/** Load logs from Nexus file. Logs are expected to be in
* /run/sample group of the file.
* @param ws :: The workspace to load the logs to.
* @param entry :: The Nexus entry
* @param period :: The period of this workspace
*/
void LoadMuonNexus2::loadLogs(API::MatrixWorkspace_sptr ws, NXEntry &entry,
int period) {
// Avoid compiler warning
(void)period;
std::string start_time = entry.getString("start_time");
std::string sampleName = entry.getString("sample/name");
NXMainClass runlogs = entry.openNXClass<NXMainClass>("sample");
ws->mutableSample().setName(sampleName);
for (std::vector<NXClassInfo>::const_iterator it = runlogs.groups().begin();
it != runlogs.groups().end(); ++it) {
NXLog nxLog = runlogs.openNXLog(it->nxname);
Kernel::Property *logv = nxLog.createTimeSeries(start_time);
if (!logv)
continue;
ws->mutableRun().addLogData(logv);
}
ws->setTitle(entry.getString("title"));
if (entry.containsDataSet("notes")) {
ws->setComment(entry.getString("notes"));
}
std::string run_num = std::to_string(entry.getInt("run_number"));
// The sample is left to delete the property
ws->mutableRun().addLogData(
new PropertyWithValue<std::string>("run_number", run_num));
ws->populateInstrumentParameters();
}
/**
* Sets the start date on a dummy workspace. If there is a detector table file
* available we update the dummy workspace with the start date from this file.
* @param workspace: dummy workspace
*/
void CreateSimulationWorkspace::setStartDate(
API::MatrixWorkspace_sptr workspace) {
const std::string detTableFile = getProperty("DetectorTableFilename");
auto hasDetTableFile = !detTableFile.empty();
auto &run = workspace->mutableRun();
Kernel::DateAndTime startTime;
Kernel::DateAndTime endTime;
try {
// The start and end times might not be valid, and hence can throw
startTime = run.startTime();
endTime = run.endTime();
} catch (std::runtime_error &) {
startTime = Kernel::DateAndTime::getCurrentTime();
endTime = Kernel::DateAndTime::getCurrentTime();
}
if (hasDetTableFile) {
if (boost::algorithm::ends_with(detTableFile, ".raw") ||
boost::algorithm::ends_with(detTableFile, ".RAW")) {
auto startAndEndTime = getStartAndEndTimesFromRawFile(detTableFile);
startTime = startAndEndTime.startTime;
endTime = startAndEndTime.endTime;
} else if (boost::algorithm::ends_with(detTableFile, ".nxs") ||
boost::algorithm::ends_with(detTableFile, ".NXS")) {
auto startAndEndTime =
getStartAndEndTimesFromNexusFile(detTableFile, startTime, endTime);
startTime = startAndEndTime.startTime;
endTime = startAndEndTime.endTime;
}
}
run.setStartAndEndTime(startTime, endTime);
}
void HFIRLoad::exec() {
// Reduction property manager
const std::string reductionManagerName = getProperty("ReductionProperties");
boost::shared_ptr<PropertyManager> reductionManager;
if (PropertyManagerDataService::Instance().doesExist(reductionManagerName)) {
reductionManager =
PropertyManagerDataService::Instance().retrieve(reductionManagerName);
} else {
reductionManager = boost::make_shared<PropertyManager>();
PropertyManagerDataService::Instance().addOrReplace(reductionManagerName,
reductionManager);
}
Progress progress(this, 0, 1, 5);
progress.report();
// If the load algorithm isn't in the reduction properties, add it
if (!reductionManager->existsProperty("LoadAlgorithm")) {
auto algProp = make_unique<AlgorithmProperty>("LoadAlgorithm");
algProp->setValue(toString());
reductionManager->declareProperty(std::move(algProp));
}
const std::string fileName = getPropertyValue("Filename");
// Output log
std::string output_message = "";
const double wavelength_input = getProperty("Wavelength");
const double wavelength_spread_input = getProperty("WavelengthSpread");
progress.report("LoadSpice2D...");
IAlgorithm_sptr loadAlg = createChildAlgorithm("LoadSpice2D", 0, 0.2);
loadAlg->setProperty("Filename", fileName);
if (!isEmpty(wavelength_input)) {
loadAlg->setProperty("Wavelength", wavelength_input);
loadAlg->setProperty("WavelengthSpread", wavelength_spread_input);
}
try {
loadAlg->executeAsChildAlg();
} catch (...) {
// The only way HFIR SANS can load Nexus files is if it's loading data that
// has already
// been processed. This will only happen with sensitivity data.
