:41:18 +0100 Subject: [PATCH 43/52] Refs #10348 Rudimentary hint tooltips --- .../MantidQtMantidWidgets/HintingLineEdit.h | 6 ++- .../MantidWidgets/src/HintingLineEdit.cpp | 49 +++++++++++++++++-- 2 files changed, 50 insertions(+), 5 deletions(-) diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h index 1c193f08d3c0..13df47d8c975 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h @@ -23,9 +23,13 @@ namespace MantidQt HintingLineEdit(QWidget *parent, const std::map &hints); virtual ~HintingLineEdit(); protected: + void updateMatches(); + std::string m_curKey; + std::map m_matches; std::map m_hints; public slots: - void showHint(const QString& keyword); + void showHint(); + void updateHint(const QString& text); }; } //namespace MantidWidgets } //namepsace MantidQt diff --git a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp index 6a166fedeae2..dadec397eec1 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp +++ b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp @@ -1,5 +1,6 @@ #include "MantidQtMantidWidgets/HintingLineEdit.h" +#include #include namespace MantidQt @@ -9,21 +10,61 @@ namespace MantidQt HintingLineEdit::HintingLineEdit(QWidget *parent, const std::map &hints) : QLineEdit(parent), m_hints(hints) { - connect(this, SIGNAL(textEdited(const QString&)), this, SLOT(showHint(const QString&))); + connect(this, SIGNAL(textEdited(const QString&)), this, SLOT(updateHint(const QString&))); } HintingLineEdit::~HintingLineEdit() { } - void HintingLineEdit::showHint(const QString& keyword) + void HintingLineEdit::updateMatches() { - //Get the current word from the cursor position + m_matches.clear(); + for(auto it = m_hints.begin(); it != m_hints.end(); ++it) + { + const std::string& hint = it->first; + + if(hint.length() < m_curKey.length()) + continue; + + const std::string hintPrefix = hint.substr(0, m_curKey.length()); + + if(m_curKey == hintPrefix) + m_matches[hint] = it->second; + } + } + + void HintingLineEdit::updateHint(const QString& text) + { + const size_t curPos = (size_t)cursorPosition(); + const std::string line = text.toStdString(); + + //Get text from start -> cursor + std::string prefix = line.substr(0, curPos); + + std::size_t startPos = prefix.find_last_of(","); + if(startPos != std::string::npos) + prefix = prefix.substr(startPos + 1, prefix.size() - (startPos + 1)); + + boost::trim(prefix); + + m_curKey = prefix; + showHint(); + } + + void HintingLineEdit::showHint() + { + updateMatches(); //If we're typing the key, auto complete and show matching keys //If we're typing the value, show the detailed description for this key - QToolTip::showText(mapToGlobal(QPoint(0, 5)), "You have entered:\n" + keyword); + QString matchList; + + for(auto mIt = m_matches.begin(); mIt != m_matches.end(); ++mIt) + matchList += QString::fromStdString(mIt->first) + " : " + QString::fromStdString(mIt->second) + "\n"; + + QToolTip::showText(mapToGlobal(QPoint(0, 5)), matchList.trimmed()); } } //namespace MantidWidgets } //namepsace MantidQt From 9a5fba2b9344741755abc7a8f9b8b78b639a0647 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Wed, 22 Oct 2014 11:39:40 +0100 Subject: [PATCH 44/52] Refs #10348 Implement autocompletion --- .../MantidQtMantidWidgets/HintingLineEdit.h | 3 ++ .../MantidWidgets/src/HintingLineEdit.cpp | 38 +++++++++++++++---- 2 files changed, 34 insertions(+), 7 deletions(-) diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h index 13df47d8c975..a43c78436592 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h @@ -23,10 +23,13 @@ namespace MantidQt HintingLineEdit(QWidget *parent, const std::map &hints); virtual ~HintingLineEdit(); protected: + virtual void keyPressEvent(QKeyEvent* e); + void insertSuggestion(); void updateMatches(); std::string m_curKey; std::map m_matches; std::map m_hints; + bool m_dontComplete; public slots: void showHint(); void updateHint(const QString& text); diff --git a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp index dadec397eec1..d955b432fef8 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp +++ b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp @@ -8,7 +8,7 @@ namespace MantidQt namespace MantidWidgets { - HintingLineEdit::HintingLineEdit(QWidget *parent, const std::map &hints) : QLineEdit(parent), m_hints(hints) + HintingLineEdit::HintingLineEdit(QWidget *parent, const std::map &hints) : QLineEdit(parent), m_hints(hints), m_dontComplete(false) { connect(this, SIGNAL(textEdited(const QString&)), this, SLOT(updateHint(const QString&))); } @@ -17,6 +17,12 @@ namespace MantidQt { } + void HintingLineEdit::keyPressEvent(QKeyEvent* e) + { + m_dontComplete = (e->key() == Qt::Key_Backspace || e->key() == Qt::Key_Delete || e->key() == Qt::Key_Space); + QLineEdit::keyPressEvent(e); + } + void HintingLineEdit::updateMatches() { m_matches.clear(); @@ -53,18 +59,36 @@ namespace MantidQt showHint(); } + void HintingLineEdit::insertSuggestion() + { + if(m_curKey.length() < 1 || m_matches.size() < 1 || m_dontComplete) + return; + + const std::string key = m_matches.begin()->first; + QString line = text(); + const int curPos = cursorPosition(); + + //Don't perform insertions mid-word + if(curPos + 1 < line.size() && line[curPos+1].isLetterOrNumber()) + return; + + line = line.left(curPos) + QString::fromStdString(key).mid((int)m_curKey.size()) + line.mid(curPos); + + setText(line); + setSelection(curPos, (int)key.size()); + } + void HintingLineEdit::showHint() { updateMatches(); - //If we're typing the key, auto complete and show matching keys - - //If we're typing the value, show the detailed description for this key - QString matchList; + QString hintList; for(auto mIt = m_matches.begin(); mIt != m_matches.end(); ++mIt) - matchList += QString::fromStdString(mIt->first) + " : " + QString::fromStdString(mIt->second) + "\n"; + hintList += QString::fromStdString(mIt->first) + " : " + QString::fromStdString(mIt->second) + "\n"; + + QToolTip::showText(mapToGlobal(QPoint(0, 5)), hintList.trimmed()); - QToolTip::showText(mapToGlobal(QPoint(0, 5)), matchList.trimmed()); + insertSuggestion(); } } //namespace MantidWidgets } //namepsace MantidQt From 9ff5789b906e0570619b61c23d9b1bdff576e3b3 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Wed, 22 Oct 2014 12:00:51 +0100 Subject: [PATCH 45/52] Refs #10348 Blacklist uninteresting properties --- .../ReflOptionsDelegate.h | 19 +++++++++++++++++-- .../CustomInterfaces/src/QtReflMainView.cpp | 3 +-- .../src/ReflMainViewPresenter.cpp | 4 ++++ 3 files changed, 22 insertions(+), 4 deletions(-) diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h index 2d344b80099f..7af51cc65ae8 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h +++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h @@ -26,11 +26,26 @@ namespace MantidQt std::map hints; - //Create hints + //Dynamically produce a list of hints and their descriptions from the algorithm IAlgorithm_sptr algReflOne = AlgorithmManager::Instance().create("ReflectometryReductionOneAuto"); auto properties = algReflOne->getProperties(); for(auto it = properties.begin(); it != properties.end(); ++it) - hints[(*it)->name()] = (*it)->briefDocumentation(); + { + const std::string name = (*it)->name(); + + //Blacklist some properties from being suggested + //These are either useless to the user (such as ThetaOut), or are handled by the presenter + if(name == "ThetaIn" || + name == "ThetaOut" || + name == "InputWorkspace" || + name == "OutputWorkspace" || + name == "OutputWorkspaceWavelength" || + name == "FirstTransmissionRun" || + name == "SecondTransmissionRun") + continue; + + hints[name] = (*it)->briefDocumentation(); + } auto editor = new HintingLineEdit(parent, hints); editor->setFrame(false); diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp index a882bf64c978..abc78ee6e688 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp @@ -57,8 +57,7 @@ namespace MantidQt connect(ui.actionProcess, SIGNAL(triggered()), this, SLOT(actionProcess())); connect(ui.actionGroupRows, SIGNAL(triggered()), this, SLOT(actionGroupRows())); - QAbstractItemDelegate* delegate = new ReflOptionsDelegate(); - ui.viewTable->setItemDelegateForColumn(ReflMainViewPresenter::COL_OPTIONS, delegate); + ui.viewTable->setItemDelegateForColumn(ReflMainViewPresenter::COL_OPTIONS, new ReflOptionsDelegate()); //Finally, create a presenter to do the thinking for us m_presenter = boost::shared_ptr(new ReflMainViewPresenter(this)); diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp index c92af568545d..ac8878d13fad 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp @@ -398,6 +398,10 @@ namespace MantidQt if(!transStr.empty()) transWS = makeTransWS(transStr); + /* If you add/remove any properties given to ReflectometryReductionOneAuto you should consider + * updating the list of suggestions provided by the options column in the UI. + * See Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h + */ IAlgorithm_sptr algReflOne = AlgorithmManager::Instance().create("ReflectometryReductionOneAuto"); algReflOne->initialize(); algReflOne->setProperty("InputWorkspace", runWS); From 5d9ea12e63ba2cc3944f77e5576312bbe0c3e749 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Tue, 21 Oct 2014 13:26:49 +0100 Subject: [PATCH 46/52] Refs #10398 Add more aggressive testing These invalid inputs should throw an exception. --- .../CustomInterfaces/test/ReflMainViewPresenterTest.h | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/Code/Mantid/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h b/Code/Mantid/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h index 24a0c8dac295..769ec5c82693 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h +++ b/Code/Mantid/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h @@ -712,6 +712,12 @@ class ReflMainViewPresenterTest : public CxxTest::TestSuite TS_ASSERT_EQUALS(kvp["e"], "4,5,6"); TS_ASSERT_EQUALS(kvp["f"], "1+1=2"); TS_ASSERT_EQUALS(kvp["g"], "'"); + + TS_ASSERT_THROWS(ReflMainViewPresenter::parseKeyValueString("a = 1, b = 2, c = 3,"), std::runtime_error); + TS_ASSERT_THROWS(ReflMainViewPresenter::parseKeyValueString("a = 1, b = 2, c = 3,d"), std::runtime_error); + TS_ASSERT_THROWS(ReflMainViewPresenter::parseKeyValueString(",a = 1"), std::runtime_error); + TS_ASSERT_THROWS(ReflMainViewPresenter::parseKeyValueString(",a = 1 = 2,="), std::runtime_error); + TS_ASSERT_THROWS(ReflMainViewPresenter::parseKeyValueString("=,=,="), std::runtime_error); } }; From b94de72e3e6357407de02cc1cf608fd0f021f1dd Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Tue, 21 Oct 2014 13:28:09 +0100 Subject: [PATCH 47/52] Refs #10398 Update parseKeyValueString to satisfy unit test --- .../CustomInterfaces/src/ReflMainViewPresenter.cpp | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp index fa0b58a7fc27..e146390b2b0e 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp @@ -123,6 +123,7 @@ namespace MantidQt /** Parses a string in the format `a = 1,b=2, c = "1,2,3,4", d = 5.0, e='a,b,c'` into a map of key/value pairs @param str The input string + @throws std::runtime_error on an invalid input string */ std::map ReflMainViewPresenter::parseKeyValueString(const std::string& str) { @@ -149,8 +150,16 @@ namespace MantidQt boost::trim(key); boost::trim(value); + if(key.empty() || value.empty()) + throw std::runtime_error("Invalid key value pair, '" + *it + "'"); + + kvp[key] = value; } + else + { + throw std::runtime_error("Invalid key value pair, '" + *it + "'"); + } } return kvp; } From cfb22f50b246d6e3b3d662836fc40a96e857b1b4 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Wed, 22 Oct 2014 15:28:51 +0100 Subject: [PATCH 48/52] Refs #10348 Refactor hint map creation --- .../MantidQtCustomInterfaces/QtReflMainView.h | 1 + .../MantidQtCustomInterfaces/ReflMainView.h | 2 + .../ReflOptionsDelegate.h | 59 ------------------- .../CustomInterfaces/src/QtReflMainView.cpp | 13 +++- .../src/ReflMainViewPresenter.cpp | 15 +++++ .../test/ReflMainViewMockObjects.h | 1 + .../AlgorithmHintStrategy.h | 45 ++++++++++++++ .../inc/MantidQtMantidWidgets/HintStrategy.h | 23 ++++++++ .../HintingLineEditFactory.h | 42 +++++++++++++ 9 files changed, 139 insertions(+), 62 deletions(-) delete mode 100644 Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h create mode 100644 Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/AlgorithmHintStrategy.h create mode 100644 Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintStrategy.h create mode 100644 Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEditFactory.h diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h index 2dcee3bf647c..d8dd8e235b8d 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h +++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h @@ -63,6 +63,7 @@ namespace MantidQt //Settor methods virtual void setInstrumentList(const std::vector& instruments, const std::string& defaultInstrument); + virtual void setOptionsHintStrategy(HintStrategy* hintStrategy); //Accessor methods virtual std::vector getSelectedRowIndexes() const; diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h index 7507cf17e664..374536c5f7c2 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h +++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h @@ -3,6 +3,7 @@ #include "MantidKernel/System.h" #include "MantidAPI/ITableWorkspace.h" +#include "MantidQtMantidWidgets/HintStrategy.h" namespace MantidQt { @@ -55,6 +56,7 @@ namespace MantidQt //Settor methods virtual void setInstrumentList(const std::vector& instruments, const std::string& defaultInstrument) = 0; + virtual void setOptionsHintStrategy(HintStrategy* hintStrategy) = 0; //Accessor methods virtual std::vector getSelectedRowIndexes() const = 0; diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h deleted file mode 100644 index 7af51cc65ae8..000000000000 --- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h +++ /dev/null @@ -1,59 +0,0 @@ -#ifndef MANTID_CUSTOMINTERFACES_REFLOPTIONSDELEGATE_H -#define MANTID_CUSTOMINTERFACES_REFLOPTIONSDELEGATE_H - -#include - -#include "MantidAPI/AlgorithmManager.h" -#include "MantidQtMantidWidgets/HintingLineEdit.h" - -using