/**
* Handles completion of the algorithm.
*
* @param error If the algorithm failed
*/
void ISISDiagnostics::algorithmComplete(bool error) {
disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(algorithmComplete(bool)));
if (error)
return;
WorkspaceGroup_sptr sliceOutputGroup =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
"IndirectDiagnostics_Workspaces");
if (sliceOutputGroup->size() == 0) {
g_log.warning("No result workspaces, cannot plot preview.");
return;
}
for (size_t i = 0; i < sliceOutputGroup->size(); i++) {
QString wsName =
QString::fromStdString(sliceOutputGroup->getItem(i)->name());
}
// Enable plot and save buttons
m_uiForm.pbSave->setEnabled(true);
m_uiForm.pbPlot->setEnabled(true);
// Update the preview plots
sliceAlgDone(false);
m_batchAlgoRunner->executeBatchAsync();
}
/** Execute the algorithm.
*/
void PolarizationCorrectionFredrikze::exec() {
WorkspaceGroup_sptr inWS = getProperty("InputWorkspace");
const std::string analysisMode = getProperty("PolarizationAnalysis");
const size_t nWorkspaces = inWS->size();
validateInputWorkspace(inWS);
WorkspaceGroup_sptr outWS;
if (analysisMode == pALabel) {
if (nWorkspaces != 4) {
throw std::invalid_argument(
"For PA analysis, input group must have 4 periods.");
}
g_log.notice("PA polarization correction");
outWS = execPA(inWS);
} else if (analysisMode == pNRLabel) {
if (nWorkspaces != 2) {
throw std::invalid_argument(
"For PNR analysis, input group must have 2 periods.");
}
outWS = execPNR(inWS);
g_log.notice("PNR polarization correction");
}
this->setProperty("OutputWorkspace", outWS);
}
/**
* Sum over transmission group workspaces to produce one
* workspace.
* @param transGroup : The transmission group to be processed
* @return A workspace pointer containing the sum of transmission workspaces.
*/
Mantid::API::Workspace_sptr
ReflectometryReductionOneAuto::sumOverTransmissionGroup(
WorkspaceGroup_sptr &transGroup) {
// Handle transmission runs
// we clone the first member of transmission group as to
// avoid addition in place which would affect the original
// workspace member.
//
// We used .release because clone() will return a unique_ptr.
// we need to release the ownership of the pointer so that it
// can be cast into a shared_ptr of type Workspace.
Workspace_sptr transmissionRunSum(transGroup->getItem(0)->clone().release());
// make a variable to store the overall total of the summation
MatrixWorkspace_sptr total;
// set up and initialize plus algorithm.
auto plusAlg = this->createChildAlgorithm("Plus");
plusAlg->setChild(true);
// plusAlg->setRethrows(true);
plusAlg->initialize();
// now accumalate the group members
for (size_t item = 1; item < transGroup->size(); ++item) {
plusAlg->setProperty("LHSWorkspace", transmissionRunSum);
plusAlg->setProperty("RHSWorkspace", transGroup->getItem(item));
plusAlg->setProperty("OutputWorkspace", transmissionRunSum);
plusAlg->execute();
total = plusAlg->getProperty("OutputWorkspace");
}
return total;
}
/**
* Handles completion of the algorithm.
*
* Sets result workspace for Python export and ungroups result WorkspaceGroup.
*
* @param error True if the algorithm was stopped due to error, false otherwise
*/
void ISISEnergyTransfer::algorithmComplete(bool error) {
disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(algorithmComplete(bool)));
if (error)
return;
WorkspaceGroup_sptr energyTransferOutputGroup =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
"IndirectEnergyTransfer_Workspaces");
if (energyTransferOutputGroup->size() == 0)
return;
// Set workspace for Python export as the first result workspace
m_pythonExportWsName = energyTransferOutputGroup->getNames()[0];
m_outputWorkspaces = energyTransferOutputGroup->getNames();
// Ungroup the output workspace
energyTransferOutputGroup->removeAll();
AnalysisDataService::Instance().remove("IndirectEnergyTransfer_Workspaces");
// Enable plotting and saving
m_uiForm.pbPlot->setEnabled(true);
m_uiForm.cbPlotType->setEnabled(true);
m_uiForm.pbSave->setEnabled(true);
m_uiForm.ckSaveAclimax->setEnabled(true);
m_uiForm.ckSaveASCII->setEnabled(true);
m_uiForm.ckSaveDaveGrp->setEnabled(true);
m_uiForm.ckSaveNexus->setEnabled(true);
m_uiForm.ckSaveNXSPE->setEnabled(true);
m_uiForm.ckSaveSPE->setEnabled(true);
}
/**
* Replots the energy mini plot
*/
void ISISCalibration::calPlotEnergy()
{
if ( ! m_uiForm.leRunNo->isValid() )
{
emit showMessageBox("Run number not valid.");
return;
}
QString files = m_uiForm.leRunNo->getFilenames().join(",");
QFileInfo fi(m_uiForm.leRunNo->getFirstFilename());
QString detRange = QString::number(m_dblManager->value(m_properties["ResSpecMin"])) + ","
+ QString::number(m_dblManager->value(m_properties["ResSpecMax"]));
IAlgorithm_sptr reductionAlg = AlgorithmManager::Instance().create("ISISIndirectEnergyTransfer");
reductionAlg->initialize();
reductionAlg->setProperty("Instrument", getInstrumentConfiguration()->getInstrumentName().toStdString());
reductionAlg->setProperty("Analyser", getInstrumentConfiguration()->getAnalyserName().toStdString());
reductionAlg->setProperty("Reflection", getInstrumentConfiguration()->getReflectionName().toStdString());
reductionAlg->setProperty("InputFiles", files.toStdString());
reductionAlg->setProperty("OutputWorkspace", "__IndirectCalibration_reduction");
reductionAlg->setProperty("SpectraRange", detRange.toStdString());
reductionAlg->execute();
if(!reductionAlg->isExecuted())
{
g_log.warning("Could not generate energy preview plot.");
return;
}
WorkspaceGroup_sptr reductionOutputGroup = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>("__IndirectCalibration_reduction");
if(reductionOutputGroup->size() == 0)
{
g_log.warning("No result workspaces, cannot plot energy preview.");
return;
}
MatrixWorkspace_sptr energyWs = boost::dynamic_pointer_cast<MatrixWorkspace>(reductionOutputGroup->getItem(0));
if(!energyWs)
{
g_log.warning("No result workspaces, cannot plot energy preview.");
return;
}
const Mantid::MantidVec & dataX = energyWs->readX(0);
QPair<double, double> range(dataX.front(), dataX.back());
auto resBackground = m_uiForm.ppResolution->getRangeSelector("ResBackground");
setPlotPropertyRange(resBackground, m_properties["ResStart"], m_properties["ResEnd"], range);
m_uiForm.ppResolution->clear();
m_uiForm.ppResolution->addSpectrum("Energy", energyWs, 0);
m_uiForm.ppResolution->resizeX();
calSetDefaultResolution(energyWs);
m_uiForm.ppResolution->replot();
}
/** Execute the algorithm.
