LoadBankFromDiskTask.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 +
#include "MantidDataHandling/LoadBankFromDiskTask.h"
#include "MantidDataHandling/BankPulseTimes.h"
#include "MantidDataHandling/DefaultEventLoader.h"
#include "MantidDataHandling/LoadEventNexus.h"
#include "MantidDataHandling/ProcessBankData.h"
#include "MantidKernel/Unit.h"
#include <algorithm>

#include "MantidNexus/NexusIOHelper.h"

namespace Mantid {
namespace DataHandling {

/** Constructor
 *
 * @param loader :: Handle to the main loader
 * @param entry_name :: The pathname of the bank to load
 * @param entry_type :: The classtype of the entry to load
 * @param numEvents :: The number of events in the bank.
 * @param oldNeXusFileNames :: Identify if file is of old variety.
 * @param prog :: an optional Progress object
 * @param ioMutex :: a mutex shared for all Disk I-O tasks
 * @param scheduler :: the ThreadScheduler that runs this task.
 * @param framePeriodNumbers :: Period numbers corresponding to each frame
 */
LoadBankFromDiskTask::LoadBankFromDiskTask(
    DefaultEventLoader &loader, const std::string &entry_name,
    const std::string &entry_type, const std::size_t numEvents,
    const bool oldNeXusFileNames, API::Progress *prog,
    boost::shared_ptr<std::mutex> ioMutex, Kernel::ThreadScheduler &scheduler,
    const std::vector<int> &framePeriodNumbers)
    : m_loader(loader), entry_name(entry_name), entry_type(entry_type),
      prog(prog), scheduler(scheduler), m_loadError(false),
      m_oldNexusFileNames(oldNeXusFileNames), m_have_weight(false),
      m_framePeriodNumbers(framePeriodNumbers) {
  setMutex(ioMutex);
  m_cost = static_cast<double>(numEvents);
  m_min_id = std::numeric_limits<uint32_t>::max();
  m_max_id = 0;
}

/** Load the pulse times, if needed. This sets
 * thisBankPulseTimes to the right pointer.
 * */
void LoadBankFromDiskTask::loadPulseTimes(::NeXus::File &file) {
  try {
    // First, get info about the event_time_zero field in this bank
    file.openData("event_time_zero");
  } catch (::NeXus::Exception &) {
    // Field not found error is most likely.
    // Use the "proton_charge" das logs.
    thisBankPulseTimes = m_loader.alg->m_allBanksPulseTimes;
    return;
  }
  std::string thisStartTime;
  size_t thisNumPulses = 0;
  file.getAttr("offset", thisStartTime);
  if (!file.getInfo().dims.empty())
    thisNumPulses = file.getInfo().dims[0];
  file.closeData();

  // Now, we look through existing ones to see if it is already loaded
  // thisBankPulseTimes = NULL;
  for (auto &bankPulseTime : m_loader.m_bankPulseTimes) {
    if (bankPulseTime->equals(thisNumPulses, thisStartTime)) {
      thisBankPulseTimes = bankPulseTime;
      return;
    }
  }

  // Not found? Need to load and add it
  thisBankPulseTimes = boost::make_shared<BankPulseTimes>(boost::ref(file),
                                                          m_framePeriodNumbers);
  m_loader.m_bankPulseTimes.emplace_back(thisBankPulseTimes);
}

/** Load the event_index field
 * (a list of size of # of pulses giving the index in the event list for that
    pulse)
 * @param file :: File handle for the NeXus file
 */
std::vector<uint64_t>
LoadBankFromDiskTask::loadEventIndex(::NeXus::File &file) {
  // Get the event_index (a list of size of # of pulses giving the index in
  // the event list for that pulse) as a uint64 vector.
  // The Nexus standard does not specify if this is to be 32-bit or 64-bit
  // integers, so we use the NeXusIOHelper to do the conversion on the fly.
  auto event_index =
      NeXus::NeXusIOHelper::readNexusVector<uint64_t>(file, "event_index");

  // Look for the sign that the bank is empty
  if (event_index.size() == 1) {
    if (event_index[0] == 0) {
      // One entry, only zero. This means NO events in this bank.
      m_loadError = true;
      m_loader.alg->getLogger().debug()
          << "Bank " << entry_name << " is empty.\n";
    }
  }
  return event_index;
}

/** Open the event_id field and validate the contents
 *
 * @param file :: File handle for the NeXus file
 * @param start_event :: set to the index of the first event
 * @param stop_event :: set to the index of the last event + 1
 * @param event_index ::  (a list of size of # of pulses giving the index in
 *the event list for that pulse)
 */
void LoadBankFromDiskTask::prepareEventId(
    ::NeXus::File &file, int64_t &start_event, int64_t &stop_event,
    const std::vector<uint64_t> &event_index) {
  // Get the list of pixel ID's
  if (m_oldNexusFileNames)
    file.openData("event_pixel_id");
  else
    file.openData("event_id");