namespace Mantid::API; -using namespace Mantid::Kernel; -using namespace MantidQt::MantidWidgets; - -namespace MantidQt -{ - namespace CustomInterfaces - { - class ReflOptionsDelegate : public QStyledItemDelegate - { - public: - ReflOptionsDelegate() {}; - virtual ~ReflOptionsDelegate() {}; - virtual QWidget* createEditor(QWidget* parent, const QStyleOptionViewItem& option, const QModelIndex& index) const - { - Q_UNUSED(option); - Q_UNUSED(index); - - std::map hints; - - //Dynamically produce a list of hints and their descriptions from the algorithm - IAlgorithm_sptr algReflOne = AlgorithmManager::Instance().create("ReflectometryReductionOneAuto"); - auto properties = algReflOne->getProperties(); - for(auto it = properties.begin(); it != properties.end(); ++it) - { - const std::string name = (*it)->name(); - - //Blacklist some properties from being suggested - //These are either useless to the user (such as ThetaOut), or are handled by the presenter - if(name == "ThetaIn" || - name == "ThetaOut" || - name == "InputWorkspace" || - name == "OutputWorkspace" || - name == "OutputWorkspaceWavelength" || - name == "FirstTransmissionRun" || - name == "SecondTransmissionRun") - continue; - - hints[name] = (*it)->briefDocumentation(); - } - - auto editor = new HintingLineEdit(parent, hints); - editor->setFrame(false); - - return editor; - } - }; - } -} - -#endif /* MANTID_CUSTOMINTERFACES_REFLOPTIONSDELEGATE_H */ diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp index abc78ee6e688..6f23d2f9649c 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/QtReflMainView.cpp @@ -1,7 +1,7 @@ #include "MantidQtCustomInterfaces/QtReflMainView.h" #include "MantidQtCustomInterfaces/QReflTableModel.h" #include "MantidQtCustomInterfaces/ReflMainViewPresenter.h" -#include "MantidQtCustomInterfaces/ReflOptionsDelegate.h" +#include "MantidQtMantidWidgets/HintingLineEditFactory.h" #include "MantidAPI/ITableWorkspace.h" #include "MantidKernel/ConfigService.h" #include @@ -57,8 +57,6 @@ namespace MantidQt connect(ui.actionProcess, SIGNAL(triggered()), this, SLOT(actionProcess())); connect(ui.actionGroupRows, SIGNAL(triggered()), this, SLOT(actionGroupRows())); - ui.viewTable->setItemDelegateForColumn(ReflMainViewPresenter::COL_OPTIONS, new ReflOptionsDelegate()); - //Finally, create a presenter to do the thinking for us m_presenter = boost::shared_ptr(new ReflMainViewPresenter(this)); } @@ -242,6 +240,15 @@ namespace MantidQt ui.comboProcessInstrument->setCurrentIndex(index); } + /** + Set the strategy used for generating hints for the autocompletion in the options column. + @param hintStrategy The hinting strategy to use + */ + void QtReflMainView::setOptionsHintStrategy(HintStrategy* hintStrategy) + { + ui.viewTable->setItemDelegateForColumn(ReflMainViewPresenter::COL_OPTIONS, new HintingLineEditFactory(hintStrategy)); + } + /** Get the selected instrument for searching @returns the selected instrument to search for diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp index ac8878d13fad..aa2344a6d198 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp @@ -7,6 +7,7 @@ #include "MantidKernel/TimeSeriesProperty.h" #include "MantidKernel/Utils.h" #include "MantidQtCustomInterfaces/ReflMainView.h" +#include "MantidQtMantidWidgets/AlgorithmHintStrategy.h" #include @@ -86,6 +87,20 @@ namespace MantidQt else m_view->setInstrumentList(instruments, "INTER"); + //Provide autocompletion hints for the options column. We use the algorithm's properties minus + //those we blacklist. We blacklist any useless properties or ones we're handling that the user + //should'nt touch. + IAlgorithm_sptr alg = AlgorithmManager::Instance().create("ReflectometryReductionOneAuto"); + std::set blacklist; + blacklist.insert("ThetaIn"); + blacklist.insert("ThetaOut"); + blacklist.insert("InputWorkspace"); + blacklist.insert("OutputWorkspace"); + blacklist.insert("OutputWorkspaceWavelength"); + blacklist.insert("FirstTransmissionRun"); + blacklist.insert("SecondTransmissionRun"); + m_view->setOptionsHintStrategy(new AlgorithmHintStrategy(alg, blacklist)); + newTable(); } diff --git a/Code/Mantid/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h b/Code/Mantid/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h index 616829c8e952..b41952ecf7b5 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h +++ b/Code/Mantid/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h @@ -34,6 +34,7 @@ class MockView : public ReflMainView public: MockView(){}; virtual void showTable(Mantid::API::ITableWorkspace_sptr model){ m_model = model;} + virtual void setOptionsHintStrategy(HintStrategy*) {}; MOCK_METHOD3(askUserString, std::string(const std::string& prompt, const std::string& title, const std::string& defaultValue)); MOCK_METHOD2(askUserYesNo, bool(std::string, std::string)); MOCK_METHOD2(giveUserCritical, void(std::string, std::string)); diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/AlgorithmHintStrategy.