/** Set up an Event workspace
* @param numentries :: number of log entries to output
* @param times :: vector of Kernel::DateAndTime
* @param values :: vector of log value in double
*/
void ExportTimeSeriesLog::setupEventWorkspace(int numentries,
vector<DateAndTime> ×,
vector<double> values) {
Kernel::DateAndTime runstart(
m_dataWS->run().getProperty("run_start")->value());
// Get some stuff from the input workspace
const size_t numberOfSpectra = 1;
const int YLength = static_cast<int>(m_dataWS->blocksize());
// Make a brand new EventWorkspace
EventWorkspace_sptr outEventWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create(
"EventWorkspace", numberOfSpectra, YLength + 1, YLength));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(m_dataWS, outEventWS,
false);
m_outWS = boost::dynamic_pointer_cast<MatrixWorkspace>(outEventWS);
if (!m_outWS)
throw runtime_error(
"Output workspace cannot be casted to a MatrixWorkspace.");
g_log.debug("[DBx336] An output workspace is generated.!");
// Create the output event list (empty)
EventList &outEL = outEventWS->getOrAddEventList(0);
outEL.switchTo(WEIGHTED_NOTIME);
// Allocate all the required memory
outEL.reserve(numentries);
outEL.clearDetectorIDs();
for (size_t i = 0; i < static_cast<size_t>(numentries); i++) {
Kernel::DateAndTime tnow = times[i];
int64_t dt = tnow.totalNanoseconds() - runstart.totalNanoseconds();
// convert to microseconds
double dtmsec = static_cast<double>(dt) / 1000.0;
outEL.addEventQuickly(WeightedEventNoTime(dtmsec, values[i], values[i]));
}
// Ensure thread-safety
outEventWS->sortAll(TOF_SORT, NULL);
// Now, create a default X-vector for histogramming, with just 2 bins.
Kernel::cow_ptr<MantidVec> axis;
MantidVec &xRef = axis.access();
xRef.resize(2);
std::vector<WeightedEventNoTime> &events = outEL.getWeightedEventsNoTime();
xRef[0] = events.begin()->tof();
xRef[1] = events.rbegin()->tof();
// Set the binning axis using this.
outEventWS->setX(0, axis);
return;
}
/** Executes the algorithm */
void FilterBadPulses::exec()
{
// the input workspace into the event workspace we already know it is
EventWorkspace_sptr inputWS = this->getProperty("InputWorkspace");
// get the proton charge exists in the run object
const API::Run& runlogs = inputWS->run();
if (!runlogs.hasProperty("proton_charge"))
{
throw std::runtime_error("Failed to find \"proton_charge\" in sample logs");
}
Kernel::TimeSeriesProperty<double> * pcharge_log
= dynamic_cast<Kernel::TimeSeriesProperty<double> *>( runlogs.getLogData("proton_charge") );
Kernel::TimeSeriesPropertyStatistics stats = pcharge_log->getStatistics();
// set the range
double min_percent = this->getProperty("LowerCutoff");
min_percent *= .01; // convert it to a percentage (0<x<1)
double min_pcharge = stats.mean * min_percent;
double max_pcharge = stats.maximum * 1.1; // make sure everything high is in
if (min_pcharge >= max_pcharge) {
throw std::runtime_error("proton_charge window filters out all of the data");
}
this->g_log.information() << "Filtering pcharge outside of " << min_pcharge
<< " to " << max_pcharge << std::endl;
size_t inputNumEvents = inputWS->getNumberEvents();
// sub-algorithme does all of the actual work - do not set the output workspace
IAlgorithm_sptr filterAlgo = createSubAlgorithm("FilterByLogValue", 0., 1.);
filterAlgo->setProperty("InputWorkspace", inputWS);
filterAlgo->setProperty("LogName", "proton_charge");
filterAlgo->setProperty("MinimumValue", min_pcharge);
filterAlgo->setProperty("MaximumValue", max_pcharge);
filterAlgo->execute();
// just grab the child's output workspace
EventWorkspace_sptr outputWS = filterAlgo->getProperty("OutputWorkspace");
size_t outputNumEvents = outputWS->getNumberEvents();
this->setProperty("OutputWorkspace", outputWS);
// log the number of events deleted
double percent = static_cast<double>(inputNumEvents - outputNumEvents)
/ static_cast<double>(inputNumEvents);
percent *= 100.;
if (percent > 10.)
{
this->g_log.warning() << "Deleted " << (inputNumEvents - outputNumEvents)
<< " of " << inputNumEvents
<< " events (" << static_cast<int>(percent) << "%)\n";
}
else
{
this->g_log.information() << "Deleted " << (inputNumEvents - outputNumEvents)
<< " of " << inputNumEvents
<< " events (" << static_cast<int>(percent) << "%)\n";
}
}
/** Executes the algorithm
* @throw std::invalid_argument If the input workspaces do not meet the requirements of this algorithm
*/
void ConjoinWorkspaces::execEvent()
{
//We do not need to check that binning is compatible, just that there is no overlap
this->checkForOverlap(event_ws1, event_ws2, false);
// Create the output workspace
const size_t totalHists = event_ws1->getNumberHistograms() + event_ws2->getNumberHistograms();
// Have the minimum # of histograms in the output.
EventWorkspace_sptr output = boost::dynamic_pointer_cast<EventWorkspace>(
WorkspaceFactory::Instance().create("EventWorkspace",
1, event_ws1->readX(0).size(), event_ws1->readY(0).size())
);
// Copy over geometry (but not data) from first input workspace
WorkspaceFactory::Instance().initializeFromParent(event_ws1,output,true);
// Create the X values inside a cow pointer - they will be shared in the output workspace
cow_ptr<MantidVec> XValues;
XValues.access() = event_ws1->readX(0);
// Initialize the progress reporting object
m_progress = new API::Progress(this, 0.0, 1.0, totalHists);
const int64_t& nhist1 = event_ws1->getNumberHistograms();
for (int64_t i = 0; i < nhist1; ++i)
{
//Copy the events over
output->getOrAddEventList(i) = event_ws1->getEventList(i); //Should fire the copy constructor
m_progress->report();
}
//For second loop we use the offset from the first
const int64_t& nhist2 = event_ws2->getNumberHistograms();
for (int64_t j = 0; j < nhist2; ++j)
{
//This is the workspace index at which we assign in the output
int64_t output_wi = j + nhist1;
//Copy the events over
output->getOrAddEventList(output_wi) = event_ws2->getEventList(j); //Should fire the copy constructor
m_progress->report();
}
//This will make the spectramap axis.
output->doneAddingEventLists();
//Set the same bins for all output pixels
output->setAllX(XValues);
this->fixSpectrumNumbers(event_ws1, event_ws2, output);
// Delete the input workspaces from the ADS
AnalysisDataService::Instance().remove(getPropertyValue("InputWorkspace1"));
AnalysisDataService::Instance().remove(getPropertyValue("InputWorkspace2"));
// Create & assign an output workspace property with the workspace name the same as the first input
declareProperty(new WorkspaceProperty<>("Output",getPropertyValue("InputWorkspace1"),Direction::Output));
setProperty("Output", boost::dynamic_pointer_cast<MatrixWorkspace>(output) );
}
/** Execute the algorithm for a EventWorkspace input
* @param ws :: EventWorkspace
*/
void SmoothNeighbours::execEvent(Mantid::DataObjects::EventWorkspace_sptr ws) {
m_progress->resetNumSteps(inWS->getNumberHistograms(), 0.5, 1.0);
// Get some stuff from the input workspace
const size_t numberOfSpectra = outWI;
const int YLength = static_cast<int>(inWS->blocksize());
EventWorkspace_sptr outWS;
// Make a brand new EventWorkspace
outWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create(
"EventWorkspace", numberOfSpectra, YLength + 1, YLength));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(*ws, *outWS, false);
// Ensure thread-safety
outWS->sortAll(TOF_SORT, nullptr);
this->setProperty("OutputWorkspace",
boost::dynamic_pointer_cast<MatrixWorkspace>(outWS));
// Go through all the output workspace
PARALLEL_FOR_IF(Kernel::threadSafe(*ws, *outWS))
for (int outWIi = 0; outWIi < int(numberOfSpectra); outWIi++) {
PARALLEL_START_INTERUPT_REGION
// Create the output event list (empty)
EventList &outEL = outWS->getSpectrum(outWIi);
// Which are the neighbours?
std::vector<weightedNeighbour> &neighbours = m_neighbours[outWIi];
std::vector<weightedNeighbour>::iterator it;
for (it = neighbours.begin(); it != neighbours.end(); ++it) {
size_t inWI = it->first;
// if(sum)outEL.copyInfoFrom(*ws->getSpectrum(inWI));
double weight = it->second;
// Copy the event list
EventList tmpEL = ws->getSpectrum(inWI);
// Scale it
tmpEL *= weight;
// Add it
outEL += tmpEL;
}
// Copy the single detector ID (of the center) and spectrum number from the
// input workspace
// if (!sum) outEL.copyInfoFrom(*ws->getSpectrum(outWIi));
m_progress->report("Summing");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Give the 0-th X bins to all the output spectra.
outWS->setAllX(inWS->binEdges(0));
if (expandSumAllPixels)
spreadPixels(outWS);
}
/** Generate mapping file name from Event workspace's instrument
*/
static string generateMappingfileName(EventWorkspace_sptr &wksp) {
// get the name of the mapping file as set in the parameter files
std::vector<string> temp =
wksp->getInstrument()->getStringParameter("TS_mapping_file");
if (temp.empty())
return "";
string mapping = temp[0];
// Try to get it from the working directory
Poco::File localmap(mapping);
if (localmap.exists())
return mapping;
// Try to get it from the data directories
string dataversion = Mantid::API::FileFinder::Instance().getFullPath(mapping);
if (!dataversion.empty())
return dataversion;
// get a list of all proposal directories
string instrument = wksp->getInstrument()->getName();
Poco::File base("/SNS/" + instrument + "/");
// try short instrument name
if (!base.exists()) {
instrument =
Kernel::ConfigService::Instance().getInstrument(instrument).shortName();
base = Poco::File("/SNS/" + instrument + "/");
if (!base.exists())
return "";
}
vector<string> dirs; // poco won't let me reuse temp
base.list(dirs);
// check all of the proposals for the mapping file in the canonical place
const string CAL("_CAL");
const size_t CAL_LEN = CAL.length(); // cache to make life easier
vector<string> files;
for (auto &dir : dirs) {
if ((dir.length() > CAL_LEN) &&
(dir.compare(dir.length() - CAL.length(), CAL.length(), CAL) == 0)) {
std::string path = std::string(base.path())
.append("/")
.append(dir)
.append("/calibrations/")
.append(mapping);
if (Poco::File(path).exists())
files.push_back(path);
}
}
if (files.empty())
return "";
else if (files.size() == 1)
return files[0];
else // just assume that the last one is the right one, this should never be
// fired
return *(files.rbegin());
}
/// Called by the foreground thread to fetch data that's accumulated in
/// the temporary workspace. The temporary workspace is left empty and
/// ready to receive more data.
