WorkspaceGroup_sptr
PolarizationCorrectionFredrikze::execPNR(WorkspaceGroup_sptr inWS) {
size_t itemIndex = 0;
MatrixWorkspace_sptr Ip =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr Ia =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
const auto rho = this->getEfficiencyWorkspace(crhoLabel);
const auto pp = this->getEfficiencyWorkspace(cppLabel);
const auto D = pp * (rho + 1);
const auto nIp = (Ip * (rho * pp + 1.0) + Ia * (pp - 1.0)) / D;
const auto nIa = (Ip * (rho * pp - 1.0) + Ia * (pp + 1.0)) / D;
// Preserve the history of the inside workspaces
nIp->history().addHistory(Ip->getHistory());
nIa->history().addHistory(Ia->getHistory());
WorkspaceGroup_sptr dataOut = boost::make_shared<WorkspaceGroup>();
dataOut->addWorkspace(nIp);
dataOut->addWorkspace(nIa);
return dataOut;
}
WorkspaceGroup_sptr PolarizationCorrection::execPNR(WorkspaceGroup_sptr inWS) {
size_t itemIndex = 0;
MatrixWorkspace_sptr Ip =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr Ia =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr ones = copyShapeAndFill(Ip, 1.0);
const VecDouble c_rho = getProperty(crhoLabel());
const VecDouble c_pp = getProperty(cppLabel());
const auto rho = this->execPolynomialCorrection(
ones, c_rho); // Execute polynomial expression
const auto pp = this->execPolynomialCorrection(
ones, c_pp); // Execute polynomial expression
const auto D = pp * (rho + 1);
const auto nIp = (Ip * (rho * pp + 1.0) + Ia * (pp - 1.0)) / D;
const auto nIa = (Ip * (rho * pp - 1.0) + Ia * (pp + 1.0)) / D;
// Preserve the history of the inside workspaces
nIp->history().addHistory(Ip->getHistory());
nIa->history().addHistory(Ia->getHistory());
WorkspaceGroup_sptr dataOut = boost::make_shared<WorkspaceGroup>();
dataOut->addWorkspace(nIp);
dataOut->addWorkspace(nIa);
return dataOut;
}
/**
* Add a workspace to a group. The group and the workspace must be in the ADS.
* @param groupName :: A group name.
* @param wsName :: Name of a workspace to add to the group.
*/
void AnalysisDataServiceImpl::addToGroup(const std::string &groupName,
const std::string &wsName) {
WorkspaceGroup_sptr group = retrieveWS<WorkspaceGroup>(groupName);
if (!group) {
throw std::runtime_error("Workspace " + groupName +
" is not a workspace group.");
}
auto ws = retrieve(wsName);
group->addWorkspace(ws);
notificationCenter.postNotification(new GroupUpdatedNotification(groupName));
}
MatrixWorkspace_sptr MuonPairingAsymmetry::execGroupWorkspaceInput() {
// Get the input workspace into a useful form
Workspace_sptr tmpWS1 = getProperty("InputWorkspace1");
Workspace_sptr tmpWS2 = getProperty("InputWorkspace2");
WorkspaceGroup_sptr ws1 = workspaceToWorkspaceGroup(tmpWS1);
WorkspaceGroup_sptr ws2 = workspaceToWorkspaceGroup(tmpWS2);
WorkspaceGroup_sptr groupedPeriods = boost::make_shared<WorkspaceGroup>();
for (int i = 0; i < countPeriods(ws1); i++) {
groupedPeriods->addWorkspace(
appendSpectra(getWorkspace(ws1, i), getWorkspace(ws2, i)));
}
// Do the asymmetry calculation
const double alpha = static_cast<double>(getProperty("Alpha"));
std::vector<int> summedPeriods = getProperty("SummedPeriods");
std::vector<int> subtractedPeriods = getProperty("SubtractedPeriods");
return calcPairAsymmetryWithSummedAndSubtractedPeriods(
summedPeriods, subtractedPeriods, groupedPeriods, alpha);
}
/// Executes the algorithm
void PoldiFitPeaks2D::exec() {
std::vector<PoldiPeakCollection_sptr> peakCollections =
getPeakCollectionsFromInput();
// Try to setup the 2D data and poldi instrument
MatrixWorkspace_sptr ws = getProperty("InputWorkspace");
setDeltaTFromWorkspace(ws);
setPoldiInstrument(boost::make_shared<PoldiInstrumentAdapter>(ws));
setTimeTransformerFromInstrument(m_poldiInstrument);
// If a profile function is selected, set it on the peak collections.
