#include "MantidAlgorithms/DetectorEfficiencyVariation.h"
#include "MantidAPI/HistogramValidator.h"
#include "MantidAPI/SpectrumInfo.h"
#include "MantidKernel/BoundedValidator.h"

#include <boost/math/special_functions/fpclassify.hpp>

namespace Mantid {
namespace Algorithms {

// Register the class into the algorithm factory
DECLARE_ALGORITHM(DetectorEfficiencyVariation)

const std::string DetectorEfficiencyVariation::category() const {
  return "Diagnostics";
}

using namespace Kernel;
using namespace API;
using DataObjects::MaskWorkspace_sptr;
using Geometry::IDetector_const_sptr;

/// Initialize the algorithm
void DetectorEfficiencyVariation::init() {
  auto val = boost::make_shared<HistogramValidator>();
  declareProperty(make_unique<WorkspaceProperty<MatrixWorkspace>>(
                      "WhiteBeamBase", "", Direction::Input, val),
                  "Name of a white beam vanadium workspace");
  // The histograms, the detectors in each histogram and their first and last
  // bin boundary must match
  declareProperty(
      make_unique<WorkspaceProperty<MatrixWorkspace>>("WhiteBeamCompare", "",
                                                      Direction::Input, val),
      "Name of a matching second white beam vanadium run from the same "
      "instrument");
  declareProperty(make_unique<WorkspaceProperty<MatrixWorkspace>>(
                      "OutputWorkspace", "", Direction::Output),
                  "A MaskWorkpace where each spectra that failed the test is "
                  "masked. Each histogram from the input workspace maps to a "
                  "histogram in this workspace with one value that indicates "
                  "if there was a dead detector.");
  auto moreThanZero = boost::make_shared<BoundedValidator<double>>();
  moreThanZero->setLower(0.0);
  declareProperty("Variation", 1.1, moreThanZero,
                  "Identify histograms whose total number of counts has "
                  "changed by more than this factor of the median change "
                  "between the two input workspaces.");
  auto mustBePosInt = boost::make_shared<BoundedValidator<int>>();
  mustBePosInt->setLower(0);
  declareProperty("StartWorkspaceIndex", 0, mustBePosInt,
                  "The index number of the first spectrum to include in the "
                  "calculation (default: 0)");

  // Mantid::EMPTY_INT() and EMPTY_DBL() are tags that indicate that no
  // value has been set and we want to use the default
  declareProperty("EndWorkspaceIndex", Mantid::EMPTY_INT(), mustBePosInt,
                  "The index number of the last spectrum to include in the "
                  "calculation (default: the last spectrum in the workspace)");
  declareProperty(
      "RangeLower", Mantid::EMPTY_DBL(),
      "No bin with a boundary at an x value less than this will be included "
      "in the summation used to decide if a detector is 'bad' (default: the "
      "start of each histogram)");
  declareProperty(
      "RangeUpper", Mantid::EMPTY_DBL(),
      "No bin with a boundary at an x value higher than this value will "
      "be included in the summation used to decide if a detector is 'bad' "
      "(default: the end of each histogram)");
  declareProperty("NumberOfFailures", 0, Direction::Output);
}

/** Executes the algorithm that includes calls to SolidAngle and Integration
 *
 *  @throw invalid_argument if there is an incapatible property value and so the
 *algorithm can't continue
 *  @throw runtime_error if a Child Algorithm cannot execute
 */
void DetectorEfficiencyVariation::exec() {
  MatrixWorkspace_sptr WB1;
  MatrixWorkspace_sptr WB2;
  double variation = Mantid::EMPTY_DBL();
  int minSpec = 0;
  int maxSpec = Mantid::EMPTY_INT();
  retrieveProperties(WB1, WB2, variation, minSpec, maxSpec);

  const double rangeLower = getProperty("RangeLower");
  const double rangeUpper = getProperty("RangeUpper");

  MatrixWorkspace_sptr counts1 =
      integrateSpectra(WB1, minSpec, maxSpec, rangeLower, rangeUpper);
  MatrixWorkspace_sptr counts2 =
      integrateSpectra(WB2, minSpec, maxSpec, rangeLower, rangeUpper);
  MatrixWorkspace_sptr countRatio;
  try {
    // Note. This can produce NAN/INFs. Leave for now and sort it out in the
    // later tests
    countRatio = counts1 / counts2;
  } catch (std::invalid_argument &) {
    g_log.error() << "The two white beam workspaces size must match.";
    throw;
  }
  double average =
      calculateMedian(*countRatio, false, makeInstrumentMap(*countRatio))
          .at(0); // Include zeroes
  g_log.notice() << name()
                 << ": The median of the ratio of the integrated counts is: "
                 << average << '\n';
  //
  int numFailed = doDetectorTests(counts1, counts2, average, variation);

  g_log.notice() << "Tests failed " << numFailed << " spectra. "
                 << "These have been masked on the OutputWorkspace\n";

  // counts1 was overwriten by the last function, now register it
  setProperty("NumberOfFailures", numFailed);
}