/// @return shared pointer to a workspace containing the accumulated data
boost::shared_ptr<Workspace> TOPAZLiveEventDataListener::extractData() {
// Check to see if the background thread has thrown an exception. If so,
// re-throw it here.
if (m_backgroundException) {
throw(*m_backgroundException);
}
// Sanity check - make sure the workspace has been initialized
if (!m_workspaceInitialized) {
throw std::runtime_error("TOPAZLiveEventDataListener: "
"The workspace has not been initialized.");
}
using namespace DataObjects;
// Make a brand new EventWorkspace
EventWorkspace_sptr temp = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create(
"EventWorkspace", m_eventBuffer->getNumberHistograms(), 2, 1));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(*m_eventBuffer, *temp,
false);
// Clear out the old logs, except for the most recent entry
temp->mutableRun().clearOutdatedTimeSeriesLogValues();
// Clear out old monitor logs
// TODO: At present, there's no way for monitor logs to be added
// to m_monitorLogs. Either implement this feature, or remove
// m_monitorLogs!
for (auto &monitorLog : m_monitorLogs) {
temp->mutableRun().removeProperty(monitorLog);
}
m_monitorLogs.clear();
// Create a fresh monitor workspace and insert into the new 'main' workspace
auto monitorBuffer = m_eventBuffer->monitorWorkspace();
auto newMonitorBuffer = WorkspaceFactory::Instance().create(
"EventWorkspace", monitorBuffer->getNumberHistograms(), 1, 1);
WorkspaceFactory::Instance().initializeFromParent(*monitorBuffer,
*newMonitorBuffer, false);
temp->setMonitorWorkspace(newMonitorBuffer);
// Lock the mutex and swap the workspaces
{
std::lock_guard<std::mutex> scopedLock(m_mutex);
std::swap(m_eventBuffer, temp);
} // mutex automatically unlocks here
return temp;
}
/** Converts an EventWorkspace to an equivalent Workspace2D
* @param inputMatrixW :: input event workspace
* @return a MatrixWorkspace_sptr
*/
MatrixWorkspace_sptr
EventWorkspaceHelpers::convertEventTo2D(MatrixWorkspace_sptr inputMatrixW) {
EventWorkspace_sptr inputW =
boost::dynamic_pointer_cast<EventWorkspace>(inputMatrixW);
if (!inputW)
throw std::invalid_argument("EventWorkspaceHelpers::convertEventTo2D(): "
"Input workspace is not an EventWorkspace.");
size_t numBins = inputW->blocksize();
// Make a workspace 2D version of it
MatrixWorkspace_sptr outputW;
outputW = WorkspaceFactory::Instance().create(
"Workspace2D", inputW->getNumberHistograms(), numBins + 1, numBins);
WorkspaceFactory::Instance().initializeFromParent(inputW, outputW, false);
// Now let's set all the X bins and values
for (size_t i = 0; i < inputW->getNumberHistograms(); i++) {
outputW->getSpectrum(i).copyInfoFrom(inputW->getSpectrum(i));
outputW->setX(i, inputW->refX(i));
MantidVec &Yout = outputW->dataY(i);
const MantidVec &Yin = inputW->readY(i);
for (size_t j = 0; j < numBins; j++)
Yout[j] = Yin[j];
MantidVec &Eout = outputW->dataE(i);
const MantidVec &Ein = inputW->readE(i);
for (size_t j = 0; j < numBins; j++)
Eout[j] = Ein[j];
}
return outputW;
}
void ScaleX::execEvent()
{
g_log.information("Processing event workspace");
const MatrixWorkspace_const_sptr matrixInputWS = this->getProperty("InputWorkspace");
EventWorkspace_const_sptr inputWS
= boost::dynamic_pointer_cast<const EventWorkspace>(matrixInputWS);
// generate the output workspace pointer
API::MatrixWorkspace_sptr matrixOutputWS = this->getProperty("OutputWorkspace");
EventWorkspace_sptr outputWS;
if (matrixOutputWS == matrixInputWS)
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(matrixOutputWS);
else
{
//Make a brand new EventWorkspace
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace", inputWS->getNumberHistograms(), 2, 1));
//Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS, false);
//You need to copy over the data as well.
outputWS->copyDataFrom( (*inputWS) );
//Cast to the matrixOutputWS and save it
matrixOutputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(outputWS);
this->setProperty("OutputWorkspace", matrixOutputWS);
}
int numHistograms = static_cast<int>(inputWS->getNumberHistograms());
PARALLEL_FOR1(outputWS)
for (int i=0; i < numHistograms; ++i)
{
PARALLEL_START_INTERUPT_REGION
//Do the offsetting
if ((i >= wi_min) && (i <= wi_max))
{
outputWS->getEventList(i).scaleTof(factor);
if( factor < 0 )
{
outputWS->getEventList(i).reverse();
}
}
m_progress->report("Scaling X");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
outputWS->clearMRU();
}
/** Executes the algorithm
*
*/
void SmoothNeighbours::exec() {
inWS = getProperty("InputWorkspace");
PreserveEvents = getProperty("PreserveEvents");
expandSumAllPixels = getProperty("ExpandSumAllPixels");
// Use the unit type to translate the entered radius into meters.
Radius = translateToMeters(getProperty("RadiusUnits"), getProperty("Radius"));
setWeightingStrategy(getProperty("WeightedSum"), Radius);
AdjX = getProperty("AdjX");
AdjY = getProperty("AdjY");
Edge = getProperty("ZeroEdgePixels");
nNeighbours = getProperty("NumberOfNeighbours");
// Progress reporting, first for the sorting
m_progress =
make_unique<Progress>(this, 0.0, 0.2, inWS->getNumberHistograms());
// Run the appropriate method depending on the type of the instrument
if (inWS->getInstrument()->containsRectDetectors() ==
Instrument::ContainsState::Full)
findNeighboursRectangular();
else
findNeighboursUbiqutious();
EventWorkspace_sptr wsEvent =
boost::dynamic_pointer_cast<EventWorkspace>(inWS);
if (wsEvent)
wsEvent->sortAll(TOF_SORT, m_progress.get());
if (!wsEvent || !PreserveEvents)
this->execWorkspace2D();
else if (wsEvent)
this->execEvent(wsEvent);
else
throw std::runtime_error("This algorithm requires a Workspace2D or "
"EventWorkspace as its input.");
}
void GatherWorkspaces::execEvent() {
// Every process in an MPI job must hit this next line or everything hangs!
mpi::communicator included; // The communicator containing all processes
// The root process needs to create a workspace of the appropriate size
EventWorkspace_sptr outputWorkspace;
if (included.rank() == 0) {
g_log.debug() << "Total number of spectra is " << totalSpec << "\n";
// Create the workspace for the output
outputWorkspace = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace", sumSpec,
numBins + hist, numBins));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(
eventW, outputWorkspace, true);
setProperty("OutputWorkspace", outputWorkspace);
ExperimentInfo_sptr inWS = inputWorkspace;
outputWorkspace->copyExperimentInfoFrom(inWS.get());
}
for (size_t wi = 0; wi < totalSpec; wi++) {
if (included.rank() == 0) {
// How do we accumulate the data?
std::string accum = this->getPropertyValue("AccumulationMethod");
std::vector<Mantid::DataObjects::EventList> out_values;
gather(included, eventW->getEventList(wi), out_values, 0);
for (int i = 0; i < included.size(); i++) {
size_t index = wi; // accum == "Add"
if (accum == "Append")
index = wi + i * totalSpec;
outputWorkspace->dataX(index) = eventW->readX(wi);
outputWorkspace->getOrAddEventList(index) += out_values[i];
const ISpectrum *inSpec = eventW->getSpectrum(wi);
ISpectrum *outSpec = outputWorkspace->getSpectrum(index);
outSpec->clearDetectorIDs();
outSpec->addDetectorIDs(inSpec->getDetectorIDs());
}
} else {
gather(included, eventW->getEventList(wi), 0);
}
}
}
/** Validate the input event workspaces
*
* @param inputWorkspaces The names of the input workspaces
* @throw invalid_argument if there is an incompatibility.
* @return true if all workspaces are event workspaces and valid. False if any
*are not found,
*/
bool MergeRuns::validateInputsForEventWorkspaces(
const std::vector<std::string> &inputWorkspaces) {
std::string xUnitID;
std::string YUnit;
bool dist(false);
m_inEventWS.clear();
// Going to check that name of instrument matches - think that's the best
// possible at the moment
// because if instrument is created from raw file it'll be a different
// object
std::string instrument;
for (size_t i = 0; i < inputWorkspaces.size(); ++i) {
// Fetch the next input workspace as an - throw an error if it's not there
EventWorkspace_sptr ws =
AnalysisDataService::Instance().retrieveWS<EventWorkspace>(
inputWorkspaces[i]);
if (!ws) { // Either it is not found, or it is not an EventWorkspace
return false;
}
m_inEventWS.push_back(ws);
// Check a few things are the same for all input workspaces
if (i == 0) {
xUnitID = ws->getAxis(0)->unit()->unitID();
YUnit = ws->YUnit();
dist = ws->isDistribution();
instrument = ws->getInstrument()->getName();
} else {
testCompatibility(ws, xUnitID, YUnit, dist, instrument);
}
} // for each input WS name
// We got here: all are event workspaces
return true;
}
void CompressEvents::exec()
{
// Get the input workspace
EventWorkspace_sptr inputWS = getProperty("InputWorkspace");
EventWorkspace_sptr outputWS = getProperty("OutputWorkspace");
double tolerance = getProperty("Tolerance");
// Some starting things
bool inplace = (inputWS == outputWS);
const int noSpectra = static_cast<int>(inputWS->getNumberHistograms());
Progress prog(this,0.0,1.0, noSpectra*2);
// Sort the input workspace in-place by TOF. This can be faster if there are few event lists.
inputWS->sortAll(TOF_SORT, &prog);
// Are we making a copy of the input workspace?
if (!inplace)
{
//Make a brand new EventWorkspace
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace", inputWS->getNumberHistograms(), 2, 1));
//Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS, false);
// We DONT copy the data though
// Do we want to parallelize over event lists, or in each event list
bool parallel_in_each = noSpectra < PARALLEL_GET_MAX_THREADS;
//parallel_in_each = false;
// Loop over the histograms (detector spectra)
// Don't parallelize the loop if we are going to parallelize each event list.
// cppcheck-suppress syntaxError
PRAGMA_OMP( parallel for schedule(dynamic) if (!parallel_in_each) )
for (int i = 0; i < noSpectra; ++i)
{
PARALLEL_START_INTERUPT_REGION
//the loop variable i can't be signed because of OpenMp rules inforced in Linux. Using this signed type suppresses warnings below
const size_t index = static_cast<size_t>(i);
// The input event list
EventList& input_el = inputWS->getEventList(index);
// And on the output side
EventList & output_el = outputWS->getOrAddEventList(index);
// Copy other settings into output
output_el.setX( input_el.ptrX() );
// The EventList method does the work.
input_el.compressEvents(tolerance, &output_el, parallel_in_each);
prog.report("Compressing");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
}
/** Executes the rebin algorithm
*
* @throw runtime_error Thrown if the bin range does not intersect the range of the input workspace
*/
void SortEvents::exec()
{
// Get the input workspace
EventWorkspace_sptr eventW = getProperty("InputWorkspace");
//And other properties
std::string sortoption = getPropertyValue("SortBy");
//------- EventWorkspace ---------------------------
const size_t histnumber = eventW->getNumberHistograms();
//Initialize progress reporting.
Progress prog(this,0.0,1.0, histnumber);
DataObjects::EventSortType sortType = DataObjects::TOF_SORT;
if (sortoption == "Pulse Time")
sortType = DataObjects::PULSETIME_SORT;
else if (sortoption == "Pulse Time + TOF")
sortType = DataObjects::PULSETIMETOF_SORT;
//This runs the SortEvents algorithm in parallel
eventW->sortAll(sortType, &prog);
return;
}
void SANSSolidAngleCorrection::execEvent() {
MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
EventWorkspace_sptr inputEventWS =
boost::dynamic_pointer_cast<EventWorkspace>(inputWS);
const int numberOfSpectra =
static_cast<int>(inputEventWS->getNumberHistograms());
Progress progress(this, 0.0, 1.0, inputEventWS->getNumberHistograms());
// generate the output workspace pointer
MatrixWorkspace_sptr outputWS = this->getProperty("OutputWorkspace");
EventWorkspace_sptr outputEventWS;
if (outputWS == inputWS)
outputEventWS = boost::dynamic_pointer_cast<EventWorkspace>(outputWS);
else {
// Make a brand new EventWorkspace
outputEventWS = boost::dynamic_pointer_cast<EventWorkspace>(
WorkspaceFactory::Instance().create(
"EventWorkspace", inputEventWS->getNumberHistograms(), 2, 1));
// Copy geometry over.
