/**
* Removes error columns from the table if all errors are zero,
* as these columns correspond to fixed parameters.
* @param table :: [input, output] Pointer to TableWorkspace to edit
*/
void MuonAnalysisResultTableCreator::removeFixedParameterErrors(
const ITableWorkspace_sptr table) const {
assert(table);
const size_t nRows = table->rowCount();
const auto colNames = table->getColumnNames();
std::vector<std::string> zeroErrorColumns;
for (const auto &name : colNames) {
// if name does not end with "Error", continue
const size_t nameLength = name.length();
if (nameLength < ERROR_LENGTH ||
name.compare(nameLength - ERROR_LENGTH, ERROR_LENGTH, ERROR_STRING)) {
continue;
}
auto col = table->getColumn(name);
bool allZeros = true;
// Check if all values in the column are zero
for (size_t iRow = 0; iRow < nRows; ++iRow) {
const double val = col->toDouble(iRow);
if (std::abs(val) > std::numeric_limits<double>::epsilon()) {
allZeros = false;
break;
}
}
if (allZeros) {
zeroErrorColumns.push_back(name);
}
}
for (const auto &name : zeroErrorColumns) {
table->removeColumn(name);
}
}
/** Parse profile table workspace to a map (the new ...
*/
void SaveGSASInstrumentFile::parseProfileTableWorkspace(
ITableWorkspace_sptr ws,
map<unsigned int, map<string, double>> &profilemap) {
size_t numbanks = ws->columnCount() - 1;
size_t numparams = ws->rowCount();
vector<map<string, double>> vec_maptemp(numbanks);
vector<unsigned int> vecbankindex(numbanks);
// Check
vector<string> colnames = ws->getColumnNames();
if (colnames[0].compare("Name"))
throw runtime_error("The first column must be Name");
// Parse
for (size_t irow = 0; irow < numparams; ++irow) {
TableRow tmprow = ws->getRow(irow);
string parname;
tmprow >> parname;
if (parname.compare("BANK")) {
for (size_t icol = 0; icol < numbanks; ++icol) {
double tmpdbl;
tmprow >> tmpdbl;
vec_maptemp[icol].insert(make_pair(parname, tmpdbl));
}
} else {
for (size_t icol = 0; icol < numbanks; ++icol) {
double tmpint;
tmprow >> tmpint;
vecbankindex[icol] = static_cast<unsigned int>(tmpint);
}
}
}
/** Execute the algorithm.
*/
void ConvertDiffCal::exec() {
OffsetsWorkspace_const_sptr offsetsWS = getProperty("OffsetsWorkspace");
// initial setup of new style config
ITableWorkspace_sptr configWksp = boost::make_shared<TableWorkspace>();
configWksp->addColumn("int", "detid");
configWksp->addColumn("double", "difc");
configWksp->addColumn("double", "difa");
configWksp->addColumn("double", "tzero");
// create values in the table
const size_t numberOfSpectra = offsetsWS->getNumberHistograms();
Progress progress(this, 0.0, 1.0, numberOfSpectra);
for (size_t i = 0; i < numberOfSpectra; ++i) {
API::TableRow newrow = configWksp->appendRow();
newrow << static_cast<int>(getDetID(offsetsWS, i));
newrow << calculateDIFC(offsetsWS, i);
newrow << 0.; // difa
newrow << 0.; // tzero
progress.report();
}
// sort the results
IAlgorithm_sptr sortTable = createChildAlgorithm("SortTableWorkspace");
sortTable->setProperty("InputWorkspace", configWksp);
sortTable->setProperty("OutputWorkspace", configWksp);
sortTable->setPropertyValue("Columns", "detid");
sortTable->executeAsChildAlg();
// copy over the results
configWksp = sortTable->getProperty("OutputWorkspace");
setProperty("OutputWorkspace", configWksp);
}
ITableWorkspace_sptr ReflCatalogSearcher::search(const std::string &text) {
auto sessions = CatalogManager::Instance().getActiveSessions();
if (sessions.empty())
throw std::runtime_error("You are not logged into any catalogs.");
const std::string sessionId = sessions.front()->getSessionId();
auto algSearch = AlgorithmManager::Instance().create("CatalogGetDataFiles");
algSearch->initialize();
algSearch->setChild(true);
algSearch->setLogging(false);
algSearch->setProperty("Session", sessionId);
algSearch->setProperty("InvestigationId", text);
algSearch->setProperty("OutputWorkspace", "_ReflSearchResults");
algSearch->execute();
ITableWorkspace_sptr results = algSearch->getProperty("OutputWorkspace");
// Now, tidy up the data
std::set<size_t> toRemove;
for (size_t i = 0; i < results->rowCount(); ++i) {
std::string &run = results->String(i, 0);
// Too short to be more than ".raw or .nxs"
if (run.size() < 5) {
toRemove.insert(i);
}
}
// Sets are sorted so if we go from back to front we won't trip over ourselves
for (auto row = toRemove.rbegin(); row != toRemove.rend(); ++row)
results->removeRow(*row);
return results;
}
/**
* Calculates binning parameters.
