SaveHKL.cpp

Go to the documentation of this file.

// 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 +
#include "MantidCrystal/SaveHKL.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/Sample.h"
#include "MantidCrystal/AnvredCorrection.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Instrument/ComponentInfo.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidGeometry/Objects/ShapeFactory.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/Material.h"
#include "MantidKernel/Strings.h"
#include "MantidKernel/Unit.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/Utils.h"
#include <cmath>
#include <filesystem>
#include <fstream>
 
using namespace Mantid::Geometry;
using namespace Mantid::DataObjects;
using namespace Mantid::Kernel;
using namespace Mantid::Kernel::Strings;
using namespace Mantid::API;
using namespace Mantid::PhysicalConstants;
 
namespace Mantid::Crystal {
 
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(SaveHKL)
 
 
void SaveHKL::init() {
  declareProperty(std::make_unique<WorkspaceProperty<PeaksWorkspace>>("InputWorkspace", "", Direction::Input),
                  "An input PeaksWorkspace.");
 
  auto mustBePositive = std::make_shared<BoundedValidator<double>>();
  mustBePositive->setLower(0.0);
  declareProperty("ScalePeaks", 1.0, mustBePositive, "Multiply FSQ and sig(FSQ) by scaleFactor");
  declareProperty("MinDSpacing", 0.0, "Minimum d-spacing (Angstroms)");
  declareProperty("MinWavelength", 0.0, "Minimum wavelength (Angstroms)");
  declareProperty("MaxWavelength", 100.0, "Maximum wavelength (Angstroms)");
 
  declareProperty("AppendFile", false,
                  "Append to file if true. Use same corrections as file.\n"
                  "If false, new file (default).");
  declareProperty("ApplyAnvredCorrections", false,
                  "Apply anvred corrections to peaks if true.\n"
                  "If false, no corrections during save (default).");
  declareProperty("LinearScatteringCoef", EMPTY_DBL(), mustBePositive,
                  "Linear scattering coefficient in 1/cm if not set with "
                  "SetSampleMaterial");
  declareProperty("LinearAbsorptionCoef", EMPTY_DBL(), mustBePositive,
                  "Linear absorption coefficient at 1.8 Angstroms in 1/cm if "
                  "not set with SetSampleMaterial");
  declareProperty("Radius", EMPTY_DBL(), mustBePositive, "Radius of the sample in centimeters");
  declareProperty("PowerLambda", 4.0, "Power of lambda ");
  declareProperty(std::make_unique<FileProperty>("SpectraFile", "", API::FileProperty::OptionalLoad, ".dat"),
                  " Spectrum data read from a spectrum file.");
 
  declareProperty(std::make_unique<FileProperty>("Filename", "", FileProperty::Save, ".hkl"),
                  "Path to an hkl file to save.");
 
  std::vector<std::string> histoTypes{"Bank", "RunNumber", ""};
  declareProperty("SortBy", histoTypes[2], std::make_shared<StringListValidator>(histoTypes),
                  "Sort the histograms by bank, run number or both (default).");
  declareProperty("MinIsigI", EMPTY_DBL(), mustBePositive, "The minimum I/sig(I) ratio");
  declareProperty("WidthBorder", EMPTY_INT(), "Width of border of detectors");
  declareProperty("MinIntensity", EMPTY_DBL(), mustBePositive, "The minimum Intensity");
  declareProperty(
      std::make_unique<WorkspaceProperty<PeaksWorkspace>>("OutputWorkspace", "SaveHKLOutput", Direction::Output),
      "Output PeaksWorkspace");
  declareProperty("HKLDecimalPlaces", EMPTY_INT(),
                  "Number of decimal places for fractional HKL.  Default is integer HKL.");
  declareProperty("DirectionCosines", false,
                  "Extra columns (22 total) in file if true for direction cosines.\n"
                  "If false, original 14 columns (default).");
  const std::vector<std::string> exts{".mat", ".ub", ".txt"};
  declareProperty(std::make_unique<FileProperty>("UBFilename", "", FileProperty::OptionalLoad, exts),
                  "Path to an ISAW-style UB matrix text file only needed for "
                  "DirectionCosines if workspace does not have lattice.");
}
 
void SaveHKL::exec() {
 
  std::string filename = getPropertyValue("Filename");
  m_ws = getProperty("InputWorkspace");
 
