size_t PawleyFunction::calculateFunctionValues(
const API::IPeakFunction_sptr &peak, const API::FunctionDomain1D &domain,
API::FunctionValues &localValues) const {
size_t domainSize = domain.size();
const double *domainBegin = domain.getPointerAt(0);
const double *domainEnd = domain.getPointerAt(domainSize);
double centre = peak->centre();
double dx = m_peakRadius * peak->fwhm();
auto lb = std::lower_bound(domainBegin, domainEnd, centre - dx);
auto ub = std::upper_bound(lb, domainEnd, centre + dx);
size_t n = std::distance(lb, ub);
if (n == 0) {
throw std::invalid_argument("Null-domain");
}
FunctionDomain1DView localDomain(lb, n);
localValues.reset(localDomain);
peak->functionLocal(localValues.getPointerToCalculated(0),
localDomain.getPointerAt(0), n);
return std::distance(domainBegin, lb);
}
/// Populates a spectrum with peaks of type given by peakShape argument.
/// @param spectrum :: A composite function that is a collection of peaks.
/// @param peakShape :: A shape of each peak as a name of an IPeakFunction.
/// @param centresAndIntensities :: A FunctionValues object containing centres
/// and intensities for the peaks. First nPeaks calculated values are the
/// centres and the following nPeaks values are the intensities.
/// @param xVec :: x-values of a tabulated width function.
/// @param yVec :: y-values of a tabulated width function.
/// @param fwhmVariation :: A variation in the peak width allowed in a fit.
/// @param defaultFWHM :: A default value for the FWHM to use if xVec and yVec
/// are empty.
/// @param nRequiredPeaks :: A number of peaks required to be created.
/// @param fixAllPeaks :: If true fix all peak parameters
/// @return :: The number of peaks that will be actually fitted.
size_t buildSpectrumFunction(API::CompositeFunction &spectrum,
const std::string &peakShape,
const API::FunctionValues ¢resAndIntensities,
const std::vector<double> &xVec,
const std::vector<double> &yVec,
double fwhmVariation, double defaultFWHM,
size_t nRequiredPeaks, bool fixAllPeaks) {
if (xVec.size() != yVec.size()) {
throw std::runtime_error("WidthX and WidthY must have the same size.");
}
auto nPeaks = calculateNPeaks(centresAndIntensities);
auto maxNPeaks = calculateMaxNPeaks(nPeaks);
if (nRequiredPeaks > maxNPeaks) {
maxNPeaks = nRequiredPeaks;
}
for (size_t i = 0; i < maxNPeaks; ++i) {
const bool isGood = i < nPeaks;
const auto centre = isGood ? centresAndIntensities.getCalculated(i) : 0.0;
const auto intensity =
isGood ? centresAndIntensities.getCalculated(i + nPeaks) : 0.0;
auto peak = createPeak(peakShape, centre, intensity, xVec, yVec,
fwhmVariation, defaultFWHM, isGood, fixAllPeaks);
spectrum.addFunction(peak);
}
return nPeaks;
}
//----------------------------------------------------------------------------------------------
/// Extract values from domain and values objects to vectors.
/// @param domain :: A domain with fitting data arguments.
/// @param values :: A FunctionValues object with the fitting data.
/// @param x :: A vector to store the domain values
/// @param y :: A vector to store the fitting data values.
void extractValues(const API::FunctionDomain1D &domain,
const API::FunctionValues &values, std::vector<double> &x,
std::vector<double> &y) {
size_t n = domain.size();
double start = domain[0];
double end = domain[n - 1];
auto dBegin = domain.getPointerAt(0);
auto startIter = std::lower_bound(dBegin, dBegin + n, start);
auto istart = static_cast<size_t>(std::distance(dBegin, startIter));
if (istart == n) {
x.clear();
y.clear();
return;
}
auto endIter = std::lower_bound(startIter, dBegin + n, end);
auto iend = static_cast<size_t>(std::distance(dBegin, endIter));
if (iend <= istart) {
x.clear();
y.clear();
return;
}
n = iend - istart;
x.resize(n);
y.resize(n);
for (size_t i = istart; i < iend; ++i) {
auto j = i - istart;
x[j] = domain[i];
y[j] = values.getFitData(i);
}
}
/**
* @param index Index value into functionValues array
* @param signal Calculated signal value
* @param functionValues [InOut] Final calculated values
*/
void ResolutionConvolvedCrossSection::storeCalculatedWithMutex(
const size_t index, const double signal,
API::FunctionValues &functionValues) const {
std::lock_guard<std::mutex> lock(m_valuesMutex);
functionValues.setCalculated(index, signal);
}
/// Calculate the number of visible peaks.
