/**
* 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();
}
void
SaveNXTomo::writeImageKeyValue(const DataObjects::Workspace2D_sptr workspace,
::NeXus::File &nxFile, int thisFileInd) {
// Add ImageKey to instrument/image_key if present, use 0 if not
try {
nxFile.openPath("/entry1/tomo_entry/instrument/detector");
} catch (...) {
throw std::runtime_error("Unable to create a valid NXTomo file");
}
// Set the default key value for this WS
std::vector<double> keyValue;
keyValue.push_back(0);
if (workspace->run().hasProperty("ImageKey")) {
std::string tmpVal = workspace->run().getLogData("ImageKey")->value();
try {
keyValue[0] = boost::lexical_cast<double>(tmpVal);
} catch (...) {
}
// Invalid Cast is handled below
}
nxFile.openData("image_key");
nxFile.putSlab(keyValue, thisFileInd, 1);
nxFile.closeData();
nxFile.closeGroup();
}
void
SaveNXTomo::writeIntensityValue(const DataObjects::Workspace2D_sptr workspace,
::NeXus::File &nxFile, int thisFileInd) {
// Add Intensity to control if present, use 1 if not
try {
nxFile.openPath("/entry1/tomo_entry/control");
} catch (...) {
throw std::runtime_error("Unable to create a valid NXTomo file");
}
std::vector<double> intensityValue;
intensityValue.push_back(1);
if (workspace->run().hasProperty("Intensity")) {
std::string tmpVal = workspace->run().getLogData("Intensity")->value();
try {
intensityValue[0] = boost::lexical_cast<double>(tmpVal);
} catch (...) {
}
// Invalid Cast is handled below
}
nxFile.openData("data");
nxFile.putSlab(intensityValue, thisFileInd, 1);
nxFile.closeData();
}
/** 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.push_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
* @param event_index :: ref to the vector
*/
void LoadBankFromDiskTask::loadEventIndex(::NeXus::File &file,
std::vector<uint64_t> &event_index) {
// Get the event_index (a list of size of # of pulses giving the index in
// the event list for that pulse)
file.openData("event_index");
// Must be uint64
if (file.getInfo().type == ::NeXus::UINT64)
file.getData(event_index);
else {
m_loader.alg->getLogger().warning()
<< "Entry " << entry_name
<< "'s event_index field is not UINT64! It will be skipped.\n";
m_loadError = true;
}
file.closeData();
// 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";
}
}
}
/**
* Open the first NXentry of the supplied nexus file.
*
* @param handle Object to work on.
*/
void MuonNexusReader::openFirstNXentry(NeXus::File &handle) {
std::map<string, string> entries = handle.getEntries();
const auto entry =
std::find_if(entries.cbegin(), entries.cend(),
[](const auto entry) { return entry.second == NXENTRY; });
if (entry == entries.cend())
throw std::runtime_error("Failed to find NXentry");
handle.openGroup(entry->first, NXENTRY);
}
void SaveNXTomo::writeLogValues(const DataObjects::Workspace2D_sptr workspace,
::NeXus::File &nxFile, int thisFileInd) {
// Add Log information (minus special values - Rotation, ImageKey, Intensity)
// Unable to add multidimensional string data, storing strings as
// multidimensional data set of uint8 values
try {
nxFile.openPath("/entry1/log_info");
} catch (...) {
throw std::runtime_error("Unable to create a valid NXTomo file");
}
// Loop through all log values, create it if it doesn't exist. Then append
// value
std::vector<Property *> logVals = workspace->run().getLogData();
for (auto it = logVals.begin(); it != logVals.end(); ++it) {
auto prop = *it;
if (prop->name() != "ImageKey" && prop->name() != "Rotation" &&
prop->name() != "Intensity" && prop->name() != "Axis1" &&
prop->name() != "Axis2") {
try {
nxFile.openData(prop->name());
} catch (::NeXus::Exception &) {
// Create the data entry if it doesn't exist yet, and open.
std::vector<int64_t> infDim;
infDim.push_back(NX_UNLIMITED);
infDim.push_back(NX_UNLIMITED);
nxFile.makeData(prop->name(), ::NeXus::UINT8, infDim, true);
}
size_t strSize = prop->value().length();
char *val = new char[80]();
// If log value is from FITS file as it should be,
// it won't be greater than this. Otherwise Shorten it
if (strSize > 80)
strSize = 80;
strncpy(val, prop->value().c_str(), strSize);
std::vector<int64_t> start, size;
start.push_back(thisFileInd);
start.push_back(0);
size.push_back(1);
size.push_back(strSize);
// single item
nxFile.putSlab(val, start, size);
nxFile.closeData();
}
}
}
/**
* Open the first NXentry of the supplied nexus file.
*
* @param handle Object to work on.
*/
void MuonNexusReader::openFirstNXentry(NeXus::File &handle) {
std::map<string, string> entries = handle.getEntries();
bool found = false;
for (auto &entrie : entries) {
if (entrie.second == NXENTRY) {
handle.openGroup(entrie.first, NXENTRY);
found = true;
break;
}
}
if (!found)
throw std::runtime_error("Failed to find NXentry");
}
/**
* Can we get a histogram (non event data) for every monitor?