Property *profileFunctionProperty =
getPointerToProperty("PeakProfileFunction");
if (!profileFunctionProperty->isDefault()) {
for (auto &peakCollection : peakCollections) {
peakCollection->setProfileFunctionName(profileFunctionProperty->value());
}
}
// Perform 2D-fit and return Fit algorithm to extract various information
IAlgorithm_sptr fitAlgorithm = calculateSpectrum(peakCollections, ws);
// The FitFunction is used to generate...
IFunction_sptr fitFunction = getFunction(fitAlgorithm);
// ...a calculated 1D-spectrum...
MatrixWorkspace_sptr outWs1D = get1DSpectrum(fitFunction, ws);
// ...a vector of peak collections.
std::vector<PoldiPeakCollection_sptr> integralPeaks =
getCountPeakCollections(fitFunction);
for (size_t i = 0; i < peakCollections.size(); ++i) {
assignMillerIndices(peakCollections[i], integralPeaks[i]);
}
// Get the calculated 2D workspace
setProperty("OutputWorkspace", getWorkspace(fitAlgorithm));
// Set the output peaks depending on whether it's one or more workspaces
if (integralPeaks.size() == 1) {
setProperty("RefinedPoldiPeakWorkspace",
integralPeaks.front()->asTableWorkspace());
} else {
WorkspaceGroup_sptr peaksGroup = boost::make_shared<WorkspaceGroup>();
for (auto &integralPeak : integralPeaks) {
peaksGroup->addWorkspace(integralPeak->asTableWorkspace());
}
setProperty("RefinedPoldiPeakWorkspace", peaksGroup);
}
// Set the 1D-spectrum output
setProperty("Calculated1DSpectrum", outWs1D);
// If it was a PawleyFit, also produce one or more cell parameter tables.
bool isPawleyFit = getProperty("PawleyFit");
if (isPawleyFit) {
Poldi2DFunction_sptr poldi2DFunction =
boost::dynamic_pointer_cast<Poldi2DFunction>(fitFunction);
std::vector<ITableWorkspace_sptr> cells;
if (poldi2DFunction) {
for (size_t i = 0; i < poldi2DFunction->nFunctions(); ++i) {
try {
ITableWorkspace_sptr cell =
getRefinedCellParameters(poldi2DFunction->getFunction(i));
cells.push_back(cell);
} catch (const std::invalid_argument &) {
// do nothing
}
}
if (cells.size() == 1) {
setProperty("RefinedCellParameters", cells.front());
} else {
WorkspaceGroup_sptr cellsGroup = boost::make_shared<WorkspaceGroup>();
for (auto &cell : cells) {
cellsGroup->addWorkspace(cell);
}
setProperty("RefinedCellParameters", cellsGroup);
}
} else {
g_log.warning() << "Warning: Cell parameter table is empty.";
}
}
// Optionally output the raw fitting parameters.
Property *rawFitParameters = getPointerToProperty("RawFitParameters");
if (!rawFitParameters->isDefault()) {
ITableWorkspace_sptr parameters =
fitAlgorithm->getProperty("OutputParameters");
setProperty("RawFitParameters", parameters);
}
}
WorkspaceGroup_sptr PolarizationCorrection::execPA(WorkspaceGroup_sptr inWS) {
if (isPropertyDefault(cAlphaLabel())) {
throw std::invalid_argument("Must provide as input for PA: " +
cAlphaLabel());
}
if (isPropertyDefault(cApLabel())) {
throw std::invalid_argument("Must provide as input for PA: " + cApLabel());
}
size_t itemIndex = 0;
MatrixWorkspace_sptr Ipp =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr Ipa =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr Iap =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr Iaa =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
Ipp->setTitle("Ipp");
Iaa->setTitle("Iaa");
Ipa->setTitle("Ipa");
Iap->setTitle("Iap");
auto cropAlg = this->createChildAlgorithm("CropWorkspace");
cropAlg->initialize();
cropAlg->setProperty("InputWorkspace", Ipp);
cropAlg->setProperty("EndWorkspaceIndex", 0);
cropAlg->execute();
MatrixWorkspace_sptr croppedIpp = cropAlg->getProperty("OutputWorkspace");
MatrixWorkspace_sptr ones = copyShapeAndFill(croppedIpp, 1.0);
// The ones workspace is now identical to the input workspaces in x, but has 1
// as y values. It can therefore be used to build real polynomial functions.
