/**
* 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;
}
/**
* Returns a Poldi2DFunction that encapsulates individual peaks
*
* This function takes all peaks from the supplied peak collection and
* generates an IPeakFunction of the type given in the name parameter, wraps
* them in a Poldi2DFunction and returns it.
*
* @param profileFunctionName :: Profile function name.
* @param peakCollection :: Peak collection with peaks to be used in the fit.
* @return :: A Poldi2DFunction with peak profile functions.
*/
Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionIndividualPeaks(
std::string profileFunctionName,
const PoldiPeakCollection_sptr &peakCollection) const {
auto mdFunction = boost::make_shared<Poldi2DFunction>();
for (size_t i = 0; i < peakCollection->peakCount(); ++i) {
PoldiPeak_sptr peak = peakCollection->peak(i);
boost::shared_ptr<PoldiSpectrumDomainFunction> peakFunction =
boost::dynamic_pointer_cast<PoldiSpectrumDomainFunction>(
FunctionFactory::Instance().createFunction(
"PoldiSpectrumDomainFunction"));
if (!peakFunction) {
throw std::invalid_argument(
"Cannot process null pointer poldi function.");
}
peakFunction->setDecoratedFunction(profileFunctionName);
IPeakFunction_sptr wrappedProfile =
boost::dynamic_pointer_cast<IPeakFunction>(
peakFunction->getProfileFunction());
if (wrappedProfile) {
wrappedProfile->setCentre(peak->d());
wrappedProfile->setFwhm(peak->fwhm(PoldiPeak::AbsoluteD));
wrappedProfile->setIntensity(peak->intensity());
}
mdFunction->addFunction(peakFunction);
}
return mdFunction;
}
/** Creates a vector of IndexCandidatePair-objects.
*
* This function iterates through all peaks in the measured
*PoldiPeakCollection, getting possible indexing candidates
* for each peak (see PoldiIndexKnownCompounds::getIndexCandidatePairs). If no
*candidates are found it means that
* there are no reflections with similar d-spacings from the known compounds,
*so it is treated as an unindexed peak.
* Otherwise, all candidates for this peak are appended to the list of existing
*candidate pairs.
*
* @param measured :: Measured peaks.
* @param knownCompoundPeaks :: Collections of expected peaks.
* @return Vector of index candidates.
*/
std::vector<IndexCandidatePair>
PoldiIndexKnownCompounds::getAllIndexCandidatePairs(
const PoldiPeakCollection_sptr &measured,
const std::vector<PoldiPeakCollection_sptr> &knownCompoundPeaks) {
std::vector<IndexCandidatePair> candidates;
size_t peakCount = measured->peakCount();
for (size_t i = 0; i < peakCount; ++i) {
PoldiPeak_sptr currentPeak = measured->peak(i);
std::vector<IndexCandidatePair> currentCandidates =
getIndexCandidatePairs(currentPeak, knownCompoundPeaks);
if (currentCandidates.empty()) {
collectUnindexedPeak(currentPeak);
} else {
candidates.insert(candidates.end(), currentCandidates.begin(),
currentCandidates.end());
}
g_log.information() << " Peak at d="
<< static_cast<double>(currentPeak->d()) << " has "
<< currentCandidates.size() << " candidates."
<< std::endl;
}
return candidates;
}
/// Assign Miller indices from one peak collection to another.
void PoldiFitPeaks2D::assignMillerIndices(const PoldiPeakCollection_sptr &from,
PoldiPeakCollection_sptr &to) const {
if (!from || !to) {
throw std::invalid_argument("Cannot process invalid peak collections.");
}
if (from->peakCount() != to->peakCount()) {
throw std::runtime_error(
"Cannot assign indices if number of peaks does not match.");
}
for (size_t i = 0; i < from->peakCount(); ++i) {
PoldiPeak_sptr fromPeak = from->peak(i);
PoldiPeak_sptr toPeak = to->peak(i);
toPeak->setHKL(fromPeak->hkl());
}
}
std::vector<RefinedRange_sptr> PoldiFitPeaks1D2::getRefinedRanges(
const PoldiPeakCollection_sptr &peaks) const {
std::vector<RefinedRange_sptr> ranges;
for (size_t i = 0; i < peaks->peakCount(); ++i) {
ranges.push_back(
boost::make_shared<RefinedRange>(peaks->peak(i), m_fwhmMultiples));
}
return ranges;
}
/**
* Returns a Poldi2DFunction that encapsulates a PawleyFunction
*
* This function creates a PawleyFunction using the supplied profile function
* name and the crystal system as well as initial cell from the input
* properties of the algorithm and wraps it in a Poldi2DFunction.
*
* The cell is refined using LatticeFunction to get better starting values.
*
* Because the peak intensities are integral at this step but PawleyFunction
* expects peak heights, a profile function is created and
* setIntensity/height-methods are used to convert.
