Exemplo n.º 1
0
/*
 * Write a certain number of log entries (from beginning) to file
 */
void ProcessDasNexusLog::writeLogtoFile(API::MatrixWorkspace_sptr ws,
                                        std::string logname,
                                        size_t numentriesoutput,
                                        std::string outputfilename) {
  // 1. Get log
  Kernel::Property *log = ws->run().getProperty(logname);
  Kernel::TimeSeriesProperty<double> *tslog =
      dynamic_cast<Kernel::TimeSeriesProperty<double> *>(log);
  if (!tslog)
    throw std::runtime_error("Invalid time series log: it could not be cast "
                             "(interpreted) as a time series property");
  std::vector<Kernel::DateAndTime> times = tslog->timesAsVector();
  std::vector<double> values = tslog->valuesAsVector();

  // 2. Write out
  std::ofstream ofs;
  ofs.open(outputfilename.c_str(), std::ios::out);
  ofs << "# Absolute Time (nanosecond)\tPulse Time (nanosecond)\tTOF (ms)\n";

  Kernel::DateAndTime prevtime(0);
  std::vector<double> tofs;

  for (size_t i = 0; i < numentriesoutput; i++) {
    Kernel::DateAndTime tnow = times[i];

    if (tnow > prevtime) {
      // (a) Process previous logs
      std::sort(tofs.begin(), tofs.end());
      for (double tof : tofs) {
        Kernel::DateAndTime temptime =
            prevtime + static_cast<int64_t>(tof * 100);
        ofs << temptime.totalNanoseconds() << "\t" << tnow.totalNanoseconds()
            << "\t" << tof * 0.1 << '\n';
      }
      // (b) Clear
      tofs.clear();
      // (c) Update time
      prevtime = tnow;
    }

    // (d) Push the current value
    tofs.push_back(values[i]);
  } // ENDFOR
  // Clear the last
  if (!tofs.empty()) {
    // (a) Process previous logs: note value is in unit of 100 nano-second
    std::sort(tofs.begin(), tofs.end());
    for (double tof : tofs) {
      Kernel::DateAndTime temptime = prevtime + static_cast<int64_t>(tof * 100);
      ofs << temptime.totalNanoseconds() << "\t" << prevtime.totalNanoseconds()
          << "\t" << tof * 0.1 << '\n';
    }
  } else {
    throw std::runtime_error("Impossible for this to happen!");
  }

  ofs.close();
} // END Function
Exemplo n.º 2
0
/*
 * Convert DAS log to a vector of absolute time
 * @param  orderedtofs: tofs with abstimevec
 */
void ProcessDasNexusLog::convertToAbsoluteTime(
    API::MatrixWorkspace_sptr ws, std::string logname,
    std::vector<Kernel::DateAndTime> &abstimevec,
    std::vector<double> &orderedtofs) {
  // 1. Get log
  Kernel::Property *log = ws->run().getProperty(logname);
  Kernel::TimeSeriesProperty<double> *tslog =
      dynamic_cast<Kernel::TimeSeriesProperty<double> *>(log);
  if (!tslog)
    throw std::runtime_error("Invalid time series log: it could not be cast "
                             "(interpreted) as a time series property");
  std::vector<Kernel::DateAndTime> times = tslog->timesAsVector();
  std::vector<double> values = tslog->valuesAsVector();

  // 2. Get converted
  size_t numsamepulses = 0;
  std::vector<double> tofs;
  Kernel::DateAndTime prevtime(0);

  for (size_t i = 0; i < times.size(); i++) {
    Kernel::DateAndTime tnow = times[i];
    if (tnow > prevtime) {
      // (a) Process previous logs
      std::sort(tofs.begin(), tofs.end());
      for (size_t j = 0; j < tofs.size(); j++) {
        Kernel::DateAndTime temptime =
            prevtime + static_cast<int64_t>(tofs[j] * 100);
        abstimevec.push_back(temptime);
        orderedtofs.push_back(tofs[j]);
      }
      // (b) Clear
      tofs.clear();
      // (c) Update time
      prevtime = tnow;
    } else {
      numsamepulses++;
    }
    // (d) Push the current value
    tofs.push_back(values[i]);
  } // ENDFOR
  // Clear the last
  if (!tofs.empty()) {
    // (a) Process previous logs: note value is in unit of 100 nano-second
    std::sort(tofs.begin(), tofs.end());
    for (size_t j = 0; j < tofs.size(); j++) {
      Kernel::DateAndTime temptime =
          prevtime + static_cast<int64_t>(tofs[j] * 100);
      abstimevec.push_back(temptime);
      orderedtofs.push_back(tofs[j]);
    }
  } else {
    throw std::runtime_error("Impossible for this to happen!");
  }