const VecDouble c_rho = getProperty(crhoLabel());
const VecDouble c_alpha = getProperty(cAlphaLabel());
const VecDouble c_pp = getProperty(cppLabel());
const VecDouble c_ap = getProperty(cApLabel());
const auto rho = this->execPolynomialCorrection(
ones, c_rho); // Execute polynomial expression
const auto pp = this->execPolynomialCorrection(
ones, c_pp); // Execute polynomial expression
const auto alpha = this->execPolynomialCorrection(
ones, c_alpha); // Execute polynomial expression
const auto ap = this->execPolynomialCorrection(
ones, c_ap); // Execute polynomial expression
const auto A0 = (Iaa * pp * ap) + (ap * Ipa * rho * pp) +
(ap * Iap * alpha * pp) + (Ipp * ap * alpha * rho * pp);
const auto A1 = pp * Iaa;
const auto A2 = pp * Iap;
const auto A3 = ap * Iaa;
const auto A4 = ap * Ipa;
const auto A5 = ap * alpha * Ipp;
const auto A6 = ap * alpha * Iap;
const auto A7 = pp * rho * Ipp;
const auto A8 = pp * rho * Ipa;
const auto D = pp * ap * (rho + alpha + 1.0 + (rho * alpha));
const auto nIpp =
(A0 - A1 + A2 - A3 + A4 + A5 - A6 + A7 - A8 + Ipp + Iaa - Ipa - Iap) / D;
const auto nIaa =
(A0 + A1 - A2 + A3 - A4 - A5 + A6 - A7 + A8 + Ipp + Iaa - Ipa - Iap) / D;
const auto nIpa =
(A0 - A1 + A2 + A3 - A4 - A5 + A6 + A7 - A8 - Ipp - Iaa + Ipa + Iap) / D;
const auto nIap =
(A0 + A1 - A2 - A3 + A4 + A5 - A6 - A7 + A8 - Ipp - Iaa + Ipa + Iap) / D;
WorkspaceGroup_sptr dataOut = boost::make_shared<WorkspaceGroup>();
dataOut->addWorkspace(nIpp);
dataOut->addWorkspace(nIpa);
dataOut->addWorkspace(nIap);
dataOut->addWorkspace(nIaa);
size_t totalGroupEntries(dataOut->getNumberOfEntries());
for (size_t i = 1; i < totalGroupEntries; i++) {
auto alg = this->createChildAlgorithm("ReplaceSpecialValues");
alg->setProperty("InputWorkspace", dataOut->getItem(i));
alg->setProperty("OutputWorkspace", "dataOut_" + std::to_string(i));
alg->setProperty("NaNValue", 0.0);
alg->setProperty("NaNError", 0.0);
alg->setProperty("InfinityValue", 0.0);
alg->setProperty("InfinityError", 0.0);
alg->execute();
}
// Preserve the history of the inside workspaces
nIpp->history().addHistory(Ipp->getHistory());
nIaa->history().addHistory(Iaa->getHistory());
nIpa->history().addHistory(Ipa->getHistory());
nIap->history().addHistory(Iap->getHistory());
return dataOut;
}
/**
* Create FITS file information for each file selected. Loads headers
* and data from the files and creates and fills the output
* workspace(s).
*
* @param paths File names as given in the algorithm input property
*
* @param outWSName name of the output (group) workspace to create
*
* @param loadAsRectImg Load files with 1 spectrum per row and 1 bin
* per column, so a color fill plot displays the image
*
* @param binSize size to rebin (1 == no re-bin == default)
*
* @param noiseThresh threshold for noise filtering
*
* @throw std::runtime_error when load fails (for example a memory
* allocation issue, wrong rebin requested, etc.)
*/
void LoadFITS::doLoadFiles(const std::vector<std::string> &paths,
const std::string &outWSName, bool loadAsRectImg,
int binSize, double noiseThresh) {
std::vector<FITSInfo> headers;
headers.resize(paths.size());
loadHeader(paths[0], headers[0]);
// No extension is set -> it's the standard format which we can parse.
if (headers[0].numberOfAxis > 0)
m_pixelCount += headers[0].axisPixelLengths[0];
// Presumably 2 axis, but futureproofing.
for (int i = 1; i < headers[0].numberOfAxis; ++i) {
m_pixelCount *= headers[0].axisPixelLengths[i];
}
// Check consistency of binSize asap
for (int i = 0; i < headers[0].numberOfAxis; ++i) {
if (0 != (headers[0].axisPixelLengths[i] % binSize)) {
throw std::runtime_error(
"Cannot rebin this image in blocks of " + std::to_string(binSize) +
" x " + std::to_string(binSize) +
" pixels as requested because the size of dimension " +
std::to_string(i + 1) + " (" +
std::to_string(headers[0].axisPixelLengths[i]) +
") is not a multiple of the bin size.");
}
}
MantidImage imageY(headers[0].axisPixelLengths[1],
std::vector<double>(headers[0].axisPixelLengths[0]));
MantidImage imageE(headers[0].axisPixelLengths[1],
std::vector<double>(headers[0].axisPixelLengths[0]));
size_t bytes = (headers[0].bitsPerPixel / 8) * m_pixelCount;
std::vector<char> buffer;
try {
buffer.resize(bytes);
} catch (std::exception &) {
throw std::runtime_error(
"Could not allocate enough memory to run when trying to allocate " +
std::to_string(bytes) + " bytes.");
}
// Create a group for these new workspaces, if the group already exists, add
// to it.
