PoldiIndexKnownCompounds.h

// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2014 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 +
#pragma once

#include "MantidAPI/Algorithm.h"
#include "MantidSINQ/DllConfig.h"
#include "MantidSINQ/PoldiUtilities/PoldiPeakCollection.h"

namespace Mantid {
namespace Poldi {

/** IndexCandidatePair :

    IndexCandidatePair is a small helper struct that holds a pointer
    to a measured peak and a pointer to a candidate that may be a
    suitable candidate for indexing. It also calculates a score
    for this pair (see wiki for details).
  */
struct MANTID_SINQ_DLL IndexCandidatePair {
  /// Default constructor
  IndexCandidatePair() : observed(), candidate(), positionMatch(0.0), candidateCollectionIndex(0) {}

  IndexCandidatePair(const PoldiPeak_sptr &measuredPeak, const PoldiPeak_sptr &candidatePeak, size_t index);

  /// Comparison operator, position matches are compared.
  bool operator<(const IndexCandidatePair &other) const { return positionMatch < other.positionMatch; }

  PoldiPeak_sptr observed;
  PoldiPeak_sptr candidate;
  double positionMatch;
  size_t candidateCollectionIndex;
};

/** PoldiIndexKnownCompounds :

    Algorithm that assigns Miller indices to measured peaks using
    reflections of known structures present in the sample.

        @author Michael Wedel, Paul Scherrer Institut - SINQ
        @date 23/09/2014
  */
class MANTID_SINQ_DLL PoldiIndexKnownCompounds : public API::Algorithm {
public:
  const std::string name() const override;
  int version() const override;
  const std::string category() const override;
  const std::string summary() const override;

  std::map<std::string, std::string> validateInputs() override;

  void setMeasuredPeaks(const PoldiPeakCollection_sptr &measuredPeaks);
  void setExpectedPhases(const std::vector<PoldiPeakCollection_sptr> &expectedPhases);
  void setExpectedPhaseNames(const std::vector<std::string> &phaseNames);

  void initializeUnindexedPeaks();
  void initializeIndexedPeaks(const std::vector<PoldiPeakCollection_sptr> &expectedPhases);

  static double fwhmToSigma(double fwhm);
  static double sigmaToFwhm(double sigma);

protected:
  // Workspace and name-handling
  std::vector<API::Workspace_sptr> getWorkspaces(const std::vector<std::string> &workspaceNames) const;
  std::vector<PoldiPeakCollection_sptr> getPeakCollections(const std::vector<API::Workspace_sptr> &workspaces) const;

  std::vector<std::string> getWorkspaceNames(const std::vector<API::Workspace_sptr> &workspaces) const;

  // Input vector checks
  std::vector<double> reshapeVector(const std::vector<double> &vector, size_t size) const;

  std::vector<double> getContributions(size_t size) const;
  std::vector<double> getNormalizedContributions(const std::vector<double> &contributions) const;

  void scaleIntensityEstimates(const std::vector<PoldiPeakCollection_sptr> &peakCollections,
                               const std::vector<double> &normalizedContributions) const;
  void scaleIntensityEstimates(const PoldiPeakCollection_sptr &peakCollection, double contribution) const;

  void scaleToExperimentalValues(const std::vector<PoldiPeakCollection_sptr> &peakCollections,
                                 const PoldiPeakCollection_sptr &measuredPeaks) const;

  double getMaximumIntensity(const PoldiPeakCollection_sptr &peakCollection) const;
  size_t getMaximumIntensityPeakIndex(const PoldiPeakCollection_sptr &peakCollection) const;

  std::vector<double> getTolerances(size_t size) const;
  void assignFwhmEstimates(const std::vector<PoldiPeakCollection_sptr> &peakCollections,
                           const std::vector<double> &tolerances) const;
  void assignFwhmEstimates(const PoldiPeakCollection_sptr &peakCollection, double tolerance) const;

  // Indexing algorithm
  void indexPeaks(const PoldiPeakCollection_sptr &measured,
                  const std::vector<PoldiPeakCollection_sptr> &knownCompoundPeaks);

  std::vector<IndexCandidatePair>
  getAllIndexCandidatePairs(const PoldiPeakCollection_sptr &measured,
                            const std::vector<PoldiPeakCollection_sptr> &knownCompoundPeaks);
  std::vector<IndexCandidatePair>
  getIndexCandidatePairs(const PoldiPeak_sptr &peak,
                         const std::vector<PoldiPeakCollection_sptr> &candidateCollections) const;
  bool isCandidate(const PoldiPeak_sptr &measuredPeak, const PoldiPeak_sptr &possibleCandidate) const;
  void collectUnindexedPeak(const PoldiPeak_sptr &unindexedPeak);

  void assignCandidates(const std::vector<IndexCandidatePair> &candidates);
  bool inPeakSet(const std::set<PoldiPeak_sptr> &peakSet, const PoldiPeak_sptr &peak) const;
  void assignPeakIndex(const IndexCandidatePair &candidate);

  // Finalization
  PoldiPeakCollection_sptr getIntensitySortedPeakCollection(const PoldiPeakCollection_sptr &peaks) const;

  void assignCrystalStructureParameters(PoldiPeakCollection_sptr &indexedPeaks,
                                        const PoldiPeakCollection_sptr &phasePeaks) const;

  PoldiPeakCollection_sptr m_measuredPeaks;
  std::vector<PoldiPeakCollection_sptr> m_expectedPhases;
  std::vector<std::string> m_phaseNames;

  PoldiPeakCollection_sptr m_unindexedPeaks;
  std::vector<PoldiPeakCollection_sptr> m_indexedPeaks;

private:
  void init() override;
  void exec() override;
};

} // namespace Poldi
} // namespace Mantid