/**
* This function: 1. loads the instrument and gets the value of deltaE-mode parameter
* 2. Based on this value, makes the necessary changes to the form setup (direct or indirect).
* @param name :: name of the instrument from the QComboBox
*/
void IndirectDataReduction::instrumentSelectChanged(const QString& name)
{
QString defFile = (Mantid::API::ExperimentInfo::getInstrumentFilename(name.toStdString())).c_str();
if((defFile == "") || !m_uiForm.cbInst->isVisible())
{
g_log.error("Instument loading failed!");
m_uiForm.cbInst->setEnabled(true);
m_uiForm.pbRun->setEnabled(true);
return;
}
QString outWS = "__empty_" + m_uiForm.cbInst->currentText();
m_curInterfaceSetup = name;
//Load the empty instrument into the workspace __empty_[name]
//This used to be done in Python
Mantid::API::IAlgorithm_sptr instLoader = Mantid::API::AlgorithmManager::Instance().create("LoadEmptyInstrument", -1);
instLoader->initialize();
instLoader->setProperty("Filename", defFile.toStdString());
instLoader->setProperty("OutputWorkspace", outWS.toStdString());
//Ensure no other algorithm is running
m_algRunner->cancelRunningAlgorithm();
m_algRunner->startAlgorithm(instLoader);
}
/**
* Get the viewable peaks. Essentially copied from the slice viewer.
* @returns A vector indicating which of the peaks are viewable.
*/
std::vector<bool> ConcretePeaksPresenterVsi::getViewablePeaks() const {
// Need to apply a transform.
// Don't bother to find peaks in the region if there are no peaks to find.
Mantid::API::ITableWorkspace_sptr outTable;
if (this->m_peaksWorkspace->getNumberPeaks() >= 1) {
double effectiveRadius = 1e-2;
std::string viewable = m_viewableRegion->toExtentsAsString();
Mantid::API::IPeaksWorkspace_sptr peaksWS = m_peaksWorkspace;
Mantid::API::IAlgorithm_sptr alg =
Mantid::API::AlgorithmManager::Instance().create("PeaksInRegion");
alg->setChild(true);
alg->setRethrows(true);
alg->initialize();
alg->setProperty("InputWorkspace", peaksWS);
alg->setProperty("OutputWorkspace", peaksWS->name() + "_peaks_in_region");
alg->setProperty("Extents", viewable);
alg->setProperty("CheckPeakExtents", true);
alg->setProperty("PeakRadius", effectiveRadius);
alg->setPropertyValue("CoordinateFrame", m_frame);
alg->execute();
outTable = alg->getProperty("OutputWorkspace");
std::vector<bool> viewablePeaks(outTable->rowCount());
for (size_t i = 0; i < outTable->rowCount(); ++i) {
viewablePeaks[i] = outTable->cell<Mantid::API::Boolean>(i, 1);
}
m_viewablePeaks = viewablePeaks;
} else {
// No peaks will be viewable
m_viewablePeaks = std::vector<bool>();
}
return m_viewablePeaks;
}
/// execute getdatafIles algorithm
ITableWorkspace_sptr ICatInvestigation::executeGetdataFiles()
{
QString algName("CatalogGetDataFiles");
const int version=1;
Mantid::API::ITableWorkspace_sptr ws_sptr;
Mantid::API::IAlgorithm_sptr alg;
try
{
alg = Mantid::API::AlgorithmManager::Instance().create(algName.toStdString(),version);
}
catch(...)
{
throw std::runtime_error("Error when loading the data files associated to the selected investigation ");
}
try
{
alg->setProperty("InvestigationId",m_invstId);
alg->setProperty("FilterLogFiles",isDataFilesChecked());
alg->setPropertyValue("OutputWorkspace","datafiles");
}
catch(std::invalid_argument& e)
{
emit error(e.what());
return ws_sptr;
}
catch (Mantid::Kernel::Exception::NotFoundError& e)
{
emit error(e.what());
return ws_sptr;
}
try
{
Poco::ActiveResult<bool> result(alg->executeAsync());
while( !result.available() )
{
QCoreApplication::processEvents();
}
}
catch(...)
