/** Open and load the times-of-flight data
*/
void LoadBankFromDiskTask::loadTof(::NeXus::File &file) {
// Allocate the array
auto temp = new float[m_loadSize[0]];
delete[] m_event_time_of_flight;
m_event_time_of_flight = temp;
// Get the list of event_time_of_flight's
if (!m_oldNexusFileNames)
file.openData("event_time_offset");
else
file.openData("event_time_of_flight");
// 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;
}
// Check that the type is what it is supposed to be
if (tof_info.type == ::NeXus::FLOAT32)
file.getSlab(m_event_time_of_flight, m_loadStart, m_loadSize);
else {
m_loader.alg->getLogger().warning()
<< "Entry " << entry_name
<< "'s event_time_offset field is not FLOAT32! It will be skipped.\n";
m_loadError = true;
}
if (!m_loadError) {
std::string units;
file.getAttr("units", units);
if (units != "microsecond") {
m_loader.alg->getLogger().warning()
<< "Entry " << entry_name << "'s event_time_offset field's units are "
"not microsecond. It will be skipped.\n";
m_loadError = true;
}
file.closeData();
} // no error
}
/** 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 = Mantid::Kernel::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;
}
/** 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 =
Mantid::Kernel::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 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 = Mantid::Kernel::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
for (int64_t i = 0; i < m_loadSize[0]; ++i) {
const auto id = event_id[i];
if (id < m_min_id)
m_min_id = id;
if (id > m_max_id)
m_max_id = id;
}
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 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";
}