  // By default, use all available indices
  start_event = 0;
  ::NeXus::Info id_info = file.getInfo();
  // dims[0] can be negative in ISIS meaning 2^32 + dims[0]. Take that into
  // account
  int64_t dim0 = recalculateDataSize(id_info.dims[0]);
  stop_event = dim0;

  // Handle the time filtering by changing the start/end offsets.
  for (size_t i = 0; i < thisBankPulseTimes->numPulses; i++) {
    if (thisBankPulseTimes->pulseTimes[i] >= m_loader.alg->filter_time_start) {
      start_event = static_cast<int64_t>(event_index[i]);
      break; // stop looking
    }
  }

  if (start_event > dim0) {
    // If the frame indexes are bad then we can't construct the times of the
    // events properly and filtering by time
    // will not work on this data
    m_loader.alg->getLogger().warning()
        << this->entry_name
        << "'s field 'event_index' seems to be invalid (start_index > than "
           "the number of events in the bank)."
        << "All events will appear in the same frame and filtering by time "
           "will not be possible on this data.\n";
    start_event = 0;
    stop_event = dim0;
  } else {
    for (size_t i = 0; i < thisBankPulseTimes->numPulses; i++) {
      if (thisBankPulseTimes->pulseTimes[i] > m_loader.alg->filter_time_stop) {
        stop_event = event_index[i];
        break;
      }
    }
  }
  // We are loading part - work out the event number range
  if (m_loader.chunk != EMPTY_INT()) {
    start_event =
        static_cast<int64_t>(m_loader.chunk - m_loader.firstChunkForBank) *
        static_cast<int64_t>(m_loader.eventsPerChunk);
    // Don't change stop_event for the final chunk
    if (start_event + static_cast<int64_t>(m_loader.eventsPerChunk) <
        stop_event)
      stop_event = start_event + static_cast<int64_t>(m_loader.eventsPerChunk);
  }

  // Make sure it is within range
  if (stop_event > dim0)
    stop_event = dim0;

  m_loader.alg->getLogger().debug()
      << entry_name << ": start_event " << start_event << " stop_event "
      << stop_event << "\n";
}

/** Load the event_id field, which has been opened
 * @param file An NeXus::File object opened at the correct group
 * @returns A new array containing the event Ids for this bank
 */
std::unique_ptr<uint32_t[]>
LoadBankFromDiskTask::loadEventId(::NeXus::File &file) {
  // This is the data size
  ::NeXus::Info id_info = file.getInfo();
  int64_t dim0 = recalculateDataSize(id_info.dims[0]);

  // Now we allocate the required arrays
  auto event_id = std::make_unique<uint32_t[]>(m_loadSize[0]);

  // Check that the required space is there in the file.
  if (dim0 < m_loadSize[0] + m_loadStart[0]) {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name << "'s event_id field is too small (" << dim0
        << ") to load the desired data size (" << m_loadSize[0] + m_loadStart[0]
        << ").\n";
    m_loadError = true;
  }

  if (m_loader.alg->getCancel())
    m_loadError = true; // To allow cancelling the algorithm

  if (!m_loadError) {
    // Must be uint32
    if (id_info.type == ::NeXus::UINT32)
      file.getSlab(event_id.get(), m_loadStart, m_loadSize);
    else {
      m_loader.alg->getLogger().warning()
          << "Entry " << entry_name
          << "'s event_id field is not UINT32! It will be skipped.\n";
      m_loadError = true;
    }
    file.closeData();

    // determine the range of pixel ids
    m_min_id =
        *(std::min_element(event_id.get(), event_id.get() + m_loadSize[0]));
    m_max_id =
        *(std::max_element(event_id.get(), event_id.get() + m_loadSize[0]));

    if (m_min_id > static_cast<uint32_t>(m_loader.eventid_max)) {
      // All the detector IDs in the bank are higher than the highest 'known'
      // (from the IDF)
      // ID. Setting this will abort the loading of the bank.
      m_loadError = true;
    }
    // fixup the minimum pixel id in the case that it's lower than the lowest
    // 'known' id. We test this by checking that when we add the offset we
    // would not get a negative index into the vector. Note that m_min_id is
    // a uint so we have to be cautious about adding it to an int which may be
    // negative.
    if (static_cast<int32_t>(m_min_id) + m_loader.pixelID_to_wi_offset < 0) {
      m_min_id = static_cast<uint32_t>(abs(m_loader.pixelID_to_wi_offset));
    }
    // fixup the maximum pixel id in the case that it's higher than the
    // highest 'known' id
    if (m_max_id > static_cast<uint32_t>(m_loader.eventid_max))
      m_max_id = static_cast<uint32_t>(m_loader.eventid_max);
  }
  return event_id;
}