size_t fileNumberInGroup = 0;
WorkspaceGroup_sptr wsGroup;
if (!AnalysisDataService::Instance().doesExist(outWSName)) {
wsGroup = boost::make_shared<WorkspaceGroup>();
wsGroup->setTitle(outWSName);
} else {
// Get the name of the latest file in group to start numbering from
if (AnalysisDataService::Instance().doesExist(outWSName))
wsGroup =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outWSName);
std::string latestName = wsGroup->getNames().back();
// Set next file number
fileNumberInGroup = fetchNumber(latestName) + 1;
}
size_t totalWS = headers.size();
// Create a progress reporting object
API::Progress progress(this, 0, 1, totalWS + 1);
progress.report(0, "Loading file(s) into workspace(s)");
// Create first workspace (with instrument definition). This is also used as
// a template for creating others
Workspace2D_sptr imgWS;
imgWS = makeWorkspace(headers[0], fileNumberInGroup, buffer, imageY, imageE,
imgWS, loadAsRectImg, binSize, noiseThresh);
progress.report(1, "First file loaded.");
wsGroup->addWorkspace(imgWS);
if (isInstrOtherThanIMAT(headers[0])) {
// For now we assume IMAT except when specific headers are found by
// isInstrOtherThanIMAT()
//
// TODO: do this conditional on INSTR='IMAT' when we have proper IMAT .fits
// files
try {
IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrument");
std::string directoryName =
Kernel::ConfigService::Instance().getInstrumentDirectory();
directoryName = directoryName + "/IMAT_Definition.xml";
loadInst->setPropertyValue("Filename", directoryName);
loadInst->setProperty<MatrixWorkspace_sptr>(
"Workspace", boost::dynamic_pointer_cast<MatrixWorkspace>(imgWS));
loadInst->execute();
} catch (std::exception &ex) {
g_log.information("Cannot load the instrument definition. " +
std::string(ex.what()));
}
}
// don't feel tempted to parallelize this loop as it is - it uses the same
// imageY and imageE buffers for all the workspaces
for (int64_t i = 1; i < static_cast<int64_t>(totalWS); ++i) {
loadHeader(paths[i], headers[i]);
// Check each header is valid/supported: standard (no extension to
// FITS), has two axis, and it is consistent with the first header
headerSanityCheck(headers[i], headers[0]);
imgWS = makeWorkspace(headers[i], fileNumberInGroup, buffer, imageY, imageE,
imgWS, loadAsRectImg, binSize, noiseThresh);
progress.report("Loaded file " + std::to_string(i + 1) + " of " +
std::to_string(totalWS));
wsGroup->addWorkspace(imgWS);
}
setProperty("OutputWorkspace", wsGroup);
}
/** Execute the algorithm.
*/
void PoldiIndexKnownCompounds::exec() {
g_log.information() << "Starting POLDI peak indexing." << std::endl;
DataObjects::TableWorkspace_sptr peakTableWorkspace =
getProperty("InputWorkspace");
PoldiPeakCollection_sptr unindexedPeaks =
boost::make_shared<PoldiPeakCollection>(peakTableWorkspace);
g_log.information() << " Number of peaks: " << unindexedPeaks->peakCount()
<< std::endl;
std::vector<Workspace_sptr> workspaces =
getWorkspaces(getProperty("CompoundWorkspaces"));
std::vector<PoldiPeakCollection_sptr> peakCollections =
getPeakCollections(workspaces);
g_log.information() << " Number of phases: " << peakCollections.size()
<< std::endl;
/* The procedure is much easier to formulate with some state stored in member
* variables,
* which are initialized either from user input or from some defaults.
*/
setMeasuredPeaks(unindexedPeaks);
setExpectedPhases(peakCollections);
setExpectedPhaseNames(getWorkspaceNames(workspaces));
initializeUnindexedPeaks();
initializeIndexedPeaks(m_expectedPhases);
/* For calculating scores in the indexing procedure, scattering contributions
* are used.
* The structure factors are scaled accordingly.
