PeaksWorkspace.cpp

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// 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 "MantidDataObjects/PeaksWorkspace.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/Sample.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Instrument/Goniometer.h"
#include "MantidKernel/IPropertyManager.h"
#include "MantidKernel/Logger.h"
#include "MantidKernel/UnitConversion.h"
#include "MantidNexus/NexusFile.h"
 
#include <cmath>
 
using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::Geometry;
 
namespace Mantid::DataObjects {
DECLARE_WORKSPACE(PeaksWorkspace)
 
Mantid::Kernel::Logger g_log("PeaksWorkspace");
 
//---------------------------------------------------------------------------------------------
PeaksWorkspace::PeaksWorkspace() : IPeaksWorkspace(), m_peaks(), m_columns(), m_columnNames(), m_coordSystem(None) {
  initColumns();
  // PeaksWorkspace does not use the grouping mechanism of ExperimentInfo.
  setNumberOfDetectorGroups(0);
}
 
//---------------------------------------------------------------------------------------------
// PeaksWorkspace::PeaksWorkspace(const PeaksWorkspace &other) = default;
PeaksWorkspace::PeaksWorkspace(const PeaksWorkspace &other)
    : IPeaksWorkspace(other), m_peaks(other.m_peaks), m_columns(), m_columnNames(), m_coordSystem(other.m_coordSystem) {
  initColumns();
  // PeaksWorkspace does not use the grouping mechanism of ExperimentInfo.
  setNumberOfDetectorGroups(0);
}
 
class PeakComparator {
public:
  using ColumnAndDirection = PeaksWorkspace::ColumnAndDirection;
  std::vector<ColumnAndDirection> &criteria;
 
  explicit PeakComparator(std::vector<ColumnAndDirection> &criteria) : criteria(criteria) {}
 
  inline bool operator()(const Peak &a, const Peak &b) {
    for (const auto &name : criteria) {
      const auto &col = name.first;
      const bool ascending = name.second;
      bool lessThan = false;
      if (col == "BankName") {
        // If this criterion is equal, move on to the next one
        const std::string valA = a.getBankName();
        const std::string valB = b.getBankName();
        // Move on to lesser criterion if equal
        if (valA == valB)
          continue;
        lessThan = (valA < valB);
      } else {
        // General double comparison
        const double valA = a.getValueByColName(col);
        const double valB = b.getValueByColName(col);
        // Move on to lesser criterion if equal
        if (valA == valB)
          continue;
        lessThan = (valA < valB);
      }
      // Flip the sign of comparison if descending.
      if (ascending)
        return lessThan;
      else
        return !lessThan;
    }
    // If you reach here, all criteria were ==; so not <, so return false
    return false;
  }
};
 
//---------------------------------------------------------------------------------------------
void PeaksWorkspace::sort(std::vector<ColumnAndDirection> &criteria) {
  PeakComparator comparator(criteria);
  std::stable_sort(m_peaks.begin(), m_peaks.end(), comparator);
}
 
//---------------------------------------------------------------------------------------------
int PeaksWorkspace::getNumberPeaks() const { return int(m_peaks.size()); }
 
//---------------------------------------------------------------------------------------------
std::string PeaksWorkspace::getConvention() const { return m_convention; }
 
//---------------------------------------------------------------------------------------------
void PeaksWorkspace::removePeak(const int peakNum) {
  if (peakNum >= static_cast<int>(m_peaks.size()) || peakNum < 0) {
    throw std::invalid_argument("PeaksWorkspace::removePeak(): peakNum is out of range.");
  }
  m_peaks.erase(m_peaks.begin() + peakNum);
}
 
void PeaksWorkspace::removePeaks(std::vector<int> badPeaks) {
  if (badPeaks.empty())
    return;
  // if index of peak is in badPeaks remove
  int ip = -1;
  auto it = std::remove_if(m_peaks.begin(), m_peaks.end(), [&ip, badPeaks](const Peak &pk) {
    UNUSED_ARG(pk);
    ip++;
    return std::any_of(badPeaks.cbegin(), badPeaks.cend(), [ip](int badPeak) { return badPeak == ip; });
  });
  m_peaks.erase(it, m_peaks.end());
}
 
//---------------------------------------------------------------------------------------------
void PeaksWorkspace::addPeak(const Geometry::IPeak &ipeak) {
  if (dynamic_cast<const Peak *>(&ipeak)) {
    m_peaks.emplace_back(static_cast<const Peak &>(ipeak));
  } else {
    m_peaks.emplace_back(Peak(ipeak));
  }
}
 
