Refs #12863 New branch with all commits

Framework/API/src/IMDWorkspace.cpp

 #include "MantidAPI/IMDWorkspace.h"
 #include "MantidKernel/Exception.h"
 #include "MantidKernel/IPropertyManager.h"
+#include "MantidKernel/ConfigService.h"
 #include "MantidKernel/VMD.h"
 
 #include <sstream>
@@ -88,6 +89,14 @@ const std::string IMDWorkspace::toString() const {
     os << "Binned from '" << getOriginalWorkspace()->getName();
   }
   os << "\n";
+  std::string convention =
+      Kernel::ConfigService::Instance().getString("Q.convention");
+  if (convention == "Crystallography")
+    os << "Crystallography: ki-kf";
+  else
+    os << "Inelastic: kf-ki";
+  os << "\n";
+
   return os.str();
 }
 

Framework/API/src/MDGeometry.cpp

@@ -379,7 +379,10 @@ void MDGeometry::transformDimensions(std::vector<double> &scaling,
                   static_cast<coord_t>(offset[d]);
     coord_t max = (dim->getMaximum() * static_cast<coord_t>(scaling[d])) +
                   static_cast<coord_t>(offset[d]);
-    dim->setRange(dim->getNBins(), min, max);
+    if (min < max)
+      dim->setRange(dim->getNBins(), min, max);
+    else
+      dim->setRange(dim->getNBins(), max, min);
   }
   // Clear the original workspace
   setOriginalWorkspace(boost::shared_ptr<Workspace>());

Framework/Crystal/inc/MantidCrystal/LoadIsawPeaks.h

@@ -59,7 +59,7 @@ private:
   /// Read a single peak from peaks file
   DataObjects::Peak readPeak(DataObjects::PeaksWorkspace_sptr outWS,
                              std::string &lastStr, std::ifstream &in,
-                             int &seqNum, std::string bankName);
+                             int &seqNum, std::string bankName, double qSign);
 
   int findPixelID(Geometry::Instrument_const_sptr inst, std::string bankName,
                   int col, int row);

Framework/Crystal/src/LoadHKL.cpp

@@ -33,9 +33,11 @@ LoadHKL::~LoadHKL() {}
 /** Initialize the algorithm's properties.
  */
 void LoadHKL::init() {
-  declareProperty(
-      new FileProperty("Filename", "", FileProperty::Load, {".hkl"}),
-      "Path to an hkl file to save.");
+  std::vector<std::string> exts;
+  exts.push_back(".hkl");
+
+  declareProperty(new FileProperty("Filename", "", FileProperty::Load, exts),
+                  "Path to an hkl file to save.");
 
   declareProperty(new WorkspaceProperty<PeaksWorkspace>("OutputWorkspace", "",
                                                         Direction::Output),
@@ -58,6 +60,11 @@ void LoadHKL::exec() {
   //    % (H, K, L, FSQ, SIGFSQ, hstnum, WL, TBAR, CURHST, SEQNUM, TRANSMISSION,
   //    DN, TWOTH, DSP))
   // HKL is flipped by -1 due to different q convention in ISAW vs mantid.
+  // Default for kf-ki has -q
+  double qSign = -1.0;
+  std::string convention = ConfigService::Instance().getString("Q.convention");
+  if (convention == "Crystallography")
+    qSign = 1.0;
   Instrument_sptr inst(new Geometry::Instrument);
   Detector *detector = new Detector("det1", -1, 0);
   detector->setPos(0.0, 0.0, 0.0);
@@ -105,7 +112,7 @@ void LoadHKL::exec() {
     }
 
     Peak peak(inst, scattering, wl);
-    peak.setHKL(-h, -k, -l);
+    peak.setHKL(qSign * h, qSign * k, qSign * l);
     peak.setIntensity(Inti);
     peak.setSigmaIntensity(SigI);
     peak.setRunNumber(run);

