/***
* This will add the maximum spectrum number from ws1 to the data coming from ws2.
*
* @param ws1 The first workspace supplied to the algorithm.
* @param ws2 The second workspace supplied to the algorithm.
* @param output The workspace that is going to be returned by the algorithm.
*/
void ConjoinWorkspaces::fixSpectrumNumbers(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr /*ws2*/,
API::MatrixWorkspace_sptr output)
{
// make sure we should bother. If you don't check for overlap, you don't need to
if (this->getProperty("CheckOverlapping"))
return;
// is everything possibly ok?
specid_t min;
specid_t max;
getMinMax(output, min, max);
if (max - min >= static_cast<specid_t>(output->getNumberHistograms())) // nothing to do then
return;
// information for remapping the spectra numbers
specid_t ws1min;
specid_t ws1max;
getMinMax(ws1, ws1min, ws1max);
// change the axis by adding the maximum existing spectrum number to the current value
for (size_t i = ws1->getNumberHistograms(); i < output->getNumberHistograms(); i++)
{
specid_t origid;
origid = output->getSpectrum(i)->getSpectrumNo();
output->getSpectrum(i)->setSpectrumNo(origid + ws1max);
}
// To be deprecated:
output->generateSpectraMap();
}
/**
* Only to be used if the KeepUnGrouped property is true, moves the spectra that were not selected
* to be in a group to the end of the output spectrum
* @param unGroupedSet :: list of WORKSPACE indexes that were included in a group
* @param inputWS :: user selected input workspace for the algorithm
* @param outputWS :: user selected output workspace for the algorithm
* @param outIndex :: the next spectra index available after the grouped spectra
*/
void GroupDetectors2::moveOthers(const std::set<int64_t> &unGroupedSet, API::MatrixWorkspace_const_sptr inputWS, API::MatrixWorkspace_sptr outputWS,
size_t outIndex)
{
g_log.debug() << "Starting to copy the ungrouped spectra" << std::endl;
double prog4Copy = (1. - 1.*static_cast<double>(m_FracCompl))/static_cast<double>(unGroupedSet.size());
std::set<int64_t>::const_iterator copyFrIt = unGroupedSet.begin();
// go thorugh all the spectra in the input workspace
for ( ; copyFrIt != unGroupedSet.end(); ++copyFrIt )
{
if( *copyFrIt == USED ) continue; //Marked as not to be used
size_t sourceIndex = static_cast<size_t>(*copyFrIt);
// The input spectrum we'll copy
const ISpectrum * inputSpec = inputWS->getSpectrum(sourceIndex);
// Destination of the copying
ISpectrum * outputSpec = outputWS->getSpectrum(outIndex);
// Copy the data
outputSpec->dataX() = inputSpec->dataX();
outputSpec->dataY() = inputSpec->dataY();
outputSpec->dataE() = inputSpec->dataE();
// Spectrum numbers etc.
outputSpec->setSpectrumNo(inputSpec->getSpectrumNo());
outputSpec->clearDetectorIDs();
outputSpec->addDetectorIDs( inputSpec->getDetectorIDs() );
// go to the next free index in the output workspace
outIndex ++;
// 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();
}
}
// Refresh the spectraDetectorMap
outputWS->generateSpectraMap();
g_log.debug() << name() << " copied " << unGroupedSet.size()-1 << " ungrouped spectra\n";
}
/**
* 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;
}