//---------------------------------------------------------------------------------------------
void PeaksWorkspace::addPeak(const V3D &position, const SpecialCoordinateSystem &frame) {
  auto peak = createPeak(position, frame);
  addPeak(*peak);
}
 
//---------------------------------------------------------------------------------------------
void PeaksWorkspace::addPeak(Peak &&peak) { m_peaks.emplace_back(peak); }
 
//---------------------------------------------------------------------------------------------
Peak &PeaksWorkspace::getPeak(size_t const peakNum) {
  if (peakNum >= m_peaks.size()) {
    throw std::invalid_argument("PeaksWorkspace::getPeak(): peakNum is out of range.");
  }
  return m_peaks[peakNum];
}
 
//---------------------------------------------------------------------------------------------
const Peak &PeaksWorkspace::getPeak(size_t const peakNum) const {
  if (peakNum >= m_peaks.size()) {
    throw std::invalid_argument("PeaksWorkspace::getPeak(): peakNum is out of range.");
  }
  return m_peaks[peakNum];
}
 
//---------------------------------------------------------------------------------------------
std::unique_ptr<Geometry::IPeak> PeaksWorkspace::createPeak(const Kernel::V3D &QLabFrame,
                                                            std::optional<double> detectorDistance) const {
  // create a peak using the qLab frame
  std::unique_ptr<IPeak> peak = std::make_unique<Peak>(this->getInstrument(), QLabFrame, detectorDistance);
  // Set the goniometer
  peak->setGoniometerMatrix(this->run().getGoniometer().getR());
  // Take the run number from this
  peak->setRunNumber(this->getRunNumber());
 
  return peak;
}
 
//---------------------------------------------------------------------------------------------
std::unique_ptr<Geometry::IPeak> PeaksWorkspace::createPeak(const Kernel::V3D &position,
                                                            const Kernel::SpecialCoordinateSystem &frame) const {
  if (frame == Mantid::Kernel::HKL) {
    return createPeakHKL(position);
  } else if (frame == Mantid::Kernel::QLab) {
    return createPeak(position);
  } else {
    return createPeakQSample(position);
  }
}
 
//---------------------------------------------------------------------------------------------
std::unique_ptr<IPeak> PeaksWorkspace::createPeakQSample(const V3D &position) const {
  // Create a peak from QSampleFrame
 
  Geometry::Goniometer goniometer;
 
  LogManager_const_sptr props = getLogs();
  // See if we can get a wavelength/energy
  // Then assume constant wavelenth
  double wavelength(0);
  if (props->hasProperty("wavelength")) {
    wavelength = props->getPropertyValueAsType<double>("wavelength");
  } else if (props->hasProperty("energy")) {
    wavelength = Kernel::UnitConversion::run("Energy", "Wavelength", props->getPropertyValueAsType<double>("energy"), 0,
                                             0, 0, Kernel::DeltaEMode::Elastic, 0);
  } else if (getInstrument()->hasParameter("wavelength")) {
    wavelength = getInstrument()->getNumberParameter("wavelength").at(0);
  }
 
  if (wavelength > 0) {
    goniometer.calcFromQSampleAndWavelength(position, wavelength);
    g_log.information() << "Found goniometer rotation to be " << goniometer.getEulerAngles()[0]
                        << " degrees for Q sample = " << position << "\n";
  } else {
    goniometer = run().getGoniometer();
  }
  // create a peak using the qLab frame
  std::unique_ptr<IPeak> peak = std::make_unique<Peak>(getInstrument(), position, goniometer.getR());
  // Take the run number from this
  peak->setRunNumber(getRunNumber());
  return peak;
}
 
std::vector<std::pair<std::string, std::string>> PeaksWorkspace::peakInfo(const Kernel::V3D &qFrame,
                                                                          bool labCoords) const {
  std::vector<std::pair<std::string, std::string>> Result;
  std::ostringstream oss;
  oss << std::setw(12) << std::fixed << std::setprecision(3) << (qFrame.norm());
  std::pair<std::string, std::string> QMag("|Q|", oss.str());
  Result.emplace_back(QMag);
 
  oss.str("");
  oss.clear();
  oss << std::setw(12) << std::fixed << std::setprecision(3) << (2.0 * M_PI / qFrame.norm());
 