*
* @param file :: NeXus file object (open)
* @param monitorNames :: names of monitors of interest
* @return If there seems to be histograms for all monitors (they have "data")
**/
bool LoadNexusMonitors2::allMonitorsHaveHistoData(
::NeXus::File &file, const std::vector<std::string> &monitorNames) {
bool res = true;
try {
for (std::size_t i = 0; i < m_monitor_count; ++i) {
file.openGroup(monitorNames[i], "NXmonitor");
file.openData("data");
file.closeData();
file.closeGroup();
}
} catch (::NeXus::Exception &) {
file.closeGroup();
res = false;
}
return res;
}
/**
*
* @param nxsFile A reference to the open NeXus fileIt should be opened at the
* "full_reference_detector" group
* @param detInfo A reference to the struct that will hold the data from the file
*/
void LoadDetectorInfo::readLibisisNxs(::NeXus::File & nxsFile, DetectorInfo & detInfo) const
{
nxsFile.readData<int32_t>("det_no", detInfo.ids);
nxsFile.readData<int32_t>("det_type", detInfo.codes);
nxsFile.readData<double>("delay_time", detInfo.delays);
const size_t numDets = detInfo.ids.size();
if(m_moveDets)
{
nxsFile.readData<double>("L2", detInfo.l2);
nxsFile.readData<double>("theta", detInfo.theta);
nxsFile.readData<double>("phi", detInfo.phi);
}
else
{
// these will get ignored
detInfo.l2.resize(numDets, -1.0);
detInfo.theta.resize(numDets, -1.0);
detInfo.phi.resize(numDets, -1.0);
}
// pressure & wall thickness are global here
double pressure = -1.0;
double thickness = -1.0;
nxsFile.openGroup("det_he3", "NXIXTdet_he3");
nxsFile.readData<double>("gas_pressure", pressure);
nxsFile.readData<double>("wall_thickness", thickness);
nxsFile.closeGroup();
if(pressure <= 0.0)
{
g_log.warning("The data file does not contain correct He3 pressure, "
"default value of 10 bar is used instead");
pressure = 10.0;
}
if(thickness <= 0.0)
{
g_log.warning("The data file does not contain correct detector's wall "
"thickness, default value of 0.8mm is used instead");
thickness = 0.0008;
}
detInfo.pressures.resize(numDets, pressure);
detInfo.thicknesses.resize(numDets, thickness);
}
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 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;
}
/** 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();
}
/** 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 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);
} else if (log_class == "NXcollection") {
int jj = 0;
++jj;
}
}
loadVetoPulses(file, workspace);
file.closeGroup();
}
/**
* Fix the detector numbers if the defaults are not correct. Currently checks
* the isis_vms_compat block and reads them from there if possible.
*
* @param det_ids :: An array of prefilled detector IDs
* @param file :: A reference to the NeXus file opened at the root entry
* @param spec_ids :: An array of spectrum numbers that the monitors have
* @param nmonitors :: The size of the det_ids and spec_ids arrays
*/
void LoadNexusMonitors2::fixUDets(boost::scoped_array<detid_t> &det_ids,
::NeXus::File &file,
const boost::scoped_array<specid_t> &spec_ids,
const size_t nmonitors) const {
try {
file.openGroup("isis_vms_compat", "IXvms");
} catch (::NeXus::Exception &) {
return;
}
// UDET
file.openData("UDET");
std::vector<int32_t> udet;
file.getData(udet);
file.closeData();
// SPEC
file.openData("SPEC");
std::vector<int32_t> spec;
file.getData(spec);
file.closeData();
// This is a little complicated: Each value in the spec_id array is a value
// found in the
// SPEC block of isis_vms_compat. The index that this value is found at then
// corresponds
// to the index within the UDET block that holds the detector ID
std::vector<int32_t>::const_iterator beg = spec.begin();
for (size_t mon_index = 0; mon_index < nmonitors; ++mon_index) {
std::vector<int32_t>::const_iterator itr =
std::find(spec.begin(), spec.end(), spec_ids[mon_index]);
if (itr == spec.end()) {
det_ids[mon_index] = -1;
continue;
}
std::vector<int32_t>::difference_type udet_index = std::distance(beg, itr);
det_ids[mon_index] = udet[udet_index];
}
file.closeGroup();
}
/** 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 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";
}
/**
* Read histogram data
* @param histogramEntries map of the file entries that have histogram
* @param outputGroup pointer to the workspace group
* @param nxFile Reads data from inside first first top entry
*/
void LoadMcStas::readHistogramData(
const std::map<std::string, std::string> &histogramEntries,
WorkspaceGroup_sptr &outputGroup, ::NeXus::File &nxFile) {
std::string nameAttrValueYLABEL;
for (const auto &histogramEntry : histogramEntries) {
const std::string &dataName = histogramEntry.first;