Framework/Crystal/src/LoadIsawPeaks.cpp

@@ -328,12 +328,13 @@ std::string LoadIsawPeaks::readHeader(PeaksWorkspace_sptr outWS,
  * @param in :: input stream
  * @param seqNum [out] :: the sequence number of the peak
  * @param bankName :: the bank number from the ISAW file.
+ * @param qSign :: For inelastic this is 1; for crystallography this is -1
  * @return the Peak the Peak object created
  */
 DataObjects::Peak LoadIsawPeaks::readPeak(PeaksWorkspace_sptr outWS,
                                           std::string &lastStr,
                                           std::ifstream &in, int &seqNum,
-                                          std::string bankName) {
+                                          std::string bankName, double qSign) {
   double h;
   double k;
   double l;
@@ -406,8 +407,7 @@ DataObjects::Peak LoadIsawPeaks::readPeak(PeaksWorkspace_sptr outWS,
 
   // Create the peak object
   Peak peak(outWS->getInstrument(), pixelID, wl);
-  // HKL's are flipped by -1 because of the internal Q convention
-  peak.setHKL(-h, -k, -l);
+  peak.setHKL(qSign * h, qSign * k, qSign * l);
   peak.setIntensity(Inti);
   peak.setSigmaIntensity(SigI);
   peak.setBinCount(IPK);
@@ -504,7 +504,12 @@ std::string LoadIsawPeaks::readPeakBlockHeader(std::string lastStr,
  */
 void LoadIsawPeaks::appendFile(PeaksWorkspace_sptr outWS,
                                std::string filename) {
-
+  // HKL's are flipped by -1 because of the internal Q convention
+  // unless Crystallography convention
+  double qSign = -1.0;
+  std::string convention = ConfigService::Instance().getString("Q.convention");
+  if (convention == "Crystallography")
+    qSign = 1.0;
   // Open the file
   std::ifstream in(filename.c_str());
 
@@ -564,7 +569,7 @@ void LoadIsawPeaks::appendFile(PeaksWorkspace_sptr outWS,
 
     try {
       // Read the peak
-      Peak peak = readPeak(outWS, s, in, seqNum, bankName);
+      Peak peak = readPeak(outWS, s, in, seqNum, bankName, qSign);
 
       // Get the calculated goniometer matrix
       Matrix<double> gonMat = uniGonio.getR();

Framework/Crystal/src/SaveHKL.cpp

@@ -126,6 +126,12 @@ void SaveHKL::exec() {
   int runSequence = 0;
   int bankold = -1;
   int runold = -1;
+  // HKL is flipped by -1 due to different q convention in ISAW vs mantid.
+  // Default for kf-ki has -q
+  double qSign = -1.0;
+  std::string convention = ConfigService::Instance().getString("Q.convention");
+  if (convention == "Crystallography")
+    qSign = 1.0;
 
   std::fstream out;
   bool append = getProperty("AppendFile");
@@ -308,14 +314,14 @@ void SaveHKL::exec() {
     // hklFile.write('%4d%4d%4d%8.2f%8.2f%4d%8.4f%7.4f%7d%7d%7.4f%4d%9.5f%9.4f\n'
     //    % (H, K, L, FSQ, SIGFSQ, hstnum, WL, TBAR, CURHST, SEQNUM,
     //    TRANSMISSION, DN, TWOTH, DSP))
-    // HKL is flipped by -1 due to different q convention in ISAW vs mantid.
     if (p.getH() == 0 && p.getK() == 0 && p.getL() == 0) {
       banned.push_back(wi);
       continue;
     }
     if (decimalHKL == EMPTY_INT())
-      out << std::setw(4) << Utils::round(-p.getH()) << std::setw(4)
-          << Utils::round(-p.getK()) << std::setw(4) << Utils::round(-p.getL());
+      out << std::setw(4) << Utils::round(qSign * p.getH()) << std::setw(4)
+          << Utils::round(qSign * p.getK()) << std::setw(4)
+          << Utils::round(qSign * p.getL());
     else
       out << std::setw(5 + decimalHKL) << std::fixed
           << std::setprecision(decimalHKL) << -p.getH()

Framework/Crystal/src/SaveIsawPeaks.cpp

@@ -247,7 +247,12 @@ void SaveIsawPeaks::exec() {
       }
     }
   }
-
+  // HKL's are flipped by -1 because of the internal Q convention
+  // unless Crystallography convention
+  double qSign = -1.0;
+  std::string convention = ConfigService::Instance().getString("Q.convention");
+  if (convention == "Crystallography")
+    qSign = 1.0;
   // ============================== Save all Peaks
   // =========================================
   // Sequence number
@@ -305,11 +310,11 @@ void SaveIsawPeaks::exec() {
           // Sequence (run) number
           out << "3" << std::setw(7) << seqNum;
 