WorkspaceFactory::Instance().initializeFromParent(inputEventWS,
outputEventWS, false);
// You need to copy over the data as well.
outputEventWS->copyDataFrom((*inputEventWS));
// Cast to the matrixOutputWS and save it
outputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(outputEventWS);
this->setProperty("OutputWorkspace", outputWS);
}
progress.report("Solid Angle Correction");
PARALLEL_FOR2(inputEventWS, outputEventWS)
for (int i = 0; i < numberOfSpectra; i++) {
PARALLEL_START_INTERUPT_REGION
IDetector_const_sptr det;
try {
det = inputEventWS->getDetector(i);
} catch (Exception::NotFoundError &) {
g_log.warning() << "Spectrum index " << i
<< " has no detector assigned to it - discarding"
<< std::endl;
// Catch if no detector. Next line tests whether this happened - test
// placed
// outside here because Mac Intel compiler doesn't like 'continue' in a
// catch
// in an openmp block.
}
if (!det)
continue;
// Skip if we have a monitor or if the detector is masked.
if (det->isMonitor() || det->isMasked())
continue;
// Compute solid angle correction factor
const bool is_tube = getProperty("DetectorTubes");
const double tanTheta = tan(inputEventWS->detectorTwoTheta(det));
const double theta_term = sqrt(tanTheta * tanTheta + 1.0);
double corr;
if (is_tube) {
const double tanAlpha = tan(getYTubeAngle(det, inputWS));
const double alpha_term = sqrt(tanAlpha * tanAlpha + 1.0);
corr = alpha_term * theta_term * theta_term;
} else {
corr = theta_term * theta_term * theta_term;
}
EventList &el = outputEventWS->getEventList(i);
el *= corr;
progress.report("Solid Angle Correction");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
setProperty("OutputMessage", "Solid angle correction applied");
}
/// Executes the algorithm for events
void UnaryOperation::execEvent() {
g_log.information("Processing event workspace");
const MatrixWorkspace_const_sptr matrixInputWS =
this->getProperty(inputPropName());
EventWorkspace_const_sptr inputWS =
boost::dynamic_pointer_cast<const EventWorkspace>(matrixInputWS);
// generate the output workspace pointer
API::MatrixWorkspace_sptr matrixOutputWS =
this->getProperty(outputPropName());
EventWorkspace_sptr outputWS;
if (matrixOutputWS == matrixInputWS) {
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(matrixOutputWS);
} else {
// Make a brand new EventWorkspace
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create(
"EventWorkspace", inputWS->getNumberHistograms(), 2, 1));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS,
false);
// You need to copy over the data as well.
outputWS->copyDataFrom((*inputWS));
// Cast to the matrixOutputWS and save it
matrixOutputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(outputWS);
this->setProperty("OutputWorkspace", matrixOutputWS);
}
// Now fetch any properties defined by concrete algorithm
retrieveProperties();
int64_t numHistograms = static_cast<int64_t>(inputWS->getNumberHistograms());
API::Progress prog = API::Progress(this, 0.0, 1.0, numHistograms);
PARALLEL_FOR1(outputWS)
for (int64_t i = 0; i < numHistograms; ++i) {
PARALLEL_START_INTERUPT_REGION
// switch to weighted events if needed, and use the appropriate helper
// function
EventList *evlist = outputWS->getEventListPtr(i);
switch (evlist->getEventType()) {
case TOF:
// Switch to weights if needed.
evlist->switchTo(WEIGHTED);
/* no break */
// Fall through
case WEIGHTED:
unaryOperationEventHelper(evlist->getWeightedEvents());
break;
case WEIGHTED_NOTIME:
unaryOperationEventHelper(evlist->getWeightedEventsNoTime());
break;
}
prog.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
outputWS->clearMRU();
if (inputWS->getNumberEvents() != outputWS->getNumberEvents()) {
g_log.information() << "Number of events has changed!!!" << std::endl;
}
}
/** Executes the algorithm
*/
void FilterByTime::exec()
{
EventWorkspace_const_sptr inputWS = this->getProperty("InputWorkspace");
// ---- Find the start/end times ----
DateAndTime start, stop;
double start_dbl, stop_dbl;
start_dbl = getProperty("StartTime");
stop_dbl = getProperty("StopTime");
std::string start_str, stop_str;
start_str = getPropertyValue("AbsoluteStartTime");
stop_str = getPropertyValue("AbsoluteStopTime");
if ( (start_str != "") && (stop_str != "") && (start_dbl <= 0.0) && (stop_dbl <= 0.0) )
{
// Use the absolute string
start = DateAndTime( start_str );
stop = DateAndTime( stop_str );
}
else if ( (start_str == "") && (stop_str == "") && ((start_dbl > 0.0) || (stop_dbl > 0.0)) )
{
// Use the relative times in seconds.
DateAndTime first = inputWS->getFirstPulseTime();
DateAndTime last = inputWS->getLastPulseTime();
start = first + start_dbl;
if (stop_dbl > 0.0)
{
stop = first + stop_dbl;
}
else
{
this->getLogger().debug() << "No end filter time specified - assuming last pulse" << std::endl;
stop = last + 10000.0; // so we get all events - needs to be past last pulse
}
}
else
{
//Either both or none were specified
throw std::invalid_argument("You need to specify either the StartTime or StopTime parameters; or both the AbsoluteStartTime and AbsoluteStopTime parameters; but not other combinations.");
}
if (stop <= start)
throw std::invalid_argument("The stop time should be larger than the start time.");
// Make a brand new EventWorkspace
EventWorkspace_sptr outputWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace", inputWS->getNumberHistograms(), 2, 1));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS, false);
// But we don't copy the data.
setProperty("OutputWorkspace", outputWS);
size_t numberOfSpectra = inputWS->getNumberHistograms();
// Initialise the progress reporting object
Progress prog(this,0.0,1.0,numberOfSpectra);
// Loop over the histograms (detector spectra)
PARALLEL_FOR_NO_WSP_CHECK()
for (int64_t i = 0; i < int64_t(numberOfSpectra); ++i)
{
PARALLEL_START_INTERUPT_REGION
//Get the output event list (should be empty)
EventList& output_el = outputWS->getEventList(i);
//and this is the input event list
const EventList& input_el = inputWS->getEventList(i);
//Perform the filtering
input_el.filterByPulseTime(start, stop, output_el);
prog.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
//Now filter out the run, using the DateAndTime type.
outputWS->mutableRun().filterByTime(start, stop);
}
/** Convert the workspace units using TOF as an intermediate step in the
* conversion
* @param fromUnit :: The unit of the input workspace
* @param outputWS :: The output workspace
*/
void ConvertUnitsUsingDetectorTable::convertViaTOF(
Kernel::Unit_const_sptr fromUnit, API::MatrixWorkspace_sptr outputWS) {
using namespace Geometry;
// Let's see if we are using a TableWorkspace to override parameters
TableWorkspace_sptr paramWS = getProperty("DetectorParameters");
// See if we have supplied a DetectorParameters Workspace
// TODO: Check if paramWS is NULL and if so throw an exception
// const std::string l1ColumnLabel("l1");
// Let's check all the columns exist and are readable
try {
auto spectraColumnTmp = paramWS->getColumn("spectra");
auto l1ColumnTmp = paramWS->getColumn("l1");
auto l2ColumnTmp = paramWS->getColumn("l2");
auto twoThetaColumnTmp = paramWS->getColumn("twotheta");
auto efixedColumnTmp = paramWS->getColumn("efixed");
auto emodeColumnTmp = paramWS->getColumn("emode");
} catch (...) {
throw Exception::InstrumentDefinitionError(
"DetectorParameter TableWorkspace is not defined correctly.");
}
// Now let's read them into some vectors.
auto l1Column = paramWS->getColVector<double>("l1");
auto l2Column = paramWS->getColVector<double>("l2");
auto twoThetaColumn = paramWS->getColVector<double>("twotheta");
auto efixedColumn = paramWS->getColVector<double>("efixed");
auto emodeColumn = paramWS->getColVector<int>("emode");
auto spectraColumn = paramWS->getColVector<int>("spectra");
EventWorkspace_sptr eventWS =
boost::dynamic_pointer_cast<EventWorkspace>(outputWS);
assert(static_cast<bool>(eventWS) == m_inputEvents); // Sanity check
Progress prog(this, 0.2, 1.0, m_numberOfSpectra);
int64_t numberOfSpectra_i =
static_cast<int64_t>(m_numberOfSpectra); // cast to make openmp happy
// Get the unit object for each workspace
Kernel::Unit_const_sptr outputUnit = outputWS->getAxis(0)->unit();
std::vector<double> emptyVec;
int failedDetectorCount = 0;
// ConstColumnVector<int> spectraNumber = paramWS->getVector("spectra");
// TODO: Check why this parallel stuff breaks
// Loop over the histograms (detector spectra)
// PARALLEL_FOR1(outputWS)
for (int64_t i = 0; i < numberOfSpectra_i; ++i) {
// Lets find what row this spectrum ID appears in our detector table.
// PARALLEL_START_INTERUPT_REGION
std::size_t wsid = i;
try {
double deg2rad = M_PI / 180.;
auto det = outputWS->getDetector(i);
int specid = det->getID();
// int spectraNumber = static_cast<int>(spectraColumn->toDouble(i));
// wsid = outputWS->getIndexFromSpectrumNumber(spectraNumber);
g_log.debug() << "###### Spectra #" << specid
<< " ==> Workspace ID:" << wsid << std::endl;
// Now we need to find the row that contains this spectrum
std::vector<int>::iterator specIter;
specIter = std::find(spectraColumn.begin(), spectraColumn.end(), specid);
if (specIter != spectraColumn.end()) {
size_t detectorRow = std::distance(spectraColumn.begin(), specIter);
double l1 = l1Column[detectorRow];
double l2 = l2Column[detectorRow];
double twoTheta = twoThetaColumn[detectorRow] * deg2rad;
double efixed = efixedColumn[detectorRow];
int emode = emodeColumn[detectorRow];
g_log.debug() << "specId from detector table = "
<< spectraColumn[detectorRow] << std::endl;
// l1 = l1Column->toDouble(detectorRow);
// l2 = l2Column->toDouble(detectorRow);
// twoTheta = deg2rad * twoThetaColumn->toDouble(detectorRow);
// efixed = efixedColumn->toDouble(detectorRow);
// emode = static_cast<int>(emodeColumn->toDouble(detectorRow));
g_log.debug() << "###### Spectra #" << specid
<< " ==> Det Table Row:" << detectorRow << std::endl;
g_log.debug() << "\tL1=" << l1 << ",L2=" << l2 << ",TT=" << twoTheta
<< ",EF=" << efixed << ",EM=" << emode << std::endl;
// Make local copies of the units. This allows running the loop in
// parallel
Unit *localFromUnit = fromUnit->clone();
Unit *localOutputUnit = outputUnit->clone();
/// @todo Don't yet consider hold-off (delta)
const double delta = 0.0;
// Convert the input unit to time-of-flight
localFromUnit->toTOF(outputWS->dataX(wsid), emptyVec, l1, l2, twoTheta,
emode, efixed, delta);
// Convert from time-of-flight to the desired unit
localOutputUnit->fromTOF(outputWS->dataX(wsid), emptyVec, l1, l2,
twoTheta, emode, efixed, delta);
// EventWorkspace part, modifying the EventLists.