const std::string &dataType = histogramEntry.second;
// open second level entry
nxFile.openGroup(dataName, dataType);
// grap title to use to e.g. create workspace name
std::string nameAttrValueTITLE;
nxFile.getAttr("filename", nameAttrValueTITLE);
if (nxFile.hasAttr("ylabel")) {
nxFile.getAttr("ylabel", nameAttrValueYLABEL);
}
// Find the axis names
auto nxdataEntries = nxFile.getEntries();
std::string axis1Name, axis2Name;
for (auto &nxdataEntry : nxdataEntries) {
if (nxdataEntry.second == "NXparameters")
continue;
if (nxdataEntry.first == "ncount")
continue;
nxFile.openData(nxdataEntry.first);
if (nxFile.hasAttr("axis")) {
int axisNo(0);
nxFile.getAttr("axis", axisNo);
if (axisNo == 1)
axis1Name = nxdataEntry.first;
else if (axisNo == 2)
axis2Name = nxdataEntry.first;
else
throw std::invalid_argument("Unknown axis number");
}
nxFile.closeData();
}
std::vector<double> axis1Values, axis2Values;
nxFile.readData<double>(axis1Name, axis1Values);
if (axis2Name.length() == 0) {
axis2Name = nameAttrValueYLABEL;
axis2Values.push_back(0.0);
} else {
nxFile.readData<double>(axis2Name, axis2Values);
}
const size_t axis1Length = axis1Values.size();
const size_t axis2Length = axis2Values.size();
g_log.debug() << "Axis lengths=" << axis1Length << " " << axis2Length
<< '\n';
// Require "data" field
std::vector<double> data;
nxFile.readData<double>("data", data);
// Optional errors field
std::vector<double> errors;
try {
nxFile.readData<double>("errors", errors);
} catch (::NeXus::Exception &) {
g_log.information() << "Field " << dataName
<< " contains no error information.\n";
}
// close second level entry
nxFile.closeGroup();
MatrixWorkspace_sptr ws = WorkspaceFactory::Instance().create(
"Workspace2D", axis2Length, axis1Length, axis1Length);
Axis *axis1 = ws->getAxis(0);
axis1->title() = axis1Name;
// Set caption
auto lblUnit = boost::make_shared<Units::Label>();
lblUnit->setLabel(axis1Name, "");
axis1->unit() = lblUnit;
Axis *axis2 = new NumericAxis(axis2Length);
axis2->title() = axis2Name;
// Set caption
lblUnit = boost::make_shared<Units::Label>();
lblUnit->setLabel(axis2Name, "");
axis2->unit() = lblUnit;
ws->setYUnit(axis2Name);
ws->replaceAxis(1, axis2);
for (size_t wsIndex = 0; wsIndex < axis2Length; ++wsIndex) {
auto &dataY = ws->dataY(wsIndex);
auto &dataE = ws->dataE(wsIndex);
auto &dataX = ws->dataX(wsIndex);
for (size_t j = 0; j < axis1Length; ++j) {
// Data is stored in column-major order so we are translating to
// row major for Mantid
const size_t fileDataIndex = j * axis2Length + wsIndex;
dataY[j] = data[fileDataIndex];
dataX[j] = axis1Values[j];
if (!errors.empty())
dataE[j] = errors[fileDataIndex];
}
axis2->setValue(wsIndex, axis2Values[wsIndex]);
}
// set the workspace title
ws->setTitle(nameAttrValueTITLE);
// use the workspace title to create the workspace name
std::replace(nameAttrValueTITLE.begin(), nameAttrValueTITLE.end(), ' ',
'_');
// ensure that specified name is given to workspace (eventWS) when added to
// outputGroup
std::string nameOfGroupWS = getProperty("OutputWorkspace");
std::string nameUserSee = nameAttrValueTITLE + "_" + nameOfGroupWS;
std::string extraProperty =
"Outputworkspace_dummy_" + std::to_string(m_countNumWorkspaceAdded);
declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
extraProperty, nameUserSee, Direction::Output));
setProperty(extraProperty, boost::static_pointer_cast<Workspace>(ws));
m_countNumWorkspaceAdded++; // need to increment to ensure extraProperty are
// unique
// Make Mantid store the workspace in the group
outputGroup->addWorkspace(ws);
}
nxFile.closeGroup();
} // finish
/**
* Writes a single workspace into the file
* @param workspace the workspace to get data from
* @param nxFile the nexus file to save data into
*/
void SaveNXTomo::writeSingleWorkspace(const Workspace2D_sptr workspace,
::NeXus::File &nxFile) {
try {
nxFile.openPath("/entry1/tomo_entry/data");
} catch (...) {
throw std::runtime_error("Unable to create a valid NXTomo file");
}
int numFiles = 0;
nxFile.getAttr<int>("NumFiles", numFiles);
// Change slab start to after last data position
m_slabStart[0] = numFiles;
m_slabSize[0] = 1;
// Set the rotation value for this WS
std::vector<double> rotValue;
rotValue.push_back(0);
if (workspace->run().hasProperty("Rotation")) {
std::string tmpVal = workspace->run().getLogData("Rotation")->value();
try {
rotValue[0] = boost::lexical_cast<double>(tmpVal);
} catch (...) {
}
// Invalid Cast is handled below
}
nxFile.openData("rotation_angle");
nxFile.putSlab(rotValue, numFiles, 1);
nxFile.closeData();
// Copy data out, remake data with dimension of old size plus new elements.
