/** Write out all of the event lists in the given workspace
* @param ws :: an EventWorkspace */
int NexusFileIO::writeNexusProcessedDataEvent( const DataObjects::EventWorkspace_const_sptr& ws)
{
//write data entry
NXstatus status=NXmakegroup(fileID,"event_workspace","NXdata");
if(status==NX_ERROR) return(2);
NXopengroup(fileID,"event_workspace","NXdata");
for (size_t wi=0; wi < ws->getNumberHistograms(); wi++)
{
std::ostringstream group_name;
group_name << "event_list_" << wi;
this->writeEventList( ws->getEventList(wi), group_name.str());
}
// Close up the overall group
status=NXclosegroup(fileID);
return((status==NX_ERROR)?3:0);
}
void ConvertToMatrixWorkspace::exec()
{
MatrixWorkspace_const_sptr inputWorkspace = getProperty("InputWorkspace");
// Let's see if we have to do anything first. Basically we want to avoid the data copy if we can
DataObjects::EventWorkspace_const_sptr eventW =
boost::dynamic_pointer_cast<const DataObjects::EventWorkspace>(inputWorkspace);
MatrixWorkspace_sptr outputWorkspace;
if( eventW )
{
g_log.information() << "Converting EventWorkspace to Workspace2D.\n";
const size_t numHists = inputWorkspace->getNumberHistograms();
Progress prog(this,0.0,1.0,numHists*2);
// Sort the input workspace in-place by TOF. This can be faster if there are few event lists.
eventW->sortAll(TOF_SORT, &prog);
// Create the output workspace. This will copy many aspects fron the input one.
outputWorkspace = WorkspaceFactory::Instance().create(inputWorkspace);
// ...but not the data, so do that here.
PARALLEL_FOR2(inputWorkspace,outputWorkspace)
for (int64_t i = 0; i < (int64_t)numHists; ++i)
{
PARALLEL_START_INTERUPT_REGION
const ISpectrum * inSpec = inputWorkspace->getSpectrum(i);
ISpectrum * outSpec = outputWorkspace->getSpectrum(i);
outSpec->copyInfoFrom(*inSpec);
outSpec->setX(inSpec->ptrX());
outSpec->dataY() = inSpec->dataY();
outSpec->dataE() = inSpec->dataE();
prog.report("Binning");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
outputWorkspace->generateSpectraMap();
}
else
{
/** Write out a combined chunk of event data
*
* @param ws :: an EventWorkspace
* @param indices :: array of event list indexes
* @param tofs :: array of TOFs
* @param weights :: array of event weights
* @param errorSquareds :: array of event squared errors
* @param pulsetimes :: array of pulsetimes
* @param compress :: if true, compress the entry
*/
int NexusFileIO::writeNexusProcessedDataEventCombined( const DataObjects::EventWorkspace_const_sptr& ws,
std::vector<int64_t> & indices,
double * tofs, float * weights, float * errorSquareds, int64_t * pulsetimes,
bool compress) const
{
NXopengroup(fileID,"event_workspace","NXdata");
// The array of indices for each event list #
int dims_array[1] = { static_cast<int>(indices.size()) };
if (indices.size() > 0)
{
if (compress)
NXcompmakedata(fileID, "indices", NX_INT64, 1, dims_array, m_nexuscompression, dims_array);
else
NXmakedata(fileID, "indices", NX_INT64, 1, dims_array);
NXopendata(fileID, "indices");
NXputdata(fileID, (void*)(indices.data()) );
std::string yUnits=ws->YUnit();
std::string yUnitLabel=ws->YUnitLabel();
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>(yUnits.c_str())), static_cast<int>(yUnits.size()), NX_CHAR);
NXputattr (fileID, "unit_label", reinterpret_cast<void*>(const_cast<char*>(yUnitLabel.c_str())), static_cast<int>(yUnitLabel.size()), NX_CHAR);
NXclosedata(fileID);
}
// Write out each field
