SaveISISNexus.cpp

// 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 +
// SaveISISNexus
// @author Freddie Akeroyd, STFC ISIS Faility
// @author Ronald Fowler, STFC eScience. Modified to fit with
// SaveISISNexusProcessed
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/SaveISISNexus.h"
#include "MantidAPI/FileProperty.h"

#include <boost/date_time/posix_time/posix_time.hpp>
#include <boost/regex.hpp>
#include <boost/scoped_array.hpp>

#include <Poco/DateTimeFormat.h>
#include <Poco/DateTimeParser.h>
#include <Poco/DirectoryIterator.h>
#include <Poco/File.h>
#include <Poco/Path.h>

#include <algorithm>
#include <fstream>
#include <iterator>
#include <map>
#include <sstream>

namespace Mantid {
namespace DataHandling {

// Register the algorithm into the algorithm factory
DECLARE_ALGORITHM(SaveISISNexus)

using namespace Kernel;
using namespace API;

/// Empty default constructor
SaveISISNexus::SaveISISNexus()
    : Algorithm(), m_isisRaw(), handle(), rawFile(), nper(0), nsp(0), ntc(0),
      nmon(0), ndet(0), counts_link(), period_index_link(),
      spectrum_index_link(), time_of_flight_link(), time_of_flight_raw_link() {}

/** Initialisation method.
 *
 */
void SaveISISNexus::init() {
  const std::vector<std::string> inputExts{".raw", ".s*", ".add"};
  declareProperty(
      std::make_unique<FileProperty>("InputFilename", "", FileProperty::Load,
                                     inputExts),
      "The name of the RAW file to read, including its full or relative\n"
      "path. (N.B. case sensitive if running on Linux).");

  // Declare required parameters, filename with ext {.nx,.nx5,xml} and input
  // workspace
  const std::vector<std::string> outputExts{".nxs", ".nx5", ".xml"};
  declareProperty(std::make_unique<FileProperty>(
                      "OutputFilename", "", FileProperty::Save, outputExts),
                  "The name of the Nexus file to write, as a full or relative\n"
                  "path");
}

/**
 * To be used with std::generate to copy only those values from a dataset that
 * don't relate to monitors
 */
template <typename T> class getWithoutMonitors {
public:
  /**
   * Constructor.
   * @param alg This algorithm.
   * @param data Pointer to the data to be copied from
   */
  getWithoutMonitors(SaveISISNexus *alg, T *data)
      : m_alg(alg), m_data(data), m_index(-1) {}
  /** function operator.
   * @return copies of data values that don't relate to monitors
   */
  T operator()() {
    ++m_index;
    while (m_alg->monitor_index.find(m_index) != m_alg->monitor_index.end())
      ++m_index;
    return m_data[m_index];
  }

private:
  SaveISISNexus *m_alg; ///< this algorithm
  T *m_data;            ///< pointer to the data
  int m_index;          ///< index to m_data array
};

/** Execute the algorithm. Currently just calls SaveISISNexusProcessed but could
 *  call write other formats if support added
 *
 *  @throw runtime_error Thrown if algorithm cannot execute
 */
void SaveISISNexus::exec() {
  // Retrieve the filename from the properties
  inputFilename = getPropertyValue("InputFileName");

  m_isisRaw = ISISRAW2();
  rawFile = fopen(inputFilename.c_str(), "rb");
  if (rawFile == nullptr) {
    throw Exception::FileError("Cannot open file ", inputFilename);
  }
  m_isisRaw.ioRAW(rawFile, true);

  nper = m_isisRaw.t_nper; // number of periods
  nsp = m_isisRaw.t_nsp1;  // number of spectra
  ntc = m_isisRaw.t_ntc1;  // number of time channels
  nmon = m_isisRaw.i_mon;  // number of monitors
  ndet = m_isisRaw.i_det;  // number of detectors

  std::string outputFilename = getPropertyValue("OutputFileName");

  NXstatus status;
  float flt;

  status = NXopen(outputFilename.c_str(), NXACC_CREATE5, &handle);
  if (status != NX_OK) {
    throw std::runtime_error("Cannot open file " + outputFilename +
                             " for writing.");
  }
  NXmakegroup(handle, "raw_data_1", "NXentry");
  NXopengroup(handle, "raw_data_1", "NXentry");
  write_isis_vms_compat();
  saveString("beamline", " ");

  flt = static_cast<float>(m_isisRaw.rpb.r_dur); // could be wrong
  saveFloatOpen("collection_time", &flt, 1);
  putAttr("units", "second");
  close();

  saveStringOpen("definition", "TOFRAW");
  putAttr("version", "1.0");
  putAttr("url",
          "http://definition.nexusformat.org/instruments/TOFRAW/?version=1.0");
  close();

  saveStringOpen("definition_local", "ISISTOFRAW");
  putAttr("version", "1.0");
  putAttr("url",
          "http://svn.isis.rl.ac.uk/instruments/ISISTOFRAW/?version=1.0");
  close();

  flt = static_cast<float>(m_isisRaw.rpb.r_dur);
  saveFloatOpen("duration", &flt, 1);
  putAttr("units", "second");
  close();