// Insert previous data.
nxFile.openData("data");
double *dataArr = new double[m_spectraCount];
for (int64_t i = 0; i < m_dimensions[1]; ++i) {
for (int64_t j = 0; j < m_dimensions[2]; ++j) {
dataArr[i * m_dimensions[1] + j] =
workspace->dataY(i * m_dimensions[1] + j)[0];
}
}
nxFile.putSlab(dataArr, m_slabStart, m_slabSize);
nxFile.closeData();
nxFile.putAttr("NumFiles", numFiles + 1);
nxFile.closeGroup();
// Write additional log information, intensity and image key
writeLogValues(workspace, nxFile, numFiles);
writeIntensityValue(workspace, nxFile, numFiles);
writeImageKeyValue(workspace, nxFile, numFiles);
++numFiles;
delete[] dataArr;
}
bool MuonNexusReader::readMuonLogData(NeXus::File &handle) {
const string NAME("name");
const string VALUES("values");
const string TIME("time");
// read name of Log data
string dataName;
handle.readData(NAME, dataName);
// read data values
try {
handle.openData(VALUES);
} catch (NeXus::Exception &) {
g_log.warning() << "No " << VALUES << " set in " << handle.getPath()
<< "\n";
return false;
}
std::vector<float> values;
std::vector<std::string> stringValues;
bool isNumeric(false);
NeXus::Info info = handle.getInfo();
if (info.type == NX_FLOAT32 && info.dims.size() == 1) {
isNumeric = true;
boost::scoped_array<float> dataVals(new float[info.dims[0]]);
handle.getData(dataVals.get());
values.assign(dataVals.get(), dataVals.get() + info.dims[0]);
stringValues.resize(info.dims[0]); // Leave empty
} else if (info.type == NX_CHAR && info.dims.size() == 2) {
boost::scoped_array<char> dataVals(
new char[info.dims[0] * info.dims[1] + 1]);
handle.getData(dataVals.get());
dataVals[info.dims[0] * info.dims[1]] = 0;
for (int i = 0; i < info.dims[0]; ++i) {
std::string str(&dataVals[i * info.dims[1]],
&dataVals[(i + 1) * info.dims[1]]);
stringValues.push_back(str);
}
values.resize(info.dims[0]); // Leave empty
} else {
// Leave both empty
values.resize(info.dims[0]);
stringValues.resize(info.dims[0]);
}
handle.closeData();
// read time values
try {
handle.openData(TIME);
} catch (NeXus::Exception &) {
g_log.warning() << "No " << TIME << " set in " << handle.getPath() << "\n";
return false;
}
info = handle.getInfo();
boost::scoped_array<float> timeVals(new float[info.dims[0]]);
if (info.type == NX_FLOAT32 && info.dims.size() == 1) {
handle.getData(timeVals.get());
} else {
throw std::runtime_error(
"Error in MuonNexusReader: expected float array for log times");
}
handle.closeData();
// Add loaded values to vectors
logNames.push_back(dataName);
std::vector<float> tmp(timeVals.get(), timeVals.get() + info.dims[0]);
logTimes.push_back(tmp);
logType.push_back(isNumeric);
logValues.push_back(values);
logStringValues.push_back(stringValues);
return true;
}
/**
* Update the detector information from a NeXus file
* @param nxFile :: Handle to a NeXus file where the root group has been opened
*/
void UpdateInstrumentFromFile::updateFromNeXus(::NeXus::File & nxFile)
{
try
{
nxFile.openGroup("isis_vms_compat","IXvms");
}
catch(::NeXus::Exception&)
{
throw std::runtime_error("Unknown NeXus flavour. Cannot update instrument positions using this type of file");
}
// Det ID
std::vector<int32_t> detID;
nxFile.openData("UDET");
nxFile.getData(detID);
nxFile.closeData();
// Position information
std::vector<float> l2, theta,phi;
nxFile.openData("LEN2");
nxFile.getData(l2);
nxFile.closeData();
nxFile.openData("TTHE");
nxFile.getData(theta);
nxFile.closeData();
nxFile.openData("UT01");
nxFile.getData(phi);
nxFile.closeData();
g_log.information() << "Setting detector postions from NeXus file.\n";
setDetectorPositions(detID, l2, theta, phi);
}
/**
* Return the confidence with with this algorithm can load the file
* @param eventEntries map of the file entries that have events
* @param outputGroup pointer to the workspace group
* @param nxFile Reads data from inside first first top entry
*/
void LoadMcStas::readEventData(
const std::map<std::string, std::string> &eventEntries,
WorkspaceGroup_sptr &outputGroup, ::NeXus::File &nxFile) {
std::string filename = getPropertyValue("Filename");
auto entries = nxFile.getEntries();
// will assume that each top level entry contain one mcstas
// generated IDF and any event data entries within this top level
// entry are data collected for that instrument
// This code for loading the instrument is for now adjusted code from
// ExperimentalInfo.
// Close data folder and go back to top level. Then read and close the
// Instrument folder.
