/** Integrate the peaks of the workspace using parameters saved in the algorithm
* class
*/
void CentroidPeaks::integrateEvent() {
/// Peak workspace to centroid
Mantid::DataObjects::PeaksWorkspace_sptr inPeakWS =
getProperty("InPeaksWorkspace");
/// Output peaks workspace, create if needed
Mantid::DataObjects::PeaksWorkspace_sptr peakWS =
getProperty("OutPeaksWorkspace");
if (peakWS != inPeakWS)
peakWS = inPeakWS->clone();
/// Radius to use around peaks
int PeakRadius = getProperty("PeakRadius");
int MinPeaks = -1;
int MaxPeaks = -1;
size_t Numberwi = inWS->getNumberHistograms();
int NumberPeaks = peakWS->getNumberPeaks();
for (int i = 0; i < NumberPeaks; ++i) {
auto &peak = peakWS->getPeak(i);
int pixelID = peak.getDetectorID();
// Find the workspace index for this detector ID
if (wi_to_detid_map.find(pixelID) != wi_to_detid_map.end()) {
size_t wi = wi_to_detid_map[pixelID];
if (MinPeaks == -1 && peak.getRunNumber() == inWS->getRunNumber() &&
wi < Numberwi)
MinPeaks = i;
if (peak.getRunNumber() == inWS->getRunNumber() && wi < Numberwi)
MaxPeaks = i;
}
}
int Edge = getProperty("EdgePixels");
Progress prog(this, MinPeaks, 1.0, MaxPeaks);
PARALLEL_FOR_IF(Kernel::threadSafe(*inWS, *peakWS))
for (int i = MinPeaks; i <= MaxPeaks; ++i) {
PARALLEL_START_INTERUPT_REGION
// Get a direct ref to that peak.
auto &peak = peakWS->getPeak(i);
int col = peak.getCol();
int row = peak.getRow();
double TOFPeakd = peak.getTOF();
std::string bankName = peak.getBankName();
int nCols = 0, nRows = 0;
sizeBanks(bankName, nCols, nRows);
double intensity = 0.0;
double tofcentroid = 0.0;
if (edgePixel(inst, bankName, col, row, Edge))
continue;
double tofstart = TOFPeakd * std::pow(1.004, -PeakRadius);
double tofend = TOFPeakd * std::pow(1.004, PeakRadius);
double rowcentroid = 0.0;
int rowstart = std::max(0, row - PeakRadius);
int rowend = std::min(nRows - 1, row + PeakRadius);
double colcentroid = 0.0;
int colstart = std::max(0, col - PeakRadius);
int colend = std::min(nCols - 1, col + PeakRadius);
for (int irow = rowstart; irow <= rowend; ++irow) {
for (int icol = colstart; icol <= colend; ++icol) {
if (edgePixel(inst, bankName, icol, irow, Edge))
continue;
auto it1 = wi_to_detid_map.find(findPixelID(bankName, icol, irow));
size_t workspaceIndex = (it1->second);
EventList el = eventW->getSpectrum(workspaceIndex);
el.switchTo(WEIGHTED_NOTIME);
std::vector<WeightedEventNoTime> events = el.getWeightedEventsNoTime();
// Check for events in tof range
for (const auto &event : events) {
double tof = event.tof();
if (tof > tofstart && tof < tofend) {
double weight = event.weight();
intensity += weight;
rowcentroid += irow * weight;
colcentroid += icol * weight;
tofcentroid += tof * weight;
}
}
}
}
// Set pixelID to change row and col
row = int(rowcentroid / intensity);
boost::algorithm::clamp(row, 0, nRows - 1);
col = int(colcentroid / intensity);
boost::algorithm::clamp(col, 0, nCols - 1);
if (!edgePixel(inst, bankName, col, row, Edge)) {
peak.setDetectorID(findPixelID(bankName, col, row));
// Set wavelength to change tof for peak object
double tof = tofcentroid / intensity;