*/
void Iqt::calculateBinning() {
using namespace Mantid::API;
disconnect(m_dblManager, SIGNAL(valueChanged(QtProperty *, double)), this,
SLOT(updatePropertyValues(QtProperty *, double)));
QString wsName = m_uiForm.dsInput->getCurrentDataName();
QString resName = m_uiForm.dsResolution->getCurrentDataName();
if (wsName.isEmpty() || resName.isEmpty())
return;
double energyMin = m_dblManager->value(m_properties["ELow"]);
double energyMax = m_dblManager->value(m_properties["EHigh"]);
double numBins = m_dblManager->value(m_properties["SampleBinning"]);
if (numBins == 0)
return;
IAlgorithm_sptr furyAlg =
AlgorithmManager::Instance().create("TransformToIqt");
furyAlg->initialize();
furyAlg->setProperty("SampleWorkspace", wsName.toStdString());
furyAlg->setProperty("ResolutionWorkspace", resName.toStdString());
furyAlg->setProperty("ParameterWorkspace", "__FuryProperties_temp");
furyAlg->setProperty("EnergyMin", energyMin);
furyAlg->setProperty("EnergyMax", energyMax);
furyAlg->setProperty("BinReductionFactor", numBins);
furyAlg->setProperty("DryRun", true);
furyAlg->execute();
// Get property table from algorithm
ITableWorkspace_sptr propsTable =
AnalysisDataService::Instance().retrieveWS<ITableWorkspace>(
"__FuryProperties_temp");
// Get data from property table
double energyWidth = propsTable->getColumn("EnergyWidth")->cell<float>(0);
int sampleBins = propsTable->getColumn("SampleOutputBins")->cell<int>(0);
int resolutionBins = propsTable->getColumn("ResolutionBins")->cell<int>(0);
// Update data in property editor
m_dblManager->setValue(m_properties["EWidth"], energyWidth);
m_dblManager->setValue(m_properties["ResolutionBins"], resolutionBins);
m_dblManager->setValue(m_properties["SampleBins"], sampleBins);
connect(m_dblManager, SIGNAL(valueChanged(QtProperty *, double)), this,
SLOT(updatePropertyValues(QtProperty *, double)));
// Warn for low number of resolution bins
int numResolutionBins =
static_cast<int>(m_dblManager->value(m_properties["ResolutionBins"]));
if (numResolutionBins < 5)
showMessageBox("Number of resolution bins is less than 5.\nResults may be "
"inaccurate.");
}
/**
* Run new CompareWorkspaces algorithm as a child algorithm.
*
* Result string formatted the same way as before; "Success!" when workspaces
* match or a newline separated list of mismatch messages.
*
* @param group_compare Should output be formatted like group comparison?
* @return A string containing either successString() or mismatch messages
*/
std::string CheckWorkspacesMatch::runCompareWorkspaces(bool group_compare) {
// This algorithm produces a single result string
std::string result;
// Use new CompareWorkspaces algorithm to perform comparison
Algorithm_sptr compare = this->createChildAlgorithm("CompareWorkspaces");
compare->setRethrows(true);
compare->setLogging(false);
// Forward workspace properties
Workspace_sptr ws1 = getProperty("Workspace1");
Workspace_sptr ws2 = getProperty("Workspace2");
compare->setProperty("Workspace1", ws1);
compare->setProperty("Workspace2", ws2);
// Copy any other non-default properties
const std::vector<Property *> &allProps = this->getProperties();
auto propCount = allProps.size();
for (size_t i = 0; i < propCount; ++i) {
Property *prop = allProps[i];
const std::string &pname = prop->name();
if (!prop->isDefault() && pname != "Workspace1" && pname != "Workspace2" &&
pname != "Result")
compare->setPropertyValue(pname, prop->value());
}
// Execute comparison
compare->execute();
// Generate result string
if (!compare->getProperty("Result")) {
ITableWorkspace_sptr table = compare->getProperty("Messages");
auto rowcount = table->rowCount();
for (size_t i = 0; i < rowcount; ++i) {
result += table->cell<std::string>(i, 0);
// Emulate special case output format when comparing groups
if (group_compare &&
table->cell<std::string>(i, 0) !=
"Type mismatch. One workspace is a group, the other is not." &&
table->cell<std::string>(i, 0) != "GroupWorkspaces size mismatch.") {
result += ". Inputs=[" + table->cell<std::string>(i, 1) + "," +
table->cell<std::string>(i, 2) + "]";
}
if (i < (rowcount - 1))
result += "\n";
}
} else {
result = successString();
}
return result;
}
ITableWorkspace_sptr ReflCatalogSearcher::search(const std::string& text, const std::string& instrument)
{
auto sessions = CatalogManager::Instance().getActiveSessions();
if(sessions.empty())
throw std::runtime_error("You are not logged into any catalogs.");
const std::string sessionId = sessions.front()->getSessionId();
auto algSearch = AlgorithmManager::Instance().create("CatalogGetDataFiles");
algSearch->initialize();
algSearch->setChild(true);
algSearch->setLogging(false);
algSearch->setProperty("Session", sessionId);
algSearch->setProperty("InvestigationId", text);
algSearch->setProperty("OutputWorkspace", "_ReflSearchResults");
algSearch->execute();
ITableWorkspace_sptr results = algSearch->getProperty("OutputWorkspace");
//Now, tidy up the data
std::set<size_t> toRemove;
for(size_t i = 0; i < results->rowCount(); ++i)
{
std::string& run = results->String(i,0);
//Too short to be more than ".raw"
if(run.size() < 5)
{
toRemove.insert(i);
}
//If this isn't the right instrument, remove it
else if(run.substr(0, instrument.size()) != instrument)
{
toRemove.insert(i);
}
//If it's not a raw file, remove it
else if(run.substr(run.size() - 4, 4) != ".raw")
{
toRemove.insert(i);
}
//It's a valid run, so let's trim the instrument prefix and ".raw" suffix
run = run.substr(instrument.size(), run.size() - (instrument.size() + 4));
//Let's also get rid of any leading zeros
size_t numZeros = 0;
while(run[numZeros] == '0')
numZeros++;
run = run.substr(numZeros, run.size() - numZeros);
}
//Sets are sorted so if we go from back to front we won't trip over ourselves
for(auto row = toRemove.rbegin(); row != toRemove.rend(); ++row)
results->removeRow(*row);
return results;
}
/**
* Creates a domain from an ITableWorkspace
*
* This method creates a LatticeDomain from a table workspace that contains two
* columns, HKL and d. HKL can either be a V3D-column or a string column,
* containing three integers separated by space, comma, semi-colon and
* optionally surrounded by []. The d-column can be double or a string that can
* be parsed as a double number.