nxFile.closeGroup();
Geometry::Instrument_sptr instrument;
// Initialize progress reporting
int reports = 2;
const double progressFractionInitial = 0.1;
Progress progInitial(this, 0.0, progressFractionInitial, reports);
try {
nxFile.openGroup("instrument", "NXinstrument");
std::string instrumentXML;
nxFile.openGroup("instrument_xml", "NXnote");
nxFile.readData("data", instrumentXML);
nxFile.closeGroup();
nxFile.closeGroup();
progInitial.report("Loading instrument");
Geometry::InstrumentDefinitionParser parser;
std::string instrumentName = "McStas";
parser.initialize(filename, instrumentName, instrumentXML);
std::string instrumentNameMangled = parser.getMangledName();
// Check whether the instrument is already in the InstrumentDataService
if (InstrumentDataService::Instance().doesExist(instrumentNameMangled)) {
// If it does, just use the one from the one stored there
instrument =
InstrumentDataService::Instance().retrieve(instrumentNameMangled);
} else {
// Really create the instrument
instrument = parser.parseXML(NULL);
// Add to data service for later retrieval
InstrumentDataService::Instance().add(instrumentNameMangled, instrument);
}
} catch (...) {
// Loader should not stop if there is no IDF.xml
g_log.warning()
<< "\nCould not find the instrument description in the Nexus file:"
<< filename << " Ignore evntdata from data file" << std::endl;
return;
}
// Finished reading Instrument. Then open new data folder again
nxFile.openGroup("data", "NXdetector");
// create and prepare an event workspace ready to receive the mcstas events
progInitial.report("Set up EventWorkspace");
EventWorkspace_sptr eventWS(new EventWorkspace());
// initialize, where create up front number of eventlists = number of
// detectors
eventWS->initialize(instrument->getNumberDetectors(), 1, 1);
// Set the units
eventWS->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
eventWS->setYUnit("Counts");
// set the instrument
eventWS->setInstrument(instrument);
// assign detector ID to eventlists
std::vector<detid_t> detIDs = instrument->getDetectorIDs();
for (size_t i = 0; i < instrument->getNumberDetectors(); i++) {
eventWS->getEventList(i).addDetectorID(detIDs[i]);
// spectrum number are treated as equal to detector IDs for McStas data
eventWS->getEventList(i).setSpectrumNo(detIDs[i]);
}
// the one is here for the moment for backward compatibility
eventWS->rebuildSpectraMapping(true);
bool isAnyNeutrons = false;
// to store shortest and longest recorded TOF
double shortestTOF(0.0);
double longestTOF(0.0);
const size_t numEventEntries = eventEntries.size();
Progress progEntries(this, progressFractionInitial, 1.0, numEventEntries * 2);
for (auto eit = eventEntries.begin(); eit != eventEntries.end(); ++eit) {
std::string dataName = eit->first;
std::string dataType = eit->second;
// open second level entry
nxFile.openGroup(dataName, dataType);
std::vector<double> data;
nxFile.openData("events");
progEntries.report("read event data from nexus");
// Need to take into account that the nexus readData method reads a
// multi-column data entry
// into a vector
// The number of data column for each neutron is here hardcoded to (p, x,
// y, n, id, t)
// Thus we have
// column 0 : p neutron wight
// column 1 : x x coordinate
// column 2 : y y coordinate
// column 3 : n accumulated number of neutrons
// column 4 : id pixel id
// column 5 : t time
// get info about event data
::NeXus::Info id_info = nxFile.getInfo();
if (id_info.dims.size() != 2) {
g_log.error() << "Event data in McStas nexus file not loaded. Expected "
"event data block to be two dimensional" << std::endl;
return;
}
int64_t nNeutrons = id_info.dims[0];
int64_t numberOfDataColumn = id_info.dims[1];
if (nNeutrons && numberOfDataColumn != 6) {
g_log.error() << "Event data in McStas nexus file expecting 6 columns"
<< std::endl;
return;
}
if (isAnyNeutrons == false && nNeutrons > 0)
isAnyNeutrons = true;
std::vector<int64_t> start(2);
std::vector<int64_t> step(2);
// read the event data in blocks. 1 million event is 1000000*6*8 doubles
// about 50Mb
int64_t nNeutronsInBlock = 1000000;
int64_t nOfFullBlocks = nNeutrons / nNeutronsInBlock;
int64_t nRemainingNeutrons = nNeutrons - nOfFullBlocks * nNeutronsInBlock;
// sum over number of blocks + 1 to cover the remainder
for (int64_t iBlock = 0; iBlock < nOfFullBlocks + 1; iBlock++) {
if (iBlock == nOfFullBlocks) {
// read remaining neutrons
start[0] = nOfFullBlocks * nNeutronsInBlock;
start[1] = 0;
step[0] = nRemainingNeutrons;
step[1] = numberOfDataColumn;
} else {
// read neutrons in a full block
start[0] = iBlock * nNeutronsInBlock;
start[1] = 0;
step[0] = nNeutronsInBlock;
step[1] = numberOfDataColumn;
}
const int64_t nNeutronsForthisBlock =
step[0]; // number of neutrons read for this block
data.resize(nNeutronsForthisBlock * numberOfDataColumn);
// Check that the type is what it is supposed to be
if (id_info.type == ::NeXus::FLOAT64) {
nxFile.getSlab(&data[0], start, step);
} else {
g_log.warning()
<< "Entry event field is not FLOAT64! It will be skipped.\n";
continue;
}
// populate workspace with McStas events
const detid2index_map detIDtoWSindex_map =
eventWS->getDetectorIDToWorkspaceIndexMap(true);
progEntries.report("read event data into workspace");
for (int64_t in = 0; in < nNeutronsForthisBlock; in++) {
const int detectorID =
static_cast<int>(data[4 + numberOfDataColumn * in]);
const double detector_time = data[5 + numberOfDataColumn * in] *
1.0e6; // convert to microseconds
if (in == 0 && iBlock == 0) {
shortestTOF = detector_time;