-          // HKL is flipped by -1 due to different q convention in ISAW vs
-          // mantid.
-          out << std::setw(5) << Utils::round(-p.getH()) << std::setw(5)
-              << Utils::round(-p.getK()) << std::setw(5)
-              << Utils::round(-p.getL());
+          // HKL's are flipped by -1 because of the internal Q convention
+          // unless Crystallography convention
+          out << std::setw(5) << Utils::round(qSign * p.getH()) << std::setw(5)
+              << Utils::round(qSign * p.getK()) << std::setw(5)
+              << Utils::round(qSign * p.getL());
 
           // Row/column
           out << std::setw(8) << std::fixed << std::setprecision(2)

Framework/Crystal/src/SaveLauenorm.cpp

@@ -111,6 +111,12 @@ void SaveLauenorm::exec() {
 
   // ============================== Save all Peaks
   // =========================================
+  // HKL is flipped by -1 due to different q convention in ISAW vs mantid.
+  // Default for kf-ki has -q
+  double qSign = -1.0;
+  std::string convention = ConfigService::Instance().getString("Q.convention");
+  if (convention == "Crystallography")
+    qSign = 1.0;
 
   // Go through each peak at this run / bank
   for (int wi = 0; wi < ws->getNumberPeaks(); wi++) {
@@ -170,10 +176,12 @@ void SaveLauenorm::exec() {
     // h k l lambda theta intensity and  sig(intensity)  in format
     // (3I5,2F10.5,2I10)
     // HKL is flipped by -1 due to different q convention in ISAW vs mantid.
+    // unless Crystallography convention
     if (p.getH() == 0 && p.getK() == 0 && p.getL() == 0)
       continue;
-    out << std::setw(5) << Utils::round(-p.getH()) << std::setw(5)
-        << Utils::round(-p.getK()) << std::setw(5) << Utils::round(-p.getL());
+    out << std::setw(5) << Utils::round(qSign * p.getH()) << std::setw(5)
+        << Utils::round(qSign * p.getK()) << std::setw(5)
+        << Utils::round(qSign * p.getL());
     out << std::setw(10) << std::fixed << std::setprecision(5) << lambda;
     // Assume that want theta not two-theta
     out << std::setw(10) << std::fixed << std::setprecision(5)

Framework/DataHandling/src/LoadNexusProcessed.cpp

@@ -1071,6 +1071,14 @@ API::Workspace_sptr LoadNexusProcessed::loadPeaksEntry(NXEntry &entry) {
   // peaks_workspace
   m_cppFile->closeGroup();
 
+  // HKL is flipped by -1 due to different q convention in Crystallography.
+  // Always write out in ki-kf so consistent with old files
+  double qSign = 1.0;
+  std::string convention =
+      ConfigService::Instance().getString("default.convention");
+  if (convention == "Crystallography")
+    qSign = -1.0;
+
   for (int r = 0; r < numberPeaks; r++) {
     Kernel::V3D v3d;
     v3d[2] = 1.0;
@@ -1097,7 +1105,7 @@ API::Workspace_sptr LoadNexusProcessed::loadPeaksEntry(NXEntry &entry) {
       nxDouble.load();
 
       for (int r = 0; r < numberPeaks; r++) {
-        double val = nxDouble[r];
+        double val = qSign * nxDouble[r];
         peakWS->getPeak(r).setH(val);
       }
     }
@@ -1107,7 +1115,7 @@ API::Workspace_sptr LoadNexusProcessed::loadPeaksEntry(NXEntry &entry) {
       nxDouble.load();
 
       for (int r = 0; r < numberPeaks; r++) {
-        double val = nxDouble[r];
+        double val = qSign * nxDouble[r];
         peakWS->getPeak(r).setK(val);
       }
     }
@@ -1117,7 +1125,7 @@ API::Workspace_sptr LoadNexusProcessed::loadPeaksEntry(NXEntry &entry) {
       nxDouble.load();
 
       for (int r = 0; r < numberPeaks; r++) {
-        double val = nxDouble[r];
+        double val = qSign * nxDouble[r];
         peakWS->getPeak(r).setL(val);
       }
     }
@@ -1629,20 +1637,11 @@ void LoadNexusProcessed::readInstrumentGroup(
 
