/**
* Removes exponential decay from a workspace
* @param wsInput :: [input] Workspace to work on
* @return :: Workspace with decay removed
*/
API::MatrixWorkspace_sptr CalMuonDetectorPhases::removeExpDecay(
const API::MatrixWorkspace_sptr &wsInput) {
API::IAlgorithm_sptr remove = createChildAlgorithm("RemoveExpDecay");
remove->setProperty("InputWorkspace", wsInput);
remove->executeAsChildAlg();
API::MatrixWorkspace_sptr wsRem = remove->getProperty("OutputWorkspace");
return wsRem;
}
/** Call diffraction focus to a matrix workspace.
*/
API::MatrixWorkspace_sptr
AlignAndFocusPowder::diffractionFocus(API::MatrixWorkspace_sptr ws) {
if (!m_groupWS) {
g_log.information() << "not focussing data\n";
return ws;
}
g_log.information() << "running DiffractionFocussing. \n";
API::IAlgorithm_sptr focusAlg = createChildAlgorithm("DiffractionFocussing");
focusAlg->setProperty("InputWorkspace", ws);
focusAlg->setProperty("OutputWorkspace", ws);
focusAlg->setProperty("GroupingWorkspace", m_groupWS);
focusAlg->setProperty("PreserveEvents", m_preserveEvents);
focusAlg->executeAsChildAlg();
ws = focusAlg->getProperty("OutputWorkspace");
return ws;
}
/** Rebin
*/
API::MatrixWorkspace_sptr
AlignAndFocusPowder::rebin(API::MatrixWorkspace_sptr matrixws) {
if (m_resampleX != 0) {
// ResampleX
g_log.information() << "running ResampleX(NumberBins=" << abs(m_resampleX)
<< ", LogBinning=" << (m_resampleX < 0) << ", dMin("
<< m_dmins.size() << "), dmax(" << m_dmaxs.size()
<< ")) started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr alg = createChildAlgorithm("ResampleX");
alg->setProperty("InputWorkspace", matrixws);
alg->setProperty("OutputWorkspace", matrixws);
if ((!m_dmins.empty()) && (!m_dmaxs.empty())) {
size_t numHist = m_outputW->getNumberHistograms();
if ((numHist == m_dmins.size()) && (numHist == m_dmaxs.size())) {
alg->setProperty("XMin", m_dmins);
alg->setProperty("XMax", m_dmaxs);
} else {
g_log.information()
<< "Number of dmin and dmax values don't match the "
<< "number of workspace indices. Ignoring the parameters.\n";
}
}
alg->setProperty("NumberBins", abs(m_resampleX));
alg->setProperty("LogBinning", (m_resampleX < 0));
alg->executeAsChildAlg();
matrixws = alg->getProperty("OutputWorkspace");
return matrixws;
} else {
g_log.information() << "running Rebin( ";
for (double param : m_params)
g_log.information() << param << " ";
g_log.information() << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr rebin3Alg = createChildAlgorithm("Rebin");
rebin3Alg->setProperty("InputWorkspace", matrixws);
rebin3Alg->setProperty("OutputWorkspace", matrixws);
rebin3Alg->setProperty("Params", m_params);
rebin3Alg->executeAsChildAlg();
matrixws = rebin3Alg->getProperty("OutputWorkspace");
return matrixws;
}
}
void LoadILLSANS::moveDetectorVertical(double shift,
const std::string &componentName) {
API::IAlgorithm_sptr mover = createChildAlgorithm("MoveInstrumentComponent");
V3D pos = getComponentPosition(componentName);
try {
mover->setProperty<MatrixWorkspace_sptr>("Workspace", m_localWorkspace);
mover->setProperty("ComponentName", componentName);
mover->setProperty("X", pos.X());
mover->setProperty("Y", shift);
mover->setProperty("Z", pos.Z());
mover->setProperty("RelativePosition", false);
mover->executeAsChildAlg();
g_log.debug() << "Moving component '" << componentName
<< "' to Y = " << shift << '\n';
} catch (std::exception &e) {
g_log.error() << "Cannot move the component '" << componentName
<< "' to Y = " << shift << '\n';
g_log.error() << e.what() << '\n';
}
}
/** Call edit instrument geometry
*/
API::MatrixWorkspace_sptr AlignAndFocusPowder::editInstrument(
API::MatrixWorkspace_sptr ws, std::vector<double> polars,
std::vector<specnum_t> specids, std::vector<double> l2s,
std::vector<double> phis) {
g_log.information() << "running EditInstrumentGeometry started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr editAlg = createChildAlgorithm("EditInstrumentGeometry");
editAlg->setProperty("Workspace", ws);
if (m_l1 > 0.)
editAlg->setProperty("PrimaryFlightPath", m_l1);
if (!polars.empty())
editAlg->setProperty("Polar", polars);
if (!specids.empty())
editAlg->setProperty("SpectrumIDs", specids);
if (!l2s.empty())
editAlg->setProperty("L2", l2s);
if (!phis.empty())
editAlg->setProperty("Azimuthal", phis);
editAlg->executeAsChildAlg();
ws = editAlg->getProperty("Workspace");
return ws;
}
/** Perform SortHKL on the output workspaces
*
* @param ws :: any PeaksWorkspace
* @param runName :: string to put in statistics table
*/
void StatisticsOfPeaksWorkspace::doSortHKL(Mantid::API::Workspace_sptr ws,
std::string runName) {
std::string pointGroup = getPropertyValue("PointGroup");
std::string latticeCentering = getPropertyValue("LatticeCentering");
std::string wkspName = getPropertyValue("OutputWorkspace");
std::string tableName = getPropertyValue("StatisticsTable");
API::IAlgorithm_sptr statsAlg = createChildAlgorithm("SortHKL");
statsAlg->setProperty("InputWorkspace", ws);
statsAlg->setPropertyValue("OutputWorkspace", wkspName);
statsAlg->setPropertyValue("StatisticsTable", tableName);
statsAlg->setProperty("PointGroup", pointGroup);
statsAlg->setProperty("LatticeCentering", latticeCentering);
statsAlg->setProperty("RowName", runName);
if (runName.compare("Overall") != 0)
statsAlg->setProperty("Append", true);
statsAlg->executeAsChildAlg();
PeaksWorkspace_sptr statsWksp = statsAlg->getProperty("OutputWorkspace");
ITableWorkspace_sptr tablews = statsAlg->getProperty("StatisticsTable");
if (runName.compare("Overall") == 0)
setProperty("OutputWorkspace", statsWksp);
setProperty("StatisticsTable", tablews);
}
/**
* Places the detector at the right sample_detector_distance
*/
void LoadSpice2D::moveDetector(double sample_detector_distance) {
// Move the detector to the right position
API::IAlgorithm_sptr mover = createChildAlgorithm("MoveInstrumentComponent");
// Finding the name of the detector object.
std::string detID =
m_workspace->getInstrument()->getStringParameter("detector-name")[0];
g_log.information("Moving " + detID);
try {
mover->setProperty<API::MatrixWorkspace_sptr>("Workspace", m_workspace);
mover->setProperty("ComponentName", detID);
mover->setProperty("Z", sample_detector_distance / 1000.0);
mover->execute();
} catch (std::invalid_argument &e) {
g_log.error("Invalid argument to MoveInstrumentComponent Child Algorithm");
g_log.error(e.what());
} catch (std::runtime_error &e) {
g_log.error(
"Unable to successfully run MoveInstrumentComponent Child Algorithm");
g_log.error(e.what());
}
}
/** Fit function
* Minimizer: "Levenberg-MarquardtMD"/"Simplex"
*/
bool RefinePowderInstrumentParameters2::doFitFunction(IFunction_sptr function, Workspace2D_sptr dataws, int wsindex,
string minimizer, int numiters, double& chi2, string& fitstatus)
{
// 0. Debug output
stringstream outss;
outss << "Fit function: " << m_positionFunc->asString() << endl << "Data To Fit: \n";
for (size_t i = 0; i < dataws->readX(0).size(); ++i)
outss << dataws->readX(wsindex)[i] << "\t\t" << dataws->readY(wsindex)[i] << "\t\t"
<< dataws->readE(wsindex)[i] << "\n";
g_log.information() << outss.str();
// 1. Create and setup fit algorithm
API::IAlgorithm_sptr fitalg = createChildAlgorithm("Fit", 0.0, 0.2, true);
fitalg->initialize();
fitalg->setProperty("Function", function);
fitalg->setProperty("InputWorkspace", dataws);
fitalg->setProperty("WorkspaceIndex", wsindex);
fitalg->setProperty("Minimizer", minimizer);
fitalg->setProperty("CostFunction", "Least squares");
fitalg->setProperty("MaxIterations", numiters);
fitalg->setProperty("CalcErrors", true);
// 2. Fit
bool successfulfit = fitalg->execute();
if (!fitalg->isExecuted() || ! successfulfit)
{
// Early return due to bad fit
g_log.warning("Fitting to instrument geometry function failed. ");
chi2 = DBL_MAX;
fitstatus = "Minimizer throws exception.";
return false;
}
// 3. Understand solution
chi2 = fitalg->getProperty("OutputChi2overDoF");
string tempfitstatus = fitalg->getProperty("OutputStatus");
fitstatus = tempfitstatus;
bool goodfit = fitstatus.compare("success") == 0;
stringstream dbss;
dbss << "Fit Result (GSL): Chi^2 = " << chi2
<< "; Fit Status = " << fitstatus << ", Return Bool = " << goodfit << std::endl;
vector<string> funcparnames = function->getParameterNames();
for (size_t i = 0; i < funcparnames.size(); ++i)
dbss << funcparnames[i] << " = " << setw(20) << function->getParameter(funcparnames[i])
<< " +/- " << function->getError(i) << "\n";
g_log.debug() << dbss.str();
return goodfit;
}
/// Run ConvertUnits as a sub-algorithm to convert to dSpacing
MatrixWorkspace_sptr DiffractionFocussing::convertUnitsToDSpacing(const API::MatrixWorkspace_sptr& workspace)
{
const std::string CONVERSION_UNIT = "dSpacing";
Unit_const_sptr xUnit = workspace->getAxis(0)->unit();
g_log.information() << "Converting units from "<< xUnit->label() << " to " << CONVERSION_UNIT<<".\n";
API::IAlgorithm_sptr childAlg = createSubAlgorithm("ConvertUnits", 0.34, 0.66);
childAlg->setProperty("InputWorkspace", workspace);
childAlg->setPropertyValue("Target",CONVERSION_UNIT);
childAlg->executeAsSubAlg();
return childAlg->getProperty("OutputWorkspace");
}
/** Run the Child Algorithm LoadInstrument (as for LoadRaw)
* @param inst_name :: The name written in the Nexus file
* @param localWorkspace :: The workspace to insert the instrument into
*/
void LoadSpice2D::runLoadInstrument(
const std::string &inst_name,
DataObjects::Workspace2D_sptr localWorkspace) {
API::IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrument");
// Now execute the Child Algorithm. Catch and log any error, but don't stop.
