/**
* Normalized the intensities of the given integrated peaks
*
* This function normalizes the peak intensities according to the source
* spectrum, the number of chopper slits and the number of detector elements.
*
* @param peakCollection :: PoldiPeakCollection with integrated intensities
* @return PoldiPeakCollection with normalized intensities
*/
PoldiPeakCollection_sptr PoldiFitPeaks2D::getNormalizedPeakCollection(
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 normalizedPeakCollection =
boost::make_shared<PoldiPeakCollection>(PoldiPeakCollection::Integral);
normalizedPeakCollection->setProfileFunctionName(
peakCollection->getProfileFunctionName());
// Carry over unit cell and point group
assignCrystalData(normalizedPeakCollection, 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 normalizedPeak = peak->clone();
normalizedPeak->setIntensity(peak->intensity() / calculatedIntensity);
normalizedPeakCollection->addPeak(normalizedPeak);
}
return normalizedPeakCollection;
}
/**
* 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;
}
/**
* 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;
}
bool PoldiPeakSearch::isLessThanMinimum(PoldiPeak_sptr peak) {
return peak->intensity().value() <= m_minimumPeakHeight;
}
/** Assigns most likely indices to measured peaks.
*
* This method takes a list of index candidate pairs and sorts it according to
*their score, because
* a high score corresponds to a high probability of the assignment being
*correct. Then the function
* takes the element with the highest score and inspects the
*IndexCandidatePair. If the measured reflection
* does not have an index yet, it checks whether the candidate index has
*already been used. In that case,
* the measured peak is stored in a buffer. Otherwise, the candidate presents
*the best solution for the
* measured peak (because the current pair has the highest score in the list of
*remaining candidate pairs) and
* the solution is accepted. This means that the measured as well as the
*candidate peak are marked as "used" and
* the measured peak is stored in the PoldiPeakCollection that is located at
*the index of the current pair.
*
* Then the next element is checked and so on. Whenever a "next best" solution
*for a measured peak in the mentioned
* buffer is found, the peak is removed from that buffer. Once all candidate
*pairs have been evaluated, the peaks
* that are still in the buffer are considered unindexed and treated
*accordingly.
*
* For a more complete explanation of the principle, please check the
*documentation in the wiki.
*
* @param candidates :: Vector of possible index candidates.
*/
void PoldiIndexKnownCompounds::assignCandidates(
const std::vector<IndexCandidatePair> &candidates) {
// Make a copy since this is going to be modified
std::vector<IndexCandidatePair> workCandidates = candidates;
/* The vector is sorted by score (see comparison operator of PeakCandidate),
* so the first element has the lowest score (lowest probability of being
* a good guess).
*/
std::sort(workCandidates.begin(), workCandidates.end());
std::set<PoldiPeak_sptr> usedMeasuredPeaks;
std::set<PoldiPeak_sptr> usedExpectedPeaks;
std::set<PoldiPeak_sptr> unassignedMeasuredPeaks;
/* The candidate at the back of the vector has the highest score,
* so it's the candidate with the highest probability of being correct.
* Consequently, the vector is iterated from end to beginning.
*/
for (auto it = workCandidates.rbegin(); it != workCandidates.rend(); ++it) {
IndexCandidatePair currentCandidate = *it;
PoldiPeak_sptr measuredPeak = currentCandidate.observed;
PoldiPeak_sptr expectedPeak = currentCandidate.candidate;
g_log.information() << " Candidate d="
<< static_cast<double>(measuredPeak->d()) << " -> "
<< "Phase: "
<< currentCandidate.candidateCollectionIndex << " ["
<< MillerIndicesIO::toString(expectedPeak->hkl())
<< "] (d=" << static_cast<double>(expectedPeak->d())
<< "), "
<< "Score=(" << currentCandidate.positionMatch << "): ";
/* If the peak has not been indexed yet, it is not stored in the set
* that holds measured peaks that are already indexed, so the candidate
* needs to be examined further.
*/
if (!inPeakSet(usedMeasuredPeaks, measuredPeak)) {
/* If the theoretical reflection of this index-candidate has already been
* assigned to a measured peak, the measured peak is inserted into
* a second set where it is kept in case there is another candidate
* for this measured peak.
*/
if (inPeakSet(usedExpectedPeaks, expectedPeak)) {
unassignedMeasuredPeaks.insert(measuredPeak);
g_log.information()
<< " Candidate rejected: Candidate has been already used."
<< std::endl;
} else {
/* Otherwise, the indexed candidate is accepted and the measured peak
* is removed from the set of peaks that are waiting for another
* solution.
*/
if (inPeakSet(unassignedMeasuredPeaks, measuredPeak)) {
unassignedMeasuredPeaks.erase(measuredPeak);
}
usedExpectedPeaks.insert(expectedPeak);
usedMeasuredPeaks.insert(measuredPeak);
assignPeakIndex(currentCandidate);
g_log.information() << " Candidate accepted." << std::endl;
}
} else {
g_log.information()
<< " Candidate rejected: peak has already been indexed: ["
<< MillerIndicesIO::toString(measuredPeak->hkl()) << "]."
<< std::endl;
}
}
/* All peaks that are still in this set at this point are not indexed and thus
* inserted into the
* peak collection that holds unindexed peaks.
*/
for (auto it = unassignedMeasuredPeaks.begin();
it != unassignedMeasuredPeaks.end(); ++it) {
collectUnindexedPeak(*it);
}
}
bool PoldiFitPeaks1D2::peakIsAcceptable(const PoldiPeak_sptr &peak) const {
return peak->intensity() > 0 &&
peak->fwhm(PoldiPeak::Relative) < m_maxRelativeFwhm &&
peak->fwhm(PoldiPeak::Relative) > 0.001;
}
