PoldiFitPeaks1D2.cpp

// 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
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidAPI/WorkspaceProperty.h"

#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/TableRow.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidSINQ/PoldiFitPeaks1D2.h"

#include "MantidSINQ/PoldiUtilities/UncertainValue.h"
#include "MantidSINQ/PoldiUtilities/UncertainValueIO.h"

#include "MantidAPI/CompositeFunction.h"
#include <boost/make_shared.hpp>

#include <boost/math/distributions/normal.hpp>
#include <functional>

namespace Mantid {
namespace Poldi {

using namespace Kernel;
using namespace API;
using namespace DataObjects;
using namespace CurveFitting;

RefinedRange::RefinedRange(const PoldiPeak_sptr &peak, double fwhmMultiples)
    : m_peaks(1, peak) {

  if (!peak) {
    throw std::invalid_argument(
        "Cannot construct RefinedRange from null-peak.");
  }

  if (fwhmMultiples < 0) {
    throw std::invalid_argument("Cannot construct a RefinedRange of width 0.");
  }

  double width = peak->fwhm();
  double extent = std::max(0.002, width) * fwhmMultiples;

  setRangeBorders(peak->q() - extent, peak->q() + extent);
}

RefinedRange::RefinedRange(double xStart, double xEnd,
                           const std::vector<PoldiPeak_sptr> &peaks)
    : m_peaks(peaks) {

  setRangeBorders(xStart, xEnd);
}

double RefinedRange::getWidth() const { return m_width; }

bool RefinedRange::operator<(const RefinedRange &other) const {
  return m_xStart < other.m_xStart;
}

bool RefinedRange::overlaps(const RefinedRange &other) const {
  return overlaps(other, 0.0);
}

bool RefinedRange::overlaps(const RefinedRange &other, double fraction) const {
  return getOverlapFraction(other) > fraction;
}

bool RefinedRange::contains(const RefinedRange &other) const {
  return (other.m_xStart > m_xStart && other.m_xEnd < m_xEnd);
}

double RefinedRange::getOverlapFraction(const RefinedRange &other) const {
  double reference = getWidth();

  if (contains(other)) {
    return other.getWidth() / reference;
  }

  if (other.contains(*this)) {
    return reference / other.getWidth();
  }

  if (*this < other) {
    return std::max(0.0, m_xEnd - other.m_xStart) / reference;
  } else {
    return std::max(0.0, other.m_xEnd - m_xStart) / reference;
  }
}

void RefinedRange::merge(const RefinedRange &other) {
  m_peaks.insert(m_peaks.end(), other.m_peaks.begin(), other.m_peaks.end());

  setRangeBorders(std::min(m_xStart, other.m_xStart),
                  std::max(m_xEnd, other.m_xEnd));
}

void RefinedRange::setRangeBorders(double start, double end) {
  if (start >= end) {
    throw std::invalid_argument("Range start is larger than range end.");
  }

  m_xStart = start;
  m_xEnd = end;
  m_width = end - start;
}

bool operator<(const RefinedRange_sptr &lhs, const RefinedRange_sptr &rhs) {
  return (*lhs) < (*rhs);
}

// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(PoldiFitPeaks1D2)

PoldiFitPeaks1D2::PoldiFitPeaks1D2()
    : m_peaks(), m_profileTemplate(),
      m_fitplots(boost::make_shared<WorkspaceGroup>()), m_fwhmMultiples(1.0),
      m_maxRelativeFwhm(0.02) {}

/// Algorithm's name for identification. @see Algorithm::name
const std::string PoldiFitPeaks1D2::name() const { return "PoldiFitPeaks1D"; }

/// Algorithm's version for identification. @see Algorithm::version
int PoldiFitPeaks1D2::version() const { return 2; }