{
return ws_sptr;
}
if(AnalysisDataService::Instance().doesExist("datafiles"))
{
ws_sptr = boost::dynamic_pointer_cast<Mantid::API::ITableWorkspace>
(AnalysisDataService::Instance().retrieve("datafiles"));
}
return ws_sptr;
}
void WorkspacePresenter::ungroupWorkspaces() {
auto view = lockView();
auto selected = view->getSelectedWorkspaceNames();
if (selected.size() == 0) {
view->showCriticalUserMessage("Error Ungrouping Workspaces",
"Select a group workspace to Ungroup.");
return;
}
try {
// workspace name
auto wsname = selected[0];
std::string algName("UnGroupWorkspace");
Mantid::API::IAlgorithm_sptr alg =
Mantid::API::AlgorithmManager::Instance().create(algName, -1);
alg->initialize();
alg->setProperty("InputWorkspace", wsname);
// execute the algorithm
bool bStatus = alg->execute();
if (!bStatus) {
view->showCriticalUserMessage("MantidPlot - Algorithm error",
" Error in UnGroupWorkspace algorithm");
}
} catch (...) {
view->showCriticalUserMessage("MantidPlot - Algorithm error",
" Error in UnGroupWorkspace algorithm");
}
}
/**
@param inname Name of workspace containing peaks
@param params optimized cell parameters
@param out residuals from optimization
*/
void OptimizeLatticeForCellType::optLattice(std::string inname,
std::vector<double> ¶ms,
double *out) {
PeaksWorkspace_sptr ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
AnalysisDataService::Instance().retrieve(inname));
const std::vector<Peak> &peaks = ws->getPeaks();
size_t n_peaks = ws->getNumberPeaks();
std::vector<V3D> q_vector;
std::vector<V3D> hkl_vector;
for (size_t i = 0; i < params.size(); i++)
params[i] = std::abs(params[i]);
for (size_t i = 0; i < n_peaks; i++) {
q_vector.push_back(peaks[i].getQSampleFrame());
hkl_vector.push_back(peaks[i].getHKL());
}
Mantid::API::IAlgorithm_sptr alg = createChildAlgorithm("CalculateUMatrix");
alg->setPropertyValue("PeaksWorkspace", inname);
alg->setProperty("a", params[0]);
alg->setProperty("b", params[1]);
alg->setProperty("c", params[2]);
alg->setProperty("alpha", params[3]);
alg->setProperty("beta", params[4]);
alg->setProperty("gamma", params[5]);
alg->executeAsChildAlg();
ws = alg->getProperty("PeaksWorkspace");
OrientedLattice latt = ws->mutableSample().getOrientedLattice();
DblMatrix UB = latt.getUB();
DblMatrix A = aMatrix(params);
DblMatrix Bc = A;
Bc.Invert();
DblMatrix U1_B1 = UB * A;
OrientedLattice o_lattice;
o_lattice.setUB(U1_B1);
DblMatrix U1 = o_lattice.getU();
DblMatrix U1_Bc = U1 * Bc;
for (size_t i = 0; i < hkl_vector.size(); i++) {
V3D error = U1_Bc * hkl_vector[i] - q_vector[i] / (2.0 * M_PI);
out[i] = error.norm2();
}
return;
}
void ConvFit::setupFit(Mantid::API::IAlgorithm_sptr fitAlgorithm) {
if (boolSettingValue("UseTempCorrection"))
m_convFittingModel->setTemperature(doubleSettingValue("TempCorrection"));
else
m_convFittingModel->setTemperature(boost::none);
fitAlgorithm->setProperty("ExtractMembers",
boolSettingValue("ExtractMembers"));
IndirectFitAnalysisTab::setupFit(fitAlgorithm);
}
/**
* Set the "search" properties to their related input fields.
* @param catalogAlgorithm :: Algorithm to set the search properties for.
* @param userInputFields :: The search properties to set against the algorithm.
*/
void CatalogHelper::setSearchProperties(const Mantid::API::IAlgorithm_sptr &catalogAlgorithm,
const std::map<std::string, std::string> &userInputFields)
{
// This will be the workspace where the content of the search result is output to.
catalogAlgorithm->setProperty("OutputWorkspace", "__searchResults");
// Iterate over the provided map of user input fields. For each field that isn't empty (e.g. a value was input by the user)
// then we will set the algorithm property with the key and value of that specific value.
for (auto it = userInputFields.begin(); it != userInputFields.end(); it++)
{
std::string value = it->second;
// If the user has input any search terms.
if (!value.empty())
{
// Set the property that the search algorithm uses to: (key => FieldName, value => FieldValue) (e.g., (Keywords, bob))
catalogAlgorithm->setProperty(it->first, value);
}
}
}
/**
* Sorts the peak workspace by a specified column name in ascending or
* descending order.