*/
std::vector<double> contributions = getContributions(m_expectedPhases.size());
std::vector<double> normalizedContributions =
getNormalizedContributions(contributions);
scaleIntensityEstimates(peakCollections, normalizedContributions);
scaleToExperimentalValues(peakCollections, unindexedPeaks);
// Tolerances on the other hand are handled as "FWHM".
std::vector<double> tolerances = getTolerances(m_expectedPhases.size());
assignFwhmEstimates(peakCollections, tolerances);
// With all necessary state assigned, the indexing procedure can be executed
indexPeaks(unindexedPeaks, peakCollections);
g_log.information() << " Unindexed peaks: " << m_unindexedPeaks->peakCount()
<< std::endl;
/* Finally, the peaks are put into separate workspaces, determined by
* the phase they have been attributed to, plus unindexed peaks.
*/
std::string inputWorkspaceName = getPropertyValue("InputWorkspace");
WorkspaceGroup_sptr outputWorkspaces = boost::make_shared<WorkspaceGroup>();
for (size_t i = 0; i < m_indexedPeaks.size(); ++i) {
PoldiPeakCollection_sptr intensitySorted =
getIntensitySortedPeakCollection(m_indexedPeaks[i]);
assignCrystalStructureParameters(intensitySorted, m_expectedPhases[i]);
ITableWorkspace_sptr tableWs = intensitySorted->asTableWorkspace();
AnalysisDataService::Instance().addOrReplace(
inputWorkspaceName + "_indexed_" + m_phaseNames[i], tableWs);
outputWorkspaces->addWorkspace(tableWs);
}
ITableWorkspace_sptr unindexedTableWs = m_unindexedPeaks->asTableWorkspace();
AnalysisDataService::Instance().addOrReplace(
inputWorkspaceName + "_unindexed", unindexedTableWs);
outputWorkspaces->addWorkspace(unindexedTableWs);
setProperty("OutputWorkspace", outputWorkspaces);
}
/**
* Read histogram data
* @param histogramEntries map of the file entries that have histogram
* @param outputGroup pointer to the workspace group
* @param nxFile Reads data from inside first first top entry
*/
void LoadMcStas::readHistogramData(
const std::map<std::string, std::string> &histogramEntries,
WorkspaceGroup_sptr &outputGroup, ::NeXus::File &nxFile) {
std::string nameAttrValueYLABEL;
for (const auto &histogramEntry : histogramEntries) {
const std::string &dataName = histogramEntry.first;
const std::string &dataType = histogramEntry.second;
// open second level entry
nxFile.openGroup(dataName, dataType);
// grap title to use to e.g. create workspace name
std::string nameAttrValueTITLE;
nxFile.getAttr("filename", nameAttrValueTITLE);
if (nxFile.hasAttr("ylabel")) {
nxFile.getAttr("ylabel", nameAttrValueYLABEL);
}
// Find the axis names
auto nxdataEntries = nxFile.getEntries();
std::string axis1Name, axis2Name;
for (auto &nxdataEntry : nxdataEntries) {
if (nxdataEntry.second == "NXparameters")
continue;
if (nxdataEntry.first == "ncount")
continue;
nxFile.openData(nxdataEntry.first);
if (nxFile.hasAttr("axis")) {
int axisNo(0);
nxFile.getAttr("axis", axisNo);
if (axisNo == 1)
axis1Name = nxdataEntry.first;
else if (axisNo == 2)
axis2Name = nxdataEntry.first;
else
throw std::invalid_argument("Unknown axis number");
}
nxFile.closeData();
}
std::vector<double> axis1Values, axis2Values;
nxFile.readData<double>(axis1Name, axis1Values);
if (axis2Name.length() == 0) {
axis2Name = nameAttrValueYLABEL;
axis2Values.push_back(0.0);
} else {
nxFile.readData<double>(axis2Name, axis2Values);
}
const size_t axis1Length = axis1Values.size();
const size_t axis2Length = axis2Values.size();
g_log.debug() << "Axis lengths=" << axis1Length << " " << axis2Length
<< '\n';
// Require "data" field
std::vector<double> data;
nxFile.readData<double>("data", data);
// Optional errors field
std::vector<double> errors;
try {
nxFile.readData<double>("errors", errors);
} catch (::NeXus::Exception &) {
g_log.information() << "Field " << dataName
<< " contains no error information.\n";
}
// close second level entry
nxFile.closeGroup();
MatrixWorkspace_sptr ws = WorkspaceFactory::Instance().create(
"Workspace2D", axis2Length, axis1Length, axis1Length);
Axis *axis1 = ws->getAxis(0);
axis1->title() = axis1Name;
// Set caption
auto lblUnit = boost::make_shared<Units::Label>();
lblUnit->setLabel(axis1Name, "");
axis1->unit() = lblUnit;
Axis *axis2 = new NumericAxis(axis2Length);
axis2->title() = axis2Name;
// Set caption
lblUnit = boost::make_shared<Units::Label>();
lblUnit->setLabel(axis2Name, "");
axis2->unit() = lblUnit;
ws->setYUnit(axis2Name);
ws->replaceAxis(1, axis2);
for (size_t wsIndex = 0; wsIndex < axis2Length; ++wsIndex) {
auto &dataY = ws->dataY(wsIndex);