  std::pair<std::string, std::string> dspc("d-spacing", oss.str());
  oss.str("");
  oss.clear();
  Result.emplace_back(dspc);
 
  int seqNum = -1;
  bool hasOneRunNumber = true;
  int runNum = -1;
  try {
    int NPeaks = getNumberPeaks();
    double minDist = 10000000;
    for (int i = 0; i < NPeaks; i++) {
      Peak pk = getPeak(i);
      V3D Q = pk.getQLabFrame();
      if (!labCoords)
        Q = pk.getQSampleFrame();
      double D = qFrame.distance(Q);
      if (D < minDist) {
        minDist = D;
        seqNum = i;
      }
 
      int run = pk.getRunNumber();
      if (runNum < 0)
        runNum = run;
      else if (runNum != run)
        hasOneRunNumber = false;
    }
  } catch (...) {
    seqNum = -1; // peak could have been removed
  }
  V3D Qlab = qFrame;
  V3D Qsamp;
  Kernel::Matrix<double> Gon(3, 3, true);
 
  if (seqNum >= 0)
    Gon = getPeak(seqNum).getGoniometerMatrix();
  if (labCoords) {
 
    Kernel::Matrix<double> InvGon(Gon);
    InvGon.Invert();
    Qsamp = InvGon * Qlab;
 
  } else {
    Qsamp = qFrame;
    Qlab = Gon * Qsamp;
  }
 
  if (labCoords || seqNum >= 0)
 
  {
    std::pair<std::string, std::string> QlabStr("Qlab", boost::lexical_cast<std::string>(Qlab));
    Result.emplace_back(QlabStr);
  }
 
  if (!labCoords || seqNum >= 0) {
 
    std::pair<std::string, std::string> QsampStr("QSample", boost::lexical_cast<std::string>(Qsamp));
    Result.emplace_back(QsampStr);
  }
 
  try {
    IPeak_uptr iPeak = createPeak(Qlab);
    Peak_uptr peak(static_cast<DataObjects::Peak *>(iPeak.release()));
 
    if (sample().hasOrientedLattice()) {
 
      peak->setGoniometerMatrix(Gon);
      const Geometry::OrientedLattice &lat = (sample().getOrientedLattice());
 
      const Kernel::Matrix<double> &UB0 = lat.getUB();
      Kernel::Matrix<double> UB(UB0);
      UB.Invert();
      V3D hkl = UB * Qsamp / 2 / M_PI;
 
      std::pair<std::string, std::string> HKL("HKL", boost::lexical_cast<std::string>(hkl));
      Result.emplace_back(HKL);
    }
 
    if (hasOneRunNumber) {
      std::pair<std::string, std::string> runn("RunNumber", "   " + std::to_string(runNum));
      Result.emplace_back(runn);
    }
 
    //------- Now get phi, chi and omega ----------------
    Geometry::Goniometer GonG(Gon);
    std::vector<double> OmegaChiPhi = GonG.getEulerAngles("YZY");
    Kernel::V3D PhiChiOmega(OmegaChiPhi[2], OmegaChiPhi[1], OmegaChiPhi[0]);
 
    std::pair<std::string, std::string> GRead("Goniometer Angles", boost::lexical_cast<std::string>(PhiChiOmega));
    Result.emplace_back(GRead);
 
    std::pair<std::string, std::string> SeqNum("Seq Num,1st=1", "    " + std::to_string(seqNum + 1));
    Result.emplace_back(SeqNum);
 
    oss << std::setw(12) << std::fixed << std::setprecision(3) << (peak->getWavelength());
    std::pair<std::string, std::string> wl("Wavelength", oss.str());
    Result.emplace_back(wl);
    oss.str("");
    oss.clear();
 
    if (peak->findDetector()) {
      std::pair<std::string, std::string> detpos("Position(x,y,z)",
                                                 boost::lexical_cast<std::string>(peak->getDetPos()));
      Result.emplace_back(detpos);
 
      oss << std::setw(15) << std::fixed << std::setprecision(3) << (peak->getTOF());
      std::pair<std::string, std::string> tof("TOF", oss.str());
      Result.emplace_back(tof);
      oss.str("");
      oss.clear();
 
      oss << std::setw(12) << std::fixed << std::setprecision(3) << (peak->getFinalEnergy());
      std::pair<std::string, std::string> Energy("Energy", oss.str());
      Result.emplace_back(Energy);
      oss.str("");
      oss.clear();
 
      std::pair<std::string, std::string> row("Row", "    " + std::to_string(peak->getRow()));
      Result.emplace_back(row);
 
      std::pair<std::string, std::string> col("Col", "    " + std::to_string(peak->getCol()));
      Result.emplace_back(col);
 
      std::pair<std::string, std::string> bank("Bank", "    " + peak->getBankName());
      Result.emplace_back(bank);
 
      oss << std::setw(12) << std::fixed << std::setprecision(3) << (peak->getScattering());
      std::pair<std::string, std::string> scat("Scattering Angle", oss.str());
      Result.emplace_back(scat);
    }
 
