/** 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(const MantidVec::const_iterator &baseListStart,
const MantidVec::const_iterator &baseListEnd,
std::list<MantidVec::const_iterator> peakPositions,
const MantidVec &xData, const Unit_sptr &unit) 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);
double xDataD = getTransformedCenter(xData[index], unit);
double fwhmEstimate =
getFWHMEstimate(baseListStart, baseListEnd, *peak, xData);
UncertainValue fwhm(fwhmEstimate / xData[index]);
PoldiPeak_sptr newPeak = PoldiPeak::create(
MillerIndices(), UncertainValue(xDataD), UncertainValue(**peak), fwhm);
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;
}
/**
* Tries to refine the initial cell using the supplied peaks
*
* This method tries to refine the initial unit cell using the indexed peaks
* that are supplied in the PoldiPeakCollection. If there are unindexed peaks,
* the cell will not be refined at all, instead the unmodified initial cell
* is returned.
*
* @param initialCell :: String with the initial unit cell
* @param crystalSystem :: Crystal system name
* @param peakCollection :: Collection of bragg peaks, must be indexed
*
* @return String for refined unit cell
*/
std::string PoldiFitPeaks2D::getRefinedStartingCell(
const std::string &initialCell, const std::string &latticeSystem,
const PoldiPeakCollection_sptr &peakCollection) {
Geometry::UnitCell cell = Geometry::strToUnitCell(initialCell);
ILatticeFunction_sptr latticeFunction =
boost::dynamic_pointer_cast<ILatticeFunction>(
FunctionFactory::Instance().createFunction("LatticeFunction"));
latticeFunction->setLatticeSystem(latticeSystem);
latticeFunction->fix(latticeFunction->parameterIndex("ZeroShift"));
latticeFunction->setUnitCell(cell);
// Remove errors from d-values
PoldiPeakCollection_sptr clone = peakCollection->clone();
for (size_t i = 0; i < clone->peakCount(); ++i) {
PoldiPeak_sptr peak = clone->peak(i);
// If there are unindexed peaks, don't refine, just return the initial cell
if (peak->hkl() == MillerIndices()) {
return initialCell;
}
peak->setD(UncertainValue(peak->d().value()));
}
TableWorkspace_sptr peakTable = clone->asTableWorkspace();
IAlgorithm_sptr fit = createChildAlgorithm("Fit");
fit->setProperty("Function",
boost::static_pointer_cast<IFunction>(latticeFunction));
fit->setProperty("InputWorkspace", peakTable);
fit->setProperty("CostFunction", "Unweighted least squares");
fit->execute();
Geometry::UnitCell refinedCell = latticeFunction->getUnitCell();
return Geometry::unitCellToStr(refinedCell);
}
void PoldiPeakCollection::setPeaks(const std::vector<V3D> &hkls,
const std::vector<double> &dValues,
const std::vector<double> &fSquared) {
if (hkls.size() != dValues.size()) {
throw std::invalid_argument(
"hkl-vector and d-vector do not have the same length.");
}
if (!m_pointGroup) {
throw std::runtime_error("Cannot set peaks without point group.");
}
m_peaks.clear();
for (size_t i = 0; i < hkls.size(); ++i) {
double multiplicity =
static_cast<double>(m_pointGroup->getEquivalents(hkls[i]).size());
addPeak(PoldiPeak::create(
MillerIndices(hkls[i]), UncertainValue(dValues[i]),
UncertainValue(multiplicity * fSquared[i]), UncertainValue(0.0)));
}
}