try {
loadInst->setPropertyValue("InstrumentName", inst_name);
loadInst->setProperty<API::MatrixWorkspace_sptr>("Workspace",
localWorkspace);
loadInst->setProperty("RewriteSpectraMap",
Mantid::Kernel::OptionalBool(true));
loadInst->execute();
} catch (std::invalid_argument &) {
g_log.information("Invalid argument to LoadInstrument Child Algorithm");
} catch (std::runtime_error &) {
g_log.information(
"Unable to successfully run LoadInstrument Child Algorithm");
}
}
/** Select background automatically
*/
DataObjects::Workspace2D_sptr
ProcessBackground::autoBackgroundSelection(Workspace2D_sptr bkgdWS) {
// Get background type and create bakground function
BackgroundFunction_sptr bkgdfunction = createBackgroundFunction(m_bkgdType);
int bkgdorder = getProperty("BackgroundOrder");
if (bkgdorder == 0)
g_log.warning("(Input) background function order is 0. It might not be "
"able to give a good estimation.");
bkgdfunction->setAttributeValue("n", bkgdorder);
bkgdfunction->initialize();
g_log.information() << "Input background points has "
<< bkgdWS->readX(0).size() << " data points for fit "
<< bkgdorder << "-th order " << bkgdfunction->name()
<< " (background) function" << bkgdfunction->asString()
<< "\n";
// Fit input (a few) background pionts to get initial guess
API::IAlgorithm_sptr fit;
try {
fit = this->createChildAlgorithm("Fit", 0.0, 0.2, true);
} catch (Exception::NotFoundError &) {
g_log.error() << "Requires CurveFitting library." << std::endl;
throw;
}
double startx = m_lowerBound;
double endx = m_upperBound;
fit->setProperty("Function",
boost::dynamic_pointer_cast<API::IFunction>(bkgdfunction));
fit->setProperty("InputWorkspace", bkgdWS);
fit->setProperty("WorkspaceIndex", 0);
fit->setProperty("MaxIterations", 500);
fit->setProperty("StartX", startx);
fit->setProperty("EndX", endx);
fit->setProperty("Minimizer", "Levenberg-Marquardt");
fit->setProperty("CostFunction", "Least squares");
fit->executeAsChildAlg();
// Get fit result
// a) Status
std::string fitStatus = fit->getProperty("OutputStatus");
bool allowedfailure = (fitStatus.find("cannot") < fitStatus.size()) &&
(fitStatus.find("tolerance") < fitStatus.size());
if (fitStatus.compare("success") != 0 && !allowedfailure) {
g_log.error() << "ProcessBackground: Fit Status = " << fitStatus
<< ". Not to update fit result" << std::endl;
throw std::runtime_error("Bad Fit");
}
// b) check that chi2 got better
const double chi2 = fit->getProperty("OutputChi2overDoF");
g_log.information() << "Fit background: Fit Status = " << fitStatus
<< ", chi2 = " << chi2 << "\n";
// Filter and construct for the output workspace
Workspace2D_sptr outws = filterForBackground(bkgdfunction);
return outws;
} // END OF FUNCTION
/** Fit background function
*/
void ProcessBackground::fitBackgroundFunction(std::string bkgdfunctiontype) {
// Get background type and create bakground function
BackgroundFunction_sptr bkgdfunction =
createBackgroundFunction(bkgdfunctiontype);
int bkgdorder = getProperty("OutputBackgroundOrder");
bkgdfunction->setAttributeValue("n", bkgdorder);
if (bkgdfunctiontype == "Chebyshev") {
double xmin = m_outputWS->readX(0).front();
double xmax = m_outputWS->readX(0).back();
g_log.information() << "Chebyshev Fit range: " << xmin << ", " << xmax
<< "\n";
bkgdfunction->setAttributeValue("StartX", xmin);
bkgdfunction->setAttributeValue("EndX", xmax);
}
g_log.information() << "Fit selected background " << bkgdfunctiontype
<< " to data workspace with "
<< m_outputWS->getNumberHistograms() << " spectra."
<< "\n";
// Fit input (a few) background pionts to get initial guess
API::IAlgorithm_sptr fit;
try {
fit = this->createChildAlgorithm("Fit", 0.9, 1.0, true);
} catch (Exception::NotFoundError &) {
g_log.error() << "Requires CurveFitting library." << std::endl;
throw;
}
g_log.information() << "Fitting background function: "
<< bkgdfunction->asString() << "\n";
double startx = m_lowerBound;
double endx = m_upperBound;
fit->setProperty("Function",
boost::dynamic_pointer_cast<API::IFunction>(bkgdfunction));
fit->setProperty("InputWorkspace", m_outputWS);
fit->setProperty("WorkspaceIndex", 0);
fit->setProperty("MaxIterations", 500);
fit->setProperty("StartX", startx);
fit->setProperty("EndX", endx);
fit->setProperty("Minimizer", "Levenberg-MarquardtMD");
fit->setProperty("CostFunction", "Least squares");
fit->executeAsChildAlg();
// Get fit status and chi^2
std::string fitStatus = fit->getProperty("OutputStatus");
bool allowedfailure = (fitStatus.find("cannot") < fitStatus.size()) &&
(fitStatus.find("tolerance") < fitStatus.size());
if (fitStatus.compare("success") != 0 && !allowedfailure) {
g_log.error() << "ProcessBackground: Fit Status = " << fitStatus
<< ". Not to update fit result" << std::endl;
throw std::runtime_error("Bad Fit");
}
const double chi2 = fit->getProperty("OutputChi2overDoF");
g_log.information() << "Fit background: Fit Status = " << fitStatus
<< ", chi2 = " << chi2 << "\n";
// Get out the parameter names
API::IFunction_sptr funcout = fit->getProperty("Function");
TableWorkspace_sptr outbkgdparws = boost::make_shared<TableWorkspace>();
outbkgdparws->addColumn("str", "Name");
outbkgdparws->addColumn("double", "Value");
TableRow typerow = outbkgdparws->appendRow();
typerow << bkgdfunctiontype << 0.;
vector<string> parnames = funcout->getParameterNames();
size_t nparam = funcout->nParams();
for (size_t i = 0; i < nparam; ++i) {
TableRow newrow = outbkgdparws->appendRow();
newrow << parnames[i] << funcout->getParameter(i);
}
TableRow chi2row = outbkgdparws->appendRow();
chi2row << "Chi-square" << chi2;
g_log.information() << "Set table workspace (#row = "
<< outbkgdparws->rowCount()
<< ") to OutputBackgroundParameterTable. "
<< "\n";
setProperty("OutputBackgroundParameterWorkspace", outbkgdparws);
// Set output workspace
const MantidVec &vecX = m_outputWS->readX(0);
const MantidVec &vecY = m_outputWS->readY(0);
FunctionDomain1DVector domain(vecX);
FunctionValues values(domain);
funcout->function(domain, values);
MantidVec &dataModel = m_outputWS->dataY(1);
MantidVec &dataDiff = m_outputWS->dataY(2);
for (size_t i = 0; i < dataModel.size(); ++i) {
dataModel[i] = values[i];
dataDiff[i] = vecY[i] - dataModel[i];
}
return;
}
void MaskBinsFromTable::exec()
{
MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
DataObjects::TableWorkspace_sptr paramWS = getProperty("MaskingInformation");
// 1. Check input table workspace and column order
g_log.debug() << "Lines of parameters workspace = " << paramWS->rowCount() << std::endl;
bool colname_specx = false;
if (!paramWS)
{
throw std::invalid_argument("Input table workspace is not accepted.");
}
else
{
std::vector<std::string> colnames = paramWS->getColumnNames();
// check colum name order
if (colnames.size() < 3)
{
g_log.error() << "Input MaskingInformation table workspace has fewer than 3 columns. " << colnames.size()
<< " columns indeed" << std::endl;
throw std::invalid_argument("MaskingInformation (TableWorkspace) has too few columns.");
}
if (colnames[0].compare("XMin") == 0)
{
// 1. Style XMin, XMax, SpectraList. Check rest
if (colnames[1].compare("XMax") != 0 || colnames[2].compare("SpectraList") != 0)
{
g_log.error() << "INput MaskingInformation table workspace has wrong column order. " << std::endl;
throw std::invalid_argument("MaskingInformation (TableWorkspace) has too few columns.");
}
}
else if (colnames[0].compare("SpectraList") == 0)
{
// 2. Style SpectraList, XMin, XMax
colname_specx = true;
if (colnames[1].compare("XMin") != 0 || colnames[2].compare("XMax") != 0)
{
g_log.error() << "INput MaskingInformation table workspace has wrong column order. " << std::endl;
throw std::invalid_argument("MaskingInformation (TableWorkspace) has too few columns.");
}
}
else
{
g_log.error() << "INput MaskingInformation table workspace has wrong column order. " << std::endl;
throw std::invalid_argument("MaskingInformation (TableWorkspace) has too few columns.");
}
}
// 2. Loop over all rows
bool firstloop = true;
API::MatrixWorkspace_sptr outputws = this->getProperty("OutputWorkspace");
for (size_t ib = 0; ib < paramWS->rowCount(); ++ib)
{
API::TableRow therow = paramWS->getRow(ib);
double xmin, xmax;
std::string speclist;
if (colname_specx)
{
therow >> speclist >> xmin >> xmax;
}
else
{
therow >> xmin >> xmax >> speclist;
}
g_log.debug() << "Row " << ib << " XMin = " << xmin << " XMax = " << xmax << " SpectraList = " << speclist << std::endl;
API::IAlgorithm_sptr maskbins = this->createChildAlgorithm("MaskBins", 0, 0.3, true);
maskbins->initialize();
if (firstloop)
{
maskbins->setProperty("InputWorkspace", inputWS);
firstloop = false;
}
else
{
maskbins->setProperty("InputWorkspace", outputws);
}
maskbins->setProperty("OutputWorkspace", outputws);
maskbins->setPropertyValue("SpectraList", speclist);
maskbins->setProperty("XMin", xmin);
maskbins->setProperty("XMax", xmax);
bool isexec = maskbins->execute();
if (!isexec)
{
g_log.error() << "MaskBins() is not executed for row " << ib << std::endl;
throw std::runtime_error("MaskBins() is not executed");
}
outputws = maskbins->getProperty("OutputWorkspace");
if (!outputws)
{
g_log.error() << "OutputWorkspace is not retrieved for row " << ib << ". " << std::endl;
throw std::runtime_error("OutputWorkspace is not got from MaskBins");
}
}
void GetDetOffsetsMultiPeaks::fitSpectra(const int64_t s, MatrixWorkspace_sptr inputW, const std::vector<double> &peakPositions,
const std::vector<double> &fitWindows, size_t &nparams, double &minD, double &maxD,
std::vector<double>&peakPosToFit, std::vector<double>&peakPosFitted,
std::vector<double> &chisq)
{
const MantidVec & X = inputW->readX(s);
minD = X.front();
maxD = X.back();
bool useFitWindows = (!fitWindows.empty());
std::vector<double> fitWindowsToUse;
for (int i = 0; i < static_cast<int>(peakPositions.size()); ++i)
{
if((peakPositions[i] > minD) && (peakPositions[i] < maxD))
{
peakPosToFit.push_back(peakPositions[i]);
if (useFitWindows)
{
fitWindowsToUse.push_back(std::max(fitWindows[2*i], minD));
fitWindowsToUse.push_back(std::min(fitWindows[2*i+1], maxD));
}
}
}
API::IAlgorithm_sptr findpeaks = createChildAlgorithm("FindPeaks", -1, -1, false);
findpeaks->setProperty("InputWorkspace", inputW);
findpeaks->setProperty<int>("FWHM",7);
findpeaks->setProperty<int>("Tolerance",4);
// FindPeaks will do the checking on the validity of WorkspaceIndex
findpeaks->setProperty("WorkspaceIndex",static_cast<int>(s));
//Get the specified peak positions, which is optional
findpeaks->setProperty("PeakPositions", peakPosToFit);
if (useFitWindows)
findpeaks->setProperty("FitWindows", fitWindowsToUse);
findpeaks->setProperty<std::string>("PeakFunction", m_peakType);
findpeaks->setProperty<std::string>("BackgroundType", m_backType);
findpeaks->setProperty<bool>("HighBackground", this->getProperty("HighBackground"));
findpeaks->setProperty<int>("MinGuessedPeakWidth",4);
findpeaks->setProperty<int>("MaxGuessedPeakWidth",4);
findpeaks->executeAsChildAlg();
ITableWorkspace_sptr peakslist = findpeaks->getProperty("PeaksList");
std::vector<size_t> banned;
std::vector<double> peakWidFitted;
std::vector<double> peakHighFitted;
std::vector<double> peakBackground;
for (size_t i = 0; i < peakslist->rowCount(); ++i)
{
// peak value
double centre = peakslist->getRef<double>("centre",i);
double width = peakslist->getRef<double>("width",i);
double height = peakslist->getRef<double>("height", i);
// background value
double back_intercept = peakslist->getRef<double>("backgroundintercept", i);
double back_slope = peakslist->getRef<double>("backgroundslope", i);
double back_quad = peakslist->getRef<double>("A2", i);
double background = back_intercept + back_slope * centre
+ back_quad * centre * centre;
// goodness of fit
double chi2 = peakslist->getRef<double>("chi2",i);
// Get references to the data
peakPosFitted.push_back(centre);
peakWidFitted.push_back(width);
peakHighFitted.push_back(height);
peakBackground.push_back(background);
chisq.push_back(chi2);
}
// first remove things that just didn't fit (center outside of window, bad chisq, ...)
