/** Makes sure that the input properties are set correctly
* @param inputWorkspace The input workspace
* @throw std::runtime_error If the properties are invalid
*/
void NormaliseToMonitor::checkProperties(API::MatrixWorkspace_sptr inputWorkspace)
{
// Check where the monitor spectrum should come from
Property* monSpec = getProperty("MonitorSpectrum");
Property* monWS = getProperty("MonitorWorkspace");
Property* monID = getProperty("MonitorID");
// Is the monitor spectrum within the main input workspace
const bool inWS = !monSpec->isDefault();
// Or is it in a separate workspace
bool sepWS = !monWS->isDefault();
// or monitor ID
bool monIDs = !monID->isDefault();
// something has to be set
if ( !inWS && !sepWS && !monIDs)
{
const std::string mess("Neither the MonitorSpectrum, nor the MonitorID or the MonitorWorkspace property has been set");
g_log.error()<<mess<<std::endl;
throw std::runtime_error(mess);
}
// One and only one of these properties should have been set
// input from separate workspace is owerwritten by monitor spectrum
if ( inWS && sepWS ){
g_log.information("Both input workspace MonitorSpectrum number and monitor workspace are specified. Ignoring Monitor Workspace");
sepWS = false;
}
// input from detector ID is rejected in favour of monitor sp
if ( inWS && monIDs ){
g_log.information("Both input workspace MonitorSpectrum number and detector ID are specified. Ignoring Detector ID");
monIDs = false;
}
// separate ws takes over detectorID (this logic is dublicated within getInWSMonitorSpectrum)
if ( sepWS && monIDs ){
g_log.information("Both input MonitorWorkspace and detector ID are specified. Ignoring Detector ID");
}
// Do a check for common binning and store
m_commonBins = API::WorkspaceHelpers::commonBoundaries(inputWorkspace);
int spec_num(-1);
// Check the monitor spectrum or workspace and extract into new workspace
m_monitor = sepWS ? this->getMonitorWorkspace(inputWorkspace,spec_num) : this->getInWSMonitorSpectrum(inputWorkspace,spec_num) ;
// Check that the 'monitor' spectrum actually relates to a monitor - warn if not
try {
Geometry::IDetector_const_sptr mon = m_monitor->getDetector(0);
if ( !mon->isMonitor() )
{
g_log.warning()<<"The spectrum N: "<<spec_num<<" in MonitorWorkspace does not refer to a monitor.\n"
<<"Continuing with normalisation regardless.";
}
} catch (Kernel::Exception::NotFoundError &) {
g_log.warning("Unable to check if the spectrum provided relates to a monitor - "
"the instrument is not fully specified.\n"
"Continuing with normalisation regardless.");
}
}
void CalculateDIFC::calculate(API::Progress &progress,
API::MatrixWorkspace_sptr &outputWs,
DataObjects::OffsetsWorkspace_sptr &offsetsWS,
double l1, double beamlineNorm,
Kernel::V3D &beamline, Kernel::V3D &samplePos,
detid2det_map &allDetectors) {
SpecialWorkspace2D_sptr localWS =
boost::dynamic_pointer_cast<SpecialWorkspace2D>(outputWs);
// Now go through all
detid2det_map::const_iterator it = allDetectors.begin();
for (; it != allDetectors.end(); ++it) {
Geometry::IDetector_const_sptr det = it->second;
if ((!det->isMasked()) && (!det->isMonitor())) {
const detid_t detID = it->first;
double offset = 0.;
if (offsetsWS)
offset = offsetsWS->getValue(detID, 0.);
double difc = Geometry::Instrument::calcConversion(
l1, beamline, beamlineNorm, samplePos, det, offset);
difc = 1. / difc; // calcConversion gives 1/DIFC
localWS->setValue(detID, difc);
}
progress.report("Calculate DIFC");
}
}
void FindDetectorsPar::populate_values_from_file(
const API::MatrixWorkspace_sptr &inputWS) {
size_t nHist = inputWS->getNumberHistograms();
if (this->current_ASCII_file.Type == PAR_type) {
// in this case data in azimuthal width and polar width are in fact real
// sizes in meters; have to transform it in into angular values
for (size_t i = 0; i < nHist; i++) {
azimuthalWidth[i] =
atan2(azimuthalWidth[i], secondaryFlightpath[i]) * rad2deg;
polarWidth[i] = atan2(polarWidth[i], secondaryFlightpath[i]) * rad2deg;
}
m_SizesAreLinear = false;
} else {
Geometry::IComponent_const_sptr sample =
inputWS->getInstrument()->getSample();
secondaryFlightpath.resize(nHist);
// Loop over the spectra
for (size_t i = 0; i < nHist; i++) {
Geometry::IDetector_const_sptr spDet;
try {
spDet = inputWS->getDetector(i);
} catch (Kernel::Exception::NotFoundError &) {
continue;
}
// Check that we aren't writing a monitor...