size_t calculateNPeaks(const API::FunctionValues ¢resAndIntensities) {
return centresAndIntensities.size() / 2;
}
/**
* Create an output event workspace filled with data simulated with the fitting
* function.
* @param baseName :: The base name for the workspace
* @param inputWorkspace :: The input workspace.
* @param values :: The calculated values
* @param outputWorkspacePropertyName :: The property name
*/
boost::shared_ptr<API::Workspace> FitMD::createEventOutputWorkspace(
const std::string &baseName, const API::IMDEventWorkspace &inputWorkspace,
const API::FunctionValues &values,
const std::string &outputWorkspacePropertyName) {
auto outputWS =
MDEventFactory::CreateMDWorkspace(inputWorkspace.getNumDims(), "MDEvent");
// Add events
// TODO: Generalize to ND (the current framework is a bit limiting)
auto mdWS = boost::dynamic_pointer_cast<
DataObjects::MDEventWorkspace<DataObjects::MDEvent<4>, 4>>(outputWS);
if (!mdWS) {
return boost::shared_ptr<API::Workspace>();
}
// Bins extents and meta data
for (size_t i = 0; i < 4; ++i) {
boost::shared_ptr<const Geometry::IMDDimension> inputDim =
inputWorkspace.getDimension(i);
Geometry::MDHistoDimensionBuilder builder;
builder.setName(inputDim->getName());
builder.setId(inputDim->getDimensionId());
builder.setUnits(inputDim->getUnits());
builder.setNumBins(inputDim->getNBins());
builder.setMin(inputDim->getMinimum());
builder.setMax(inputDim->getMaximum());
builder.setFrameName(inputDim->getMDFrame().name());
outputWS->addDimension(builder.create());
}
// Run information
outputWS->copyExperimentInfos(inputWorkspace);
// Coordinates
outputWS->setCoordinateSystem(inputWorkspace.getSpecialCoordinateSystem());
// Set sensible defaults for splitting behaviour
BoxController_sptr bc = outputWS->getBoxController();
bc->setSplitInto(3);
bc->setSplitThreshold(3000);
outputWS->initialize();
outputWS->splitBox();
auto inputIter = inputWorkspace.createIterator();
size_t resultValueIndex(0);
const float errorSq = 0.0;
do {
const size_t numEvents = inputIter->getNumEvents();
const float signal =
static_cast<float>(values.getCalculated(resultValueIndex));
for (size_t i = 0; i < numEvents; ++i) {
coord_t centers[4] = {
inputIter->getInnerPosition(i, 0), inputIter->getInnerPosition(i, 1),
inputIter->getInnerPosition(i, 2), inputIter->getInnerPosition(i, 3)};
mdWS->addEvent(MDEvent<4>(signal, errorSq, inputIter->getInnerRunIndex(i),
inputIter->getInnerDetectorID(i), centers));
}
++resultValueIndex;
} while (inputIter->next());
delete inputIter;
// This splits up all the boxes according to split thresholds and sizes.
auto threadScheduler = new Kernel::ThreadSchedulerFIFO();
Kernel::ThreadPool threadPool(threadScheduler);
outputWS->splitAllIfNeeded(threadScheduler);
threadPool.joinAll();
outputWS->refreshCache();
// Store it
if (!outputWorkspacePropertyName.empty()) {
declareProperty(
new API::WorkspaceProperty<API::IMDEventWorkspace>(
outputWorkspacePropertyName, "", Direction::Output),
"Name of the output Workspace holding resulting simulated spectrum");
m_manager->setPropertyValue(outputWorkspacePropertyName,
baseName + "Workspace");
m_manager->setProperty(outputWorkspacePropertyName, outputWS);
}
return outputWS;
}