/** Open and load the times-of-flight data
 * @param file An NeXus::File object opened at the correct group
 * @returns A new array containing the time of flights for this bank
 */
std::unique_ptr<float[]> LoadBankFromDiskTask::loadTof(::NeXus::File &file) {
  // Allocate the array
  auto event_time_of_flight = std::make_unique<float[]>(m_loadSize[0]);

  // Get the list of event_time_of_flight's
  std::string key, tof_unit;
  if (!m_oldNexusFileNames)
    key = "event_time_offset";
  else
    key = "event_time_of_flight";
  file.openData(key);

  // Check that the required space is there in the file.
  ::NeXus::Info tof_info = file.getInfo();
  int64_t tof_dim0 = recalculateDataSize(tof_info.dims[0]);
  if (tof_dim0 < m_loadSize[0] + m_loadStart[0]) {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name
        << "'s event_time_offset field is too small "
           "to load the desired data.\n";
    m_loadError = true;
  }

  // The Nexus standard does not specify if event_time_offset should be float or
  // integer, so we use the NeXusIOHelper to perform the conversion to float on
  // the fly. If the data field already contains floats, the conversion is
  // skipped.
  auto vec = NeXus::NeXusIOHelper::readNexusSlab<float>(file, key, m_loadStart,
                                                        m_loadSize);
  file.getAttr("units", tof_unit);
  file.closeData();
  // Convert Tof to microseconds
  Kernel::Units::timeConversionVector(vec, tof_unit, "microseconds");
  std::copy(vec.begin(), vec.end(), event_time_of_flight.get());

  return event_time_of_flight;
}

/** Load weight of weigthed events if they exist
 * @param file An NeXus::File object opened at the correct group
 * @returns A new array containing the weights or a nullptr if the weights
 * are not present
 */
std::unique_ptr<float[]>
LoadBankFromDiskTask::loadEventWeights(::NeXus::File &file) {
  try {
    // First, get info about the event_weight field in this bank
    file.openData("event_weight");
  } catch (::NeXus::Exception &) {
    // Field not found error is most likely.
    m_have_weight = false;
    return std::unique_ptr<float[]>();
  }
  // OK, we've got them
  m_have_weight = true;

  // Allocate the array
  auto event_weight = std::make_unique<float[]>(m_loadSize[0]);

  ::NeXus::Info weight_info = file.getInfo();
  int64_t weight_dim0 = recalculateDataSize(weight_info.dims[0]);
  if (weight_dim0 < m_loadSize[0] + m_loadStart[0]) {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name
        << "'s event_weight field is too small to load the desired data.\n";
    m_loadError = true;
  }

  // Check that the type is what it is supposed to be
  if (weight_info.type == ::NeXus::FLOAT32)
    file.getSlab(event_weight.get(), m_loadStart, m_loadSize);
  else {
    m_loader.alg->getLogger().warning()
        << "Entry " << entry_name
        << "'s event_weight field is not FLOAT32! It will be skipped.\n";
    m_loadError = true;
  }

  if (!m_loadError) {
    file.closeData();
  }
  return event_weight;
}

void LoadBankFromDiskTask::run() {
  // These give the limits in each file as to which events we actually load
  // (when filtering by time).
  m_loadStart.resize(1, 0);
  m_loadSize.resize(1, 0);

  m_loadError = false;
  m_have_weight = m_loader.m_haveWeights;

  prog->report(entry_name + ": load from disk");

  // arrays to load into
  std::unique_ptr<uint32_t[]> event_id;
  std::unique_ptr<float[]> event_time_of_flight;
  std::unique_ptr<float[]> event_weight;
  std::vector<uint64_t> event_index;

  // Open the file
  ::NeXus::File file(m_loader.alg->m_filename);
  try {
    // Navigate into the file
    file.openGroup(m_loader.alg->m_top_entry_name, "NXentry");
    // Open the bankN_event group
    file.openGroup(entry_name, entry_type);

    // Load the event_index field.
    event_index = this->loadEventIndex(file);

    if (!m_loadError) {
      // Load and validate the pulse times
      this->loadPulseTimes(file);

      // The event_index should be the same length as the pulse times from DAS
      // logs.
      if (event_index.size() != thisBankPulseTimes->numPulses)
        m_loader.alg->getLogger().warning()
            << "Bank " << entry_name
            << " has a mismatch between the number of event_index entries "
               "and the number of pulse times in event_time_zero.\n";

      // Open and validate event_id field.
      int64_t start_event = 0;
      int64_t stop_event = 0;
      this->prepareEventId(file, start_event, stop_event, event_index);

