LoadNexusLogs.cpp

#include "MantidDataHandling/LoadNexusLogs.h"
#include <nexus/NeXusException.hpp>
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/Run.h"
#include <locale>

#include <Poco/Path.h>
#include <Poco/DateTimeFormatter.h>
#include <Poco/DateTimeParser.h>
#include <Poco/DateTimeFormat.h>

#include <boost/scoped_array.hpp>
#include "MantidDataHandling/LoadTOFRawNexus.h"

namespace Mantid {
namespace DataHandling {
// Register the algorithm into the algorithm factory
DECLARE_ALGORITHM(LoadNexusLogs)

using namespace Kernel;
using API::WorkspaceProperty;
using API::MatrixWorkspace;
using API::MatrixWorkspace_sptr;
using API::FileProperty;
using std::size_t;

namespace {

/**
 * @brief loadAndApplyMeasurementInfo
 * @param file : Nexus::File pointer
 * @param workspace : Pointer to the workspace to set logs on
 * @return True only if reading and execution successful.
 */
bool loadAndApplyMeasurementInfo(::NeXus::File *const file,
                                 API::MatrixWorkspace &workspace) {

  bool successfullyApplied = false;
  try {
    file->openGroup("measurement", "NXcollection");

    // If we can open the measurement group. We assume that the following will
    // be avaliable.
    file->openData("id");
    workspace.mutableRun().addLogData(
        new Mantid::Kernel::PropertyWithValue<std::string>("measurement_id",
                                                           file->getStrData()));
    file->closeData();
    file->openData("label");
    workspace.mutableRun().addLogData(
        new Mantid::Kernel::PropertyWithValue<std::string>("measurement_label",
                                                           file->getStrData()));
    file->closeData();
    file->openData("subid");
    workspace.mutableRun().addLogData(
        new Mantid::Kernel::PropertyWithValue<std::string>("measurement_subid",
                                                           file->getStrData()));
    file->closeData();
    file->openData("type");
    workspace.mutableRun().addLogData(
        new Mantid::Kernel::PropertyWithValue<std::string>("measurement_type",
                                                           file->getStrData()));
    file->closeData();
    file->closeGroup();
    successfullyApplied = true;
  } catch (::NeXus::Exception &) {
    successfullyApplied = false;
  }
  return successfullyApplied;
}

/**
* @brief loadAndApplyRunTitle
* @param file : Nexus::File pointer
* @param workspace : Pointer to the workspace to set logs on
* @return True only if reading and execution successful.
*/
bool loadAndApplyRunTitle(::NeXus::File *const file,
                          API::MatrixWorkspace &workspace) {

  bool successfullyApplied = false;
  try {
    file->openData("title");
    workspace.mutableRun().addLogData(
        new Mantid::Kernel::PropertyWithValue<std::string>("run_title",
                                                           file->getStrData()));
    file->closeData();
    successfullyApplied = true;
  } catch (::NeXus::Exception &) {
    successfullyApplied = false;
  }
  return successfullyApplied;
}
}

/// Empty default constructor
LoadNexusLogs::LoadNexusLogs() {}

/// Initialisation method.
void LoadNexusLogs::init() {
  declareProperty(
      make_unique<WorkspaceProperty<MatrixWorkspace>>("Workspace", "Anonymous",
                                                      Direction::InOut),
      "The name of the workspace that will be filled with the logs.");
  const std::vector<std::string> exts{".nxs", ".n*"};
  declareProperty(Kernel::make_unique<FileProperty>("Filename", "",
                                                    FileProperty::Load, exts),
                  "Path to the .nxs file to load. Can be an EventNeXus or a "
                  "histogrammed NeXus.");
  declareProperty(
      make_unique<PropertyWithValue<bool>>("OverwriteLogs", true,
                                           Direction::Input),
      "If true then some existing logs will be overwritten, if false they will "
      "not.");
  declareProperty(make_unique<PropertyWithValue<std::string>>("NXentryName", "",
                                                              Direction::Input),
                  "Entry in the nexus file from which to read the logs");
}

/** Executes the algorithm. Reading in the file and creating and populating
*  the output workspace
*
*  @throw Exception::FileError If the Nexus file cannot be found/opened
*  @throw std::invalid_argument If the optional properties are set to invalid
*values
*/
void LoadNexusLogs::exec() {
  std::string filename = getPropertyValue("Filename");
  MatrixWorkspace_sptr workspace = getProperty("Workspace");

  std::string entry_name = getPropertyValue("NXentryName");
  // Find the entry name to use (normally "entry" for SNS, "raw_data_1" for
  // ISIS) if entry name is empty
  if (entry_name.empty()) {
    entry_name = LoadTOFRawNexus::getEntryName(filename);
  }
  ::NeXus::File file(filename);
  // Find the root entry
  try {
    file.openGroup(entry_name, "NXentry");
  } catch (::NeXus::Exception &) {
    throw std::invalid_argument("Unknown NeXus file format found in file '" +
                                filename + "', or '" + entry_name +
                                "' is not a valid NXentry");
  }