auto &dataE = ws->dataE(wsIndex);
auto &dataX = ws->dataX(wsIndex);
for (size_t j = 0; j < axis1Length; ++j) {
// Data is stored in column-major order so we are translating to
// row major for Mantid
const size_t fileDataIndex = j * axis2Length + wsIndex;
dataY[j] = data[fileDataIndex];
dataX[j] = axis1Values[j];
if (!errors.empty())
dataE[j] = errors[fileDataIndex];
}
axis2->setValue(wsIndex, axis2Values[wsIndex]);
}
// set the workspace title
ws->setTitle(nameAttrValueTITLE);
// use the workspace title to create the workspace name
std::replace(nameAttrValueTITLE.begin(), nameAttrValueTITLE.end(), ' ',
'_');
// ensure that specified name is given to workspace (eventWS) when added to
// outputGroup
std::string nameOfGroupWS = getProperty("OutputWorkspace");
std::string nameUserSee = nameAttrValueTITLE + "_" + nameOfGroupWS;
std::string extraProperty =
"Outputworkspace_dummy_" + std::to_string(m_countNumWorkspaceAdded);
declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
extraProperty, nameUserSee, Direction::Output));
setProperty(extraProperty, boost::static_pointer_cast<Workspace>(ws));
m_countNumWorkspaceAdded++; // need to increment to ensure extraProperty are
// unique
// Make Mantid store the workspace in the group
outputGroup->addWorkspace(ws);
}
nxFile.closeGroup();
} // finish
WorkspaceGroup_sptr
PolarizationCorrectionFredrikze::execPA(WorkspaceGroup_sptr inWS) {
size_t itemIndex = 0;
MatrixWorkspace_sptr Ipp =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr Ipa =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr Iap =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
MatrixWorkspace_sptr Iaa =
boost::dynamic_pointer_cast<MatrixWorkspace>(inWS->getItem(itemIndex++));
Ipp->setTitle("Ipp");
Iaa->setTitle("Iaa");
Ipa->setTitle("Ipa");
Iap->setTitle("Iap");
const auto rho = this->getEfficiencyWorkspace(crhoLabel);
const auto pp = this->getEfficiencyWorkspace(cppLabel);
const auto alpha = this->getEfficiencyWorkspace(cAlphaLabel);
const auto ap = this->getEfficiencyWorkspace(cApLabel);
const auto A0 = (Iaa * pp * ap) + (Ipa * ap * rho * pp) +
(Iap * ap * alpha * pp) + (Ipp * ap * alpha * rho * pp);
const auto A1 = Iaa * pp;
const auto A2 = Iap * pp;
const auto A3 = Iaa * ap;
const auto A4 = Ipa * ap;
const auto A5 = Ipp * ap * alpha;
const auto A6 = Iap * ap * alpha;
const auto A7 = Ipp * pp * rho;
const auto A8 = Ipa * pp * rho;
const auto D = pp * ap * (rho + alpha + 1.0 + (rho * alpha));
const auto nIpp =
(A0 - A1 + A2 - A3 + A4 + A5 - A6 + A7 - A8 + Ipp + Iaa - Ipa - Iap) / D;
const auto nIaa =
(A0 + A1 - A2 + A3 - A4 - A5 + A6 - A7 + A8 + Ipp + Iaa - Ipa - Iap) / D;
const auto nIap =
(A0 - A1 + A2 + A3 - A4 - A5 + A6 + A7 - A8 - Ipp - Iaa + Ipa + Iap) / D;
const auto nIpa =
(A0 + A1 - A2 - A3 + A4 + A5 - A6 - A7 + A8 - Ipp - Iaa + Ipa + Iap) / D;
WorkspaceGroup_sptr dataOut = boost::make_shared<WorkspaceGroup>();
dataOut->addWorkspace(nIpp);
dataOut->addWorkspace(nIpa);
dataOut->addWorkspace(nIap);
dataOut->addWorkspace(nIaa);
size_t totalGroupEntries(dataOut->getNumberOfEntries());
for (size_t i = 1; i < totalGroupEntries; i++) {
auto alg = this->createChildAlgorithm("ReplaceSpecialValues");
alg->setProperty("InputWorkspace", dataOut->getItem(i));
alg->setProperty("OutputWorkspace", "dataOut_" + std::to_string(i));
alg->setProperty("NaNValue", 0.0);
alg->setProperty("NaNError", 0.0);
alg->setProperty("InfinityValue", 0.0);
alg->setProperty("InfinityError", 0.0);
alg->execute();
}
// Preserve the history of the inside workspaces
nIpp->history().addHistory(Ipp->getHistory());
nIaa->history().addHistory(Iaa->getHistory());
nIpa->history().addHistory(Ipa->getHistory());
nIap->history().addHistory(Iap->getHistory());
return dataOut;
}
/**
* Return the confidence with with this algorithm can load the file
* @param eventEntries map of the file entries that have events
* @param outputGroup pointer to the workspace group
* @param nxFile Reads data from inside first first top entry
*/
void LoadMcStas::readEventData(
const std::map<std::string, std::string> &eventEntries,
WorkspaceGroup_sptr &outputGroup, ::NeXus::File &nxFile) {
std::string filename = getPropertyValue("Filename");
auto entries = nxFile.getEntries();
// will assume that each top level entry contain one mcstas
// generated IDF and any event data entries within this top level
// entry are data collected for that instrument
// This code for loading the instrument is for now adjusted code from
// ExperimentalInfo.