// So if we make it here and are still unable to load the file, assume it's
// a sensitivity file.
// This will cover the special case where the instrument scientist uses a
// reduced data set
// as a sensitivity data set.
g_log.warning() << "Unable to load file as a SPICE file. Trying to load as "
"a Nexus file.\n";
loadAlg = createChildAlgorithm("Load", 0, 0.2);
loadAlg->setProperty("Filename", fileName);
loadAlg->executeAsChildAlg();
Workspace_sptr dataWS_tmp = loadAlg->getProperty("OutputWorkspace");
MatrixWorkspace_sptr dataWS =
boost::dynamic_pointer_cast<MatrixWorkspace>(dataWS_tmp);
dataWS->mutableRun().addProperty("is_sensitivity", 1, "", true);
setProperty<MatrixWorkspace_sptr>("OutputWorkspace", dataWS);
g_log.notice() << "Successfully loaded " << fileName
<< " and setting sensitivity flag to True\n";
return;
}
Workspace_sptr dataWS_tmp = loadAlg->getProperty("OutputWorkspace");
API::MatrixWorkspace_sptr dataWS =
boost::dynamic_pointer_cast<MatrixWorkspace>(dataWS_tmp);
// Get the sample-detector distance
// If SampleDetectorDistance is provided, use it!
// Otherwise get's "sample-detector-distance" from the data file
// And uses SampleDetectorDistanceOffset if given!
double sdd = 0.0;
const double sample_det_dist = getProperty("SampleDetectorDistance");
if (!isEmpty(sample_det_dist)) {
sdd = sample_det_dist;
} else {
const std::string sddName = "sample-detector-distance";
Mantid::Kernel::Property *prop = dataWS->run().getProperty(sddName);
Mantid::Kernel::PropertyWithValue<double> *dp =
dynamic_cast<Mantid::Kernel::PropertyWithValue<double> *>(prop);
if (!dp) {
throw std::runtime_error("Could not cast (interpret) the property " +
sddName + " as a floating point numeric value.");
}
sdd = *dp;
// Modify SDD according to offset if given
const double sample_det_offset =
getProperty("SampleDetectorDistanceOffset");
if (!isEmpty(sample_det_offset)) {
sdd += sample_det_offset;
}
}
dataWS->mutableRun().addProperty("sample_detector_distance", sdd, "mm", true);
progress.report("MoveInstrumentComponent...");
// Move the detector to its correct position
IAlgorithm_sptr mvAlg =
createChildAlgorithm("MoveInstrumentComponent", 0.2, 0.4);
mvAlg->setProperty<MatrixWorkspace_sptr>("Workspace", dataWS);
mvAlg->setProperty("ComponentName", "detector1");
mvAlg->setProperty("Z", sdd / 1000.0);
mvAlg->setProperty("RelativePosition", false);
mvAlg->executeAsChildAlg();
g_log.information() << "Moving detector to " << sdd / 1000.0 << '\n';
output_message += " Detector position: " +
Poco::NumberFormatter::format(sdd / 1000.0, 3) + " m\n";
// Compute beam diameter at the detector
double src_to_sample = 0.0;
try {
src_to_sample = HFIRInstrument::getSourceToSampleDistance(dataWS);
dataWS->mutableRun().addProperty("source-sample-distance", src_to_sample,
"mm", true);
output_message += " Computed SSD from number of guides: " +
Poco::NumberFormatter::format(src_to_sample / 1000.0, 3) +
" \n";
} catch (...) {
Mantid::Kernel::Property *prop =
dataWS->run().getProperty("source-sample-distance");
Mantid::Kernel::PropertyWithValue<double> *dp =
dynamic_cast<Mantid::Kernel::PropertyWithValue<double> *>(prop);
src_to_sample = *dp;
output_message +=
" Could not compute SSD from number of guides, taking: " +
Poco::NumberFormatter::format(src_to_sample / 1000.0, 3) + " \n";
}
const std::string sampleADName = "sample-aperture-diameter";
Mantid::Kernel::Property *prop = dataWS->run().getProperty(sampleADName);
Mantid::Kernel::PropertyWithValue<double> *dp =
dynamic_cast<Mantid::Kernel::PropertyWithValue<double> *>(prop);
if (!dp) {
throw std::runtime_error("Could not cast (interpret) the property " +
sampleADName +
" as a floating point numeric value.");
}
double sample_apert = *dp;
const std::string sourceADName = "source-aperture-diameter";
prop = dataWS->run().getProperty(sourceADName);
dp = dynamic_cast<Mantid::Kernel::PropertyWithValue<double> *>(prop);
if (!dp) {
throw std::runtime_error("Could not cast (interpret) the property " +
sourceADName +
" as a floating point numeric value.");
}
double source_apert = *dp;
const double beam_diameter =
sdd / src_to_sample * (source_apert + sample_apert) + sample_apert;
dataWS->mutableRun().addProperty("beam-diameter", beam_diameter, "mm", true);
progress.report("Move to center beam...");
double center_x = 0;
double center_y = 0;
// Move the beam center to its proper position
const bool noBeamCenter = getProperty("NoBeamCenter");
if (!noBeamCenter) {
center_x = getProperty("BeamCenterX");
center_y = getProperty("BeamCenterY");
if (isEmpty(center_x) && isEmpty(center_y)) {
if (reductionManager->existsProperty("LatestBeamCenterX") &&
reductionManager->existsProperty("LatestBeamCenterY")) {
center_x = reductionManager->getProperty("LatestBeamCenterX");
center_y = reductionManager->getProperty("LatestBeamCenterY");
}
}
moveToBeamCenter(dataWS, center_x, center_y);
progress.report();
// Add beam center to reduction properties, as the last beam center position
// that was used.