  /// Use frequency start for Monitor19 and Special1_19 logs with "No Time" for
  /// SNAP
  try {
    file.openPath("DASlogs");
    try {
      file.openGroup("frequency", "NXlog");
      try {
        file.openData("time");

        //----- Start time is an ISO8601 string date and time. ------
        try {
          file.getAttr("start", freqStart);

        } catch (::NeXus::Exception &) {
          // Some logs have "offset" instead of start
          try {
            file.getAttr("offset", freqStart);
          } catch (::NeXus::Exception &) {
            g_log.warning() << "Log entry has no start time indicated.\n";
            file.closeData();
            throw;
          }
        }
        file.closeData();
      } catch (::NeXus::Exception &) {
        // No time. This is not an SNS SNAP file
      }
      file.closeGroup();
    } catch (::NeXus::Exception &) {
      // No time. This is not an SNS frequency group
    }
    file.closeGroup();
  } catch (::NeXus::Exception &) {
    // No time. This is not an SNS group
  }
  // print out the entry level fields
  std::map<std::string, std::string> entries = file.getEntries();
  std::map<std::string, std::string>::const_iterator iend = entries.end();
  for (std::map<std::string, std::string>::const_iterator it = entries.begin();
       it != iend; ++it) {
    std::string group_name(it->first);
    std::string group_class(it->second);
    if (group_name == "DASlogs" || group_class == "IXrunlog" ||
        group_class == "IXselog" || group_name == "framelog") {
      loadLogs(file, group_name, group_class, workspace);
    }
    if (group_class == "IXperiods") {
      loadNPeriods(file, workspace);
    }
  }

  // If there's measurement information, load that info as logs.
  loadAndApplyMeasurementInfo(&file, *workspace);
  // If there's title information, load that info as logs.
  loadAndApplyRunTitle(&file, *workspace);

  // Freddie Akeroyd 12/10/2011
  // current ISIS implementation contains an additional indirection between
  // collected frames via an
  // "event_frame_number" array in NXevent_data (which eliminates frames with no
  // events).
  // the proton_log is for all frames and so is longer than the event_index
  // array, so we need to
  // filter the proton_charge log based on event_frame_number
  // This difference will be removed in future for compatibility with SNS, but
  // the code below will allow current SANS2D files to load
  if (workspace->mutableRun().hasProperty("proton_log")) {
    std::vector<int> event_frame_number;
    this->getLogger().notice()
        << "Using old ISIS proton_log and event_frame_number indirection...\n";
    try {
      // Find the bank/name corresponding to the first event data entry, i.e.
      // one with type NXevent_data.
      file.openPath("/" + entry_name);
      std::map<std::string, std::string> entries = file.getEntries();
      std::map<std::string, std::string>::const_iterator it = entries.begin();
      std::string eventEntry;
      for (; it != entries.end(); ++it) {
        if (it->second == "NXevent_data") {
          eventEntry = it->first;
          break;
        }
      }
      this->getLogger().debug()
          << "Opening"
          << " /" + entry_name + "/" + eventEntry + "/event_frame_number"
          << " to find the event_frame_number\n";
      file.openPath("/" + entry_name + "/" + eventEntry +
                    "/event_frame_number");
      file.getData(event_frame_number);
    } catch (const ::NeXus::Exception &) {
      this->getLogger().warning()
          << "Unable to load event_frame_number - "
             "filtering events by time will not work \n";
    }
    file.openPath("/" + entry_name);
    if (!event_frame_number.empty()) // ISIS indirection - see above comments
    {
      Kernel::TimeSeriesProperty<double> *plog =
          dynamic_cast<Kernel::TimeSeriesProperty<double> *>(
              workspace->mutableRun().getProperty("proton_log"));
      if (!plog)
        throw std::runtime_error(
            "Could not cast (interpret) proton_log as a time "
            "series property. Cannot continue.");
      Kernel::TimeSeriesProperty<double> *pcharge =
          new Kernel::TimeSeriesProperty<double>("proton_charge");
      std::vector<double> pval;
      std::vector<Mantid::Kernel::DateAndTime> ptime;
      pval.reserve(event_frame_number.size());
      ptime.reserve(event_frame_number.size());
      std::vector<Mantid::Kernel::DateAndTime> plogt = plog->timesAsVector();
      std::vector<double> plogv = plog->valuesAsVector();
      for (auto number : event_frame_number) {
        ptime.push_back(plogt[number]);
        pval.push_back(plogv[number]);
      }
      pcharge->create(ptime, pval);
      pcharge->setUnits("uAh");
      workspace->mutableRun().addProperty(pcharge, true);
    }
  }
  try {
    // Read the start and end time strings
    file.openData("start_time");
    Kernel::DateAndTime start(file.getStrData());
    file.closeData();
    file.openData("end_time");
    Kernel::DateAndTime end(file.getStrData());
    file.closeData();
    workspace->mutableRun().setStartAndEndTime(start, end);
  } catch (::NeXus::Exception &) {
  }

