LoadBankFromDiskTask.cpp

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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
//   NScD Oak Ridge National Laboratory, European Spallation Source,
//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidDataHandling/LoadBankFromDiskTask.h"
#include "MantidDataHandling/BankPulseTimes.h"
#include "MantidDataHandling/DefaultEventLoader.h"
#include "MantidDataHandling/LoadEventNexus.h"
#include "MantidDataHandling/ProcessBankData.h"
#include "MantidKernel/Unit.h"
#include "MantidNexus/NexusIOHelper.h"
 
// clang-format off
#include <nexus/NeXusFile.hpp>
#include <nexus/NeXusException.hpp>
// clang-format on
 
#include <algorithm>
#include <utility>
 
namespace Mantid::DataHandling {
 
LoadBankFromDiskTask::LoadBankFromDiskTask(DefaultEventLoader &loader, std::string entry_name, std::string entry_type,
                                           const std::size_t numEvents, const bool oldNeXusFileNames,
                                           API::Progress *prog, std::shared_ptr<std::mutex> ioMutex,
                                           Kernel::ThreadScheduler &scheduler, std::vector<int> framePeriodNumbers)
    : m_loader(loader), entry_name(std::move(entry_name)), entry_type(std::move(entry_type)), prog(prog),
      scheduler(scheduler), m_loadError(false), m_oldNexusFileNames(oldNeXusFileNames), m_have_weight(false),
      m_framePeriodNumbers(std::move(framePeriodNumbers)) {
  setMutex(ioMutex);
  m_cost = static_cast<double>(numEvents);
  m_min_id = std::numeric_limits<uint32_t>::max();
  m_max_id = 0;
}
 
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 thispulseTimes = 0;
  // If the offset is not present, use Unix epoch
  if (!file.hasAttr("offset")) {
    thisStartTime = "1970-01-01T00:00:00Z";
    m_loader.alg->getLogger().warning() << "In loadPulseTimes: no ISO8601 offset attribute provided for "
                                           "event_time_zero, using UNIX epoch instead\n";
  } else {
    file.getAttr("offset", thisStartTime);
  }
 
  if (!file.getInfo().dims.empty())
    thispulseTimes = 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(thispulseTimes, thisStartTime)) {
      thisBankPulseTimes = bankPulseTime;
      return;
    }
  }
 
  // Not found? Need to load and add it
  thisBankPulseTimes = std::make_shared<BankPulseTimes>(boost::ref(file), m_framePeriodNumbers);
  m_loader.m_bankPulseTimes.emplace_back(thisBankPulseTimes);
}
 
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 = Mantid::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;
}
 
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 = event_index[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;
 
  // 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";
}
 
std::unique_ptr<std::vector<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<std::vector<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->data(), 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->data(), event_id->data() + m_loadSize[0]));
    m_max_id = *(std::max_element(event_id->data(), event_id->data() + 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;
}
 
std::unique_ptr<std::vector<float>> LoadBankFromDiskTask::loadTof(::NeXus::File &file) {
  // Allocate the array
  auto event_time_of_flight = std::make_unique<std::vector<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;
  }
 
  // Mantid assumes event_time_offset to be float.
  // Nexus only requires event_time_offset to be a NXNumber.
  // We thus have to consider 32-bit or 64-bit options, and we
  // explicitly allow downcasting using the additional AllowDowncasting
  // template argument.
  auto vec = Mantid::NeXus::NeXusIOHelper::readNexusSlab<float, Mantid::NeXus::NeXusIOHelper::AllowNarrowing>(
      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->data());
 
  return event_time_of_flight;
}
 
std::unique_ptr<std::vector<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<std::vector<float>>();
  }
  // OK, we've got them
  m_have_weight = true;
 
  // Allocate the array
  auto event_weight = std::make_unique<std::vector<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->data(), 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<std::vector<uint32_t>> event_id;
  std::unique_ptr<std::vector<float>> event_time_of_flight;
  std::unique_ptr<std::vector<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->pulseTimes.size())
        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
  std::shared_ptr<std::vector<uint32_t>> event_id_shrd(event_id.release());
  std::shared_ptr<std::vector<float>> event_time_of_flight_shrd(event_time_of_flight.release());
  std::shared_ptr<std::vector<float>> event_weight_shrd(event_weight.release());
  auto event_index_shrd = std::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);
  }
}
 
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 Mantid::DataHandling