dims_array[0] = static_cast<int>(indices.back()); // TODO big truncation error! This is the # of events
if (tofs)
NXwritedata("tof", NX_FLOAT64, 1, dims_array, (void *)(tofs), compress);
if (pulsetimes)
NXwritedata("pulsetime", NX_INT64, 1, dims_array, (void *)(pulsetimes), compress);
if (weights)
NXwritedata("weight", NX_FLOAT32, 1, dims_array, (void *)(weights), compress);
if (errorSquareds)
NXwritedata("error_squared", NX_FLOAT32, 1, dims_array, (void *)(errorSquareds), compress);
// Close up the overall group
NXstatus status=NXclosegroup(fileID);
return((status==NX_ERROR)?3:0);
}
/**
* 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::moveOthersEvent(const std::set<int64_t> &unGroupedSet, DataObjects::EventWorkspace_const_sptr inputWS,
DataObjects::EventWorkspace_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 EventList & inputSpec = inputWS->getEventList(sourceIndex);
// Destination of the copying
EventList & outputSpec=outputWS->getEventList(outIndex);
// Copy the data
outputSpec+=inputSpec;
// 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->doneAddingEventLists();
g_log.debug() << name() << " copied " << unGroupedSet.size()-1 << " ungrouped spectra\n";
}
/**
* Create an output EventWorkspace w/o any events
*/
DataObjects::EventWorkspace_sptr CountEventsInPulses::createEventWorkspace(
DataObjects::EventWorkspace_const_sptr parentws, bool sumspectrum) {
size_t numspec;
bool diffsize;
if (sumspectrum) {
numspec = 1;
diffsize = true;
} else {
numspec = parentws->getNumberHistograms();
diffsize = false;
}
DataObjects::EventWorkspace_sptr outputWS =
boost::dynamic_pointer_cast<DataObjects::EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace", numspec, 1,
1));
API::WorkspaceFactory::Instance().initializeFromParent(parentws, outputWS,
diffsize);
outputWS->getAxis(0)->unit() = Kernel::UnitFactory::Instance().create("Time");
return outputWS;
}
/**
* 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;
}
/** Executes the algorithm
*/
void FilterByTime2::exec() {
DataObjects::EventWorkspace_const_sptr inWS =
this->getProperty("InputWorkspace");
if (!inWS) {
g_log.error() << "Input is not EventWorkspace" << std::endl;
throw std::invalid_argument("Input is not EventWorksapce");
} else {
g_log.debug() << "DB5244 InputWorkspace Name = " << inWS->getName()
<< std::endl;
}
double starttime = this->getProperty("StartTime");
double stoptime = this->getProperty("StopTime");
std::string absstarttime = this->getProperty("AbsoluteStartTime");
std::string absstoptime = this->getProperty("AbsoluteStopTime");
std::string start, stop;
if ((absstarttime != "") && (absstoptime != "") && (starttime <= 0.0) &&
(stoptime <= 0.0)) {
// Use the absolute string
start = absstarttime;
stop = absstoptime;
} else if ((absstarttime != "" || absstoptime != "") &&
(starttime > 0.0 || stoptime > 0.0)) {
throw std::invalid_argument(
"It is not allowed to provide both absolute time and relative time.");
} else {
// Use second
std::stringstream ss;
ss << starttime;
start = ss.str();
std::stringstream ss2;
ss2 << stoptime;
stop = ss2.str();
}
// 1. Generate Filters
g_log.debug() << "\nDB441: About to generate Filter. StartTime = "
<< starttime << " StopTime = " << stoptime << std::endl;
API::Algorithm_sptr genfilter =
createChildAlgorithm("GenerateEventsFilter", 0.0, 20.0, true, 1);
genfilter->initialize();
genfilter->setPropertyValue("InputWorkspace", inWS->getName());
genfilter->setPropertyValue("OutputWorkspace", "FilterWS");