  start_time_str.assign(m_isisRaw.hdr.hd_date, m_isisRaw.hdr.hd_date + 12);
  toISO8601(start_time_str);
  start_time_str += 'T';
  start_time_str +=
      std::string(m_isisRaw.hdr.hd_time, m_isisRaw.hdr.hd_time + 8);
  saveCharOpen("start_time", &start_time_str[0], 19);
  putAttr("units", "ISO8601");
  close();

  std::string str;
  str.assign(m_isisRaw.rpb.r_enddate, m_isisRaw.rpb.r_enddate + 12);
  toISO8601(str);
  str += 'T';
  str += std::string(m_isisRaw.rpb.r_endtime, m_isisRaw.rpb.r_endtime + 8);
  saveCharOpen("end_time", &str[0], 19);
  putAttr("units", "ISO8601");
  close();

  saveChar("title", m_isisRaw.r_title, 80);
  saveInt("good_frames", &m_isisRaw.rpb.r_goodfrm);

  std::string experiment_identifier = std::to_string(m_isisRaw.rpb.r_prop);
  saveChar("experiment_identifier", &experiment_identifier[0],
           static_cast<int>(experiment_identifier.size()));
  int tmp_int(0);
  saveInt("measurement_first_run", &tmp_int);
  saveString("measurement_id", " ");
  saveString("measurement_label", " ");
  saveString("measurement_subid", " ");
  saveString("measurement_type", " ");

  saveCharOpen("name", &m_isisRaw.i_inst, 8);
  putAttr("short_name", m_isisRaw.hdr.inst_abrv, 3);
  close();

  logNotes();

  saveString("program_name", "isisicp");

  saveFloatOpen("proton_charge", &m_isisRaw.rpb.r_gd_prtn_chrg, 1);
  putAttr("units", "uamp.hour");
  close();

  saveFloatOpen("proton_charge_raw", &m_isisRaw.rpb.r_tot_prtn_chrg, 1);
  putAttr("units", "uamp.hour");
  close();

  saveInt("raw_frames", &m_isisRaw.rpb.r_rawfrm);

  run_cycle();

  saveInt("run_number", &m_isisRaw.r_number);

  // script_name
  // seci_config

  instrument();

  make_detector_1_link();

  write_monitors();

  user();

  sample();

  runlog();

  selog();

  NXclosegroup(handle); // raw_data_1
  NXclose(&handle);
}

/**
 * Save int data.
 * @param name Name of the data set
 * @param data Pointer to the data source
 * @param size size of the data in sizeof(int)
 */
void SaveISISNexus::saveInt(const char *name, void *data, int size) {
  saveIntOpen(name, data, size);
  close();
}

/**
 * Save char data.
 * @param name Name of the data set
 * @param data Pointer to the data source
 * @param size size of the data in sizeof(char)
 */
void SaveISISNexus::saveChar(const char *name, void *data, int size) {
  saveCharOpen(name, data, size);
  close();
}

/**
 * Save float data.
 * @param name Name of the data set
 * @param data Pointer to the data source
 * @param size size of the data in sizeof(float)
 */
void SaveISISNexus::saveFloat(const char *name, void *data, int size) {
  saveFloatOpen(name, data, size);
  close();
}

/**
 * Save int data and leave the dataset open.
 * @param name Name of the data set
 * @param data Pointer to the data source
 * @param size size of the data in sizeof(int)
 */
void SaveISISNexus::saveIntOpen(const char *name, void *data, int size) {
  int dim[1];
  dim[0] = size;
  // If we aren't going to anything with the status, then don't bother asking
  // for it!  (NXstatus status = NXblah())
  NXmakedata(handle, name, NX_INT32, 1, dim);
  NXopendata(handle, name);
  NXputdata(handle, data);
}

/**
 * Save char data and leave the dataset open.
 * @param name Name of the data set
 * @param data Pointer to the data source
 * @param size size of the data in sizeof(char)
 */
void SaveISISNexus::saveCharOpen(const char *name, void *data, int size) {
  int dim[1];
  dim[0] = size;
  // If we aren't going to anything with the status, then don't bother asking
  // for it!  (NXstatus status = NXblah())
  NXmakedata(handle, name, NX_CHAR, 1, dim);
  NXopendata(handle, name);
  NXputdata(handle, data);
}

/**
 * Save float data ald leave the dataset open.
 * @param name Name of the data set
 * @param data Pointer to the data source
 * @param size size of the data in sizeof(float)
 */
void SaveISISNexus::saveFloatOpen(const char *name, void *data, int size) {
  int dim[1];
  dim[0] = size;
  // If we aren't going to anything with the status, then don't bother asking
  // for it!  (NXstatus status = NXblah())
  NXmakedata(handle, name, NX_FLOAT32, 1, dim);
  NXopendata(handle, name);
  NXputdata(handle, data);
}

