/**
* Loads a file into a *hidden* workspace.
*
* @param fileName :: file name to load.
* @param wsName :: workspace name, which will be prefixed by a "__"
*
* @returns a pointer to the loaded workspace
*/
API::Workspace_sptr Load::loadFileToWs(const std::string &fileName,
const std::string &wsName) {
Mantid::API::IAlgorithm_sptr loadAlg = createChildAlgorithm("Load", 1);
// Get the list properties for the concrete loader load algorithm
const std::vector<Kernel::Property *> &props = getProperties();
// Loop through and set the properties on the Child Algorithm
for (auto prop : props) {
const std::string &propName = prop->name();
if (this->existsProperty(propName)) {
if (propName == "Filename") {
loadAlg->setPropertyValue("Filename", fileName);
} else if (propName == "OutputWorkspace") {
loadAlg->setPropertyValue("OutputWorkspace", wsName);
} else {
loadAlg->setPropertyValue(propName, getPropertyValue(propName));
}
}
}
loadAlg->executeAsChildAlg();
Workspace_sptr ws = loadAlg->getProperty("OutputWorkspace");
// ws->setName(wsName);
AnalysisDataService::Instance().addOrReplace(wsName, ws);
return ws;
}
/** Run any algorithm with a variable number of parameters
*
* @param algorithmName
* @param count :: number of arguments given.
* @return the algorithm created
*/
IAlgorithm_sptr FrameworkManagerImpl::exec(const std::string& algorithmName, int count, ...)
{
// Create the algorithm
Mantid::API::IAlgorithm_sptr alg;
alg = Mantid::API::AlgorithmManager::Instance().createUnmanaged(algorithmName, -1);
alg->initialize();
if (!alg->isInitialized())
throw std::runtime_error(algorithmName + " was not initialized.");
if (count % 2 == 1)
{
throw std::runtime_error("Must have an even number of parameter/value string arguments");
}
va_list Params;
va_start(Params, count);
for(int i = 0; i < count; i += 2 )
{
std::string paramName = va_arg(Params, const char *);
std::string paramValue = va_arg(Params, const char *);
alg->setPropertyValue(paramName, paramValue);
}
va_end(Params);
alg->execute();
return alg;
}
/**
* 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;
}
/**
* 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();
}
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;
}
/// 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 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);
}
/**
* 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;
}
/**
@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;
}
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;
}
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");
}
}
/**
* Fill m_uiForm.logBox with names of the log values read from one of the input files
*/
void PlotAsymmetryByLogValueDialog::fillLogBox(const QString&)
{
QString nexusFileName = m_uiForm.firstRunBox->text();
QFileInfo file(nexusFileName);
if (!file.exists())
{
return;
}
m_uiForm.logBox->clear();
Mantid::API::IAlgorithm_sptr alg = Mantid::API::AlgorithmFactory::Instance().create("LoadNexus",-1);
alg->initialize();
try
{
alg->setPropertyValue("Filename",nexusFileName.toStdString());
alg->setPropertyValue("OutputWorkspace","PlotAsymmetryByLogValueDialog_tmp");
alg->setPropertyValue("SpectrumMin","0");
alg->setPropertyValue("SpectrumMax","0");
alg->execute();
if (alg->isExecuted())
{
std::string wsName = alg->getPropertyValue("OutputWorkspace");
Mantid::API::Workspace_sptr ws = Mantid::API::AnalysisDataService::Instance().retrieve(wsName);
if ( !ws )
{
return;
}
Mantid::API::MatrixWorkspace_sptr mws = boost::dynamic_pointer_cast<Mantid::API::MatrixWorkspace>(ws);
Mantid::API::WorkspaceGroup_sptr gws = boost::dynamic_pointer_cast<Mantid::API::WorkspaceGroup>(ws);
if (gws)
{
if (gws->getNumberOfEntries() < 2) return;
mws = boost::dynamic_pointer_cast<Mantid::API::MatrixWorkspace>(
Mantid::API::AnalysisDataService::Instance().retrieve(gws->getNames()[1])
);
}
const std::vector< Mantid::Kernel::Property* >& props = mws->run().getLogData();
if (gws)
{
std::vector<std::string> wsNames = gws->getNames();
for(std::vector<std::string>::iterator it=wsNames.begin();it!=wsNames.end();++it)
{
Mantid::API::AnalysisDataService::Instance().remove(*it);
}
}
else
{
Mantid::API::AnalysisDataService::Instance().remove("PlotAsymmetryByLogValueDialog_tmp");
}
for(size_t i=0;i<props.size();i++)
{
m_uiForm.logBox->addItem(QString::fromStdString(props[i]->name()));
}
// Display the appropriate value
QString displayed("");
if( !isForScript() )
{
displayed = MantidQt::API::AlgorithmInputHistory::Instance().previousInput("PlotAsymmetryByLogValue", "LogValue");
}
if( !displayed.isEmpty() )
{
int index = m_uiForm.logBox->findText(displayed);
if( index >= 0 )
{
m_uiForm.logBox->setCurrentIndex(index);
}
}
}
}
catch(std::exception& )
{
}
}