  if (!workspace->run().hasProperty("gd_prtn_chrg")) {
    // Try pulling it from the main proton_charge entry first
    try {
      file.openData("proton_charge");
      std::vector<double> values;
      file.getDataCoerce(values);
      std::string units;
      file.getAttr("units", units);
      double charge = values.front();
      if (units.find("picoCoulomb") != std::string::npos) {
        charge *= 1.e-06 / 3600.;
      }
      workspace->mutableRun().setProtonCharge(charge);
    } catch (::NeXus::Exception &) {
      // Try and integrate the proton logs
      try {
        // Use the DAS logs to integrate the proton charge (if any).
        workspace->mutableRun().getProtonCharge();
      } catch (Exception::NotFoundError &) {
        // Ignore not found property error.
      }
    }
  }

  // Close the file
  file.close();
}

/** Try to load the "Veto_pulse" field in DASLogs
 * and convert it to a sample log.
 *
 * @param file :: open nexus file at the DASLogs group
 * @param workspace :: workspace to add to.
 */
void LoadNexusLogs::loadVetoPulses(
    ::NeXus::File &file,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  try {
    file.openGroup("Veto_pulse", "NXgroup");
  } catch (::NeXus::Exception &) {
    // No group. This is common in older files
    return;
  }
  file.openData("veto_pulse_time");

  // Load the start date/time as ISO8601 string.
  std::string start_time;
  file.getAttr("start_time", start_time);
  DateAndTime start(start_time);

  // Read the offsets
  std::vector<double> time_double;
  file.getData(time_double);

  // Fake values with zeroes.
  std::vector<double> values(time_double.size(), 0.0);
  TimeSeriesProperty<double> *tsp =
      new TimeSeriesProperty<double>("veto_pulse_time");
  tsp->create(start, time_double, values);
  tsp->setUnits("");

  // Add the log
  workspace->mutableRun().addProperty(tsp);

  file.closeData();
  file.closeGroup();
}

void LoadNexusLogs::loadNPeriods(
    ::NeXus::File &file,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  int value = 1; // Default to 1-period unless
  try {
    file.openGroup("periods", "IXperiods");
    file.openData("number");
    file.getData(&value);
    file.closeData();
    file.closeGroup();
  } catch (::NeXus::Exception &) {
    // Likely missing IXperiods.
    return;
  }

  API::Run &run = workspace->mutableRun();
  const std::string nPeriodsLabel = "nperiods";
  if (!run.hasProperty(nPeriodsLabel)) {
    run.addProperty(new PropertyWithValue<int>(nPeriodsLabel, value));
  }
}

/**
 * Load log entries from the given group
 * @param file :: A reference to the NeXus file handle opened such that the
 * next call can be to open the named group
 * @param entry_name :: The name of the log entry
 * @param entry_class :: The class type of the log entry
 * @param workspace :: A pointer to the workspace to store the logs
 */
void LoadNexusLogs::loadLogs(
    ::NeXus::File &file, const std::string &entry_name,
    const std::string &entry_class,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  file.openGroup(entry_name, entry_class);
  std::map<std::string, std::string> entries = file.getEntries();
  std::map<std::string, std::string>::const_iterator iend = entries.end();
  for (std::map<std::string, std::string>::const_iterator itr = entries.begin();
       itr != iend; ++itr) {
    std::string log_class = itr->second;
    if (log_class == "NXlog" || log_class == "NXpositioner") {
      loadNXLog(file, itr->first, log_class, workspace);
    } else if (log_class == "IXseblock") {
      loadSELog(file, itr->first, workspace);
    }
  }
  loadVetoPulses(file, workspace);

