SaveCanSAS1D2.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 "MantidDataHandling/SaveCanSAS1D2.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/BinEdgeAxis.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/WorkspaceUnitValidator.h"
#include "MantidDataHandling/FormattingHelpers.h"
#include "MantidGeometry/IComponent.h"
#include "MantidGeometry/Instrument.h"
#include "MantidKernel/Exception.h"
#include "MantidKernel/MantidVersion.h"
#include "MantidKernel/Unit.h"
 
namespace {
void encode(std::string &data) {
  std::string buffer;
  buffer.reserve(data.size());
 
  for (auto const &element : data) {
    switch (element) {
    case '&':
      buffer.append("&");
      break;
    case '\"':
      buffer.append(""");
      break;
    case '\'':
      buffer.append("'");
      break;
    case '<':
      buffer.append("&lt;");
      break;
    case '>':
      buffer.append("&gt;");
      break;
    default:
      buffer.push_back(element);
    }
  }
 
  data.swap(buffer);
}
} // namespace
 
using namespace Mantid::Kernel;
using namespace Mantid::Geometry;
using namespace Mantid::API;
 
namespace Mantid::DataHandling {
 
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(SaveCanSAS1D2)
 
 
void SaveCanSAS1D2::init() {
  SaveCanSAS1D::init();
 
  declareProperty(
      std::make_unique<API::WorkspaceProperty<>>("Transmission", "", Kernel::Direction::Input, PropertyMode::Optional,
                                                 std::make_shared<API::WorkspaceUnitValidator>("Wavelength")),
      "The transmission workspace. Optional. If given, will be saved at "
      "TransmissionSpectrum");
 
  declareProperty(std::make_unique<API::WorkspaceProperty<>>(
                      "TransmissionCan", "", Kernel::Direction::Input, PropertyMode::Optional,
                      std::make_shared<API::WorkspaceUnitValidator>("Wavelength")),
                  "The transmission workspace of the Can. Optional. If given, will be "
                  "saved at TransmissionSpectrum");
 
  declareProperty("SampleTransmissionRunNumber", "", "The run number for the sample transmission workspace. Optional.");
  declareProperty("SampleDirectRunNumber", "", "The run number for the sample direct workspace. Optional.");
  declareProperty("CanScatterRunNumber", "", "The run number for the can scatter workspace. Optional.");
  declareProperty("CanDirectRunNumber", "", "The run number for the can direct workspace. Optional.");
  declareProperty("OneSpectrumPerFile", false, "If true, each spectrum will be saved in an invididual file");
 
  declareProperty(
      "BackgroundSubtractionWorkspace", "",
      "The name of the workspace used in the scaled background subtraction, to be included in the metadata. Optional.");
  declareProperty(
      "BackgroundSubtractionScaleFactor", 0.0,
      "The scale factor used in the scaled background subtraction, to be included in the metadata. Optional.");
}
 
void SaveCanSAS1D2::exec() {
  m_workspace = getProperty("InputWorkspace");
  m_trans_ws = getProperty("Transmission");
  m_transcan_ws = getProperty("TransmissionCan");
  if (!m_workspace) {
    throw std::invalid_argument("Invalid inputworkspace ,Error in  SaveCanSAS1D");
  }
 
  if ((m_trans_ws && m_trans_ws->getNumberHistograms() > 1) ||
      (m_transcan_ws && m_transcan_ws->getNumberHistograms() > 1)) {
    throw std::invalid_argument("Error in SaveCanSAS1D - more than one "
                                "histogram for the transmission workspaces");
  }
 
  // write xml manually as the user requires a specific format were the
  // placement of new line characters is controled
  // and this can't be done in using the stylesheet part in Poco or libXML
 
  size_t i = 0;
  while (i < m_workspace->getNumberHistograms()) {
    std::string fileName;
    if (getProperty("OneSpectrumPerFile")) {
      fileName = getPropertyValue("FileName");
      size_t extPosition = fileName.find(".xml");
      if (extPosition == std::string::npos)
        extPosition = fileName.size();
      std::ostringstream ss;
      ss << std::string(fileName, 0, extPosition) << "_" << i;
      auto axis = m_workspace->getAxis(1);
      if (axis->isNumeric()) {
        auto binEdgeAxis = dynamic_cast<BinEdgeAxis *>(axis);
        if (binEdgeAxis)
          ss << "_" << binEdgeAxis->label(i);
        else
          ss << "_" << axis->getValue(i) << axis->unit()->label().ascii();
      } else if (axis->isText())
        ss << "_" << axis->label(i);
      ss << std::string(fileName, extPosition);
      fileName = ss.str();
    } else {
      fileName = getPropertyValue("FileName");
    }
 
    prepareFileToWriteEntry(fileName);
    m_outFile << "\n\t<SASentry name=\"" << m_workspace->getName() << "\">";
 
