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);
}
}
}
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");
}
}
/**
* 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;
}
/** 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++;
}
}
/**
* Move the user selected spectra in the input workspace into groups in the output workspace
* @param inputWS :: user selected input workspace for the algorithm
* @param outputWS :: user selected output workspace for the algorithm
* @param prog4Copy :: the amount of algorithm progress to attribute to moving a single spectra
* @return number of new grouped spectra
*/
size_t GroupDetectors2::formGroupsEvent( DataObjects::EventWorkspace_const_sptr inputWS, DataObjects::EventWorkspace_sptr outputWS,
const double prog4Copy)
{
// get "Behaviour" string
const std::string behaviour = getProperty("Behaviour");
int bhv = 0;
if ( behaviour == "Average" ) bhv = 1;
API::MatrixWorkspace_sptr beh = API::WorkspaceFactory::Instance().create(
"Workspace2D", static_cast<int>(m_GroupSpecInds.size()), 1, 1);
g_log.debug() << name() << ": Preparing to group spectra into " << m_GroupSpecInds.size() << " groups\n";
// where we are copying spectra to, we start copying to the start of the output workspace
size_t outIndex = 0;
// Only used for averaging behaviour. We may have a 1:1 map where a Divide would be waste as it would be just dividing by 1
bool requireDivide(false);
for ( storage_map::const_iterator it = m_GroupSpecInds.begin(); it != m_GroupSpecInds.end() ; ++it )
{
// This is the grouped spectrum
EventList & outEL = outputWS->getEventList(outIndex);
// The spectrum number of the group is the key
outEL.setSpectrumNo(it->first);
// Start fresh with no detector IDs
outEL.clearDetectorIDs();
// the Y values and errors from spectra being grouped are combined in the output spectrum
// Keep track of number of detectors required for masking
size_t nonMaskedSpectra(0);
beh->dataX(outIndex)[0] = 0.0;
beh->dataE(outIndex)[0] = 0.0;
for( std::vector<size_t>::const_iterator wsIter = it->second.begin(); wsIter != it->second.end(); ++wsIter)
{
const size_t originalWI = *wsIter;
const EventList & fromEL=inputWS->getEventList(originalWI);
//Add the event lists with the operator
outEL += fromEL;
// detectors to add to the output spectrum
outEL.addDetectorIDs(fromEL.getDetectorIDs() );
try
{
Geometry::IDetector_const_sptr det = inputWS->getDetector(originalWI);
if( !det->isMasked() ) ++nonMaskedSpectra;
}
catch(Exception::NotFoundError&)
{
// If a detector cannot be found, it cannot be masked
++nonMaskedSpectra;
}
}
if( nonMaskedSpectra == 0 ) ++nonMaskedSpectra; // Avoid possible divide by zero
if(!requireDivide) requireDivide = (nonMaskedSpectra > 1);
beh->dataY(outIndex)[0] = static_cast<double>(nonMaskedSpectra);
// make regular progress reports and check for cancelling the algorithm
if ( outIndex % INTERVAL == 0 )
{
m_FracCompl += INTERVAL*prog4Copy;
if ( m_FracCompl > 1.0 )
m_FracCompl = 1.0;
progress(m_FracCompl);
interruption_point();
}
outIndex ++;
}
// Refresh the spectraDetectorMap
outputWS->doneAddingEventLists();
if ( bhv == 1 && requireDivide )
{
g_log.debug() << "Running Divide algorithm to perform averaging.\n";
Mantid::API::IAlgorithm_sptr divide = createChildAlgorithm("Divide");
divide->initialize();
divide->setProperty<API::MatrixWorkspace_sptr>("LHSWorkspace", outputWS);
divide->setProperty<API::MatrixWorkspace_sptr>("RHSWorkspace", beh);
divide->setProperty<API::MatrixWorkspace_sptr>("OutputWorkspace", outputWS);
divide->execute();
}
g_log.debug() << name() << " created " << outIndex << " new grouped spectra\n";
return outIndex;
}
/**
* Move the user selected spectra in the input workspace into groups in the output workspace
* @param inputWS :: user selected input workspace for the algorithm
* @param outputWS :: user selected output workspace for the algorithm
* @param prog4Copy :: the amount of algorithm progress to attribute to moving a single spectra