longestTOF = detector_time;
} else {
if (detector_time < shortestTOF)
shortestTOF = detector_time;
if (detector_time > longestTOF)
longestTOF = detector_time;
}
const size_t workspaceIndex =
detIDtoWSindex_map.find(detectorID)->second;
int64_t pulse_time = 0;
// eventWS->getEventList(workspaceIndex) +=
// TofEvent(detector_time,pulse_time);
// eventWS->getEventList(workspaceIndex) += TofEvent(detector_time);
eventWS->getEventList(workspaceIndex) += WeightedEvent(
detector_time, pulse_time, data[numberOfDataColumn * in], 1.0);
}
} // end reading over number of blocks of an event dataset
// nxFile.getData(data);
nxFile.closeData();
nxFile.closeGroup();
} // end reading over number of event datasets
// Create a default TOF-vector for histogramming, for now just 2 bins
// 2 bins is the standard. However for McStas simulation data it may make
// sense to
// increase this number for better initial visual effect
Kernel::cow_ptr<MantidVec> axis;
MantidVec &xRef = axis.access();
xRef.resize(2, 0.0);
// if ( nNeutrons > 0)
if (isAnyNeutrons) {
xRef[0] = shortestTOF - 1; // Just to make sure the bins hold it all
xRef[1] = longestTOF + 1;
}
// Set the binning axis
eventWS->setAllX(axis);
// ensure that specified name is given to workspace (eventWS) when added to
// outputGroup
std::string nameOfGroupWS = getProperty("OutputWorkspace");
std::string nameUserSee = std::string("EventData_") + nameOfGroupWS;
std::string extraProperty =
"Outputworkspace_dummy_" +
boost::lexical_cast<std::string>(m_countNumWorkspaceAdded);
declareProperty(new WorkspaceProperty<Workspace>(extraProperty, nameUserSee,
Direction::Output));
setProperty(extraProperty, boost::static_pointer_cast<Workspace>(eventWS));
m_countNumWorkspaceAdded++; // need to increment to ensure extraProperty are
// unique
outputGroup->addWorkspace(eventWS);
}
/** Loads an entry from a previously-open NXS file as a log entry
* in the workspace's run.
*
* @param file: NXS file handle. MUST BE PASSED BY REFERENCE otherwise there
* occurs a segfault.
* @param entry_name, entry_class: name and class of NXlog to open.
*/
void LoadLogsFromSNSNexus::loadSampleLog(::NeXus::File& file, std::string entry_name, std::string entry_class)
{
// whether or not to overwrite logs on workspace
bool overwritelogs = this->getProperty("OverwriteLogs");
file.openGroup(entry_name, entry_class);
// Validate the NX log class.
map<string, 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;
}
::NeXus::Info info;
//Two possible types of properties:
vector<double> values;
vector<int> values_int;
bool isTimeSeries = false;
bool isInt = false;
file.openData("value");
//Get the units of the property
std::string units("");
try
{
file.getAttr("units", units);
}
catch (::NeXus::Exception &)
{
//Ignore missing units field.
units = "";
}
//If there is more than one entry, it is a timeseries
info = file.getInfo();
//isTimeSeries = (info.dims[0] > 1);
isTimeSeries = true;
Timer timer1;
try
{
//Get the data (convert types if necessary)
if (file.isDataInt())
{
isInt = true;
file.getDataCoerce(values_int);
// if (values_int.size() == 1)
// {
// WS->mutableRun().addProperty(entry_name, values_int[0], units);
// }
}
else
{
//Try to get as doubles.
file.getDataCoerce(values);
// if (values.size() == 1)
// {
// WS->mutableRun().addProperty(entry_name, values[0], units);
// }
}
}
catch (::NeXus::Exception &e)
{
g_log.warning() << "NXlog entry " << entry_name << " gave an error when loading 'value' data:'" << e.what() << "'.\n";
file.closeData();
file.closeGroup();
return;
}
if (VERBOSE) std::cout << "getDataCoerce took " << timer1.elapsed() << " sec.\n";
file.closeData();
if (isTimeSeries)
{
// --- Time series property ---
//Get the times
vector<double> time_double;
vector<DateAndTime> times;
try {
file.openData("time");
}
catch (::NeXus::Exception &e)
{
g_log.warning() << "NXlog entry " << entry_name << " gave an error when opening the time field '" << e.what() << "'.\n";
file.closeGroup();
return;
}
//----- 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() << "NXlog entry " << entry_name << " has no start time indicated.\n";
file.closeData();
file.closeGroup();
return;
}
}
//Convert to date and time
Kernel::DateAndTime start_time = Kernel::DateAndTime(start);
std::string time_units;
file.getAttr("units", time_units);
if (time_units != "second")
{
g_log.warning() << "NXlog entry " << entry_name << " has time units of '" << time_units << "', which are unsupported. 'second' is the only supported time unit.\n";
file.closeData();
file.closeGroup();
return;
}
Timer timer2;
//--- Load the seconds into a double array ---
try {
file.getDataCoerce(time_double);
}
catch (::NeXus::Exception &e)
{
g_log.warning() << "NXlog entry " << entry_name << "'s time field could not be loaded: '" << e.what() << "'.\n";
file.closeData();
file.closeGroup();
return;
}
file.closeData();
if (VERBOSE) std::cout << "getDataCoerce for the seconds field took " << timer2.elapsed() << " sec.\n";
if (isInt)
{
//Make an int TSP
TimeSeriesProperty<int> * tsp = new TimeSeriesProperty<int>(entry_name);
tsp->create(start_time, time_double, values_int);
tsp->setUnits( units );
WS->mutableRun().addProperty( tsp, overwritelogs );
}
else
{
//Make a double TSP
TimeSeriesProperty<double> * tsp = new TimeSeriesProperty<double>(entry_name);
Timer timer3;
tsp->create(start_time, time_double, values);
if (VERBOSE) std::cout << "creating a TSP took " << timer3.elapsed() << " sec.\n";
tsp->setUnits( units );
WS->mutableRun().addProperty( tsp, overwritelogs );
// Trick to free memory?