if (m_inputEvents) {
eventWS->getEventList(wsid)
.convertUnitsViaTof(localFromUnit, localOutputUnit);
}
// Clear unit memory
delete localFromUnit;
delete localOutputUnit;
} else {
// Not found
g_log.debug() << "Spectrum " << specid << " not found!" << std::endl;
failedDetectorCount++;
outputWS->maskWorkspaceIndex(wsid);
}
} catch (Exception::NotFoundError &) {
// Get to here if exception thrown when calculating distance to detector
failedDetectorCount++;
// Since you usually (always?) get to here when there's no attached
// detectors, this call is
// the same as just zeroing out the data (calling clearData on the
// spectrum)
outputWS->maskWorkspaceIndex(i);
}
prog.report("Convert to " + m_outputUnit->unitID());
// PARALLEL_END_INTERUPT_REGION
} // loop over spectra
// PARALLEL_CHECK_INTERUPT_REGION
if (failedDetectorCount != 0) {
g_log.information() << "Something went wrong for " << failedDetectorCount
<< " spectra. Masking spectrum." << std::endl;
}
if (m_inputEvents)
eventWS->clearMRU();
}
void ModeratorTzero::execEvent()
{
g_log.information("Processing event workspace");
const MatrixWorkspace_const_sptr matrixInputWS = getProperty("InputWorkspace");
EventWorkspace_const_sptr inputWS= boost::dynamic_pointer_cast<const EventWorkspace>(matrixInputWS);
// generate the output workspace pointer
const size_t numHists = static_cast<size_t>(inputWS->getNumberHistograms());
Mantid::API::MatrixWorkspace_sptr matrixOutputWS = getProperty("OutputWorkspace");
EventWorkspace_sptr outputWS;
if (matrixOutputWS == matrixInputWS)
{
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(matrixOutputWS);
}
else
{
//Make a brand new EventWorkspace
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(WorkspaceFactory::Instance().create("EventWorkspace", numHists, 2, 1));
//Copy geometry over.
WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS, false);
//You need to copy over the data as well.
outputWS->copyDataFrom( (*inputWS) );
//Cast to the matrixOutputWS and save it
matrixOutputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(outputWS);
setProperty("OutputWorkspace", matrixOutputWS);
}
//Get a pointer to the sample
IComponent_const_sptr sample = outputWS->getInstrument()->getSample();
// Loop over the spectra
Progress prog(this,0.0,1.0,numHists); //report progress of algorithm
PARALLEL_FOR1(outputWS)
for (int i = 0; i < static_cast<int>(numHists); ++i)
{
PARALLEL_START_INTERUPT_REGION
size_t wsIndex = static_cast<size_t>(i);
EventList &evlist=outputWS->getEventList(wsIndex);
if( evlist.getNumberEvents() > 0 ) //don't bother with empty lists
{
double L1=CalculateL1(matrixOutputWS, wsIndex); // distance from source to sample or monitor
double t2=CalculateT2(matrixOutputWS, wsIndex); // time from sample to detector
if(t2>=0) //t2 < 0 when no detector info is available
{
double tof, E1;
mu::Parser parser;
parser.DefineVar("incidentEnergy", &E1); // associate variable E1 to this parser
parser.SetExpr(m_formula);
E1=m_convfactor*(L1/m_t1min)*(L1/m_t1min);
double min_t0_next=parser.Eval(); // fast neutrons are shifted by min_t0_next, irrespective of tof
// fix the histogram bins
MantidVec &x=evlist.dataX();
for (MantidVec::iterator iter=x.begin(); iter!=x.end(); ++iter)
{
tof=*iter;
if(tof<m_t1min+t2)
tof-=min_t0_next;
else
tof-=CalculateT0(tof, L1, t2, E1, parser);
*iter=tof;
}
MantidVec tofs=evlist.getTofs();
for(unsigned int itof=0; itof<tofs.size(); itof++)
{
tof=tofs[itof]+0.002*(rand()%100 -50); // add a [-0.1,0.1] microsecond noise to avoid artifacts resulting from original tof data
if(tof<m_t1min+t2)
tof-=min_t0_next;
else
tof-=CalculateT0(tof, L1, t2, E1, parser);
tofs[itof]=tof;
}
evlist.setTofs(tofs);
evlist.setSortOrder(Mantid::DataObjects::EventSortType::UNSORTED);
}
}
prog.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
outputWS->clearMRU(); // Clears the Most Recent Used lists */
} // end of void ModeratorTzero::execEvent()
/** 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));
}
/** Process the event file properly.
* @param workspace :: EventWorkspace to write to.
*/
void
LoadEventPreNexus::procEvents(DataObjects::EventWorkspace_sptr &workspace) {
this->num_error_events = 0;
this->num_good_events = 0;
this->num_ignored_events = 0;
// Default values in the case of no parallel
size_t loadBlockSize = Mantid::Kernel::DEFAULT_BLOCK_SIZE * 2;
shortest_tof = static_cast<double>(MAX_TOF_UINT32) * TOF_CONVERSION;
longest_tof = 0.;
// Initialize progress reporting.
size_t numBlocks = (max_events + loadBlockSize - 1) / loadBlockSize;
// We want to pad out empty pixels.
detid2det_map detector_map;
workspace->getInstrument()->getDetectors(detector_map);
// -------------- Determine processing mode
std::string procMode = getProperty("UseParallelProcessing");
if (procMode == "Serial")
parallelProcessing = false;
else if (procMode == "Parallel")
parallelProcessing = true;
else {
// Automatic determination. Loading serially (for me) is about 3 million
// events per second,
// (which is sped up by ~ x 3 with parallel processing, say 10 million per
// second, e.g. 7 million events more per seconds).
// compared to a setup time/merging time of about 10 seconds per million
// detectors.
double setUpTime = double(detector_map.size()) * 10e-6;
parallelProcessing = ((double(max_events) / 7e6) > setUpTime);
g_log.debug() << (parallelProcessing ? "Using" : "Not using")
<< " parallel processing." << std::endl;
}
// determine maximum pixel id
detid2det_map::iterator it;
detid_max = 0; // seems like a safe lower bound
for (it = detector_map.begin(); it != detector_map.end(); it++)
if (it->first > detid_max)
detid_max = it->first;
// Pad all the pixels
prog->report("Padding Pixels");
this->pixel_to_wkspindex.reserve(
detid_max + 1); // starting at zero up to and including detid_max
// Set to zero
this->pixel_to_wkspindex.assign(detid_max + 1, 0);
size_t workspaceIndex = 0;
for (it = detector_map.begin(); it != detector_map.end(); it++) {
if (!it->second->isMonitor()) {
this->pixel_to_wkspindex[it->first] = workspaceIndex;
EventList &spec = workspace->getOrAddEventList(workspaceIndex);
spec.addDetectorID(it->first);
// Start the spectrum number at 1
spec.setSpectrumNo(specid_t(workspaceIndex + 1));
workspaceIndex += 1;
}
}
// For slight speed up
loadOnlySomeSpectra = (this->spectra_list.size() > 0);
// Turn the spectra list into a map, for speed of access
for (std::vector<int64_t>::iterator it = spectra_list.begin();
it != spectra_list.end(); it++)
spectraLoadMap[*it] = true;
CPUTimer tim;
// --------------- Create the partial workspaces
// ------------------------------------------
// Vector of partial workspaces, for parallel processing.
std::vector<EventWorkspace_sptr> partWorkspaces;
std::vector<DasEvent *> buffers;
/// Pointer to the vector of events
typedef std::vector<TofEvent> *EventVector_pt;
/// Bare array of arrays of pointers to the EventVectors
EventVector_pt **eventVectors;
/// How many threads will we use?
size_t numThreads = 1;
if (parallelProcessing)
numThreads = size_t(PARALLEL_GET_MAX_THREADS);
partWorkspaces.resize(numThreads);
buffers.resize(numThreads);
eventVectors = new EventVector_pt *[numThreads];
// cppcheck-suppress syntaxError
PRAGMA_OMP( parallel for if (parallelProcessing) )
for (int i = 0; i < int(numThreads); i++) {
// This is the partial workspace we are about to create (if in parallel)
EventWorkspace_sptr partWS;
if (parallelProcessing) {
prog->report("Creating Partial Workspace");
// Create a partial workspace
partWS = EventWorkspace_sptr(new EventWorkspace());
// Make sure to initialize.
partWS->initialize(1, 1, 1);
// Copy all the spectra numbers and stuff (no actual events to copy
// though).
partWS->copyDataFrom(*workspace);
// Push it in the array
partWorkspaces[i] = partWS;
} else
partWS = workspace;
// Allocate the buffers
buffers[i] = new DasEvent[loadBlockSize];
// For each partial workspace, make an array where index = detector ID and
// value = pointer to the events vector
eventVectors[i] = new EventVector_pt[detid_max + 1];
EventVector_pt *theseEventVectors = eventVectors[i];
for (detid_t j = 0; j < detid_max + 1; j++) {
size_t wi = pixel_to_wkspindex[j];
// Save a POINTER to the vector<tofEvent>
theseEventVectors[j] = &partWS->getEventList(wi).getEvents();
}
}
g_log.debug() << tim << " to create " << partWorkspaces.size()
<< " workspaces for parallel loading." << std::endl;
prog->resetNumSteps(numBlocks, 0.1, 0.8);
// ---------------------------------- LOAD THE DATA --------------------------
PRAGMA_OMP( parallel for schedule(dynamic, 1) if (parallelProcessing) )
for (int blockNum = 0; blockNum < int(numBlocks); blockNum++) {
PARALLEL_START_INTERUPT_REGION
// Find the workspace for this particular thread
EventWorkspace_sptr ws;
size_t threadNum = 0;
if (parallelProcessing) {
threadNum = PARALLEL_THREAD_NUMBER;
ws = partWorkspaces[threadNum];
} else
ws = workspace;
// Get the buffer (for this thread)
DasEvent *event_buffer = buffers[threadNum];
// Get the speeding-up array of vector<tofEvent> where index = detid.
EventVector_pt *theseEventVectors = eventVectors[threadNum];
// Where to start in the file?
size_t fileOffset = first_event + (loadBlockSize * blockNum);
// May need to reduce size of last (or only) block
size_t current_event_buffer_size =
(blockNum == int(numBlocks - 1))
? (max_events - (numBlocks - 1) * loadBlockSize)
: loadBlockSize;
// Load this chunk of event data (critical block)
PARALLEL_CRITICAL(LoadEventPreNexus_fileAccess) {
current_event_buffer_size = eventfile->loadBlockAt(
event_buffer, fileOffset, current_event_buffer_size);
}
// This processes the events. Can be done in parallel!
procEventsLinear(ws, theseEventVectors, event_buffer,
current_event_buffer_size, fileOffset);
// Report progress
prog->report("Load Event PreNeXus");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
g_log.debug() << tim << " to load the data." << std::endl;
// ---------------------------------- MERGE WORKSPACES BACK TOGETHER
// --------------------------
if (parallelProcessing) {
PARALLEL_START_INTERUPT_REGION
prog->resetNumSteps(workspace->getNumberHistograms(), 0.8, 0.95);
size_t memoryCleared = 0;
MemoryManager::Instance().releaseFreeMemory();
// Merge all workspaces, index by index.