*/
void PolarizationCorrection::exec() {
WorkspaceGroup_sptr inWS = getProperty("InputWorkspace");
const std::string analysisMode = getProperty("PolarizationAnalysis");
const size_t nWorkspaces = inWS->size();
validateInputWorkspace(inWS);
Instrument_const_sptr instrument = fetchInstrument(inWS.get());
// Check if we need to fetch polarization parameters from the instrument's
// parameters
std::map<std::string, std::string> loadableProperties;
loadableProperties[crhoLabel()] = "crho";
loadableProperties[cppLabel()] = "cPp";
// In PA mode, we also require cap and calpha
if (analysisMode == pALabel()) {
loadableProperties[cApLabel()] = "cAp";
loadableProperties[cAlphaLabel()] = "calpha";
}
for (auto propName = loadableProperties.begin();
propName != loadableProperties.end(); ++propName) {
Property *prop = getProperty(propName->first);
if (!prop)
continue;
if (prop->isDefault()) {
auto vals = instrument->getStringParameter(propName->second);
if (vals.empty())
throw std::runtime_error(
"Cannot find value for " + propName->first +
" in parameter file. Please specify this property manually.");
prop->setValue(vals[0]);
}
}
WorkspaceGroup_sptr outWS;
if (analysisMode == pALabel()) {
if (nWorkspaces != 4) {
throw std::invalid_argument(
"For PA analysis, input group must have 4 periods.");
}
g_log.notice("PA polarization correction");
outWS = execPA(inWS);
} else if (analysisMode == pNRLabel()) {
if (nWorkspaces != 2) {
throw std::invalid_argument(
"For PNR analysis, input group must have 2 periods.");
}
outWS = execPNR(inWS);
g_log.notice("PNR polarization correction");
}
this->setProperty("OutputWorkspace", outWS);
}
void IqtFit::updatePlot() {
if (!m_ffInputWS) {
g_log.error("No workspace loaded, cannot create preview plot.");
return;
}
int specNo = m_uiForm.spPlotSpectrum->value();
m_uiForm.ppPlot->clear();
m_uiForm.ppPlot->addSpectrum("Sample", m_ffInputWS, specNo);
try {
const QPair<double, double> curveRange =
m_uiForm.ppPlot->getCurveRange("Sample");
const std::pair<double, double> range(curveRange.first, curveRange.second);
m_uiForm.ppPlot->getRangeSelector("FuryFitRange")
->setRange(range.first, range.second);
m_ffRangeManager->setRange(m_properties["StartX"], range.first,
range.second);
m_ffRangeManager->setRange(m_properties["EndX"], range.first, range.second);
setDefaultParameters("Exponential1");
setDefaultParameters("Exponential2");
setDefaultParameters("StretchedExp");
m_uiForm.ppPlot->resizeX();
m_uiForm.ppPlot->setAxisRange(qMakePair(0.0, 1.0), QwtPlot::yLeft);
} catch (std::invalid_argument &exc) {
showMessageBox(exc.what());
}
// If there is a result plot then plot it
if (AnalysisDataService::Instance().doesExist(m_pythonExportWsName)) {
WorkspaceGroup_sptr outputGroup =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
m_pythonExportWsName);
if (specNo >= static_cast<int>(outputGroup->size()))
return;
MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
outputGroup->getItem(specNo));
if (ws) {
if (m_uiForm.ckPlotGuess->isChecked()) {
m_uiForm.ppPlot->removeSpectrum("Guess");
}
m_uiForm.ppPlot->addSpectrum("Fit", ws, 1, Qt::red);
m_uiForm.ppPlot->addSpectrum("Diff", ws, 2, Qt::blue);
}
}
}
/**
* Validate the multiperiods workspace groups. Gives the opportunity to exit
* processing if things don't look right.
* @param vecMultiPeriodGroups : vector of multiperiod groups.
