IndexSXPeaks.cpp

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// 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 +
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidCrystal/IndexSXPeaks.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidGeometry/Crystal/IPeak.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/VectorHelper.h"
 
namespace Mantid::Crystal {
 
// Register the class into the algorithm factory
DECLARE_ALGORITHM(IndexSXPeaks)
 
using namespace Geometry;
using namespace API;
using namespace Kernel;
 
void IndexSXPeaks::init() {
  auto mustBePositive = std::make_shared<BoundedValidator<double>>();
  mustBePositive->setLower(0.0);
 
  auto reasonable_angle = std::make_shared<BoundedValidator<double>>();
  reasonable_angle->setLower(5.0);
  reasonable_angle->setUpper(175.0);
 
  declareProperty(
      std::make_unique<WorkspaceProperty<Mantid::DataObjects::PeaksWorkspace>>("PeaksWorkspace", "", Direction::InOut),
      "Input Peaks Workspace");
 
  declareProperty(std::make_unique<PropertyWithValue<double>>("a", -1.0, mustBePositive->clone(), Direction::Input),
                  "Lattice parameter a");
 
  declareProperty(std::make_unique<PropertyWithValue<double>>("b", -1.0, mustBePositive->clone(), Direction::Input),
                  "Lattice parameter b");
 
  declareProperty(std::make_unique<PropertyWithValue<double>>("c", -1.0, std::move(mustBePositive), Direction::Input),
                  "Lattice parameter c");
 
  declareProperty(
      std::make_unique<PropertyWithValue<double>>("alpha", -1.0, reasonable_angle->clone(), Direction::Input),
      "Lattice parameter alpha");
 
  declareProperty(
      std::make_unique<PropertyWithValue<double>>("beta", -1.0, reasonable_angle->clone(), Direction::Input),
      "Lattice parameter beta");
 
  declareProperty(
      std::make_unique<PropertyWithValue<double>>("gamma", -1.0, std::move(reasonable_angle), Direction::Input),
      "Lattice parameter gamma");
 
  declareProperty(std::make_unique<ArrayProperty<int>>("PeakIndices"),
                  "Index of the peaks in the table workspace to be used. If no "
                  "index are provided, all will be used.");
 
  declareProperty("dTolerance", 0.01, "Tolerance for peak positions in d-spacing");
 
  std::vector<int> extents(6, 0);
  const int range = 20;
  extents[0] = -range;
  extents[1] = range;
  extents[2] = -range;
  extents[3] = range;
  extents[4] = -range;
  extents[5] = range;
  declareProperty(std::make_unique<ArrayProperty<int>>("SearchExtents", std::move(extents)),
                  "A comma separated list of min, max for each of H, K and L,\n"
                  "Specifies the search extents applied for H K L values "
                  "associated with the peaks.");
}
 
void IndexSXPeaks::cullHKLs(std::vector<PeakCandidate> &peakCandidates, Mantid::Geometry::UnitCell &unitcell) {
  size_t npeaks = peakCandidates.size();
  for (std::size_t p = 0; p < npeaks; p++) {
    for (std::size_t q = 0; q < npeaks; q++) {
      if (p == q) // Don't do a self comparison
      {
        continue;
      }
      peakCandidates[p].clean(peakCandidates[q], unitcell,
                              0.5 * M_PI / 180.0); // Half a degree tolerance
    }
  }
}
 
void IndexSXPeaks::validateNotColinear(const std::vector<PeakCandidate> &peakCandidates) const {
  // Find two non-colinear peaks
  bool all_collinear = true;
  size_t npeaks = peakCandidates.size();
  for (std::size_t i = 0; i < npeaks; i++) {
    for (std::size_t j = i; j < npeaks; j++) {
      double anglerad = peakCandidates[i].angle(peakCandidates[j]);
      if (anglerad > 2.0 * M_PI / 180.0 && anglerad < 178.0 * M_PI / 180.0) {
        all_collinear = false;
        break;
      }
    }
  }
  // Throw if all collinear
  if (all_collinear) {
    throw std::runtime_error("Angles between all pairs of peaks are too small");
  }
}
 
void IndexSXPeaks::exec() {
  using namespace Mantid::DataObjects;
  std::vector<int> peakindices = getProperty("PeakIndices");
 
  PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
 
  // Need a least two peaks
  std::size_t npeaks = peakindices.size();
  if (npeaks > size_t(ws->getNumberPeaks())) {
    throw std::runtime_error("Cannot have more peaks indices than actual peaks");
  }
  if (npeaks == 1 || ws->getNumberPeaks() < 2) {
    throw std::runtime_error("At least 2 peaks are required for this algorithm to work");
  }
  if (npeaks == 0) {
    // If the user provides no peaks we default to use all the available peaks.
    npeaks = ws->getNumberPeaks();
    peakindices.reserve(npeaks);
    for (int i = 1; i <= int(npeaks); i++) // create indexes corresponding to all peak indexes
    {
      peakindices.emplace_back(i);
    }
    g_log.information("No peak indexes provided. Algorithm will use all peaks "
                      "in the workspace for the calculation.");
  }
 
  // Get the effective unit cell
  double a = getProperty("a");
  double b = getProperty("b");
  double c = getProperty("c");
  double alpha = getProperty("alpha");
  double beta = getProperty("beta");
  double gamma = getProperty("gamma");
 
  std::vector<int> extents = getProperty("SearchExtents");
  if (extents.size() != 6) {
    std::stringstream stream;
    stream << "Expected 6 elements for the extents. Got: " << extents.size();
    throw std::runtime_error(stream.str());
  }
 
  // Create the Unit-Cell.
  Mantid::Geometry::UnitCell unitcell(a, b, c, alpha, beta, gamma);
 
  std::vector<PeakCandidate> peaks;
 
  for (std::size_t i = 0; i < npeaks; i++) {
    int row = peakindices[i] - 1;
    if (row < 0) {
      throw std::runtime_error("Cannot have a peak index < 0.");
    }
    IPeak &peak = ws->getPeak(row);
    V3D Qs = peak.getQSampleFrame() / (2.0 * M_PI);
    peaks.emplace_back(Qs[0], Qs[1], Qs[2]);
  }
  assert(peaks.size() >= 2);
 
  // Sanity check the generated peaks.
  validateNotColinear(peaks);
 
  // Generate HKL possibilities for each peak.
  double dtol = getProperty("dTolerance");
  Progress prog(this, 0.0, 1.0, 4);
  for (int h = extents[0]; h < extents[1]; h++) {
    for (int k = extents[2]; k < extents[3]; k++) {
      for (int l = extents[4]; l < extents[5]; l++) {
        double dspacing = unitcell.d(h, k, l); // Create a fictional d spacing
        for (std::size_t p = 0; p < npeaks; p++) {
          double dSpacingPeaks = peaks[p].getdSpacing();
          if (std::abs(dspacing - dSpacingPeaks) < dtol)
            peaks[p].addHKL(h, k, l); // If the peak position and the fictional
                                      // d spacing are within tolerance, add it
        }
      }
    }
  }
  prog.report(); // 1st Progress report.
 
  cullHKLs(peaks, unitcell);
 
  prog.report();       // 2nd progress report.
  peaks[0].setFirst(); // On the first peak, now only the first candidate hkl is
                       // considered, others are erased,
  // This means the design space of possible peak-hkl alignments has been
  // reduced, will improve future refinements.
 
  cullHKLs(peaks, unitcell);
  prog.report(); // 3rd progress report.
 
  peaks[1].setFirst();
 
  cullHKLs(peaks, unitcell);
  prog.report(); // 4th progress report.
 
  // Now we can index the input/output peaks workspace
  // If there are peak indexes uses those to find actual peaks in the workspace
  // and overrite HKL
  for (std::size_t i = 0; i < npeaks; i++) {
    int row = 0;
    try {
      row = peakindices[i] - 1;
      IPeak &peak = ws->getPeak(row);
      const V3D hkl = peaks[i].getHKL();
      peak.setHKL(hkl);
      std::stringstream stream;
      stream << "Peak Index: " << row << " HKL: " << hkl;
      g_log.information(stream.str());
    } catch (std::logic_error &) {
      std::stringstream msg;
      msg << "Peak Index: " << row + 1 << " cannot be assigned a single HKL set.";
      g_log.warning(msg.str());
      continue;
    }
  }
}
} // namespace Mantid::Crystal