if (spDet->isMonitor())
continue;
/// this is the only value, which is not defined in phx file, so we
/// calculate it
secondaryFlightpath[i] = spDet->getDistance(*sample);
}
}
}
/** Retrieves the detector postion for a given spectrum
* @param index :: The workspace index of the spectrum
* @param l1 :: Returns the source-sample distance
* @param l2 :: Returns the sample-detector distance
* @param twoTheta :: Returns the detector's scattering angle
*/
void RemoveBins::calculateDetectorPosition(const int& index, double& l1, double& l2, double& twoTheta)
{
// Get a pointer to the instrument contained in the workspace
Geometry::Instrument_const_sptr instrument = m_inputWorkspace->getInstrument();
// Get the distance between the source and the sample (assume in metres)
Geometry::IObjComponent_const_sptr sample = instrument->getSample();
// Check for valid instrument
if (sample == NULL)
{
throw Exception::InstrumentDefinitionError("Instrument not sufficiently defined: failed to get sample");
}
l1 = instrument->getSource()->getDistance(*sample);
Geometry::IDetector_const_sptr det = m_inputWorkspace->getDetector(index);
// Get the sample-detector distance for this detector (in metres)
if ( ! det->isMonitor() )
{
l2 = det->getDistance(*sample);
// The scattering angle for this detector (in radians).
twoTheta = m_inputWorkspace->detectorTwoTheta(det);
}
else // If this is a monitor then make l1+l2 = source-detector distance and twoTheta=0
{
l2 = det->getDistance(*(instrument->getSource()));
l2 = l2 - l1;
twoTheta = 0.0;
}
g_log.debug() << "Detector for index " << index << " has L1+L2=" << l1+l2 << " & 2theta= " << twoTheta << std::endl;
return;
}
void CalculateDIFC::calculate() {
Instrument_const_sptr instrument = m_inputWS->getInstrument();
SpecialWorkspace2D_sptr localWS =
boost::dynamic_pointer_cast<SpecialWorkspace2D>(m_outputWS);
double l1;
Kernel::V3D beamline, samplePos;
double beamline_norm;
instrument->getInstrumentParameters(l1, beamline, beamline_norm, samplePos);
// To get all the detector ID's
detid2det_map allDetectors;
instrument->getDetectors(allDetectors);
// Now go through all
detid2det_map::const_iterator it = allDetectors.begin();
for (; it != allDetectors.end(); ++it) {
Geometry::IDetector_const_sptr det = it->second;
if ((!det->isMasked()) && (!det->isMonitor())) {
const detid_t detID = it->first;
double offset = 0.;
if (m_offsetsWS)
offset = m_offsetsWS->getValue(detID, 0.);
double difc = Geometry::Instrument::calcConversion(
l1, beamline, beamline_norm, samplePos, det, offset);
difc = 1. / difc; // calcConversion gives 1/DIFC
localWS->setValue(detID, difc);
}
}
}
/** Calculates the total flightpath for the given detector.
* This is L1+L2 normally, but is the source-detector distance for a monitor.