// This will give us our default position next time.
if (!reductionManager->existsProperty("LatestBeamCenterX"))
reductionManager->declareProperty(make_unique<PropertyWithValue<double>>(
"LatestBeamCenterX", center_x));
else
reductionManager->setProperty("LatestBeamCenterX", center_x);
if (!reductionManager->existsProperty("LatestBeamCenterY"))
reductionManager->declareProperty(make_unique<PropertyWithValue<double>>(
"LatestBeamCenterY", center_y));
else
reductionManager->setProperty("LatestBeamCenterY", center_y);
dataWS->mutableRun().addProperty("beam_center_x", center_x, "pixel", true);
dataWS->mutableRun().addProperty("beam_center_y", center_y, "pixel", true);
output_message += " Beam center: " +
Poco::NumberFormatter::format(center_x, 1) + ", " +
Poco::NumberFormatter::format(center_y, 1) + "\n";
} else {
HFIRInstrument::getDefaultBeamCenter(dataWS, center_x, center_y);
dataWS->mutableRun().addProperty("beam_center_x", center_x, "pixel", true);
dataWS->mutableRun().addProperty("beam_center_y", center_y, "pixel", true);
output_message += " Default beam center: " +
Poco::NumberFormatter::format(center_x, 1) + ", " +
Poco::NumberFormatter::format(center_y, 1) + "\n";
}
setProperty<MatrixWorkspace_sptr>(
"OutputWorkspace", boost::dynamic_pointer_cast<MatrixWorkspace>(dataWS));
setPropertyValue("OutputMessage", output_message);
}
void LoadSpiceAscii::addProperty(API::MatrixWorkspace_sptr ws,
const std::string &pname, T pvalue) {
ws->mutableRun().addLogData(new PropertyWithValue<T>(pname, pvalue));
}
/*
* Add and check log from processed absolute time stamps
*/
void ProcessDasNexusLog::addLog(API::MatrixWorkspace_sptr ws,
std::vector<Kernel::DateAndTime> timevec,
double unifylogvalue, std::string logname,
std::vector<Kernel::DateAndTime> pulsetimes,
std::vector<double> orderedtofs, bool docheck) {
// 1. Do some static
g_log.notice() << "Vector size = " << timevec.size() << std::endl;
double sum1dtms = 0.0; // sum(dt^2)
double sum2dtms = 0.0; // sum(dt^2)
size_t numinvert = 0;
size_t numsame = 0;
size_t numnormal = 0;
double maxdtms = 0;
double mindtms = 1.0E20;
size_t numdtabove10p = 0;
size_t numdtbelow10p = 0;
double sampledtms = 0.00832646 * 1.0E6;
double dtmsA10p = sampledtms * 1.1;
double dtmsB10p = sampledtms / 1.0;
for (size_t i = 1; i < timevec.size(); i++) {
int64_t dtns =
timevec[i].totalNanoseconds() - timevec[i - 1].totalNanoseconds();
double dtms = static_cast<double>(dtns) * 1.0E-3;
sum1dtms += dtms;
sum2dtms += dtms * dtms;
if (dtns == 0)
numsame++;
else if (dtns < 0)
numinvert++;
else
numnormal++;
if (dtms > maxdtms)
maxdtms = dtms;
if (dtms < mindtms)
mindtms = dtms;
if (dtms > dtmsA10p)
numdtabove10p++;
else if (dtms < dtmsB10p)
numdtbelow10p++;
} // ENDFOR
double dt = sum1dtms / static_cast<double>(timevec.size()) * 1.0E-6;
double stddt =
sqrt(sum2dtms / static_cast<double>(timevec.size()) * 1.0E-12 - dt * dt);
g_log.notice() << "Normal dt = " << numnormal << std::endl;
g_log.notice() << "Zero dt = " << numsame << std::endl;