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/AlgorithmHintStrategy.h new file mode 100644 index 000000000000..161168e5c460 --- /dev/null +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/AlgorithmHintStrategy.h @@ -0,0 +1,45 @@ +#ifndef MANTID_MANTIDWIDGETS_ALGORITHMHINTSTRATEGY_H +#define MANTID_MANTIDWIDGETS_ALGORITHMHINTSTRATEGY_H + +#include "MantidAPI/IAlgorithm.h" +#include "MantidQtMantidWidgets/HintStrategy.h" + +using namespace Mantid::API; + +namespace MantidQt +{ + namespace CustomInterfaces + { + class AlgorithmHintStrategy : public HintStrategy + { + public: + AlgorithmHintStrategy(IAlgorithm_sptr algorithm, std::set blacklist) : m_algorithm(algorithm), m_blacklist(blacklist) + { + } + + virtual ~AlgorithmHintStrategy() {}; + + virtual std::map createHints() + { + std::map hints; + + auto properties = m_algorithm->getProperties(); + for(auto it = properties.begin(); it != properties.end(); ++it) + { + const std::string name = (*it)->name(); + + //If it's not in the blacklist, add the property to our hints + if(m_blacklist.find(name) == m_blacklist.end()) + hints[name] = (*it)->briefDocumentation(); + } + + return hints; + } + private: + IAlgorithm_sptr m_algorithm; + std::set m_blacklist; + }; + } +} + +#endif /* MANTID_MANTIDWIDGETS_ALGORITHMHINTSTRATEGY_H */ diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintStrategy.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintStrategy.h new file mode 100644 index 000000000000..9fbe15852f13 --- /dev/null +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintStrategy.h @@ -0,0 +1,23 @@ +#ifndef MANTID_MANTIDWIDGETS_HINTSTRATEGY_H +#define MANTID_MANTIDWIDGETS_HINTSTRATEGY_H + +#include +#include + +namespace MantidQt +{ + namespace CustomInterfaces + { + class HintStrategy + { + public: + HintStrategy() {}; + virtual ~HintStrategy() {}; + + //Provides a map of hints to be used by a HintingLineEdit widget + virtual std::map createHints() = 0; + }; + } +} + +#endif /* MANTID_MANTIDWIDGETS_HINTSTRATEGY_H */ diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEditFactory.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEditFactory.h new file mode 100644 index 000000000000..ecf8f839026a --- /dev/null +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEditFactory.h @@ -0,0 +1,42 @@ +#ifndef MANTID_MANTIDWIDGETS_HINTINGLINEEDITFACTORY_H +#define MANTID_MANTIDWIDGETS_HINTINGLINEEDITFACTORY_H + +#include + +#include "MantidAPI/AlgorithmManager.h" +#include "MantidQtMantidWidgets/HintingLineEdit.h" +#include "MantidQtMantidWidgets/HintStrategy.h" + +using namespace Mantid::API; +using namespace Mantid::Kernel; +using namespace MantidQt::MantidWidgets; + +namespace MantidQt +{ + namespace CustomInterfaces + { + class HintingLineEditFactory : public QStyledItemDelegate + { + public: + HintingLineEditFactory(HintStrategy* hintStrategy) : m_strategy(hintStrategy) {}; + virtual ~HintingLineEditFactory() + { + delete m_strategy; + }; + virtual QWidget* createEditor(QWidget* parent, const QStyleOptionViewItem& option, const QModelIndex& index) const + { + Q_UNUSED(option); + Q_UNUSED(index); + + auto editor = new HintingLineEdit(parent, m_strategy->createHints()); + editor->setFrame(false); + + return editor; + } + protected: + HintStrategy* m_strategy; + }; + } +} + +#endif /* MANTID_MANTIDWIDGETS_HINTINGLINEEDITFACTORY_H */ From 9158daa74ea43635651c8e4eba9ad4719f23c532 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Wed, 22 Oct 2014 15:35:57 +0100 Subject: [PATCH 49/52] Refs #10348 Remove obsolete comment --- .../MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp | 4 ---- 1 file changed, 4 deletions(-) diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp index aa2344a6d198..516878053c43 100644 --- a/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp +++ b/Code/Mantid/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp @@ -413,10 +413,6 @@ namespace MantidQt if(!transStr.empty()) transWS = makeTransWS(transStr); - /* If you add/remove any properties given to ReflectometryReductionOneAuto you should consider - * updating the list of suggestions provided by the options column in the UI. - * See Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflOptionsDelegate.h - */ IAlgorithm_sptr algReflOne = AlgorithmManager::Instance().create("ReflectometryReductionOneAuto"); algReflOne->initialize(); algReflOne->setProperty("InputWorkspace", runWS); From 