  return;
} // END Function
Exemplo n.º 3
0
/*
 * Check log in workspace
 */
void ProcessDasNexusLog::checkLog(API::MatrixWorkspace_sptr ws,
                                  std::string logname) {
  // 1. Get log
  Kernel::Property *log = ws->run().getProperty(logname);
  if (!log) {
    g_log.error() << "Log " << logname << " does not exist!" << std::endl;
    throw std::invalid_argument("Non-exising log name");
  }
  Kernel::TimeSeriesProperty<double> *tslog =
      dynamic_cast<Kernel::TimeSeriesProperty<double> *>(log);
  if (!tslog) {
    g_log.error() << "Log " << logname << " is not time series log"
                  << std::endl;
    throw std::invalid_argument("Log type error!");
  }

  // 2. Survey
  std::vector<Kernel::DateAndTime> times = tslog->timesAsVector();
  g_log.information() << "Entries of times = " << times.size() << std::endl;
  size_t countsame = 0;
  size_t countinverse = 0;
  for (size_t i = 1; i < times.size(); i++) {
    Kernel::DateAndTime tprev = times[i - 1];
    Kernel::DateAndTime tpres = times[i];
    if (tprev == tpres)
      countsame++;
    else if (tprev > tpres)
      countinverse++;
  }

  // 3. Output
  Kernel::DateAndTime t0(ws->run().getProperty("run_start")->value());
  Kernel::time_duration dts = times[0] - t0;
  Kernel::time_duration dtf = times[times.size() - 1] - t0;
  size_t f = times.size() - 1;

  g_log.information() << "Number of Equal Time Stamps    = " << countsame
                      << std::endl;
  g_log.information() << "Number of Inverted Time Stamps = " << countinverse
                      << std::endl;
  g_log.information() << "Run Start = " << t0.totalNanoseconds() << std::endl;
  g_log.information() << "First Log (Absolute Time, Relative Time): "
                      << times[0].totalNanoseconds() << ", "
                      << Kernel::DateAndTime::nanosecondsFromDuration(dts)
                      << std::endl;
  g_log.information() << "Last  Log (Absolute Time, Relative Time): "
                      << times[f].totalNanoseconds() << ", "
                      << Kernel::DateAndTime::nanosecondsFromDuration(dtf)
                      << std::endl;

  return;
}
Exemplo n.º 4
0
/** Export part of designated log to an file in column format and a output file
  * @param logname :: name of log to export
  * @param numentries :: number of log entries to export
  * @param outputeventws :: boolean.  output workspace is event workspace if
 * true.
 */
void ExportTimeSeriesLog::exportLog(string logname, int numentries,
                                    bool outputeventws) {

  // 1.  Get log, time, and etc.
  std::vector<Kernel::DateAndTime> times;
  std::vector<double> values;

  if (logname.size() > 0) {
    // Log
    Kernel::TimeSeriesProperty<double> *tlog =
        dynamic_cast<Kernel::TimeSeriesProperty<double> *>(
            m_dataWS->run().getProperty(logname));
    if (!tlog) {
      std::stringstream errmsg;
      errmsg << "TimeSeriesProperty Log " << logname
             << " does not exist in workspace " << m_dataWS->getName();
      g_log.error(errmsg.str());
      throw std::invalid_argument(errmsg.str());
    }
    times = tlog->timesAsVector();
    values = tlog->valuesAsVector();
  } else {
    throw std::runtime_error("Log name cannot be left empty.");
  }

  // 2. Determine number of export log
  if (numentries == EMPTY_INT()) {
    numentries = static_cast<int>(times.size());
  } else if (numentries <= 0) {
    stringstream errmsg;
    errmsg << "For Export Log, NumberEntriesExport must be greater than 0.  "
              "Input = " << numentries;
    g_log.error(errmsg.str());
    throw std::runtime_error(errmsg.str());
  } else if (static_cast<size_t>(numentries) > times.size()) {
    numentries = static_cast<int>(times.size());
  }