  file.closeGroup();
}

/**
 * Load an NX log entry a group type that has value and time entries.
 * @param file :: A reference to the NeXus file handle opened at the parent
 * group
 * @param entry_name :: The name of the log entry
 * @param entry_class :: The type of the entry
 * @param workspace :: A pointer to the workspace to store the logs
 */
void LoadNexusLogs::loadNXLog(
    ::NeXus::File &file, const std::string &entry_name,
    const std::string &entry_class,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  g_log.debug() << "processing " << entry_name << ":" << entry_class << "\n";

  file.openGroup(entry_name, entry_class);
  // Validate the NX log class.
  std::map<std::string, std::string> entries = file.getEntries();
  if ((entries.find("value") == entries.end()) ||
      (entries.find("time") == entries.end())) {
    g_log.warning() << "Invalid NXlog entry " << entry_name
                    << " found. Did not contain 'value' and 'time'.\n";
    file.closeGroup();
    return;
  }
  // whether or not to overwrite logs on workspace
  bool overwritelogs = this->getProperty("OverwriteLogs");
  try {
    if (overwritelogs || !(workspace->run().hasProperty(entry_name))) {
      Kernel::Property *logValue = createTimeSeries(file, entry_name);
      workspace->mutableRun().addProperty(logValue, overwritelogs);
    }
  } catch (::NeXus::Exception &e) {
    g_log.warning() << "NXlog entry " << entry_name
                    << " gave an error when loading:'" << e.what() << "'.\n";
  }

  file.closeGroup();
}

/**
 * Load an SE log entry
 * @param file :: A reference to the NeXus file handle opened at the parent
 * group
 * @param entry_name :: The name of the log entry
 * @param workspace :: A pointer to the workspace to store the logs
 */
void LoadNexusLogs::loadSELog(
    ::NeXus::File &file, const std::string &entry_name,
    boost::shared_ptr<API::MatrixWorkspace> workspace) const {
  // Open the entry
  file.openGroup(entry_name, "IXseblock");
  std::string propName = entry_name;
  if (workspace->run().hasProperty(propName)) {
    propName = "selog_" + propName;
  }
  // There are two possible entries:
  //   value_log - A time series entry. This can contain a corrupt value entry
  //   so if it does use the value one
  //   value - A single value float entry
  Kernel::Property *logValue(nullptr);
  std::map<std::string, std::string> entries = file.getEntries();
  if (entries.find("value_log") != entries.end()) {
    try {
      try {
        file.openGroup("value_log", "NXlog");
      } catch (::NeXus::Exception &) {
        file.closeGroup();
        throw;
      }
      logValue = createTimeSeries(file, propName);
      file.closeGroup();
    } catch (::NeXus::Exception &e) {
      g_log.warning() << "IXseblock entry '" << entry_name
                      << "' gave an error when loading "
                      << "a time series:'" << e.what() << "'. Skipping entry\n";
      file.closeGroup(); // value_log
      file.closeGroup(); // entry_name
      return;
    }
  } else if (entries.find("value") != entries.end()) {
    try {
      // This may have a larger dimension than 1 bit it has no time field so
      // take the first entry
      file.openData("value");
      ::NeXus::Info info = file.getInfo();
      if (info.type == ::NeXus::FLOAT32) {
        boost::scoped_array<float> value(new float[info.dims[0]]);
        file.getData(value.get());
        file.closeData();
        logValue = new Kernel::PropertyWithValue<double>(
            propName, static_cast<double>(value[0]), true);
      } else {
        file.closeGroup();
        return;
      }
    } catch (::NeXus::Exception &e) {
      g_log.warning() << "IXseblock entry " << entry_name
                      << " gave an error when loading "
                      << "a single value:'" << e.what() << "'.\n";
      file.closeData();
      file.closeGroup();
      return;
    }
  } else {
    g_log.warning() << "IXseblock entry " << entry_name
                    << " cannot be read, skipping entry.\n";
    file.closeGroup();
    return;
  }
  workspace->mutableRun().addProperty(logValue);
  file.closeGroup();
}

/**
 * Creates a time series property from the currently opened log entry. It is
 * assumed to
 * have been checked to have a time field and the value entry's name is given as
 * an argument
 * @param file :: A reference to the file handle
 * @param prop_name :: The name of the property
 * @returns A pointer to a new property containing the time series
 */
Kernel::Property *
LoadNexusLogs::createTimeSeries(::NeXus::File &file,
                                const std::string &prop_name) const {
  file.openData("time");
  //----- Start time is an ISO8601 string date and time. ------
  std::string start;
  try {
    file.getAttr("start", start);
  } catch (::NeXus::Exception &) {
    // Some logs have "offset" instead of start
    try {
      file.getAttr("offset", start);
    } catch (::NeXus::Exception &) {
      g_log.warning() << "Log entry has no start time indicated.\n";
      file.closeData();
      throw;
    }
  }
  if (start.compare("No Time") == 0) {
    start = freqStart;
  }

