FindPeaks.h

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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2008 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/IBackgroundFunction.h"
#include "MantidAPI/IPeakFunction.h"
#include "MantidAPI/ParallelAlgorithm.h"
#include "MantidAlgorithms/DllConfig.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidIndexing/SpectrumIndexSet.h"
#include "MantidKernel/cow_ptr.h"
 
namespace Mantid {
 
namespace HistogramData {
class Histogram;
class HistogramX;
class HistogramY;
} // namespace HistogramData
 
namespace Algorithms {
class MANTID_ALGORITHMS_DLL FindPeaks : public API::ParallelAlgorithm {
public:
  FindPeaks();
  ~FindPeaks() override = default;
  const std::string name() const override { return "FindPeaks"; }
  const std::string summary() const override { return "Searches for peaks in a dataset."; }
 
  int version() const override { return (1); }
  const std::vector<std::string> seeAlso() const override { return {"MatchPeaks", "FindPeaksMD", "GeneratePeaks"}; }
  const std::string category() const override { return "Optimization\\PeakFinding"; }
  int getIndex(const HistogramData::HistogramX &vecX, double x);
 
private:
  void init() override;
  void exec() override;
 
  void processAlgorithmProperties();
 
  void findPeaksUsingMariscotti();
 
  void findPeaksGivenStartingPoints(const std::vector<double> &peakcentres, const std::vector<double> &fitwindows);
 
  std::vector<HistogramData::Histogram> calculateSecondDifference(const API::MatrixWorkspace_const_sptr &input);
  void smoothData(std::vector<HistogramData::Histogram> &histograms, const int w, const int g_z);
  void calculateStandardDeviation(const API::MatrixWorkspace_const_sptr &input,
                                  std::vector<HistogramData::Histogram> &smoothed, const int &w);
  long long computePhi(const int &w) const;
 
  void fitPeakInWindow(const API::MatrixWorkspace_sptr &input, const int spectrum, const double centre_guess,
                       const double xmin, const double xmax);
 
  void fitPeakGivenFWHM(const API::MatrixWorkspace_sptr &input, const int spectrum, const double center_guess,
                        const int fitWidth, const bool hasleftpeak, const double leftpeakcentre,
                        const bool hasrightpeak, const double rightpeakcentre);
 
  void fitSinglePeak(const API::MatrixWorkspace_sptr &input, const int spectrum, const int i_min, const int i_max,
                     const int i_centre);
 
  void fitPeakHighBackground(const API::MatrixWorkspace_sptr &input, const size_t spectrum, int i_centre, int i_min,
                             int i_max, double &in_bg0, double &in_bg1, double &in_bg2, int i_peakmin, int i_peakmax);
 
  void fitPeakOneStep(const API::MatrixWorkspace_sptr &input, const int spectrum, const int &i0, const int &i2,
                      const int &i4, const double &in_bg0, const double &in_bg1, const double &in_bg2);
 
  void addInfoRow(const size_t spectrum, const API::IPeakFunction_const_sptr &peakfunction,
                  const API::IBackgroundFunction_sptr &bkgdfunction, const bool isoutputraw, const double mincost);
 
  void addNonFitRecord(const size_t spectrum, const double centre);
 
  void createFunctions();
 
  int findPeakBackground(const API::MatrixWorkspace_sptr &input, int spectrum, size_t i_min, size_t i_max,
                         std::vector<double> &vecBkgdParamValues, std::vector<double> &vecpeakrange);
 
  void estimateBackground(const HistogramData::HistogramX &X, const HistogramData::HistogramY &Y, const size_t i_min,
                          const size_t i_max, std::vector<double> &vecbkgdparvalues);
 
  void estimatePeakRange(const HistogramData::HistogramX &vecX, size_t i_centre, size_t i_min, size_t i_max,
                         const double &leftfwhm, const double &rightfwhm, std::vector<double> &vecpeakrange);
 
  std::string estimatePeakParameters(const HistogramData::HistogramX &vecX, const HistogramData::HistogramY &vecY,
                                     size_t i_min, size_t i_max, const std::vector<double> &vecbkgdparvalues,
                                     size_t &iobscentre, double &height, double &fwhm, double &leftfwhm,
                                     double &rightfwhm);
 
  void generateOutputPeakParameterTable();
 
  std::vector<double> getStartingPeakValues();
  std::vector<double> getStartingBkgdValues();
 
  double callFitPeak(const API::MatrixWorkspace_sptr &dataws, int wsindex, const API::IPeakFunction_sptr &peakfunction,
                     const API::IBackgroundFunction_sptr &backgroundfunction, const std::vector<double> &vec_fitwindow,
                     const std::vector<double> &vec_peakrange, int minGuessFWHM, int maxGuessFWHM, int guessedFWHMStep,
                     int estBackResult = 0);
 
  std::vector<std::string> m_peakParameterNames;
  std::vector<std::string> m_bkgdParameterNames;
  size_t m_bkgdOrder;
 
  static const int g_z = 5;
 
  API::ITableWorkspace_sptr m_outPeakTableWS;
  std::unique_ptr<API::Progress> m_progress = nullptr;
 
  // Properties saved in the algo.
  API::MatrixWorkspace_sptr m_dataWS;    
  int m_inputPeakFWHM;                   
  Indexing::SpectrumIndexSet m_indexSet; 
  bool m_highBackground;                 
  bool m_rawPeaksTable; 
  std::size_t m_numTableParams; //<Number of parameters in the output table workspace
  std::size_t m_centreIndex;    //< Column in output table of peak centre
  std::string m_peakFuncType;   //< The name of the peak function to fit
  std::string m_backgroundType; //< The type of background to fit
 
  // Peaks positions
  std::vector<double> m_vecPeakCentre;
  std::vector<double> m_vecFitWindows;
 
  // Functions for reused
  API::IBackgroundFunction_sptr m_backgroundFunction;
  API::IPeakFunction_sptr m_peakFunction;
 
  int m_minGuessedPeakWidth;
  int m_maxGuessedPeakWidth;
  int m_stepGuessedPeakWidth;
 
  bool m_usePeakPositionTolerance;
  double m_peakPositionTolerance;
 
  std::vector<API::IFunction_sptr> m_fitFunctions;
  std::vector<size_t> m_peakLeftIndexes;
  std::vector<size_t> m_peakRightIndexes;
 
  std::string m_minimizer;
  std::string m_costFunction;
 
  double m_minHeight;
  double m_leastMaxObsY;
 
  bool m_useObsCentre;
};
 
} // namespace Algorithms
} // namespace Mantid