    std::string sasTitle;
    createSASTitleElement(sasTitle);
    m_outFile << sasTitle;
 
    std::string sasRun;
    createSASRunElement(sasRun);
    m_outFile << sasRun;
 
    std::string dataUnit = m_workspace->YUnitLabel();
    // look for xml special characters and replace with entity refrence
    searchandreplaceSpecialChars(dataUnit);
 
    std::string sasData;
    if (getProperty("OneSpectrumPerFile")) {
      createSASDataElement(sasData, i);
      i++;
    } else {
      while (i < m_workspace->getNumberHistograms()) {
        createSASDataElement(sasData, i);
        i++;
      }
    }
    m_outFile << sasData;
 
    if (m_trans_ws) {
      std::string transData;
      createSASTransElement(transData, "sample");
      m_outFile << transData;
    }
    if (m_transcan_ws) {
      std::string transData;
      createSASTransElement(transData, "can");
      m_outFile << transData;
    }
 
    std::string sasSample;
    createSASSampleElement(sasSample);
    m_outFile << sasSample;
 
    // Recording the SAS instrument can throw, if there
    // are no detecors present
    std::string sasInstrument;
    try {
      createSASInstrument(sasInstrument);
    } catch (Kernel::Exception::NotFoundError &) {
      throw;
    } catch (std::runtime_error &) {
      throw;
    }
    m_outFile << sasInstrument;
 
    std::string sasProcess;
    createSASProcessElement(sasProcess);
    m_outFile << sasProcess;
 
    std::string sasNote = "\n\t\t<SASnote>";
    sasNote += "\n\t\t</SASnote>";
    m_outFile << sasNote;
 
    m_outFile << "\n\t</SASentry>";
    m_outFile << "\n</SASroot>";
    m_outFile.close();
  }
}
 
void SaveCanSAS1D2::createSASRootElement(std::string &rootElem) {
  rootElem = "<SASroot version=\"1.1\"";
  rootElem += "\n\t\t xmlns=\"urn:cansas1d:1.1\"";
  rootElem += "\n\t\t xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"";
  rootElem += "\n\t\t xsi:schemaLocation=\"urn:cansas1d:1.1 "
              "http://www.cansas.org/formats/1.1/cansas1d.xsd\"\n\t\t>";
}
 
void SaveCanSAS1D2::createSASProcessElement(std::string &sasProcess) {
  sasProcess = "\n\t\t<SASprocess>";
  // outFile<<sasProcess;
 
  std::string sasProcname = "\n\t\t\t<name>";
  sasProcname += "Mantid generated CanSAS1D XML";
  sasProcname += "</name>";
  sasProcess += sasProcname;
 
  time_t rawtime;
  time(&rawtime);
 
  char temp[25];
  strftime(temp, 25, "%d-%b-%Y %H:%M:%S", localtime(&rawtime));
  std::string sasDate(temp);
 
  std::string sasProcdate = "\n\t\t\t<date>";
  sasProcdate += sasDate;
  sasProcdate += "</date>";
  sasProcess += sasProcdate;
 
  std::string sasProcsvn = "\n\t\t\t<term name=\"svn\">";
  sasProcsvn += MantidVersion::version();
  sasProcsvn += "</term>";
  sasProcess += sasProcsvn;
 
  const API::Run &run = m_workspace->run();
  std::string user_file;
  if (run.hasProperty("UserFile")) {
    user_file = run.getLogData("UserFile")->value();
  } else {
    g_log.information("No user file was found in the input workspace.");
  }
 
  std::string sasProcuserfile = "\n\t\t\t<term name=\"user_file\">";
  sasProcuserfile += user_file;
  sasProcuserfile += "</term>";
  // outFile<<sasProcuserfile;
  sasProcess += sasProcuserfile;
 
  std::string batch_file;
  if (run.hasProperty("BatchFile")) {
    batch_file = run.getLogData("BatchFile")->value();
  }
  std::string sasProcbatchfile = "\n\t\t\t<term name=\"batch_file\">";
  sasProcbatchfile += batch_file;
  sasProcbatchfile += "</term>";
  sasProcess += sasProcbatchfile;
 
  if (m_trans_ws) {
    // Add other run numbers
    // SampleTransmission
    const auto sample_trans_run = getPropertyValue("SampleTransmissionRunNumber");
    sasProcess += "\n\t\t\t<term name=\"sample_trans_run\">";
    sasProcess += sample_trans_run + "</term>";
 
    // SampleDirect
    const auto sample_direct_run = getPropertyValue("SampleDirectRunNumber");
    sasProcess += "\n\t\t\t<term name=\"sample_direct_run\">";
    sasProcess += sample_direct_run + "</term>";
  }
 