*
* @param workspace :: ITableWorkspace with format specified above.
* @param domain :: Pointer to outgoing FunctionDomain instance.
* @param values :: Pointer to outgoing FunctionValues object.
* @param i0 :: Size offset for values object if it already contains data.
*/
void LatticeDomainCreator::createDomainFromPeakTable(
const ITableWorkspace_sptr &workspace,
boost::shared_ptr<FunctionDomain> &domain,
boost::shared_ptr<FunctionValues> &values, size_t i0) {
size_t peakCount = workspace->rowCount();
if (peakCount < 1) {
throw std::range_error("Cannot create a domain for 0 peaks.");
}
try {
Column_const_sptr hklColumn = workspace->getColumn("HKL");
Column_const_sptr dColumn = workspace->getColumn("d");
std::vector<V3D> hkls;
hkls.reserve(peakCount);
std::vector<double> dSpacings;
dSpacings.reserve(peakCount);
V3DFromHKLColumnExtractor extractor;
for (size_t i = 0; i < peakCount; ++i) {
try {
V3D hkl = extractor(hklColumn, i);
if (hkl != V3D(0, 0, 0)) {
hkls.push_back(hkl);
double d = (*dColumn)[i];
dSpacings.push_back(d);
}
} catch (const std::bad_alloc &) {
// do nothing.
}
}
domain = boost::make_shared<LatticeDomain>(hkls);
if (!values) {
values = boost::make_shared<FunctionValues>(*domain);
} else {
values->expand(i0 + domain->size());
}
values->setFitData(dSpacings);
values->setFitWeights(1.0);
} catch (const std::runtime_error &) {
// Column does not exist
throw std::runtime_error("Can not process table, the following columns are "
"required: HKL, d.");
}
}
/// Returns a TableWorkspace with refined cell parameters and error.
ITableWorkspace_sptr PoldiFitPeaks2D::getRefinedCellParameters(
const IFunction_sptr &fitFunction) const {
Poldi2DFunction_sptr poldi2DFunction =
boost::dynamic_pointer_cast<Poldi2DFunction>(fitFunction);
if (!poldi2DFunction || poldi2DFunction->nFunctions() < 1) {
throw std::invalid_argument(
"Cannot process function that is not a Poldi2DFunction.");
}
// Create a new table for lattice parameters
ITableWorkspace_sptr latticeParameterTable =
WorkspaceFactory::Instance().createTable();
latticeParameterTable->addColumn("str", "Parameter");
latticeParameterTable->addColumn("double", "Value");
latticeParameterTable->addColumn("double", "Error");
// The first function should be PoldiSpectrumPawleyFunction
boost::shared_ptr<PoldiSpectrumPawleyFunction> poldiPawleyFunction =
boost::dynamic_pointer_cast<PoldiSpectrumPawleyFunction>(
poldi2DFunction->getFunction(0));
if (!poldiPawleyFunction) {
throw std::invalid_argument("First function in Poldi2DFunction is not "
"PoldiSpectrumPawleyFunction.");
}
// Get the actual PawleyFunction to extract parameters.
IPawleyFunction_sptr pawleyFunction =
boost::dynamic_pointer_cast<IPawleyFunction>(
poldiPawleyFunction->getDecoratedFunction());
if (pawleyFunction) {
CompositeFunction_sptr pawleyParts =
boost::dynamic_pointer_cast<CompositeFunction>(
pawleyFunction->getDecoratedFunction());
// The first function in PawleyFunction contains the parameters
IFunction_sptr pawleyParameters = pawleyParts->getFunction(0);
for (size_t i = 0; i < pawleyParameters->nParams(); ++i) {
TableRow newRow = latticeParameterTable->appendRow();
newRow << pawleyParameters->parameterName(i)
<< pawleyParameters->getParameter(i)
<< pawleyParameters->getError(i);
}
}
return latticeParameterTable;
}
/** Creates grouping table from supplied forward and backward spectra
* @param fwd :: [Input] Forward spectra
* @param bwd :: [Input] Backward spectra
* @return :: Workspace containing custom grouping
*/
Workspace_sptr
PlotAsymmetryByLogValue::createCustomGrouping(const std::vector<int> &fwd,
const std::vector<int> &bwd) {
ITableWorkspace_sptr group =
WorkspaceFactory::Instance().createTable("TableWorkspace");
group->addColumn("vector_int", "group");
TableRow row = group->appendRow();
row << fwd;
row = group->appendRow();
row << bwd;
return boost::dynamic_pointer_cast<Workspace>(group);
}
/**
* Handles completion of the preview algorithm.
*
* @param error If the algorithm failed
*/
void IndirectSymmetrise::previewAlgDone(bool error) {
if (error)
return;
QString workspaceName = m_uiForm.dsInput->getCurrentDataName();
int spectrumNumber =
static_cast<int>(m_dblManager->value(m_properties["PreviewSpec"]));
MatrixWorkspace_sptr sampleWS =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
workspaceName.toStdString());
ITableWorkspace_sptr propsTable =
AnalysisDataService::Instance().retrieveWS<ITableWorkspace>(
"__SymmetriseProps_temp");
MatrixWorkspace_sptr symmWS =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
"__Symmetrise_temp");
// Get the index of XCut on each side of zero
int negativeIndex = propsTable->getColumn("NegativeXMinIndex")->cell<int>(0);
int positiveIndex = propsTable->getColumn("PositiveXMinIndex")->cell<int>(0);
// Get the Y values for each XCut and the difference between them
double negativeY = sampleWS->dataY(0)[negativeIndex];
double positiveY = sampleWS->dataY(0)[positiveIndex];
double deltaY = fabs(negativeY - positiveY);
// Show values in property tree
m_dblManager->setValue(m_properties["NegativeYValue"], negativeY);
m_dblManager->setValue(m_properties["PositiveYValue"], positiveY);
m_dblManager->setValue(m_properties["DeltaY"], deltaY);
// Set indicator positions
m_uiForm.ppRawPlot->getRangeSelector("NegativeEMinYPos")
->setMinimum(negativeY);
m_uiForm.ppRawPlot->getRangeSelector("PositiveEMinYPos")
->setMinimum(positiveY);
// Plot preview plot
size_t spectrumIndex = symmWS->getIndexFromSpectrumNumber(spectrumNumber);
m_uiForm.ppPreviewPlot->clear();
m_uiForm.ppPreviewPlot->addSpectrum("Symmetrised", "__Symmetrise_temp",
spectrumIndex);
// Don't want this to trigger when the algorithm is run for all spectra
disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(previewAlgDone(bool)));
}
/**
* Parse the stream for the characterization file information.
