void SaveNexusProcessed::doExec(Workspace_sptr inputWorkspace,
Mantid::NeXus::NexusFileIO_sptr &nexusFile,
const bool keepFile,
optional_size_t entryNumber) {
// TODO: Remove?
NXMEnableErrorReporting();
// Retrieve the filename from the properties
m_filename = getPropertyValue("Filename");
// m_entryname = getPropertyValue("EntryName");
m_title = getPropertyValue("Title");
// Do we prserve events?
bool PreserveEvents = getProperty("PreserveEvents");
MatrixWorkspace_const_sptr matrixWorkspace =
boost::dynamic_pointer_cast<const MatrixWorkspace>(inputWorkspace);
ITableWorkspace_const_sptr tableWorkspace =
boost::dynamic_pointer_cast<const ITableWorkspace>(inputWorkspace);
PeaksWorkspace_const_sptr peaksWorkspace =
boost::dynamic_pointer_cast<const PeaksWorkspace>(inputWorkspace);
OffsetsWorkspace_const_sptr offsetsWorkspace =
boost::dynamic_pointer_cast<const OffsetsWorkspace>(inputWorkspace);
if (peaksWorkspace)
g_log.debug("We have a peaks workspace");
// check if inputWorkspace is something we know how to save
if (!matrixWorkspace && !tableWorkspace) {
// get the workspace name for the error message
std::string name = getProperty("InputWorkspace");
// md workspaces should be saved using SaveMD
if (bool(boost::dynamic_pointer_cast<const IMDEventWorkspace>(
inputWorkspace)) ||
bool(boost::dynamic_pointer_cast<const IMDHistoWorkspace>(
inputWorkspace)))
g_log.warning() << name << " can be saved using SaveMD\n";
// standard error message
std::stringstream msg;
msg << "Workspace \"" << name
<< "\" not saved because it is not of a type we can presently save.";
throw std::runtime_error(msg.str());
}
m_eventWorkspace =
boost::dynamic_pointer_cast<const EventWorkspace>(matrixWorkspace);
const std::string workspaceID = inputWorkspace->id();
if ((workspaceID.find("Workspace2D") == std::string::npos) &&
(workspaceID.find("RebinnedOutput") == std::string::npos) &&
!m_eventWorkspace && !tableWorkspace && !offsetsWorkspace)
throw Exception::NotImplementedError(
"SaveNexusProcessed passed invalid workspaces. Must be Workspace2D, "
"EventWorkspace, ITableWorkspace, or OffsetsWorkspace.");
// Create progress object for initial part - depends on whether events are
// processed
if (PreserveEvents && m_eventWorkspace) {
m_timeProgInit = 0.07; // Events processed 0.05 to 1.0
} else {
m_timeProgInit = 1.0; // All work is done in the initial part
}
Progress prog_init(this, 0.0, m_timeProgInit, 7);
// If no title's been given, use the workspace title field
if (m_title.empty())
m_title = inputWorkspace->getTitle();
// get the workspace name to write to file
std::string wsName = inputWorkspace->getName();
// If we don't want to append then remove the file if it already exists
bool append_to_file = getProperty("Append");
if (!append_to_file && !keepFile) {
Poco::File file(m_filename);
if (file.exists())
file.remove();
}
nexusFile->resetProgress(&prog_init);
nexusFile->openNexusWrite(m_filename, entryNumber);
// Equivalent C++ API handle
auto cppFile = new ::NeXus::File(nexusFile->fileID);
prog_init.reportIncrement(1, "Opening file");
if (nexusFile->writeNexusProcessedHeader(m_title, wsName) != 0)
throw Exception::FileError("Failed to write to file", m_filename);
prog_init.reportIncrement(1, "Writing header");
// write instrument data, if present and writer enabled
if (matrixWorkspace) {
// Save the instrument names, ParameterMap, sample, run
matrixWorkspace->saveExperimentInfoNexus(cppFile);
prog_init.reportIncrement(1, "Writing sample and instrument");
// check if all X() are in fact the same array
const bool uniformSpectra =
API::WorkspaceHelpers::commonBoundaries(*matrixWorkspace);
// Retrieve the workspace indices (from params)
std::vector<int> spec;
this->getSpectrumList(spec, matrixWorkspace);
prog_init.reportIncrement(1, "Writing data");
// Write out the data (2D or event)
if (m_eventWorkspace && PreserveEvents) {
this->execEvent(nexusFile.get(), uniformSpectra, spec);
} else if (offsetsWorkspace) {
g_log.warning() << "Writing SpecialWorkspace2D ID=" << workspaceID
<< "\n";
nexusFile->writeNexusProcessedData2D(matrixWorkspace, uniformSpectra,
spec, "offsets_workspace", true);
} else {
nexusFile->writeNexusProcessedData2D(matrixWorkspace, uniformSpectra,
spec, "workspace", true);
}
cppFile->openGroup("instrument", "NXinstrument");
matrixWorkspace->saveSpectraMapNexus(cppFile, spec, ::NeXus::LZW);
cppFile->closeGroup();
} // finish matrix workspace specifics
if (peaksWorkspace) {
// Save the instrument names, ParameterMap, sample, run
peaksWorkspace->saveExperimentInfoNexus(cppFile);
prog_init.reportIncrement(1, "Writing sample and instrument");
}
// peaks workspace specifics
if (peaksWorkspace) {
// g_log.information("Peaks Workspace saving to Nexus would be done");
// int pNum = peaksWorkspace->getNumberPeaks();
peaksWorkspace->saveNexus(cppFile);
} // finish peaks workspace specifics
else if (tableWorkspace) // Table workspace specifics
{
nexusFile->writeNexusTableWorkspace(tableWorkspace, "table_workspace");
} // finish table workspace specifics
// Switch to the Cpp API for the algorithm history
if (trackingHistory()) {
m_history->fillAlgorithmHistory(
this, Mantid::Kernel::DateAndTime::getCurrentTime(), 0,
Algorithm::g_execCount);
if (!isChild()) {
inputWorkspace->history().addHistory(m_history);
}
// this is a child algorithm, but we still want to keep the history.