* @return number of new grouped spectra
*/
size_t GroupDetectors2::formGroups( API::MatrixWorkspace_const_sptr inputWS, API::MatrixWorkspace_sptr outputWS,
const double prog4Copy)
{
// get "Behaviour" string
const std::string behaviour = getProperty("Behaviour");
int bhv = 0;
if ( behaviour == "Average" ) bhv = 1;
API::MatrixWorkspace_sptr beh = API::WorkspaceFactory::Instance().create(
"Workspace2D", static_cast<int>(m_GroupSpecInds.size()), 1, 1);
g_log.debug() << name() << ": Preparing to group spectra into " << m_GroupSpecInds.size() << " groups\n";
// where we are copying spectra to, we start copying to the start of the output workspace
size_t outIndex = 0;
// Only used for averaging behaviour. We may have a 1:1 map where a Divide would be waste as it would be just dividing by 1
bool requireDivide(false);
for ( storage_map::const_iterator it = m_GroupSpecInds.begin(); it != m_GroupSpecInds.end() ; ++it )
{
// This is the grouped spectrum
ISpectrum * outSpec = outputWS->getSpectrum(outIndex);
// The spectrum number of the group is the key
outSpec->setSpectrumNo(it->first);
// Start fresh with no detector IDs
outSpec->clearDetectorIDs();
// Copy over X data from first spectrum, the bin boundaries for all spectra are assumed to be the same here
outSpec->dataX() = inputWS->readX(0);
// the Y values and errors from spectra being grouped are combined in the output spectrum
// Keep track of number of detectors required for masking
size_t nonMaskedSpectra(0);
beh->dataX(outIndex)[0] = 0.0;
beh->dataE(outIndex)[0] = 0.0;
for( std::vector<size_t>::const_iterator wsIter = it->second.begin(); wsIter != it->second.end(); ++wsIter)
{
const size_t originalWI = *wsIter;
// detectors to add to firstSpecNum
const ISpectrum * fromSpectrum = inputWS->getSpectrum(originalWI);
// Add up all the Y spectra and store the result in the first one
// Need to keep the next 3 lines inside loop for now until ManagedWorkspace mru-list works properly
MantidVec &firstY = outSpec->dataY();
MantidVec::iterator fYit;
MantidVec::iterator fEit = outSpec->dataE().begin();
MantidVec::const_iterator Yit = fromSpectrum->dataY().begin();
MantidVec::const_iterator Eit = fromSpectrum->dataE().begin();
for (fYit = firstY.begin(); fYit != firstY.end(); ++fYit, ++fEit, ++Yit, ++Eit)
{
*fYit += *Yit;
// Assume 'normal' (i.e. Gaussian) combination of errors
*fEit = std::sqrt( (*fEit)*(*fEit) + (*Eit)*(*Eit) );
}
// detectors to add to the output spectrum
outSpec->addDetectorIDs(fromSpectrum->getDetectorIDs() );
try
{
Geometry::IDetector_const_sptr det = inputWS->getDetector(originalWI);
if( !det->isMasked() ) ++nonMaskedSpectra;
}
catch(Exception::NotFoundError&)
{
// If a detector cannot be found, it cannot be masked
++nonMaskedSpectra;
}
}
if( nonMaskedSpectra == 0 ) ++nonMaskedSpectra; // Avoid possible divide by zero
if(!requireDivide) requireDivide = (nonMaskedSpectra > 1);
beh->dataY(outIndex)[0] = static_cast<double>(nonMaskedSpectra);
// make regular progress reports and check for cancelling the algorithm
if ( outIndex % INTERVAL == 0 )
{
m_FracCompl += INTERVAL*prog4Copy;
if ( m_FracCompl > 1.0 )
m_FracCompl = 1.0;
progress(m_FracCompl);
interruption_point();
}
outIndex ++;
}
// Refresh the spectraDetectorMap
outputWS->generateSpectraMap();
if ( bhv == 1 && requireDivide )
{
g_log.debug() << "Running Divide algorithm to perform averaging.\n";
Mantid::API::IAlgorithm_sptr divide = createChildAlgorithm("Divide");
divide->initialize();
divide->setProperty<API::MatrixWorkspace_sptr>("LHSWorkspace", outputWS);
divide->setProperty<API::MatrixWorkspace_sptr>("RHSWorkspace", beh);
divide->setProperty<API::MatrixWorkspace_sptr>("OutputWorkspace", outputWS);
divide->execute();
}
g_log.debug() << name() << " created " << outIndex << " new grouped spectra\n";
return outIndex;
}
/** 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];
}
}
}
/** Write GSAS file based on user-specified request
*/