*
* @param file The stream to parse.
* @param wksp The table workspace to fill in.
*/
void PDLoadCharacterizations::readCharInfo(std::ifstream &file, ITableWorkspace_sptr &wksp)
{
// end early if already at the end of the file
if (file.eof()) return;
// parse the file
for (std::string line = Strings::getLine(file); !file.eof(); line = Strings::getLine(file))
{
line = Strings::strip(line);
// skip empty lines and "comments"
if (line.empty()) continue;
if (line.substr(0,1) == "#") continue;
// parse the line
std::vector<std::string> splitted;
boost::split(splitted, line, boost::is_any_of("\t "), boost::token_compress_on);
while (splitted.size() < 10)
splitted.push_back(ZERO); // extra values default to zero
// add the row
API::TableRow row = wksp->appendRow();
row << boost::lexical_cast<double>(splitted[0]); // frequency
row << boost::lexical_cast<double>(splitted[1]); // wavelength
row << boost::lexical_cast<int32_t>(splitted[2]); // bank
row << boost::lexical_cast<int32_t>(splitted[3]); // vanadium
row << boost::lexical_cast<int32_t>(splitted[4]); // container
row << boost::lexical_cast<int32_t>(splitted[5]); // empty
row << splitted[6]; // d_min
row << splitted[7]; // d_max
row << boost::lexical_cast<double>(splitted[8]); // tof_min
row << boost::lexical_cast<double>(splitted[9]); // tof_max
}
}
/**
* Convert a grouping table to a grouping struct.
* @param table :: A table to convert
* @return Grouping info
*/
boost::shared_ptr<Grouping> tableToGrouping(ITableWorkspace_sptr table)
{
auto grouping = boost::make_shared<Grouping>();
for ( size_t row = 0; row < table->rowCount(); ++row )
{
std::vector<int> detectors = table->cell< std::vector<int> >(row,0);
// toString() expects the sequence to be sorted
std::sort( detectors.begin(), detectors.end() );
// Convert to a range string, i.e. 1-5,6-8,9
std::string detectorRange = Strings::toString(detectors);
grouping->groupNames.push_back(boost::lexical_cast<std::string>(row + 1));
grouping->groups.push_back(detectorRange);
}
// If we have 2 groups only - create a longitudinal pair
if ( grouping->groups.size() == 2 )
{
grouping->pairNames.push_back("long");
grouping->pairAlphas.push_back(1.0);
grouping->pairs.push_back(std::make_pair(0,1));
}
return grouping;
}
/**
* Write log and parameter values to the table for the case of a single fit.
* @param table :: [input, output] Table to write to
* @param paramsByLabel :: [input] Map of <label name, <workspace name,
* <parameter, value>>>
* @param paramsToDisplay :: [input] List of parameters to display in table
*/
void MuonAnalysisResultTableCreator::writeDataForSingleFit(
ITableWorkspace_sptr &table,
const QMap<QString, WSParameterList> ¶msByLabel,
const QStringList ¶msToDisplay) const {
assert(!m_multiple);
assert(m_logValues);
for (const auto &wsName : m_items) {
Mantid::API::TableRow row = table->appendRow();
row << wsName.toStdString();
// Get log values for this row
const auto &logValues = m_logValues->value(wsName);
// Write log values in each column
for (int i = 0; i < m_logs.size(); ++i) {
Mantid::API::Column_sptr col = table->getColumn(i);
const auto &log = m_logs[i];
const QVariant &val = logValues[log];
QString valueToWrite;
// Special case: if log is time in sec, subtract the first start time
if (log.endsWith(" (s)")) {
auto seconds =
val.toDouble() - static_cast<double>(m_firstStart_ns) * 1.e-9;
valueToWrite = QString::number(seconds);
} else if (MuonAnalysisHelper::isNumber(val.toString()) &&
!log.endsWith(" (text)")) {
valueToWrite = QString::number(val.toDouble());
} else {
valueToWrite = val.toString();
}
if (MuonAnalysisHelper::isNumber(val.toString()) &&
!log.endsWith(" (text)")) {
row << valueToWrite.toDouble();
} else {
row << valueToWrite.toStdString();
}
}
// Add param values (params same for all workspaces)
QMap<QString, double> paramsList = paramsByLabel.begin()->value(wsName);
for (const auto ¶mName : paramsToDisplay) {
row << paramsList[paramName];
}
}
}
/// Execute
void EstimatePeakErrors::exec() {
IFunction_sptr function = getProperty("Function");
ITableWorkspace_sptr results =
WorkspaceFactory::Instance().createTable("TableWorkspace");
results->addColumn("str", "Parameter");
results->addColumn("double", "Value");
results->addColumn("double", "Error");
auto matrix = function->getCovarianceMatrix();
if (!matrix) {
g_log.warning() << "Function doesn't have covariance matrix.\n";
setProperty("OutputWorkspace", results);
return;
}
IPeakFunction *peak = dynamic_cast<IPeakFunction *>(function.get());
if (peak) {