* @param spectrum :: The workspace index
* @param L1 :: The primary flightpath
* @param isMonitor :: Output: true is this detector is a monitor
* @return The flightpath (Ld) for the detector linked to spectrum
* @throw Kernel::Exception::InstrumentDefinitionError if the detector position
* can't be obtained
*/
double UnwrapMonitor::calculateFlightpath(const int &spectrum, const double &L1,
bool &isMonitor) const {
double Ld = -1.0;
try {
// Get the detector object for this histogram
Geometry::IDetector_const_sptr det = m_inputWS->getDetector(spectrum);
// Get the sample-detector distance for this detector (or source-detector if
// a monitor)
// This is the total flightpath
isMonitor = det->isMonitor();
// Get the L2 distance if this detector is not a monitor
if (!isMonitor) {
double L2 = det->getDistance(*(m_inputWS->getInstrument()->getSample()));
Ld = L1 + L2;
}
// If it is a monitor, then the flightpath is the distance to the source
else {
Ld = det->getDistance(*(m_inputWS->getInstrument()->getSource()));
}
} catch (Exception::NotFoundError &) {
// If the detector information is missing, return a negative number
}
return Ld;
}
/**
* Corrects a spectra for the detector efficiency calculated from detector
* information. Gets the detector information and uses this to calculate its
* efficiency
* @param spectraIndex :: index of the spectrum to get the efficiency for
* @throw invalid_argument if the shape of a detector is isn't a cylinder
* aligned along one axis
* @throw runtime_error if the SpectraDetectorMap has not been filled
* @throw NotFoundError if the detector or its gas pressure or wall thickness
* were not found
*/
void He3TubeEfficiency::correctForEfficiency(std::size_t spectraIndex)
{
Geometry::IDetector_const_sptr det = this->inputWS->getDetector(spectraIndex);
if( det->isMonitor() || det->isMasked() )
{
return;
}
const double exp_constant = this->calculateExponential(spectraIndex, det);
const double scale = this->getProperty("ScaleFactor");
Mantid::MantidVec &yout = this->outputWS->dataY(spectraIndex);
Mantid::MantidVec &eout = this->outputWS->dataE(spectraIndex);
// Need the original values so this is not a reference
const Mantid::MantidVec yValues = this->inputWS->readY(spectraIndex);
const Mantid::MantidVec eValues = this->inputWS->readE(spectraIndex);
std::vector<double>::const_iterator yinItr = yValues.begin();
std::vector<double>::const_iterator einItr = eValues.begin();
Mantid::MantidVec::const_iterator xItr = this->inputWS->readX(spectraIndex).begin();
Mantid::MantidVec::iterator youtItr = yout.begin();
Mantid::MantidVec::iterator eoutItr = eout.begin();
for( ; youtItr != yout.end(); ++youtItr, ++eoutItr)
{
const double wavelength = (*xItr + *(xItr + 1)) / 2.0;
const double effcorr = this->detectorEfficiency(exp_constant * wavelength, scale);
*youtItr = (*yinItr) * effcorr;
*eoutItr = (*einItr) * effcorr;
++yinItr; ++einItr;
++xItr;
}
return;
}
/// helper function to preprocess the detectors directions
void
ConvertToQ3DdE::process_detectors_positions(const DataObjects::Workspace2D_const_sptr inputWS)
{
const size_t nHist = inputWS->getNumberHistograms();
det_loc.det_dir.resize(nHist);
det_loc.det_id.resize(nHist);
// Loop over the spectra
size_t ic(0);
for (size_t i = 0; i < nHist; i++){
Geometry::IDetector_const_sptr spDet;
try{
spDet= inputWS->getDetector(i);
}catch(Kernel::Exception::NotFoundError &){
continue;
}
// Check that we aren't dealing with monitor...
if (spDet->isMonitor())continue;
det_loc.det_id[ic] = spDet->getID();
// dist = spDet->getDistance(*sample);
double polar = inputWS->detectorTwoTheta(spDet);
double azim = spDet->getPhi();
double sPhi=sin(polar);
double ez = cos(polar);
double ex = sPhi*cos(azim);
double ey = sPhi*sin(azim);
det_loc.det_dir[ic].setX(ex);
det_loc.det_dir[ic].setY(ey);
det_loc.det_dir[ic].setZ(ez);
ic++;
}
//
if(ic<nHist){
det_loc.det_dir.resize(ic);
det_loc.det_id.resize(ic);
}
}
/**
* Set the new detector position given the r,theta and phi.