else if (isRecordingHistoryForChild() && m_parentHistory) {
m_parentHistory->addChildHistory(m_history);
}
}
inputWorkspace->history().saveNexus(cppFile);
nexusFile->closeGroup();
}
/** Executes the algorithm.
*
* @throw runtime_error Thrown if algorithm cannot execute
*/
void SaveNexusProcessed::exec()
{
//TODO: Remove?
NXMEnableErrorReporting();
Workspace_sptr inputWorkspace = getProperty("InputWorkspace");
// Retrieve the filename from the properties
m_filename = getPropertyValue("Filename");
//m_entryname = getPropertyValue("EntryName");
m_title = getPropertyValue("Title");
// Do we prserve events?
bool PreserveEvents = getProperty("PreserveEvents");
MatrixWorkspace_const_sptr matrixWorkspace = boost::dynamic_pointer_cast<const MatrixWorkspace>(inputWorkspace);
ITableWorkspace_const_sptr tableWorkspace = boost::dynamic_pointer_cast<const ITableWorkspace>(inputWorkspace);
PeaksWorkspace_const_sptr peaksWorkspace = boost::dynamic_pointer_cast<const PeaksWorkspace>(inputWorkspace);
OffsetsWorkspace_const_sptr offsetsWorkspace = boost::dynamic_pointer_cast<const OffsetsWorkspace>(inputWorkspace);
if(peaksWorkspace) g_log.debug("We have a peaks workspace");
// check if inputWorkspace is something we know how to save
if (!matrixWorkspace && !tableWorkspace) {
g_log.debug() << "Workspace " << m_title << " not saved because it is not of a type we can presently save.\n";
return;
}
m_eventWorkspace = boost::dynamic_pointer_cast<const EventWorkspace>(matrixWorkspace);
const std::string workspaceID = inputWorkspace->id();
if ((workspaceID.find("Workspace2D") == std::string::npos) &&
(workspaceID.find("RebinnedOutput") == std::string::npos) &&
!m_eventWorkspace && !tableWorkspace && !offsetsWorkspace)
throw Exception::NotImplementedError("SaveNexusProcessed passed invalid workspaces. Must be Workspace2D, EventWorkspace, ITableWorkspace, or OffsetsWorkspace.");
// Create progress object for initial part - depends on whether events are processed
if( PreserveEvents && m_eventWorkspace)
{
m_timeProgInit = 0.07; // Events processed 0.05 to 1.0
}
else
{
m_timeProgInit = 1.0; // All work is done in the initial part
}
Progress prog_init(this, 0.0, m_timeProgInit, 7);
// If no title's been given, use the workspace title field
if (m_title.empty())
m_title = inputWorkspace->getTitle();
// If we don't want to append then remove the file if it already exists
bool append_to_file = getProperty("Append");
if( !append_to_file )
{
Poco::File file(m_filename);
if( file.exists() )
file.remove();
}
// Then immediately open the file
Mantid::NeXus::NexusFileIO *nexusFile= new Mantid::NeXus::NexusFileIO( &prog_init );
nexusFile->openNexusWrite( m_filename );
// Equivalent C++ API handle
::NeXus::File * cppFile = new ::NeXus::File(nexusFile->fileID);
prog_init.reportIncrement(1, "Opening file");
if( nexusFile->writeNexusProcessedHeader( m_title ) != 0 )
throw Exception::FileError("Failed to write to file", m_filename);
prog_init.reportIncrement(1, "Writing header");
// write instrument data, if present and writer enabled
if (matrixWorkspace)
{
// Save the instrument names, ParameterMap, sample, run
matrixWorkspace->saveExperimentInfoNexus(cppFile);
prog_init.reportIncrement(1, "Writing sample and instrument");
// check if all X() are in fact the same array
const bool uniformSpectra = API::WorkspaceHelpers::commonBoundaries(matrixWorkspace);
// Retrieve the workspace indices (from params)
std::vector<int> spec;
this->getSpectrumList(spec, matrixWorkspace);
prog_init.reportIncrement(1, "Writing data");
// Write out the data (2D or event)
if (m_eventWorkspace && PreserveEvents)