/**
 * Save a vector of string in a dataset.
 * @param name :: Name of the data set
 * @param str_vec :: The vector to save
 * @param max_str_size :: The maximum string size
 * @return The line size
 */
int SaveISISNexus::saveStringVectorOpen(const char *name,
                                        const std::vector<std::string> &str_vec,
                                        int max_str_size) {
  if (str_vec.empty()) {
    saveStringOpen(name, " ");
    return 0;
  }
  int buff_size = max_str_size;
  if (buff_size <= 0)
    for (const auto &str : str_vec) {
      buff_size = std::max(buff_size, int(str.size()));
    }
  if (buff_size <= 0)
    buff_size = 1;
  auto buff = new char[buff_size];
  int dim[2];
  dim[0] = static_cast<int>(str_vec.size());
  dim[1] = buff_size;
  NXmakedata(handle, name, NX_CHAR, 2, dim);
  NXopendata(handle, name);
  for (std::size_t i = 0; i < str_vec.size(); ++i) {
    int start[] = {static_cast<int>(i), 0};
    int sizes[] = {1, buff_size};
    const char *str = str_vec[i].c_str();
    std::fill_n(buff, buff_size, ' ');
    int n = std::min(buff_size, int(str_vec[i].size()));
    std::copy(str, str + n, buff);
    NXputslab(handle, buff, start, sizes);
  }
  delete[] buff;
  return buff_size;
}

/**
 * Save a string in a dataset.
 * @param name :: Name of the data set
 * @param str :: The vector to save
 */
void SaveISISNexus::saveString(const char *name, const std::string &str) {
  if (str.empty())
    return;
  std::string buff(str);
  saveChar(name, &buff[0], static_cast<int>(buff.size()));
}

/**
 * Save a string in a dataset.
 * @param name :: Name of the data set
 * @param str :: The vector to save
 */
void SaveISISNexus::saveStringOpen(const char *name, const std::string &str) {
  if (str.empty())
    return;
  std::string buff(str);
  saveCharOpen(name, &buff[0], static_cast<int>(buff.size()));
}

void SaveISISNexus::putAttr(const char *name, const std::string &value) {
  boost::scoped_array<char> buff(new char[value.size()]);
  std::copy(value.begin(), value.end(), buff.get());
  NXputattr(handle, name, buff.get(), static_cast<int>(value.size()), NX_CHAR);
}

void SaveISISNexus::putAttr(const char *name, char *value, int size) {
  NXputattr(handle, name, value, size, NX_CHAR);
}

void SaveISISNexus::putAttr(const char *name, int value, int size) {
  NXputattr(handle, name, &value, size, NX_INT32);
}

void SaveISISNexus::toISO8601(std::string &str) {
  static const std::string months[] = {"JAN", "FEB", "MAR", "APR",
                                       "MAY", "JUN", "JUL", "AUG",
                                       "SEP", "OCT", "NOV", "DEC"};
  static const std::string monthsn[] = {"01", "02", "03", "04", "05", "06",
                                        "07", "08", "09", "10", "11", "12"};
  const std::string mon = str.substr(3, 3);
  const std::string *i = std::find(months, months + 12, mon);
  std::string iso8601 =
      str.substr(7, 4) + "-" + monthsn[i - months] + "-" + str.substr(0, 2);
  str = iso8601;
}

/// Write isis_vms_compat
void SaveISISNexus::write_isis_vms_compat() {
  NXmakegroup(handle, "isis_vms_compat", "IXvms");
  NXopengroup(handle, "isis_vms_compat", "IXvms");
  int ndet = m_isisRaw.i_det;
  int nmon = m_isisRaw.i_mon;

  saveInt("ADD", &m_isisRaw.add, 9);
  saveInt("CODE", m_isisRaw.code, ndet);
  saveInt("CRAT", m_isisRaw.crat, ndet);