  PeaksWorkspace_sptr peaksW = getProperty("OutputWorkspace");
  if (peaksW != m_ws)
    peaksW = m_ws->clone();
  auto inst = peaksW->getInstrument();
  std::vector<Peak> &peaks = peaksW->getPeaks();
  double scaleFactor = getProperty("ScalePeaks");
  double dMin = getProperty("MinDSpacing");
  double wlMin = getProperty("MinWavelength");
  double wlMax = getProperty("MaxWavelength");
  std::string type = getProperty("SortBy");
  double minIsigI = getProperty("MinIsigI");
  double minIntensity = getProperty("MinIntensity");
  int widthBorder = getProperty("WidthBorder");
  int decimalHKL = getProperty("HKLDecimalPlaces");
  bool cosines = getProperty("DirectionCosines");
  OrientedLattice ol;
  if (cosines) {
    if (peaksW->sample().hasOrientedLattice()) {
      ol = peaksW->sample().getOrientedLattice();
    } else {
      // Find OrientedLattice
      std::string fileUB = getProperty("UBFilename");
      // Open the file
      std::ifstream in(fileUB.c_str());
      if (!in)
        throw std::runtime_error("A file containing the UB matrix must be input into UBFilename.");
 
      auto UB_alg = createChildAlgorithm("LoadIsawUB", -1, -1, false);
      UB_alg->setProperty("PeaksWorkspace", peaksW);
      UB_alg->setProperty("Filename", fileUB);
      UB_alg->executeAsChildAlg();
    }
  }
 
  // Sequence and run number
  int bankSequence = 0;
  int runSequence = 0;
  // HKL is flipped by -1 due to different q convention in ISAW vs mantid.
  // Default for kf-ki has -q
  double qSign = -1.0;
  std::string convention = ConfigService::Instance().getString("Q.convention");
  if (convention == "Crystallography") {
    qSign = 1.0;
  }
 
  std::fstream out;
  out.open(filename.c_str(), std::ios::out);
 
  // We cannot assume the peaks have bank type detector modules, so we have a
  // string to check this
  std::string bankPart = "?";
  // We must sort the peaks first by run, then bank #, and save the list of
  // workspace indices of it
  using bankMap_t = std::map<int, std::vector<size_t>>;
  using runMap_t = std::map<int, bankMap_t>;
  std::set<int> uniqueBanks;
  std::set<int> uniqueRuns;
  runMap_t runMap;
  for (size_t i = 0; i < peaks.size(); ++i) {
    Peak const &p = peaks[i];
    int run = p.getRunNumber();
    int bank = 0;
    std::string bankName = p.getBankName();
    if (bankName.size() <= 4) {
      g_log.information() << "Could not interpret bank number of peak " << i << "(" << bankName << ")\n";
      continue;
    }
    // Save the "bank" part once to check whether it really is a bank
    if (bankPart == "?")
      bankPart = bankName.substr(0, 4);
    // Take out the "bank" part of the bank name and convert to an int
    if (bankPart == "bank")
      bankName = bankName.substr(4, bankName.size() - 4);
    else if (bankPart == "WISH")
      bankName = bankName.substr(9, bankName.size() - 9);
    Strings::convert(bankName, bank);
 
    // Save in the map
    if (type.compare(0, 2, "Ru") == 0)
      runMap[run][bank].emplace_back(i);
    else
      runMap[bank][run].emplace_back(i);
    // Track unique bank numbers
    uniqueBanks.insert(bank);
    uniqueRuns.insert(run);
  }
 
  bool correctPeaks = getProperty("ApplyAnvredCorrections");
  std::vector<std::vector<double>> spectra;
  std::vector<std::vector<double>> time;
  int iSpec = 0;
 
  m_smu = getProperty("LinearScatteringCoef"); // in 1/cm
  m_amu = getProperty("LinearAbsorptionCoef"); // in 1/cm
  m_power_th = getProperty("PowerLambda");     // in cm
 