for (size_t i = 0; i < peakslist->rowCount(); ++i)
{
if (peakPosFitted[i] <= minD || peakPosFitted[i] >= maxD)
{
banned.push_back(i);
continue;
}
else if (useFitWindows) // be more restrictive if fit windows were specified
{
if (peakPosFitted[i] <= fitWindowsToUse[2*i]
|| peakPosFitted[i] >= fitWindowsToUse[2*i+1])
{
banned.push_back(i);
continue;
}
}
if (chisq[i] > m_maxChiSq)
{
banned.push_back(i);
continue;
}
}
// delete banned peaks
g_log.debug() << "Deleting " << banned.size() << " of " << peakPosFitted.size()
<< " peaks in wkspindex = " << s << "\n";
deletePeaks(banned, peakPosToFit, peakPosFitted,
peakWidFitted, peakHighFitted, peakBackground,
chisq);
// ban peaks that are low intensity compared to their widths
for (size_t i = 0; i < peakWidFitted.size(); ++i)
{
if (peakHighFitted[i] * FWHM_TO_SIGMA / peakWidFitted[i] < 5.)
{
g_log.debug() << "Banning peak at " << peakPosFitted[i] << " in wkspindex = " << s
<< " I/sigma = " << (peakHighFitted[i] * FWHM_TO_SIGMA / peakWidFitted[i]) << "\n";
banned.push_back(i);
continue;
}
}
// delete banned peaks
g_log.debug() << "Deleting " << banned.size() << " of " << peakPosFitted.size()
<< " peaks in wkspindex = " << s << "\n";
deletePeaks(banned, peakPosToFit, peakPosFitted,
peakWidFitted, peakHighFitted, peakBackground,
chisq);
// determine the (z-value) for constant "width" - (delta d)/d
std::vector<double> widthDivPos(peakWidFitted.size(), 0.); // DELETEME
for (size_t i = 0; i < peakWidFitted.size(); ++i)
{
widthDivPos[i] = peakWidFitted[i] / peakPosFitted[i]; // DELETEME
}
std::vector<double> Zscore = getZscore(widthDivPos);
for (size_t i = 0; i < peakWidFitted.size(); ++i)
{
if (Zscore[i] > 2.0)
{
g_log.debug() << "Banning peak at " << peakPosFitted[i] << " in wkspindex = " << s
<< " sigma/d = " << widthDivPos[i] << "\n";
banned.push_back(i);
continue;
}
}
// delete banned peaks
g_log.debug() << "Deleting " << banned.size() << " of " << peakPosFitted.size()
<< " peaks in wkspindex = " << s << "\n";
deletePeaks(banned, peakPosToFit, peakPosFitted,
peakWidFitted, peakHighFitted, peakBackground,
chisq);
// ban peaks that are not outside of error bars for the background
for (size_t i = 0; i < peakWidFitted.size(); ++i)
{
if (peakHighFitted[i] < 0.5 * std::sqrt(peakHighFitted[i] + peakBackground[i]))
{
g_log.debug() << "Banning peak at " << peakPosFitted[i] << " in wkspindex = " << s
<< " " << peakHighFitted[i] << " < "
<< 0.5 * std::sqrt(peakHighFitted[i] + peakBackground[i]) << "\n";
banned.push_back(i);
continue;
}
}
// delete banned peaks
g_log.debug() << "Deleting " << banned.size() << " of " << peakPosFitted.size()
<< " peaks in wkspindex = " << s << "\n";
deletePeaks(banned, peakPosToFit, peakPosFitted,
peakWidFitted, peakHighFitted, peakBackground,
chisq);
nparams = peakPosFitted.size();
return;
}
/// Overwrites Algorithm exec method
void LoadSpice2D::exec()
{
std::string fileName = getPropertyValue("Filename");
const double wavelength_input = getProperty("Wavelength");
const double wavelength_spread_input = getProperty("WavelengthSpread");
// Set up the DOM parser and parse xml file
DOMParser pParser;
Document* pDoc;
try
{
pDoc = pParser.parse(fileName);
} catch (...)
{
throw Kernel::Exception::FileError("Unable to parse File:", fileName);
}
// Get pointer to root element
Element* pRootElem = pDoc->documentElement();
if (!pRootElem->hasChildNodes())
{
throw Kernel::Exception::NotFoundError("No root element in Spice XML file", fileName);
}
// Read in start time
const std::string start_time = pRootElem->getAttribute("start_time");
Element* sasEntryElem = pRootElem->getChildElement("Header");
throwException(sasEntryElem, "Header", fileName);
// Read in scan title
Element* element = sasEntryElem->getChildElement("Scan_Title");
throwException(element, "Scan_Title", fileName);
std::string wsTitle = element->innerText();
// Read in instrument name
element = sasEntryElem->getChildElement("Instrument");
throwException(element, "Instrument", fileName);
std::string instrument = element->innerText();
// Read sample thickness
double sample_thickness = 0;
from_element<double>(sample_thickness, sasEntryElem, "Sample_Thickness", fileName);
double source_apert = 0.0;
from_element<double>(source_apert, sasEntryElem, "source_aperture_size", fileName);
double sample_apert = 0.0;
from_element<double>(sample_apert, sasEntryElem, "sample_aperture_size", fileName);
double source_distance = 0.0;
from_element<double>(source_distance, sasEntryElem, "source_distance", fileName);
// Read in wavelength and wavelength spread
double wavelength = 0;
double dwavelength = 0;
if ( isEmpty(wavelength_input) ) {
from_element<double>(wavelength, sasEntryElem, "wavelength", fileName);
from_element<double>(dwavelength, sasEntryElem, "wavelength_spread", fileName);
}
else
{
wavelength = wavelength_input;
dwavelength = wavelength_spread_input;
}
// Read in positions
sasEntryElem = pRootElem->getChildElement("Motor_Positions");
throwException(sasEntryElem, "Motor_Positions", fileName);
// Read in the number of guides
int nguides = 0;
from_element<int>(nguides, sasEntryElem, "nguides", fileName);
// Read in sample-detector distance in mm
double distance = 0;
from_element<double>(distance, sasEntryElem, "sample_det_dist", fileName);
distance *= 1000.0;
// Read in beam trap positions
double highest_trap = 0;
double trap_pos = 0;
from_element<double>(trap_pos, sasEntryElem, "trap_y_25mm", fileName);
double beam_trap_diam = 25.4;
from_element<double>(highest_trap, sasEntryElem, "trap_y_101mm", fileName);
if (trap_pos>highest_trap)
{
highest_trap = trap_pos;
beam_trap_diam = 101.6;
}
from_element<double>(trap_pos, sasEntryElem, "trap_y_50mm", fileName);
if (trap_pos>highest_trap)
{
highest_trap = trap_pos;
beam_trap_diam = 50.8;
}
from_element<double>(trap_pos, sasEntryElem, "trap_y_76mm", fileName);
if (trap_pos>highest_trap)
{
highest_trap = trap_pos;
beam_trap_diam = 76.2;
}
// Read in counters
sasEntryElem = pRootElem->getChildElement("Counters");
throwException(sasEntryElem, "Counters", fileName);
double countingTime = 0;
from_element<double>(countingTime, sasEntryElem, "time", fileName);
double monitorCounts = 0;
from_element<double>(monitorCounts, sasEntryElem, "monitor", fileName);
// Read in the data image
Element* sasDataElem = pRootElem->getChildElement("Data");
throwException(sasDataElem, "Data", fileName);
// Read in the data buffer
element = sasDataElem->getChildElement("Detector");
throwException(element, "Detector", fileName);
std::string data_str = element->innerText();
// Read in the detector dimensions from the Detector tag
int numberXPixels = 0;
int numberYPixels = 0;
std::string data_type = element->getAttribute("type");
boost::regex b_re_sig("INT\\d+\\[(\\d+),(\\d+)\\]");
if (boost::regex_match(data_type, b_re_sig))
{
boost::match_results<std::string::const_iterator> match;
boost::regex_search(data_type, match, b_re_sig);
// match[0] is the full string
Kernel::Strings::convert(match[1], numberXPixels);
Kernel::Strings::convert(match[2], numberYPixels);
}
if (numberXPixels==0 || numberYPixels==0)
g_log.notice() << "Could not read in the number of pixels!" << std::endl;
// We no longer read from the meta data because that data is wrong
//from_element<int>(numberXPixels, sasEntryElem, "Number_of_X_Pixels", fileName);
//from_element<int>(numberYPixels, sasEntryElem, "Number_of_Y_Pixels", fileName);
// Store sample-detector distance
declareProperty("SampleDetectorDistance", distance, Kernel::Direction::Output);
// Create the output workspace
// Number of bins: we use a single dummy TOF bin
int nBins = 1;
// Number of detectors: should be pulled from the geometry description. Use detector pixels for now.
// The number of spectram also includes the monitor and the timer.
int numSpectra = numberXPixels*numberYPixels + LoadSpice2D::nMonitors;
DataObjects::Workspace2D_sptr ws = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
API::WorkspaceFactory::Instance().create("Workspace2D", numSpectra, nBins+1, nBins));
ws->setTitle(wsTitle);
ws->getAxis(0)->unit() = Kernel::UnitFactory::Instance().create("Wavelength");
ws->setYUnit("");
API::Workspace_sptr workspace = boost::static_pointer_cast<API::Workspace>(ws);
setProperty("OutputWorkspace", workspace);
// Parse out each pixel. Pixels can be separated by white space, a tab, or an end-of-line character
Poco::StringTokenizer pixels(data_str, " \n\t", Poco::StringTokenizer::TOK_TRIM | Poco::StringTokenizer::TOK_IGNORE_EMPTY);
Poco::StringTokenizer::Iterator pixel = pixels.begin();
// Check that we don't keep within the size of the workspace
size_t pixelcount = pixels.count();
if( pixelcount != static_cast<size_t>(numberXPixels*numberYPixels) )
{
throw Kernel::Exception::FileError("Inconsistent data set: "
"There were more data pixels found than declared in the Spice XML meta-data.", fileName);
}
if( numSpectra == 0 )
{
throw Kernel::Exception::FileError("Empty data set: the data file has no pixel data.", fileName);
}
// Go through all detectors/channels
int ipixel = 0;
// Store monitor count
store_value(ws, ipixel++, monitorCounts, monitorCounts>0 ? sqrt(monitorCounts) : 0.0,
wavelength, dwavelength);
// Store counting time
store_value(ws, ipixel++, countingTime, 0.0, wavelength, dwavelength);
// Store detector pixels
while (pixel != pixels.end())
{
//int ix = ipixel%npixelsx;
//int iy = (int)ipixel/npixelsx;
// Get the count value and assign it to the right bin
double count = 0.0;
from_string<double>(count, *pixel, std::dec);
// Data uncertainties, computed according to the HFIR/IGOR reduction code
// The following is what I would suggest instead...