47f2b704dbdc8817f027625252cf9e0d24460195 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Wed, 22 Oct 2014 16:57:31 +0100 Subject: [PATCH 50/52] Refs #10348 Allow user to cycle through suggestions Up/Down arrow keys allow the user to switch between the available suggestions rapidly. --- .../MantidQtMantidWidgets/HintingLineEdit.h | 4 ++ .../MantidWidgets/src/HintingLineEdit.cpp | 61 ++++++++++++++++++- 2 files changed, 62 insertions(+), 3 deletions(-) diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h index a43c78436592..b5711092c7f5 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h @@ -26,7 +26,11 @@ namespace MantidQt virtual void keyPressEvent(QKeyEvent* e); void insertSuggestion(); void updateMatches(); + void clearSuggestion(); + void nextSuggestion(); + void prevSuggestion(); std::string m_curKey; + std::string m_curMatch; std::map m_matches; std::map m_hints; bool m_dontComplete; diff --git a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp index d955b432fef8..a798d0df1e6e 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp +++ b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp @@ -20,11 +20,23 @@ namespace MantidQt void HintingLineEdit::keyPressEvent(QKeyEvent* e) { m_dontComplete = (e->key() == Qt::Key_Backspace || e->key() == Qt::Key_Delete || e->key() == Qt::Key_Space); + + if(e->key() == Qt::Key_Up) + { + prevSuggestion(); + } + + if(e->key() == Qt::Key_Down) + { + nextSuggestion(); + return; + } QLineEdit::keyPressEvent(e); } void HintingLineEdit::updateMatches() { + m_curMatch.clear(); m_matches.clear(); for(auto it = m_hints.begin(); it != m_hints.end(); ++it) @@ -64,7 +76,9 @@ namespace MantidQt if(m_curKey.length() < 1 || m_matches.size() < 1 || m_dontComplete) return; - const std::string key = m_matches.begin()->first; + if(m_curMatch.empty()) + m_curMatch = m_matches.begin()->first; + QString line = text(); const int curPos = cursorPosition(); @@ -72,10 +86,51 @@ namespace MantidQt if(curPos + 1 < line.size() && line[curPos+1].isLetterOrNumber()) return; - line = line.left(curPos) + QString::fromStdString(key).mid((int)m_curKey.size()) + line.mid(curPos); + line = line.left(curPos) + QString::fromStdString(m_curMatch).mid((int)m_curKey.size()) + line.mid(curPos); setText(line); - setSelection(curPos, (int)key.size()); + setSelection(curPos, (int)m_curMatch.size()); + } + + void HintingLineEdit::clearSuggestion() + { + if(!hasSelectedText()) + return; + + //Remove the selected text + QString line = text(); + line = line.left(selectionStart()) + line.mid(selectionStart() + selectedText().length()); + setText(line); + } + + void HintingLineEdit::nextSuggestion() + { + clearSuggestion(); + auto it = m_matches.find(m_curMatch); + if(it != m_matches.end()) + { + it++; + if(it == m_matches.end()) + m_curMatch = m_matches.begin()->first; + else + m_curMatch = it->first; + insertSuggestion(); + } + } + + void HintingLineEdit::prevSuggestion() + { + clearSuggestion(); + auto it = m_matches.find(m_curMatch); + if(it != m_matches.end()) + { + it--; + if(it == m_matches.end()) + m_curMatch = m_matches.rbegin()->first; + else + m_curMatch = it->first; + insertSuggestion(); + } } void HintingLineEdit::showHint() From bbc9bd655ad5522a16982696d10cf8f26d7738f9 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Thu, 23 Oct 2014 09:12:27 +0100 Subject: [PATCH 51/52] Refs #10348 Tidy up HintingLineEdit * Reorder and rename some methods for clarity * Improve commenting --- .../MantidQtMantidWidgets/HintingLineEdit.h | 8 +-- .../MantidWidgets/src/HintingLineEdit.cpp | 71 +++++++++++-------- 2 files changed, 45 insertions(+), 34 deletions(-) diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h index b5711092c7f5..ab4821d7699c 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h @@ -24,8 +24,9 @@ namespace MantidQt virtual ~HintingLineEdit(); protected: virtual void keyPressEvent(QKeyEvent* e); - void insertSuggestion(); void updateMatches(); + void showToolTip(); + void insertSuggestion(); void clearSuggestion(); void nextSuggestion(); void prevSuggestion(); @@ -34,9 +35,8 @@ namespace MantidQt std::map m_matches; std::map m_hints; bool m_dontComplete; - public slots: - void showHint(); - void updateHint(const QString& text); + protected slots: + void updateHints(const QString& text); }; } //namespace MantidWidgets } //namepsace MantidQt diff --git a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp index a798d0df1e6e..083646c4bd6d 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp +++ b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp @@ -7,10 +7,9 @@ namespace MantidQt { namespace MantidWidgets { - HintingLineEdit::HintingLineEdit(QWidget *parent, const std::map &hints) : QLineEdit(parent), m_hints(hints), m_dontComplete(false) { - connect(this, SIGNAL(textEdited(const QString&)), this, SLOT(updateHint(const QString&))); + connect(this, SIGNAL(textEdited(const QString&)), this, SLOT(updateHints(const QString&))); } HintingLineEdit::~HintingLineEdit() @@ -24,6 +23,7 @@ namespace MantidQt if(e->key() == Qt::Key_Up) { prevSuggestion(); + return; } if(e->key() == Qt::Key_Down) @@ -34,6 +34,35 @@ namespace MantidQt QLineEdit::keyPressEvent(e); } + void HintingLineEdit::updateHints(const QString& text) + { + const size_t curPos = (size_t)cursorPosition(); + const std::string line = text.toStdString(); + + //Get everything before the cursor + std::string prefix = line.substr(0, curPos); + + //Now remove everything before the last ',' to give us the current word + std::size_t startPos = prefix.find_last_of(","); + if(startPos != std::string::npos) + prefix = prefix.substr(startPos + 1, prefix.size() - (startPos + 1)); + + //Remove any leading or trailing whitespace + boost::trim(prefix); + + //Set the current key/prefix + m_curKey = prefix; + + //Update our current list of matches + updateMatches(); + + //Show the potential matches in a tooltip + showToolTip(); + + //Suggest one of them to the user via auto-completion + insertSuggestion(); + } + void HintingLineEdit::updateMatches() { m_curMatch.clear(); @@ -53,22 +82,13 @@ namespace MantidQt } } - void HintingLineEdit::updateHint(const QString& text) + void HintingLineEdit::showToolTip() { - const size_t curPos = (size_t)cursorPosition(); - const std::string line = text.toStdString(); - - //Get text from start -> cursor - std::string prefix = line.substr(0, curPos); - - std::size_t startPos = prefix.find_last_of(","); - if(startPos != std::string::npos) - prefix = prefix.substr(startPos + 1, prefix.size() - (startPos + 1)); - - boost::trim(prefix); + QString hintList; + for(auto mIt = m_matches.begin(); mIt != m_matches.end(); ++mIt) + hintList += QString::fromStdString(mIt->first) + " : " + QString::fromStdString(mIt->second) + "\n"; - m_curKey = prefix; - showHint(); + QToolTip::showText(mapToGlobal(QPoint(0, 5)), hintList.trimmed()); } void HintingLineEdit::insertSuggestion() @@ -76,6 +96,7 @@ namespace MantidQt if(m_curKey.length() < 1 || m_matches.size() < 1 || m_dontComplete) return; + //If we don't have a match, just use the first one in the map if(m_curMatch.empty()) m_curMatch = m_matches.begin()->first; @@ -86,6 +107,7 @@ namespace MantidQt if(curPos + 1 < line.size() && line[curPos+1].isLetterOrNumber()) return; + //Insert a suggestion under the cursor, then select it line = line.left(curPos) + QString::fromStdString(m_curMatch).mid((int)m_curKey.size()) + line.mid(curPos); setText(line); @@ -97,7 +119,7 @@ namespace MantidQt if(!hasSelectedText()) return; - //Remove the selected text + //Carefully cut out the selected text QString line = text(); line = line.left(selectionStart()) + line.mid(selectionStart() + selectedText().length()); setText(line); @@ -106,6 +128,7 @@ namespace MantidQt void HintingLineEdit::nextSuggestion() { clearSuggestion(); + //Find the next suggestion in the hint map auto it = m_matches.find(m_curMatch); if(it != m_matches.end()) { @@ -121,6 +144,7 @@ namespace MantidQt void HintingLineEdit::prevSuggestion() { clearSuggestion(); + //Find the previous suggestion in the hint map auto it = m_matches.find(m_curMatch); if(it != m_matches.end()) { @@ -132,18 +156,5 @@ namespace MantidQt insertSuggestion(); } } - - void HintingLineEdit::showHint() - { - updateMatches(); - - QString hintList; - for(auto mIt = m_matches.begin(); mIt != m_matches.end(); ++mIt) - hintList += QString::fromStdString(mIt->first) + " : " + QString::fromStdString(mIt->second) + "\n"; - - QToolTip::showText(mapToGlobal(QPoint(0, 5)), hintList.trimmed()); - - insertSuggestion(); - } } //namespace MantidWidgets } //namepsace MantidQt From aa64548b4fb656b1ffccb93c7758ca852fe4b578 Mon Sep 17 00:00:00 2001 From: Harry Jeffery Date: Thu, 23 Oct 2014 09:34:48 +0100 Subject: [PATCH 52/52] Refs #10348 Add copyright headers and doxygen comments --- .../AlgorithmHintStrategy.h | 22 +++++++++++++++ .../inc/MantidQtMantidWidgets/HintStrategy.h | 27 ++++++++++++++++++- .../MantidQtMantidWidgets/HintingLineEdit.h | 22 +++++++++++++++ .../HintingLineEditFactory.h | 22 +++++++++++++++ .../MantidWidgets/src/HintingLineEdit.cpp | 15 +++++++++++ 5 files changed, 107 insertions(+), 1 deletion(-) diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/AlgorithmHintStrategy.