  write_rpb();
  write_spb();
  write_vpb();
  saveInt("DAEP", &m_isisRaw.daep, 64);
  saveInt("DELT", m_isisRaw.delt, ndet);
  saveInt("FORM", &m_isisRaw.data_format);
  saveChar("HDR", &m_isisRaw.hdr, 80);
  saveFloat("LEN2", m_isisRaw.len2, ndet);
  saveInt("MDET", m_isisRaw.mdet, nmon);
  saveInt("MODN", m_isisRaw.modn, ndet);
  saveInt("MONP", m_isisRaw.monp, nmon);
  saveInt("MPOS", m_isisRaw.mpos, ndet);
  saveChar("NAME", m_isisRaw.i_inst, 8);
  saveInt("NDET", &ndet);
  saveInt("NFPP", &m_isisRaw.t_nfpp);
  saveInt("NMON", &nmon);
  saveInt("NPER", &m_isisRaw.t_nper);
  saveInt("NSER", &m_isisRaw.e_nse);
  saveInt("NSP1", &m_isisRaw.t_nsp1);
  saveInt("NTC1", &m_isisRaw.t_ntc1);
  saveInt("NTRG", &m_isisRaw.t_ntrg);
  saveInt("NUSE", &m_isisRaw.i_use);
  saveInt("PMAP", &m_isisRaw.t_pmap, 256);
  saveInt("PRE1", &m_isisRaw.t_pre1);
  saveInt("RUN", &m_isisRaw.r_number);
  saveInt("SPEC", m_isisRaw.spec, ndet);
  saveInt("TCM1", &m_isisRaw.t_tcm1);
  saveFloat("TCP1", m_isisRaw.t_tcp1, 20);
  saveInt("TIMR", m_isisRaw.timr, ndet);
  saveChar("TITL", m_isisRaw.r_title, 80);
  saveFloat("TTHE", m_isisRaw.tthe, ndet);
  saveInt("UDET", m_isisRaw.udet, ndet);
  saveInt("ULEN", &m_isisRaw.u_len);
  std::string user_info(160, ' ');
  if (m_isisRaw.u_len > 0) {
    std::copy(reinterpret_cast<char *>(&m_isisRaw.user),
              reinterpret_cast<char *>(&m_isisRaw.user) + m_isisRaw.u_len,
              user_info.begin());
  }
  saveString("USER", user_info);
  saveInt("VER1", &m_isisRaw.frmt_ver_no);
  saveInt("VER2", &m_isisRaw.ver2);
  saveInt("VER3", &m_isisRaw.ver3);
  saveInt("VER4", &m_isisRaw.ver4);
  saveInt("VER5", &m_isisRaw.ver5);
  saveInt("VER6", &m_isisRaw.ver6);
  saveInt("VER7", &m_isisRaw.ver7);
  saveInt("VER8", &m_isisRaw.ver8);
  int tmp_int(0);
  saveInt("VER9", &tmp_int);

  int n = m_isisRaw.logsect.nlines;
  log_notes.resize(n);
  for (int i = 0; i < n; ++i) {
    log_notes[i].assign(m_isisRaw.logsect.lines[i].data,
                        m_isisRaw.logsect.lines[i].len);
  }
  int ll = saveStringVectorOpen("NOTE", log_notes);
  saveInt("NTNL", &n);
  saveInt("NTLL", &ll);

  NXclosegroup(handle); // isis_vms_compat
}

void SaveISISNexus::instrument() {
  NXmakegroup(handle, "instrument", "NXinstrument");
  NXopengroup(handle, "instrument", "NXinstrument");
  saveCharOpen("name", &m_isisRaw.i_inst, 8);
  putAttr("short_name", m_isisRaw.hdr.inst_abrv, 3);
  close();
  dae();
  detector_1();
  moderator();
  source();
  NXclosegroup(handle);
}

void SaveISISNexus::detector_1() {
  NXmakegroup(handle, "detector_1", "NXdata");
  NXopengroup(handle, "detector_1", "NXdata");

  for (int i = 0; i < nmon; ++i) {
    auto si = int(std::distance(
        m_isisRaw.spec,
        std::find(m_isisRaw.spec, m_isisRaw.spec + nsp, m_isisRaw.mdet[i])));
    monitor_index[si] = i;
  }

  // write counts
  int dim[3];
  dim[0] = nper;
  dim[1] = nsp - nmon;
  dim[2] = ntc;
  NXmakedata(handle, "counts", NX_INT32, 3, dim);
  NXopendata(handle, "counts");
  putAttr("units", "counts");
  putAttr("signal", 1);
  putAttr("axes", "period_index,spectrum_index,time_of_flight");

  int size[] = {1, 1, ntc};
  int index = 0;
  for (int p = 0; p < nper; ++p) {
    int ispec = 0;
    m_isisRaw.skipData(rawFile, index++);
    for (int si = 0; si < nsp; ++si) {
      if (monitor_index.find(si) != monitor_index.end()) {
        m_isisRaw.readData(rawFile, index);
        monitorData.insert(monitorData.end(), m_isisRaw.dat1 + 1,
                           m_isisRaw.dat1 + ntc + 1);
      } else {
        m_isisRaw.readData(rawFile, index);
        int start[] = {p, ispec, 0};
        NXputslab(handle, m_isisRaw.dat1 + 1, start, size);
        ++ispec;
      }
      ++index;
    }
  }
  NXgetdataID(handle, &counts_link);
  NXclosedata(handle);

  NXmakelink(handle, &period_index_link);

  std::vector<int> spec_minus_monitors(nsp - nmon);
  std::generate(spec_minus_monitors.begin(), spec_minus_monitors.end(),
                getWithoutMonitors<int>(this, m_isisRaw.spec));
  saveIntOpen("spectrum_index", &spec_minus_monitors[0], nsp - nmon);
  NXgetdataID(handle, &spectrum_index_link);
  close();

  NXmakelink(handle, &time_of_flight_link);
  NXmakelink(handle, &time_of_flight_raw_link);

  std::vector<float> float_vec(ndet - nmon);
  std::generate(float_vec.begin(), float_vec.end(),
                getWithoutMonitors<float>(this, m_isisRaw.delt));
  saveFloat("delt", &float_vec[0], ndet - nmon);

  saveFloat("source_detector_distance", &m_isisRaw.ivpb.i_sddist, 1);