* @param det :: A pointer to the detector
* @param l2 :: A single l2
* @param theta :: A single theta
* @param phi :: A single phi
*/
void UpdateInstrumentFromFile::setDetectorPosition(const Geometry::IDetector_const_sptr & det, const float l2,
const float theta, const float phi)
{
if( m_ignoreMonitors && det->isMonitor() ) return;
Geometry::ParameterMap & pmap = m_workspace->instrumentParameters();
Kernel::V3D pos;
if (!m_ignorePhi)
{
pos.spherical(l2, theta, phi);
}
else
{
double r,t,p;
det->getPos().getSpherical(r,t,p);
pos.spherical(l2, theta, p);
}
Geometry::ComponentHelper::moveComponent(*det, pmap, pos, Geometry::ComponentHelper::Absolute);
}
std::pair<double, double> LoadILLSANS::calculateQMaxQMin() {
double min = std::numeric_limits<double>::max(),
max = std::numeric_limits<double>::min();
g_log.debug("Calculating Qmin Qmax...");
std::size_t nHist = m_localWorkspace->getNumberHistograms();
for (std::size_t i = 0; i < nHist; ++i) {
Geometry::IDetector_const_sptr det = m_localWorkspace->getDetector(i);
if (!det->isMonitor()) {
const MantidVec &lambdaBinning = m_localWorkspace->readX(i);
Kernel::V3D detPos = det->getPos();
double r, theta, phi;
detPos.getSpherical(r, theta, phi);
double v1 = calculateQ(*(lambdaBinning.begin()), theta);
double v2 = calculateQ(*(lambdaBinning.end() - 1), theta);
// std::cout << "i=" << i << " theta="<<theta << " lambda_i=" <<
// *(lambdaBinning.begin()) << " lambda_f=" << *(lambdaBinning.end()-1) <<
// " v1=" << v1 << " v2=" << v2 << '\n';
if (i == 0) {
min = v1;
max = v1;
}
if (v1 < min) {
min = v1;
}
if (v2 < min) {
min = v2;
}
if (v1 > max) {
max = v1;
}
if (v2 > max) {
max = v2;
}
} else
g_log.debug() << "Detector " << i << " is a Monitor : " << det->getID()
<< '\n';
}
g_log.debug() << "Calculating Qmin Qmax. Done : [" << min << "," << max
<< "]\n";
return std::pair<double, double>(min, max);
}
/** Method updates the column, which describes if current detector/spectra is
masked
It is used if one tries to process multiple workspaces obtained from a
series of experiments where the masked detectors can change */
void PreprocessDetectorsToMD::updateMasksState(
const API::MatrixWorkspace_const_sptr &inputWS,
DataObjects::TableWorkspace_sptr &targWS) {
int *pMasksArray = targWS->getColDataArray<int>("detMask");
if (!pMasksArray)
throw std::invalid_argument(
"target workspace " + targWS->getName() +
" does not have defined masks column to update");
size_t nHist = targWS->rowCount();
const size_t nRows = inputWS->getNumberHistograms();
if (nHist != nRows)
throw std::invalid_argument(
" source workspace " + inputWS->getName() + " and target workspace " +
targWS->getName() +
" are inconsistent as have different numner of detectors");
uint32_t liveDetectorsCount(0);
for (size_t i = 0; i < nHist; i++) {
// get detector or detector group which corresponds to the spectra i
Geometry::IDetector_const_sptr spDet;
try {
spDet = inputWS->getDetector(i);
} catch (Kernel::Exception::NotFoundError &) {
continue;
}
// Check that we aren't dealing with monitor...
if (spDet->isMonitor())
continue;
// if masked detectors state is not used, masked detectors just ignored;
bool maskDetector = spDet->isMasked();
*(pMasksArray + liveDetectorsCount) = maskDetector ? 1 : 0;
liveDetectorsCount++;
}
}
/** Executes the algorithm
*@param localworkspace :: the input workspace
*@param indices :: set of indices to sum up
*/
void SumSpectra::execEvent(EventWorkspace_const_sptr localworkspace,
std::set<int> &indices) {
// Make a brand new EventWorkspace
EventWorkspace_sptr outputWorkspace =
boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace", 1, 2, 1));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(localworkspace,
outputWorkspace, true);
Progress progress(this, 0, 1, indices.size());
// Get the pointer to the output event list
EventList &outEL = outputWorkspace->getEventList(0);
outEL.setSpectrumNo(m_outSpecId);
outEL.clearDetectorIDs();
// Loop over spectra
std::set<int>::iterator it;
size_t numSpectra(0);
size_t numMasked(0);
size_t numZeros(0);
// for (int i = m_minSpec; i <= m_maxSpec; ++i)
for (it = indices.begin(); it != indices.end(); ++it) {
int i = *it;
// Don't go outside the range.