/** Loads, checks and passes back the values passed to the algorithm
 * @param whiteBeam1 :: A white beam vanadium spectrum that will be used to
 * check detector efficiency variations
 * @param whiteBeam2 :: The other white beam vanadium spectrum from the same
 * instrument to use for comparison
 * @param variation :: The maximum fractional variation above the median that is
 * allowed for god detectors
 * @param startWsIndex :: Index number of the first spectrum to use
 * @param endWsIndex :: Index number of the last spectrum to use
 * @throw invalid_argument if there is an incapatible property value and so the
 * algorithm can't continue
 */
void DetectorEfficiencyVariation::retrieveProperties(
    API::MatrixWorkspace_sptr &whiteBeam1,
    API::MatrixWorkspace_sptr &whiteBeam2, double &variation, int &startWsIndex,
    int &endWsIndex) {
  whiteBeam1 = getProperty("WhiteBeamBase");
  whiteBeam2 = getProperty("WhiteBeamCompare");
  if (whiteBeam1->getInstrument()->getName() !=
      whiteBeam2->getInstrument()->getName()) {
    throw std::invalid_argument("The two input white beam vanadium workspaces "
                                "must be from the same instrument");
  }
  int maxWsIndex = static_cast<int>(whiteBeam1->getNumberHistograms()) - 1;
  if (maxWsIndex !=
      static_cast<int>(whiteBeam2->getNumberHistograms()) -
          1) { // we would get a crash later on if this were not true
    throw std::invalid_argument("The input white beam vanadium workspaces must "
                                "be have the same number of histograms");
  }

  variation = getProperty("Variation");

  startWsIndex = getProperty("StartWorkspaceIndex");
  if ((startWsIndex < 0) || (startWsIndex > maxWsIndex)) {
    g_log.warning("StartWorkspaceIndex out of range, changed to 0");
    startWsIndex = 0;
  }
  endWsIndex = getProperty("EndWorkspaceIndex");
  if (endWsIndex == Mantid::EMPTY_INT())
    endWsIndex = maxWsIndex;
  if ((endWsIndex < 0) || (endWsIndex > maxWsIndex)) {
    g_log.warning(
        "EndWorkspaceIndex out of range, changed to max Workspace number");
    endWsIndex = maxWsIndex;
  }
  if ((endWsIndex < startWsIndex)) {
    g_log.warning(
        "EndWorkspaceIndex can not be less than the StartWorkspaceIndex, "
        "changed to max Workspace number");
    endWsIndex = maxWsIndex;
  }
}

/**
 * Apply the detector test criterion
 * @param counts1 :: A workspace containing the integrated counts of the first
 * white beam run
 * @param counts2 :: A workspace containing the integrated counts of the first
 * white beam run
 * @param average :: The computed median
 * @param variation :: The allowed variation in terms of number of medians, i.e
 * those spectra where
 * the ratio of the counts outside this range will fail the tests and will be
 * masked on counts1
 * @return number of detectors for which tests failed
 */
int DetectorEfficiencyVariation::doDetectorTests(
    API::MatrixWorkspace_const_sptr counts1,
    API::MatrixWorkspace_const_sptr counts2, const double average,
    double variation) {
  // DIAG in libISIS did this.  A variation of less than 1 doesn't make sense in
  // this algorithm
  if (variation < 1) {
    variation = 1.0 / variation;
  }
  // criterion for if the the first spectrum is larger than expected
  double largest = average * variation;
  // criterion for if the the first spectrum is lower than expected
  double lowest = average / variation;

  const int numSpec = static_cast<int>(counts1->getNumberHistograms());
  const int progStep = static_cast<int>(std::ceil(numSpec / 30.0));

  // Create a workspace for the output
  MaskWorkspace_sptr maskWS = this->generateEmptyMask(counts1);

  bool checkForMask = false;
  Geometry::Instrument_const_sptr instrument = counts1->getInstrument();
  if (instrument != nullptr) {
    checkForMask = ((instrument->getSource() != nullptr) &&
                    (instrument->getSample() != nullptr));
  }

  const double deadValue(1.0);
  int numFailed(0);
  const auto &spectrumInfo = counts1->spectrumInfo();
  PARALLEL_FOR3(counts1, counts2, maskWS)
  for (int i = 0; i < numSpec; ++i) {
    PARALLEL_START_INTERUPT_REGION
    // move progress bar
    if (i % progStep == 0) {
      advanceProgress(progStep * static_cast<double>(RTMarkDetects) / numSpec);
      progress(m_fracDone);
      interruption_point();
    }

    if (checkForMask) {
      if (spectrumInfo.isMonitor(i))
        continue;
      if (spectrumInfo.isMasked(i)) {
        // Ensure it is masked on the output
        maskWS->mutableY(i)[0] = deadValue;
        continue;
      }
    }

    const double signal1 = counts1->y(i)[0];
    const double signal2 = counts2->y(i)[0];

    // Mask out NaN and infinite
    if (boost::math::isinf(signal1) || boost::math::isnan(signal1) ||
        boost::math::isinf(signal2) || boost::math::isnan(signal2)) {
      maskWS->mutableY(i)[0] = deadValue;
      PARALLEL_ATOMIC
      ++numFailed;
      continue;
    }

    // Check the ratio is within the given range
    const double ratio = signal1 / signal2;
    if (ratio < lowest || ratio > largest) {
      maskWS->mutableY(i)[0] = deadValue;
      PARALLEL_ATOMIC
      ++numFailed;
    }

    PARALLEL_END_INTERUPT_REGION
  }
  PARALLEL_CHECK_INTERUPT_REGION

  // Register the results with the ADS
  setProperty("OutputWorkspace", maskWS);

  return numFailed;
}

} // namespace Algorithm
} // namespace Mantid