* @param byColumnName The column by which the workspace is to be sorted.
* @param ascending If the workspace is to be sorted in a ascending or
* descending manner.
*/
void ConcretePeaksPresenterVsi::sortPeaksWorkspace(
const std::string &byColumnName, const bool ascending) {
Mantid::API::IPeaksWorkspace_sptr peaksWS =
boost::const_pointer_cast<Mantid::API::IPeaksWorkspace>(
this->m_peaksWorkspace);
// Sort the Peaks in-place.
Mantid::API::IAlgorithm_sptr alg =
Mantid::API::AlgorithmManager::Instance().create("SortPeaksWorkspace");
alg->setChild(true);
alg->setRethrows(true);
alg->initialize();
alg->setProperty("InputWorkspace", peaksWS);
alg->setPropertyValue("OutputWorkspace", "SortedPeaksWorkspace");
alg->setProperty("OutputWorkspace", peaksWS);
alg->setProperty("SortAscending", ascending);
alg->setPropertyValue("ColumnNameToSortBy", byColumnName);
alg->execute();
}
std::vector<size_t>
ConcretePeaksPresenter::findVisiblePeakIndexes(const PeakBoundingBox &box) {
std::vector<size_t> indexes;
// Don't bother to find peaks in the region if there are no peaks to find.
if (this->m_peaksWS->getNumberPeaks() >= 1) {
double radius =
m_viewPeaks
->getRadius(); // Effective radius of each peak representation.
Mantid::API::IPeaksWorkspace_sptr peaksWS =
boost::const_pointer_cast<Mantid::API::IPeaksWorkspace>(
this->m_peaksWS);
PeakBoundingBox transformedViewableRegion = box.makeSliceBox(radius);
transformedViewableRegion.transformBox(m_transform);
Mantid::API::IAlgorithm_sptr alg =
AlgorithmManager::Instance().create("PeaksInRegion");
alg->setChild(true);
alg->setRethrows(true);
alg->initialize();
alg->setProperty("InputWorkspace", peaksWS);
alg->setProperty("OutputWorkspace", peaksWS->name() + "_peaks_in_region");
alg->setProperty("Extents", transformedViewableRegion.toExtents());
alg->setProperty("CheckPeakExtents", false); // consider all peaks as points
alg->setProperty("PeakRadius", radius);
alg->setPropertyValue("CoordinateFrame", m_transform->getFriendlyName());
alg->execute();
ITableWorkspace_sptr outTable = alg->getProperty("OutputWorkspace");
for (size_t i = 0; i < outTable->rowCount(); ++i) {
const bool insideRegion = outTable->cell<Boolean>(i, 1);
if (insideRegion) {
indexes.push_back(i);
}
}
}
return indexes;
}
bool ConcretePeaksPresenter::addPeakAt(double plotCoordsPointX,
double plotCoordsPointY) {
V3D plotCoordsPoint(plotCoordsPointX, plotCoordsPointY,
m_slicePoint.slicePoint());
V3D hkl = m_transform->transformBack(plotCoordsPoint);
Mantid::API::IPeaksWorkspace_sptr peaksWS =
boost::const_pointer_cast<Mantid::API::IPeaksWorkspace>(this->m_peaksWS);
Mantid::API::IAlgorithm_sptr alg =
AlgorithmManager::Instance().create("AddPeakHKL");
alg->setChild(true);
alg->setRethrows(true);
alg->initialize();
alg->setProperty("Workspace", peaksWS);
alg->setProperty("HKL", std::vector<double>(hkl));
// Execute the algorithm
try {
alg->execute();
} catch (...) {
g_log.warning("ConcretePeaksPresenter: Could not add the peak. Make sure "
"that it is added within a valid workspace region");
}
// Reproduce the views. Proxy representations recreated for all peaks.
this->produceViews();
// Refind visible peaks and Set the proxy representations to be visible or
// not.
doFindPeaksInRegion();
// Upstream controls need to be regenerated.
this->informOwnerUpdate();
return alg->isExecuted();
}
void ConcretePeaksPresenter::sortPeaksWorkspace(const std::string &byColumnName,
const bool ascending) {
Mantid::API::IPeaksWorkspace_sptr peaksWS =
boost::const_pointer_cast<Mantid::API::IPeaksWorkspace>(this->m_peaksWS);
// Sort the Peaks in-place.