GSLMatrix covariance(*matrix);
calculatePeakValues(*peak, *results, covariance, "");
} else {
CompositeFunction *cf = dynamic_cast<CompositeFunction *>(function.get());
if (cf) {
size_t ip = 0;
for (size_t i = 0; i < cf->nFunctions(); ++i) {
IFunction *fun = cf->getFunction(i).get();
size_t np = fun->nParams();
peak = dynamic_cast<IPeakFunction *>(fun);
if (peak) {
std::string prefix = "f" + std::to_string(i) + ".";
GSLMatrix covariance(*matrix, ip, ip, np, np);
calculatePeakValues(*peak, *results, covariance, prefix);
}
ip += np;
}
} else {
g_log.warning() << "Function has no peaks.\n";
}
}
setProperty("OutputWorkspace", results);
}
/** Constructor
@param tableWorkspace : The table workspace to wrap
@param whitelist : A DataProcessorWhiteList containing the columns
*/
QDataProcessorOneLevelTreeModel::QDataProcessorOneLevelTreeModel(
ITableWorkspace_sptr tableWorkspace,
const DataProcessorWhiteList &whitelist)
: m_tWS(tableWorkspace), m_whitelist(whitelist) {
if (tableWorkspace->columnCount() != m_whitelist.size())
throw std::invalid_argument(
"Invalid table workspace. Table workspace must "
"have the same number of columns as the white list");
}
int PoldiFitPeaks1D2::getBestChebyshevPolynomialDegree(
const Workspace2D_sptr &dataWorkspace, const RefinedRange_sptr &range) {
double chiSquareMin = 1e10;
int nMin = -1;
try {
int n = 0;
while ((n < 3)) {
IAlgorithm_sptr fit = getFitAlgorithm(dataWorkspace, range, n);
bool fitSuccess = fit->execute();
if (fitSuccess) {
ITableWorkspace_sptr fitCharacteristics =
fit->getProperty("OutputParameters");
TableRow row =
fitCharacteristics->getRow(fitCharacteristics->rowCount() - 1);
double chiSquare = row.Double(1);
if (fabs(chiSquare - 1) < fabs(chiSquareMin - 1)) {
chiSquareMin = chiSquare;
nMin = n;
}
}
++n;
}
} catch (std::runtime_error) {
nMin = -1;
}
if (nMin == -1) {
g_log.information() << "Range [" << range->getXStart() << " - "
<< range->getXEnd() << "] is excluded.";
} else {
g_log.information() << "Chi^2 for range [" << range->getXStart() << " - "
<< range->getXEnd() << "] is minimal at n = " << nMin
<< " with Chi^2 = " << chiSquareMin << std::endl;
}
return nMin;
}
/** Constructor
@param tableWorkspace : The table workspace to wrap
@param whitelist : A DataProcessorWhiteList containing information about the
columns, their indices and descriptions
*/
QDataProcessorTreeModel::QDataProcessorTreeModel(
ITableWorkspace_sptr tableWorkspace,
const DataProcessorWhiteList &whitelist)
: m_tWS(tableWorkspace), m_whitelist(whitelist) {
if (tableWorkspace->columnCount() != m_whitelist.size() + 1)
throw std::invalid_argument("Invalid table workspace. Table workspace must "
"have one extra column accounting for groups");
setupModelData(tableWorkspace);
}
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 ConvertTableToMatrixWorkspace::exec()
{
ITableWorkspace_sptr inputWorkspace = getProperty("InputWorkspace");
std::string columnX = getProperty("ColumnX");
std::string columnY = getProperty("ColumnY");
std::string columnE = getProperty("ColumnE");
size_t nrows = inputWorkspace->rowCount();
std::vector<double> X(nrows);
std::vector<double> Y(nrows);
std::vector<double> E(nrows);
inputWorkspace->getColumn(columnX)->numeric_fill(X);
inputWorkspace->getColumn(columnY)->numeric_fill(Y);
if (!columnE.empty())
{
inputWorkspace->getColumn(columnE)->numeric_fill(E);
}
else
{
E.assign(X.size(),1.0);
}
MatrixWorkspace_sptr outputWorkspace = WorkspaceFactory::Instance().create("Workspace2D",1,X.size(),X.size());
outputWorkspace->dataX(0).assign(X.begin(),X.end());
outputWorkspace->dataY(0).assign(Y.begin(),Y.end());
outputWorkspace->dataE(0).assign(E.begin(),E.end());
outputWorkspace->generateSpectraMap();
boost::shared_ptr<Kernel::Units::Label> labelX = boost::dynamic_pointer_cast<Kernel::Units::Label>(
Kernel::UnitFactory::Instance().create("Label")
);
labelX->setLabel(columnX);
outputWorkspace->getAxis(0)->unit() = labelX;
outputWorkspace->setYUnitLabel(columnY);
setProperty("OutputWorkspace", outputWorkspace);
}
ITableWorkspace_sptr ALCBaselineModellingModel::exportSections() {
if (!m_sections.empty()) {
ITableWorkspace_sptr table =
WorkspaceFactory::Instance().createTable("TableWorkspace");
table->addColumn("double", "Start X");
table->addColumn("double", "End X");
for (auto it = m_sections.begin(); it != m_sections.end(); ++it) {
TableRow newRow = table->appendRow();
newRow << it->first << it->second;
}
return table;
} else {
return ITableWorkspace_sptr();
}
}
/**
* Sets a new preview spectrum for the mini plot.