PARALLEL_FOR_NO_WSP_CHECK()
for (int iwi = 0; iwi < int(workspace->getNumberHistograms()); iwi++) {
size_t wi = size_t(iwi);
// The output event list.
EventList &el = workspace->getEventList(wi);
el.clear(false);
// How many events will it have?
size_t numEvents = 0;
for (size_t i = 0; i < numThreads; i++)
numEvents += partWorkspaces[i]->getEventList(wi).getNumberEvents();
// This will avoid too much copying.
el.reserve(numEvents);
// Now merge the event lists
for (size_t i = 0; i < numThreads; i++) {
EventList &partEl = partWorkspaces[i]->getEventList(wi);
el += partEl.getEvents();
// Free up memory as you go along.
partEl.clear(false);
}
// With TCMalloc, release memory when you accumulate enough to make sense
PARALLEL_CRITICAL(LoadEventPreNexus_trackMemory) {
memoryCleared += numEvents;
if (memoryCleared > 10000000) // ten million events = about 160 MB
{
MemoryManager::Instance().releaseFreeMemory();
memoryCleared = 0;
}
}
prog->report("Merging Workspaces");
}
// Final memory release
MemoryManager::Instance().releaseFreeMemory();
g_log.debug() << tim << " to merge workspaces together." << std::endl;
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Delete the buffers for each thread.
for (size_t i = 0; i < numThreads; i++) {
delete[] buffers[i];
delete[] eventVectors[i];
}
delete[] eventVectors;
// delete [] pulsetimes;
prog->resetNumSteps(3, 0.94, 1.00);
// finalize loading
prog->report("Deleting Empty Lists");
if (loadOnlySomeSpectra)
workspace->deleteEmptyLists();
prog->report("Setting proton charge");
this->setProtonCharge(workspace);
g_log.debug() << tim << " to set the proton charge log." << std::endl;
// Make sure the MRU is cleared
workspace->clearMRU();
// Now, create a default X-vector for histogramming, with just 2 bins.
Kernel::cow_ptr<MantidVec> axis;
MantidVec &xRef = axis.access();
xRef.resize(2);
xRef[0] = shortest_tof - 1; // Just to make sure the bins hold it all
xRef[1] = longest_tof + 1;
workspace->setAllX(axis);
this->pixel_to_wkspindex.clear();
g_log.information() << "Read " << this->num_good_events << " events + "
<< this->num_error_events << " errors"
<< ". Shortest TOF: " << shortest_tof
<< " microsec; longest TOF: " << longest_tof
<< " microsec." << std::endl;
}
/** Carries out the bin-by-bin normalisation
* @param inputWorkspace The input workspace
* @param outputWorkspace The result workspace
*/
void NormaliseToMonitor::normaliseBinByBin(API::MatrixWorkspace_sptr inputWorkspace,
API::MatrixWorkspace_sptr& outputWorkspace)
{
EventWorkspace_sptr inputEvent = boost::dynamic_pointer_cast<EventWorkspace>(inputWorkspace);
EventWorkspace_sptr outputEvent;
// Only create output workspace if different to input one
if (outputWorkspace != inputWorkspace )
{
if (inputEvent)
{
//Make a brand new EventWorkspace
outputEvent = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace", inputEvent->getNumberHistograms(), 2, 1));
//Copy geometry and data
API::WorkspaceFactory::Instance().initializeFromParent(inputEvent, outputEvent, false);
outputEvent->copyDataFrom( (*inputEvent) );
outputWorkspace = boost::dynamic_pointer_cast<MatrixWorkspace>(outputEvent);
}
else
outputWorkspace = WorkspaceFactory::Instance().create(inputWorkspace);
}
// Get hold of the monitor spectrum
const MantidVec& monX = m_monitor->readX(0);
MantidVec& monY = m_monitor->dataY(0);
MantidVec& monE = m_monitor->dataE(0);
// Calculate the overall normalisation just the once if bins are all matching
if (m_commonBins) this->normalisationFactor(m_monitor->readX(0),&monY,&monE);
const size_t numHists = inputWorkspace->getNumberHistograms();
MantidVec::size_type specLength = inputWorkspace->blocksize();
Progress prog(this,0.0,1.0,numHists);
// Loop over spectra
PARALLEL_FOR3(inputWorkspace,outputWorkspace,m_monitor)
for (int64_t i = 0; i < int64_t(numHists); ++i)
{
PARALLEL_START_INTERUPT_REGION
prog.report();
const MantidVec& X = inputWorkspace->readX(i);
// If not rebinning, just point to our monitor spectra, otherwise create new vectors
MantidVec* Y = ( m_commonBins ? &monY : new MantidVec(specLength) );
MantidVec* E = ( m_commonBins ? &monE : new MantidVec(specLength) );
if (!m_commonBins)
{
// ConvertUnits can give X vectors of all zeroes - skip these, they cause problems
if (X.back() == 0.0 && X.front() == 0.0) continue;
// Rebin the monitor spectrum to match the binning of the current data spectrum
VectorHelper::rebinHistogram(monX,monY,monE,X,*Y,*E,false);
// Recalculate the overall normalisation factor
this->normalisationFactor(X,Y,E);
}
if (inputEvent)
{
// ----------------------------------- EventWorkspace ---------------------------------------
EventList & outEL = outputEvent->getEventList(i);
outEL.divide(X, *Y, *E);
}
else
{
// ----------------------------------- Workspace2D ---------------------------------------
const MantidVec& inY = inputWorkspace->readY(i);
const MantidVec& inE = inputWorkspace->readE(i);
MantidVec& YOut = outputWorkspace->dataY(i);
MantidVec& EOut = outputWorkspace->dataE(i);
outputWorkspace->dataX(i) = inputWorkspace->readX(i);
// The code below comes more or less straight out of Divide.cpp
for (MantidVec::size_type k = 0; k < specLength; ++k)
{
// Get references to the input Y's
const double& leftY = inY[k];
const double& rightY = (*Y)[k];
// Calculate result and store in local variable to avoid overwriting original data if
// output workspace is same as one of the input ones
const double newY = leftY/rightY;
if (fabs(rightY)>1.0e-12 && fabs(newY)>1.0e-12)
{
const double lhsFactor = (inE[k]<1.0e-12|| fabs(leftY)<1.0e-12) ? 0.0 : pow((inE[k]/leftY),2);
const double rhsFactor = (*E)[k]<1.0e-12 ? 0.0 : pow(((*E)[k]/rightY),2);
EOut[k] = std::abs(newY) * sqrt(lhsFactor+rhsFactor);
}
// Now store the result
YOut[k] = newY;
} // end Workspace2D case
} // end loop over current spectrum
if (!m_commonBins) { delete Y; delete E; }
PARALLEL_END_INTERUPT_REGION
} // end loop over spectra
PARALLEL_CHECK_INTERUPT_REGION
}
/** Load the event_workspace field
*
* @param wksp_cls
* @param progressStart
* @param progressRange
* @return
*/
API::MatrixWorkspace_sptr LoadNexusProcessed::loadEventEntry(NXData & wksp_cls, NXDouble & xbins,
const double& progressStart, const double& progressRange)
{
NXDataSetTyped<int64_t> indices_data = wksp_cls.openNXDataSet<int64_t>("indices");
indices_data.load();
boost::shared_array<int64_t> indices = indices_data.sharedBuffer();
int numspec = indices_data.dim0()-1;
int num_xbins = xbins.dim0();
if (num_xbins < 2) num_xbins = 2;
EventWorkspace_sptr ws = boost::dynamic_pointer_cast<EventWorkspace>
(WorkspaceFactory::Instance().create("EventWorkspace", numspec, num_xbins, num_xbins-1));
// Set the YUnit label
ws->setYUnit(indices_data.attributes("units"));
std::string unitLabel = indices_data.attributes("unit_label");
if (unitLabel.empty()) unitLabel = indices_data.attributes("units");
ws->setYUnitLabel(unitLabel);
//Handle optional fields.
// TODO: Handle inconsistent sizes
boost::shared_array<int64_t> pulsetimes;
if (wksp_cls.isValid("pulsetime"))
{
NXDataSetTyped<int64_t> pulsetime = wksp_cls.openNXDataSet<int64_t>("pulsetime");
pulsetime.load();
pulsetimes = pulsetime.sharedBuffer();
}
boost::shared_array<double> tofs;
if (wksp_cls.isValid("tof"))
{
NXDouble tof = wksp_cls.openNXDouble("tof");
tof.load();
tofs = tof.sharedBuffer();
}
boost::shared_array<float> error_squareds;
if (wksp_cls.isValid("error_squared"))
{
NXFloat error_squared = wksp_cls.openNXFloat("error_squared");
error_squared.load();
error_squareds = error_squared.sharedBuffer();
}
boost::shared_array<float> weights;
if (wksp_cls.isValid("weight"))
{
NXFloat weight = wksp_cls.openNXFloat("weight");
weight.load();
weights = weight.sharedBuffer();
}
// What type of event lists?
EventType type = TOF;
if (tofs && pulsetimes && weights && error_squareds)
type = WEIGHTED;
else if ((tofs && weights && error_squareds))
type = WEIGHTED_NOTIME;
else if (pulsetimes && tofs)
type = TOF;
else
throw std::runtime_error("Could not figure out the type of event list!");
// Create all the event lists
PARALLEL_FOR_NO_WSP_CHECK()
for (int wi=0; wi < numspec; wi++)
{
PARALLEL_START_INTERUPT_REGION
int64_t index_start = indices[wi];
int64_t index_end = indices[wi+1];
if (index_end >= index_start)
{
EventList & el = ws->getEventList(wi);
el.switchTo(type);
// Allocate all the required memory
el.reserve(index_end - index_start);
el.clearDetectorIDs();
for (long i=index_start; i<index_end; i++)
switch (type)
{
case TOF:
el.addEventQuickly( TofEvent( tofs[i], DateAndTime(pulsetimes[i])) );
break;
case WEIGHTED:
el.addEventQuickly( WeightedEvent( tofs[i], DateAndTime(pulsetimes[i]), weights[i], error_squareds[i]) );
break;
case WEIGHTED_NOTIME:
el.addEventQuickly( WeightedEventNoTime( tofs[i], weights[i], error_squareds[i]) );
break;
}
// Set the X axis
if (this->m_shared_bins)
el.setX(this->m_xbins);
else
{
MantidVec x;
x.resize(xbins.dim0());
for (int i=0; i < xbins.dim0(); i++)
x[i] = xbins(wi, i);
el.setX(x);
}
}
progress(progressStart + progressRange*(1.0/numspec));
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Clean up some stuff
ws->doneAddingEventLists();
return ws;
}
void TOFSANSResolution::exec()
{
Workspace2D_sptr iqWS = getProperty("InputWorkspace");
MatrixWorkspace_sptr reducedWS = getProperty("ReducedWorkspace");
EventWorkspace_sptr reducedEventWS = boost::dynamic_pointer_cast<EventWorkspace>(reducedWS);
const double min_wl = getProperty("MinWavelength");
const double max_wl = getProperty("MaxWavelength");
double pixel_size_x = getProperty("PixelSizeX");
double pixel_size_y = getProperty("PixelSizeY");
double R1 = getProperty("SourceApertureRadius");
double R2 = getProperty("SampleApertureRadius");
// Convert to meters
pixel_size_x /= 1000.0;
pixel_size_y /= 1000.0;
R1 /= 1000.0;
R2 /= 1000.0;
wl_resolution = getProperty("DeltaT");
// Although we want the 'ReducedWorkspace' to be an event workspace for this algorithm to do
// anything, we don't want the algorithm to 'fail' if it isn't
if (!reducedEventWS)
{
g_log.warning() << "An Event Workspace is needed to compute dQ. Calculation skipped." << std::endl;
return;
}
// Calculate the output binning
const std::vector<double> binParams = getProperty("OutputBinning");
// Count histogram for normalization
const int xLength = static_cast<int>(iqWS->readX(0).size());
std::vector<double> XNorm(xLength-1, 0.0);
// Create workspaces with each component of the resolution for debugging purposes
MatrixWorkspace_sptr thetaWS = WorkspaceFactory::Instance().create(iqWS);
declareProperty(new WorkspaceProperty<>("ThetaError","",Direction::Output));
setPropertyValue("ThetaError","__"+iqWS->getName()+"_theta_error");
setProperty("ThetaError",thetaWS);
thetaWS->setX(0,iqWS->readX(0));
MantidVec& ThetaY = thetaWS->dataY(0);
MatrixWorkspace_sptr tofWS = WorkspaceFactory::Instance().create(iqWS);
declareProperty(new WorkspaceProperty<>("TOFError","",Direction::Output));
setPropertyValue("TOFError","__"+iqWS->getName()+"_tof_error");
setProperty("TOFError",tofWS);
tofWS->setX(0,iqWS->readX(0));
MantidVec& TOFY = tofWS->dataY(0);
// Initialize Dq
MantidVec& DxOut = iqWS->dataDx(0);
for ( int i = 0; i<xLength-1; i++ ) DxOut[i] = 0.0;
const V3D samplePos = reducedWS->getInstrument()->getSample()->getPos();
const V3D sourcePos = reducedWS->getInstrument()->getSource()->getPos();
const V3D SSD = samplePos - sourcePos;
const double L1 = SSD.norm();
const int numberOfSpectra = static_cast<int>(reducedWS->getNumberHistograms());
Progress progress(this,0.0,1.0,numberOfSpectra);
PARALLEL_FOR2(reducedEventWS, iqWS)
for (int i = 0; i < numberOfSpectra; i++)
{
PARALLEL_START_INTERUPT_REGION
IDetector_const_sptr det;
try {
det = reducedEventWS->getDetector(i);
} catch (Exception::NotFoundError&) {
g_log.warning() << "Spectrum index " << i << " has no detector assigned to it - discarding" << std::endl;
// Catch if no detector. Next line tests whether this happened - test placed
// outside here because Mac Intel compiler doesn't like 'continue' in a catch
// in an openmp block.