Mantid::API::IAlgorithm_sptr alg =
AlgorithmManager::Instance().create("SortPeaksWorkspace");
alg->setChild(true);
alg->setRethrows(true);
alg->initialize();
alg->setProperty("InputWorkspace", peaksWS);
alg->setPropertyValue("OutputWorkspace", "SortedPeaksWorkspace");
alg->setProperty("OutputWorkspace", peaksWS);
alg->setProperty("SortAscending", ascending);
alg->setPropertyValue("ColumnNameToSortBy", byColumnName);
alg->execute();
// Reproduce the views.
this->produceViews();
// Give the new views the current slice point.
m_viewPeaks->setSlicePoint(this->m_slicePoint.slicePoint(), m_viewablePeaks);
}
bool ConcretePeaksPresenter::deletePeaksIn(PeakBoundingBox box) {
Left left(box.left());
Right right(box.right());
Bottom bottom(box.bottom());
Top top(box.top());
SlicePoint slicePoint(box.slicePoint());
if (slicePoint() < 0) { // indicates that it should not be used.
slicePoint = SlicePoint(m_slicePoint.slicePoint());
}
PeakBoundingBox accurateBox(
left, right, top, bottom,
slicePoint /*Use the current slice position, previously unknown.*/);
// Tranform box from plot coordinates into orderd HKL, Qx,Qy,Qz etc, then find
// the visible peaks.
std::vector<size_t> deletionIndexList = findVisiblePeakIndexes(accurateBox);
// If we have things to remove, do that in one-step.
if (!deletionIndexList.empty()) {
Mantid::API::IPeaksWorkspace_sptr peaksWS =
boost::const_pointer_cast<Mantid::API::IPeaksWorkspace>(
this->m_peaksWS);
// Sort the Peaks in-place.
Mantid::API::IAlgorithm_sptr alg =
AlgorithmManager::Instance().create("DeleteTableRows");
alg->setChild(true);
alg->setRethrows(true);
alg->initialize();
alg->setProperty("TableWorkspace", peaksWS);
alg->setProperty("Rows", deletionIndexList);
alg->execute();
// Reproduce the views. Proxy representations recreated for all peaks.
this->produceViews();
// Refind visible peaks and Set the proxy representations to be visible or
// not.
doFindPeaksInRegion();
// Upstream controls need to be regenerated.
this->informOwnerUpdate();
}
return !deletionIndexList.empty();
}
Mantid::API::MatrixWorkspace_sptr SANSPlotSpecial::runIQTransform() {
// Run the IQTransform algorithm for the current settings on the GUI
Mantid::API::IAlgorithm_sptr iqt =
Mantid::API::AlgorithmManager::Instance().create("IQTransform");
iqt->initialize();
try {
iqt->setPropertyValue("InputWorkspace",
m_uiForm.wsInput->currentText().toStdString());
} catch (std::invalid_argument &) {
m_uiForm.lbPlotOptionsError->setText(
"Selected input workspace is not appropriate for the IQTransform "
"algorithm. Please refer to the documentation for guidelines.");
return Mantid::API::MatrixWorkspace_sptr();
}
iqt->setPropertyValue("OutputWorkspace", "__sans_isis_display_iqt");
iqt->setPropertyValue("TransformType",
m_uiForm.cbPlotType->currentText().toStdString());
if (m_uiForm.cbBackground->currentText() == "Value") {
iqt->setProperty<double>("BackgroundValue", m_uiForm.dsBackground->value());
} else {
iqt->setPropertyValue("BackgroundWorkspace",
m_uiForm.wsBackground->currentText().toStdString());
}
if (m_uiForm.cbPlotType->currentText() == "General") {
std::vector<double> constants =
m_transforms["General"]->functionConstants();
iqt->setProperty("GeneralFunctionConstants", constants);
}
iqt->execute();
Mantid::API::MatrixWorkspace_sptr result =
boost::dynamic_pointer_cast<Mantid::API::MatrixWorkspace>(
Mantid::API::AnalysisDataService::Instance().retrieve(
"__sans_isis_display_iqt"));
return result;
}
void WorkspacePresenter::groupWorkspaces() {
auto view = lockView();
auto selected = view->getSelectedWorkspaceNames();
std::string groupName("NewGroup");
// get selected workspaces
if (selected.size() < 2) {
view->showCriticalUserMessage("Cannot Group Workspaces",
"Select at least two workspaces to group ");
return;
}
if (m_adapter->doesWorkspaceExist(groupName)) {
if (!view->askUserYesNo("",
"Workspace " + groupName +
" already exists. Do you want to replace it?"))