  } catch (...) // Impossible position
  {
  }
  return Result;
}
 
std::unique_ptr<IPeak> PeaksWorkspace::createPeakHKL(const V3D &HKL) const {
  /*
   The following allows us to add peaks where we have a single UB to work from.
   */
  const auto &lattice = this->sample().getOrientedLattice();
  const auto &goniometer = this->run().getGoniometer();
 
  // Calculate qLab from q HKL. As per Busing and Levy 1967, q_lab_frame = 2pi *
  // Goniometer * UB * HKL
  const V3D qLabFrame = goniometer.getR() * lattice.getUB() * HKL * 2 * M_PI;
 
  // create a peak using the qLab frame
  // This should calculate the detector positions too
  std::unique_ptr<IPeak> peak = std::make_unique<Peak>(this->getInstrument(), qLabFrame);
  // We need to set HKL separately to keep things consistent.
  peak->setHKL(HKL[0], HKL[1], HKL[2]);
  peak->setIntHKL(peak->getHKL());
  // Set the goniometer
  peak->setGoniometerMatrix(goniometer.getR());
  // Take the run number from this
  peak->setRunNumber(this->getRunNumber());
 
  return peak;
}
 
std::unique_ptr<IPeak> PeaksWorkspace::createPeak() const { return std::make_unique<Peak>(); }
 
int PeaksWorkspace::peakInfoNumber(const Kernel::V3D &qFrame, bool labCoords) const {
  std::vector<std::pair<std::string, std::string>> Result;
  std::ostringstream oss;
  oss << std::setw(12) << std::fixed << std::setprecision(3) << (qFrame.norm());
  std::pair<std::string, std::string> QMag("|Q|", oss.str());
  Result.emplace_back(QMag);
 
  oss.str("");
  oss.clear();
  oss << std::setw(12) << std::fixed << std::setprecision(3) << (2.0 * M_PI / qFrame.norm());
 
  std::pair<std::string, std::string> dspc("d-spacing", oss.str());
  oss.str("");
  oss.clear();
  Result.emplace_back(dspc);
 
  int seqNum = -1;
  double minDist = 10000000;
 
  for (int i = 0; i < getNumberPeaks(); i++) {
    Peak pk = getPeak(i);
    V3D Q = pk.getQLabFrame();
    if (!labCoords)
      Q = pk.getQSampleFrame();
    double D = qFrame.distance(Q);
    if (D < minDist) {
      minDist = D;
      seqNum = i + 1;
    }
  }
  return seqNum;
}
 
//---------------------------------------------------------------------------------------------
std::vector<Peak> &PeaksWorkspace::getPeaks() { return m_peaks; }
 
const std::vector<Peak> &PeaksWorkspace::getPeaks() const { return m_peaks; }
 
bool PeaksWorkspace::hasIntegratedPeaks() const {
  bool ret = false;
  const std::string peaksIntegrated = "PeaksIntegrated";
  if (this->run().hasProperty(peaksIntegrated)) {
    const auto value = boost::lexical_cast<int>(this->run().getProperty(peaksIntegrated)->value());
    ret = (value != 0);
  }
  return ret;
}
 
//---------------------------------------------------------------------------------------------
size_t PeaksWorkspace::getMemorySize() const { return getNumberPeaks() * sizeof(Peak); }
 