  // 3. Create otuput workspace
  if (outputeventws) {
    setupEventWorkspace(numentries, times, values);
  } else {
    setupWorkspace2D(numentries, times, values);
  }

  return;
}
Exemplo n.º 5
0
/** Export part of designated log to an file in column format and a output file
 * @brief ExportTimeSeriesLog::exportLog
 * @param logname ::  name of log to export
 * @param timeunit :: unit of time for input start/stop time and output
 * @param starttime :: relative start time of the output time series log
 * @param stoptime :: relative stop time of the output time series log
 * @param exportepoch :: flag to output time as epoch time/absolute time
 * @param outputeventws :: boolean.  output workspace is event workspace if
 * @param numentries :: number of log entries to export
 */
void ExportTimeSeriesLog::exportLog(const std::string &logname,
                                    const std::string timeunit,
                                    const double &starttime,
                                    const double &stoptime,
                                    const bool exportepoch, bool outputeventws,
                                    int numentries) {

  // Get log, time, and etc.
  std::vector<Kernel::DateAndTime> times;
  std::vector<double> values;

  if (logname.size() > 0) {
    // Log
    Kernel::TimeSeriesProperty<double> *tlog =
        dynamic_cast<Kernel::TimeSeriesProperty<double> *>(
            m_inputWS->run().getProperty(logname));
    if (!tlog) {
      std::stringstream errmsg;
      errmsg << "TimeSeriesProperty Log " << logname
             << " does not exist in workspace " << m_inputWS->getName();
      g_log.error(errmsg.str());
      throw std::invalid_argument(errmsg.str());
    }
    times = tlog->timesAsVector();
    values = tlog->valuesAsVector();
  } else {
    throw std::runtime_error("Log name cannot be left empty.");
  }

  // Get start time, stop time and unit factor
  double timeunitfactor = 1.;
  if (timeunit.compare("Seconds") == 0)
    timeunitfactor = 1.E-9;

  // Get index for start time
  size_t i_start = 0;
  size_t i_stop = times.size() - 1;
  // Rule out the case that start time is behind last log entry
  bool i_start_cal = false;
  if (starttime != EMPTY_DBL()) {
    int64_t timerangens =
        times.back().totalNanoseconds() - times.front().totalNanoseconds();
    double timerange = static_cast<double>(timerangens) * timeunitfactor;
    g_log.debug() << "Time range is " << timerange << ", Start time is "
                  << starttime << "\n";
    if (timerange < starttime) {
      i_start = times.size() - 1;
      i_start_cal = true;
    }
  }

  if ((!i_start_cal) && (starttime != EMPTY_DBL() || stoptime != EMPTY_DBL())) {
    bool export_partial = calculateTimeSeriesRangeByTime(
        times, starttime, i_start, stoptime, i_stop, timeunitfactor);
    if (!export_partial)
      throw std::runtime_error(
          "Unable to find proton_charge for run start time. "
          "Failed to get partial time series.");
  }

  // Determine number of export log
  if (numentries == EMPTY_INT()) {
    numentries = static_cast<int>(times.size());
  } else if (numentries <= 0) {
    stringstream errmsg;
    errmsg << "For Export Log, NumberEntriesExport must be greater than 0.  "
              "Input = " << numentries;
    g_log.error(errmsg.str());
    throw std::runtime_error(errmsg.str());
  } else if (static_cast<size_t>(numentries) > times.size()) {
    numentries = static_cast<int>(times.size());
  }

  // Create otuput workspace
  if (outputeventws) {
    setupEventWorkspace(i_start, i_stop, numentries, times, values,
                        exportepoch);
  } else {
    setupWorkspace2D(i_start, i_stop, numentries, times, values, exportepoch,
                     timeunitfactor);
  }

  return;
}
Exemplo n.º 6
0
/** 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");

  // Find the entry name to use (normally "entry" for SNS, "raw_data_1" for
  // ISIS)
  std::string 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 + "'");
  }

  /// 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);

  // 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..."
        << std::endl;
    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 "
                                  << std::endl;
    }
    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();
}