Mantid::Kernel::Units::Wavelength wl;
std::vector<double> timeflight;
timeflight.push_back(tof);
double scattering = peak.getScattering();
double L1 = peak.getL1();
double L2 = peak.getL2();
wl.fromTOF(timeflight, timeflight, L1, L2, scattering, 0, 0, 0);
const double lambda = timeflight[0];
timeflight.clear();
peak.setWavelength(lambda);
peak.setBinCount(intensity);
}
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
removeEdgePeaks(*peakWS);
// Save the output
setProperty("OutPeaksWorkspace", peakWS);
}
void CentroidPeaksMD::integrate(typename MDEventWorkspace<MDE, nd>::sptr ws) {
if (nd != 3)
throw std::invalid_argument("For now, we expect the input MDEventWorkspace "
"to have 3 dimensions only.");
/// Peak workspace to centroid
Mantid::DataObjects::PeaksWorkspace_sptr inPeakWS =
getProperty("PeaksWorkspace");
/// Output peaks workspace, create if needed
Mantid::DataObjects::PeaksWorkspace_sptr peakWS =
getProperty("OutputWorkspace");
if (peakWS != inPeakWS)
peakWS.reset(inPeakWS->clone().release());
std::string CoordinatesToUseStr = getPropertyValue("CoordinatesToUse");
int CoordinatesToUse = ws->getSpecialCoordinateSystem();
if (CoordinatesToUse == 1 && CoordinatesToUseStr != "Q (lab frame)")
g_log.warning() << "Warning: used Q (lab frame) coordinates for MD "
"workspace, not CoordinatesToUse from input "
<< std::endl;
else if (CoordinatesToUse == 2 && CoordinatesToUseStr != "Q (sample frame)")
g_log.warning() << "Warning: used Q (sample frame) coordinates for MD "
"workspace, not CoordinatesToUse from input "
<< std::endl;
else if (CoordinatesToUse == 3 && CoordinatesToUseStr != "HKL")
g_log.warning() << "Warning: used HKL coordinates for MD workspace, not "
"CoordinatesToUse from input " << std::endl;
/// Radius to use around peaks
double PeakRadius = getProperty("PeakRadius");
// cppcheck-suppress syntaxError
PRAGMA_OMP(parallel for schedule(dynamic, 10) )
for (int i = 0; i < int(peakWS->getNumberPeaks()); ++i) {
// Get a direct ref to that peak.
IPeak &p = peakWS->getPeak(i);
double detectorDistance = p.getL2();
// Get the peak center as a position in the dimensions of the workspace
V3D pos;
if (CoordinatesToUse == 1) //"Q (lab frame)"
pos = p.getQLabFrame();
else if (CoordinatesToUse == 2) //"Q (sample frame)"
pos = p.getQSampleFrame();
else if (CoordinatesToUse == 3) //"HKL"
pos = p.getHKL();
// Build the sphere transformation
bool dimensionsUsed[nd];
coord_t center[nd];
for (size_t d = 0; d < nd; ++d) {
dimensionsUsed[d] = true; // Use all dimensions
center[d] = static_cast<coord_t>(pos[d]);
}
CoordTransformDistance sphere(nd, center, dimensionsUsed);
// Initialize the centroid to 0.0
signal_t signal = 0;
coord_t centroid[nd];
for (size_t d = 0; d < nd; d++)
centroid[d] = 0.0;
// Perform centroid
ws->getBox()->centroidSphere(
sphere, static_cast<coord_t>(PeakRadius * PeakRadius), centroid,
signal);
// Normalize by signal
if (signal != 0.0) {
for (size_t d = 0; d < nd; d++)
centroid[d] /= static_cast<coord_t>(signal);
V3D vecCentroid(centroid[0], centroid[1], centroid[2]);
// Save it back in the peak object, in the dimension specified.