}
// If no detector found or if it's masked or a monitor, skip onto the next spectrum
if ( !det || det->isMonitor() || det->isMasked() ) continue;
// Get the flight path from the sample to the detector pixel
const V3D scattered_flight_path = det->getPos() - samplePos;
// Multiplicative factor to go from lambda to Q
// Don't get fooled by the function name...
const double theta = reducedEventWS->detectorTwoTheta(det);
const double factor = 4.0 * M_PI * sin( theta/2.0 );
EventList& el = reducedEventWS->getEventList(i);
el.switchTo(WEIGHTED);
std::vector<WeightedEvent>::iterator itev;
std::vector<WeightedEvent>::iterator itev_end = el.getWeightedEvents().end();
for (itev = el.getWeightedEvents().begin(); itev != itev_end; ++itev)
{
if ( itev->m_weight != itev->m_weight ) continue;
if (std::abs(itev->m_weight) == std::numeric_limits<double>::infinity()) continue;
if ( !isEmpty(min_wl) && itev->m_tof < min_wl ) continue;
if ( !isEmpty(max_wl) && itev->m_tof > max_wl ) continue;
const double q = factor/itev->m_tof;
int iq = 0;
// Bin assignment depends on whether we have log or linear bins
if(binParams[1]>0.0)
{
iq = (int)floor( (q-binParams[0])/ binParams[1] );
} else {
iq = (int)floor(log(q/binParams[0])/log(1.0-binParams[1]));
}
const double L2 = scattered_flight_path.norm();
const double src_to_pixel = L1+L2;
const double dTheta2 = ( 3.0*R1*R1/(L1*L1) + 3.0*R2*R2*src_to_pixel*src_to_pixel/(L1*L1*L2*L2)
+ 2.0*(pixel_size_x*pixel_size_x+pixel_size_y*pixel_size_y)/(L2*L2) )/12.0;
const double dwl_over_wl = 3.9560*getTOFResolution(itev->m_tof)/(1000.0*(L1+L2)*itev->m_tof);
const double dq_over_q = std::sqrt(dTheta2/(theta*theta)+dwl_over_wl*dwl_over_wl);
PARALLEL_CRITICAL(iq) /* Write to shared memory - must protect */
if (iq>=0 && iq < xLength-1 && !dq_over_q!=dq_over_q && dq_over_q>0)
{
DxOut[iq] += q*dq_over_q*itev->m_weight;
XNorm[iq] += itev->m_weight;
TOFY[iq] += q*std::fabs(dwl_over_wl)*itev->m_weight;
ThetaY[iq] += q*std::sqrt(dTheta2)/theta*itev->m_weight;
}
}
progress.report("Computing Q resolution");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Normalize according to the chosen weighting scheme
for ( int i = 0; i<xLength-1; i++ )
{
if (XNorm[i]>0)
{
DxOut[i] /= XNorm[i];
TOFY[i] /= XNorm[i];
ThetaY[i] /= XNorm[i];
}
}
}
/**
* Execute the align detectors algorithm for an event workspace.
*/
void AlignDetectors::execEvent() {
// g_log.information("Processing event workspace");
// the calibration information is already read in at this point
// convert the input workspace into the event workspace we already know it is
const MatrixWorkspace_const_sptr matrixInputWS =
this->getProperty("InputWorkspace");
EventWorkspace_const_sptr inputWS =
boost::dynamic_pointer_cast<const EventWorkspace>(matrixInputWS);
// generate the output workspace pointer
API::MatrixWorkspace_sptr matrixOutputWS =
this->getProperty("OutputWorkspace");
EventWorkspace_sptr outputWS;
if (matrixOutputWS == matrixInputWS)
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(matrixOutputWS);
else {
// Make a brand new EventWorkspace
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create(
"EventWorkspace", inputWS->getNumberHistograms(), 2, 1));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS,
false);
// You need to copy over the data as well.
outputWS->copyDataFrom((*inputWS));
// Cast to the matrixOutputWS and save it
matrixOutputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(outputWS);
this->setProperty("OutputWorkspace", matrixOutputWS);
}
// Set the final unit that our output workspace will have
setXAxisUnits(outputWS);
ConversionFactors converter = ConversionFactors(m_calibrationWS);
Progress progress(this, 0.0, 1.0, m_numberOfSpectra);
PARALLEL_FOR_NO_WSP_CHECK()
for (int64_t i = 0; i < m_numberOfSpectra; ++i) {
PARALLEL_START_INTERUPT_REGION
auto toDspacing = converter.getConversionFunc(
inputWS->getSpectrum(size_t(i))->getDetectorIDs());
outputWS->getEventList(i).convertTof(toDspacing);
progress.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
if (outputWS->getTofMin() < 0.) {
std::stringstream msg;
msg << "Something wrong with the calibration. Negative minimum d-spacing "
"created. d_min = " << outputWS->getTofMin() << " d_max "
<< outputWS->getTofMax();
g_log.warning(msg.str());
}
outputWS->clearMRU();
}
void GroupDetectors2::execEvent()
{
// Get the input workspace
const MatrixWorkspace_const_sptr matrixInputWS = getProperty("InputWorkspace");
EventWorkspace_const_sptr inputWS= boost::dynamic_pointer_cast<const EventWorkspace>(matrixInputWS);
const size_t numInHists = inputWS->getNumberHistograms();
progress( m_FracCompl = CHECKBINS );
interruption_point();
// some values loaded into this vector can be negative so this needs to be a signed type
std::vector<int64_t> unGroupedInds;
//the ungrouped list could be very big but might be none at all
unGroupedInds.reserve(numInHists);
for( size_t i = 0; i < numInHists ; i++ )
{
unGroupedInds.push_back(i);
}
// read in the input parameters to make that map, if KeepUngroupedSpectra was set we'll need a list of the ungrouped spectrra too
getGroups(inputWS, unGroupedInds);
// converting the list into a set gets rid of repeated values, here the multiple GroupDetectors2::USED become one USED at the start
const std::set<int64_t> unGroupedSet(unGroupedInds.begin(), unGroupedInds.end());
// Check what the user asked to be done with ungrouped spectra
const bool keepAll = getProperty("KeepUngroupedSpectra");
// ignore the one USED value in set or ignore all the ungrouped if the user doesn't want them
const size_t numUnGrouped = keepAll ? unGroupedSet.size()-1 : 0;
//Make a brand new EventWorkspace
EventWorkspace_sptr outputWS = boost::dynamic_pointer_cast<EventWorkspace>(
WorkspaceFactory::Instance().create("EventWorkspace", m_GroupSpecInds.size()+ numUnGrouped,
inputWS->readX(0).size(), inputWS->blocksize()));
//Copy geometry over.
WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS, true);
// prepare to move the requested histograms into groups, first estimate how long for progress reporting. +1 in the demonator gets rid of any divide by zero risk
double prog4Copy=( (1.0 - m_FracCompl)/(static_cast<double>(numInHists-unGroupedSet.size())+1.) )*
(keepAll ? static_cast<double>(numInHists-unGroupedSet.size())/static_cast<double>(numInHists): 1.);
// Build a new map
const size_t outIndex = formGroupsEvent(inputWS, outputWS, prog4Copy);
// If we're keeping ungrouped spectra
if (keepAll)
{
// copy them into the output workspace
moveOthersEvent(unGroupedSet, inputWS, outputWS, outIndex);
}
//Set all X bins on the output
cow_ptr<MantidVec> XValues;
XValues.access() = inputWS->readX(0);
outputWS->setAllX(XValues);
g_log.information() << name() << " algorithm has finished\n";
setProperty("OutputWorkspace",outputWS);
}
/** Execute the algorithm.