*/
void MultiPeriodGroupWorker::validateMultiPeriodGroupInputs(
const VecWSGroupType &vecMultiPeriodGroups) const {
const size_t multiPeriodGroupsSize = vecMultiPeriodGroups.size();
if (multiPeriodGroupsSize > 0) {
const size_t benchMarkGroupSize = vecMultiPeriodGroups[0]->size();
for (size_t i = 0; i < multiPeriodGroupsSize; ++i) {
WorkspaceGroup_sptr currentGroup = vecMultiPeriodGroups[i];
if (currentGroup->size() != benchMarkGroupSize) {
throw std::runtime_error("Not all the input Multi-period-group input "
"workspaces are the same size.");
}
for (size_t j = 0; j < currentGroup->size(); ++j) {
MatrixWorkspace_const_sptr currentNestedWS =
boost::dynamic_pointer_cast<const MatrixWorkspace>(
currentGroup->getItem(j));
Property *nPeriodsProperty =
currentNestedWS->run().getLogData("nperiods");
size_t nPeriods = std::stoul(nPeriodsProperty->value());
if (nPeriods != benchMarkGroupSize) {
throw std::runtime_error("Missmatch between nperiods log and the "
"number of workspaces in the input group: " +
vecMultiPeriodGroups[i]->getName());
}
Property *currentPeriodProperty =
currentNestedWS->run().getLogData("current_period");
size_t currentPeriod = std::stoul(currentPeriodProperty->value());
if (currentPeriod != (j + 1)) {
throw std::runtime_error("Multiperiod group workspaces must be "
"ordered by current_period. Correct: " +
currentNestedWS->getName());
}
}
}
}
}
/**
* Handles completion of the correction algorithm.
*
* @param error True of the algorithm failed
*/
void CalculatePaalmanPings::absCorComplete(bool error) {
disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(absCorComplete(bool)));
if (error) {
emit showMessageBox("Absorption correction calculation failed.\nSee "
"Results Log for more details.");
return;
}
// Convert the spectrum axis of correction factors to Q
const auto sampleWsName =
m_uiForm.dsSample->getCurrentDataName().toStdString();
MatrixWorkspace_sptr sampleWs =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(sampleWsName);
WorkspaceGroup_sptr corrections =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
m_pythonExportWsName);
for (size_t i = 0; i < corrections->size(); i++) {
MatrixWorkspace_sptr factorWs =
boost::dynamic_pointer_cast<MatrixWorkspace>(corrections->getItem(i));
if (!factorWs || !sampleWs)
continue;
if (getEMode(sampleWs) == "Indirect") {
API::BatchAlgorithmRunner::AlgorithmRuntimeProps convertSpecProps;
IAlgorithm_sptr convertSpecAlgo =
AlgorithmManager::Instance().create("ConvertSpectrumAxis");
convertSpecAlgo->initialize();
convertSpecAlgo->setProperty("InputWorkspace", factorWs);
convertSpecAlgo->setProperty("OutputWorkspace", factorWs->getName());
convertSpecAlgo->setProperty("Target", "ElasticQ");
convertSpecAlgo->setProperty("EMode", "Indirect");
try {
convertSpecAlgo->setProperty("EFixed", getEFixed(factorWs));
} catch (std::runtime_error &) {
}
m_batchAlgoRunner->addAlgorithm(convertSpecAlgo);
}
}
// Run algorithm queue
connect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(postProcessComplete(bool)));
m_batchAlgoRunner->executeBatchAsync();
}
/**
* Handles completion of the algorithm.
*
* Sets result workspace for Python export and ungroups result WorkspaceGroup.
*
* @param error True if the algorithm was stopped due to error, false otherwise
*/
void IndirectConvertToEnergy::algorithmComplete(bool error)
{
disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this, SLOT(algorithmComplete(bool)));
if(error)
return;
WorkspaceGroup_sptr energyTransferOutputGroup = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>("IndirectEnergyTransfer_Workspaces");
if(energyTransferOutputGroup->size() == 0)
return;
// Set workspace for Python export as the first result workspace
m_pythonExportWsName = energyTransferOutputGroup->getNames()[0];
// Ungroup the output workspace
energyTransferOutputGroup->removeAll();
AnalysisDataService::Instance().remove("IndirectEnergyTransfer_Workspaces");
}
/**
* Returns a workspace for the first period as specified using FirstPeriod
* property.
* @param group :: Loaded group of workspaces to use
* @return Workspace for the period
*/
MatrixWorkspace_sptr MuonLoad::getFirstPeriodWS(WorkspaceGroup_sptr group) {
int firstPeriod = getProperty("FirstPeriod");
MatrixWorkspace_sptr resultWS;
if (firstPeriod < 0 || firstPeriod >= static_cast<int>(group->size()))
throw std::invalid_argument(
"Workspace doesn't contain specified first period");
resultWS =
boost::dynamic_pointer_cast<MatrixWorkspace>(group->getItem(firstPeriod));
if (!resultWS)
throw std::invalid_argument(
"First period workspace is not a MatrixWorkspace");
return resultWS;
}
/**
* Remove a workspace group and all its members from the ADS.
* @param name :: A group to remove.
*/
void AnalysisDataServiceImpl::deepRemoveGroup(const std::string &name) {
WorkspaceGroup_sptr group = retrieveWS<WorkspaceGroup>(name);
if (!group) {
throw std::runtime_error("Workspace " + name +
" is not a workspace group.");
}
group->observeADSNotifications(false);
for (size_t i = 0; i < group->size(); ++i) {
auto ws = group->getItem(i);
WorkspaceGroup_sptr gws = boost::dynamic_pointer_cast<WorkspaceGroup>(ws);
if (gws) {
// if a member is a group remove its items as well
deepRemoveGroup(gws->name());
} else {
remove(ws->name());
}
}
remove(name);
}
/**
* Returns a workspace for the second period as specified using SecondPeriod
* property.