*
* @param value workspace index
*/
void ResNorm::previewSpecChanged(int value) {
m_previewSpec = value;
// Update vanadium plot
if (m_uiForm.dsVanadium->isValid())
m_uiForm.ppPlot->addSpectrum(
"Vanadium", m_uiForm.dsVanadium->getCurrentDataName(), m_previewSpec);
// Update fit plot
std::string fitWsGroupName(m_pythonExportWsName + "_Fit_Workspaces");
std::string fitParamsName(m_pythonExportWsName + "_Fit");
if (AnalysisDataService::Instance().doesExist(fitWsGroupName)) {
WorkspaceGroup_sptr fitWorkspaces =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(
fitWsGroupName);
ITableWorkspace_sptr fitParams =
AnalysisDataService::Instance().retrieveWS<ITableWorkspace>(
fitParamsName);
if (fitWorkspaces && fitParams) {
Column_const_sptr scaleFactors = fitParams->getColumn("Scaling");
std::string fitWsName(fitWorkspaces->getItem(m_previewSpec)->name());
MatrixWorkspace_const_sptr fitWs =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
fitWsName);
MatrixWorkspace_sptr fit = WorkspaceFactory::Instance().create(fitWs, 1);
fit->setX(0, fitWs->readX(1));
fit->getSpectrum(0)->setData(fitWs->readY(1), fitWs->readE(1));
for (size_t i = 0; i < fit->blocksize(); i++)
fit->dataY(0)[i] /= scaleFactors->cell<double>(m_previewSpec);
m_uiForm.ppPlot->addSpectrum("Fit", fit, 0, Qt::red);
}
}
}
void LoadDNSSCD::loadHuber(ITableWorkspace_sptr tws) {
ColumnVector<double> huber = tws->getVector("Huber(degrees)");
// set huber[0] for each run in m_data
for (auto &ds : m_data) {
ds.huber = huber[0];
}
// dublicate runs for each huber in the table
std::vector<ExpData> old(m_data);
for (size_t i = 1; i < huber.size(); ++i) {
for (auto &ds : old) {
ds.huber = huber[i];
m_data.push_back(ds);
}
}
}
/**
* Creates an output workspace from calculated and observed values
*
* This method creates a table workspace for an ILatticeFunction, containing
* observed and calculated d-values for each HKL, as well as the difference
* between those two values.
*
* @param baseName :: Basename for output workspace.
* @param function :: An ILatticeFunction
* @param domain :: Pointer to LatticeDomain instance.
* @param values :: Pointer to FunctionValues instance.
* @param outputWorkspacePropertyName :: Name of output workspace property.
* @return TableWorkspace with calculated and observed d-values.
*/
Workspace_sptr LatticeDomainCreator::createOutputWorkspace(
const std::string &baseName, IFunction_sptr function,
boost::shared_ptr<FunctionDomain> domain,
boost::shared_ptr<FunctionValues> values,
const std::string &outputWorkspacePropertyName) {
boost::shared_ptr<LatticeDomain> latticeDomain =
boost::dynamic_pointer_cast<LatticeDomain>(domain);
if (!latticeDomain) {
throw std::invalid_argument("LatticeDomain is required.");
}
ILatticeFunction_sptr latticeFunction =
boost::dynamic_pointer_cast<ILatticeFunction>(function);
if (!latticeFunction) {
throw std::invalid_argument(
"LatticeDomainCreator can only process ILatticeFunction.");
}
// Calculate function values again.
latticeFunction->functionLattice(*latticeDomain, *values);
ITableWorkspace_sptr tableWorkspace =
WorkspaceFactory::Instance().createTable();
if (tableWorkspace) {
tableWorkspace->addColumn("V3D", "HKL");
tableWorkspace->addColumn("double", "d(obs)");
tableWorkspace->addColumn("double", "d(calc)");
tableWorkspace->addColumn("double", "d(obs) - d(calc)");
for (size_t i = 0; i < values->size(); ++i) {
double dObs = values->getFitData(i);
double dCalc = values->getCalculated(i);
TableRow newRow = tableWorkspace->appendRow();
newRow << (*latticeDomain)[i] << dObs << dCalc << dObs - dCalc;
}
}
if (m_manager && !outputWorkspacePropertyName.empty()) {
declareProperty(
new WorkspaceProperty<ITableWorkspace>(outputWorkspacePropertyName, "",
Kernel::Direction::Output),
"Result workspace");
m_manager->setPropertyValue(outputWorkspacePropertyName,
baseName + "Workspace");
m_manager->setProperty(outputWorkspacePropertyName, tableWorkspace);
}
return tableWorkspace;
}
/** Setup the data, initialize member variables using a table workspace and
* whitelist
* @param table : A table workspace containing the data
*/
void QDataProcessorTreeModel::setupModelData(ITableWorkspace_sptr table) {
int nrows = static_cast<int>(table->rowCount());
int lastIndex = 0;
std::map<std::string, int> groupIndex;
for (int r = 0; r < nrows; r++) {
const std::string &groupName = m_tWS->String(r, 0);
if (groupIndex.count(groupName) == 0) {
groupIndex[groupName] = lastIndex++;
m_groupName.push_back(groupName);
m_rowsOfGroup.push_back(std::vector<int>());
}
m_rowsOfGroup[groupIndex[groupName]].push_back(r);
}
}
/**
* Construct a Grouping from a table
* @param table :: [input] Table to construct from
*/
Grouping::Grouping(ITableWorkspace_sptr table) {
for (size_t row = 0; row < table->rowCount(); ++row) {
std::vector<int> detectors = table->cell<std::vector<int>>(row, 0);
// toString() expects the sequence to be sorted
std::sort(detectors.begin(), detectors.end());
// Convert to a range string, i.e. 1-5,6-8,9
std::string detectorRange = Kernel::Strings::toString(detectors);
this->groupNames.push_back(std::to_string(row + 1));
this->groups.push_back(detectorRange);
}
// If we have 2 groups only - create a longitudinal pair
if (this->groups.size() == 2) {
this->pairNames.emplace_back("long");
this->pairAlphas.push_back(1.0);
this->pairs.emplace_back(0, 1);
}
}
/// Inserts statistics the supplied PeaksStatistics-objects into the supplied
/// TableWorkspace.
void SortHKL::insertStatisticsIntoTable(
const ITableWorkspace_sptr &table,
const PeaksStatistics &statistics) const {
if (!table) {
throw std::runtime_error("Can't store statistics into Null-table.");
}
std::string name = getProperty("RowName");
double completeness = 0.0;
if (name.substr(0, 4) != "bank") {
completeness = static_cast<double>(statistics.m_completeness);
}
// append to the table workspace
API::TableRow newrow = table->appendRow();
newrow << name << statistics.m_uniqueReflections << statistics.m_dspacingMin
<< statistics.m_dspacingMax << statistics.m_redundancy
<< statistics.m_meanIOverSigma << 100.0 * statistics.m_rMerge
<< 100.0 * statistics.m_rPim << 100.0 * completeness;
}
/** Execute the algorithm.