  // can run number if available
  if (m_transcan_ws) {
    std::string can_run;
    if (m_transcan_ws->run().hasProperty("run_number")) {
      Kernel::Property const *const logP = m_transcan_ws->run().getLogData("run_number");
      can_run = logP->value();
    } else {
      g_log.debug() << "Didn't find RunNumber log in workspace. Writing "
                       "<Run></Run> to the CANSAS file\n";
    }
    std::string sasProcCanRun = "\n\t\t\t<term name=\"can_trans_run\">";
    sasProcCanRun += can_run;
    sasProcCanRun += "</term>";
    sasProcess += sasProcCanRun;
 
    // CanScatter
    const auto can_scatter_run = getPropertyValue("CanScatterRunNumber");
    sasProcess += "\n\t\t\t<term name=\"can_scatter_run\">";
    sasProcess += can_scatter_run + "</term>";
 
    // CanDirect
    const auto can_direct_run = getPropertyValue("CanDirectRunNumber");
    sasProcess += "\n\t\t\t<term name=\"can_direct_run\">";
    sasProcess += can_direct_run + "</term>";
  }
 
  // Scaled Background Subtraction information.
  auto const &bgsubWsName = getPropertyValue("BackgroundSubtractionWorkspace");
  auto const &bgsubScaleFactor = getPropertyValue("BackgroundSubtractionScaleFactor");
  if (!bgsubWsName.empty()) {
    sasProcess += "\n\t\t\t<term name=\"scaled_bgsub_workspace\">";
    sasProcess += bgsubWsName + "</term>";
    sasProcess += "\n\t\t\t<term name=\"scaled_bgsub_scale_factor\">";
    sasProcess += bgsubScaleFactor + "</term>";
  }
 
  // Reduction process note, if available
  std::string process_xml = getProperty("Process");
  if (!process_xml.empty()) {
    std::string processNote = "\n\t\t\t<SASprocessnote>";
    encode(process_xml);
    processNote += process_xml;
    processNote += "</SASprocessnote>";
    sasProcess += processNote;
  } else {
    sasProcess += "\n\t\t\t<SASprocessnote/>";
  }
 
  sasProcess += "\n\t\t</SASprocess>";
}
 
void SaveCanSAS1D2::createSASTransElement(std::string &sasTrans, const std::string &name) {
  API::MatrixWorkspace_const_sptr m_ws;
  if (name == "sample") {
    m_ws = m_trans_ws;
  } else if (name == "can") {
    m_ws = m_transcan_ws;
  } else {
    return; // does not change sasTrans... it will add nothing
  }
 
  if (m_ws->getNumberHistograms() != 1)
    return; // does not change sasTrans
 
  std::stringstream trans;
 
  trans << "\n\t\t<SAStransmission_spectrum name=\"" << name << "\">";
  std::string t_unit = m_ws->YUnit();
  std::string lambda_unit = m_ws->getAxis(0)->unit()->label();
  if (t_unit.empty())
    t_unit = "none";
  if (lambda_unit.empty() || lambda_unit == "Angstrom")
    lambda_unit = "A";
 
  // x data is the Lambda in xml. If histogramdata take the mean
  const auto lambda = m_ws->points(0);
  // y data is the T in xml.
  const auto &trans_value = m_ws->y(0);
  // e data is the Tdev in xml.
  const auto &trans_err = m_ws->e(0);
  for (size_t j = 0; j < trans_value.size(); ++j) {
    trans << "\n\t\t\t<Tdata><Lambda unit=\"" << lambda_unit << "\">";
    if (std::isnan(lambda[j]))
      trans << "NaN";
    else
      trans << formatDouble(lambda[j]);
    trans << "</Lambda>"
          << "<T unit=\"" << t_unit << "\">";
    if (std::isnan(trans_value[j]))
      trans << "NaN";
    else
      trans << formatDouble(trans_value[j]);
    trans << "</T><Tdev unit=\"none\">";
    if (std::isnan(trans_err[j]))
      trans << "NaN";
    else
      trans << formatDouble(trans_err[j]);
    trans << "</Tdev></Tdata>";
  }
  trans << "\n\t\t</SAStransmission_spectrum>";
  sasTrans += trans.str();
}
 
void SaveCanSAS1D2::writeHeader(const std::string &fileName) {
  try {
    m_outFile.open(fileName.c_str(), std::ios::out | std::ios::trunc);
    // write the file header
    m_outFile << "<?xml version=\"1.0\"?>\n"
              << "<?xml-stylesheet type=\"text/xsl\" href=\"cansas1d.xsl\" ?>\n";
    std::string sasroot;
    createSASRootElement(sasroot);
    m_outFile << sasroot;
  } catch (std::fstream::failure &) {
    throw Exception::FileError("Error opening the output file for writing", fileName);
  }
}
 
} // namespace Mantid::DataHandling