//---------------------------------------------------------------------------------------------
API::ITableWorkspace_sptr PeaksWorkspace::createDetectorTable() const {
  auto table = API::WorkspaceFactory::Instance().createTable("TableWorkspace");
  table->addColumn("int", "Index");
  table->addColumn("int", "DetectorID");
 
  const auto npeaks(static_cast<int>(this->rowCount()));
  int nrows(0);
  for (int i = 0; i < npeaks; ++i) {
    const Peak &peak = this->m_peaks[i];
    auto detIDs = peak.getContributingDetIDs();
    auto itEnd = detIDs.end();
    for (auto it = detIDs.begin(); it != itEnd; ++it) {
      table->appendRow();
      table->cell<int>(nrows, 0) = i;
      table->cell<int>(nrows, 1) = *it;
      ++nrows;
    }
  }
 
  return table;
}
 
//---------------------------------------------------------------------------------------------
void PeaksWorkspace::initColumns() {
  // Note: The column types are controlled in PeakColumn.cpp
  addPeakColumn("RunNumber");
  addPeakColumn("DetID");
  addPeakColumn("h");
  addPeakColumn("k");
  addPeakColumn("l");
  addPeakColumn("Wavelength");
  addPeakColumn("Energy");
  addPeakColumn("TOF");
  addPeakColumn("DSpacing");
  addPeakColumn("Intens");
  addPeakColumn("SigInt");
  addPeakColumn("Intens/SigInt");
  addPeakColumn("BinCount");
  addPeakColumn("BankName");
  addPeakColumn("Row");
  addPeakColumn("Col");
  addPeakColumn("QLab");
  addPeakColumn("QSample");
  addPeakColumn("PeakNumber");
  addPeakColumn("TBar");
  addPeakColumn("IntHKL");
  addPeakColumn("IntMNP");
}
 
//---------------------------------------------------------------------------------------------
void PeaksWorkspace::addPeakColumn(const std::string &name) {
  // Create the PeakColumn.
  m_columns.emplace_back(std::make_shared<DataObjects::PeakColumn<Peak>>(this->m_peaks, name));
  // Cache the names
  m_columnNames.emplace_back(name);
}
 
//---------------------------------------------------------------------------------------------
size_t PeaksWorkspace::getColumnIndex(const std::string &name) const {
  for (size_t i = 0; i < m_columns.size(); i++)
    if (m_columns[i]->name() == name)
      return i;
  throw std::invalid_argument("Column named " + name + " was not found in the PeaksWorkspace.");
}
 
//---------------------------------------------------------------------------------------------
std::shared_ptr<Mantid::API::Column> PeaksWorkspace::getColumn(size_t index) {
  if (index >= m_columns.size())
    throw std::invalid_argument("PeaksWorkspace::getColumn() called with invalid index.");
  return m_columns[index];
}
 
//---------------------------------------------------------------------------------------------
std::shared_ptr<const Mantid::API::Column> PeaksWorkspace::getColumn(size_t index) const {
  if (index >= m_columns.size())
    throw std::invalid_argument("PeaksWorkspace::getColumn() called with invalid index.");
  return m_columns[index];
}
 
void PeaksWorkspace::saveNexus(Nexus::File *file) const {
 
  // Number of Peaks
  const size_t np(m_peaks.size());
 
  // Column vectors for peaks table
  std::vector<int> detectorID(np);
  std::vector<double> H(np);
  std::vector<double> K(np);
  std::vector<double> L(np);
  std::vector<double> intensity(np);
  std::vector<double> sigmaIntensity(np);
  std::vector<double> binCount(np);
  std::vector<double> initialEnergy(np);
  std::vector<double> finalEnergy(np);
  std::vector<double> waveLength(np);
  std::vector<double> scattering(np);
  std::vector<double> dSpacing(np);
  std::vector<double> TOF(np);
  std::vector<int> runNumber(np);
  std::vector<int> peakNumber(np);
  std::vector<double> tbar(np);
  std::vector<double> intHKL(3 * np);
  std::vector<double> intMNP(3 * np);
  std::vector<double> goniometerMatrix(9 * np);
  std::vector<std::string> shapes(np);
 