if (CoordinatesToUse == 1) //"Q (lab frame)"
{
p.setQLabFrame(vecCentroid, detectorDistance);
p.findDetector();
} else if (CoordinatesToUse == 2) //"Q (sample frame)"
{
p.setQSampleFrame(vecCentroid, detectorDistance);
p.findDetector();
} else if (CoordinatesToUse == 3) //"HKL"
{
p.setHKL(vecCentroid);
}
g_log.information() << "Peak " << i << " at " << pos << ": signal "
<< signal << ", centroid " << vecCentroid << " in "
<< CoordinatesToUse << std::endl;
} else {
g_log.information() << "Peak " << i << " at " << pos
<< " had no signal, and could not be centroided."
<< std::endl;
}
}
// Save the output
setProperty("OutputWorkspace", peakWS);
}
void CentroidPeaksMD::integrate(typename MDEventWorkspace<MDE, nd>::sptr ws)
{
if (nd != 3)
throw std::invalid_argument("For now, we expect the input MDEventWorkspace to have 3 dimensions only.");
/// Peak workspace to centroid
Mantid::DataObjects::PeaksWorkspace_sptr inPeakWS = getProperty("PeaksWorkspace");
/// Output peaks workspace, create if needed
Mantid::DataObjects::PeaksWorkspace_sptr peakWS = getProperty("OutputWorkspace");
if (peakWS != inPeakWS)
peakWS = inPeakWS->clone();
/// Value of the CoordinatesToUse property.
std::string CoordinatesToUse = getPropertyValue("CoordinatesToUse");
// TODO: Confirm that the coordinates requested match those in the MDEventWorkspace
/// Radius to use around peaks
double PeakRadius = getProperty("PeakRadius");
PRAGMA_OMP(parallel for schedule(dynamic, 10) )
for (int i=0; i < int(peakWS->getNumberPeaks()); ++i)
{
// Get a direct ref to that peak.
IPeak & p = peakWS->getPeak(i);
double detectorDistance = p.getL2();
// Get the peak center as a position in the dimensions of the workspace
V3D pos;
if (CoordinatesToUse == "Q (lab frame)")
pos = p.getQLabFrame();
else if (CoordinatesToUse == "Q (sample frame)")
pos = p.getQSampleFrame();
else if (CoordinatesToUse == "HKL")
pos = p.getHKL();
// Build the sphere transformation
bool dimensionsUsed[nd];
coord_t center[nd];
for (size_t d=0; d<nd; ++d)
{
dimensionsUsed[d] = true; // Use all dimensions
center[d] = pos[d];
}
CoordTransformDistance sphere(nd, center, dimensionsUsed);
// Initialize the centroid to 0.0
signal_t signal = 0;
coord_t centroid[nd];
for (size_t d=0; d<nd; d++)
centroid[d] = 0.0;
// Perform centroid
ws->getBox()->centroidSphere(sphere, PeakRadius*PeakRadius, centroid, signal);
// Normalize by signal
if (signal != 0.0)
{
for (size_t d=0; d<nd; d++)
centroid[d] /= signal;
V3D vecCentroid(centroid[0], centroid[1], centroid[2]);
// Save it back in the peak object, in the dimension specified.
if (CoordinatesToUse == "Q (lab frame)")
{
p.setQLabFrame( vecCentroid, detectorDistance);
p.findDetector();
}
else if (CoordinatesToUse == "Q (sample frame)")
{
p.setQSampleFrame( vecCentroid, detectorDistance);
p.findDetector();
}
else if (CoordinatesToUse == "HKL")
{
p.setHKL( vecCentroid );
}
g_log.information() << "Peak " << i << " at " << pos << ": signal "
<< signal << ", centroid " << vecCentroid
<< " in " << CoordinatesToUse
<< std::endl;
}
else
{
g_log.information() << "Peak " << i << " at " << pos << " had no signal, and could not be centroided."
<< std::endl;
}
}
// Save the output
setProperty("OutputWorkspace", peakWS);
}