*/
void CreateChunkingFromInstrument::exec() {
// get the instrument
Instrument_const_sptr inst = this->getInstrument();
// setup the output workspace
ITableWorkspace_sptr strategy =
WorkspaceFactory::Instance().createTable("TableWorkspace");
strategy->addColumn("str", "BankName");
this->setProperty("OutputWorkspace", strategy);
// get the correct level of grouping
string groupLevel = this->getPropertyValue(PARAM_CHUNK_BY);
vector<string> groupNames =
getGroupNames(this->getPropertyValue(PARAM_CHUNK_NAMES));
if (groupLevel.compare("All") == 0) {
return; // nothing to do
} else if (inst->getName().compare("SNAP") == 0 &&
groupLevel.compare("Group") == 0) {
groupNames.clear();
groupNames.push_back("East");
groupNames.push_back("West");
}
// set up a progress bar with the "correct" number of steps
int maxBankNum = this->getProperty(PARAM_MAX_BANK_NUM);
Progress progress(this, .2, 1., maxBankNum);
// search the instrument for the bank names
int maxRecurseDepth = this->getProperty(PARAM_MAX_RECURSE);
map<string, vector<string>> grouping;
// cppcheck-suppress syntaxError
PRAGMA_OMP(parallel for schedule(dynamic, 1) )
for (int num = 0; num < maxBankNum; ++num) {
PARALLEL_START_INTERUPT_REGION
ostringstream mess;
mess << "bank" << num;
IComponent_const_sptr comp =
inst->getComponentByName(mess.str(), maxRecurseDepth);
PARALLEL_CRITICAL(grouping)
if (comp) {
// get the name of the correct parent
string parent;
if (groupNames.empty()) {
parent = parentName(comp, groupLevel);
} else {
parent = parentName(comp, groupNames);
}
// add it to the correct chunk
if (!parent.empty()) {
if (grouping.count(parent) == 0)
grouping[parent] = vector<string>();
grouping[parent].push_back(comp->getName());
}
}
progress.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// check to see that something happened
if (grouping.empty())
throw std::runtime_error("Failed to find any banks in the instrument");
// fill in the table workspace
for (auto group = grouping.begin(); group != grouping.end(); ++group) {
stringstream banks;
for (auto bank = group->second.begin(); bank != group->second.end();
++bank)
banks << (*bank) << ",";
// remove the trailing comma
string banksStr = banks.str();
banksStr = banksStr.substr(0, banksStr.size() - 1);
// add it to the table
TableRow row = strategy->appendRow();
row << banksStr;
}
}
//----------------------------------------------------------------------------------------------
/// Run the algorithm
void QueryMDWorkspace::exec() {
// Extract the required normalisation.
std::string strNormalisation = getPropertyValue("Normalisation");
MDNormalization requestedNormalisation = whichNormalisation(strNormalisation);
IMDWorkspace_sptr input = getProperty("InputWorkspace");
const bool transformCoordsToOriginal = getProperty("TransformCoordsToOriginal");
// Define a table workspace with a specific column schema.
ITableWorkspace_sptr output = WorkspaceFactory::Instance().createTable();
const std::string signalColumnName = "Signal/" + strNormalisation;
const std::string errorColumnName = "Error/" + strNormalisation;
output->addColumn("double", signalColumnName);
output->addColumn("double", errorColumnName);
output->addColumn("int", "Number of Events");
const size_t ndims = input->getNumDims();
for (size_t index = 0; index < ndims; ++index) {
Mantid::Geometry::IMDDimension_const_sptr dim = input->getDimension(index);
std::string dimInUnit = dim->getName() + "/" + dim->getUnits().ascii();
output->addColumn("double", dimInUnit);
// Magic numbers required to configure the X axis.
output->getColumn(dimInUnit)->setPlotType(1);
}
// Magic numbers required to configure the Y axis.
output->getColumn(signalColumnName)->setPlotType(2);
output->getColumn(errorColumnName)->setPlotType(5);
IMDIterator *it = input->createIterator();
it->setNormalization(requestedNormalisation);
bool bLimitRows = getProperty("LimitRows");
int maxRows = 0;
if (bLimitRows) {
maxRows = getProperty("MaximumRows");
}
// Use the iterator to loop through each MDBoxBase and create a row for each
// entry.
int rowCounter = 0;
Progress progress(this, 0, 1, int64_t(input->getNPoints()));
while (true) {
size_t cellIndex = 0;
output->appendRow();
output->cell<double>(rowCounter, cellIndex++) = it->getNormalizedSignal();
output->cell<double>(rowCounter, cellIndex++) = it->getNormalizedError();
output->cell<int>(rowCounter, cellIndex++) = int(it->getNumEvents());
VMD center = it->getCenter();
const size_t numberOriginal = input->getNumberTransformsToOriginal();
if (transformCoordsToOriginal && numberOriginal > 0) {
const size_t index = numberOriginal - 1;
CoordTransform const *transform = input->getTransformToOriginal(index);
VMD temp = transform->applyVMD(center);
center = temp;
}
for (size_t index = 0; index < ndims; ++index) {
output->cell<double>(rowCounter, cellIndex++) = center[index];
}
progress.report();
if (!it->next() || (bLimitRows && ((rowCounter + 1) >= maxRows))) {
break;
}
rowCounter++;
}
setProperty("OutputWorkspace", output);
delete it;
//
IMDEventWorkspace_sptr mdew;
CALL_MDEVENT_FUNCTION(this->getBoxData, input);
}
/**
* Executes the algorithm.
