/**
* 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;
}
PoldiPeakCollection_sptr PoldiFitPeaks1D2::getReducedPeakCollection(
const PoldiPeakCollection_sptr &peaks) const {
PoldiPeakCollection_sptr reducedPeaks =
boost::make_shared<PoldiPeakCollection>();
reducedPeaks->setProfileFunctionName(peaks->getProfileFunctionName());
for (size_t i = 0; i < peaks->peakCount(); ++i) {
PoldiPeak_sptr currentPeak = peaks->peak(i);
if (peakIsAcceptable(currentPeak)) {
reducedPeaks->addPeak(currentPeak);
}
}
return reducedPeaks;
}
PoldiPeakCollection_sptr
PoldiIndexKnownCompounds::getIntensitySortedPeakCollection(
const PoldiPeakCollection_sptr &peaks) const {
std::vector<PoldiPeak_sptr> peakVector(peaks->peaks());
std::sort(peakVector.begin(), peakVector.end(),
boost::bind<bool>(&PoldiPeak::greaterThan, _1, _2,
&PoldiPeak::intensity));
PoldiPeakCollection_sptr sortedPeaks =
boost::make_shared<PoldiPeakCollection>(peaks->intensityType());
for (size_t i = 0; i < peakVector.size(); ++i) {
sortedPeaks->addPeak(peakVector[i]->clone());
}
return sortedPeaks;
}
/**
* Construct a PoldiPeakCollection from a Poldi2DFunction
*
* This method performs the opposite operation of
*getFunctionFromPeakCollection.
* It takes a function, checks if it's of the proper type and turns the
* information into a PoldiPeakCollection.
*
* @param Poldi2DFunction with one PoldiSpectrumDomainFunction per peak
* @return PoldiPeakCollection containing peaks with normalized intensities
*/
PoldiPeakCollection_sptr PoldiFitPeaks2D::getPeakCollectionFromFunction(
const IFunction_sptr &fitFunction) {
Poldi2DFunction_sptr poldi2DFunction =
boost::dynamic_pointer_cast<Poldi2DFunction>(fitFunction);
if (!poldi2DFunction) {
throw std::invalid_argument(
"Cannot process function that is not a Poldi2DFunction.");
}
PoldiPeakCollection_sptr normalizedPeaks =
boost::make_shared<PoldiPeakCollection>(PoldiPeakCollection::Integral);
boost::shared_ptr<const Kernel::DblMatrix> covarianceMatrix =
poldi2DFunction->getCovarianceMatrix();
size_t offset = 0;
for (size_t i = 0; i < poldi2DFunction->nFunctions(); ++i) {
boost::shared_ptr<PoldiSpectrumPawleyFunction> poldiPawleyFunction =
boost::dynamic_pointer_cast<PoldiSpectrumPawleyFunction>(
poldi2DFunction->getFunction(i));
// If it's a Pawley function, there are several peaks in one function.
if (poldiPawleyFunction) {
IPawleyFunction_sptr pawleyFunction =
poldiPawleyFunction->getPawleyFunction();
if (pawleyFunction) {
CompositeFunction_sptr decoratedFunction =
boost::dynamic_pointer_cast<CompositeFunction>(
pawleyFunction->getDecoratedFunction());
offset = decoratedFunction->getFunction(0)->nParams();
for (size_t j = 0; j < pawleyFunction->getPeakCount(); ++j) {
IPeakFunction_sptr profileFunction =
pawleyFunction->getPeakFunction(j);
size_t nLocalParams = profileFunction->nParams();
boost::shared_ptr<Kernel::DblMatrix> localCov =
getLocalCovarianceMatrix(covarianceMatrix, offset, nLocalParams);
profileFunction->setCovarianceMatrix(localCov);
// Increment offset for next function
offset += nLocalParams;
V3D peakHKL = pawleyFunction->getPeakHKL(j);
PoldiPeak_sptr peak =
getPeakFromPeakFunction(profileFunction, peakHKL);
normalizedPeaks->addPeak(peak);
}
}
break;
}
// Otherwise, it's just one peak in this function.
boost::shared_ptr<PoldiSpectrumDomainFunction> peakFunction =
boost::dynamic_pointer_cast<PoldiSpectrumDomainFunction>(
poldi2DFunction->getFunction(i));
if (peakFunction) {
IPeakFunction_sptr profileFunction =
boost::dynamic_pointer_cast<IPeakFunction>(
peakFunction->getProfileFunction());
// Get local covariance matrix
size_t nLocalParams = profileFunction->nParams();
boost::shared_ptr<Kernel::DblMatrix> localCov =
getLocalCovarianceMatrix(covarianceMatrix, offset, nLocalParams);
profileFunction->setCovarianceMatrix(localCov);
// Increment offset for next function
offset += nLocalParams;
PoldiPeak_sptr peak =
getPeakFromPeakFunction(profileFunction, V3D(0, 0, 0));
normalizedPeaks->addPeak(peak);
}
}
return normalizedPeaks;
}
/**
* 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;
}