// Close data folder and go back to top level. Then read and close the
// Instrument folder.
nxFile.closeGroup();
Geometry::Instrument_sptr instrument;
// Initialize progress reporting
int reports = 2;
const double progressFractionInitial = 0.1;
Progress progInitial(this, 0.0, progressFractionInitial, reports);
try {
nxFile.openGroup("instrument", "NXinstrument");
std::string instrumentXML;
nxFile.openGroup("instrument_xml", "NXnote");
nxFile.readData("data", instrumentXML);
nxFile.closeGroup();
nxFile.closeGroup();
progInitial.report("Loading instrument");
Geometry::InstrumentDefinitionParser parser;
std::string instrumentName = "McStas";
parser.initialize(filename, instrumentName, instrumentXML);
std::string instrumentNameMangled = parser.getMangledName();
// Check whether the instrument is already in the InstrumentDataService
if (InstrumentDataService::Instance().doesExist(instrumentNameMangled)) {
// If it does, just use the one from the one stored there
instrument =
InstrumentDataService::Instance().retrieve(instrumentNameMangled);
} else {
// Really create the instrument
instrument = parser.parseXML(NULL);
// Add to data service for later retrieval
InstrumentDataService::Instance().add(instrumentNameMangled, instrument);
}
} catch (...) {
// Loader should not stop if there is no IDF.xml
g_log.warning()
<< "\nCould not find the instrument description in the Nexus file:"
<< filename << " Ignore evntdata from data file" << std::endl;
return;
}
// Finished reading Instrument. Then open new data folder again
nxFile.openGroup("data", "NXdetector");
// create and prepare an event workspace ready to receive the mcstas events
progInitial.report("Set up EventWorkspace");
EventWorkspace_sptr eventWS(new EventWorkspace());
// initialize, where create up front number of eventlists = number of
// detectors
eventWS->initialize(instrument->getNumberDetectors(), 1, 1);
// Set the units
eventWS->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
eventWS->setYUnit("Counts");
// set the instrument
eventWS->setInstrument(instrument);
// assign detector ID to eventlists
std::vector<detid_t> detIDs = instrument->getDetectorIDs();
for (size_t i = 0; i < instrument->getNumberDetectors(); i++) {
eventWS->getEventList(i).addDetectorID(detIDs[i]);
// spectrum number are treated as equal to detector IDs for McStas data
eventWS->getEventList(i).setSpectrumNo(detIDs[i]);
}
// the one is here for the moment for backward compatibility
eventWS->rebuildSpectraMapping(true);
bool isAnyNeutrons = false;
// to store shortest and longest recorded TOF
double shortestTOF(0.0);
double longestTOF(0.0);
const size_t numEventEntries = eventEntries.size();
Progress progEntries(this, progressFractionInitial, 1.0, numEventEntries * 2);
for (auto eit = eventEntries.begin(); eit != eventEntries.end(); ++eit) {
std::string dataName = eit->first;
std::string dataType = eit->second;
// open second level entry
nxFile.openGroup(dataName, dataType);
std::vector<double> data;
nxFile.openData("events");
progEntries.report("read event data from nexus");
// Need to take into account that the nexus readData method reads a
// multi-column data entry
// into a vector
// The number of data column for each neutron is here hardcoded to (p, x,
// y, n, id, t)
// Thus we have
// column 0 : p neutron wight
// column 1 : x x coordinate
// column 2 : y y coordinate
// column 3 : n accumulated number of neutrons
// column 4 : id pixel id
// column 5 : t time
// get info about event data
::NeXus::Info id_info = nxFile.getInfo();
if (id_info.dims.size() != 2) {
g_log.error() << "Event data in McStas nexus file not loaded. Expected "
"event data block to be two dimensional" << std::endl;
return;
}
