SaveZODS.cpp

Go to the documentation of this file.

// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
//   NScD Oak Ridge National Laboratory, European Spallation Source,
//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidMDAlgorithms/SaveZODS.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/IMDHistoWorkspace.h"
#include "MantidAPI/Sample.h"
#include "MantidDataObjects/MDHistoWorkspace.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidKernel/Strings.h"
 
using namespace Mantid::Kernel;
using namespace Mantid::API;
using namespace Mantid::Geometry;
using namespace Mantid::DataObjects;
 
namespace Mantid::MDAlgorithms {
 
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(SaveZODS)
 
 
const std::string SaveZODS::name() const { return "SaveZODS"; }
 
int SaveZODS::version() const { return 1; }
 
const std::string SaveZODS::category() const { return "MDAlgorithms\\DataHandling"; }
 
void SaveZODS::init() {
  declareProperty(std::make_unique<WorkspaceProperty<IMDHistoWorkspace>>("InputWorkspace", "", Direction::Input),
                  "An input MDHistoWorkspace in HKL space.");
 
  declareProperty(std::make_unique<FileProperty>("Filename", "", FileProperty::Save, ".h5"),
                  "The name of the HDF5 file to write, as a full or relative path.");
}
 
void SaveZODS::exec() {
  IMDHistoWorkspace_sptr inWS = getProperty("InputWorkspace");
  std::string Filename = getPropertyValue("Filename");
  MDHistoWorkspace_sptr ws = std::dynamic_pointer_cast<MDHistoWorkspace>(inWS);
  if (!ws)
    throw std::runtime_error("InputWorkspace is not a MDHistoWorkspace");
  if (ws->getNumDims() != 3)
    throw std::runtime_error("InputWorkspace must have 3 dimensions (having "
                             "one bin in the 3rd dimension is OK).");
 
  if (ws->getDimension(0)->getName() != "[H,0,0]")
    g_log.warning() << "SaveZODS expects the workspace to be in HKL space! "
                       "Saving anyway...\n";
 
  // Create a HDF5 file
  auto file = std::make_unique<Nexus::File>(Filename, NXaccess::CREATE5);
 
  // ----------- Coordinate system -----------
  uint32_t isLocal = 1;
  file->makeGroup("CoordinateSystem", "NXgroup", true);
  file->putAttr("isLocal", isLocal);
 
  if (ws->getNumExperimentInfo() > 0) {
    ExperimentInfo_const_sptr ei = ws->getExperimentInfo(0);
    if (ei) {
      if (ei->sample().hasOrientedLattice()) {
        std::vector<double> unitCell;
        const OrientedLattice &latt = ei->sample().getOrientedLattice();
        unitCell.emplace_back(latt.a());
        unitCell.emplace_back(latt.b());
        unitCell.emplace_back(latt.c());
        unitCell.emplace_back(latt.alpha());
        unitCell.emplace_back(latt.beta());
        unitCell.emplace_back(latt.gamma());
 
        // Now write out the 6D vector
        const Nexus::DimVector unit_cell_size(1, 6);
        file->writeData("unit_cell", unitCell, unit_cell_size);
      }
    }
  }
 
  file->closeGroup();
 
  uint64_t numPoints = ws->getNPoints();
 
  file->makeGroup("Data", "NXgroup", true);
  file->makeGroup("Data_0", "NXgroup", true);
 
  // ----------- Attributes ------------------
  std::vector<double> origin(3, 0.0);
 
  // Size in each dimension (in the "C" style order, so z,y,x
  // That is, data[z][y][x] = etc.
  Nexus::DimVector size(3, 0);
 
  // And this will be the "size" field we save, in the usual XYZ order.
  std::vector<int> size_field(3, 0);
 
  // Dimension_X attributes give the step size for each dimension
  for (size_t d = 0; d < 3; d++) {
    IMDDimension_const_sptr dim = ws->getDimension(d);
    std::vector<double> direction(3, 0.0);
    direction[d] = dim->getBinWidth();
    // Origin of the CENTER of the first bin
    origin[d] = dim->getMinimum() + dim->getBinWidth() / 2;
    // Size in each dimension (reverse order for RANK)
    size[2 - d] = int(dim->getNBins());
    // Size in each dimension (in the XYZ order)
    size_field[d] = int(dim->getNBins());
    file->writeData("direction_" + Strings::toString(d + 1), direction);
  }
  file->writeData("origin", origin);
  file->writeData("size", size_field);
 
  // Copy data into a vector
  const auto signal = ws->getSignalArray();
  std::vector<double> data;
 
  for (int i = 0; i < size_field[0]; i++)
    for (int j = 0; j < size_field[1]; j++)
      for (int k = 0; k < size_field[2]; k++) {
        int l = i + size_field[0] * j + size_field[0] * size_field[1] * k;
        data.emplace_back(signal[l]);
      }
 
  file->writeData("Data", data, size);
 
  // Copy errors (not squared) into a vector called sigma
  const auto errorSquared = ws->getErrorSquaredArray();
  std::vector<double> sigma;
  sigma.reserve(numPoints);
  for (int i = 0; i < size_field[0]; i++)
    for (int j = 0; j < size_field[1]; j++)
      for (int k = 0; k < size_field[2]; k++) {
        int l = i + size_field[0] * j + size_field[0] * size_field[1] * k;
        sigma.emplace_back(sqrt(errorSquared[l]));
      }
  file->writeData("sigma", sigma, size);
 
  // Close Data_0 group
  file->closeGroup();
  // Close Data group
  file->closeGroup();
 
  file->close();
}
 
} // namespace Mantid::MDAlgorithms