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());
}
void PoldiPeakSearch::exec() {
g_log.information() << "PoldiPeakSearch:" << std::endl;
Workspace2D_sptr correlationWorkspace = getProperty("InputWorkspace");
MantidVec correlationQValues = correlationWorkspace->readX(0);
MantidVec correlatedCounts = correlationWorkspace->readY(0);
g_log.information() << " Auto-correlation data read." << std::endl;
Unit_sptr xUnit = correlationWorkspace->getAxis(0)->unit();
if (xUnit->caption() == "") {
g_log.information()
<< " Workspace does not have unit, defaulting to MomentumTransfer."
<< std::endl;
xUnit = UnitFactory::Instance().create("MomentumTransfer");
} else {
g_log.information() << " Unit of workspace is " << xUnit->caption() << "."
<< std::endl;
}
setMinimumDistance(getProperty("MinimumPeakSeparation"));
setMinimumPeakHeight(getProperty("MinimumPeakHeight"));
setMaximumPeakNumber(getProperty("MaximumPeakNumber"));
if (m_doubleMinimumDistance > static_cast<int>(correlatedCounts.size())) {
throw(std::runtime_error("MinimumPeakSeparation is smaller than number of "
"spectrum points - no peaks possible."));
}
g_log.information() << " Parameters set." << std::endl;
MantidVec summedNeighborCounts = getNeighborSums(correlatedCounts);
g_log.information() << " Neighboring counts summed, contains "
<< summedNeighborCounts.size() << " data points."
<< std::endl;
std::list<MantidVec::const_iterator> peakPositionsSummed =
findPeaks(summedNeighborCounts.begin(), summedNeighborCounts.end());
g_log.information() << " Peaks detected in summed spectrum: "
<< peakPositionsSummed.size() << std::endl;
/* This step is required because peaks are actually searched in the
* "sum-of-neighbors"-spectrum.
* The mapping removes the offset from the peak position which results from
* different beginning
* of this vector compared to the original correlation counts.
*/
std::list<MantidVec::const_iterator> peakPositionsCorrelation =
mapPeakPositionsToCorrelationData(peakPositionsSummed,
summedNeighborCounts.begin(),
correlatedCounts.begin());
g_log.information() << " Peak positions transformed to original spectrum."
<< std::endl;
/* Since intensities are required for filtering, they are extracted from the
* original count data,
* along with the Q-values.
*/
std::vector<PoldiPeak_sptr> peakCoordinates =
getPeaks(correlatedCounts.begin(), correlatedCounts.end(),
peakPositionsCorrelation, correlationQValues, xUnit);
g_log.information()
<< " Extracted peak positions in Q and intensity guesses." << std::endl;
UncertainValue backgroundWithSigma =
getBackgroundWithSigma(peakPositionsCorrelation, correlatedCounts);
g_log.information() << " Calculated average background and deviation: "
<< UncertainValueIO::toString(backgroundWithSigma)
<< std::endl;
if ((*getProperty("MinimumPeakHeight")).isDefault()) {
setMinimumPeakHeight(minimumPeakHeightFromBackground(backgroundWithSigma));
}
std::vector<PoldiPeak_sptr> intensityFilteredPeaks(peakCoordinates.size());
auto newEnd = std::remove_copy_if(
peakCoordinates.begin(), peakCoordinates.end(),
intensityFilteredPeaks.begin(),
boost::bind(&PoldiPeakSearch::isLessThanMinimum, this, _1));
intensityFilteredPeaks.resize(
std::distance(intensityFilteredPeaks.begin(), newEnd));
g_log.information() << " Peaks above minimum intensity ("
<< m_minimumPeakHeight
<< "): " << intensityFilteredPeaks.size() << std::endl;
std::sort(intensityFilteredPeaks.begin(), intensityFilteredPeaks.end(),
boost::bind<bool>(&PoldiPeak::greaterThan, _1, _2,
&PoldiPeak::intensity));
for (std::vector<PoldiPeak_sptr>::const_iterator peak =
intensityFilteredPeaks.begin();
peak != intensityFilteredPeaks.end(); ++peak) {
m_peaks->addPeak(*peak);
}
/* The derived background error is set as error in the workspace containing
* correlation data, so it may be used as weights for peak fitting later on.
*/
setErrorsOnWorkspace(correlationWorkspace, backgroundWithSigma.error());
setProperty("OutputWorkspace", m_peaks->asTableWorkspace());
}
/** Returns the minimum height a peak should have.
*
* This method is used when no user estimate of minimum required peak height is
*given. It is set to background
* plus 3 times Sn.
*
* @param backgroundWithSigma :: Background with error estimate.
* @return Minimum peak height.
*/
double PoldiPeakSearch::minimumPeakHeightFromBackground(
UncertainValue backgroundWithSigma) const {
return 3.0 * backgroundWithSigma.error() + backgroundWithSigma.value();
}