genfilter->setProperty("StartTime", start);
genfilter->setProperty("StopTime", stop);
genfilter->setProperty("UnitOfTime", "Seconds");
genfilter->setProperty("FastLog", false);
bool sucgen = genfilter->execute();
if (!sucgen) {
g_log.error() << "Unable to generate event filters" << std::endl;
throw std::runtime_error("Unable to generate event filters");
} else {
g_log.debug() << "Filters are generated. " << std::endl;
}
API::Workspace_sptr filterWS = genfilter->getProperty("OutputWorkspace");
if (!filterWS) {
g_log.error() << "Unable to retrieve generated SplittersWorkspace object "
"from AnalysisDataService." << std::endl;
throw std::runtime_error("Unable to retrieve Splittersworkspace. ");
}
// 2. Filter events
g_log.debug() << "\nAbout to filter events. "
<< "\n";
API::Algorithm_sptr filter =
createChildAlgorithm("FilterEvents", 20.0, 100.0, true, 1);
filter->initialize();
filter->setPropertyValue("InputWorkspace", inWS->getName());
filter->setPropertyValue("OutputWorkspaceBaseName", "ResultWS");
filter->setProperty("SplitterWorkspace", filterWS);
filter->setProperty("FilterByPulseTime", true);
bool sucfilt = filter->execute();
if (!sucfilt) {
g_log.error() << "Unable to filter events" << std::endl;
throw std::runtime_error("Unable to filter events");
} else {
g_log.debug() << "Filter events is successful. " << std::endl;
}
DataObjects::EventWorkspace_sptr optws =
filter->getProperty("OutputWorkspace_0");
this->setProperty("OutputWorkspace", optws);
}
/** Check whether 2 event lists are identical
*/
bool CompareWorkspaces::compareEventWorkspaces(
DataObjects::EventWorkspace_const_sptr ews1,
DataObjects::EventWorkspace_const_sptr ews2) {
bool checkallspectra = getProperty("CheckAllData");
int numspec2print = getProperty("NumberMismatchedSpectraToPrint");
int wsindex2print = getProperty("DetailedPrintIndex");
// Compare number of spectra
if (ews1->getNumberHistograms() != ews2->getNumberHistograms()) {
recordMismatch("Mismatched number of histograms.");
return false;
}
if (ews1->getEventType() != ews2->getEventType()) {
recordMismatch("Mismatched type of events in the EventWorkspaces.");
return false;
}
// Both will end up sorted anyway
ews1->sortAll(PULSETIMETOF_SORT, m_Prog);
ews2->sortAll(PULSETIMETOF_SORT, m_Prog);
// Determine the tolerance for "tof" attribute and "weight" of events
double toleranceWeight = Tolerance; // Standard tolerance
int64_t tolerancePulse = 1;
double toleranceTOF = 0.05;
if ((ews1->getAxis(0)->unit()->label().ascii() != "microsecond") ||
(ews2->getAxis(0)->unit()->label().ascii() != "microsecond")) {
g_log.warning() << "Event workspace has unit as "
<< ews1->getAxis(0)->unit()->label().ascii() << " and "
<< ews2->getAxis(0)->unit()->label().ascii()
<< ". Tolerance of TOF is set to 0.05 still. "
<< "\n";
toleranceTOF = 0.05;
}
g_log.notice() << "TOF Tolerance = " << toleranceTOF << "\n";
bool mismatchedEvent = false;
int mismatchedEventWI = 0;
size_t numUnequalNumEventsSpectra = 0;
size_t numUnequalEvents = 0;
size_t numUnequalTOFEvents = 0;
size_t numUnequalPulseEvents = 0;
size_t numUnequalBothEvents = 0;
std::vector<int> vec_mismatchedwsindex;
PARALLEL_FOR_IF(m_ParallelComparison && ews1->threadSafe() &&
ews2->threadSafe())
for (int i = 0; i < static_cast<int>(ews1->getNumberHistograms()); ++i) {
PARALLEL_START_INTERUPT_REGION
m_Prog->report("EventLists");
if (!mismatchedEvent ||
checkallspectra) // This guard will avoid checking unnecessarily
{
const EventList &el1 = ews1->getEventList(i);