// error = count > 0 ? sqrt((double)count) : 0.0;
double error = sqrt( 0.5 + fabs( count - 0.5 ));
store_value(ws, ipixel, count, error, wavelength, dwavelength);
// Set the spectrum number
ws->getAxis(1)->setValue(ipixel, ipixel);
++pixel;
ipixel++;
}
// run load instrument
runLoadInstrument(instrument, ws);
runLoadMappingTable(ws, numberXPixels, numberYPixels);
// Set the run properties
ws->mutableRun().addProperty("sample-detector-distance", distance, "mm", true);
ws->mutableRun().addProperty("beam-trap-diameter", beam_trap_diam, "mm", true);
ws->mutableRun().addProperty("number-of-guides", nguides, true);
ws->mutableRun().addProperty("source-sample-distance", source_distance, "mm", true);
ws->mutableRun().addProperty("source-aperture-diameter", source_apert, "mm", true);
ws->mutableRun().addProperty("sample-aperture-diameter", sample_apert, "mm", true);
ws->mutableRun().addProperty("sample-thickness", sample_thickness, "cm", true);
ws->mutableRun().addProperty("wavelength", wavelength, "Angstrom", true);
ws->mutableRun().addProperty("wavelength-spread", dwavelength, "Angstrom", true);
ws->mutableRun().addProperty("timer", countingTime, "sec", true);
ws->mutableRun().addProperty("monitor", monitorCounts, "", true);
ws->mutableRun().addProperty("start_time", start_time, "", true);
ws->mutableRun().addProperty("run_start", start_time, "", true);
// Move the detector to the right position
API::IAlgorithm_sptr mover = createChildAlgorithm("MoveInstrumentComponent");
// Finding the name of the detector object.
std::string detID = ws->getInstrument()->getStringParameter("detector-name")[0];
g_log.information("Moving "+detID);
try
{
mover->setProperty<API::MatrixWorkspace_sptr> ("Workspace", ws);
mover->setProperty("ComponentName", detID);
mover->setProperty("Z", distance/1000.0);
mover->execute();
} catch (std::invalid_argument& e)
{
g_log.error("Invalid argument to MoveInstrumentComponent Child Algorithm");
g_log.error(e.what());
} catch (std::runtime_error& e)
{
g_log.error("Unable to successfully run MoveInstrumentComponent Child Algorithm");
g_log.error(e.what());
}
// Release the XML document memory
pDoc->release();
}
/** Executes the algorithm
* @throw Exception::FileError If the grouping file cannot be opened or read
* successfully
* @throw runtime_error If unable to run one of the Child Algorithms
* successfully
*/
void AlignAndFocusPowder::exec() {
// retrieve the properties
m_inputW = getProperty("InputWorkspace");
m_inputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_inputW);
m_instName = m_inputW->getInstrument()->getName();
m_instName =
Kernel::ConfigService::Instance().getInstrument(m_instName).shortName();
std::string calFilename = getPropertyValue("CalFileName");
std::string groupFilename = getPropertyValue("GroupFilename");
m_calibrationWS = getProperty("CalibrationWorkspace");
m_maskWS = getProperty("MaskWorkspace");
m_groupWS = getProperty("GroupingWorkspace");
DataObjects::TableWorkspace_sptr maskBinTableWS = getProperty("MaskBinTable");
m_l1 = getProperty("PrimaryFlightPath");
specids = getProperty("SpectrumIDs");
l2s = getProperty("L2");
tths = getProperty("Polar");
phis = getProperty("Azimuthal");
m_params = getProperty("Params");
dspace = getProperty("DSpacing");
auto dmin = getVecPropertyFromPmOrSelf("DMin", m_dmins);
auto dmax = getVecPropertyFromPmOrSelf("DMax", m_dmaxs);
LRef = getProperty("UnwrapRef");
DIFCref = getProperty("LowResRef");
minwl = getProperty("CropWavelengthMin");
maxwl = getProperty("CropWavelengthMax");
if (maxwl == 0.)
maxwl = EMPTY_DBL(); // python can only specify 0 for unused
tmin = getProperty("TMin");
tmax = getProperty("TMax");
m_preserveEvents = getProperty("PreserveEvents");
m_resampleX = getProperty("ResampleX");
// determine some bits about d-space and binning
if (m_resampleX != 0) {
m_params.clear(); // ignore the normal rebin parameters
} else if (m_params.size() == 1) {
if (dmax > 0.)
dspace = true;
else
dspace = false;
}
if (dspace) {
if (m_params.size() == 1 && dmax > 0) {
double step = m_params[0];
m_params.clear();
if (step > 0 || dmin > 0) {
m_params.push_back(dmin);
m_params.push_back(step);
m_params.push_back(dmax);
g_log.information() << "d-Spacing Binning: " << m_params[0] << " "
<< m_params[1] << " " << m_params[2] << "\n";
}
}
} else {
if (m_params.size() == 1 && tmax > 0) {
double step = m_params[0];
if (step > 0 || tmin > 0) {
m_params[0] = tmin;
m_params.push_back(step);
m_params.push_back(tmax);
g_log.information() << "TOF Binning: " << m_params[0] << " "
<< m_params[1] << " " << m_params[2] << "\n";
}
}
}
xmin = 0.;
xmax = 0.;
if (tmin > 0.) {
xmin = tmin;
}
if (tmax > 0.) {
xmax = tmax;
}
if (!dspace && m_params.size() == 3) {
xmin = m_params[0];
xmax = m_params[2];
}
// Low resolution
int lowresoffset = getProperty("LowResSpectrumOffset");
if (lowresoffset < 0) {
m_processLowResTOF = false;
} else {
m_processLowResTOF = true;
m_lowResSpecOffset = static_cast<size_t>(lowresoffset);
}
loadCalFile(calFilename, groupFilename);
// Now setup the output workspace
m_outputW = getProperty("OutputWorkspace");
if (m_inputEW) {
if (m_outputW != m_inputW) {
m_outputEW = m_inputEW->clone();
}
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
} else {
if (m_outputW != m_inputW) {
m_outputW = WorkspaceFactory::Instance().create(m_inputW);
}
}
if (m_processLowResTOF) {
if (!m_inputEW) {
throw std::runtime_error(
"Input workspace is not EventWorkspace. It is not supported now.");
} else {
// Make a brand new EventWorkspace
m_lowResEW = boost::dynamic_pointer_cast<EventWorkspace>(
WorkspaceFactory::Instance().create(
"EventWorkspace", m_inputEW->getNumberHistograms(), 2, 1));
// Cast to the matrixOutputWS and save it
m_lowResW = boost::dynamic_pointer_cast<MatrixWorkspace>(m_lowResEW);
// m_lowResW->setName(lowreswsname);
}
}
// set up a progress bar with the "correct" number of steps
m_progress = new Progress(this, 0., 1., 22);
if (m_inputEW) {
double tolerance = getProperty("CompressTolerance");
if (tolerance > 0.) {
g_log.information() << "running CompressEvents(Tolerance=" << tolerance
<< ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr compressAlg = createChildAlgorithm("CompressEvents");
compressAlg->setProperty("InputWorkspace", m_outputEW);
compressAlg->setProperty("OutputWorkspace", m_outputEW);
compressAlg->setProperty("OutputWorkspace", m_outputEW);
compressAlg->setProperty("Tolerance", tolerance);
compressAlg->executeAsChildAlg();
m_outputEW = compressAlg->getProperty("OutputWorkspace");
m_outputW = boost::dynamic_pointer_cast<MatrixWorkspace>(m_outputEW);
} else {
g_log.information() << "Not compressing event list\n";
doSortEvents(m_outputW); // still sort to help some thing out
}
}
m_progress->report();
if (xmin > 0. || xmax > 0.) {
double tempmin;
double tempmax;
m_outputW->getXMinMax(tempmin, tempmax);
g_log.information() << "running CropWorkspace(TOFmin=" << xmin
<< ", TOFmax=" << xmax << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr cropAlg = createChildAlgorithm("CropWorkspace");
cropAlg->setProperty("InputWorkspace", m_outputW);
cropAlg->setProperty("OutputWorkspace", m_outputW);
if ((xmin > 0.) && (xmin > tempmin))
cropAlg->setProperty("Xmin", xmin);
if ((xmax > 0.) && (xmax < tempmax))
cropAlg->setProperty("Xmax", xmax);
cropAlg->executeAsChildAlg();
m_outputW = cropAlg->getProperty("OutputWorkspace");
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
}
m_progress->report();
// filter the input events if appropriate
double removePromptPulseWidth = getProperty("RemovePromptPulseWidth");
if (removePromptPulseWidth > 0.) {
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if (m_outputEW->getNumberEvents() > 0) {
g_log.information() << "running RemovePromptPulse(Width="
<< removePromptPulseWidth << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr filterPAlg =
createChildAlgorithm("RemovePromptPulse");
filterPAlg->setProperty("InputWorkspace", m_outputW);
filterPAlg->setProperty("OutputWorkspace", m_outputW);
filterPAlg->setProperty("Width", removePromptPulseWidth);
filterPAlg->executeAsChildAlg();
m_outputW = filterPAlg->getProperty("OutputWorkspace");
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
} else {
g_log.information("skipping RemovePromptPulse on empty EventWorkspace");
}
}
m_progress->report();
if (maskBinTableWS) {
g_log.information() << "running MaskBinsFromTable started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr alg = createChildAlgorithm("MaskBinsFromTable");
alg->setProperty("InputWorkspace", m_outputW);
alg->setProperty("OutputWorkspace", m_outputW);
alg->setProperty("MaskingInformation", maskBinTableWS);
alg->executeAsChildAlg();
m_outputW = alg->getProperty("OutputWorkspace");
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
}
m_progress->report();
if (m_maskWS) {
g_log.information() << "running MaskDetectors started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr maskAlg = createChildAlgorithm("MaskDetectors");
maskAlg->setProperty("Workspace", m_outputW);
maskAlg->setProperty("MaskedWorkspace", m_maskWS);
maskAlg->executeAsChildAlg();
Workspace_sptr tmpW = maskAlg->getProperty("Workspace");
m_outputW = boost::dynamic_pointer_cast<MatrixWorkspace>(tmpW);
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
}
m_progress->report();
if (!dspace)
m_outputW = rebin(m_outputW);
m_progress->report();
if (m_calibrationWS) {
g_log.information() << "running AlignDetectors started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr alignAlg = createChildAlgorithm("AlignDetectors");
alignAlg->setProperty("InputWorkspace", m_outputW);
alignAlg->setProperty("OutputWorkspace", m_outputW);
alignAlg->setProperty("CalibrationWorkspace", m_calibrationWS);
alignAlg->executeAsChildAlg();
m_outputW = alignAlg->getProperty("OutputWorkspace");
} else {
m_outputW = convertUnits(m_outputW, "dSpacing");
}
m_progress->report();
if (LRef > 0. || minwl > 0. || DIFCref > 0. || (!isEmpty(maxwl))) {
m_outputW = convertUnits(m_outputW, "TOF");
}
m_progress->report();
// Beyond this point, low resolution TOF workspace is considered.