   // Now build the spectra list
   int index = 0;
-  bool haveSpectraAxis = local_workspace->getAxis(1)->isSpectra();
 
   for (int i = 1; i <= spectraInfo.nSpectra; ++i) {
     int spectrum(-1);
-    // prefer the spectra number from the instrument section
-    // over anything else. If not there then use a spectra axis
-    // number if we have one, else make one up as nothing was
-    // written to the file. We should always set it so that
-    // CompareWorkspaces gives the expected answer on a Save/Load
-    // round trip.
     if (spectraInfo.hasSpectra) {
       spectrum = spectraInfo.spectraNumbers[i - 1];
-    } else if (haveSpectraAxis && !m_axis1vals.empty()) {
-      spectrum = static_cast<specid_t>(m_axis1vals[i - 1]);
     } else {
       spectrum = i + 1;
     }
@@ -1652,7 +1651,11 @@ void LoadNexusProcessed::readInstrumentGroup(
          find(m_spec_list.begin(), m_spec_list.end(), i) !=
              m_spec_list.end())) {
       ISpectrum *spec = local_workspace->getSpectrum(index);
-      spec->setSpectrumNo(spectrum);
+      if (m_axis1vals.empty()) {
+        spec->setSpectrumNo(spectrum);
+      } else {
+        spec->setSpectrumNo(static_cast<specid_t>(m_axis1vals[i - 1]));
+      }
       ++index;
 
       int start = spectraInfo.detectorIndex[i - 1];

Framework/DataObjects/inc/MantidDataObjects/MDBox.tcc

@@ -690,6 +690,7 @@ TMDE(void MDBox)::centroidSphere(Mantid::API::CoordTransform &radiusTransform,
 TMDE(void MDBox)::transformDimensions(std::vector<double> &scaling,
                                       std::vector<double> &offset) {
   MDBoxBase<MDE, nd>::transformDimensions(scaling, offset);
+  this->calculateCentroid(this->m_centroid);
   std::vector<MDE> &events = this->getEvents();
   typename std::vector<MDE>::iterator it;
   typename std::vector<MDE>::iterator it_end = events.end();

Framework/DataObjects/inc/MantidDataObjects/MDEventWorkspace.tcc

@@ -16,6 +16,8 @@
 #include "MantidDataObjects/MDFramesToSpecialCoordinateSystem.h"
 #include "MantidDataObjects/MDGridBox.h"
 #include "MantidDataObjects/MDLeanEvent.h"
+#include "MantidKernel/ConfigService.h"
+
 #include <iomanip>
 #include <functional>
 #include <algorithm>
@@ -327,6 +329,7 @@ TMDE(signal_t MDEventWorkspace)::getSignalWithMaskAtCoord(
   }
   // Check if masked
   const API::IMDNode *box = data->getBoxAtCoord(coords);
+  if (!box) return MDMaskValue;
   if (box->getIsMasked()) {
     return MDMaskValue;
   }
@@ -376,6 +379,7 @@ TMDE(std::vector<Mantid::Geometry::MDDimensionExtents<coord_t>>
 TMDE(std::vector<std::string> MDEventWorkspace)::getBoxControllerStats() const {
   std::vector<std::string> out;
   std::ostringstream mess;
+ 
   size_t mem;
   mem = (this->m_BoxController->getTotalNumMDBoxes() * sizeof(MDBox<MDE, nd>)) /
         1024;

Framework/DataObjects/inc/MantidDataObjects/Peak.h

@@ -9,6 +9,7 @@
 #include "MantidKernel/PhysicalConstants.h"
 #include "MantidKernel/System.h"
 #include "MantidGeometry/Crystal/PeakShape.h"
+#include "MantidKernel/ConfigService.h"
 #include <boost/shared_ptr.hpp>
 #include <boost/optional.hpp>
 
@@ -214,6 +215,10 @@ private:
 