  API::Run &run = peaksW->mutableRun();
 
  double radius = getProperty("Radius"); // in cm
  if (radius != EMPTY_DBL()) {
    run.addProperty<double>("Radius", radius, true);
  } else {
    if (run.hasProperty("Radius"))
      radius = run.getPropertyValueAsType<double>("Radius");
  }
 
  const Material &sampleMaterial = peaksW->sample().getMaterial();
  const IObject *sampleShape{nullptr};
  // special case of sphere else assume the sample shape and material have been
  // set already
  if (radius != EMPTY_DBL()) {
    // create sphere shape
    auto sphere = ShapeFactory::createSphere(V3D(), radius * 0.01);
    if (m_smu != EMPTY_DBL() && m_amu != EMPTY_DBL()) {
      // Save input in Sample with wrong atomic number and name
      NeutronAtom neutron(0, 0, 0.0, 0.0, m_smu, 0.0, m_smu, m_amu);
      sphere->setMaterial(Material("SetInSaveHKL", neutron, 1.0));
    } else {
      sphere->setMaterial(sampleMaterial);
      const double rho = sampleMaterial.numberDensity();
      m_smu = sampleMaterial.totalScatterXSection() * rho;
      m_amu = sampleMaterial.absorbXSection(NeutronAtom::ReferenceLambda) * rho;
    }
    peaksW->mutableSample().setShape(sphere);
  } else if (peaksW->sample().getShape().hasValidShape()) {
    sampleShape = &(peaksW->sample().getShape());
    // if AddAbsorptionWeightedPathLengths has already been run on the workspace
    // then keep those tbar values
    if (std::all_of(peaks.cbegin(), peaks.cend(), [](auto &p) { return p.getAbsorptionWeightedPathLength() == 0; })) {
      auto alg = createChildAlgorithm("AddAbsorptionWeightedPathLengths");
      alg->setProperty("InputWorkspace", peaksW);
      alg->setProperty("UseSinglePath", true);
      alg->executeAsChildAlg();
    }
  }
 
  if (correctPeaks) {
    std::ifstream infile;
    std::string spectraFile = getPropertyValue("SpectraFile");
    infile.open(spectraFile.c_str());
    if (infile.is_open()) {
      std::string ignoreLine;
      size_t a = 1;
      for (int wi = 0; wi < 8; wi++)
        getline(infile, ignoreLine);
      while (!infile.eof()) {
        time.resize(a + 1);
        spectra.resize(a + 1);
        std::string line;
        getline(infile, line);
        std::stringstream ss(line);
        if (line.find("Bank") == std::string::npos) {
          double time0, spectra0;
          ss >> time0 >> spectra0;
          time[a].emplace_back(time0);
          spectra[a].emplace_back(spectra0);
 
        } else {
          std::string temp;
          size_t a0 = 1;
          ss >> temp >> a0 >> temp >> a;
        }
      }
      infile.close();
    }
  }
  // =================== Save all Peaks ======================================
  std::set<size_t> banned;
  // Go through each peak at this run / bank
  int maxOrder = 0;
  if (peaksW->sample().hasOrientedLattice()) {
    maxOrder = peaksW->sample().getOrientedLattice().getMaxOrder();
  }
  // Go in order of run numbers
  runMap_t::iterator runMap_it;
  for (runMap_it = runMap.begin(); runMap_it != runMap.end(); ++runMap_it) {
    // Start of a new run
    // int run = runMap_it->first;
    bankMap_t &bankMap = runMap_it->second;
 
    bankMap_t::iterator bankMap_it;
    for (bankMap_it = bankMap.begin(); bankMap_it != bankMap.end(); ++bankMap_it) {
      // Start of a new bank.
      // int bank = bankMap_it->first;
      std::vector<size_t> &ids = bankMap_it->second;
 
