/// Returns true if d-spacing of measured and candidate peak are less than three
/// sigma (of the candidate) apart.
bool PoldiIndexKnownCompounds::isCandidate(
const PoldiPeak_sptr &measuredPeak,
const PoldiPeak_sptr &possibleCandidate) const {
if (!measuredPeak || !possibleCandidate) {
throw std::invalid_argument("Cannot check null-peaks.");
}
return (fabs(static_cast<double>(measuredPeak->d()) -
possibleCandidate->d()) /
fwhmToSigma(possibleCandidate->fwhm(PoldiPeak::AbsoluteD))) < 3.0;
}
/**
* 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;
}
/**
* 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;
}
/** 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;
}
void PoldiPeakSummary::storePeakSummary(TableRow tableRow,
const PoldiPeak_sptr &peak) const {
UncertainValue q = peak->q();
UncertainValue d = peak->d();
tableRow << MillerIndicesIO::toString(peak->hkl())
<< UncertainValueIO::toString(q) << UncertainValueIO::toString(d)
<< d.error() / d.value() * 1e3
<< UncertainValueIO::toString(peak->fwhm(PoldiPeak::Relative) * 1e3)
<< UncertainValueIO::toString(peak->intensity());
}
/**
* 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;
}
/**
* 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);
}
/** 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);
}
}