if (LRef > 0.) {
g_log.information() << "running UnwrapSNS(LRef=" << LRef << ",Tmin=" << tmin
<< ",Tmax=" << tmax << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr removeAlg = createChildAlgorithm("UnwrapSNS");
removeAlg->setProperty("InputWorkspace", m_outputW);
removeAlg->setProperty("OutputWorkspace", m_outputW);
removeAlg->setProperty("LRef", LRef);
if (tmin > 0.)
removeAlg->setProperty("Tmin", tmin);
if (tmax > tmin)
removeAlg->setProperty("Tmax", tmax);
removeAlg->executeAsChildAlg();
m_outputW = removeAlg->getProperty("OutputWorkspace");
}
m_progress->report();
if (minwl > 0. || (!isEmpty(maxwl))) { // just crop the worksapce
// turn off the low res stuff
m_processLowResTOF = false;
EventWorkspace_sptr ews =
boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if (ews)
g_log.information() << "Number of events = " << ews->getNumberEvents()
<< ". ";
g_log.information("\n");
m_outputW = convertUnits(m_outputW, "Wavelength");
g_log.information() << "running CropWorkspace(WavelengthMin=" << minwl;
if (!isEmpty(maxwl))
g_log.information() << ", WavelengthMax=" << maxwl;
g_log.information() << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr removeAlg = createChildAlgorithm("CropWorkspace");
removeAlg->setProperty("InputWorkspace", m_outputW);
removeAlg->setProperty("OutputWorkspace", m_outputW);
removeAlg->setProperty("XMin", minwl);
removeAlg->setProperty("XMax", maxwl);
removeAlg->executeAsChildAlg();
m_outputW = removeAlg->getProperty("OutputWorkspace");
if (ews)
g_log.information() << "Number of events = " << ews->getNumberEvents()
<< ".\n";
} else if (DIFCref > 0.) {
g_log.information() << "running RemoveLowResTof(RefDIFC=" << DIFCref
<< ",K=3.22) started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
EventWorkspace_sptr ews =
boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if (ews)
g_log.information() << "Number of events = " << ews->getNumberEvents()
<< ". ";
g_log.information("\n");
API::IAlgorithm_sptr removeAlg = createChildAlgorithm("RemoveLowResTOF");
removeAlg->setProperty("InputWorkspace", m_outputW);
removeAlg->setProperty("OutputWorkspace", m_outputW);
removeAlg->setProperty("ReferenceDIFC", DIFCref);
removeAlg->setProperty("K", 3.22);
if (tmin > 0.)
removeAlg->setProperty("Tmin", tmin);
if (m_processLowResTOF)
removeAlg->setProperty("LowResTOFWorkspace", m_lowResW);
removeAlg->executeAsChildAlg();
m_outputW = removeAlg->getProperty("OutputWorkspace");
if (m_processLowResTOF)
m_lowResW = removeAlg->getProperty("LowResTOFWorkspace");
}
m_progress->report();
EventWorkspace_sptr ews =
boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if (ews) {
size_t numhighevents = ews->getNumberEvents();
if (m_processLowResTOF) {
EventWorkspace_sptr lowes =
boost::dynamic_pointer_cast<EventWorkspace>(m_lowResW);
size_t numlowevents = lowes->getNumberEvents();
g_log.information() << "Number of high TOF events = " << numhighevents
<< "; "
<< "Number of low TOF events = " << numlowevents
<< ".\n";
}
}
m_progress->report();
// Convert units
if (LRef > 0. || minwl > 0. || DIFCref > 0. || (!isEmpty(maxwl))) {
m_outputW = convertUnits(m_outputW, "dSpacing");
if (m_processLowResTOF)
m_lowResW = convertUnits(m_lowResW, "dSpacing");
}
m_progress->report();
if (dspace) {
m_outputW = rebin(m_outputW);
if (m_processLowResTOF)
m_lowResW = rebin(m_lowResW);
}
m_progress->report();
doSortEvents(m_outputW);
if (m_processLowResTOF)
doSortEvents(m_lowResW);
m_progress->report();
// Diffraction focus
m_outputW = diffractionFocus(m_outputW);
if (m_processLowResTOF)
m_lowResW = diffractionFocus(m_lowResW);
m_progress->report();
doSortEvents(m_outputW);
if (m_processLowResTOF)
doSortEvents(m_lowResW);
m_progress->report();
// this next call should probably be in for rebin as well
// but it changes the system tests
if (dspace && m_resampleX != 0) {
m_outputW = rebin(m_outputW);
if (m_processLowResTOF)
m_lowResW = rebin(m_lowResW);
}
m_progress->report();
// edit the instrument geometry
if (m_groupWS &&
(m_l1 > 0 || !tths.empty() || !l2s.empty() || !phis.empty())) {
size_t numreg = m_outputW->getNumberHistograms();
try {
// set up the vectors for doing everything
auto specidsSplit = splitVectors(specids, numreg, "specids");
auto tthsSplit = splitVectors(tths, numreg, "two-theta");
auto l2sSplit = splitVectors(l2s, numreg, "L2");
auto phisSplit = splitVectors(phis, numreg, "phi");
// Edit instrument
m_outputW = editInstrument(m_outputW, tthsSplit.reg, specidsSplit.reg,
l2sSplit.reg, phisSplit.reg);
if (m_processLowResTOF) {
m_lowResW = editInstrument(m_lowResW, tthsSplit.low, specidsSplit.low,
l2sSplit.low, phisSplit.low);
}
} catch (std::runtime_error &e) {
g_log.warning("Not editing instrument geometry:");
g_log.warning(e.what());
}
}
m_progress->report();
// Conjoin 2 workspaces if there is low resolution
if (m_processLowResTOF) {
m_outputW = conjoinWorkspaces(m_outputW, m_lowResW, m_lowResSpecOffset);
}
m_progress->report();
// Convert units to TOF
m_outputW = convertUnits(m_outputW, "TOF");
m_progress->report();
// compress again if appropriate
double tolerance = getProperty("CompressTolerance");
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if ((m_outputEW) && (tolerance > 0.)) {
g_log.information() << "running CompressEvents(Tolerance=" << tolerance
<< ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr compressAlg = createChildAlgorithm("CompressEvents");
compressAlg->setProperty("InputWorkspace", m_outputEW);
compressAlg->setProperty("OutputWorkspace", m_outputEW);
compressAlg->setProperty("OutputWorkspace", m_outputEW);
compressAlg->setProperty("Tolerance", tolerance);
compressAlg->executeAsChildAlg();
m_outputEW = compressAlg->getProperty("OutputWorkspace");
m_outputW = boost::dynamic_pointer_cast<MatrixWorkspace>(m_outputEW);
}
m_progress->report();
if ((!m_params.empty()) && (m_params.size() != 1)) {
m_params.erase(m_params.begin());
m_params.pop_back();
}
if (!m_dmins.empty())
m_dmins.clear();
if (!m_dmaxs.empty())
m_dmaxs.clear();
m_outputW = rebin(m_outputW);
m_progress->report();
// return the output workspace
setProperty("OutputWorkspace", m_outputW);
}
/**
* Gaussian fit to determine peak position if no user position given.
*
* @return :: detector position of the peak: Gaussian fit and position
* of the maximum (serves as start value for the optimization)
*/
double LoadILLReflectometry::reflectometryPeak() {
if (!isDefault("BeamCentre")) {
return getProperty("BeamCentre");
}
size_t startIndex;
size_t endIndex;
std::tie(startIndex, endIndex) =
fitIntegrationWSIndexRange(*m_localWorkspace);
IAlgorithm_sptr integration = createChildAlgorithm("Integration");
integration->initialize();
integration->setProperty("InputWorkspace", m_localWorkspace);
integration->setProperty("OutputWorkspace", "__unused_for_child");
integration->setProperty("StartWorkspaceIndex", static_cast<int>(startIndex));
integration->setProperty("EndWorkspaceIndex", static_cast<int>(endIndex));
integration->execute();
MatrixWorkspace_sptr integralWS = integration->getProperty("OutputWorkspace");
IAlgorithm_sptr transpose = createChildAlgorithm("Transpose");
transpose->initialize();
transpose->setProperty("InputWorkspace", integralWS);
transpose->setProperty("OutputWorkspace", "__unused_for_child");
transpose->execute();
integralWS = transpose->getProperty("OutputWorkspace");
rebinIntegralWorkspace(*integralWS);
// determine initial height: maximum value
const auto maxValueIt =
std::max_element(integralWS->y(0).cbegin(), integralWS->y(0).cend());
const double height = *maxValueIt;
// determine initial centre: index of the maximum value
const size_t maxIndex = std::distance(integralWS->y(0).cbegin(), maxValueIt);
const double centreByMax = static_cast<double>(maxIndex);
g_log.debug() << "Peak maximum position: " << centreByMax << '\n';
// determine sigma
const auto &ys = integralWS->y(0);
auto lessThanHalfMax = [height](const double x) { return x < 0.5 * height; };
using IterType = HistogramData::HistogramY::const_iterator;
std::reverse_iterator<IterType> revMaxValueIt{maxValueIt};
auto revMinFwhmIt = std::find_if(revMaxValueIt, ys.crend(), lessThanHalfMax);
auto maxFwhmIt = std::find_if(maxValueIt, ys.cend(), lessThanHalfMax);
std::reverse_iterator<IterType> revMaxFwhmIt{maxFwhmIt};
if (revMinFwhmIt == ys.crend() || maxFwhmIt == ys.cend()) {
g_log.warning() << "Couldn't determine fwhm of beam, using position of max "
"value as beam center.\n";
return centreByMax;
}
const double fwhm =
static_cast<double>(std::distance(revMaxFwhmIt, revMinFwhmIt) + 1);
g_log.debug() << "Initial fwhm (full width at half maximum): " << fwhm
<< '\n';
// generate Gaussian
auto func =
API::FunctionFactory::Instance().createFunction("CompositeFunction");
auto sum = boost::dynamic_pointer_cast<API::CompositeFunction>(func);
func = API::FunctionFactory::Instance().createFunction("Gaussian");
auto gaussian = boost::dynamic_pointer_cast<API::IPeakFunction>(func);
gaussian->setHeight(height);
gaussian->setCentre(centreByMax);
gaussian->setFwhm(fwhm);
sum->addFunction(gaussian);
func = API::FunctionFactory::Instance().createFunction("LinearBackground");
func->setParameter("A0", 0.);
func->setParameter("A1", 0.);
sum->addFunction(func);
// call Fit child algorithm
API::IAlgorithm_sptr fit = createChildAlgorithm("Fit");
fit->initialize();
fit->setProperty("Function",
boost::dynamic_pointer_cast<API::IFunction>(sum));
fit->setProperty("InputWorkspace", integralWS);
fit->setProperty("StartX", centreByMax - 3 * fwhm);
fit->setProperty("EndX", centreByMax + 3 * fwhm);
fit->execute();
const std::string fitStatus = fit->getProperty("OutputStatus");
if (fitStatus != "success") {
g_log.warning("Fit not successful, using position of max value.\n");
return centreByMax;
}
const auto centre = gaussian->centre();
g_log.debug() << "Sigma: " << gaussian->fwhm() << '\n';
g_log.debug() << "Estimated peak position: " << centre << '\n';
return centre;
}
/**
* Execute the algorithm.