   /// Static logger
   static Mantid::Kernel::Logger g_log;
+
+  // ki-kf for Inelastic convention; kf-ki for Crystallography convention
+  std::string convention =
+      Kernel::ConfigService::Instance().getString("Q.convention");
 };
 
 } // namespace Mantid

Framework/DataObjects/src/MDBoxFlatTree.cpp

@@ -749,6 +749,12 @@ void MDBoxFlatTree::saveWSGenericInfo(::NeXus::File *const file,
   file->writeData("coordinate_system",
                   static_cast<uint32_t>(ws->getSpecialCoordinateSystem()));
 
+  // Write out the Qconvention
+  // ki-kf for Inelastic convention; kf-ki for Crystallography convention
+  std::string m_QConvention =
+      Kernel::ConfigService::Instance().getString("Q.convention");
+  file->writeData("QConvention", m_QConvention);
+
   // Write out the set display normalization
   file->writeData("visual_normalization",
                   static_cast<uint32_t>(ws->displayNormalization()));
@@ -808,6 +814,8 @@ void MDBoxFlatTree::saveAffineTransformMatricies(
 void MDBoxFlatTree::saveAffineTransformMatrix(
     ::NeXus::File *const file, API::CoordTransform const *transform,
     std::string entry_name) {
+  if (!transform)
+    return;
   Kernel::Matrix<coord_t> matrix = transform->makeAffineMatrix();
   g_log.debug() << "TRFM: " << matrix.str() << std::endl;
   saveMatrix<coord_t>(file, entry_name, matrix, ::NeXus::FLOAT32,

Framework/DataObjects/src/Peak.cpp

@@ -452,7 +452,11 @@ Mantid::Kernel::V3D Peak::getQLabFrame() const {
   // Now calculate the wavevector of the scattered neutron
   double wvf = (2.0 * M_PI) / this->getWavelength();
   // And Q in the lab frame
-  return beamDir * wvi - detDir * wvf;
+  // Default for ki-kf is positive
+  double qSign = 1.0;
+  if (convention == "Crystallography")
+    qSign = -1.0;
+  return (beamDir * wvi - detDir * wvf) * qSign;
 }
 
 //----------------------------------------------------------------------------------------------
@@ -528,7 +532,11 @@ void Peak::setQLabFrame(Mantid::Kernel::V3D QLabFrame,
   boost::shared_ptr<const ReferenceFrame> refFrame =
       this->m_inst->getReferenceFrame();
   const V3D refBeamDir = refFrame->vecPointingAlongBeam();
-  const double qBeam = q.scalar_prod(refBeamDir);
+  // Default for ki-kf has -q
+  double qSign = 1.0;
+  if (convention == "Crystallography")
+    qSign = -1.0;
+  const double qBeam = q.scalar_prod(refBeamDir) * qSign;
 
   if (norm_q == 0.0)
     throw std::invalid_argument("Peak::setQLabFrame(): Q cannot be 0,0,0.");
@@ -548,7 +556,12 @@ void Peak::setQLabFrame(Mantid::Kernel::V3D QLabFrame,
   // Save the wavelength
   this->setWavelength(wl);
 
-  V3D detectorDir = q * -1.0;
+  // Default for ki-kf has -q
+  qSign = -1.0;
+  if (convention == "Crystallography")
+    qSign = 1.0;
+
+  V3D detectorDir = q * qSign;
   detectorDir[refFrame->pointingAlongBeam()] = one_over_wl - qBeam;
   detectorDir.normalize();
 

Framework/DataObjects/src/PeaksWorkspace.cpp

@@ -605,14 +605,21 @@ void PeaksWorkspace::saveNexus(::NeXus::File *file) const {
   std::vector<double> goniometerMatrix(9 * np);
   std::vector<std::string> shapes(np);
 
+  // HKL is flipped by -1 due to different q convention in Crystallography.
+  // Always write out in ki-kf so consistent with old files
+  double qSign = 1.0;
+  std::string convention = ConfigService::Instance().getString("Q.convention");
+  if (convention == "Crystallography")
+    qSign = -1.0;
+
   // Populate column vectors from Peak Workspace
   size_t maxShapeJSONLength = 0;
   for (size_t i = 0; i < np; i++) {
     Peak p = peaks[i];
     detectorID[i] = p.getDetectorID();
-    H[i] = p.getH();
-    K[i] = p.getK();
-    L[i] = p.getL();
+    H[i] = qSign * p.getH();
+    K[i] = qSign * p.getK();
+    L[i] = qSign * p.getL();
     intensity[i] = p.getIntensity();
     sigmaIntensity[i] = p.getSigmaIntensity();
     binCount[i] = p.getBinCount();