g_log.notice() << "Negative dt = " << numinvert << std::endl;
g_log.notice() << "Avg d(T) = " << dt << " seconds +/- " << stddt
<< ", Frequency = " << 1.0 / dt << std::endl;
g_log.notice() << "d(T) (unit ms) is in range [" << mindtms << ", " << maxdtms
<< "]" << std::endl;
g_log.notice() << "Number of d(T) 10% larger than average = "
<< numdtabove10p << std::endl;
g_log.notice() << "Number of d(T) 10% smaller than average = "
<< numdtbelow10p << std::endl;
g_log.notice() << "Size of timevec, pulsestimes, orderedtofs = "
<< timevec.size() << ", " << pulsetimes.size() << ", "
<< orderedtofs.size() << std::endl;
if (docheck) {
exportErrorLog(ws, timevec, pulsetimes, orderedtofs, 1 / (0.5 * 240.1));
calDistributions(timevec, 1 / (0.5 * 240.1));
}
// 2. Add log
Kernel::TimeSeriesProperty<double> *newlog =
new Kernel::TimeSeriesProperty<double>(logname);
for (size_t i = 0; i < timevec.size(); i++) {
newlog->addValue(timevec[i], unifylogvalue);
}
ws->mutableRun().addProperty(newlog, true);
return;
}
void LoadDaveGrp::exec()
{
const std::string filename = this->getProperty("Filename");
int yLength = 0;
MantidVec *xAxis = new MantidVec();
MantidVec *yAxis = new MantidVec();
std::vector<MantidVec *> data;
std::vector<MantidVec *> errors;
this->ifile.open(filename.c_str());
if (this->ifile.is_open())
{
// Size of x axis
this->getAxisLength(this->xLength);
// Size of y axis
this->getAxisLength(yLength);
// This is also the number of groups (spectra)
this->nGroups = yLength;
// Read in the x axis values
this->getAxisValues(xAxis, static_cast<std::size_t>(this->xLength));
// Read in the y axis values
this->getAxisValues(yAxis, static_cast<std::size_t>(yLength));
// Read in the data
this->getData(data, errors);
}
this->ifile.close();
// Scale the x-axis if it is in micro-eV to get it to meV
const bool isUeV = this->getProperty("IsMicroEV");
if (isUeV)
{
MantidVec::iterator iter;
for (iter = xAxis->begin(); iter != xAxis->end(); ++iter)
{
*iter /= 1000.0;
}
}
// Create workspace
API::MatrixWorkspace_sptr outputWorkspace = \
boost::dynamic_pointer_cast<API::MatrixWorkspace>\
(API::WorkspaceFactory::Instance().create("Workspace2D", this->nGroups,
this->xLength, yLength));
// Force the workspace to be a distribution
outputWorkspace->isDistribution(true);
// Set the x-axis units
outputWorkspace->getAxis(0)->unit() = Kernel::UnitFactory::Instance().create(this->getProperty("XAxisUnits"));
API::Axis* const verticalAxis = new API::NumericAxis(yLength);
// Set the y-axis units
verticalAxis->unit() = Kernel::UnitFactory::Instance().create(this->getProperty("YAxisUnits"));
outputWorkspace->replaceAxis(1, verticalAxis);
for(int i = 0; i < this->nGroups; i++)
{
outputWorkspace->dataX(i) = *xAxis;
outputWorkspace->dataY(i) = *data[i];
outputWorkspace->dataE(i) = *errors[i];
verticalAxis->setValue(i, yAxis->at(i));
delete data[i];
delete errors[i];
}
delete xAxis;
delete yAxis;
outputWorkspace->mutableRun().addProperty("Filename",filename);
this->setProperty("OutputWorkspace", outputWorkspace);
}
/// Execute the algorithm.