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/AlgorithmHintStrategy.h index 161168e5c460..d4cc24b80664 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/AlgorithmHintStrategy.h +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/AlgorithmHintStrategy.h @@ -10,6 +10,28 @@ namespace MantidQt { namespace CustomInterfaces { + /** AlgorithmHintStrategy : Produces hints using a given algorithm's properties. + + 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 . + + File change history is stored at: + Code Documentation is available at: + */ class AlgorithmHintStrategy : public HintStrategy { public: diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintStrategy.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintStrategy.h index 9fbe15852f13..204ba658e372 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintStrategy.h +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintStrategy.h @@ -8,13 +8,38 @@ namespace MantidQt { namespace CustomInterfaces { + /** HintStrategy : Provides an interface for generating hints to be used by a HintingLineEdit. + + 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 . + + File change history is stored at: + Code Documentation is available at: + */ class HintStrategy { public: HintStrategy() {}; virtual ~HintStrategy() {}; - //Provides a map of hints to be used by a HintingLineEdit widget + /** Create a list of hints for auto completion + + @returns A map of keywords to short descriptions for the keyword. + */ virtual std::map createHints() = 0; }; } diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h index ab4821d7699c..377573916d05 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEdit.h @@ -16,6 +16,28 @@ namespace MantidQt { namespace MantidWidgets { + /** HintingLineEdit : A QLineEdit widget providing autocompletion. + + 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 . + + File change history is stored at: + Code Documentation is available at: + */ class EXPORT_OPT_MANTIDQT_MANTIDWIDGETS HintingLineEdit : public QLineEdit { Q_OBJECT diff --git a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEditFactory.h b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEditFactory.h index ecf8f839026a..e63ddcebcc49 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEditFactory.h +++ b/Code/Mantid/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/HintingLineEditFactory.h @@ -15,6 +15,28 @@ namespace MantidQt { namespace CustomInterfaces { + /** HintingLineEditFactory : A QStyledItemDelegate that produces HintingLineEdits using the given hint strategy. + + 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 . + + File change history is stored at: + Code Documentation is available at: + */ class HintingLineEditFactory : public QStyledItemDelegate { public: diff --git a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp index 083646c4bd6d..be2abe0b1379 100644 --- a/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp +++ b/Code/Mantid/MantidQt/MantidWidgets/src/HintingLineEdit.cpp @@ -16,6 +16,10 @@ namespace MantidQt { } + /** Handle a key press event. + + @param e : A pointer to the event + */ void HintingLineEdit::keyPressEvent(QKeyEvent* e) { m_dontComplete = (e->key() == Qt::Key_Backspace || e->key() == Qt::Key_Delete || e->key() == Qt::Key_Space); @@ -34,6 +38,11 @@ namespace MantidQt QLineEdit::keyPressEvent(e); } + /** Rebuild a list of hints whenever the user edits the text, and use the hints + to make auto completion suggestions. + + @param text : The new contents of the QLineEdit + */ void HintingLineEdit::updateHints(const QString& text) { const size_t curPos = (size_t)cursorPosition(); @@ -63,6 +72,7 @@ namespace MantidQt insertSuggestion(); } + /** Updates the list of hints matching the user's current input */ void HintingLineEdit::updateMatches() { m_curMatch.clear(); @@ -82,6 +92,7 @@ namespace MantidQt } } + /** Show a tooltip with the current relevant hints */ void HintingLineEdit::showToolTip() { QString hintList; @@ -91,6 +102,7 @@ namespace MantidQt QToolTip::showText(mapToGlobal(QPoint(0, 5)), hintList.trimmed()); } + /** Insert an auto completion suggestion beneath the user's cursor and select it */ void HintingLineEdit::insertSuggestion() { if(m_curKey.length() < 1 || m_matches.size() < 1 || m_dontComplete) @@ -114,6 +126,7 @@ namespace MantidQt setSelection(curPos, (int)m_curMatch.size()); } + /** Remove any existing auto completion suggestion */ void HintingLineEdit::clearSuggestion() { if(!hasSelectedText()) @@ -125,6 +138,7 @@ namespace MantidQt setText(line); } + /** Change to the next available auto completion suggestion */ void HintingLineEdit::nextSuggestion() { clearSuggestion(); @@ -141,6 +155,7 @@ namespace MantidQt } } + /** Change to the previous auto completion suggestion */ void HintingLineEdit::prevSuggestion() { clearSuggestion();