LoadSpec.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 +
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/LoadSpec.h"
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/RegisterFileLoader.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/StringTokenizer.h"
#include "MantidKernel/UnitFactory.h"
 
#include <algorithm>
#include <cstring>
#include <fstream>
 
namespace Mantid::DataHandling {
// Register the algorithm into the algorithm factory
DECLARE_FILELOADER_ALGORITHM(LoadSpec)
 
using namespace Kernel;
using namespace API;
 
LoadSpec::LoadSpec() = default;
 
int LoadSpec::confidence(Kernel::FileDescriptor &descriptor) const {
  if (!descriptor.isAscii())
    return 0;
 
  auto &file = descriptor.data();
 
  int confidence(0);
  size_t axiscols(0), datacols(0);
  std::string str;
  using tokenizer = Mantid::Kernel::StringTokenizer;
  const std::string sep = " ";
  bool snsspec(false);
 
  while (std::getline(file, str)) {
    // File is opened in binary mode so getline will leave a \r at the end of an
    // empty line if it exists
    if (str.empty() || str == "\r")
      continue;
 
    try {
      // if it's comment line
      tokenizer tok(str, sep, Mantid::Kernel::StringTokenizer::TOK_IGNORE_EMPTY);
      if (str.at(0) == '#') {
        if (str.at(1) == 'L') {
          axiscols = tok.count();
          // if the file contains a comment line starting with "#L" followed
          // by three columns this could be loadsnsspec file
          if (axiscols > 2) {
            snsspec = true;
          }
        }
      } else {
        // check first data line is a 3 column line
        datacols = tok.count();
        break;
      }
    } catch (std::out_of_range &) {
    }
  }
  if (snsspec && datacols == 3) // three column data
  {
    confidence = 80;
  }
  return confidence;
}
 
void LoadSpec::init() {
  const std::vector<std::string> exts{".dat", ".txt"};
  declareProperty(std::make_unique<FileProperty>("Filename", "", FileProperty::Load, exts),
                  "The name of the text file to read, including its full or "
                  "relative path. The file extension must be .txt or .dat.");
  declareProperty(std::make_unique<WorkspaceProperty<>>("OutputWorkspace", "", Direction::Output),
                  "The name of the workspace that will be created, filled with the read-in "
                  "data and stored in the [[Analysis Data Service]].");
 
  std::vector<std::string> units = UnitFactory::Instance().getKeys();
  units.insert(units.begin(), "MomemtumTransfer");
  declareProperty("Unit", "Energy", std::make_shared<Kernel::StringListValidator>(units),
                  "The unit to assign to the X axis (anything known to the "
                  "[[Unit Factory]] or \"Dimensionless\")");
}
 
void LoadSpec::exec() {
  std::string filename = getProperty("Filename");
  std::ifstream file(filename.c_str());
 
  file.seekg(0, std::ios::end);
  Progress progress(this, 0.0, 1.0, static_cast<int>(file.tellg()));
  file.seekg(0, std::ios::beg);
 
  std::string str;
  std::vector<double> input;
 
  const size_t nSpectra = readNumberOfSpectra(file);
  auto localWorkspace =
      std::dynamic_pointer_cast<MatrixWorkspace>(WorkspaceFactory::Instance().create("Workspace2D", nSpectra, 2, 1));
 
  localWorkspace->getAxis(0)->unit() = UnitFactory::Instance().create(getProperty("Unit"));
 
  file.clear();                 // end of file has been reached so we need to clear file state
  file.seekg(0, std::ios::beg); // go back to beginning of file
 
  int specNum = -1; // spectrum number
  while (getline(file, str)) {
    progress.report(static_cast<int>(file.tellg()));
 
    // line with data, need to be parsed by white spaces
    readLine(str, input);
 
    if (str.empty() && specNum != -1) {
      auto histogram = localWorkspace->histogram(specNum);
      readHistogram(input, histogram);
      localWorkspace->setHistogram(specNum, histogram);
    }
 
    if (str.empty()) {
      specNum++;
      input.clear();
    }
 
  } // end of read file
 
  try {
    if (nSpectra == 0)
      throw "Undefined number of spectra";
 
    if (static_cast<size_t>(specNum) == (nSpectra - 1)) {
      auto histogram = localWorkspace->histogram(specNum);
      readHistogram(input, histogram);
      localWorkspace->setHistogram(specNum, histogram);
    }
  } catch (...) {
  }
 
  setProperty("OutputWorkspace", localWorkspace);
}
 
size_t LoadSpec::readNumberOfSpectra(std::ifstream &file) const {
  // determine the number of lines starting by #L
  // as there is one per set of data
  size_t spectra_nbr = 0;
  std::string str;
  while (getline(file, str)) {
    if (str.empty())
      continue;
    if (str[0] == '#' && str[1] == 'L') {
      spectra_nbr++;
    }
  }
  return spectra_nbr;
}
 
void LoadSpec::readLine(const std::string &line, std::vector<double> &buffer) const {
  if (!line.empty() && line[0] != '#') {
    using tokenizer = Mantid::Kernel::StringTokenizer;
    const std::string sep = " ";
    tokenizer tok(line, sep, Mantid::Kernel::StringTokenizer::TOK_IGNORE_EMPTY);
    buffer.reserve(buffer.size() + tok.size());
    std::transform(tok.cbegin(), tok.cend(), std::back_inserter(buffer),
                   [](const auto &beg) { return std::stod(beg); });
  }
}
 
void LoadSpec::readHistogram(const std::vector<double> &input, HistogramData::Histogram &histogram) const {
  std::vector<double> x, y, e;
 
  auto isHist = input.size() % 3 > 0;
  auto nElements = (isHist) ? input.size() - 1 : input.size() - 2;
 
  x.reserve(nElements);
  y.reserve(nElements);
  e.reserve(nElements);
 
  for (size_t index = 0; index < nElements; index++) {
    x.emplace_back(input[index]);
    index++;
    y.emplace_back(input[index]);
    index++;
    e.emplace_back(input[index]);
  }
 
  histogram.resize(y.size());
 
  if (isHist) {
    // we're loading binned data
    // last value is final x bin
    x.emplace_back(input.back());
    histogram.setBinEdges(x);
  } else {
    histogram.setPoints(x);
  }
 
  histogram.setCounts(y);
  histogram.setCountStandardDeviations(e);
}
 
} // namespace Mantid::DataHandling