void SaveGSS::writeGSASFile(const std::string &outfilename, bool append,
int basebanknumber, bool multiplybybinwidth,
bool split, const std::string &outputFormat) {
// Initialize the file stream
using std::ios_base;
ios_base::openmode mode =
(append ? (ios_base::out | ios_base::app) : ios_base::out);
// Instrument related
Geometry::Instrument_const_sptr instrument = inputWS->getInstrument();
Geometry::IComponent_const_sptr source;
Geometry::IComponent_const_sptr sample;
bool has_instrument = false;
if (instrument != NULL) {
source = instrument->getSource();
sample = instrument->getSample();
if (source && sample)
has_instrument = true;
}
// Write GSAS file for each histogram (spectrum)
std::stringstream outbuffer;
int nHist = static_cast<int>(inputWS->getNumberHistograms());
Progress p(this, 0.0, 1.0, nHist);
for (int iws = 0; iws < nHist; iws++) {
// Determine whether to skip the spectrum due to being masked
if (has_instrument) {
try {
Geometry::IDetector_const_sptr det =
inputWS->getDetector(static_cast<size_t>(iws));
if (det->isMasked())
continue;
} catch (const Kernel::Exception::NotFoundError &) {
has_instrument = false;
g_log.warning() << "There is no detector associated with spectrum "
<< iws
<< ". Workspace is treated as NO-INSTRUMENT case. \n";
}
}
// Obtain detector information
double l1, l2, tth, difc;
if (has_instrument)
getFocusedPos(inputWS, iws, l1, l2, tth, difc);
else
l1 = l2 = tth = difc = 0;
g_log.debug() << "Spectrum " << iws << ": L1 = " << l1 << " L2 = " << l2
<< " 2theta = " << tth << "\n";
std::stringstream tmpbuffer;
// Header: 2 cases requires header: (1) first bank in non-append mode and
// (2) split
g_log.debug() << "[DB9933] Append = " << append << ", split = " << split
<< "\n";
bool writeheader = false;
std::string splitfilename("");
if (!split && iws == 0 && !append) {
// Non-split mode and first spectrum and in non-append mode
writeheader = true;
} else if (split) {
std::stringstream number;
number << "-" << iws;
Poco::Path path(outfilename);
std::string basename = path.getBaseName(); // Filename minus extension
std::string ext = path.getExtension();
// Chop off filename
path.makeParent();
path.append(basename + number.str() + "." + ext);
Poco::File fileobj(path);
const bool exists = fileobj.exists();
if (!exists || !append)
writeheader = true;
if (fileobj.exists() && !append)
g_log.warning() << "File " << path.getFileName()
<< " exists and will be overwritten."
<< "\n";
splitfilename = path.toString();
}
// Create header
if (writeheader)
writeHeaders(outputFormat, tmpbuffer, l1);
// Write bank header
if (has_instrument) {
tmpbuffer << "# Total flight path " << (l1 + l2) << "m, tth "
<< (tth * 180. / M_PI) << "deg, DIFC " << difc << "\n";
}
tmpbuffer << "# Data for spectrum :" << iws << "\n";
// Determine bank number into GSAS file
int bankid;
if (m_useSpecAsBank) {
bankid = static_cast<int>(inputWS->getSpectrum(iws)->getSpectrumNo());
} else {
bankid = basebanknumber + iws;
}
// Write data
if (RALF.compare(outputFormat) == 0) {
this->writeRALFdata(bankid, multiplybybinwidth, tmpbuffer,
inputWS->readX(iws), inputWS->readY(iws),
inputWS->readE(iws));
} else if (SLOG.compare(outputFormat) == 0) {
this->writeSLOGdata(bankid, multiplybybinwidth, tmpbuffer,
inputWS->readX(iws), inputWS->readY(iws),
inputWS->readE(iws));
} else {
throw std::runtime_error("Cannot write to the unknown " + outputFormat +
"output format");
}
// Write out to file if necessary
if (split) {
// Create a new file name and a new file with ofstream
std::ofstream out;
out.open(splitfilename.c_str(), mode);
out.write(tmpbuffer.str().c_str(), tmpbuffer.str().size());
out.close();
} else {
outbuffer << tmpbuffer.str();
}
p.report();
} // ENDFOR (iws)
// Write file
if (!split) {
std::ofstream out;
out.open(outfilename.c_str(), mode);
out.write(outbuffer.str().c_str(), outbuffer.str().length());
out.close();
}
return;
}
/** 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";
}