*/
void LoadBBY::exec() {
// Delete the output workspace name if it existed
std::string outName = getPropertyValue("OutputWorkspace");
if (API::AnalysisDataService::Instance().doesExist(outName))
API::AnalysisDataService::Instance().remove(outName);
// Get the name of the data file.
std::string filename = getPropertyValue(FilenameStr);
ANSTO::Tar::File tarFile(filename);
if (!tarFile.good())
throw std::invalid_argument("invalid BBY file");
// region of intreset
std::vector<bool> roi = createRoiVector(getPropertyValue(MaskStr));
double tofMinBoundary = getProperty(FilterByTofMinStr);
double tofMaxBoundary = getProperty(FilterByTofMaxStr);
double timeMinBoundary = getProperty(FilterByTimeStartStr);
double timeMaxBoundary = getProperty(FilterByTimeStopStr);
if (isEmpty(tofMaxBoundary))
tofMaxBoundary = std::numeric_limits<double>::infinity();
if (isEmpty(timeMaxBoundary))
timeMaxBoundary = std::numeric_limits<double>::infinity();
API::Progress prog(this, 0.0, 1.0, Progress_Total);
prog.doReport("creating instrument");
// create workspace
DataObjects::EventWorkspace_sptr eventWS =
boost::make_shared<DataObjects::EventWorkspace>();
eventWS->initialize(HISTO_BINS_Y * HISTO_BINS_X,
2, // number of TOF bin boundaries
1);
// set the units
eventWS->getAxis(0)->unit() = Kernel::UnitFactory::Instance().create("TOF");
eventWS->setYUnit("Counts");
// set title
const std::vector<std::string> &subFiles = tarFile.files();
for (const auto &subFile : subFiles)
if (subFile.compare(0, 3, "BBY") == 0) {
std::string title = subFile;
if (title.rfind(".hdf") == title.length() - 4)
title.resize(title.length() - 4);
if (title.rfind(".nx") == title.length() - 3)
title.resize(title.length() - 3);
eventWS->setTitle(title);
break;
}
// create instrument
InstrumentInfo instrumentInfo;
// Geometry::Instrument_sptr instrument =
createInstrument(tarFile, /* ref */ instrumentInfo);
// eventWS->setInstrument(instrument);
// load events
size_t numberHistograms = eventWS->getNumberHistograms();
std::vector<EventVector_pt> eventVectors(numberHistograms, nullptr);
std::vector<size_t> eventCounts(numberHistograms, 0);
// phase correction
Kernel::Property *periodMasterProperty =
getPointerToProperty(PeriodMasterStr);
Kernel::Property *periodSlaveProperty = getPointerToProperty(PeriodSlaveStr);
Kernel::Property *phaseSlaveProperty = getPointerToProperty(PhaseSlaveStr);
double periodMaster;
double periodSlave;
double phaseSlave;
if (periodMasterProperty->isDefault() || periodSlaveProperty->isDefault() ||
phaseSlaveProperty->isDefault()) {
if (!periodMasterProperty->isDefault() ||
!periodSlaveProperty->isDefault() || !phaseSlaveProperty->isDefault()) {
throw std::invalid_argument("Please specify PeriodMaster, PeriodSlave "
"and PhaseSlave or none of them.");
}
// if values have not been specified in loader then use values from hdf file
periodMaster = instrumentInfo.period_master;
periodSlave = instrumentInfo.period_slave;
phaseSlave = instrumentInfo.phase_slave;
} else {
periodMaster = getProperty(PeriodMasterStr);
periodSlave = getProperty(PeriodSlaveStr);
phaseSlave = getProperty(PhaseSlaveStr);
if ((periodMaster < 0.0) || (periodSlave < 0.0))
throw std::invalid_argument(
"Please specify a positive value for PeriodMaster and PeriodSlave.");
}
double period = periodSlave;
double shift = -1.0 / 6.0 * periodMaster - periodSlave * phaseSlave / 360.0;
// count total events per pixel to reserve necessary memory
ANSTO::EventCounter eventCounter(
roi, HISTO_BINS_Y, period, shift, tofMinBoundary, tofMaxBoundary,
timeMinBoundary, timeMaxBoundary, eventCounts);
loadEvents(prog, "loading neutron counts", tarFile, eventCounter);
// prepare event storage
ANSTO::ProgressTracker progTracker(prog, "creating neutron event lists",
numberHistograms, Progress_ReserveMemory);
for (size_t i = 0; i != numberHistograms; ++i) {
DataObjects::EventList &eventList = eventWS->getEventList(i);
eventList.setSortOrder(DataObjects::PULSETIME_SORT);
eventList.reserve(eventCounts[i]);
eventList.setDetectorID(static_cast<detid_t>(i));
eventList.setSpectrumNo(static_cast<detid_t>(i));
DataObjects::getEventsFrom(eventList, eventVectors[i]);
progTracker.update(i);
}
progTracker.complete();
ANSTO::EventAssigner eventAssigner(
roi, HISTO_BINS_Y, period, shift, tofMinBoundary, tofMaxBoundary,
timeMinBoundary, timeMaxBoundary, eventVectors);
loadEvents(prog, "loading neutron events", tarFile, eventAssigner);
Kernel::cow_ptr<MantidVec> axis;
MantidVec &xRef = axis.access();
xRef.resize(2, 0.0);
xRef[0] = std::max(
0.0,
floor(eventCounter.tofMin())); // just to make sure the bins hold it all
xRef[1] = eventCounter.tofMax() + 1;
eventWS->setAllX(axis);
// count total number of masked bins
size_t maskedBins = 0;
for (size_t i = 0; i != roi.size(); i++)
if (!roi[i])
maskedBins++;
if (maskedBins > 0) {
// create list of masked bins
std::vector<size_t> maskIndexList(maskedBins);
size_t maskIndex = 0;
for (size_t i = 0; i != roi.size(); i++)
if (!roi[i])
maskIndexList[maskIndex++] = i;
API::IAlgorithm_sptr maskingAlg = createChildAlgorithm("MaskDetectors");
maskingAlg->setProperty("Workspace", eventWS);
maskingAlg->setProperty("WorkspaceIndexList", maskIndexList);
maskingAlg->executeAsChildAlg();
}
// set log values
API::LogManager &logManager = eventWS->mutableRun();
logManager.addProperty("filename", filename);
logManager.addProperty("att_pos", static_cast<int>(instrumentInfo.att_pos));
logManager.addProperty("frame_count",
static_cast<int>(eventCounter.numFrames()));
logManager.addProperty("period", period);
// currently beam monitor counts are not available, instead number of frames
// times period is used
logManager.addProperty(
"bm_counts", static_cast<double>(eventCounter.numFrames()) * period /
1.0e6); // static_cast<double>(instrumentInfo.bm_counts)
// currently
Kernel::time_duration duration =
boost::posix_time::microseconds(static_cast<boost::int64_t>(
static_cast<double>(eventCounter.numFrames()) * period));
Kernel::DateAndTime start_time("2000-01-01T00:00:00");
Kernel::DateAndTime end_time(start_time + duration);
logManager.addProperty("start_time", start_time.toISO8601String());
logManager.addProperty("end_time", end_time.toISO8601String());
std::string time_str = start_time.toISO8601String();
AddSinglePointTimeSeriesProperty(logManager, time_str, "L1_chopper_value",
instrumentInfo.L1_chopper_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "L2_det_value",
instrumentInfo.L2_det_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "L2_curtainl_value",
instrumentInfo.L2_curtainl_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "L2_curtainr_value",
instrumentInfo.L2_curtainr_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "L2_curtainu_value",
instrumentInfo.L2_curtainu_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "L2_curtaind_value",
instrumentInfo.L2_curtaind_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "D_det_value",
instrumentInfo.D_det_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "D_curtainl_value",
instrumentInfo.D_curtainl_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "D_curtainr_value",
instrumentInfo.D_curtainr_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "D_curtainu_value",
instrumentInfo.D_curtainu_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "D_curtaind_value",
instrumentInfo.D_curtaind_value);
AddSinglePointTimeSeriesProperty(logManager, time_str, "curtain_rotation",
10.0);
API::IAlgorithm_sptr loadInstrumentAlg =
createChildAlgorithm("LoadInstrument");
loadInstrumentAlg->setProperty("Workspace", eventWS);
loadInstrumentAlg->setPropertyValue("InstrumentName", "BILBY");
loadInstrumentAlg->setProperty("RewriteSpectraMap",
Mantid::Kernel::OptionalBool(false));
loadInstrumentAlg->executeAsChildAlg();
setProperty("OutputWorkspace", eventWS);
}
/** Calls Gaussian1D as a child algorithm to fit the offset peak in a spectrum
*
* @param wi :: The Workspace Index to fit.
* @param inputW :: Input workspace.
* @param peakPositions :: Peak positions.
* @param fitWindows :: Fit windows.
* @param nparams :: Number of parameters.
* @param minD :: Min distance.
* @param maxD :: Max distance.
* @param peakPosToFit :: Actual peak positions to fit (output).
* @param peakPosFitted :: Actual peak positions fitted (output).
* @param chisq :: chisq.