void PDDetermineCharacterizations::exec() {
// setup property manager to return
const std::string managerName = getPropertyValue("ReductionProperties");
if (PropertyManagerDataService::Instance().doesExist(managerName)) {
m_propertyManager =
PropertyManagerDataService::Instance().retrieve(managerName);
} else {
m_propertyManager = boost::make_shared<Kernel::PropertyManager>();
PropertyManagerDataService::Instance().addOrReplace(managerName,
m_propertyManager);
}
setDefaultsInPropManager();
m_characterizations = getProperty(CHAR_PROP_NAME);
if (bool(m_characterizations) && (m_characterizations->rowCount() > 0)) {
API::MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
auto run = inputWS->mutableRun();
double frequency = getLogValue(run, FREQ_PROP_NAME);
double wavelength = getLogValue(run, WL_PROP_NAME);
// determine the container name
std::string container;
if (run.hasProperty("SampleContainer")) {
const auto containerProp = run.getLogData("SampleContainer");
// the property is normally a TimeSeriesProperty
const auto containerPropSeries =
dynamic_cast<TimeSeriesProperty<std::string> *>(containerProp);
if (containerPropSeries) {
// assume that only the first value matters
container = containerPropSeries->valuesAsVector().front();
} else {
// try as a normal Property
container = containerProp->value();
}
// remove whitespace from the value
container = Kernel::Strings::replaceAll(container, " ", "");
}
getInformationFromTable(frequency, wavelength, container);
}
overrideRunNumProperty("BackRun", "container");
overrideRunNumProperty("NormRun", "vanadium");
overrideRunNumProperty("NormBackRun", "vanadium_background");
overrideRunNumProperty("EmptyEnv", "empty_environment");
overrideRunNumProperty("EmptyInstr", "empty_instrument");
std::vector<std::string> expectedNames = getColumnNames();
for (auto &expectedName : expectedNames) {
if (m_propertyManager->existsProperty(expectedName)) {
g_log.debug() << expectedName << ":"
<< m_propertyManager->getPropertyValue(expectedName)
<< "\n";
} else {
g_log.warning() << expectedName << " DOES NOT EXIST\n";
}
}
}
/**
* Splits multiperiod histogram data into seperate workspaces and puts them in
* a group
*
* @param numPeriods :: number of periods
**/
void LoadNexusMonitors2::splitMutiPeriodHistrogramData(
const size_t numPeriods) {
// protection - we should not have entered the routine if these are not true
// More than 1 period
if (numPeriods < 2) {
g_log.warning()
<< "Attempted to split multiperiod histogram workspace with "
<< numPeriods << "periods, aborted." << std::endl;
return;
}
// Y array should be divisible by the number of periods
if (m_workspace->blocksize() % numPeriods != 0) {
g_log.warning()
<< "Attempted to split multiperiod histogram workspace with "
<< m_workspace->blocksize() << "data entries, into " << numPeriods
<< "periods."
" Aborted." << std::endl;
return;
}
WorkspaceGroup_sptr wsGroup(new WorkspaceGroup);
size_t yLength = m_workspace->blocksize() / numPeriods;
size_t xLength = yLength + 1;
size_t numSpectra = m_workspace->getNumberHistograms();
ISISRunLogs monLogCreator(m_workspace->run(), static_cast<int>(numPeriods));
for (size_t i = 0; i < numPeriods; i++) {
// create the period workspace
API::MatrixWorkspace_sptr wsPeriod =
API::WorkspaceFactory::Instance().create(m_workspace, numSpectra,
xLength, yLength);
// assign x values - restart at start for all periods
for (size_t specIndex = 0; specIndex < numSpectra; specIndex++) {
MantidVec &outputVec = wsPeriod->dataX(specIndex);
const MantidVec &inputVec = m_workspace->readX(specIndex);
for (size_t index = 0; index < xLength; index++) {
outputVec[index] = inputVec[index];
}
}
// assign y values - use the values offset by the period number
for (size_t specIndex = 0; specIndex < numSpectra; specIndex++) {
MantidVec &outputVec = wsPeriod->dataY(specIndex);
const MantidVec &inputVec = m_workspace->readY(specIndex);
for (size_t index = 0; index < yLength; index++) {
outputVec[index] = inputVec[(yLength * i) + index];
}
}
// assign E values
for (size_t specIndex = 0; specIndex < numSpectra; specIndex++) {
MantidVec &outputVec = wsPeriod->dataE(specIndex);
const MantidVec &inputVec = m_workspace->readE(specIndex);
for (size_t index = 0; index < yLength; index++) {
outputVec[index] = inputVec[(yLength * i) + index];
}
}
// add period logs
monLogCreator.addPeriodLogs(static_cast<int>(i + 1),
wsPeriod->mutableRun());
// add to workspace group
wsGroup->addWorkspace(wsPeriod);
}
// set the output workspace
this->setProperty("OutputWorkspace", wsGroup);
}