  // Populate column vectors from Peak Workspace
  size_t maxShapeJSONLength = 0;
  for (size_t i = 0; i < np; i++) {
    Peak p = m_peaks[i];
    detectorID[i] = p.getDetectorID();
    H[i] = p.getH();
    K[i] = p.getK();
    L[i] = p.getL();
    intensity[i] = p.getIntensity();
    sigmaIntensity[i] = p.getSigmaIntensity();
    binCount[i] = p.getBinCount();
    initialEnergy[i] = p.getInitialEnergy();
    finalEnergy[i] = p.getFinalEnergy();
    waveLength[i] = p.getWavelength();
    scattering[i] = p.getScattering();
    dSpacing[i] = p.getDSpacing();
    TOF[i] = p.getTOF();
    runNumber[i] = p.getRunNumber();
    peakNumber[i] = p.getPeakNumber();
    tbar[i] = p.getAbsorptionWeightedPathLength();
    {
      V3D hkl = p.getIntHKL();
      intHKL[3 * i + 0] = hkl[0];
      intHKL[3 * i + 1] = hkl[1];
      intHKL[3 * i + 2] = hkl[2];
      V3D mnp = p.getIntMNP();
      intMNP[3 * i + 0] = mnp[0];
      intMNP[3 * i + 1] = mnp[1];
      intMNP[3 * i + 2] = mnp[2];
      Matrix<double> gm = p.getGoniometerMatrix();
      goniometerMatrix[9 * i + 0] = gm[0][0];
      goniometerMatrix[9 * i + 1] = gm[1][0];
      goniometerMatrix[9 * i + 2] = gm[2][0];
      goniometerMatrix[9 * i + 3] = gm[0][1];
      goniometerMatrix[9 * i + 4] = gm[1][1];
      goniometerMatrix[9 * i + 5] = gm[2][1];
      goniometerMatrix[9 * i + 6] = gm[0][2];
      goniometerMatrix[9 * i + 7] = gm[1][2];
      goniometerMatrix[9 * i + 8] = gm[2][2];
    }
    const std::string shapeJSON = p.getPeakShape().toJSON();
    shapes[i] = shapeJSON;
    if (shapeJSON.size() > maxShapeJSONLength) {
      maxShapeJSONLength = shapeJSON.size();
    }
  }
 
  // Start Peaks Workspace in Nexus File
  const std::string specifyInteger = "An integer";
  const std::string specifyDouble = "A double";
  const std::string specifyString = "A string";
  file->makeGroup("peaks_workspace", "NXentry",
                  true); // For when peaksWorkspace can be loaded
 
  // Coordinate system
  file->writeData("coordinate_system", static_cast<uint32_t>(m_coordSystem));
 
  // Write out the Qconvention
  // ki-kf for Inelastic convention; kf-ki for Crystallography convention
  std::string m_QConvention = this->getConvention();
  file->putAttr("QConvention", m_QConvention);
 
  // Detectors column
  file->writeData("column_1", detectorID);
  file->openData("column_1");
  file->putAttr("name", "Detector ID");
  file->putAttr("interpret_as", specifyInteger);
  file->putAttr("units", "Not known");
  file->closeData();
 
  // H column
  file->writeData("column_2", H);
  file->openData("column_2");
  file->putAttr("name", "H");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // K column
  file->writeData("column_3", K);
  file->openData("column_3");
  file->putAttr("name", "K");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // L column
  file->writeData("column_4", L);
  file->openData("column_4");
  file->putAttr("name", "L");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Intensity column
  file->writeData("column_5", intensity);
  file->openData("column_5");
  file->putAttr("name", "Intensity");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Sigma Intensity column
  file->writeData("column_6", sigmaIntensity);
  file->openData("column_6");
  file->putAttr("name", "Sigma Intensity");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Bin Count column
  file->writeData("column_7", binCount);
  file->openData("column_7");
  file->putAttr("name", "Bin Count");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Initial Energy column
  file->writeData("column_8", initialEnergy);
  file->openData("column_8");
  file->putAttr("name", "Initial Energy");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Final Energy column
  file->writeData("column_9", finalEnergy);
  file->openData("column_9");
  file->putAttr("name", "Final Energy");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Wave Length Column
  file->writeData("column_10", waveLength);
  file->openData("column_10");
  file->putAttr("name", "Wave Length");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Scattering Column
  file->writeData("column_11", scattering);
  file->openData("column_11");
  file->putAttr("name", "Scattering");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // D Spacing Column
  file->writeData("column_12", dSpacing);
  file->openData("column_12");
  file->putAttr("name", "D Spacing");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // TOF Column
  file->writeData("column_13", TOF);
  file->openData("column_13");
  file->putAttr("name", "TOF");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Run Number column
  file->writeData("column_14", runNumber);
  file->openData("column_14");
  file->putAttr("name", "Run Number");
  file->putAttr("interpret_as", specifyInteger);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Peak Number column
  file->writeData("column_17", peakNumber);
  file->openData("column_17");
  file->putAttr("name", "Peak Number");
  file->putAttr("interpret_as", specifyInteger);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // TBar column
  file->writeData("column_18", tbar);
  file->openData("column_18");
  file->putAttr("name", "TBar");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  const Nexus::DimVector qlab_dims{m_peaks.size(), 3};
 