{
this->execEvent(nexusFile,uniformSpectra,spec);
}
else if (offsetsWorkspace)
{
g_log.warning() << "Writing SpecialWorkspace2D ID=" << workspaceID << "\n";
nexusFile->writeNexusProcessedData2D(matrixWorkspace,uniformSpectra,spec, "offsets_workspace", true);
}
else
{
nexusFile->writeNexusProcessedData2D(matrixWorkspace,uniformSpectra,spec, "workspace", true);
}
// MW 27/10/10 - don't try and save the spectra-detector map if there isn't one
if ( matrixWorkspace->getAxis(1)->isSpectra() )
{
cppFile->openGroup("instrument", "NXinstrument");
matrixWorkspace->saveSpectraMapNexus(cppFile, spec, ::NeXus::LZW);
cppFile->closeGroup();
}
} // finish matrix workspace specifics
if (peaksWorkspace)
{
// Save the instrument names, ParameterMap, sample, run
peaksWorkspace->saveExperimentInfoNexus(cppFile);
prog_init.reportIncrement(1, "Writing sample and instrument");
}
// peaks workspace specifics
if (peaksWorkspace)
{
// g_log.information("Peaks Workspace saving to Nexus would be done");
// int pNum = peaksWorkspace->getNumberPeaks();
peaksWorkspace->saveNexus( cppFile );
} // finish peaks workspace specifics
else if (tableWorkspace) // Table workspace specifics
{
nexusFile->writeNexusTableWorkspace(tableWorkspace,"table_workspace");
} // finish table workspace specifics
// Switch to the Cpp API for the algorithm history
inputWorkspace->getHistory().saveNexus(cppFile);
nexusFile->closeNexusFile();
delete nexusFile;
return;
}
/** Executes the algorithm.
*/
void CombinePeaksWorkspaces::exec()
{
PeaksWorkspace_const_sptr LHSWorkspace = getProperty("LHSWorkspace");
PeaksWorkspace_const_sptr RHSWorkspace = getProperty("RHSWorkspace");
const bool CombineMatchingPeaks = getProperty("CombineMatchingPeaks");
// Warn if not the same instrument, sample
if ( LHSWorkspace->getInstrument()->getName() != RHSWorkspace->getInstrument()->getName() )
{
g_log.warning("The two input workspaces do not appear to come from data take on the same instrument");
}
if ( LHSWorkspace->sample().getName() != RHSWorkspace->sample().getName() )
{
g_log.warning("The two input workspaces do not appear to relate to the same sample");
}
// Copy the first workspace to our output workspace
PeaksWorkspace_sptr output(LHSWorkspace->clone());
// Get hold of the peaks in the second workspace
auto & rhsPeaks = RHSWorkspace->getPeaks();
Progress progress(this, 0, 1, rhsPeaks.size());
// If not checking for matching peaks, then it's easy...
if ( ! CombineMatchingPeaks )
{
// Loop over the peaks in the second workspace, appending each one to the output
for ( size_t i = 0; i < rhsPeaks.size(); ++i )
{
output->addPeak(rhsPeaks[i]);
progress.report();
}
}
else // Check for matching peaks
{
const double Tolerance = getProperty("Tolerance");
// Get hold of the peaks in the first workspace as we'll need to examine them
auto & lhsPeaks = LHSWorkspace->getPeaks();
// Loop over the peaks in the second workspace, appending ones that don't match any in first workspace
for ( size_t i = 0; i < rhsPeaks.size(); ++i )
{
const Peak& currentPeak = rhsPeaks[i];
// Now have to go through the first workspace checking for matches
// Not doing anything clever as peaks workspace are typically not large - just a linear search
bool match = false;
for ( size_t j = 0; j < lhsPeaks.size(); ++j )
{
const V3D deltaQ = currentPeak.getQSampleFrame() - lhsPeaks[j].getQSampleFrame();
if ( deltaQ.nullVector(Tolerance) ) // Using a V3D method that does the job
{
match = true;
break;
}
}
// Only add the peak if there was no match
if ( ! match ) output->addPeak(currentPeak);
progress.report();
}
}
setProperty("OutputWorkspace", output);
}