if ((i >= m_numberOfSpectra) || (i < 0)) {
g_log.error() << "Invalid index " << i
<< " was specified. Sum was aborted.\n";
break;
}
try {
// Get the detector object for this spectrum
Geometry::IDetector_const_sptr det = localworkspace->getDetector(i);
// Skip monitors, if the property is set to do so
if (!m_keepMonitors && det->isMonitor())
continue;
// Skip masked detectors
if (det->isMasked()) {
numMasked++;
continue;
}
} catch (...) {
// if the detector not found just carry on
}
numSpectra++;
// Add the event lists with the operator
const EventList &tOutEL = localworkspace->getEventList(i);
if (tOutEL.empty()) {
++numZeros;
}
outEL += tOutEL;
progress.report();
}
// Set all X bins on the output
cow_ptr<MantidVec> XValues;
XValues.access() = localworkspace->readX(0);
outputWorkspace->setAllX(XValues);
outputWorkspace->mutableRun().addProperty("NumAllSpectra", int(numSpectra),
"", true);
outputWorkspace->mutableRun().addProperty("NumMaskSpectra", int(numMasked),
"", true);
outputWorkspace->mutableRun().addProperty("NumZeroSpectra", int(numZeros), "",
true);
// Assign it to the output workspace property
setProperty("OutputWorkspace",
boost::dynamic_pointer_cast<MatrixWorkspace>(outputWorkspace));
}
/**
* This function handles the logic for summing RebinnedOutput workspaces.
* @param outputWorkspace the workspace to hold the summed input
* @param progress the progress indicator
* @param numSpectra
* @param numMasked
* @param numZeros
*/
void SumSpectra::doRebinnedOutput(MatrixWorkspace_sptr outputWorkspace,
Progress &progress, size_t &numSpectra,
size_t &numMasked, size_t &numZeros) {
// Get a copy of the input workspace
MatrixWorkspace_sptr temp = getProperty("InputWorkspace");
// First, we need to clean the input workspace for nan's and inf's in order
// to treat the data correctly later. This will create a new private
// workspace that will be retrieved as mutable.
IAlgorithm_sptr alg = this->createChildAlgorithm("ReplaceSpecialValues");
alg->setProperty<MatrixWorkspace_sptr>("InputWorkspace", temp);
std::string outName = "_" + temp->getName() + "_clean";
alg->setProperty("OutputWorkspace", outName);
alg->setProperty("NaNValue", 0.0);
alg->setProperty("NaNError", 0.0);
alg->setProperty("InfinityValue", 0.0);
alg->setProperty("InfinityError", 0.0);
alg->executeAsChildAlg();
MatrixWorkspace_sptr localworkspace = alg->getProperty("OutputWorkspace");
// Transform to real workspace types
RebinnedOutput_sptr inWS =
boost::dynamic_pointer_cast<RebinnedOutput>(localworkspace);
RebinnedOutput_sptr outWS =
boost::dynamic_pointer_cast<RebinnedOutput>(outputWorkspace);
// Get references to the output workspaces's data vectors
ISpectrum *outSpec = outputWorkspace->getSpectrum(0);
MantidVec &YSum = outSpec->dataY();
MantidVec &YError = outSpec->dataE();
MantidVec &FracSum = outWS->dataF(0);
MantidVec Weight;
std::vector<size_t> nZeros;
if (m_calculateWeightedSum) {
Weight.assign(YSum.size(), 0);
nZeros.assign(YSum.size(), 0);
}
numSpectra = 0;
numMasked = 0;
numZeros = 0;
// Loop over spectra
std::set<int>::iterator it;
// for (int i = m_minSpec; i <= m_maxSpec; ++i)
for (it = m_indices.begin(); it != m_indices.end(); ++it) {
int i = *it;
// Don't go outside the range.
if ((i >= m_numberOfSpectra) || (i < 0)) {
g_log.error() << "Invalid index " << i
<< " was specified. Sum was aborted.\n";
break;
}
try {
// Get the detector object for this spectrum
Geometry::IDetector_const_sptr det = localworkspace->getDetector(i);
// Skip monitors, if the property is set to do so
if (!m_keepMonitors && det->isMonitor())
continue;
// Skip masked detectors
if (det->isMasked()) {
numMasked++;
continue;
}
} catch (...) {
// if the detector not found just carry on
}
numSpectra++;
// Retrieve the spectrum into a vector
const MantidVec &YValues = localworkspace->readY(i);
const MantidVec &YErrors = localworkspace->readE(i);
const MantidVec &FracArea = inWS->readF(i);
if (m_calculateWeightedSum) {
for (int k = 0; k < this->m_yLength; ++k) {
if (YErrors[k] != 0) {
double errsq = YErrors[k] * YErrors[k] * FracArea[k] * FracArea[k];
YError[k] += errsq;
Weight[k] += 1. / errsq;
YSum[k] += YValues[k] * FracArea[k] / errsq;
FracSum[k] += FracArea[k];
} else {
nZeros[k]++;
FracSum[k] += FracArea[k];
}
}
} else {
for (int k = 0; k < this->m_yLength; ++k) {
YSum[k] += YValues[k] * FracArea[k];
YError[k] += YErrors[k] * YErrors[k] * FracArea[k] * FracArea[k];
FracSum[k] += FracArea[k];
}
}
// Map all the detectors onto the spectrum of the output
outSpec->addDetectorIDs(localworkspace->getSpectrum(i)->getDetectorIDs());
progress.report();
}
if (m_calculateWeightedSum) {
numZeros = 0;
for (size_t i = 0; i < Weight.size(); i++) {
if (nZeros[i] == 0)
YSum[i] *= double(numSpectra) / Weight[i];
else
numZeros += nZeros[i];
}
}
// Create the correct representation
outWS->finalize();
}
/**
* This function deals with the logic necessary for summing a Workspace2D.