* @param group :: Loaded group of workspaces to use
* @return Workspace for the period
*/
MatrixWorkspace_sptr MuonLoad::getSecondPeriodWS(WorkspaceGroup_sptr group) {
int secondPeriod = getProperty("SecondPeriod");
MatrixWorkspace_sptr resultWS;
if (secondPeriod != EMPTY_INT()) {
if (secondPeriod < 0 || secondPeriod >= static_cast<int>(group->size()))
throw std::invalid_argument(
"Workspace doesn't contain specified second period");
resultWS = boost::dynamic_pointer_cast<MatrixWorkspace>(
group->getItem(secondPeriod));
if (!resultWS)
throw std::invalid_argument(
"Second period workspace is not a MatrixWorkspace");
}
return resultWS;
}
/**
* Updates the preview plot when the algorithm is complete.
*
* @param error True if the algorithm was stopped due to error, false otherwise
*/
void ISISDiagnostics::sliceAlgDone(bool error) {
disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(sliceAlgDone(bool)));
if (error)
return;
QStringList filenames = m_uiForm.dsInputFiles->getFilenames();
if (filenames.size() < 1)
return;
WorkspaceGroup_sptr sliceOutputGroup =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
"IndirectDiagnostics_Workspaces");
if (sliceOutputGroup->size() == 0) {
g_log.warning("No result workspaces, cannot plot preview.");
return;
}
MatrixWorkspace_sptr sliceWs = boost::dynamic_pointer_cast<MatrixWorkspace>(
sliceOutputGroup->getItem(0));
if (!sliceWs) {
g_log.warning("No result workspaces, cannot plot preview.");
return;
}
// Set workspace for Python export as the first result workspace
m_pythonExportWsName = sliceWs->getName();
// Plot result spectrum
m_uiForm.ppSlicePreview->clear();
m_uiForm.ppSlicePreview->addSpectrum("Slice", sliceWs, 0);
m_uiForm.ppSlicePreview->resizeX();
// Ungroup the output workspace
sliceOutputGroup->removeAll();
AnalysisDataService::Instance().remove("IndirectDiagnostics_Workspaces");
}
/**
* Updates the preview plot when the algorithm is complete.
*
* @param error True if the algorithm was stopped due to error, false otherwise
*/
void IndirectDiagnostics::sliceAlgDone(bool error)
{
if(error)
return;
QStringList filenames = m_uiForm.dsInputFiles->getFilenames();
if(filenames.size() < 1)
return;
WorkspaceGroup_sptr sliceOutputGroup = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>("IndirectDiagnostics_Workspaces");
if(sliceOutputGroup->size() == 0)
{
g_log.warning("No result workspaces, cannot plot preview.");
return;
}
MatrixWorkspace_sptr sliceWs = boost::dynamic_pointer_cast<MatrixWorkspace>(sliceOutputGroup->getItem(0));
if(!sliceWs)
{
g_log.warning("No result workspaces, cannot plot preview.");
return;
}
// Set workspace for Python export as the first result workspace
m_pythonExportWsName = sliceWs->getName();
// Plot result spectrum
plotMiniPlot(sliceWs, 0, "SlicePreviewPlot", "SlicePreviewCurve");
// Set X range to data range
setXAxisToCurve("SlicePreviewPlot", "SlicePreviewCurve");
m_plots["SlicePreviewPlot"]->replot();
// Ungroup the output workspace
sliceOutputGroup->removeAll();
AnalysisDataService::Instance().remove("IndirectDiagnostics_Workspaces");
}
/**
* Sum transmission workspaces that belong to a workspace group
* @param transGroup : The transmission group containing the transmission runs
* @return :: A workspace pointer containing the sum of transmission workspaces
*/
MatrixWorkspace_sptr ReflectometryReductionOneAuto2::sumTransmissionWorkspaces(
WorkspaceGroup_sptr &transGroup) {
const std::string transSum = "trans_sum";
Workspace_sptr sumWS = transGroup->getItem(0)->clone();
/// For this step to appear in the history of the output workspaces I need to
/// set child to false and work with the ADS
auto plusAlg = createChildAlgorithm("Plus");
plusAlg->setChild(false);
plusAlg->initialize();
for (size_t item = 1; item < transGroup->size(); item++) {
plusAlg->setProperty("LHSWorkspace", sumWS);
plusAlg->setProperty("RHSWorkspace", transGroup->getItem(item));
plusAlg->setProperty("OutputWorkspace", transSum);
plusAlg->execute();
sumWS = AnalysisDataService::Instance().retrieve(transSum);
}
MatrixWorkspace_sptr result =
boost::dynamic_pointer_cast<MatrixWorkspace>(sumWS);
AnalysisDataService::Instance().remove(transSum);
return result;
}
bool ReflectometryReductionOneAuto::processGroups() {
auto group = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
getPropertyValue("InputWorkspace"));
const std::string outputIvsQ = this->getPropertyValue("OutputWorkspace");
const std::string outputIvsLam =
this->getPropertyValue("OutputWorkspaceWavelength");
// Create a copy of ourselves
Algorithm_sptr alg = this->createChildAlgorithm(
this->name(), -1, -1, this->isLogging(), this->version());