*/
void IntegrateEllipsoids::exec() {
// get the input workspace
MatrixWorkspace_sptr wksp = getProperty("InputWorkspace");
EventWorkspace_sptr eventWS =
boost::dynamic_pointer_cast<EventWorkspace>(wksp);
Workspace2D_sptr histoWS = boost::dynamic_pointer_cast<Workspace2D>(wksp);
if (!eventWS && !histoWS) {
throw std::runtime_error("IntegrateEllipsoids needs either a "
"EventWorkspace or Workspace2D as input.");
}
// error out if there are not events
if (eventWS && eventWS->getNumberEvents() <= 0) {
throw std::runtime_error(
"IntegrateEllipsoids does not work for empty event lists");
}
PeaksWorkspace_sptr in_peak_ws = getProperty("PeaksWorkspace");
if (!in_peak_ws) {
throw std::runtime_error("Could not read the peaks workspace");
}
double radius = getProperty("RegionRadius");
int numSigmas = getProperty("NumSigmas");
double cutoffIsigI = getProperty("CutoffIsigI");
bool specify_size = getProperty("SpecifySize");
double peak_radius = getProperty("PeakSize");
double back_inner_radius = getProperty("BackgroundInnerSize");
double back_outer_radius = getProperty("BackgroundOuterSize");
bool hkl_integ = getProperty("IntegrateInHKL");
bool integrateEdge = getProperty("IntegrateIfOnEdge");
if (!integrateEdge) {
// This only fails in the unit tests which say that MaskBTP is not
// registered
try {
runMaskDetectors(in_peak_ws, "Tube", "edges");
runMaskDetectors(in_peak_ws, "Pixel", "edges");
} catch (...) {
g_log.error("Can't execute MaskBTP algorithm for this instrument to set "
"edge for IntegrateIfOnEdge option");
}
calculateE1(in_peak_ws->detectorInfo()); // fill E1Vec for use in detectorQ
}
Mantid::DataObjects::PeaksWorkspace_sptr peak_ws =
getProperty("OutputWorkspace");
if (peak_ws != in_peak_ws) {
peak_ws = in_peak_ws->clone();
}
// get UBinv and the list of
// peak Q's for the integrator
std::vector<Peak> &peaks = peak_ws->getPeaks();
size_t n_peaks = peak_ws->getNumberPeaks();
size_t indexed_count = 0;
std::vector<V3D> peak_q_list;
std::vector<std::pair<double, V3D>> qList;
std::vector<V3D> hkl_vectors;
for (size_t i = 0; i < n_peaks; i++) // Note: we skip un-indexed peaks
{
V3D hkl(peaks[i].getH(), peaks[i].getK(), peaks[i].getL());
if (Geometry::IndexingUtils::ValidIndex(hkl, 1.0)) // use tolerance == 1 to
// just check for (0,0,0)
{
peak_q_list.emplace_back(peaks[i].getQLabFrame());
qList.emplace_back(1., V3D(peaks[i].getQLabFrame()));
V3D miller_ind(static_cast<double>(boost::math::iround<double>(hkl[0])),
static_cast<double>(boost::math::iround<double>(hkl[1])),
static_cast<double>(boost::math::iround<double>(hkl[2])));
hkl_vectors.push_back(miller_ind);
indexed_count++;
}
}
if (indexed_count < 3) {
throw std::runtime_error(
"At least three linearly independent indexed peaks are needed.");
}
// Get UB using indexed peaks and
// lab-Q vectors
Matrix<double> UB(3, 3, false);
Geometry::IndexingUtils::Optimize_UB(UB, hkl_vectors, peak_q_list);
Matrix<double> UBinv(UB);
UBinv.Invert();
UBinv *= (1.0 / (2.0 * M_PI));
std::vector<double> PeakRadiusVector(n_peaks, peak_radius);
std::vector<double> BackgroundInnerRadiusVector(n_peaks, back_inner_radius);
std::vector<double> BackgroundOuterRadiusVector(n_peaks, back_outer_radius);
if (specify_size) {
if (back_outer_radius > radius)
throw std::runtime_error(
"BackgroundOuterSize must be less than or equal to the RegionRadius");
if (back_inner_radius >= back_outer_radius)
throw std::runtime_error(
"BackgroundInnerSize must be less BackgroundOuterSize");
if (peak_radius > back_inner_radius)
throw std::runtime_error(
"PeakSize must be less than or equal to the BackgroundInnerSize");
}
// make the integrator
Integrate3DEvents integrator(qList, UBinv, radius);
// get the events and add
// them to the inegrator
// set up a descripter of where we are going
this->initTargetWSDescr(wksp);
// set up the progress bar
const size_t numSpectra = wksp->getNumberHistograms();
Progress prog(this, 0.5, 1.0, numSpectra);
if (eventWS) {
// process as EventWorkspace
qListFromEventWS(integrator, prog, eventWS, UBinv, hkl_integ);
} else {
// process as Workspace2D
qListFromHistoWS(integrator, prog, histoWS, UBinv, hkl_integ);
}
double inti;
double sigi;
std::vector<double> principalaxis1, principalaxis2, principalaxis3;
V3D peak_q;
for (size_t i = 0; i < n_peaks; i++) {
V3D hkl(peaks[i].getH(), peaks[i].getK(), peaks[i].getL());
if (Geometry::IndexingUtils::ValidIndex(hkl, 1.0)) {
peak_q = peaks[i].getQLabFrame();
std::vector<double> axes_radii;
Mantid::Geometry::PeakShape_const_sptr shape =
integrator.ellipseIntegrateEvents(
E1Vec, peak_q, specify_size, peak_radius, back_inner_radius,
back_outer_radius, axes_radii, inti, sigi);
peaks[i].setIntensity(inti);
peaks[i].setSigmaIntensity(sigi);
peaks[i].setPeakShape(shape);
if (axes_radii.size() == 3) {
if (inti / sigi > cutoffIsigI || cutoffIsigI == EMPTY_DBL()) {
principalaxis1.push_back(axes_radii[0]);
principalaxis2.push_back(axes_radii[1]);
principalaxis3.push_back(axes_radii[2]);
}
}
} else {
peaks[i].setIntensity(0.0);
peaks[i].setSigmaIntensity(0.0);
}
}
if (principalaxis1.size() > 1) {
size_t histogramNumber = 3;
Workspace_sptr wsProfile = WorkspaceFactory::Instance().create(
"Workspace2D", histogramNumber, principalaxis1.size(),
principalaxis1.size());
Workspace2D_sptr wsProfile2D =
boost::dynamic_pointer_cast<Workspace2D>(wsProfile);
AnalysisDataService::Instance().addOrReplace("EllipsoidAxes", wsProfile2D);
for (size_t j = 0; j < principalaxis1.size(); j++) {
wsProfile2D->dataX(0)[j] = static_cast<double>(j);
wsProfile2D->dataY(0)[j] = principalaxis1[j];
wsProfile2D->dataE(0)[j] = std::sqrt(principalaxis1[j]);
wsProfile2D->dataX(1)[j] = static_cast<double>(j);
wsProfile2D->dataY(1)[j] = principalaxis2[j];
wsProfile2D->dataE(1)[j] = std::sqrt(principalaxis2[j]);
wsProfile2D->dataX(2)[j] = static_cast<double>(j);
wsProfile2D->dataY(2)[j] = principalaxis3[j];
wsProfile2D->dataE(2)[j] = std::sqrt(principalaxis3[j]);
}
Statistics stats1 = getStatistics(principalaxis1);
g_log.notice() << "principalaxis1: "
<< " mean " << stats1.mean << " standard_deviation "
<< stats1.standard_deviation << " minimum " << stats1.minimum
<< " maximum " << stats1.maximum << " median "
<< stats1.median << "\n";
Statistics stats2 = getStatistics(principalaxis2);
g_log.notice() << "principalaxis2: "
<< " mean " << stats2.mean << " standard_deviation "
<< stats2.standard_deviation << " minimum " << stats2.minimum
<< " maximum " << stats2.maximum << " median "
<< stats2.median << "\n";
Statistics stats3 = getStatistics(principalaxis3);
g_log.notice() << "principalaxis3: "
<< " mean " << stats3.mean << " standard_deviation "
<< stats3.standard_deviation << " minimum " << stats3.minimum
<< " maximum " << stats3.maximum << " median "
<< stats3.median << "\n";
if (cutoffIsigI != EMPTY_DBL()) {
principalaxis1.clear();
principalaxis2.clear();
principalaxis3.clear();
specify_size = true;
peak_radius = std::max(std::max(stats1.mean, stats2.mean), stats3.mean) +
numSigmas * std::max(std::max(stats1.standard_deviation,
stats2.standard_deviation),
stats3.standard_deviation);
back_inner_radius = peak_radius;
back_outer_radius =
peak_radius *
1.25992105; // A factor of 2 ^ (1/3) will make the background
// shell volume equal to the peak region volume.
V3D peak_q;
for (size_t i = 0; i < n_peaks; i++) {
V3D hkl(peaks[i].getH(), peaks[i].getK(), peaks[i].getL());
if (Geometry::IndexingUtils::ValidIndex(hkl, 1.0)) {
peak_q = peaks[i].getQLabFrame();
std::vector<double> axes_radii;
integrator.ellipseIntegrateEvents(
E1Vec, peak_q, specify_size, peak_radius, back_inner_radius,
back_outer_radius, axes_radii, inti, sigi);
peaks[i].setIntensity(inti);
peaks[i].setSigmaIntensity(sigi);
if (axes_radii.size() == 3) {
principalaxis1.push_back(axes_radii[0]);
principalaxis2.push_back(axes_radii[1]);
principalaxis3.push_back(axes_radii[2]);
}
} else {
peaks[i].setIntensity(0.0);
peaks[i].setSigmaIntensity(0.0);
}
}
if (principalaxis1.size() > 1) {
size_t histogramNumber = 3;
Workspace_sptr wsProfile2 = WorkspaceFactory::Instance().create(
"Workspace2D", histogramNumber, principalaxis1.size(),
principalaxis1.size());
Workspace2D_sptr wsProfile2D2 =
boost::dynamic_pointer_cast<Workspace2D>(wsProfile2);
AnalysisDataService::Instance().addOrReplace("EllipsoidAxes_2ndPass",
wsProfile2D2);
for (size_t j = 0; j < principalaxis1.size(); j++) {
wsProfile2D2->dataX(0)[j] = static_cast<double>(j);
wsProfile2D2->dataY(0)[j] = principalaxis1[j];
wsProfile2D2->dataE(0)[j] = std::sqrt(principalaxis1[j]);
wsProfile2D2->dataX(1)[j] = static_cast<double>(j);
wsProfile2D2->dataY(1)[j] = principalaxis2[j];
wsProfile2D2->dataE(1)[j] = std::sqrt(principalaxis2[j]);
wsProfile2D2->dataX(2)[j] = static_cast<double>(j);
wsProfile2D2->dataY(2)[j] = principalaxis3[j];
wsProfile2D2->dataE(2)[j] = std::sqrt(principalaxis3[j]);
}
}
}
}
// This flag is used by the PeaksWorkspace to evaluate whether it has been
// integrated.
peak_ws->mutableRun().addProperty("PeaksIntegrated", 1, true);
// These flags are specific to the algorithm.
peak_ws->mutableRun().addProperty("PeakRadius", PeakRadiusVector, true);
peak_ws->mutableRun().addProperty("BackgroundInnerRadius",
BackgroundInnerRadiusVector, true);
peak_ws->mutableRun().addProperty("BackgroundOuterRadius",
BackgroundOuterRadiusVector, true);
setProperty("OutputWorkspace", peak_ws);
}
/** Execute the algorithm.
*/
void LoadLiveData::exec() {
// The full, post-processed output workspace
m_outputWS = this->getProperty("OutputWorkspace");
// Validate inputs
if (this->hasPostProcessing()) {
if (this->getPropertyValue("AccumulationWorkspace").empty())
throw std::invalid_argument("Must specify the AccumulationWorkspace "
"parameter if using PostProcessing.");
// The accumulated but not post-processed output workspace
m_accumWS = this->getProperty("AccumulationWorkspace");
} else {
// No post-processing, so the accumulation and output are the same
m_accumWS = m_outputWS;
}
// Get or create the live listener
ILiveListener_sptr listener = this->getLiveListener();
// Do we need to reset the data?
bool dataReset = listener->dataReset();
// The listener returns a MatrixWorkspace containing the chunk of live data.