* @param peakHeights :: vector for fitted heights of peaks
* @param i_highestpeak:: index of the highest peak among all peaks
* @param resolution :: spectrum's resolution delta(d)/d
* @param dev_resolution :: standard deviation resolution
* @return The number of peaks in range
*/
int GetDetOffsetsMultiPeaks::fitSpectra(
const int64_t wi, MatrixWorkspace_sptr inputW,
const std::vector<double> &peakPositions,
const std::vector<double> &fitWindows, size_t &nparams, double &minD,
double &maxD, std::vector<double> &peakPosToFit,
std::vector<double> &peakPosFitted, std::vector<double> &chisq,
std::vector<double> &peakHeights, int &i_highestpeak, double &resolution,
double &dev_resolution) {
// Default overall fit range is the whole spectrum
const MantidVec &X = inputW->readX(wi);
minD = X.front();
maxD = X.back();
// Trim in the edges based on where the data turns off of zero
const MantidVec &Y = inputW->readY(wi);
size_t minDindex = 0;
for (; minDindex < Y.size(); ++minDindex) {
if (Y[minDindex] > 0.) {
minD = X[minDindex];
break;
}
}
if (minD >= maxD) {
// throw if minD >= maxD
std::stringstream ess;
ess << "Stuff went wrong with wkspIndex=" << wi
<< " specIndex=" << inputW->getSpectrum(wi)->getSpectrumNo();
throw std::runtime_error(ess.str());
}
size_t maxDindex = Y.size() - 1;
for (; maxDindex > minDindex; --maxDindex) {
if (Y[maxDindex] > 0.) {
maxD = X[maxDindex];
break;
}
}
std::stringstream dbss;
dbss << "D-RANGE[" << inputW->getSpectrum(wi)->getSpectrumNo()
<< "]: " << minD << " -> " << maxD;
g_log.debug(dbss.str());
// Setup the fit windows
bool useFitWindows = (!fitWindows.empty());
std::vector<double> fitWindowsToUse;
for (int i = 0; i < static_cast<int>(peakPositions.size()); ++i) {
if ((peakPositions[i] > minD) && (peakPositions[i] < maxD)) {
if (m_useFitWindowTable) {
fitWindowsToUse.push_back(std::max(m_vecFitWindow[wi][2 * i], minD));
fitWindowsToUse.push_back(
std::min(m_vecFitWindow[wi][2 * i + 1], maxD));
} else if (useFitWindows) {
fitWindowsToUse.push_back(std::max(fitWindows[2 * i], minD));
fitWindowsToUse.push_back(std::min(fitWindows[2 * i + 1], maxD));
}
peakPosToFit.push_back(peakPositions[i]);
}
}
int numPeaksInRange = static_cast<int>(peakPosToFit.size());
if (numPeaksInRange == 0) {
std::stringstream outss;
outss << "Spectrum " << wi << " has no peak in range (" << minD << ", "
<< maxD << ")";
g_log.information(outss.str());
return 0;
}
// Fit peaks
API::IAlgorithm_sptr findpeaks =
createChildAlgorithm("FindPeaks", -1, -1, false);
findpeaks->setProperty("InputWorkspace", inputW);
findpeaks->setProperty<int>("FWHM", 7);
findpeaks->setProperty<int>("Tolerance", 4);
// FindPeaks will do the checking on the validity of WorkspaceIndex
findpeaks->setProperty("WorkspaceIndex", static_cast<int>(wi));
// Get the specified peak positions, which is optional
findpeaks->setProperty("PeakPositions", peakPosToFit);
if (useFitWindows)
findpeaks->setProperty("FitWindows", fitWindowsToUse);
findpeaks->setProperty<std::string>("PeakFunction", m_peakType);
findpeaks->setProperty<std::string>("BackgroundType", m_backType);
findpeaks->setProperty<bool>("HighBackground",
this->getProperty("HighBackground"));
findpeaks->setProperty<int>("MinGuessedPeakWidth", 4);
findpeaks->setProperty<int>("MaxGuessedPeakWidth", 4);
findpeaks->setProperty<double>("MinimumPeakHeight", m_minPeakHeight);
findpeaks->setProperty("StartFromObservedPeakCentre", true);
findpeaks->executeAsChildAlg();
// Collect fitting resutl of all peaks
ITableWorkspace_sptr peakslist = findpeaks->getProperty("PeaksList");
// use tmpPeakPosToFit to shuffle the vectors
std::vector<double> tmpPeakPosToFit;
generatePeaksList(peakslist, static_cast<int>(wi), peakPosToFit,
tmpPeakPosToFit, peakPosFitted, peakHeights, chisq,
(useFitWindows || m_useFitWindowTable), fitWindowsToUse,
minD, maxD, resolution, dev_resolution);
peakPosToFit = tmpPeakPosToFit;
nparams = peakPosFitted.size();
// Find the highest peak
i_highestpeak = -1;
double maxheight = 0;
for (int i = 0; i < static_cast<int>(peakPosFitted.size()); ++i) {
double tmpheight = peakHeights[i];
if (tmpheight > maxheight) {
maxheight = tmpheight;
i_highestpeak = i;
}
}
return numPeaksInRange;
}
/**
* Executes the algorithm
*/
void PlotPeakByLogValue::exec()
{
// Create a list of the input workspace
const std::vector<InputData> wsNames = makeNames();
std::string fun = getPropertyValue("Function");
//int wi = getProperty("WorkspaceIndex");
std::string logName = getProperty("LogValue");
bool sequential = getPropertyValue("FitType") == "Sequential";
bool isDataName = false; // if true first output column is of type string and is the data source name
ITableWorkspace_sptr result = WorkspaceFactory::Instance().createTable("TableWorkspace");
if (logName == "SourceName")
{
result->addColumn("str","Source name");
isDataName = true;
}
else if (logName.empty())
{
result->addColumn("double","axis-1");
}
else
{
result->addColumn("double",logName);
}
// Create an instance of the fitting function to obtain the names of fitting parameters
IFitFunction* ifun = FunctionFactory::Instance().createInitialized(fun);
if (!ifun)
{
throw std::invalid_argument("Fitting function failed to initialize");
}
for(size_t iPar=0;iPar<ifun->nParams();++iPar)
{
result->addColumn("double",ifun->parameterName(iPar));
result->addColumn("double",ifun->parameterName(iPar)+"_Err");
}
result->addColumn("double","Chi_squared");
delete ifun;
setProperty("OutputWorkspace",result);
double dProg = 1./static_cast<double>(wsNames.size());
double Prog = 0.;
for(int i=0;i<static_cast<int>(wsNames.size());++i)
{
InputData data = getWorkspace(wsNames[i]);
if (!data.ws)
{
g_log.warning() << "Cannot access workspace " << wsNames[i].name << '\n';
continue;
}
if (data.i < 0 && data.indx.empty())
{
g_log.warning() << "Zero spectra selected for fitting in workspace " << wsNames[i].name << '\n';
continue;
}
int j,jend;
if (data.i >= 0)
{
j = data.i;
jend = j + 1;
}
else
{// no need to check data.indx.empty()
j = data.indx.front();
jend = data.indx.back() + 1;
}
dProg /= abs(jend - j);
for(;j < jend;++j)
{
// Find the log value: it is either a log-file value or simply the workspace number
double logValue;
if (logName.empty())
{
API::Axis* axis = data.ws->getAxis(1);
logValue = (*axis)(j);
}
else if (logName != "SourceName")
{
Kernel::Property* prop = data.ws->run().getLogData(logName);
if (!prop)
{
throw std::invalid_argument("Log value "+logName+" does not exist");
}
TimeSeriesProperty<double>* logp =
dynamic_cast<TimeSeriesProperty<double>*>(prop);
logValue = logp->lastValue();
}
std::string resFun = fun;
std::vector<double> errors;
double chi2;
try
{
// Fit the function
API::IAlgorithm_sptr fit = createSubAlgorithm("Fit");
fit->initialize();
fit->setProperty("InputWorkspace",data.ws);
//fit->setPropertyValue("InputWorkspace",data.ws->getName());
fit->setProperty("WorkspaceIndex",j);
fit->setPropertyValue("Function",fun);
fit->setPropertyValue("StartX",getPropertyValue("StartX"));
fit->setPropertyValue("EndX",getPropertyValue("EndX"));
fit->setPropertyValue("Minimizer",getPropertyValue("Minimizer"));
fit->setPropertyValue("CostFunction",getPropertyValue("CostFunction"));
fit->execute();
resFun = fit->getPropertyValue("Function");
errors = fit->getProperty("Errors");
chi2 = fit->getProperty("OutputChi2overDoF");
}
catch(...)
{
g_log.error("Error in Fit subalgorithm");
throw;
}
if (sequential)
{
fun = resFun;
}
// Extract the fitted parameters and put them into the result table
TableRow row = result->appendRow();
if (isDataName)
{
row << wsNames[i].name;
}
else
{
row << logValue;
}
ifun = FunctionFactory::Instance().createInitialized(resFun);
for(size_t iPar=0;iPar<ifun->nParams();++iPar)
{
row << ifun->getParameter(iPar) << errors[iPar];
}
row << chi2;
delete ifun;
Prog += dProg;
progress(Prog);
interruption_point();
} // for(;j < jend;++j)
}
}
void GoniometerAnglesFromPhiRotation::exec() {
PeaksWorkspace_sptr PeaksRun1 = getProperty("PeaksWorkspace1");
PeaksWorkspace_sptr PeaksRun2 = getProperty("PeaksWorkspace2");
double Tolerance = getProperty("Tolerance");
Kernel::Matrix<double> Gon1(3, 3);
Kernel::Matrix<double> Gon2(3, 3);
if (!CheckForOneRun(PeaksRun1, Gon1) || !CheckForOneRun(PeaksRun2, Gon2)) {
g_log.error("Each peaks workspace MUST have only one run");
throw std::invalid_argument("Each peaks workspace MUST have only one run");
}
Kernel::Matrix<double> UB1;
bool Run1HasOrientedLattice = true;
if (!PeaksRun1->sample().hasOrientedLattice()) {
Run1HasOrientedLattice = false;
const std::string fft("FindUBUsingFFT");
API::IAlgorithm_sptr findUB = this->createChildAlgorithm(fft);
findUB->initialize();
findUB->setProperty<PeaksWorkspace_sptr>("PeaksWorkspace",
getProperty("PeaksWorkspace1"));
findUB->setProperty("MIND", static_cast<double>(getProperty("MIND")));
findUB->setProperty("MAXD", static_cast<double>(getProperty("MAXD")));
findUB->setProperty("Tolerance", Tolerance);
findUB->executeAsChildAlg();
if (!PeaksRun1->sample().hasOrientedLattice()) {
g_log.notice(std::string("Could not find UB for ") +
std::string(PeaksRun1->getName()));
throw std::invalid_argument(std::string("Could not find UB for ") +
std::string(PeaksRun1->getName()));
}
}
//-------------get UB raw :No goniometer----------------
UB1 = PeaksRun1->sample().getOrientedLattice().getUB();
UB1 = getUBRaw(UB1, Gon1);
int N1;
double avErrIndx, avErrAll;
IndexRaw(PeaksRun1, UB1, N1, avErrIndx, avErrAll, Tolerance);
if (N1 < .6 * PeaksRun1->getNumberPeaks()) {
g_log.notice(std::string("UB did not index well for ") +
std::string(PeaksRun1->getName()));
throw std::invalid_argument(std::string("UB did not index well for ") +
std::string(PeaksRun1->getName()));
}
//----------------------------------------------
Geometry::OrientedLattice lat2 = PeaksRun1->sample().getOrientedLattice();
lat2.setUB(UB1);
PeaksRun2->mutableSample().setOrientedLattice(&lat2);
if (!Run1HasOrientedLattice)
PeaksRun1->mutableSample().setOrientedLattice(nullptr);
double dphi = static_cast<double>(getProperty("Phi2")) -
static_cast<double>(getProperty("Run1Phi"));
Kernel::Matrix<double> Gon22(3, 3, true);
for (int i = 0; i < PeaksRun2->getNumberPeaks(); i++) {
PeaksRun2->getPeak(i).setGoniometerMatrix(Gon22);
}
int RunNum = PeaksRun2->getPeak(0).getRunNumber();
std::string RunNumStr = std::to_string(RunNum);
int Npeaks = PeaksRun2->getNumberPeaks();
// n indexed, av err, phi, chi,omega
std::array<double, 5> MinData = {{0., 0., 0., 0., 0.}};
MinData[0] = 0.0;
std::vector<V3D> directionList = IndexingUtils::MakeHemisphereDirections(50);
API::FrameworkManager::Instance();
for (auto dir : directionList)
for (int sgn = 1; sgn > -2; sgn -= 2) {
dir.normalize();
Quat Q(sgn * dphi, dir);
Q.normalize();
Kernel::Matrix<double> Rot(Q.getRotation());
int Nindexed;
double dummyAvErrIndx, dummyAvErrAll;
IndexRaw(PeaksRun2, Rot * UB1, Nindexed, dummyAvErrIndx, dummyAvErrAll,