  // using the same float_vec, size unchanged ndet-nmon
  std::generate(float_vec.begin(), float_vec.end(),
                getWithoutMonitors<float>(this, m_isisRaw.len2));
  saveFloatOpen("distance", &float_vec[0], ndet - nmon);
  putAttr("units", "metre");
  close();

  // using the same float_vec, size unchanged ndet-nmon
  std::generate(float_vec.begin(), float_vec.end(),
                getWithoutMonitors<float>(this, m_isisRaw.tthe));
  saveFloatOpen("polar_angle", &float_vec[0], ndet - nmon);
  putAttr("units", "degree");
  close();

  NXclosegroup(handle);
}

/**
 * Write instrument/moderator group
 */
void SaveISISNexus::moderator() {
  NXmakegroup(handle, "moderator", "NXmoderator");
  NXopengroup(handle, "moderator", "NXmoderator");

  float l1 = -m_isisRaw.ivpb.i_l1;
  saveFloatOpen("distance", &l1, 1);
  putAttr("units", "metre");

  NXclosegroup(handle);
}

/**
 * Write instrument/source group
 */
void SaveISISNexus::source() {
  NXmakegroup(handle, "source", "NXsource");
  NXopengroup(handle, "source", "NXsource");

  saveString("name", "ISIS");
  saveString("probe", "neutrons");
  saveString("type", "Pulsed Neutron Source");

  NXclosegroup(handle);
}

/**
 * Create group "detector_1" at NXentry level and link to some of the data in
 * instrument/detector_1
 */
void SaveISISNexus::make_detector_1_link() {
  NXmakegroup(handle, "detector_1", "NXdata");
  NXopengroup(handle, "detector_1", "NXdata");

  NXmakelink(handle, &counts_link);
  NXmakelink(handle, &period_index_link);
  NXmakelink(handle, &spectrum_index_link);
  NXmakelink(handle, &time_of_flight_link);

  NXclosegroup(handle);
}

/**
 * Get a pointer to the saved monitor data
 * @param period Period, starts with 0
 * @param imon Monitor index (not its spectrum number)
 */
int *SaveISISNexus::getMonitorData(int period, int imon) {
  return &monitorData[period * m_isisRaw.i_mon * m_isisRaw.t_ntc1 +
                      imon * m_isisRaw.t_ntc1];
}

void SaveISISNexus::write_monitors() {
  int nmon = m_isisRaw.i_mon;
  for (int i = 0; i < nmon; ++i) {
    monitor_i(i);
  }
}

/**
 * Write monitor_i gorup
 * @param i Index of a monitor
 */
void SaveISISNexus::monitor_i(int i) {
  int nper = m_isisRaw.t_nper; // number of periods
  int ntc = m_isisRaw.t_ntc1;  // number of time channels
  int dim[] = {nper, 1, ntc};
  int size[] = {1, 1, ntc};
  std::ostringstream ostr;
  int mon_num = i + 1;
  ostr << "monitor_" << mon_num;
  NXmakegroup(handle, ostr.str().c_str(), "NXmonitor");
  NXopengroup(handle, ostr.str().c_str(), "NXmonitor");

  //  int imon = m_isisRaw.mdet[i]; // spectrum number
  NXmakedata(handle, "data", NX_INT32, 3, dim);
  NXopendata(handle, "data");
  for (int p = 0; p < nper; ++p) {
    int start[] = {p, 0, 0};
    NXputslab(handle, getMonitorData(p, i), start, size);
  }
  putAttr("units", "counts");
  putAttr("signal", 1);
  putAttr("axes", "period_index,spectrum_index,time_of_flight");
  NXclosedata(handle);

  saveInt("monitor_number", &mon_num);
  NXmakelink(handle, &period_index_link);
  saveInt("spectrum_index", &m_isisRaw.mdet[i]);
  NXmakelink(handle, &time_of_flight_link);

  NXclosegroup(handle);
}

void SaveISISNexus::dae() {
  NXmakegroup(handle, "dae", "IXdae");
  NXopengroup(handle, "dae", "IXdae");

  saveString("detector_table_file", " ");
  saveString("spectra_table_file", " ");
  saveString("wiring_table_file", " ");

  saveIntOpen("period_index", m_isisRaw.t_pmap, nper);
  NXgetdataID(handle, &period_index_link);
  close();

  NXmakegroup(handle, "time_channels_1", "IXtime_channels");
  NXopengroup(handle, "time_channels_1", "IXtime_channels");

  boost::scoped_array<float> timeChannels(new float[ntc + 1]);
  m_isisRaw.getTimeChannels(timeChannels.get(), ntc + 1);
  saveFloatOpen("time_of_flight", timeChannels.get(), ntc + 1);
  putAttr("axis", 1);
  putAttr("primary", 1);
  putAttr("units", "microseconds");
  NXgetdataID(handle, &time_of_flight_link);
  close();

  saveIntOpen("time_of_flight_raw", m_isisRaw.t_tcb1, ntc + 1);
  putAttr("units", "pulses");
  putAttr("frequency", "32 MHz");
  NXgetdataID(handle, &time_of_flight_raw_link);
  close();