/// Algorithm's category for identification. @see Algorithm::category
const std::string PoldiFitPeaks1D2::category() const { return "SINQ\\Poldi"; }

void PoldiFitPeaks1D2::init() {
  declareProperty(
      std::make_unique<WorkspaceProperty<Workspace2D>>("InputWorkspace", "",
                                                       Direction::Input),
      "An input workspace containing a POLDI auto-correlation spectrum.");
  boost::shared_ptr<BoundedValidator<double>> minFwhmPerDirection =
      boost::make_shared<BoundedValidator<double>>();
  minFwhmPerDirection->setLower(2.0);
  declareProperty(
      "FwhmMultiples", 2.0, minFwhmPerDirection,
      "Each peak will be fitted using x times FWHM data in each direction.",
      Direction::Input);

  boost::shared_ptr<BoundedValidator<double>> allowedOverlapFraction =
      boost::make_shared<BoundedValidator<double>>(0.0, 1.0);
  declareProperty("AllowedOverlap", 0.25, allowedOverlapFraction,
                  "If a fraction larger than this value overlaps with the next "
                  "range, the ranges are merged.");

  declareProperty("MaximumRelativeFwhm", 0.02,
                  "Peaks with a relative FWHM higher"
                  "than this value will be excluded.",
                  Direction::Input);

  std::vector<std::string> peakFunctions =
      FunctionFactory::Instance().getFunctionNames<IPeakFunction>();

  boost::shared_ptr<ListValidator<std::string>> peakFunctionNames(
      new ListValidator<std::string>(peakFunctions));
  declareProperty("PeakFunction", "Gaussian", peakFunctionNames,
                  "Peak function that will be fitted to all peaks.",
                  Direction::Input);

  declareProperty(std::make_unique<WorkspaceProperty<TableWorkspace>>(
                      "PoldiPeakTable", "", Direction::Input),
                  "A table workspace containing POLDI peak data.");

  declareProperty(std::make_unique<WorkspaceProperty<TableWorkspace>>(
                      "OutputWorkspace", "RefinedPeakTable", Direction::Output),
                  "Output workspace with refined peak data.");
  declareProperty(std::make_unique<WorkspaceProperty<Workspace>>(
                      "FitPlotsWorkspace", "FitPlots", Direction::Output),
                  "Plots of all peak fits.");
}

void PoldiFitPeaks1D2::setPeakFunction(const std::string &peakFunction) {
  m_profileTemplate = peakFunction;
}

PoldiPeakCollection_sptr PoldiFitPeaks1D2::getInitializedPeakCollection(
    const DataObjects::TableWorkspace_sptr &peakTable) const {
  auto peakCollection = boost::make_shared<PoldiPeakCollection>(peakTable);
  peakCollection->setProfileFunctionName(m_profileTemplate);

  return peakCollection;
}

std::vector<RefinedRange_sptr> PoldiFitPeaks1D2::getRefinedRanges(
    const PoldiPeakCollection_sptr &peaks) const {
  std::vector<RefinedRange_sptr> ranges;
  for (size_t i = 0; i < peaks->peakCount(); ++i) {
    ranges.push_back(
        boost::make_shared<RefinedRange>(peaks->peak(i), m_fwhmMultiples));
  }

  return ranges;
}

std::vector<RefinedRange_sptr> PoldiFitPeaks1D2::getReducedRanges(
    const std::vector<RefinedRange_sptr> &ranges) const {
  std::vector<RefinedRange_sptr> workingRanges(ranges);
  std::sort(workingRanges.begin(), workingRanges.end());

  std::vector<RefinedRange_sptr> reducedRanges;
  reducedRanges.push_back(
      boost::make_shared<RefinedRange>(*(workingRanges.front())));

  double allowedOverlap = getProperty("AllowedOverlap");

  for (size_t i = 1; i < workingRanges.size(); ++i) {
    RefinedRange_sptr lastReduced = reducedRanges.back();
    RefinedRange_sptr current = workingRanges[i];

    if (!lastReduced->contains(*current) &&
        !lastReduced->overlaps(*current, allowedOverlap)) {
      reducedRanges.push_back(boost::make_shared<RefinedRange>(*current));
    } else {
      lastReduced->merge(*current);
    }
  }

  return reducedRanges;
}

API::IFunction_sptr
PoldiFitPeaks1D2::getRangeProfile(const RefinedRange_sptr &range, int n) const {
  auto totalProfile = boost::make_shared<CompositeFunction>();
  totalProfile->initialize();