* @param localworkspace The input workspace for summing.
* @param outSpec The spectrum for the summed output.
* @param progress The progress indicator.
* @param numSpectra The number of spectra contributed to the sum.
* @param numMasked The spectra dropped from the summations because they are
* masked.
* @param numZeros The number of zero bins in histogram workspace or empty
* spectra for event workspace.
*/
void SumSpectra::doWorkspace2D(MatrixWorkspace_const_sptr localworkspace,
ISpectrum *outSpec, Progress &progress,
size_t &numSpectra, size_t &numMasked,
size_t &numZeros) {
// Get references to the output workspaces's data vectors
MantidVec &YSum = outSpec->dataY();
MantidVec &YError = outSpec->dataE();
MantidVec Weight;
std::vector<size_t> nZeros;
if (m_calculateWeightedSum) {
Weight.assign(YSum.size(), 0);
nZeros.assign(YSum.size(), 0);
}
numSpectra = 0;
numMasked = 0;
numZeros = 0;
// Loop over spectra
std::set<int>::iterator it;
// for (int i = m_minSpec; i <= m_maxSpec; ++i)
for (it = this->m_indices.begin(); it != this->m_indices.end(); ++it) {
int i = *it;
// Don't go outside the range.
if ((i >= this->m_numberOfSpectra) || (i < 0)) {
g_log.error() << "Invalid index " << i
<< " was specified. Sum was aborted.\n";
break;
}
try {
// Get the detector object for this spectrum
Geometry::IDetector_const_sptr det = localworkspace->getDetector(i);
// Skip monitors, if the property is set to do so
if (!m_keepMonitors && det->isMonitor())
continue;
// Skip masked detectors
if (det->isMasked()) {
numMasked++;
continue;
}
} catch (...) {
// if the detector not found just carry on
}
numSpectra++;
// Retrieve the spectrum into a vector
const MantidVec &YValues = localworkspace->readY(i);
const MantidVec &YErrors = localworkspace->readE(i);
if (m_calculateWeightedSum) {
for (int k = 0; k < this->m_yLength; ++k) {
if (YErrors[k] != 0) {
double errsq = YErrors[k] * YErrors[k];
YError[k] += errsq;
Weight[k] += 1. / errsq;
YSum[k] += YValues[k] / errsq;
} else {
nZeros[k]++;
}
}
} else {
for (int k = 0; k < this->m_yLength; ++k) {
YSum[k] += YValues[k];
YError[k] += YErrors[k] * YErrors[k];
}
}
// Map all the detectors onto the spectrum of the output
outSpec->addDetectorIDs(localworkspace->getSpectrum(i)->getDetectorIDs());
progress.report();
}
if (m_calculateWeightedSum) {
numZeros = 0;
for (size_t i = 0; i < Weight.size(); i++) {
if (nZeros[i] == 0)
YSum[i] *= double(numSpectra) / Weight[i];
else
numZeros += nZeros[i];
}
}
}
/** method does preliminary calculations of the detectors positions to convert
results into k-dE space ;
and places the results into static cash to be used in subsequent calls to this
algorithm */
void PreprocessDetectorsToMD::processDetectorsPositions(
const API::MatrixWorkspace_const_sptr &inputWS,
DataObjects::TableWorkspace_sptr &targWS) {
g_log.information()
<< "Preprocessing detector locations in a target reciprocal space\n";
//
Geometry::Instrument_const_sptr instrument = inputWS->getInstrument();
// this->pBaseInstr = instrument->baseInstrument();
//
Geometry::IComponent_const_sptr source = instrument->getSource();
Geometry::IComponent_const_sptr sample = instrument->getSample();
if ((!source) || (!sample)) {
g_log.error() << " Instrument is not fully defined. Can not identify "
"source or sample\n";
throw Kernel::Exception::InstrumentDefinitionError(
"Instrument not sufficiently defined: failed to get source and/or "
"sample");
}
// L1
try {
double L1 = source->getDistance(*sample);
targWS->logs()->addProperty<double>("L1", L1, true);
g_log.debug() << "Source-sample distance: " << L1 << std::endl;
} catch (Kernel::Exception::NotFoundError &) {
throw Kernel::Exception::InstrumentDefinitionError(
"Unable to calculate source-sample distance for workspace",
inputWS->getTitle());
}
// Instrument name
std::string InstrName = instrument->getName();
targWS->logs()->addProperty<std::string>(
"InstrumentName", InstrName,
true); // "The name which should unique identify current instrument");
targWS->logs()->addProperty<bool>("FakeDetectors", false, true);
// get access to the workspace memory