  NXclosegroup(handle); // time_channels_1

  NXclosegroup(handle); // dae
}

void SaveISISNexus::user() {
  NXmakegroup(handle, "user_1", "NXuser");
  NXopengroup(handle, "user_1", "NXuser");

  saveChar("name", m_isisRaw.user.r_user, 20);
  saveChar("affiliation", m_isisRaw.user.r_instit, 20);

  NXclosegroup(handle); // user_1
}

void SaveISISNexus::sample() {
  NXmakegroup(handle, "sample", "NXsample");
  NXopengroup(handle, "sample", "NXsample");

  saveChar("name", m_isisRaw.spb.e_name, 40);
  saveFloat("height", &m_isisRaw.spb.e_height, 1);
  saveFloat("width", &m_isisRaw.spb.e_width, 1);
  saveFloat("thickness", &m_isisRaw.spb.e_thick, 1);
  saveString("id", " ");
  float tmp(0.0);
  saveFloat("distance", &tmp, 1);
  std::string shape[] = {"cylinder", "flat plate", "HRPD slab", "unknown"};
  int i = m_isisRaw.spb.e_geom - 1;
  if (i < 0 || i > 3)
    i = 3;
  saveString("shape", shape[i]);
  std::string type[] = {"sample+can", "empty can",      "vanadium", "absorber",
                        "nothing",    "sample, no can", "unknown"};
  i = m_isisRaw.spb.e_type - 1;
  if (i < 0 || i > 6)
    i = 6;
  saveString("type", type[i]);

  NXclosegroup(handle); // sample
}

/**
 * Create and write run logs form \<RawFilename\>_ICPstatus.txt log file
 */
void SaveISISNexus::runlog() {
  progress(0);
  std::string ICPstatus_filename = inputFilename;
  std::string ICPevent_filename;
  std::string::size_type i = ICPstatus_filename.find_last_of('.');
  if (i != std::string::npos) // remove the file extension
  {
    ICPstatus_filename.erase(i);
  }
  ICPevent_filename = ICPstatus_filename + "_ICPevent.txt";
  ICPstatus_filename += "_ICPstatus.txt";

  std::ifstream fil(ICPstatus_filename.c_str());
  if (!fil) {
    g_log.warning("Cannot find the ICPstatus file. Skipping runlog");
    progress(0.5);
    return;
  }

  std::vector<float> time_vec;
  std::vector<int> period_vec;
  std::vector<int> is_running_vec;
  std::vector<int> is_waiting_vec;
  std::vector<int> good_frames_vec;
  std::vector<int> raw_frames_vec;
  std::vector<int> monitor_sum_1_vec;
  std::vector<int> total_counts_vec;
  std::vector<int> run_status_vec;
  std::vector<float> proton_charge_vec;
  std::vector<float> proton_charge_raw_vec;
  std::vector<float> dae_beam_current_vec;
  std::vector<float> count_rate_vec;
  std::vector<float> np_ratio_vec;

  start_time_str[10] = ' '; // make it compatible with boost::posix_time::ptime
  boost::posix_time::ptime start_time(
      boost::posix_time::time_from_string(start_time_str));
  start_time_str[10] = 'T'; // revert
  std::string line;
  std::getline(fil, line); // skip the first line
  while (std::getline(fil, line)) {
    std::string date_time_str;
    int period;
    int is_running;
    int is_waiting;
    int good_frames;
    int raw_frames;
    int monitor_sum_1;
    int total_counts;
    float proton_charge;
    float proton_charge_raw;
    float dae_beam_current;
    float count_rate;
    float np_ratio;
    std::istringstream istr(line);
    istr >> date_time_str >> period >> is_running >> is_waiting >>
        good_frames >> raw_frames >> proton_charge >> proton_charge_raw >>
        monitor_sum_1 >> dae_beam_current >> total_counts >> count_rate >>
        np_ratio;
    date_time_str[10] = ' ';
    boost::posix_time::ptime time(
        boost::posix_time::time_from_string(date_time_str));
    boost::posix_time::time_duration dt = time - start_time;
    time_vec.emplace_back(float(dt.total_seconds()));
    period_vec.emplace_back(period);
    is_running_vec.emplace_back(is_running);
    is_waiting_vec.emplace_back(is_waiting);
    good_frames_vec.emplace_back(good_frames);
    raw_frames_vec.emplace_back(raw_frames);
    monitor_sum_1_vec.emplace_back(monitor_sum_1);
    total_counts_vec.emplace_back(total_counts);
    proton_charge_vec.emplace_back(proton_charge);
    proton_charge_raw_vec.emplace_back(proton_charge_raw);
    dae_beam_current_vec.emplace_back(dae_beam_current);
    count_rate_vec.emplace_back(count_rate);
    np_ratio_vec.emplace_back(np_ratio);
  }
  fil.close();

  run_status_vec.resize(time_vec.size());
  using std::placeholders::_1;
  std::transform(is_running_vec.begin(), is_running_vec.end(),
                 run_status_vec.begin(), std::bind(std::plus<int>(), _1, 1));