  // Integer HKL column
  file->writeData("column_19", intHKL, qlab_dims);
  file->openData("column_19");
  file->putAttr("name", "IntHKL");
  file->putAttr("interpret_as", "A vector of 3 doubles");
  file->putAttr("units", "r.l.u.");
  file->closeData();
 
  // Integer HKL column
  file->writeData("column_20", intMNP, qlab_dims);
  file->openData("column_20");
  file->putAttr("name", "IntMNP");
  file->putAttr("interpret_as", "A vector of 3 doubles");
  file->putAttr("units", "r.l.u.");
  file->closeData();
 
  // Goniometer Matrix Column
  const Nexus::DimVector array_dims{m_peaks.size(), 9};
  file->writeData("column_15", goniometerMatrix, array_dims);
  file->openData("column_15");
  file->putAttr("name", "Goniometer Matrix");
  file->putAttr("interpret_as", "A matrix of 3x3 doubles");
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();
 
  // Shape
  Nexus::DimVector dims;
  dims.emplace_back(np);
  dims.emplace_back(static_cast<int>(maxShapeJSONLength));
  const std::string name = "column_16";
  file->makeData(name, NXnumtype::CHAR, dims, false);
  file->openData(name);
 
  auto toNexus = new char[maxShapeJSONLength * np];
  for (size_t ii = 0; ii < np; ii++) {
    std::string rowStr = shapes[ii];
    for (size_t ic = 0; ic < rowStr.size(); ic++)
      toNexus[ii * maxShapeJSONLength + ic] = rowStr[ic];
    for (size_t ic = rowStr.size(); ic < static_cast<size_t>(maxShapeJSONLength); ic++)
      toNexus[ii * maxShapeJSONLength + ic] = ' ';
  }
 
  file->putData(toNexus);
 
  delete[] toNexus;
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->putAttr("name", "Shape");
  file->putAttr("interpret_as", specifyString);
  file->closeData();
 
  // QLab & QSample are calculated and do not need to be saved
 
  file->closeGroup(); // end of peaks workpace
}
 
void PeaksWorkspace::setCoordinateSystem(const Kernel::SpecialCoordinateSystem coordinateSystem) {
  m_coordSystem = coordinateSystem;
}
 
Kernel::SpecialCoordinateSystem PeaksWorkspace::getSpecialCoordinateSystem() const { return m_coordSystem; }
 
// prevent shared pointer from deleting this
struct NullDeleter {
  template <typename T> void operator()(T * /*unused*/) {}
};
API::LogManager_sptr PeaksWorkspace::logs() { return API::LogManager_sptr(&(this->mutableRun()), NullDeleter()); }
 
API::LogManager_const_sptr PeaksWorkspace::getLogs() const {
  return API::LogManager_const_sptr(new API::LogManager(this->run()));
}
 
ITableWorkspace *PeaksWorkspace::doCloneColumns(const std::vector<std::string> & /*colNames*/) const {
  throw Kernel::Exception::NotImplementedError("PeaksWorkspace cannot clone columns.");
}
} // namespace Mantid::DataObjects
 
 
namespace Mantid::Kernel {
 
template <>
DLLExport Mantid::DataObjects::PeaksWorkspace_sptr
IPropertyManager::getValue<Mantid::DataObjects::PeaksWorkspace_sptr>(const std::string &name) const {
  if (const auto *prop =
          dynamic_cast<PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr> *>(getPointerToProperty(name))) {
    return *prop;
  } else {
    std::string message =
        "Attempt to assign property " + name + " to incorrect type. Expected shared_ptr<PeaksWorkspace>.";
    throw std::runtime_error(message);
  }
}
 
template <>
DLLExport Mantid::DataObjects::PeaksWorkspace_const_sptr
IPropertyManager::getValue<Mantid::DataObjects::PeaksWorkspace_const_sptr>(const std::string &name) const {
  if (const auto *prop =
          dynamic_cast<PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr> *>(getPointerToProperty(name))) {
    return prop->operator()();
  } else {
    std::string message =
        "Attempt to assign property " + name + " to incorrect type. Expected const shared_ptr<PeaksWorkspace>.";
    throw std::runtime_error(message);
  }
}
 
} // namespace Mantid::Kernel