*
* @param profileFunctionName :: Profile function name for PawleyFunction.
* @param peakCollection :: Peak collection with peaks to be used in the fit.
* @return :: A Poldi2DFunction with a PawleyFunction.
*/
Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionPawley(
std::string profileFunctionName,
const PoldiPeakCollection_sptr &peakCollection) {
auto mdFunction = boost::make_shared<Poldi2DFunction>();
boost::shared_ptr<PoldiSpectrumPawleyFunction> poldiPawleyFunction =
boost::dynamic_pointer_cast<PoldiSpectrumPawleyFunction>(
FunctionFactory::Instance().createFunction(
"PoldiSpectrumPawleyFunction"));
if (!poldiPawleyFunction) {
throw std::invalid_argument("Could not create pawley function.");
}
poldiPawleyFunction->setDecoratedFunction("PawleyFunction");
IPawleyFunction_sptr pawleyFunction =
poldiPawleyFunction->getPawleyFunction();
pawleyFunction->setProfileFunction(profileFunctionName);
// Extract crystal system from peak collection
PointGroup_sptr pointGroup = peakCollection->pointGroup();
if (!pointGroup) {
throw std::invalid_argument("Can not initialize pawley function properly - "
"peaks do not have point group.");
}
std::string latticeSystem = getLatticeSystemFromPointGroup(pointGroup);
pawleyFunction->setLatticeSystem(latticeSystem);
UnitCell cell = peakCollection->unitCell();
// Extract unit cell from peak collection
pawleyFunction->setUnitCell(getRefinedStartingCell(
unitCellToStr(cell), latticeSystem, peakCollection));
IPeakFunction_sptr pFun = boost::dynamic_pointer_cast<IPeakFunction>(
FunctionFactory::Instance().createFunction(profileFunctionName));
for (size_t i = 0; i < peakCollection->peakCount(); ++i) {
PoldiPeak_sptr peak = peakCollection->peak(i);
pFun->setCentre(peak->d());
pFun->setFwhm(peak->fwhm(PoldiPeak::AbsoluteD));
pFun->setIntensity(peak->intensity());
pawleyFunction->addPeak(peak->hkl().asV3D(),
peak->fwhm(PoldiPeak::AbsoluteD), pFun->height());
}
pawleyFunction->fix(pawleyFunction->parameterIndex("f0.ZeroShift"));
mdFunction->addFunction(poldiPawleyFunction);
return mdFunction;
}
TableWorkspace_sptr PoldiPeakSummary::getSummaryTable(
const PoldiPeakCollection_sptr &peakCollection) const {
if (!peakCollection) {
throw std::invalid_argument(
"Cannot create summary of a null PoldiPeakCollection.");
}
TableWorkspace_sptr peakResultWorkspace = getInitializedResultWorkspace();
for (size_t i = 0; i < peakCollection->peakCount(); ++i) {
storePeakSummary(peakResultWorkspace->appendRow(), peakCollection->peak(i));
}
return peakResultWorkspace;
}
/// 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);
}
}
/** 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);
}
}
size_t PoldiIndexKnownCompounds::getMaximumIntensityPeakIndex(
const PoldiPeakCollection_sptr &peakCollection) const {
double maxInt = 0.0;
size_t maxIndex = 0;
for (size_t i = 0; i < peakCollection->peakCount(); ++i) {
PoldiPeak_sptr currentPeak = peakCollection->peak(i);
double currentInt = currentPeak->intensity();
if (currentInt > maxInt) {
maxInt = currentInt;
maxIndex = i;
}
}
return maxIndex;
}
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;
}
/**
* 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);
}
/// Uses PoldiIndexKnownCompounds::isCandidate to find all candidates for
/// supplied peak in the candidate peak collections.
std::vector<IndexCandidatePair>
PoldiIndexKnownCompounds::getIndexCandidatePairs(
const PoldiPeak_sptr &peak,
const std::vector<PoldiPeakCollection_sptr> &candidateCollections) const {
std::vector<IndexCandidatePair> indexCandidates;
for (size_t i = 0; i < candidateCollections.size(); ++i) {
PoldiPeakCollection_sptr currentCandidateCollection =
candidateCollections[i];
size_t peakCount = currentCandidateCollection->peakCount();
for (size_t p = 0; p < peakCount; ++p) {
PoldiPeak_sptr currentCandidate = currentCandidateCollection->peak(p);
if (isCandidate(peak, currentCandidate)) {
indexCandidates.push_back(
IndexCandidatePair(peak, currentCandidate, i));
}
}
}
return indexCandidates;
}
/**
* 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;
}
double PoldiIndexKnownCompounds::getMaximumIntensity(
const PoldiPeakCollection_sptr &peakCollection) const {
size_t i = getMaximumIntensityPeakIndex(peakCollection);
return peakCollection->peak(i)->intensity();
}