int64_t nNeutrons = id_info.dims[0];
int64_t numberOfDataColumn = id_info.dims[1];
if (nNeutrons && numberOfDataColumn != 6) {
g_log.error() << "Event data in McStas nexus file expecting 6 columns"
<< std::endl;
return;
}
if (isAnyNeutrons == false && nNeutrons > 0)
isAnyNeutrons = true;
std::vector<int64_t> start(2);
std::vector<int64_t> step(2);
// read the event data in blocks. 1 million event is 1000000*6*8 doubles
// about 50Mb
int64_t nNeutronsInBlock = 1000000;
int64_t nOfFullBlocks = nNeutrons / nNeutronsInBlock;
int64_t nRemainingNeutrons = nNeutrons - nOfFullBlocks * nNeutronsInBlock;
// sum over number of blocks + 1 to cover the remainder
for (int64_t iBlock = 0; iBlock < nOfFullBlocks + 1; iBlock++) {
if (iBlock == nOfFullBlocks) {
// read remaining neutrons
start[0] = nOfFullBlocks * nNeutronsInBlock;
start[1] = 0;
step[0] = nRemainingNeutrons;
step[1] = numberOfDataColumn;
} else {
// read neutrons in a full block
start[0] = iBlock * nNeutronsInBlock;
start[1] = 0;
step[0] = nNeutronsInBlock;
step[1] = numberOfDataColumn;
}
const int64_t nNeutronsForthisBlock =
step[0]; // number of neutrons read for this block
data.resize(nNeutronsForthisBlock * numberOfDataColumn);
// Check that the type is what it is supposed to be
if (id_info.type == ::NeXus::FLOAT64) {
nxFile.getSlab(&data[0], start, step);
} else {
g_log.warning()
<< "Entry event field is not FLOAT64! It will be skipped.\n";
continue;
}
// populate workspace with McStas events
const detid2index_map detIDtoWSindex_map =
eventWS->getDetectorIDToWorkspaceIndexMap(true);
progEntries.report("read event data into workspace");
for (int64_t in = 0; in < nNeutronsForthisBlock; in++) {
const int detectorID =
static_cast<int>(data[4 + numberOfDataColumn * in]);
const double detector_time = data[5 + numberOfDataColumn * in] *
1.0e6; // convert to microseconds
if (in == 0 && iBlock == 0) {
shortestTOF = detector_time;
longestTOF = detector_time;
} else {
if (detector_time < shortestTOF)
shortestTOF = detector_time;
if (detector_time > longestTOF)
longestTOF = detector_time;
}
const size_t workspaceIndex =
detIDtoWSindex_map.find(detectorID)->second;
int64_t pulse_time = 0;
// eventWS->getEventList(workspaceIndex) +=
// TofEvent(detector_time,pulse_time);
// eventWS->getEventList(workspaceIndex) += TofEvent(detector_time);
eventWS->getEventList(workspaceIndex) += WeightedEvent(
detector_time, pulse_time, data[numberOfDataColumn * in], 1.0);
}
} // end reading over number of blocks of an event dataset
// nxFile.getData(data);
nxFile.closeData();
nxFile.closeGroup();
} // end reading over number of event datasets
// Create a default TOF-vector for histogramming, for now just 2 bins
// 2 bins is the standard. However for McStas simulation data it may make
// sense to
// increase this number for better initial visual effect
Kernel::cow_ptr<MantidVec> axis;
MantidVec &xRef = axis.access();
xRef.resize(2, 0.0);
// if ( nNeutrons > 0)
if (isAnyNeutrons) {
xRef[0] = shortestTOF - 1; // Just to make sure the bins hold it all
xRef[1] = longestTOF + 1;
}
// Set the binning axis
eventWS->setAllX(axis);
// ensure that specified name is given to workspace (eventWS) when added to
// outputGroup
std::string nameOfGroupWS = getProperty("OutputWorkspace");
std::string nameUserSee = std::string("EventData_") + nameOfGroupWS;
std::string extraProperty =
"Outputworkspace_dummy_" +
boost::lexical_cast<std::string>(m_countNumWorkspaceAdded);
declareProperty(new WorkspaceProperty<Workspace>(extraProperty, nameUserSee,
Direction::Output));
setProperty(extraProperty, boost::static_pointer_cast<Workspace>(eventWS));
m_countNumWorkspaceAdded++; // need to increment to ensure extraProperty are
// unique
outputGroup->addWorkspace(eventWS);
}