  std::vector<PoldiPeak_sptr> peaks = range->getPeaks();
  for (auto &peak : peaks) {
    totalProfile->addFunction(getPeakProfile(peak));
  }

  totalProfile->addFunction(FunctionFactory::Instance().createInitialized(
      "name=Chebyshev,n=" + std::to_string(n) +
      ",StartX=" + boost::lexical_cast<std::string>(range->getXStart()) +
      ",EndX=" + boost::lexical_cast<std::string>(range->getXEnd())));

  return totalProfile;
}

IFunction_sptr
PoldiFitPeaks1D2::getPeakProfile(const PoldiPeak_sptr &poldiPeak) const {
  IPeakFunction_sptr clonedProfile = boost::dynamic_pointer_cast<IPeakFunction>(
      FunctionFactory::Instance().createFunction(m_profileTemplate));
  clonedProfile->setCentre(poldiPeak->q());
  clonedProfile->setFwhm(poldiPeak->fwhm(PoldiPeak::AbsoluteQ));
  clonedProfile->setHeight(poldiPeak->intensity());

  return clonedProfile;
}

void PoldiFitPeaks1D2::setValuesFromProfileFunction(
    PoldiPeak_sptr poldiPeak, const IFunction_sptr &fittedFunction) const {
  IPeakFunction_sptr peakFunction =
      boost::dynamic_pointer_cast<IPeakFunction>(fittedFunction);

  if (peakFunction) {
    poldiPeak->setIntensity(
        UncertainValue(peakFunction->height(), peakFunction->getError(0)));
    poldiPeak->setQ(
        UncertainValue(peakFunction->centre(), peakFunction->getError(1)));
    poldiPeak->setFwhm(UncertainValue(peakFunction->fwhm(),
                                      getFwhmWidthRelation(peakFunction) *
                                          peakFunction->getError(2)));
  }
}

double
PoldiFitPeaks1D2::getFwhmWidthRelation(IPeakFunction_sptr peakFunction) const {
  return peakFunction->fwhm() / peakFunction->getParameter(2);
}

PoldiPeakCollection_sptr
PoldiFitPeaks1D2::fitPeaks(const PoldiPeakCollection_sptr &peaks) {
  g_log.information() << "Peaks to fit: " << peaks->peakCount() << '\n';

  std::vector<RefinedRange_sptr> rawRanges = getRefinedRanges(peaks);
  std::vector<RefinedRange_sptr> reducedRanges = getReducedRanges(rawRanges);

  g_log.information() << "Ranges used for fitting: " << reducedRanges.size()
                      << '\n';

  Workspace2D_sptr dataWorkspace = getProperty("InputWorkspace");
  m_fitplots->removeAll();

  for (const auto &currentRange : reducedRanges) {
    int nMin = getBestChebyshevPolynomialDegree(dataWorkspace, currentRange);

    if (nMin > -1) {
      IAlgorithm_sptr fit = getFitAlgorithm(dataWorkspace, currentRange, nMin);
      fit->execute();

      IFunction_sptr fitFunction = fit->getProperty("Function");
      CompositeFunction_sptr composite =
          boost::dynamic_pointer_cast<CompositeFunction>(fitFunction);

      if (!composite) {
        throw std::runtime_error("Not a composite function!");
      }

      std::vector<PoldiPeak_sptr> peaks = currentRange->getPeaks();
      for (size_t i = 0; i < peaks.size(); ++i) {
        setValuesFromProfileFunction(peaks[i], composite->getFunction(i));
        MatrixWorkspace_sptr fpg = fit->getProperty("OutputWorkspace");
        m_fitplots->addWorkspace(fpg);
      }
    }
  }

  return getReducedPeakCollection(peaks);
}

int PoldiFitPeaks1D2::getBestChebyshevPolynomialDegree(
    const Workspace2D_sptr &dataWorkspace, const RefinedRange_sptr &range) {
  double chiSquareMin = 1e10;
  int nMin = -1;

  try {
    int n = 0;

    while ((n < 3)) {
      IAlgorithm_sptr fit = getFitAlgorithm(dataWorkspace, range, n);
      bool fitSuccess = fit->execute();

      if (fitSuccess) {
        ITableWorkspace_sptr fitCharacteristics =
            fit->getProperty("OutputParameters");
        TableRow row =
            fitCharacteristics->getRow(fitCharacteristics->rowCount() - 1);

        double chiSquare = row.Double(1);

        if (fabs(chiSquare - 1) < fabs(chiSquareMin - 1)) {
          chiSquareMin = chiSquare;
          nMin = n;
        }
      }