const EventList &el2 = ews2->getEventList(i);
bool printdetail = (i == wsindex2print);
if (printdetail) {
g_log.information() << "Spectrum " << i
<< " is set to print out in details. "
<< "\n";
}
if (!el1.equals(el2, toleranceTOF, toleranceWeight, tolerancePulse)) {
size_t tempNumTof = 0;
size_t tempNumPulses = 0;
size_t tempNumBoth = 0;
int tempNumUnequal = 0;
if (el1.getNumberEvents() != el2.getNumberEvents()) {
// Number of events are different
tempNumUnequal = -1;
} else {
tempNumUnequal = compareEventsListInDetails(
el1, el2, toleranceTOF, toleranceWeight, tolerancePulse,
printdetail, tempNumPulses, tempNumTof, tempNumBoth);
}
mismatchedEvent = true;
mismatchedEventWI = i;
PARALLEL_CRITICAL(CompareWorkspaces) {
if (tempNumUnequal == -1) {
// 2 spectra have different number of events
++numUnequalNumEventsSpectra;
} else {
// 2 spectra have some events different to each other
numUnequalEvents += static_cast<size_t>(tempNumUnequal);
numUnequalTOFEvents += tempNumTof;
numUnequalPulseEvents += tempNumPulses;
numUnequalBothEvents += tempNumBoth;
}
vec_mismatchedwsindex.push_back(i);
} // Parallel critical region
} // If elist 1 is not equal to elist 2
}
PARALLEL_END_INTERUPT_REGION
}
//----------------------------------------------------------------------------------------------
/// @copydoc Mantid::API::Algorithm::exec()
void ResetNegatives::exec()
{
MatrixWorkspace_sptr inputWS = this->getProperty("InputWorkspace");
MatrixWorkspace_sptr outputWS = this->getProperty("OutputWorkspace");
// get the minimum for each spectrum
IAlgorithm_sptr alg = this->createChildAlgorithm("Min", 0., .1);
alg->setProperty<MatrixWorkspace_sptr>("InputWorkspace", inputWS);
alg->executeAsChildAlg();
MatrixWorkspace_const_sptr minWS = alg->getProperty("OutputWorkspace");
// determine if there is anything to do
int64_t nHist = static_cast<int64_t>(minWS->getNumberHistograms());
bool hasNegative = false;
for (int64_t i = 0; i < nHist; i++)
{
if (minWS->readY(i)[0] < 0)
{
hasNegative = true;
}
break;
}
// get out early if there is nothing to do
if (!hasNegative)
{
g_log.information() << "No values are negative. Copying InputWorkspace to OutputWorkspace\n";
if (inputWS != outputWS)
{
IAlgorithm_sptr alg = this->createChildAlgorithm("CloneWorkspace", .1, 1.);
alg->setProperty<Workspace_sptr>("InputWorkspace", inputWS);
alg->executeAsChildAlg();
Workspace_sptr temp = alg->getProperty("OutputWorkspace");
setProperty("OutputWorkspace", boost::dynamic_pointer_cast<MatrixWorkspace>(temp));
}
return;
}
// sort the event list to make it fast and thread safe
DataObjects::EventWorkspace_const_sptr eventWS
= boost::dynamic_pointer_cast<const DataObjects::EventWorkspace>( inputWS );
if (eventWS)
eventWS->sortAll(DataObjects::TOF_SORT, NULL);
Progress prog(this, .1, 1., 2*nHist);
// generate output workspace - copy X and dY
outputWS = API::WorkspaceFactory::Instance().create(inputWS);
PARALLEL_FOR2(inputWS,outputWS)
for (int64_t i = 0; i < nHist; i++)
{
PARALLEL_START_INTERUPT_REGION
outputWS->dataY(i) = inputWS->readY(i);
outputWS->dataE(i) = inputWS->readE(i);
outputWS->setX(i, inputWS->refX(i)); // share the pointer more
prog.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// do the actual work
if (this->getProperty("AddMinimum"))
{
this->pushMinimum(minWS, outputWS, prog);
}
else
{
this->changeNegatives(minWS, this->getProperty("ResetValue"), outputWS, prog);
}
setProperty("OutputWorkspace",outputWS);
}