/**
* Converts normalized peak intensities to count based integral intensities
*
* This operation is the opposite of getNormalizedPeakCollection and is used
* to convert the intensities back to integral intensities.
*
* @param peakCollection :: PoldiPeakCollection with normalized intensities
* @return PoldiPeakCollection with integral intensities
*/
PoldiPeakCollection_sptr PoldiFitPeaks2D::getCountPeakCollection(
const PoldiPeakCollection_sptr &peakCollection) const {
if (!peakCollection) {
throw std::invalid_argument(
"Cannot proceed with invalid PoldiPeakCollection.");
}
if (!m_timeTransformer) {
throw std::invalid_argument("Cannot proceed without PoldiTimeTransformer.");
}
PoldiPeakCollection_sptr countPeakCollection =
boost::make_shared<PoldiPeakCollection>(PoldiPeakCollection::Integral);
countPeakCollection->setProfileFunctionName(
peakCollection->getProfileFunctionName());
// Get crystal data into new peak collection
assignCrystalData(countPeakCollection, peakCollection);
for (size_t i = 0; i < peakCollection->peakCount(); ++i) {
PoldiPeak_sptr peak = peakCollection->peak(i);
double calculatedIntensity =
m_timeTransformer->calculatedTotalIntensity(peak->d());
PoldiPeak_sptr countPeak = peak->clone();
countPeak->setIntensity(peak->intensity() * calculatedIntensity);
countPeakCollection->addPeak(countPeak);
}
return countPeakCollection;
}
/** Scales the intensities of all peaks in the collection by the supplied
*scattering contribution
*
* This method scales intensities of peaks contained in the supplied
*PoldiPeakCollection
* (if it's a null-pointer, the method throws an std::invalid_argument
*exception). The original
* intensity is multiplied by the contribution factor.
*
* @param peakCollection :: PoldiPeakCollection with expected peaks of one
*phase.
* @param contribution :: Scattering contribution of that material.
*/
void PoldiIndexKnownCompounds::scaleIntensityEstimates(
const PoldiPeakCollection_sptr &peakCollection, double contribution) const {
if (!peakCollection) {
throw std::invalid_argument(
"Cannot assign intensities to invalid PoldiPeakCollection.");
}
size_t peakCount = peakCollection->peakCount();
for (size_t i = 0; i < peakCount; ++i) {
PoldiPeak_sptr peak = peakCollection->peak(i);
peak->setIntensity(peak->intensity() * contribution);
}
}
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)));
}
}
/**
* Return peak collection with integrated peaks
*
* This method takes a PoldiPeakCollection where the intensity is represented
* by the maximum. Then it takes the profile function stored in the peak
* collection, which must be the name of a registered
* IPeakFunction-implementation. The parameters height and fwhm are assigned,
* centre is set to 0 to avoid problems with the parameter transformation for
* the integration from -inf to inf. The profiles are integrated using
* a PeakFunctionIntegrator to the precision of 1e-10.
*
* The original peak collection is not modified, a new instance is created.
*
* @param rawPeakCollection :: PoldiPeakCollection
* @return PoldiPeakCollection with integrated intensities
*/
PoldiPeakCollection_sptr PoldiFitPeaks2D::getIntegratedPeakCollection(
const PoldiPeakCollection_sptr &rawPeakCollection) const {
if (!rawPeakCollection) {
throw std::invalid_argument(
"Cannot proceed with invalid PoldiPeakCollection.");
}
if (!isValidDeltaT(m_deltaT)) {
throw std::invalid_argument("Cannot proceed with invalid time bin size.");
}
if (!m_timeTransformer) {
throw std::invalid_argument(
"Cannot proceed with invalid PoldiTimeTransformer.");
}
if (rawPeakCollection->intensityType() == PoldiPeakCollection::Integral) {
/* Intensities are integral already - don't need to do anything,
* except cloning the collection, to make behavior consistent, since
* integrating also results in a new peak collection.
*/
return rawPeakCollection->clone();
}
/* If no profile function is specified, it's not possible to get integrated
* intensities at all and we try to use the one specified by the user
* instead.
*/
std::string profileFunctionName = rawPeakCollection->getProfileFunctionName();
if (!rawPeakCollection->hasProfileFunctionName()) {
profileFunctionName = getPropertyValue("PeakProfileFunction");
}
std::vector<std::string> allowedProfiles =
FunctionFactory::Instance().getFunctionNames<IPeakFunction>();
if (std::find(allowedProfiles.begin(), allowedProfiles.end(),
profileFunctionName) == allowedProfiles.end()) {
throw std::runtime_error(
"Cannot integrate peak profiles with invalid profile function.");
}
PoldiPeakCollection_sptr integratedPeakCollection =
boost::make_shared<PoldiPeakCollection>(PoldiPeakCollection::Integral);
integratedPeakCollection->setProfileFunctionName(profileFunctionName);
// Preserve unit cell, point group
assignCrystalData(integratedPeakCollection, rawPeakCollection);
for (size_t i = 0; i < rawPeakCollection->peakCount(); ++i) {
PoldiPeak_sptr peak = rawPeakCollection->peak(i);
IPeakFunction_sptr profileFunction =
boost::dynamic_pointer_cast<IPeakFunction>(
FunctionFactory::Instance().createFunction(profileFunctionName));
profileFunction->setHeight(peak->intensity());
profileFunction->setFwhm(peak->fwhm(PoldiPeak::AbsoluteD));
PoldiPeak_sptr integratedPeak = peak->clone();
integratedPeak->setIntensity(UncertainValue(profileFunction->intensity()));
integratedPeakCollection->addPeak(integratedPeak);
}
return integratedPeakCollection;
}