Framework/Geometry/inc/MantidGeometry/MDGeometry/MDDimensionExtents.h

@@ -58,6 +58,12 @@ public:
     min = static_cast<T>(min * scaling + offset);
     max = static_cast<T>(max * scaling + offset);
     m_size = static_cast<T>(m_size * scaling);
+    if (max < min) {
+      T tmp = max;
+      max = min;
+      min = tmp;
+      m_size = std::fabs(m_size);
+    }
   }
   // it looks like this loses accuracy?
   void expand(MDDimensionExtents &other) {

Framework/Kernel/src/ConfigService.cpp

@@ -673,10 +673,15 @@ void ConfigServiceImpl::createUserPropertiesFile() const {
     filestr << "## e.g.: ISIS, SNS, ILL" << std::endl;
     filestr << "default.facility=" << std::endl;
     filestr << std::endl;
-    filestr << "## Stes the default instrument" << std::endl;
+    filestr << "## Sets the default instrument" << std::endl;
     filestr << "## e.g. IRIS, HET, NIMROD" << std::endl;
     filestr << "default.instrument=" << std::endl;
     filestr << std::endl;
+    filestr << std::endl;
+    filestr << "## Sets the Q.convention" << std::endl;
+    filestr << "## Set to Crystallography for kf-ki instead of default "
+               "Inelastic which is ki-kf" << std::endl;
+    filestr << "#Q.convention=Crystallography" << std::endl;
     filestr << "##" << std::endl;
     filestr << "## DIRECTORIES" << std::endl;
     filestr << "##" << std::endl;

Framework/MDAlgorithms/inc/MantidMDAlgorithms/CalculateCoverageDGS.h

@@ -46,6 +46,9 @@ private:
   void init();
   void exec();
 
+  // ki-kf for Inelastic convention; kf-ki for Crystallography convention
+  std::string convention =
+      Kernel::ConfigService::Instance().getString("Q.convention");
   /// limits for h,k,l,dE dimensions
   coord_t m_hmin, m_hmax, m_kmin, m_kmax, m_lmin, m_lmax, m_dEmin, m_dEmax;
   /// cached values for incident energy and momentum, final momentum min/max

Framework/MDAlgorithms/inc/MantidMDAlgorithms/LoadMD.h

@@ -66,6 +66,10 @@ private:
   /// Run the algorithm
   void exec();
 
+  // ki-kf for Inelastic convention; kf-ki for Crystallography convention
+  std::string convention =
+      Kernel::ConfigService::Instance().getString("Q.convention");
+
   /// Helper method
   template <typename MDE, size_t nd>
   void doLoad(typename DataObjects::MDEventWorkspace<MDE, nd>::sptr ws);
@@ -84,6 +88,8 @@ private:
 
   void loadCoordinateSystem();
 
+  void loadQConvention();
+
   void loadVisualNormalization(
       const std::string &key,
       boost::optional<Mantid::API::MDNormalization> &normalization);
@@ -114,6 +120,8 @@ private:
   std::vector<Mantid::Geometry::IMDDimension_sptr> m_dims;
   /// Coordinate system
   Kernel::SpecialCoordinateSystem m_coordSystem;
+  /// QConvention
+  std::string m_QConvention;
   /// load only the box structure with empty boxes but do not tload boxes events
   bool m_BoxStructureAndMethadata;
 

Framework/MDAlgorithms/inc/MantidMDAlgorithms/MDNormDirectSC.h

@@ -88,6 +88,9 @@ private:
   Kernel::V3D m_samplePos;
   /// Beam direction
   Kernel::V3D m_beamDir;
+  /// ki-kf for Inelastic convention; kf-ki for Crystallography convention
+  std::string convention =
+      Kernel::ConfigService::Instance().getString("Q.convention");
 };
 
 } // namespace MDAlgorithms