/// Converts the given tolerance (interpreted as standard deviation of a normal
/// probability distribution) to FWHM and assigns that to all peaks of the
/// supplied collection.
void PoldiIndexKnownCompounds::assignFwhmEstimates(
const PoldiPeakCollection_sptr &peakCollection, double tolerance) const {
if (!peakCollection) {
throw std::invalid_argument(
"Cannot assign intensities to invalid PoldiPeakCollection.");
}
size_t peakCount = peakCollection->peakCount();
double fwhm = sigmaToFwhm(tolerance);
for (size_t i = 0; i < peakCount; ++i) {
PoldiPeak_sptr peak = peakCollection->peak(i);
peak->setFwhm(UncertainValue(fwhm), PoldiPeak::Relative);
}
}
void PoldiFitPeaks1D2::setValuesFromProfileFunction(
PoldiPeak_sptr poldiPeak, const IFunction_sptr &fittedFunction) const {
IPeakFunction_sptr peakFunction =
boost::dynamic_pointer_cast<IPeakFunction>(fittedFunction);
if (peakFunction) {
poldiPeak->setIntensity(
UncertainValue(peakFunction->height(), peakFunction->getError(0)));
poldiPeak->setQ(
UncertainValue(peakFunction->centre(), peakFunction->getError(1)));
poldiPeak->setFwhm(UncertainValue(peakFunction->fwhm(),
getFwhmWidthRelation(peakFunction) *
peakFunction->getError(2)));
}
}
/** Creates PoldiPeak-objects from peak position iterators
*
* In this method, PoldiPeak objects are created from the raw peak position data and the original x-data. Estimates for peak height and FWHM
* provided along with the position.
*
* @param baseListStart :: Starting iterator of the vector which the peak positions refer to.
* @param peakPositions :: List with peakPositions.
* @param xData :: Vector with x-values of the correlation spectrum.
* @return Vector with PoldiPeak objects constructed from the raw peak position data.
*/
std::vector<PoldiPeak_sptr> PoldiPeakSearch::getPeaks(MantidVec::const_iterator baseListStart, std::list<MantidVec::const_iterator> peakPositions, const MantidVec &xData) const
{
std::vector<PoldiPeak_sptr> peakData;
peakData.reserve(peakPositions.size());
for(std::list<MantidVec::const_iterator>::const_iterator peak = peakPositions.begin();
peak != peakPositions.end();
++peak)
{
size_t index = std::distance(baseListStart, *peak);
PoldiPeak_sptr newPeak = PoldiPeak::create(UncertainValue(xData[index]), UncertainValue(**peak));
double fwhmEstimate = getFWHMEstimate(baseListStart, *peak, xData);
newPeak->setFwhm(UncertainValue(fwhmEstimate));
peakData.push_back(newPeak);
}
return peakData;
}
/// Creates a PoldiPeak from the given profile function/hkl pair.
PoldiPeak_sptr
PoldiFitPeaks2D::getPeakFromPeakFunction(IPeakFunction_sptr profileFunction,
const V3D &hkl) {
// Use EstimatePeakErrors to calculate errors of FWHM and so on
IAlgorithm_sptr errorAlg = createChildAlgorithm("EstimatePeakErrors");
errorAlg->setProperty(
"Function", boost::dynamic_pointer_cast<IFunction>(profileFunction));
errorAlg->setPropertyValue("OutputWorkspace", "Errors");
errorAlg->execute();
double centre = profileFunction->centre();
double fwhmValue = profileFunction->fwhm();
ITableWorkspace_sptr errorTable = errorAlg->getProperty("OutputWorkspace");
double centreError = errorTable->cell<double>(0, 2);
double fwhmError = errorTable->cell<double>(2, 2);
UncertainValue d(centre, centreError);
UncertainValue fwhm(fwhmValue, fwhmError);
UncertainValue intensity;
bool useIntegratedIntensities = getProperty("OutputIntegratedIntensities");
if (useIntegratedIntensities) {
double integratedIntensity = profileFunction->intensity();
double integratedIntensityError = errorTable->cell<double>(3, 2);
intensity = UncertainValue(integratedIntensity, integratedIntensityError);
} else {
double height = profileFunction->height();
double heightError = errorTable->cell<double>(1, 2);
intensity = UncertainValue(height, heightError);
}
// Create peak with extracted parameters and supplied hkl
PoldiPeak_sptr peak =
PoldiPeak::create(MillerIndices(hkl), d, intensity, UncertainValue(1.0));
peak->setFwhm(fwhm, PoldiPeak::FwhmRelation::AbsoluteD);
return peak;
}