  // Convert to date and time
  Kernel::DateAndTime start_time = Kernel::DateAndTime(start);
  std::string time_units;
  file.getAttr("units", time_units);
  if (time_units.compare("second") < 0 && time_units != "s" &&
      time_units != "minutes") // Can be s/second/seconds/minutes
  {
    file.closeData();
    throw ::NeXus::Exception("Unsupported time unit '" + time_units + "'");
  }
  //--- Load the seconds into a double array ---
  std::vector<double> time_double;
  try {
    file.getDataCoerce(time_double);
  } catch (::NeXus::Exception &e) {
    g_log.warning() << "Log entry's time field could not be loaded: '"
                    << e.what() << "'.\n";
    file.closeData();
    throw;
  }
  file.closeData(); // Close time data
  g_log.debug() << "   done reading \"time\" array\n";

  // Convert to seconds if needed
  if (time_units == "minutes") {
    std::transform(time_double.begin(), time_double.end(), time_double.begin(),
                   std::bind2nd(std::multiplies<double>(), 60.0));
  }
  // Now the values: Could be a string, int or double
  file.openData("value");
  // Get the units of the property
  std::string value_units;
  try {
    file.getAttr("units", value_units);
  } catch (::NeXus::Exception &) {
    // Ignore missing units field.
    value_units = "";
  }

  // Now the actual data
  ::NeXus::Info info = file.getInfo();
  // Check the size
  if (size_t(info.dims[0]) != time_double.size()) {
    file.closeData();
    throw ::NeXus::Exception("Invalid value entry for time series");
  }
  if (file.isDataInt()) // Int type
  {
    std::vector<int> values;
    try {
      file.getDataCoerce(values);
      file.closeData();
    } catch (::NeXus::Exception &) {
      file.closeData();
      throw;
    }
    // Make an int TSP
    auto tsp = new TimeSeriesProperty<int>(prop_name);
    tsp->create(start_time, time_double, values);
    tsp->setUnits(value_units);
    g_log.debug() << "   done reading \"value\" array\n";
    return tsp;
  } else if (info.type == ::NeXus::CHAR) {
    std::string values;
    const int64_t item_length = info.dims[1];
    try {
      const int64_t nitems = info.dims[0];
      const int64_t total_length = nitems * item_length;
      boost::scoped_array<char> val_array(new char[total_length]);
      file.getData(val_array.get());
      file.closeData();
      values = std::string(val_array.get(), total_length);
    } catch (::NeXus::Exception &) {
      file.closeData();
      throw;
    }
    // The string may contain non-printable (i.e. control) characters, replace
    // these
    std::replace_if(values.begin(), values.end(), [&](const char &c) {
      return isControlValue(c, prop_name, g_log);
    }, ' ');
    auto tsp = new TimeSeriesProperty<std::string>(prop_name);
    std::vector<DateAndTime> times;
    DateAndTime::createVector(start_time, time_double, times);
    const size_t ntimes = times.size();
    for (size_t i = 0; i < ntimes; ++i) {
      std::string value_i =
          std::string(values.data() + i * item_length, item_length);
      tsp->addValue(times[i], value_i);
    }
    tsp->setUnits(value_units);
    g_log.debug() << "   done reading \"value\" array\n";
    return tsp;
  } else if (info.type == ::NeXus::FLOAT32 || info.type == ::NeXus::FLOAT64) {
    std::vector<double> values;
    try {
      file.getDataCoerce(values);
      file.closeData();
    } catch (::NeXus::Exception &) {
      file.closeData();
      throw;
    }
    auto tsp = new TimeSeriesProperty<double>(prop_name);
    tsp->create(start_time, time_double, values);
    tsp->setUnits(value_units);
    g_log.debug() << "   done reading \"value\" array\n";
    return tsp;
  } else {
    throw ::NeXus::Exception(
        "Invalid value type for time series. Only int, double or strings are "
        "supported");
  }
}

bool LoadNexusLogs::isControlValue(const char &c, const std::string &propName,
                                   Kernel::Logger &log) {

  // Have to check it falls within range accepted by c style check
  if (c <= -1 || c > 255) {
    log.warning("Found an invalid character in property " + propName);
    // Pretend this is a control value so it is sanitized
    return true;
  } else {
    // Use default global c++ locale within this program
    std::locale locale{};
    // Use c++ style call so we don't need to cast from int to bool
    return std::iscntrl(c, locale);
  }
}

} // namespace DataHandling
} // namespace Mantid