      // Go through each peak at this run / bank
      for (auto wi : ids) {
 
        Peak &p = peaks[wi];
        if (p.getIntensity() == 0.0 || !(std::isfinite(p.getIntensity())) || !(std::isfinite(p.getSigmaIntensity()))) {
          banned.insert(wi);
          continue;
        }
        if (minIsigI != EMPTY_DBL() && p.getIntensity() < std::abs(minIsigI * p.getSigmaIntensity())) {
          banned.insert(wi);
          continue;
        }
        if (minIntensity != EMPTY_DBL() && p.getIntensity() < minIntensity) {
          banned.insert(wi);
          continue;
        }
        const int runNumber = p.getRunNumber();
        int seqNum = p.getPeakNumber();
        int bank = 0;
        std::string bankName = p.getBankName();
        int nCols, nRows;
        sizeBanks(bankName, nCols, nRows);
        // peaks with detectorID=-1 are from LoadHKL
        if (widthBorder != EMPTY_INT() && p.getDetectorID() != -1 &&
            (p.getCol() < widthBorder || p.getRow() < widthBorder || p.getCol() > (nCols - widthBorder) ||
             p.getRow() > (nRows - widthBorder))) {
          banned.insert(wi);
          continue;
        }
        // Take out the "bank" part of the bank name and convert to an int
        bankName.erase(remove_if(bankName.begin(), bankName.end(), std::not_fn(::isdigit)), bankName.end());
        Strings::convert(bankName, bank);
 
        // Two-theta = polar angle = scattering angle = between +Z vector and
        // the
        // scattered beam
        double scattering = p.getScattering();
        double lambda = p.getWavelength();
        double dsp = p.getDSpacing();
        if (dsp < dMin || lambda < wlMin || lambda > wlMax) {
          banned.insert(wi);
          continue;
        }
 
        double transmission{0}, tbar{0};
        if (radius != EMPTY_DBL()) {
          // keep original method if radius is provided
          transmission = absorbSphere(radius, scattering, lambda, tbar);
        } else if (sampleShape) {
          tbar = p.getAbsorptionWeightedPathLength();
          transmission = exp(-tbar * 0.01 * sampleShape->material().attenuationCoefficient(lambda));
        }
 
        // Anvred write from Art Schultz/
        if (p.getH() == 0 && p.getK() == 0 && p.getL() == 0) {
          banned.insert(wi);
          continue;
        }
        if (decimalHKL == EMPTY_INT()) {
          V3D HKL = (maxOrder == 0) ? p.getHKL() : p.getIntHKL();
          out << std::setw(4) << Utils::round(qSign * HKL[0]) << std::setw(4) << Utils::round(qSign * HKL[1])
              << std::setw(4) << Utils::round(qSign * HKL[2]);
          if (maxOrder > 0) {
            V3D MNP = p.getIntMNP();
            out << std::setw(4) << Utils::round(qSign * MNP[0]) << std::setw(4) << Utils::round(qSign * MNP[1])
                << std::setw(4) << Utils::round(qSign * MNP[2]);
          }
        } else {
          out << std::setw(5 + decimalHKL) << std::fixed << std::setprecision(decimalHKL) << qSign * p.getH()
              << std::setw(5 + decimalHKL) << std::fixed << std::setprecision(decimalHKL) << qSign * p.getK()
              << std::setw(5 + decimalHKL) << std::fixed << std::setprecision(decimalHKL) << qSign * p.getL();
        }
        double correc = scaleFactor;
        double instBkg = 0;
        double relSigSpect = 0.0;
        bankSequence = static_cast<int>(std::distance(uniqueBanks.begin(), uniqueBanks.find(bank)));
        runSequence = static_cast<int>(std::distance(uniqueRuns.begin(), uniqueRuns.find(runNumber)));
        if (correctPeaks) {
          // correct for the slant path throught the scintillator glass
          double mu = (9.614 * lambda) + 0.266; // mu for GS20 glass
          double depth = 0.2;
          double eff_center = 1.0 - std::exp(-mu * depth); // efficiency at center of detector
 