Tolerance);
if (Nindexed > MinData[0]) {
MinData[0] = Nindexed;
MinData[1] = sgn;
MinData[2] = dir[0];
MinData[3] = dir[1];
MinData[4] = dir[2];
}
}
g_log.debug() << "Best direction unOptimized is ("
<< (MinData[1] * MinData[2]) << "," << (MinData[1] * MinData[3])
<< "," << (MinData[1] * MinData[4]) << ")\n";
//----------------------- Optimize around best----------------------------
auto ws = createWorkspace<Workspace2D>(1, 3 * Npeaks, 3 * Npeaks);
MantidVec Xvals;
for (int i = 0; i < Npeaks; ++i) {
Xvals.push_back(i);
Xvals.push_back(i);
Xvals.push_back(i);
}
ws->setPoints(0, Xvals);
//--------------------Set up other Fit function arguments------------------
V3D dir(MinData[2], MinData[3], MinData[4]);
dir.normalize();
Quat Q(MinData[1] * dphi, dir);
Q.normalize();
Kernel::Matrix<double> Rot(Q.getRotation());
Goniometer Gon(Rot);
std::vector<double> omchiphi = Gon.getEulerAngles("yzy");
MinData[2] = omchiphi[2];
MinData[3] = omchiphi[1];
MinData[4] = omchiphi[0];
std::string FunctionArgs =
"name=PeakHKLErrors, PeakWorkspaceName=" + PeaksRun2->getName() +
",OptRuns=" + RunNumStr + ",phi" + RunNumStr + "=" +
boost::lexical_cast<std::string>(MinData[2]) + ",chi" + RunNumStr + "=" +
boost::lexical_cast<std::string>(MinData[3]) + ",omega" + RunNumStr +
"=" + boost::lexical_cast<std::string>(MinData[4]);
std::string Constr = boost::lexical_cast<std::string>(MinData[2] - 5) +
"<phi" + RunNumStr + "<" +
boost::lexical_cast<std::string>(MinData[2] + 5);
Constr += "," + boost::lexical_cast<std::string>(MinData[3] - 5) + "<chi" +
RunNumStr + "<" + boost::lexical_cast<std::string>(MinData[3] + 5) +
",";
Constr += boost::lexical_cast<std::string>(MinData[4] - 5) + "<omega" +
RunNumStr + "<" + boost::lexical_cast<std::string>(MinData[4] + 5);
std::string Ties = "SampleXOffset=0.0,SampleYOffset=0.0,SampleZOffset=0.0,"
"GonRotx=0.0,GonRoty=0.0,GonRotz=0.0";
boost::shared_ptr<Algorithm> Fit = createChildAlgorithm("Fit");
Fit->initialize();
Fit->setProperty("Function", FunctionArgs);
Fit->setProperty("Ties", Ties);
Fit->setProperty("Constraints", Constr);
Fit->setProperty("InputWorkspace", ws);
Fit->setProperty("CreateOutput", true);
std::string outputName = "out";
Fit->setProperty("Output", outputName);
Fit->executeAsChildAlg();
boost::shared_ptr<API::ITableWorkspace> results =
Fit->getProperty("OutputParameters");
double chisq = Fit->getProperty("OutputChi2overDoF");
MinData[0] = chisq;
MinData[2] = results->Double(6, 1);
MinData[3] = results->Double(7, 1);
MinData[4] = results->Double(8, 1);
g_log.debug() << "Best direction Optimized is (" << (MinData[2]) << ","
<< (MinData[3]) << "," << (MinData[4]) << ")\n";
// ---------------------Find number indexed -----------------------
Quat Q1 = Quat(MinData[4], V3D(0, 1, 0)) * Quat(MinData[3], V3D(0, 0, 1)) *
Quat(MinData[2], V3D(0, 1, 0));
int Nindexed;
Kernel::Matrix<double> Mk(Q1.getRotation());
IndexRaw(PeaksRun2, Mk * UB1, Nindexed, avErrIndx, avErrAll, Tolerance);
//------------------------------------ Convert/Save Results
//-----------------------------
double deg, ax1, ax2, ax3;
Q1.getAngleAxis(deg, ax1, ax2, ax3);
if (dphi * deg < 0) {
deg = -deg;
ax1 = -ax1;
ax2 = -ax2;
ax3 = -ax3;
}
double phi2 = static_cast<double>(getProperty("Run1Phi")) + dphi;
double chi2 = acos(ax2) / M_PI * 180;
double omega2 = atan2(ax3, -ax1) / M_PI * 180;
g_log.notice()
<< "============================ Results ============================\n";
g_log.notice() << " phi,chi, and omega= (" << phi2 << "," << chi2 << ","
<< omega2 << ")\n";
g_log.notice() << " #indexed =" << Nindexed << '\n';
g_log.notice()
<< " ==============================================\n";
setProperty("Phi2", phi2);
setProperty("Chi2", chi2);
setProperty("Omega2", omega2);
setProperty("NIndexed", Nindexed);
setProperty("AvErrIndex", avErrIndx);
setProperty("AvErrAll", avErrAll);
Q1 = Quat(omega2, V3D(0, 1, 0)) * Quat(chi2, V3D(0, 0, 1)) *
Quat(phi2, V3D(0, 1, 0));
Kernel::Matrix<double> Gon2a(Q1.getRotation());
for (int i = 0; i < PeaksRun2->getNumberPeaks(); i++) {
PeaksRun2->getPeak(i).setGoniometerMatrix(Gon2a);
}
OrientedLattice latt2(PeaksRun2->mutableSample().getOrientedLattice());
// Kernel::Matrix<double> UB = latt2.getUB();
Rot.Invert();
Gon2a.Invert();
latt2.setUB(Gon2a * Mk * UB1);
PeaksRun2->mutableSample().setOrientedLattice(&latt2);
}
/** Executes the algorithm
*
* @throw Exception::FileError If the grouping file cannot be opened or read successfully
* @throw runtime_error If unable to run one of the sub-algorithms successfully
*/
void DiffractionFocussing::exec()
{
// retrieve the properties
std::string groupingFileName=getProperty("GroupingFileName");
// Get the input workspace
MatrixWorkspace_sptr inputW = getProperty("InputWorkspace");
bool dist = inputW->isDistribution();
//do this first to check that a valid file is available before doing any work
std::multimap<int64_t,int64_t> detectorGroups;// <group, UDET>
if (!readGroupingFile(groupingFileName, detectorGroups))
{
throw Exception::FileError("Error reading .cal file",groupingFileName);
}
//Convert to d-spacing units
API::MatrixWorkspace_sptr tmpW = convertUnitsToDSpacing(inputW);
//Rebin to a common set of bins
RebinWorkspace(tmpW);
std::set<int64_t> groupNumbers;
for(std::multimap<int64_t,int64_t>::const_iterator d = detectorGroups.begin();d!=detectorGroups.end();d++)
{
if (groupNumbers.find(d->first) == groupNumbers.end())
{
groupNumbers.insert(d->first);
}
}
int iprogress = 0;
int iprogress_count = static_cast<int>(groupNumbers.size());
int iprogress_step = iprogress_count / 100;
if (iprogress_step == 0) iprogress_step = 1;
std::vector<int64_t> resultIndeces;
for(std::set<int64_t>::const_iterator g = groupNumbers.begin();g!=groupNumbers.end();g++)
{
if (iprogress++ % iprogress_step == 0)
{
progress(0.68 + double(iprogress)/iprogress_count/3);
}
std::multimap<int64_t,int64_t>::const_iterator from = detectorGroups.lower_bound(*g);
std::multimap<int64_t,int64_t>::const_iterator to = detectorGroups.upper_bound(*g);
std::vector<detid_t> detectorList;
for(std::multimap<int64_t,int64_t>::const_iterator d = from;d!=to;d++)
detectorList.push_back(static_cast<detid_t>(d->second));
// Want version 1 of GroupDetectors here
API::IAlgorithm_sptr childAlg = createSubAlgorithm("GroupDetectors",-1.0,-1.0,true,1);
childAlg->setProperty("Workspace", tmpW);
childAlg->setProperty< std::vector<detid_t> >("DetectorList",detectorList);
childAlg->executeAsSubAlg();
try
{
// get the index of the combined spectrum
int ri = childAlg->getProperty("ResultIndex");
if (ri >= 0)
{
resultIndeces.push_back(ri);
}
}
catch(...)
{
throw std::runtime_error("Unable to get Properties from GroupDetectors sub-algorithm");
}
}
// Discard left-over spectra, but print warning message giving number discarded
int discarded = 0;
const int64_t oldHistNumber = tmpW->getNumberHistograms();
API::Axis *spectraAxis = tmpW->getAxis(1);
for(int64_t i=0; i < oldHistNumber; i++)
if ( spectraAxis->spectraNo(i) >= 0 && find(resultIndeces.begin(),resultIndeces.end(),i) == resultIndeces.end())
{
++discarded;
}
g_log.warning() << "Discarded " << discarded << " spectra that were not assigned to any group" << std::endl;
// Running GroupDetectors leads to a load of redundant spectra
// Create a new workspace that's the right size for the meaningful spectra and copy them in
int64_t newSize = tmpW->blocksize();
API::MatrixWorkspace_sptr outputW = API::WorkspaceFactory::Instance().create(tmpW,resultIndeces.size(),newSize+1,newSize);
// Copy units
outputW->getAxis(0)->unit() = tmpW->getAxis(0)->unit();
outputW->getAxis(1)->unit() = tmpW->getAxis(1)->unit();
API::Axis *spectraAxisNew = outputW->getAxis(1);
for(int64_t hist=0; hist < static_cast<int64_t>(resultIndeces.size()); hist++)
{
int64_t i = resultIndeces[hist];
double spNo = static_cast<double>(spectraAxis->spectraNo(i));
MantidVec &tmpE = tmpW->dataE(i);
MantidVec &outE = outputW->dataE(hist);
MantidVec &tmpY = tmpW->dataY(i);
MantidVec &outY = outputW->dataY(hist);
MantidVec &tmpX = tmpW->dataX(i);
MantidVec &outX = outputW->dataX(hist);
outE.assign(tmpE.begin(),tmpE.end());
outY.assign(tmpY.begin(),tmpY.end());
outX.assign(tmpX.begin(),tmpX.end());
spectraAxisNew->setValue(hist,spNo);
spectraAxis->setValue(i,-1);
}
progress(1.);
outputW->isDistribution(dist);
// Assign it to the output workspace property
setProperty("OutputWorkspace",outputW);
return;
}
/** Select background automatically
*/
DataObjects::Workspace2D_sptr ProcessBackground::autoBackgroundSelection(Workspace2D_sptr bkgdWS)
{
// Get background type and create bakground function
BackgroundFunction_sptr bkgdfunction = createBackgroundFunction(m_bkgdType);
int bkgdorder = getProperty("BackgroundOrder");
bkgdfunction->setAttributeValue("n", bkgdorder);
g_log.debug() << "DBx622 Background Workspace has " << bkgdWS->readX(0).size()
<< " data points." << std::endl;
// Fit input (a few) background pionts to get initial guess
API::IAlgorithm_sptr fit;
try
{
fit = this->createChildAlgorithm("Fit", 0.0, 0.2, true);
}
catch (Exception::NotFoundError &)
{
g_log.error() << "Requires CurveFitting library." << std::endl;
throw;
}
double startx = m_lowerBound;
double endx = m_upperBound;
fit->setProperty("Function", boost::dynamic_pointer_cast<API::IFunction>(bkgdfunction));
fit->setProperty("InputWorkspace", bkgdWS);
fit->setProperty("WorkspaceIndex", 0);
fit->setProperty("MaxIterations", 500);
fit->setProperty("StartX", startx);
fit->setProperty("EndX", endx);
fit->setProperty("Minimizer", "Levenberg-Marquardt");
fit->setProperty("CostFunction", "Least squares");
fit->executeAsChildAlg();
// Get fit result
// a) Status
std::string fitStatus = fit->getProperty("OutputStatus");
bool allowedfailure = (fitStatus.find("cannot") < fitStatus.size()) &&
(fitStatus.find("tolerance") < fitStatus.size());
if (fitStatus.compare("success") != 0 && !allowedfailure)
{
g_log.error() << "ProcessBackground: Fit Status = " << fitStatus
<< ". Not to update fit result" << std::endl;
throw std::runtime_error("Bad Fit");
}
// b) check that chi2 got better
const double chi2 = fit->getProperty("OutputChi2overDoF");
g_log.information() << "Fit background: Fit Status = " << fitStatus << ", chi2 = "
<< chi2 << "\n";
// c) get out the parameter names
API::IFunction_sptr func = fit->getProperty("Function");
/* Comment out as not being used
std::vector<std::string> parnames = func->getParameterNames();
std::map<std::string, double> parvalues;
for (size_t iname = 0; iname < parnames.size(); ++iname)
{
double value = func->getParameter(parnames[iname]);
parvalues.insert(std::make_pair(parnames[iname], value));
}
DataObject::Workspace2D_const_sptr theorybackground = AnalysisDataService::Instance().retrieve(wsname);
*/
// Filter and construct for the output workspace
Workspace2D_sptr outws = filterForBackground(bkgdfunction);
return outws;
} // END OF FUNCTION