alg->setChild(false);
alg->setRethrows(true);
// Copy all the non-workspace properties over
std::vector<Property *> props = this->getProperties();
for (auto prop = props.begin(); prop != props.end(); ++prop) {
if (*prop) {
IWorkspaceProperty *wsProp = dynamic_cast<IWorkspaceProperty *>(*prop);
if (!wsProp)
alg->setPropertyValue((*prop)->name(), (*prop)->value());
}
}
// Check if the transmission runs are groups or not
const std::string firstTrans = this->getPropertyValue("FirstTransmissionRun");
WorkspaceGroup_sptr firstTransG;
if (!firstTrans.empty()) {
auto firstTransWS =
AnalysisDataService::Instance().retrieveWS<Workspace>(firstTrans);
firstTransG = boost::dynamic_pointer_cast<WorkspaceGroup>(firstTransWS);
if (!firstTransG)
alg->setProperty("FirstTransmissionRun", firstTrans);
else if (group->size() != firstTransG->size())
throw std::runtime_error("FirstTransmissionRun WorkspaceGroup must be "
"the same size as the InputWorkspace "
"WorkspaceGroup");
}
const std::string secondTrans =
this->getPropertyValue("SecondTransmissionRun");
WorkspaceGroup_sptr secondTransG;
if (!secondTrans.empty()) {
auto secondTransWS =
AnalysisDataService::Instance().retrieveWS<Workspace>(secondTrans);
secondTransG = boost::dynamic_pointer_cast<WorkspaceGroup>(secondTransWS);
if (!secondTransG)
alg->setProperty("SecondTransmissionRun", secondTrans);
else if (group->size() != secondTransG->size())
throw std::runtime_error("SecondTransmissionRun WorkspaceGroup must be "
"the same size as the InputWorkspace "
"WorkspaceGroup");
}
std::vector<std::string> IvsQGroup, IvsLamGroup;
// Execute algorithm over each group member (or period, if this is
// multiperiod)
size_t numMembers = group->size();
for (size_t i = 0; i < numMembers; ++i) {
const std::string IvsQName =
outputIvsQ + "_" + boost::lexical_cast<std::string>(i + 1);
const std::string IvsLamName =
outputIvsLam + "_" + boost::lexical_cast<std::string>(i + 1);
alg->setProperty("InputWorkspace", group->getItem(i)->name());
alg->setProperty("OutputWorkspace", IvsQName);
alg->setProperty("OutputWorkspaceWavelength", IvsLamName);
// Handle transmission runs
if (firstTransG)
alg->setProperty("FirstTransmissionRun", firstTransG->getItem(i)->name());
if (secondTransG)
alg->setProperty("SecondTransmissionRun",
secondTransG->getItem(i)->name());
alg->execute();
IvsQGroup.push_back(IvsQName);
IvsLamGroup.push_back(IvsLamName);
// We use the first group member for our thetaout value
if (i == 0)
this->setPropertyValue("ThetaOut", alg->getPropertyValue("ThetaOut"));
}
// Group the IvsQ and IvsLam workspaces
Algorithm_sptr groupAlg = this->createChildAlgorithm("GroupWorkspaces");
groupAlg->setChild(false);
groupAlg->setRethrows(true);
groupAlg->setProperty("InputWorkspaces", IvsLamGroup);
groupAlg->setProperty("OutputWorkspace", outputIvsLam);
groupAlg->execute();
groupAlg->setProperty("InputWorkspaces", IvsQGroup);
groupAlg->setProperty("OutputWorkspace", outputIvsQ);
groupAlg->execute();
// If this is a multiperiod workspace and we have polarization corrections
// enabled
if (this->getPropertyValue("PolarizationAnalysis") !=
noPolarizationCorrectionMode()) {
if (group->isMultiperiod()) {
// Perform polarization correction over the IvsLam group
Algorithm_sptr polAlg =
this->createChildAlgorithm("PolarizationCorrection");
polAlg->setChild(false);
polAlg->setRethrows(true);
polAlg->setProperty("InputWorkspace", outputIvsLam);
polAlg->setProperty("OutputWorkspace", outputIvsLam);
polAlg->setProperty("PolarizationAnalysis",
this->getPropertyValue("PolarizationAnalysis"));
polAlg->setProperty("CPp", this->getPropertyValue(cppLabel()));
polAlg->setProperty("CRho", this->getPropertyValue(crhoLabel()));
polAlg->setProperty("CAp", this->getPropertyValue(cApLabel()));
polAlg->setProperty("CAlpha", this->getPropertyValue(cAlphaLabel()));
polAlg->execute();
// Now we've overwritten the IvsLam workspaces, we'll need to recalculate
// the IvsQ ones
alg->setProperty("FirstTransmissionRun", "");
alg->setProperty("SecondTransmissionRun", "");
for (size_t i = 0; i < numMembers; ++i) {
const std::string IvsQName =
outputIvsQ + "_" + boost::lexical_cast<std::string>(i + 1);
const std::string IvsLamName =
outputIvsLam + "_" + boost::lexical_cast<std::string>(i + 1);
alg->setProperty("InputWorkspace", IvsLamName);
alg->setProperty("OutputWorkspace", IvsQName);
alg->setProperty("OutputWorkspaceWavelength", IvsLamName);
alg->execute();
}
} else {
g_log.warning("Polarization corrections can only be performed on "
"multiperiod workspaces.");
}
}
// We finished successfully
this->setPropertyValue("OutputWorkspace", outputIvsQ);
this->setPropertyValue("OutputWorkspaceWavelength", outputIvsLam);