          // Distance to center of detector
          const double pathlength = slantPathLength(inst, m_ws->componentInfo(), p.getBankName(), p.getL2(), depth);
          double eff_R = 1.0 - exp(-mu * pathlength); // efficiency at point R
          double sp_ratio = eff_center / eff_R;       // slant path efficiency ratio
          double sinsqt = std::pow(lambda / (2.0 * dsp), 2);
          double wl4 = std::pow(lambda, m_power_th);
          double cmonx = 1.0;
          if (p.getMonitorCount() > 0) {
            cmonx = 100e6 / p.getMonitorCount();
          }
          double spect = spectrumCalc(p.getTOF(), iSpec, time, spectra, bank);
          // Find spectra at wavelength of 1 for normalization
          std::vector<double> xdata(1, 1.0); // wl = 1
          std::vector<double> ydata;
          double theta2 = p.getScattering();
          double l1 = p.getL1();
          double l2 = p.getL2();
          Mantid::Kernel::Unit_sptr unit = UnitFactory::Instance().create("Wavelength");
          unit->toTOF(xdata, ydata, l1, 0, {{UnitParams::l2, l2}, {UnitParams::twoTheta, theta2}});
          double one = xdata[0];
          double spect1 = spectrumCalc(one, iSpec, time, spectra, bank);
          relSigSpect = std::sqrt((1.0 / spect) + (1.0 / spect1));
          if (spect1 != 0.0) {
            spect /= spect1;
          } else {
            throw std::runtime_error("Wavelength for normalizing to spectrum is out of range.");
          }
          correc = scaleFactor * sinsqt * cmonx * sp_ratio / (wl4 * spect * transmission);
 
          if (inst->hasParameter("detScale" + bankName)) {
            correc *= static_cast<double>(inst->getNumberParameter("detScale" + bankName)[0]);
          }
 
          // instrument background constant for sigma
          instBkg = 0. * 12.28 / cmonx * scaleFactor;
        }
 
        // SHELX can read data without the space between the l and intensity
        if (p.getDetectorID() != -1) {
          double ckIntensity = correc * p.getIntensity();
          double cksigI = std::sqrt(std::pow(correc * p.getSigmaIntensity(), 2) +
                                    std::pow(relSigSpect * correc * p.getIntensity(), 2) + instBkg);
          p.setIntensity(ckIntensity);
          p.setSigmaIntensity(cksigI);
          if (ckIntensity > 99999.985)
            g_log.warning() << "Scaled intensity, " << ckIntensity
                            << " is too large for format.  Decrease ScalePeaks.\n";
          out << std::setw(8) << std::fixed << std::setprecision(2) << ckIntensity;
 
          out << std::setw(8) << std::fixed << std::setprecision(2) << cksigI;
        } else {
          // This is data from LoadHKL which is already corrected
          out << std::setw(8) << std::fixed << std::setprecision(2) << p.getIntensity();
 
          out << std::setw(8) << std::fixed << std::setprecision(2) << p.getSigmaIntensity();
        }
        if (type.compare(0, 2, "Ba") == 0)
          out << std::setw(4) << bankSequence + 1;
        else
          out << std::setw(4) << runSequence + 1;
 
        out << std::setw(8) << std::fixed << std::setprecision(5) << lambda;
        out << std::setw(8) << std::fixed << std::setprecision(5) << tbar;
 
        if (cosines) {
          // This is the reverse incident beam
          V3D reverse_incident_dir = p.getSourceDirectionSampleFrame();
          V3D reverse_incident_cos = ol.cosFromDir(reverse_incident_dir);
 