return;
}
try {
std::string algName("GroupWorkspaces");
Mantid::API::IAlgorithm_sptr alg =
Mantid::API::AlgorithmManager::Instance().create(algName, -1);
alg->initialize();
alg->setProperty("InputWorkspaces", selected);
alg->setPropertyValue("OutputWorkspace", groupName);
// execute the algorithm
bool bStatus = alg->execute();
if (!bStatus) {
view->showCriticalUserMessage("MantidPlot - Algorithm error",
" Error in GroupWorkspaces algorithm");
}
} catch (...) {
view->showCriticalUserMessage("MantidPlot - Algorithm error",
" Error in GroupWorkspaces algorithm");
}
}
/**
* Create a list of files from the given algorithm property.
*/
void FindFilesThread::getFilesFromAlgorithm() {
Mantid::API::IAlgorithm_sptr algorithm =
Mantid::API::AlgorithmManager::Instance().createUnmanaged(
m_algorithm.toStdString());
if (!algorithm)
throw std::invalid_argument("Cannot create algorithm " +
m_algorithm.toStdString() + ".");
algorithm->initialize();
const std::string propName = m_property.toStdString();
algorithm->setProperty(propName, m_text);
Property *prop = algorithm->getProperty(propName);
m_valueForProperty = QString::fromStdString(prop->value());
FileProperty *fileProp = dynamic_cast<FileProperty *>(prop);
MultipleFileProperty *multiFileProp =
dynamic_cast<MultipleFileProperty *>(prop);
if (fileProp) {
m_filenames.push_back(fileProp->value());
} else if (multiFileProp) {
// This flattens any summed files to a set of single files so that you lose
// the information about
// what was summed
std::vector<std::vector<std::string>> filenames =
algorithm->getProperty(propName);
std::vector<std::string> flattenedNames =
VectorHelper::flattenVector(filenames);
for (auto filename = flattenedNames.begin();
filename != flattenedNames.end(); ++filename) {
m_filenames.push_back(*filename);
}
}
}
/**
* Groups the workspace according to grouping provided.
*
* @param ws :: Workspace to group
* @param g :: The grouping information
* @return Sptr to created grouped workspace
*/
MatrixWorkspace_sptr groupWorkspace(MatrixWorkspace_const_sptr ws, const Grouping& g)
{
// As I couldn't specify multiple groups for GroupDetectors, I am going down quite a complicated
// route - for every group distinct grouped workspace is created using GroupDetectors. These
// workspaces are then merged into the output workspace.
// Create output workspace
MatrixWorkspace_sptr outWs =
WorkspaceFactory::Instance().create(ws, g.groups.size(), ws->readX(0).size(), ws->blocksize());
for(size_t gi = 0; gi < g.groups.size(); gi++)
{
Mantid::API::IAlgorithm_sptr alg = AlgorithmManager::Instance().create("GroupDetectors");
alg->setChild(true); // So Output workspace is not added to the ADS
alg->initialize();
alg->setProperty("InputWorkspace", boost::const_pointer_cast<MatrixWorkspace>(ws));
alg->setPropertyValue("SpectraList", g.groups[gi]);
alg->setPropertyValue("OutputWorkspace", "grouped"); // Is not actually used, just to make validators happy
alg->execute();
MatrixWorkspace_sptr grouped = alg->getProperty("OutputWorkspace");
// Copy the spectrum
*(outWs->getSpectrum(gi)) = *(grouped->getSpectrum(0));
// Update spectrum number
outWs->getSpectrum(gi)->setSpectrumNo(static_cast<specid_t>(gi));
// Copy to the output workspace
outWs->dataY(gi) = grouped->readY(0);
outWs->dataX(gi) = grouped->readX(0);
outWs->dataE(gi) = grouped->readE(0);
}
return outWs;
}