setExecuted(true);
notificationCenter().postNotification(
new FinishedNotification(this, isExecuted()));
return true;
}
bool ApplyPaalmanPings::validate() {
UserInputValidator uiv;
uiv.checkDataSelectorIsValid("Sample", m_uiForm.dsSample);
MatrixWorkspace_sptr sampleWs;
bool useCan = m_uiForm.ckUseCan->isChecked();
bool useCorrections = m_uiForm.ckUseCorrections->isChecked();
if (!(useCan || useCorrections))
uiv.addErrorMessage("Must use either container subtraction or corrections");
if (useCan) {
uiv.checkDataSelectorIsValid("Container", m_uiForm.dsContainer);
// Check can and sample workspaces are the same "type" (reduced or S(Q, w))
QString sample = m_uiForm.dsSample->getCurrentDataName();
QString sampleType =
sample.right(sample.length() - sample.lastIndexOf("_"));
QString container = m_uiForm.dsContainer->getCurrentDataName();
QString containerType =
container.right(container.length() - container.lastIndexOf("_"));
g_log.debug() << "Sample type is: " << sampleType.toStdString() << '\n';
g_log.debug() << "Can type is: " << containerType.toStdString() << '\n';
if (containerType != sampleType)
uiv.addErrorMessage(
"Sample and can workspaces must contain the same type of data.");
}
if (useCorrections) {
if (m_uiForm.dsCorrections->getCurrentDataName().compare("") == 0) {
uiv.addErrorMessage(
"Use Correction must contain a corrections file or workspace.");
} else {
QString correctionsWsName = m_uiForm.dsCorrections->getCurrentDataName();
WorkspaceGroup_sptr corrections =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
correctionsWsName.toStdString());
for (size_t i = 0; i < corrections->size(); i++) {
// Check it is a MatrixWorkspace
MatrixWorkspace_sptr factorWs =
boost::dynamic_pointer_cast<MatrixWorkspace>(
corrections->getItem(i));
if (!factorWs) {
QString msg = "Correction factor workspace " + QString::number(i) +
" is not a MatrixWorkspace";
uiv.addErrorMessage(msg);
continue;
}
// Check X unit is wavelength
Mantid::Kernel::Unit_sptr xUnit = factorWs->getAxis(0)->unit();
if (xUnit->caption() != "Wavelength") {
QString msg = "Correction factor workspace " +
QString::fromStdString(factorWs->name()) +
" is not in wavelength";
uiv.addErrorMessage(msg);
}
}
}
}
// Show errors if there are any
if (!uiv.isAllInputValid())
emit showMessageBox(uiv.generateErrorMessage());
return uiv.isAllInputValid();
}
void ApplyPaalmanPings::run() {
// Create / Initialize algorithm
API::BatchAlgorithmRunner::AlgorithmRuntimeProps absCorProps;
IAlgorithm_sptr applyCorrAlg =
AlgorithmManager::Instance().create("ApplyPaalmanPingsCorrection");
applyCorrAlg->initialize();
// get Sample Workspace
MatrixWorkspace_sptr sampleWs =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
m_sampleWorkspaceName);
m_originalSampleUnits = sampleWs->getAxis(0)->unit()->unitID();
// If not in wavelength then do conversion
if (m_originalSampleUnits != "Wavelength") {
g_log.information(
"Sample workspace not in wavelength, need to convert to continue.");
absCorProps["SampleWorkspace"] =
addConvertUnitsStep(sampleWs, "Wavelength");
} else {
absCorProps["SampleWorkspace"] = m_sampleWorkspaceName;
}
const bool useCan = m_uiForm.ckUseCan->isChecked();
const bool useCorrections = m_uiForm.ckUseCorrections->isChecked();
// Get Can and Clone
MatrixWorkspace_sptr canClone;
if (useCan) {
const auto canName =
m_uiForm.dsContainer->getCurrentDataName().toStdString();
const auto cloneName = "__algorithm_can";
IAlgorithm_sptr clone =
AlgorithmManager::Instance().create("CloneWorkspace");
clone->initialize();
clone->setProperty("InputWorkspace", canName);
clone->setProperty("Outputworkspace", cloneName);
clone->execute();
const bool useShift = m_uiForm.ckShiftCan->isChecked();
if (useShift) {
IAlgorithm_sptr scaleX = AlgorithmManager::Instance().create("ScaleX");
scaleX->initialize();
scaleX->setLogging(false);
scaleX->setProperty("InputWorkspace", cloneName);
scaleX->setProperty("OutputWorkspace", cloneName);
scaleX->setProperty("Factor", m_uiForm.spCanShift->value());
scaleX->setProperty("Operation", "Add");
scaleX->execute();
IAlgorithm_sptr rebin =
AlgorithmManager::Instance().create("RebinToWorkspace");
rebin->initialize();
rebin->setLogging(false);
rebin->setProperty("WorkspaceToRebin", cloneName);
rebin->setProperty("WorkspaceToMatch", m_sampleWorkspaceName);
rebin->setProperty("OutputWorkspace", cloneName);
rebin->execute();
}
canClone =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(cloneName);
// Check for same binning across sample and container
if (!checkWorkspaceBinningMatches(sampleWs, canClone)) {
const char *text =
"Binning on sample and container does not match."