          // This is the scattered beam direction
          V3D scattered_dir = p.getDetectorDirectionSampleFrame();
          V3D scattered_cos = ol.cosFromDir(scattered_dir);
 
          for (int k = 0; k < 3; ++k) {
            out << std::setw(9) << std::fixed << std::setprecision(5) << reverse_incident_cos[k];
            out << std::setw(9) << std::fixed << std::setprecision(5) << scattered_cos[k];
          }
        }
 
        out << std::setw(6) << runNumber;
 
        if (cosines) {
          out << std::setw(7) << seqNum;
        } else {
          out << std::setw(7) << wi + 1;
        }
 
        out << std::setw(7) << std::fixed << std::setprecision(4) << transmission;
 
        out << std::setw(4) << std::right << bank;
 
        out << std::setw(9) << std::fixed << std::setprecision(5) << scattering; // two-theta scattering
 
        out << std::setw(8) << std::fixed << std::setprecision(4) << dsp;
 
        if (cosines) {
          out << std::setw(7) << std::fixed << std::setprecision(2) << static_cast<double>(p.getCol());
          out << std::setw(7) << std::fixed << std::setprecision(2) << static_cast<double>(p.getRow());
        }
 
        out << '\n';
      }
    }
  }
  if (decimalHKL == EMPTY_INT()) {
    out << std::setw(4) << 0 << std::setw(4) << 0 << std::setw(4) << 0;
    if (maxOrder > 0) {
      out << std::setw(4) << 0 << std::setw(4) << 0 << std::setw(4) << 0;
    }
  } else {
    //
    out << std::setw(5 + decimalHKL) << std::fixed << std::setprecision(decimalHKL) << 0.0 << std::setw(5 + decimalHKL)
        << std::fixed << std::setprecision(decimalHKL) << 0.0 << std::setw(5 + decimalHKL) << std::fixed
        << std::setprecision(decimalHKL) << 0.0;
  }
  if (cosines) {
    out << "    0.00    0.00   0 0.00000 0.00000"
           "  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000"
           "      0      0 0.0000   0  0.00000  0.0000   0.00   0.00";
  } else {
    out << "    0.00    0.00   0 0.00000 0.00000"
           "      0      0 0.0000   0  0.00000  0.0000";
  }
  out << '\n';
  out.flush();
  out.close();
  // delete banned peaks
  std::vector<int> badPeaks;
  for (auto it = banned.crbegin(); it != banned.crend(); ++it) {
    badPeaks.emplace_back(static_cast<int>(*it));
  }
  peaksW->removePeaks(std::move(badPeaks));
 
  bool append = getProperty("AppendFile");
  if (append && std::filesystem::exists(filename)) {
    auto load_alg = createChildAlgorithm("LoadHKL");
    load_alg->setPropertyValue("Filename", filename);
    load_alg->setProperty("OutputWorkspace", "peaks");
    load_alg->executeAsChildAlg();
    // Get back the result
    DataObjects::PeaksWorkspace_sptr ws2 = load_alg->getProperty("OutputWorkspace");
    ws2->setInstrument(inst);
 
    auto plus_alg = createChildAlgorithm("CombinePeaksWorkspaces");
    plus_alg->setProperty("LHSWorkspace", peaksW);
    plus_alg->setProperty("RHSWorkspace", ws2);
    plus_alg->executeAsChildAlg();
    // Get back the result
    peaksW = plus_alg->getProperty("OutputWorkspace");
  }
 
  setProperty("OutputWorkspace", peaksW);
} // namespace Crystal
 
double SaveHKL::slantPathLength(const Instrument_const_sptr &inst, const ComponentInfo &componentInfo,
                                const std::string &bankName, const double L2, const double depth) {
  size_t detIndex = componentInfo.indexOfAny(bankName);
  if (inst->getName() == "CORELLI") // for Corelli with sixteenpack under bank
  {
    const auto children = componentInfo.children(detIndex);
    if (!children.empty()) {
      detIndex = children[0];
    }
  }
  // NOTE: take the position from ComponentInfo. Dereferencing componentID() would yield the *base* component,
  //       whose getDistance() ignores the ParameterMap and so reports uncalibrated IDF geometry.
  const double cosA = componentInfo.position(detIndex).distance(componentInfo.samplePosition()) / L2;
  return depth / cosA;
}
 