auto &sp2detMap = targWS->getColVector<size_t>("spec2detMap");
auto &detId = targWS->getColVector<int32_t>("DetectorID");
auto &detIDMap = targWS->getColVector<size_t>("detIDMap");
auto &L2 = targWS->getColVector<double>("L2");
auto &TwoTheta = targWS->getColVector<double>("TwoTheta");
auto &Azimuthal = targWS->getColVector<double>("Azimuthal");
auto &detDir = targWS->getColVector<Kernel::V3D>("DetDirections");
// Efixed; do we need one and does one exist?
double Efi = targWS->getLogs()->getPropertyValueAsType<double>("Ei");
float *pEfixedArray(nullptr);
const Geometry::ParameterMap &pmap = inputWS->constInstrumentParameters();
if (m_getEFixed)
pEfixedArray = targWS->getColDataArray<float>("eFixed");
// check if one needs to generate masked detectors column.
int *pMasksArray(nullptr);
if (m_getIsMasked)
pMasksArray = targWS->getColDataArray<int>("detMask");
//// progress message appearance
size_t div = 100;
size_t nHist = targWS->rowCount();
Mantid::API::Progress theProgress(this, 0, 1, nHist);
//// Loop over the spectra
uint32_t liveDetectorsCount(0);
for (size_t i = 0; i < nHist; i++) {
sp2detMap[i] = std::numeric_limits<uint64_t>::quiet_NaN();
detId[i] = std::numeric_limits<int32_t>::quiet_NaN();
detIDMap[i] = std::numeric_limits<uint64_t>::quiet_NaN();
L2[i] = std::numeric_limits<double>::quiet_NaN();
TwoTheta[i] = std::numeric_limits<double>::quiet_NaN();
Azimuthal[i] = std::numeric_limits<double>::quiet_NaN();
// detMask[i] = true;
// get detector or detector group which corresponds to the spectra i
Geometry::IDetector_const_sptr spDet;
try {
spDet = inputWS->getDetector(i);
} catch (Kernel::Exception::NotFoundError &) {
continue;
}
// Check that we aren't dealing with monitor...
if (spDet->isMonitor())
continue;
// if masked detectors state is not used, masked detectors just ignored;
bool maskDetector = spDet->isMasked();
if (m_getIsMasked)
*(pMasksArray + liveDetectorsCount) = maskDetector ? 1 : 0;
else if (maskDetector)
continue;
// calculate the requested values;
sp2detMap[i] = liveDetectorsCount;
detId[liveDetectorsCount] = int32_t(spDet->getID());
detIDMap[liveDetectorsCount] = i;
L2[liveDetectorsCount] = spDet->getDistance(*sample);
double polar = inputWS->detectorTwoTheta(spDet);
double azim = spDet->getPhi();
TwoTheta[liveDetectorsCount] = polar;
Azimuthal[liveDetectorsCount] = azim;
double sPhi = sin(polar);
double ez = cos(polar);
double ex = sPhi * cos(azim);
double ey = sPhi * sin(azim);
detDir[liveDetectorsCount].setX(ex);
detDir[liveDetectorsCount].setY(ey);
detDir[liveDetectorsCount].setZ(ez);
// double sinTheta=sin(0.5*polar);
// this->SinThetaSq[liveDetectorsCount] = sinTheta*sinTheta;
// specific code which should work and makes sense
// for indirect instrument but may be deployed on any code with Ei property
// defined;
if (pEfixedArray) {
try {
Geometry::Parameter_sptr par = pmap.getRecursive(spDet.get(), "eFixed");
if (par)
Efi = par->value<double>();
} catch (std::runtime_error &) {
}
// set efixed for each existing detector
*(pEfixedArray + liveDetectorsCount) = static_cast<float>(Efi);
}
liveDetectorsCount++;
if (i % div == 0)
theProgress.report(i, "Preprocessing detectors");
}
targWS->logs()->addProperty<uint32_t>("ActualDetectorsNum",
liveDetectorsCount, true);
theProgress.report();
g_log.information() << "Finished preprocessing detector locations. Found: "
<< liveDetectorsCount << " detectors out of: " << nHist
<< " histograms\n";
}
/** Read the scaling information from a file (e.g. merlin_detector.sca) or from
* the RAW file (.raw)
* @param scalingFile :: Name of scaling file .sca
* @param truepos :: V3D vector of actual positions as read from the file
* @return False if unable to open file, True otherwise
*/
bool SetScalingPSD::processScalingFile(const std::string &scalingFile,
std::vector<Kernel::V3D> &truepos) {
// Read the scaling information from a text file (.sca extension) or from a
// raw file (.raw)
// This is really corrected positions as (r,theta,phi) for each detector
// Compare these with the instrument values to determine the change in
// position and the scaling
// which may be necessary for each pixel if in a tube.