"Would you like to rebin the container to match the sample?";
int result = QMessageBox::question(NULL, tr("Rebin sample?"), tr(text),
QMessageBox::Yes, QMessageBox::No,
QMessageBox::NoButton);
if (result == QMessageBox::Yes) {
addRebinStep(QString::fromStdString(canName),
QString::fromStdString(m_sampleWorkspaceName));
} else {
m_batchAlgoRunner->clearQueue();
g_log.error("Cannot apply absorption corrections "
"using a sample and "
"container with different binning.");
return;
}
}
// If not in wavelength then do conversion
std::string originalCanUnits = canClone->getAxis(0)->unit()->unitID();
if (originalCanUnits != "Wavelength") {
g_log.information("Container workspace not in wavelength, need to "
"convert to continue.");
absCorProps["CanWorkspace"] = addConvertUnitsStep(canClone, "Wavelength");
} else {
absCorProps["CanWorkspace"] = cloneName;
}
const bool useCanScale = m_uiForm.ckScaleCan->isChecked();
if (useCanScale) {
const double canScaleFactor = m_uiForm.spCanScale->value();
applyCorrAlg->setProperty("CanScaleFactor", canScaleFactor);
}
}
if (useCorrections) {
QString correctionsWsName = m_uiForm.dsCorrections->getCurrentDataName();
WorkspaceGroup_sptr corrections =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
correctionsWsName.toStdString());
bool interpolateAll = false;
for (size_t i = 0; i < corrections->size(); i++) {
MatrixWorkspace_sptr factorWs =
boost::dynamic_pointer_cast<MatrixWorkspace>(corrections->getItem(i));
// Check for matching binning
if (sampleWs && (sampleWs->blocksize() != factorWs->blocksize())) {
int result;
if (interpolateAll) {
result = QMessageBox::Yes;
} else {
std::string text = "Number of bins on sample and " +
factorWs->name() + " workspace does not match.\n" +
"Would you like to interpolate this workspace to "
"match the sample?";
result = QMessageBox::question(
NULL, tr("Interpolate corrections?"), tr(text.c_str()),
QMessageBox::YesToAll, QMessageBox::Yes, QMessageBox::No);
}
switch (result) {
case QMessageBox::YesToAll:
interpolateAll = true;
// fall through
case QMessageBox::Yes:
addInterpolationStep(factorWs, absCorProps["SampleWorkspace"]);
break;
default:
m_batchAlgoRunner->clearQueue();
g_log.error("ApplyPaalmanPings cannot run with corrections that do "
"not match sample binning.");
return;
}
}
}
applyCorrAlg->setProperty("CorrectionsWorkspace",
correctionsWsName.toStdString());
}
// Generate output workspace name
auto QStrSampleWsName = QString::fromStdString(m_sampleWorkspaceName);
int nameCutIndex = QStrSampleWsName.lastIndexOf("_");
if (nameCutIndex == -1)
nameCutIndex = QStrSampleWsName.length();
QString correctionType;
switch (m_uiForm.cbGeometry->currentIndex()) {
case 0:
correctionType = "flt";
break;
case 1:
correctionType = "cyl";
break;
case 2:
correctionType = "anl";
break;
}
QString outputWsName = QStrSampleWsName.left(nameCutIndex);
// Using corrections
if (m_uiForm.ckUseCorrections->isChecked()) {
outputWsName += "_" + correctionType + "_Corrected";
} else {
outputWsName += "_Subtracted";
}
// Using container
if (m_uiForm.ckUseCan->isChecked()) {
const auto canName =
m_uiForm.dsContainer->getCurrentDataName().toStdString();
MatrixWorkspace_sptr containerWs =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(canName);
auto run = containerWs->run();
if (run.hasProperty("run_number")) {
outputWsName +=
"_" + QString::fromStdString(run.getProperty("run_number")->value());
} else {
auto canCutIndex = QString::fromStdString(canName).indexOf("_");
outputWsName += "_" + QString::fromStdString(canName).left(canCutIndex);
}
}
outputWsName += "_red";
applyCorrAlg->setProperty("OutputWorkspace", outputWsName.toStdString());
// Add corrections algorithm to queue
m_batchAlgoRunner->addAlgorithm(applyCorrAlg, absCorProps);
// Run algorithm queue
connect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(absCorComplete(bool)));
m_batchAlgoRunner->executeBatchAsync();
// Set the result workspace for Python script export
m_pythonExportWsName = outputWsName.toStdString();
// m_containerWorkspaceName = m_uiForm.dsContainer->getCurrentDataName();
// updateContainer();
}
bool ReflectometryReductionOneAuto::processGroups() {
// isPolarizationCorrectionOn is used to decide whether
// we should process our Transmission WorkspaceGroup members
// as individuals (not multiperiod) when PolarizationCorrection is off,
// or sum over all of the workspaces in the group
// and used that sum as our TransmissionWorkspace when PolarizationCorrection
// is on.
const bool isPolarizationCorrectionOn =
this->getPropertyValue("PolarizationAnalysis") !=
noPolarizationCorrectionMode();
// Get our input workspace group
auto group = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
getPropertyValue("InputWorkspace"));
// Get name of IvsQ workspace
const std::string outputIvsQ = this->getPropertyValue("OutputWorkspace");
// Get name of IvsLam workspace
const std::string outputIvsLam =
this->getPropertyValue("OutputWorkspaceWavelength");
// Create a copy of ourselves
Algorithm_sptr alg = this->createChildAlgorithm(
this->name(), -1, -1, this->isLogging(), this->version());
alg->setChild(false);
alg->setRethrows(true);
// Copy all the non-workspace properties over
std::vector<Property *> props = this->getProperties();
for (auto &prop : props) {
if (prop) {
IWorkspaceProperty *wsProp = dynamic_cast<IWorkspaceProperty *>(prop);
if (!wsProp)
alg->setPropertyValue(prop->name(), prop->value());
}
}
// Check if the transmission runs are groups or not
const std::string firstTrans = this->getPropertyValue("FirstTransmissionRun");
WorkspaceGroup_sptr firstTransG;
if (!firstTrans.empty()) {
auto firstTransWS =
AnalysisDataService::Instance().retrieveWS<Workspace>(firstTrans);
firstTransG = boost::dynamic_pointer_cast<WorkspaceGroup>(firstTransWS);
if (!firstTransG) {
// we only have one transmission workspace, so we use it as it is.
alg->setProperty("FirstTransmissionRun", firstTrans);
} else if (group->size() != firstTransG->size() &&
!isPolarizationCorrectionOn) {
// if they are not the same size then we cannot associate a transmission
// group workspace member with every input group workpspace member.