      ++n;
    }
  } catch (const std::runtime_error &) {
    nMin = -1;
  }

  if (nMin == -1) {
    g_log.information() << "Range [" << range->getXStart() << " - "
                        << range->getXEnd() << "] is excluded.";
  } else {
    g_log.information() << "Chi^2 for range [" << range->getXStart() << " - "
                        << range->getXEnd() << "] is minimal at n = " << nMin
                        << " with Chi^2 = " << chiSquareMin << '\n';
  }

  return nMin;
}

PoldiPeakCollection_sptr PoldiFitPeaks1D2::getReducedPeakCollection(
    const PoldiPeakCollection_sptr &peaks) const {
  PoldiPeakCollection_sptr reducedPeaks =
      boost::make_shared<PoldiPeakCollection>();
  reducedPeaks->setProfileFunctionName(peaks->getProfileFunctionName());

  for (size_t i = 0; i < peaks->peakCount(); ++i) {
    PoldiPeak_sptr currentPeak = peaks->peak(i);

    if (peakIsAcceptable(currentPeak)) {
      reducedPeaks->addPeak(currentPeak);
    }
  }

  return reducedPeaks;
}

bool PoldiFitPeaks1D2::peakIsAcceptable(const PoldiPeak_sptr &peak) const {
  return peak->intensity() > 0 &&
         peak->fwhm(PoldiPeak::Relative) < m_maxRelativeFwhm &&
         peak->fwhm(PoldiPeak::Relative) > 0.001;
}

void PoldiFitPeaks1D2::exec() {
  setPeakFunction(getProperty("PeakFunction"));

  // Number of points around the peak center to use for the fit
  m_fwhmMultiples = getProperty("FwhmMultiples");
  m_maxRelativeFwhm = getProperty("MaximumRelativeFwhm");

  // try to construct PoldiPeakCollection from provided TableWorkspace
  TableWorkspace_sptr poldiPeakTable = getProperty("PoldiPeakTable");
  m_peaks = getInitializedPeakCollection(poldiPeakTable);

  PoldiPeakCollection_sptr fittedPeaksNew = fitPeaks(m_peaks);
  PoldiPeakCollection_sptr fittedPeaksOld = m_peaks;

  int i = 0;
  while (fittedPeaksNew->peakCount() < fittedPeaksOld->peakCount() || i < 1) {
    fittedPeaksOld = fittedPeaksNew;
    fittedPeaksNew = fitPeaks(fittedPeaksOld);
    ++i;
  }

  setProperty("OutputWorkspace", fittedPeaksNew->asTableWorkspace());
  setProperty("FitPlotsWorkspace", m_fitplots);
}

IAlgorithm_sptr
PoldiFitPeaks1D2::getFitAlgorithm(const Workspace2D_sptr &dataWorkspace,
                                  const RefinedRange_sptr &range, int n) {
  IFunction_sptr rangeProfile = getRangeProfile(range, n);

  IAlgorithm_sptr fitAlgorithm = createChildAlgorithm("Fit", -1, -1, false);
  fitAlgorithm->setProperty("CreateOutput", true);
  fitAlgorithm->setProperty("Output", "FitPeaks1D");
  fitAlgorithm->setProperty("CalcErrors", true);
  fitAlgorithm->setProperty("OutputCompositeMembers", true);
  fitAlgorithm->setProperty("Function", rangeProfile);
  fitAlgorithm->setProperty("InputWorkspace", dataWorkspace);
  fitAlgorithm->setProperty("WorkspaceIndex", 0);
  fitAlgorithm->setProperty("StartX", range->getXStart());
  fitAlgorithm->setProperty("EndX", range->getXEnd());

  return fitAlgorithm;
}

} // namespace Poldi
} // namespace Mantid