// movePos is used to updated positions
std::map<int, Kernel::V3D> posMap;
std::map<int, double> scaleMap;
std::map<int, double>::iterator its;
Instrument_const_sptr instrument = m_workspace->getInstrument();
if (scalingFile.find(".sca") != std::string::npos ||
scalingFile.find(".SCA") != std::string::npos) {
// read a .sca text format file
// format consists of a short header followed by one line per detector
std::ifstream sFile(scalingFile.c_str());
if (!sFile) {
g_log.error() << "Unable to open scaling file " << scalingFile
<< std::endl;
return false;
}
std::string str;
getline(sFile,
str); // skip header line should be <filename> generated by <prog>
int detectorCount;
getline(sFile, str); // get detector count line
std::istringstream istr(str);
istr >> detectorCount;
if (detectorCount < 1) {
g_log.error("Bad detector count in scaling file");
throw std::runtime_error("Bad detector count in scaling file");
}
truepos.reserve(detectorCount);
getline(sFile, str); // skip title line
int detIdLast = -10;
Kernel::V3D truPosLast, detPosLast;
Progress prog(this, 0.0, 0.5, detectorCount);
// Now loop through lines, one for each detector/monitor. The latter are
// ignored.
while (getline(sFile, str)) {
if (str.empty() || str[0] == '#')
continue;
std::istringstream istr(str);
// read 6 values from the line to get the 3 (l2,theta,phi) of interest
int detIndex, code;
double l2, theta, phi, offset;
istr >> detIndex >> offset >> l2 >> code >> theta >> phi;
// sanity check on angles - l2 should be +ve but sample file has a few -ve
// values
// on monitors
if (theta > 181.0 || theta < -1 || phi < -181 || phi > 181) {
g_log.error("Position angle data out of range in .sca file");
throw std::runtime_error(
"Position angle data out of range in .sca file");
}
Kernel::V3D truPos;
// use abs as correction file has -ve l2 for first few detectors
truPos.spherical(fabs(l2), theta, phi);
truepos.push_back(truPos);
//
Geometry::IDetector_const_sptr det;
try {
det = instrument->getDetector(detIndex);
} catch (Kernel::Exception::NotFoundError &) {
continue;
}
Kernel::V3D detPos = det->getPos();
Kernel::V3D shift = truPos - detPos;
// scaling applied to dets that are not monitors and have sequential IDs
if (detIdLast == detIndex - 1 && !det->isMonitor()) {
Kernel::V3D diffI = detPos - detPosLast;
Kernel::V3D diffT = truPos - truPosLast;
double scale = diffT.norm() / diffI.norm();
Kernel::V3D scaleDir = diffT / diffT.norm();
// Wish to store the scaling in a map, if we already have a scaling
// for this detector (i.e. from the other side) we average the two
// values. End of tube detectors only have one scaling estimate.
scaleMap[detIndex] = scale;
its = scaleMap.find(detIndex - 1);
if (its == scaleMap.end())
scaleMap[detIndex - 1] = scale;
else
its->second = 0.5 * (its->second + scale);
// std::cout << detIndex << scale << scaleDir << std::endl;
}
detIdLast = detIndex;
detPosLast = detPos;
truPosLast = truPos;
posMap[detIndex] = shift;
//
prog.report();
}
} else if (scalingFile.find(".raw") != std::string::npos ||