throw std::runtime_error("FirstTransmissionRun WorkspaceGroup must be "
"the same size as the InputWorkspace "
"WorkspaceGroup");
}
}
const std::string secondTrans =
this->getPropertyValue("SecondTransmissionRun");
WorkspaceGroup_sptr secondTransG;
if (!secondTrans.empty()) {
auto secondTransWS =
AnalysisDataService::Instance().retrieveWS<Workspace>(secondTrans);
secondTransG = boost::dynamic_pointer_cast<WorkspaceGroup>(secondTransWS);
if (!secondTransG)
// we only have one transmission workspace, so we use it as it is.
alg->setProperty("SecondTransmissionRun", secondTrans);
else if (group->size() != secondTransG->size() &&
!isPolarizationCorrectionOn) {
// if they are not the same size then we cannot associate a transmission
// group workspace member with every input group workpspace member.
throw std::runtime_error("SecondTransmissionRun WorkspaceGroup must be "
"the same size as the InputWorkspace "
"WorkspaceGroup");
}
}
std::vector<std::string> IvsQGroup, IvsLamGroup;
// Execute algorithm over each group member (or period, if this is
// multiperiod)
size_t numMembers = group->size();
for (size_t i = 0; i < numMembers; ++i) {
const std::string IvsQName =
outputIvsQ + "_" + boost::lexical_cast<std::string>(i + 1);
const std::string IvsLamName =
outputIvsLam + "_" + boost::lexical_cast<std::string>(i + 1);
// If our transmission run is a group and PolarizationCorrection is on
// then we sum our transmission group members.
//
// This is done inside of the for loop to avoid the wrong workspace being
// used when these arguments are passed through to the exec() method.
// If this is not set in the loop, exec() will fetch the first workspace
// from the specified Transmission Group workspace that the user entered.
if (firstTransG && isPolarizationCorrectionOn) {
auto firstTransmissionSum = sumOverTransmissionGroup(firstTransG);
alg->setProperty("FirstTransmissionRun", firstTransmissionSum);
}
if (secondTransG && isPolarizationCorrectionOn) {
auto secondTransmissionSum = sumOverTransmissionGroup(secondTransG);
alg->setProperty("SecondTransmissionRun", secondTransmissionSum);
}
// Otherwise, if polarization correction is off, we process them
// using one transmission group member at a time.
if (firstTransG && !isPolarizationCorrectionOn) // polarization off
alg->setProperty("FirstTransmissionRun", firstTransG->getItem(i)->name());
if (secondTransG && !isPolarizationCorrectionOn) // polarization off
alg->setProperty("SecondTransmissionRun",
secondTransG->getItem(i)->name());
alg->setProperty("InputWorkspace", group->getItem(i)->name());
alg->setProperty("OutputWorkspace", IvsQName);
alg->setProperty("OutputWorkspaceWavelength", IvsLamName);
alg->execute();
MatrixWorkspace_sptr tempFirstTransWS =
alg->getProperty("FirstTransmissionRun");
IvsQGroup.push_back(IvsQName);
IvsLamGroup.push_back(IvsLamName);
// We use the first group member for our thetaout value
if (i == 0)
this->setPropertyValue("ThetaOut", alg->getPropertyValue("ThetaOut"));
}
// Group the IvsQ and IvsLam workspaces
Algorithm_sptr groupAlg = this->createChildAlgorithm("GroupWorkspaces");
groupAlg->setChild(false);
groupAlg->setRethrows(true);
groupAlg->setProperty("InputWorkspaces", IvsLamGroup);
groupAlg->setProperty("OutputWorkspace", outputIvsLam);
groupAlg->execute();
groupAlg->setProperty("InputWorkspaces", IvsQGroup);
groupAlg->setProperty("OutputWorkspace", outputIvsQ);
groupAlg->execute();
// If this is a multiperiod workspace and we have polarization corrections
// enabled
if (isPolarizationCorrectionOn) {
if (group->isMultiperiod()) {
// Perform polarization correction over the IvsLam group
Algorithm_sptr polAlg =
this->createChildAlgorithm("PolarizationCorrection");
polAlg->setChild(false);
polAlg->setRethrows(true);
polAlg->setProperty("InputWorkspace", outputIvsLam);
polAlg->setProperty("OutputWorkspace", outputIvsLam);
polAlg->setProperty("PolarizationAnalysis",
this->getPropertyValue("PolarizationAnalysis"));
polAlg->setProperty("CPp", this->getPropertyValue(cppLabel()));
polAlg->setProperty("CRho", this->getPropertyValue(crhoLabel()));
polAlg->setProperty("CAp", this->getPropertyValue(cApLabel()));
polAlg->setProperty("CAlpha", this->getPropertyValue(cAlphaLabel()));
polAlg->execute();
// Now we've overwritten the IvsLam workspaces, we'll need to recalculate
// the IvsQ ones
alg->setProperty("FirstTransmissionRun", "");
alg->setProperty("SecondTransmissionRun", "");
for (size_t i = 0; i < numMembers; ++i) {
const std::string IvsQName =
outputIvsQ + "_" + boost::lexical_cast<std::string>(i + 1);
const std::string IvsLamName =
outputIvsLam + "_" + boost::lexical_cast<std::string>(i + 1);
alg->setProperty("InputWorkspace", IvsLamName);
alg->setProperty("OutputWorkspace", IvsQName);
alg->setProperty("CorrectionAlgorithm", "None");
alg->setProperty("OutputWorkspaceWavelength", IvsLamName);
alg->execute();
}
} else {
g_log.warning("Polarization corrections can only be performed on "
"multiperiod workspaces.");
}
}
// We finished successfully
this->setPropertyValue("OutputWorkspace", outputIvsQ);
this->setPropertyValue("OutputWorkspaceWavelength", outputIvsLam);
setExecuted(true);
notificationCenter().postNotification(
new FinishedNotification(this, isExecuted()));
return true;
}