std::vector<double>().swap(time_double);
std::vector<double>().swap(values);
}
}
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();
}
/**
* Read Event Data
* @param eventEntries map of the file entries that have events
* @param nxFile Reads data from inside first top entry
* @return Names of workspaces to include in the output group
*/
std::vector<std::string> LoadMcStas::readEventData(
const std::map<std::string, std::string> &eventEntries,
::NeXus::File &nxFile) {
// vector to store output workspaces
std::vector<std::string> scatteringWSNames;
std::string filename = getPropertyValue("Filename");
auto entries = nxFile.getEntries();
const bool errorBarsSetTo1 = getProperty("ErrorBarsSetTo1");
// will assume that each top level entry contain one mcstas
// generated IDF and any event data entries within this top level
// entry are data collected for that instrument
// This code for loading the instrument is for now adjusted code from
// ExperimentalInfo.
// Close data folder and go back to top level. Then read and close the
// Instrument folder.
nxFile.closeGroup();
Geometry::Instrument_sptr instrument;
// Initialize progress reporting
int reports = 2;
const double progressFractionInitial = 0.1;
Progress progInitial(this, 0.0, progressFractionInitial, reports);
std::string instrumentXML;
progInitial.report("Loading instrument");
try {
nxFile.openGroup("instrument", "NXinstrument");
nxFile.openGroup("instrument_xml", "NXnote");
nxFile.readData("data", instrumentXML);
nxFile.closeGroup();
nxFile.closeGroup();
} catch (...) {
g_log.warning()
<< "\nCould not find the instrument description in the Nexus file:"
<< filename << " Ignore eventdata from the Nexus file\n";
return scatteringWSNames;
;
}
try {
std::string instrumentName = "McStas";
Geometry::InstrumentDefinitionParser parser(filename, instrumentName,
instrumentXML);
std::string instrumentNameMangled = parser.getMangledName();
// Check whether the instrument is already in the InstrumentDataService
if (InstrumentDataService::Instance().doesExist(instrumentNameMangled)) {
// If it does, just use the one from the one stored there
instrument =
InstrumentDataService::Instance().retrieve(instrumentNameMangled);
} else {
// Really create the instrument
instrument = parser.parseXML(nullptr);
// Add to data service for later retrieval
InstrumentDataService::Instance().add(instrumentNameMangled, instrument);
}
} catch (Exception::InstrumentDefinitionError &e) {
g_log.warning()
<< "When trying to read the instrument description in the Nexus file: "
<< filename << " the following error is reported: " << e.what()
<< " Ignore eventdata from the Nexus file\n";
return scatteringWSNames;
;
} catch (...) {
g_log.warning()
<< "Could not parse instrument description in the Nexus file: "
<< filename << " Ignore eventdata from the Nexus file\n";
return scatteringWSNames;
;
}
// Finished reading Instrument. Then open new data folder again
nxFile.openGroup("data", "NXdetector");
// create and prepare an event workspace ready to receive the mcstas events
progInitial.report("Set up EventWorkspace");
EventWorkspace_sptr eventWS(new EventWorkspace());
// initialize, where create up front number of eventlists = number of
// detectors
eventWS->initialize(instrument->getNumberDetectors(), 1, 1);
// Set the units
eventWS->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
eventWS->setYUnit("Counts");
// set the instrument
eventWS->setInstrument(instrument);
// assign detector ID to eventlists
std::vector<detid_t> detIDs = instrument->getDetectorIDs();
for (size_t i = 0; i < instrument->getNumberDetectors(); i++) {
eventWS->getSpectrum(i).addDetectorID(detIDs[i]);
// spectrum number are treated as equal to detector IDs for McStas data
eventWS->getSpectrum(i).setSpectrumNo(detIDs[i]);
}
// the one is here for the moment for backward compatibility
eventWS->rebuildSpectraMapping(true);
bool isAnyNeutrons = false;
// to store shortest and longest recorded TOF
double shortestTOF(0.0);
double longestTOF(0.0);
// create vector container all the event output workspaces needed
const size_t numEventEntries = eventEntries.size();
std::string nameOfGroupWS = getProperty("OutputWorkspace");
const auto eventDataTotalName = "EventData_" + nameOfGroupWS;
std::vector<std::pair<EventWorkspace_sptr, std::string>> allEventWS = {
{eventWS, eventDataTotalName}};
// if numEventEntries > 1 also create separate event workspaces
const bool onlySummedEventWorkspace =
getProperty("OutputOnlySummedEventWorkspace");
if (!onlySummedEventWorkspace && numEventEntries > 1) {
for (const auto &eventEntry : eventEntries) {
const std::string &dataName = eventEntry.first;
// create container to hold partial event data
// plus the name users will see for it