  NXmakegroup(handle, "runlog", "IXrunlog");
  NXopengroup(handle, "runlog", "IXrunlog");

  auto time_vec_size = static_cast<int>(time_vec.size());

  write_runlog("period", &time_vec[0], &period_vec[0], NX_INT32, time_vec_size,
               "none");
  write_runlog("is_running", &time_vec[0], &is_running_vec[0], NX_INT32,
               time_vec_size, "none");
  write_runlog("is_waiting", &time_vec[0], &is_waiting_vec[0], NX_INT32,
               time_vec_size, "none");
  write_runlog("good_frames", &time_vec[0], &good_frames_vec[0], NX_INT32,
               time_vec_size, "frames");
  write_runlog("raw_frames", &time_vec[0], &raw_frames_vec[0], NX_INT32,
               time_vec_size, "frames");
  write_runlog("monitor_sum_1", &time_vec[0], &monitor_sum_1_vec[0], NX_INT32,
               time_vec_size, "counts");
  write_runlog("total_counts", &time_vec[0], &total_counts_vec[0], NX_INT32,
               time_vec_size, "counts");
  write_runlog("proton_charge", &time_vec[0], &proton_charge_vec[0], NX_FLOAT32,
               time_vec_size, "uAh");
  write_runlog("proton_charge_raw", &time_vec[0], &proton_charge_raw_vec[0],
               NX_FLOAT32, time_vec_size, "uAh");
  write_runlog("dae_beam_current", &time_vec[0], &dae_beam_current_vec[0],
               NX_FLOAT32, time_vec_size, "uAh");
  write_runlog("count_rate", &time_vec[0], &count_rate_vec[0], NX_FLOAT32,
               time_vec_size, "counts");
  write_runlog("np_ratio", &time_vec[0], &np_ratio_vec[0], NX_FLOAT32,
               time_vec_size, "nones");

  write_runlog("run_status", &time_vec[0], &run_status_vec[0], NX_INT32,
               time_vec_size, "none");

  // read in ICPevent file and create icp_event log
  std::ifstream icpevent_fil(ICPevent_filename.c_str());
  if (!icpevent_fil) {
    g_log.warning("Cannot find the ICPevent file");
    progress(0.5);
    return;
  }

  time_vec.clear();
  std::vector<std::string> event_vec;
  while (std::getline(icpevent_fil, line)) {
    if (line.empty())
      continue;
    std::string date_time_str = line.substr(0, 19);
    date_time_str[10] = ' ';
    boost::posix_time::ptime time(
        boost::posix_time::time_from_string(date_time_str));
    boost::posix_time::time_duration dt = time - start_time;
    time_vec.emplace_back(float(dt.total_seconds()));
    event_vec.emplace_back(line.substr(20));
  }
  icpevent_fil.close();

  NXmakegroup(handle, "icp_event", "NXlog");
  NXopengroup(handle, "icp_event", "NXlog");

  saveFloatOpen("time", &time_vec[0], static_cast<int>(time_vec.size()));
  putAttr("start", start_time_str);
  putAttr("units", "seconds");
  close();

  saveStringVectorOpen("value", event_vec, 72);
  putAttr("units", " ");
  close();
  NXclosegroup(handle); // icp_event

  NXclosegroup(handle); // runlog
  progress(0.5);
}

/**
 * Write one run log.
 * @param name The log name
 * @param times The pointer to the time array
 * @param data The pointer to the data
 * @param type The type of the data
 * @param size The size of the data
 * @param units The units of the data
 */
void SaveISISNexus::write_runlog(const char *name, void *times, void *data,
                                 int type, int size, const std::string &units) {
  write_logOpen(name, times, data, type, size, units);
  closegroup();
}

/**
 * Writes a NXlog and leaves it open.
 * @param name The log name
 * @param times The pointer to the time array
 * @param data The pointer to the data
 * @param type The type of the data
 * @param size The size of the data
 * @param units The units of the data
 */
void SaveISISNexus::write_logOpen(const char *name, void *times, void *data,
                                  int type, int size,
                                  const std::string &units) {
  NXmakegroup(handle, name, "NXlog");
  NXopengroup(handle, name, "NXlog");

  saveFloatOpen("time", times, size);
  putAttr("start", start_time_str);
  putAttr("units", "seconds");
  close();

  if (type == NX_INT32) {
    saveIntOpen("value", data, size);
  } else if (type == NX_FLOAT32) {
    saveFloatOpen("value", data, size);
  }
  putAttr("units", units);
  close();
}

void SaveISISNexus::selog() {
  // find log files with names <RawFilenameWithoutExt>_LogName.txt and save them
  // in potentialLogFiles
  std::vector<std::string> potentialLogFiles;
  Poco::File l_path(inputFilename);
  std::string l_filenamePart = Poco::Path(l_path.path()).getFileName();
  std::string::size_type i = l_filenamePart.find_last_of('.');
  if (i != std::string::npos) // remove the file extension
  {
    l_filenamePart.erase(i);
  }
  std::string base_name = l_filenamePart;
  boost::regex regex(l_filenamePart + "_.*\\.txt",
                     boost::regex_constants::icase);
  Poco::DirectoryIterator end_iter;
  for (Poco::DirectoryIterator dir_itr(Poco::Path(inputFilename).parent());
       dir_itr != end_iter; ++dir_itr) {
    if (!Poco::File(dir_itr->path()).isFile())
      continue;

    l_filenamePart = Poco::Path(dir_itr->path()).getFileName();

    if (boost::regex_match(l_filenamePart, regex)) {
      potentialLogFiles.emplace_back(dir_itr->path());
    }
  }

