/**
* 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;
}
/**
* 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;
}
/** This method executes the ListInstruments algorithm
* and fills the instrument box with instrument lists returned by ICat API
* @return shared pointer to workspace which contains instrument names
*/
std::vector<std::string> ICatUtils::executeListInstruments()
{
QString algName("CatalogListInstruments");
const int version=-1;
Mantid::API::IAlgorithm_sptr alg;
try
{
alg = Mantid::API::AlgorithmManager::Instance().create(algName.toStdString(),version);
}
catch(...)
{
throw std::runtime_error("Error when Populating the instrument list box");
}
Poco::ActiveResult<bool> result(alg->executeAsync());
while( !result.available() )
{
QCoreApplication::processEvents();
}
if(!alg->isExecuted())
{
//if the algorithm failed check the session id passed is valid
if(!isSessionValid(alg))
{
//at this point session is invalid, popup loginbox to login
if(login())
{
//now populate instrument box
std::vector<std::string> instruments =executeListInstruments();
return instruments;
}
else
{
throw std::runtime_error("Please Login to the information catalog using the login menu provided to do the investigation search.");
}
}
else
{
return std::vector<std::string>();
}
}
std::vector<std::string>instrlist;
try
{
instrlist= alg->getProperty("InstrumentList");
}
catch (Mantid::Kernel::Exception::NotFoundError&)
{
throw;
}
return instrlist;
}
bool ICatUtils::isSessionValid(const Mantid::API::IAlgorithm_sptr& alg)
{
try
{
return alg->getProperty("IsValid");
}
catch (Mantid::Kernel::Exception::NotFoundError&)
{
throw;
}
}
/**
* 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);
}
}
}
/**
@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;
}
/**
* Create a list of file extensions from the given algorithm
* @param algName :: The name of the algorithm
* @param propName :: The name of the property
* @returns A list of file extensions
*/
QStringList
MWRunFiles::getFileExtensionsFromAlgorithm(const QString &algName,
const QString &propName) {
Mantid::API::IAlgorithm_sptr algorithm =
Mantid::API::AlgorithmManager::Instance().createUnmanaged(
algName.toStdString());
QStringList fileExts;
if (!algorithm)
return fileExts;
algorithm->initialize();
Property *prop = algorithm->getProperty(propName.toStdString());
FileProperty *fileProp = dynamic_cast<FileProperty *>(prop);
MultipleFileProperty *multiFileProp =
dynamic_cast<MultipleFileProperty *>(prop);
std::vector<std::string> allowed;
QString preferredExt;
if (fileProp) {
allowed = fileProp->allowedValues();
preferredExt = QString::fromStdString(fileProp->getDefaultExt());
} else if (multiFileProp) {
allowed = multiFileProp->allowedValues();
preferredExt = QString::fromStdString(multiFileProp->getDefaultExt());
} else {
return fileExts;
}
std::vector<std::string>::const_iterator iend = allowed.end();
int index(0);
for (std::vector<std::string>::const_iterator it = allowed.begin();
it != iend; ++it) {
if (!it->empty()) {
QString ext = QString::fromStdString(*it);
fileExts.append(ext);
if (ext == preferredExt) {
fileExts.move(index, 0);
}
++index;
}
}
return fileExts;
}
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;
}
/**
* 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;
}