*/
void LoadTBL::exec() {
std::string filename = getProperty("Filename");
std::ifstream file(filename.c_str());
if (!file) {
throw Exception::FileError("Unable to open file: ", filename);
}
std::string line;
ITableWorkspace_sptr ws = WorkspaceFactory::Instance().createTable();
std::vector<std::string> columnHeadings;
Kernel::Strings::extractToEOL(file, line);
// We want to check if the first line contains an empty string or series of
// ",,,,,"
// to see if we are loading a TBL file that actually contains data or not.
boost::split(columnHeadings, line, boost::is_any_of(","),
boost::token_compress_off);
for (auto entry = columnHeadings.begin(); entry != columnHeadings.end();) {
if (entry->empty()) {
// erase the empty values
entry = columnHeadings.erase(entry);
} else {
// keep any non-empty values
++entry;
}
}
if (columnHeadings.empty()) {
// we have an empty string or series of ",,,,,"
throw std::runtime_error("The file you are trying to load is Empty. \n "
"Please load a non-empty TBL file");
} else {
// set columns back to empty ready to populated with columnHeadings.
columnHeadings.clear();
}
// this will tell us if we need to just fill in the cell values
// or whether we will have to create the column headings as well.
bool isOld = getColumnHeadings(line, columnHeadings);
std::vector<std::string> rowVec;
if (isOld) {
/**THIS IS ESSENTIALLY THE OLD LoadReflTBL CODE**/
// create the column headings
auto colStitch = ws->addColumn("str", "StitchGroup");
auto colRuns = ws->addColumn("str", "Run(s)");
auto colTheta = ws->addColumn("str", "ThetaIn");
auto colTrans = ws->addColumn("str", "TransRun(s)");
auto colQmin = ws->addColumn("str", "Qmin");
auto colQmax = ws->addColumn("str", "Qmax");
auto colDqq = ws->addColumn("str", "dq/q");
auto colScale = ws->addColumn("str", "Scale");
auto colOptions = ws->addColumn("str", "Options");
auto colHiddenOptions = ws->addColumn("str", "HiddenOptions");
for (size_t i = 0; i < ws->columnCount(); i++) {
auto col = ws->getColumn(i);
col->setPlotType(0);
}
// we are using the old ReflTBL format
// where all of the entries are on one line
// so we must reset the stream to reread the first line.
std::ifstream file(filename.c_str());
if (!file) {
throw Exception::FileError("Unable to open file: ", filename);
}
std::string line;
int stitchID = 1;
while (Kernel::Strings::extractToEOL(file, line)) {
if (line.empty() || line == ",,,,,,,,,,,,,,,,") {
continue;
}
getCells(line, rowVec, 16, isOld);
const std::string scaleStr = rowVec.at(16);
const std::string stitchStr = boost::lexical_cast<std::string>(stitchID);
// check if the first run in the row has any data associated with it
// 0 = runs, 1 = theta, 2 = trans, 3 = qmin, 4 = qmax
if (!rowVec[0].empty() || !rowVec[1].empty() || !rowVec[2].empty() ||
!rowVec[3].empty() || !rowVec[4].empty()) {
TableRow row = ws->appendRow();
row << stitchStr;
for (int i = 0; i < 5; ++i) {
row << rowVec.at(i);
}
row << rowVec.at(15);
row << scaleStr;
}
// check if the second run in the row has any data associated with it
// 5 = runs, 6 = theta, 7 = trans, 8 = qmin, 9 = qmax
if (!rowVec[5].empty() || !rowVec[6].empty() || !rowVec[7].empty() ||
!rowVec[8].empty() || !rowVec[9].empty()) {
TableRow row = ws->appendRow();
row << stitchStr;
for (int i = 5; i < 10; ++i) {
row << rowVec.at(i);
}
row << rowVec.at(15);
row << scaleStr;
}
// check if the third run in the row has any data associated with it
// 10 = runs, 11 = theta, 12 = trans, 13 = qmin, 14 = qmax
if (!rowVec[10].empty() || !rowVec[11].empty() || !rowVec[12].empty() ||
!rowVec[13].empty() || !rowVec[14].empty()) {
TableRow row = ws->appendRow();
row << stitchStr;
for (int i = 10; i < 17; ++i) {
if (i == 16)
row << scaleStr;
else
row << rowVec.at(i);
}
}
++stitchID;
setProperty("OutputWorkspace", ws);
}
} else {
// we have a TBL format that contains column headings
// on the first row. These are now entries in the columns vector
if (!columnHeadings.empty()) {
// now we need to add the custom column headings from
// the columns vector to the TableWorkspace
for (auto heading = columnHeadings.begin();
heading != columnHeadings.end();) {
if (heading->empty()) {
// there is no need to have empty column headings.
heading = columnHeadings.erase(heading);
} else {
Mantid::API::Column_sptr col;
col = ws->addColumn("str", *heading);
col->setPlotType(0);
heading++;
}
}
}
size_t expectedCommas = columnHeadings.size() - 1;
while (Kernel::Strings::extractToEOL(file, line)) {
if (line.empty() || line == ",,,,,,,,,,,,,,,,") {
// skip over any empty lines
continue;
}
getCells(line, rowVec, columnHeadings.size() - 1, isOld);
// populate the columns with their values for this row.
TableRow row = ws->appendRow();
for (size_t i = 0; i < expectedCommas + 1; ++i) {
row << rowVec.at(i);
}
}
setProperty("OutputWorkspace", ws);
}
}