  Progress prog(this, 0.5, 1.0, potentialLogFiles.size());

  NXmakegroup(handle, "selog", "IXselog");
  NXopengroup(handle, "selog", "IXselog");

  // create a log for each of the found log files
  std::size_t nBase = base_name.size() + 1;
  for (auto &potentialLogFile : potentialLogFiles) {
    std::string logName = Poco::Path(potentialLogFile).getFileName();
    logName.erase(0, nBase);
    logName.erase(logName.size() - 4);
    if (logName.size() > 3) {
      std::string icp = logName.substr(0, 3);
      std::transform(icp.begin(), icp.end(), icp.begin(), toupper);
      if (icp == "ICP")
        continue;
    }

    std::ifstream fil(potentialLogFile.c_str());
    if (!fil) {
      g_log.warning("Cannot open log file " + potentialLogFile);
      continue;
    }

    start_time_str[10] =
        ' '; // make it compatible with boost::posix_time::ptime
    boost::posix_time::ptime start_time(
        boost::posix_time::time_from_string(start_time_str));
    start_time_str[10] = 'T'; // revert
    std::vector<float> time_vec;
    std::vector<std::string> str_vec;
    std::vector<float> flt_vec;
    std::string line;
    bool isNotNumeric = false;
    while (std::getline(fil, line)) {
      if (line.empty())
        continue;
      std::string date_time_str = line.substr(0, 19);
      date_time_str[10] = ' ';
      boost::posix_time::ptime time(
          boost::posix_time::time_from_string(date_time_str));
      boost::posix_time::time_duration dt = time - start_time;
      time_vec.emplace_back(float(dt.total_seconds()));
      std::istringstream istr(line.substr(20));
      // check if the data are numeric then save them in flt_vec
      if (!isNotNumeric) {
        float flt;
        istr >> flt;
        if (istr.bad() || istr.fail()) {
          isNotNumeric = true;
        } else {
          flt_vec.emplace_back(flt);
        }
      }
      str_vec.emplace_back(istr.str());
    }
    fil.close();
    NXmakegroup(handle, &logName[0], "IXseblock");
    NXopengroup(handle, &logName[0], "IXseblock");

    {
      saveString("vi_name", " ");
      saveString("set_control", " ");
      saveString("read_control", " ");
      float tmp = 0.0;
      saveFloatOpen("setpoint", &tmp, 1);
      putAttr("units", "mV");
      close();
    }

    NXmakegroup(handle, "value_log", "NXlog");
    NXopengroup(handle, "value_log", "NXlog");

    saveFloatOpen("time", &time_vec[0], static_cast<int>(time_vec.size()));
    putAttr("start", start_time_str);
    putAttr("units", "seconds");
    close();

    if (flt_vec.size() == str_vec.size()) {
      saveFloatOpen("value", &flt_vec[0], static_cast<int>(flt_vec.size()));
    } else {
      saveStringVectorOpen("value", str_vec);
    }
    putAttr("units", " ");
    close();

    saveString("name", " ");

    NXclosegroup(handle); // value_log

    NXclosegroup(handle); // logName

    prog.report();
  }

  NXclosegroup(handle); // selog

  progress(1);
}

void SaveISISNexus::logNotes() {
  saveStringVectorOpen("notes", log_notes);
  close();
}

void SaveISISNexus::run_cycle() { saveString("run_cycle", " "); }

void SaveISISNexus::write_rpb() {
  int dim[] = {32, 4};
  NXmakedata(handle, "CRPB", NX_CHAR, 2, dim);
  NXopendata(handle, "CRPB");
  NXputdata(handle, &m_isisRaw.rpb);
  NXclosedata(handle);

  saveInt("IRPB", &m_isisRaw.rpb, 32);
  saveFloat("RRPB", &m_isisRaw.rpb, 32);
}

void SaveISISNexus::write_spb() {
  int dim[] = {64, 4};
  NXmakedata(handle, "CSPB", NX_CHAR, 2, dim);
  NXopendata(handle, "CSPB");
  NXputdata(handle, &m_isisRaw.spb);
  NXclosedata(handle);

  saveInt("SPB", &m_isisRaw.spb, 64);
  saveInt("ISPB", &m_isisRaw.spb, 64);
  saveFloat("RSPB", &m_isisRaw.spb, 64);
}

void SaveISISNexus::write_vpb() {
  saveInt("IVPB", &m_isisRaw.ivpb, 64);
  saveFloat("RVPB", &m_isisRaw.ivpb, 64);
}

} // namespace DataHandling
} // namespace Mantid