/**
* 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);
}
/** 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";
}
}
}
/** 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();
}
/**
* 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();
}
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));
}
}
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;
}
/**
* 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();
}