const auto ws_name = dataName + "_" + nameOfGroupWS;
allEventWS.emplace_back(eventWS->clone(), ws_name);
}
}
Progress progEntries(this, progressFractionInitial, 1.0, numEventEntries * 2);
// Refer to entry in allEventWS. The first non-summed workspace index is 1
auto eventWSIndex = 1u;
// Loop over McStas event data components
for (const auto &eventEntry : eventEntries) {
const std::string &dataName = eventEntry.first;
const std::string &dataType = eventEntry.second;
// open second level entry
nxFile.openGroup(dataName, dataType);
std::vector<double> data;
nxFile.openData("events");
progEntries.report("read event data from nexus");
// Need to take into account that the nexus readData method reads a
// multi-column data entry
// into a vector
// The number of data column for each neutron is here hardcoded to (p, x,
// y, n, id, t)
// Thus we have
// column 0 : p neutron wight
// column 1 : x x coordinate
// column 2 : y y coordinate
// column 3 : n accumulated number of neutrons
// column 4 : id pixel id
// column 5 : t time
// get info about event data
::NeXus::Info id_info = nxFile.getInfo();
if (id_info.dims.size() != 2) {
g_log.error() << "Event data in McStas nexus file not loaded. Expected "
"event data block to be two dimensional\n";
return scatteringWSNames;
;
}
int64_t nNeutrons = id_info.dims[0];
int64_t numberOfDataColumn = id_info.dims[1];
if (nNeutrons && numberOfDataColumn != 6) {
g_log.error() << "Event data in McStas nexus file expecting 6 columns\n";
return scatteringWSNames;
;
}
if (!isAnyNeutrons && nNeutrons > 0)
isAnyNeutrons = true;
std::vector<int64_t> start(2);
std::vector<int64_t> step(2);
// read the event data in blocks. 1 million event is 1000000*6*8 doubles
// about 50Mb
int64_t nNeutronsInBlock = 1000000;
int64_t nOfFullBlocks = nNeutrons / nNeutronsInBlock;
int64_t nRemainingNeutrons = nNeutrons - nOfFullBlocks * nNeutronsInBlock;
// sum over number of blocks + 1 to cover the remainder
for (int64_t iBlock = 0; iBlock < nOfFullBlocks + 1; iBlock++) {
if (iBlock == nOfFullBlocks) {
// read remaining neutrons
start[0] = nOfFullBlocks * nNeutronsInBlock;
start[1] = 0;
step[0] = nRemainingNeutrons;
step[1] = numberOfDataColumn;
} else {
// read neutrons in a full block
start[0] = iBlock * nNeutronsInBlock;
start[1] = 0;
step[0] = nNeutronsInBlock;
step[1] = numberOfDataColumn;
}
const int64_t nNeutronsForthisBlock =
step[0]; // number of neutrons read for this block
data.resize(nNeutronsForthisBlock * numberOfDataColumn);
// Check that the type is what it is supposed to be
if (id_info.type == ::NeXus::FLOAT64) {
nxFile.getSlab(&data[0], start, step);
} else {
g_log.warning()
<< "Entry event field is not FLOAT64! It will be skipped.\n";
continue;
}
// populate workspace with McStas events
const detid2index_map detIDtoWSindex_map =
allEventWS[0].first->getDetectorIDToWorkspaceIndexMap(true);
progEntries.report("read event data into workspace");
for (int64_t in = 0; in < nNeutronsForthisBlock; in++) {
const int detectorID =
static_cast<int>(data[4 + numberOfDataColumn * in]);
const double detector_time = data[5 + numberOfDataColumn * in] *
1.0e6; // convert to microseconds
if (in == 0 && iBlock == 0) {
shortestTOF = detector_time;
longestTOF = detector_time;
} else {
if (detector_time < shortestTOF)
shortestTOF = detector_time;
if (detector_time > longestTOF)
longestTOF = detector_time;
}
const size_t workspaceIndex =
detIDtoWSindex_map.find(detectorID)->second;
int64_t pulse_time = 0;
auto weightedEvent = WeightedEvent();
if (errorBarsSetTo1) {
weightedEvent = WeightedEvent(detector_time, pulse_time,
data[numberOfDataColumn * in], 1.0);
} else {
weightedEvent = WeightedEvent(
detector_time, pulse_time, data[numberOfDataColumn * in],
data[numberOfDataColumn * in] * data[numberOfDataColumn * in]);
}
allEventWS[0].first->getSpectrum(workspaceIndex) += weightedEvent;
if (!onlySummedEventWorkspace && numEventEntries > 1) {
allEventWS[eventWSIndex].first->getSpectrum(workspaceIndex) +=
weightedEvent;
}
}
eventWSIndex++;
} // end reading over number of blocks of an event dataset
nxFile.closeData();
nxFile.closeGroup();
} // end reading over number of event datasets
// Create a default TOF-vector for histogramming, for now just 2 bins
// 2 bins is the standard. However for McStas simulation data it may make
// sense to
// increase this number for better initial visual effect
auto axis = HistogramData::BinEdges{shortestTOF - 1, longestTOF + 1};
// ensure that specified name is given to workspace (eventWS) when added to
// outputGroup
for (auto eventWS : allEventWS) {
const auto ws = eventWS.first;
ws->setAllX(axis);
AnalysisDataService::Instance().addOrReplace(eventWS.second, ws);
scatteringWSNames.emplace_back(eventWS.second);
}
return scatteringWSNames;
}