      // These are the arguments to getSlab()
      m_loadStart[0] = start_event;
      m_loadSize[0] = stop_event - start_event;

      if ((m_loadSize[0] > 0) && (m_loadStart[0] >= 0)) {
        // Load pixel IDs
        event_id = this->loadEventId(file);
        if (m_loader.alg->getCancel()) {
          m_loader.alg->getLogger().error()
              << "Loading bank " << entry_name << " is cancelled.\n";
          m_loadError = true; // To allow cancelling the algorithm
        }

        // And TOF.
        if (!m_loadError) {
          event_time_of_flight = this->loadTof(file);
          if (m_have_weight) {
            event_weight = this->loadEventWeights(file);
          }
        }
      } // Size is at least 1
      else {
        // Found a size that was 0 or less; stop processing
        m_loader.alg->getLogger().error()
            << "Loading bank " << entry_name
            << " is stopped due to either zero/negative loading size ("
            << m_loadStart[0] << ") or negative load start index ("
            << m_loadStart[0] << ")\n";
        m_loadError = true;
      }

    } // no error

  } // try block
  catch (std::exception &e) {
    m_loader.alg->getLogger().error()
        << "Error while loading bank " << entry_name << ":\n";
    m_loader.alg->getLogger().error() << e.what() << '\n';
    m_loadError = true;
  } catch (...) {
    m_loader.alg->getLogger().error()
        << "Unspecified error while loading bank " << entry_name << '\n';
    m_loadError = true;
  }

  // Close up the file even if errors occured.
  file.closeGroup();
  file.close();

  // Abort if anything failed
  if (m_loadError) {
    return;
  }

  const auto bank_size = m_max_id - m_min_id;
  const auto minSpectraToLoad = static_cast<uint32_t>(m_loader.alg->m_specMin);
  const auto maxSpectraToLoad = static_cast<uint32_t>(m_loader.alg->m_specMax);
  const auto emptyInt = static_cast<uint32_t>(EMPTY_INT());
  // check that if a range of spectra were requested that these fit within
  // this bank
  if (minSpectraToLoad != emptyInt && m_min_id < minSpectraToLoad) {
    if (minSpectraToLoad > m_max_id) { // the minimum spectra to load is more
                                       // than the max of this bank
      return;
    }
    // the min spectra to load is higher than the min for this bank
    m_min_id = minSpectraToLoad;
  }
  if (maxSpectraToLoad != emptyInt && m_max_id > maxSpectraToLoad) {
    if (maxSpectraToLoad < m_min_id) {
      // the maximum spectra to load is less than the minimum of this bank
      return;
    }
    // the max spectra to load is lower than the max for this bank
    m_max_id = maxSpectraToLoad;
  }
  if (m_min_id > m_max_id) {
    // the min is now larger than the max, this means the entire block of
    // spectra to load is outside this bank
    return;
  }

  // schedule the job to generate the event lists
  auto mid_id = m_max_id;
  if (m_loader.splitProcessing && m_max_id > (m_min_id + (bank_size / 4)))
    // only split if told to and the section to load is at least 1/4 the size
    // of the whole bank
    mid_id = (m_max_id + m_min_id) / 2;

  // No error? Launch a new task to process that data.
  auto numEvents = static_cast<size_t>(m_loadSize[0]);
  auto startAt = static_cast<size_t>(m_loadStart[0]);

  // convert things to shared_arrays to share between tasks
  boost::shared_array<uint32_t> event_id_shrd(event_id.release());
  boost::shared_array<float> event_time_of_flight_shrd(
      event_time_of_flight.release());
  boost::shared_array<float> event_weight_shrd(event_weight.release());
  auto event_index_shrd =
      boost::make_shared<std::vector<uint64_t>>(std::move(event_index));

  std::shared_ptr<Task> newTask1 = std::make_shared<ProcessBankData>(
      m_loader, entry_name, prog, event_id_shrd, event_time_of_flight_shrd,
      numEvents, startAt, event_index_shrd, thisBankPulseTimes, m_have_weight,
      event_weight_shrd, m_min_id, mid_id);
  scheduler.push(newTask1);
  if (m_loader.splitProcessing && (mid_id < m_max_id)) {
    std::shared_ptr<Task> newTask2 = std::make_shared<ProcessBankData>(
        m_loader, entry_name, prog, event_id_shrd, event_time_of_flight_shrd,
        numEvents, startAt, event_index_shrd, thisBankPulseTimes, m_have_weight,
        event_weight_shrd, (mid_id + 1), m_max_id);
    scheduler.push(newTask2);
  }
}

/**
 * Interpret the value describing the number of events. If the number is
 * positive return it unchanged.
 * If the value is negative (can happen at ISIS) add 2^32 to it.
 * @param size :: The size of events value.
 */
int64_t LoadBankFromDiskTask::recalculateDataSize(const int64_t &size) {
  if (size < 0) {
    const int64_t shift = int64_t(1) << 32;
    return shift + size;
  }
  return size;
}

} // namespace DataHandling
} // namespace Mantid