double SaveHKL::absorbSphere(double radius, double twoth, double wl, double &tbar) {
 
  const double mu = m_smu + (m_amu / 1.8f) * wl; // linear absorption coef
  const double mur = mu * radius;
 
  if (mur < 0. || mur > 2.5) {
    std::ostringstream s;
    s << mur;
    throw std::runtime_error("muR is not in range of Dwiggins' table :" + s.str());
  }
 
  const double theta = twoth * radtodeg * 0.5;
  if (theta < 0. || theta > 90.) {
    std::ostringstream s;
    s << theta;
    throw std::runtime_error("theta is not valid it must be in range [0, 90]");
  }
 
  const double transmission = 1.f / AnvredCorrection::calc_Astar(theta, mur);
 
  // calculate tbar as defined by coppens.
  // transmission = exp(-mu*tbar)
  if (std::fabs(mu) < 1e-300)
    tbar = 0.0;
  else
    tbar = -std::log(transmission) / mu;
 
  return transmission;
}
 
double SaveHKL::spectrumCalc(double TOF, int iSpec, const std::vector<std::vector<double>> &time,
                             const std::vector<std::vector<double>> &spectra, size_t id) {
  if (spectra[id].size() < 11) {
    throw std::runtime_error("Not enough spectral coefficients for GSAS Type 2 spectrum.");
  }
  if (time[id].size() < spectra[id].size()) {
    throw std::runtime_error("Not enough time points for the spectrum.");
  }
 
  double spect = 0;
  if (iSpec == 1) {
    //"Calculate the spectrum using spectral coefficients for the GSAS Type 2
    // incident spectrum."
    double T = TOF / 1000.; // time-of-flight in milliseconds
 
    double c1 = spectra[id][0];
    double c2 = spectra[id][1];
    double c3 = spectra[id][2];
    double c4 = spectra[id][3];
    double c5 = spectra[id][4];
    double c6 = spectra[id][5];
    double c7 = spectra[id][6];
    double c8 = spectra[id][7];
    double c9 = spectra[id][8];
    double c10 = spectra[id][9];
    double c11 = spectra[id][10];
 
    spect = c1 + c2 * exp(-c3 / std::pow(T, 2)) / std::pow(T, 5) + c4 * exp(-c5 * std::pow(T, 2)) +
            c6 * exp(-c7 * std::pow(T, 3)) + c8 * exp(-c9 * std::pow(T, 4)) + c10 * exp(-c11 * std::pow(T, 5));
  } else {
    size_t i = 1;
    for (i = 1; i < spectra[id].size(); ++i)
      if (TOF < time[id][i])
        break;
    if (i < spectra[id].size()) {
      spect = spectra[id][i - 1] +
              (TOF - time[id][i - 1]) / (time[id][i] - time[id][i - 1]) * (spectra[id][i] - spectra[id][i - 1]);
    } else {
      spect = spectra[id].back();
    }
  }
 
  return spect;
}
void SaveHKL::sizeBanks(const std::string &bankName, int &nCols, int &nRows) {
  if (bankName == "None")
    return;
  const auto &componentInfo = m_ws->componentInfo();
  size_t parentIndex;
  try {
    parentIndex = componentInfo.indexOfAny(bankName);
  } catch (std::invalid_argument &) {
    return;
  }
  if (componentInfo.isGridDetector(parentIndex)) {
    const auto grid = componentInfo.pixelGridComponent(parentIndex);
 
    nCols = grid.nX;
    nRows = grid.nY;
  } else {
    if (m_ws->getInstrumentName() == "CORELLI") // for Corelli with sixteenpack under bank
    {
      auto children = componentInfo.children(parentIndex);
      if (!children.empty()) {
        parentIndex = children[0];
      }
    }
    auto children = componentInfo.children(parentIndex);
    auto grandchildren = componentInfo.children(children[0]);
    nRows = static_cast<int>(grandchildren.size());
    nCols = static_cast<int>(children.size());
  }
}
 
} // namespace Mantid::Crystal