Workspace_sptr chunkWS;
bool dataNotYetGiven = true;
while (dataNotYetGiven) {
try {
chunkWS = listener->extractData();
dataNotYetGiven = false;
} catch (Exception::NotYet &ex) {
g_log.warning() << "The " << listener->name()
<< " is not ready to return data: " << ex.what() << "\n";
g_log.warning()
<< "Trying again in 10 seconds - cancel the algorithm to stop.\n";
const int tenSeconds = 40;
for (int i = 0; i < tenSeconds; ++i) {
Poco::Thread::sleep(10000 / tenSeconds); // 250 ms
this->interruption_point();
}
}
}
// TODO: Have the ILiveListener tell me exactly the time stamp
DateAndTime lastTimeStamp = DateAndTime::getCurrentTime();
this->setPropertyValue("LastTimeStamp", lastTimeStamp.toISO8601String());
// Now we process the chunk
Workspace_sptr processed = this->processChunk(chunkWS);
bool PreserveEvents = this->getProperty("PreserveEvents");
EventWorkspace_sptr processedEvent =
boost::dynamic_pointer_cast<EventWorkspace>(processed);
if (!PreserveEvents && processedEvent) {
// Convert the monitor workspace, if there is one and it's necessary
MatrixWorkspace_sptr monitorWS = processedEvent->monitorWorkspace();
auto monitorEventWS =
boost::dynamic_pointer_cast<EventWorkspace>(monitorWS);
if (monitorEventWS) {
auto monAlg = this->createChildAlgorithm("ConvertToMatrixWorkspace");
monAlg->setProperty("InputWorkspace", monitorEventWS);
monAlg->executeAsChildAlg();
if (!monAlg->isExecuted())
g_log.error(
"Failed to convert monitors from events to histogram form.");
monitorWS = monAlg->getProperty("OutputWorkspace");
}
// Now do the main workspace
Algorithm_sptr alg = this->createChildAlgorithm("ConvertToMatrixWorkspace");
alg->setProperty("InputWorkspace", processedEvent);
std::string outputName = "__anonymous_livedata_convert_" +
this->getPropertyValue("OutputWorkspace");
alg->setPropertyValue("OutputWorkspace", outputName);
alg->execute();
if (!alg->isExecuted())
throw std::runtime_error("Error when calling ConvertToMatrixWorkspace "
"(since PreserveEvents=False). See log.");
// Replace the "processed" workspace with the converted one.
MatrixWorkspace_sptr temp = alg->getProperty("OutputWorkspace");
if (monitorWS)
temp->setMonitorWorkspace(monitorWS); // Set back the monitor workspace
processed = temp;
}
// How do we accumulate the data?
std::string accum = this->getPropertyValue("AccumulationMethod");
// If the AccumulationWorkspace does not exist, we always replace the
// AccumulationWorkspace.
// Also, if the listener said we are resetting the data, then we clear out the
// old.
if (!m_accumWS || dataReset)
accum = "Replace";
g_log.notice() << "Performing the " << accum << " operation.\n";
// Perform the accumulation and set the AccumulationWorkspace workspace
if (accum == "Replace")
this->replaceChunk(processed);
else if (accum == "Append")
this->appendChunk(processed);
else
// Default to Add.
this->addChunk(processed);
// At this point, m_accumWS is set.
if (this->hasPostProcessing()) {
// ----------- Run post-processing -------------
this->runPostProcessing();
// Set both output workspaces
this->setProperty("AccumulationWorkspace", m_accumWS);
this->setProperty("OutputWorkspace", m_outputWS);
doSortEvents(m_outputWS);
} else {
// ----------- No post-processing -------------
m_outputWS = m_accumWS;
// We DO NOT set AccumulationWorkspace.
this->setProperty("OutputWorkspace", m_outputWS);
}
// Output group requires some additional handling
WorkspaceGroup_sptr out_gws =
boost::dynamic_pointer_cast<WorkspaceGroup>(m_outputWS);
if (out_gws) {
size_t n = static_cast<size_t>(out_gws->getNumberOfEntries());
for (size_t i = 0; i < n; ++i) {
auto ws = out_gws->getItem(i);
std::string itemName = ws->name();
std::string wsName =
getPropertyValue("OutputWorkspace") + "_" + std::to_string(i + 1);
if (wsName != itemName) {
if (AnalysisDataService::Instance().doesExist(itemName)) {
// replace the temporary name with the proper one
AnalysisDataService::Instance().rename(itemName, wsName);
}
} else {
// touch the workspace in the ADS to issue a notification to update the
// GUI
AnalysisDataService::Instance().addOrReplace(itemName, ws);
}
}
}
}
/** Executes the algorithm
*
* @throw runtime_error Thrown if algorithm cannot execute
*/
void DiffractionEventCalibrateDetectors::exec() {
// Try to retrieve optional properties
const int maxIterations = getProperty("MaxIterations");
const double peakOpt = getProperty("LocationOfPeakToOptimize");
// Get the input workspace
EventWorkspace_sptr inputW = getProperty("InputWorkspace");
// retrieve the properties
const std::string rb_params = getProperty("Params");
// Get some stuff from the input workspace
Instrument_const_sptr inst = inputW->getInstrument();
// Build a list of Rectangular Detectors
std::vector<boost::shared_ptr<RectangularDetector>> detList;
// --------- Loading only one bank ----------------------------------
std::string onebank = getProperty("BankName");
bool doOneBank = (onebank != "");
for (int i = 0; i < inst->nelements(); i++) {
boost::shared_ptr<RectangularDetector> det;
boost::shared_ptr<ICompAssembly> assem;
boost::shared_ptr<ICompAssembly> assem2;
det = boost::dynamic_pointer_cast<RectangularDetector>((*inst)[i]);
if (det) {
if (det->getName().compare(onebank) == 0)
detList.push_back(det);
if (!doOneBank)
detList.push_back(det);
} else {
// Also, look in the first sub-level for RectangularDetectors (e.g. PG3).
// We are not doing a full recursive search since that will be very long
// for lots of pixels.
assem = boost::dynamic_pointer_cast<ICompAssembly>((*inst)[i]);
if (assem) {
for (int j = 0; j < assem->nelements(); j++) {
det = boost::dynamic_pointer_cast<RectangularDetector>((*assem)[j]);
if (det) {
if (det->getName().compare(onebank) == 0)
detList.push_back(det);
if (!doOneBank)
detList.push_back(det);
} else {
// Also, look in the second sub-level for RectangularDetectors (e.g.
// PG3).
// We are not doing a full recursive search since that will be very
// long for lots of pixels.
assem2 = boost::dynamic_pointer_cast<ICompAssembly>((*assem)[j]);
if (assem2) {
for (int k = 0; k < assem2->nelements(); k++) {
det = boost::dynamic_pointer_cast<RectangularDetector>(
(*assem2)[k]);
if (det) {
if (det->getName().compare(onebank) == 0)
detList.push_back(det);
if (!doOneBank)
detList.push_back(det);
}
}
}
}
}
}
}
}
// set-up minimizer
std::string inname = getProperty("InputWorkspace");
std::string outname = inname + "2"; // getProperty("OutputWorkspace");
IAlgorithm_sptr algS = createChildAlgorithm("SortEvents");
algS->setProperty("InputWorkspace", inputW);
algS->setPropertyValue("SortBy", "X Value");
algS->executeAsChildAlg();
// Write DetCal File
std::string filename = getProperty("DetCalFilename");
std::fstream outfile;
outfile.open(filename.c_str(), std::ios::out);
if (detList.size() > 1) {
outfile << "#\n";
outfile << "# Mantid Optimized .DetCal file for SNAP with TWO detector "
"panels\n";
outfile << "# Old Panel, nominal size and distance at -90 degrees.\n";
outfile << "# New Panel, nominal size and distance at +90 degrees.\n";
outfile << "#\n";
outfile << "# Lengths are in centimeters.\n";
outfile << "# Base and up give directions of unit vectors for a local\n";
outfile << "# x,y coordinate system on the face of the detector.\n";
outfile << "#\n";
outfile << "# " << DateAndTime::getCurrentTime().toFormattedString("%c")
<< "\n";
outfile << "#\n";
outfile << "6 L1 T0_SHIFT\n";
IComponent_const_sptr source = inst->getSource();
IComponent_const_sptr sample = inst->getSample();
outfile << "7 " << source->getDistance(*sample) * 100 << " 0\n";
outfile << "4 DETNUM NROWS NCOLS WIDTH HEIGHT DEPTH DETD "
"CenterX CenterY CenterZ BaseX BaseY BaseZ "
"UpX UpY UpZ\n";
}
Progress prog(this, 0.0, 1.0, detList.size());
for (int det = 0; det < static_cast<int>(detList.size()); det++) {
std::string par[6];
par[0] = detList[det]->getName();
par[1] = inname;
par[2] = outname;
std::ostringstream strpeakOpt;
strpeakOpt << peakOpt;
par[3] = strpeakOpt.str();
par[4] = rb_params;
// --- Create a GroupingWorkspace for this detector name ------
CPUTimer tim;
IAlgorithm_sptr alg2 =
AlgorithmFactory::Instance().create("CreateGroupingWorkspace", 1);
alg2->initialize();
alg2->setProperty("InputWorkspace", inputW);
alg2->setPropertyValue("GroupNames", detList[det]->getName());
std::string groupWSName = "group_" + detList[det]->getName();
alg2->setPropertyValue("OutputWorkspace", groupWSName);
alg2->executeAsChildAlg();
par[5] = groupWSName;
std::cout << tim << " to CreateGroupingWorkspace\n";
const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex;
gsl_multimin_fminimizer *s = nullptr;
gsl_vector *ss, *x;
gsl_multimin_function minex_func;
// finally do the fitting
int nopt = 6;
int iter = 0;
int status = 0;
/* Starting point */
x = gsl_vector_alloc(nopt);
gsl_vector_set(x, 0, 0.0);
gsl_vector_set(x, 1, 0.0);
gsl_vector_set(x, 2, 0.0);
gsl_vector_set(x, 3, 0.0);
gsl_vector_set(x, 4, 0.0);
gsl_vector_set(x, 5, 0.0);
/* Set initial step sizes to 0.1 */
ss = gsl_vector_alloc(nopt);
gsl_vector_set_all(ss, 0.1);
/* Initialize method and iterate */
minex_func.n = nopt;
minex_func.f = &Mantid::Algorithms::gsl_costFunction;
minex_func.params = ∥
s = gsl_multimin_fminimizer_alloc(T, nopt);
gsl_multimin_fminimizer_set(s, &minex_func, x, ss);
do {
iter++;
status = gsl_multimin_fminimizer_iterate(s);
if (status)
break;
double size = gsl_multimin_fminimizer_size(s);
status = gsl_multimin_test_size(size, 1e-2);
} while (status == GSL_CONTINUE && iter < maxIterations &&
s->fval != -0.000);
// Output summary to log file
if (s->fval != -0.000)
movedetector(gsl_vector_get(s->x, 0), gsl_vector_get(s->x, 1),
gsl_vector_get(s->x, 2), gsl_vector_get(s->x, 3),
gsl_vector_get(s->x, 4), gsl_vector_get(s->x, 5), par[0],
getProperty("InputWorkspace"));
else {
gsl_vector_set(s->x, 0, 0.0);
gsl_vector_set(s->x, 1, 0.0);
gsl_vector_set(s->x, 2, 0.0);
gsl_vector_set(s->x, 3, 0.0);
gsl_vector_set(s->x, 4, 0.0);
gsl_vector_set(s->x, 5, 0.0);
}
std::string reportOfDiffractionEventCalibrateDetectors =
gsl_strerror(status);
if (s->fval == -0.000)
reportOfDiffractionEventCalibrateDetectors = "No events";
g_log.information() << "Detector = " << det << "\n"
<< "Method used = "
<< "Simplex"
<< "\n"
<< "Iteration = " << iter << "\n"
<< "Status = "
<< reportOfDiffractionEventCalibrateDetectors << "\n"
<< "Minimize PeakLoc-" << peakOpt << " = " << s->fval
<< "\n";
// Move in cm for small shifts
g_log.information() << "Move (X) = " << gsl_vector_get(s->x, 0) * 0.01
<< " \n";
g_log.information() << "Move (Y) = " << gsl_vector_get(s->x, 1) * 0.01
<< " \n";
g_log.information() << "Move (Z) = " << gsl_vector_get(s->x, 2) * 0.01
<< " \n";
g_log.information() << "Rotate (X) = " << gsl_vector_get(s->x, 3) << " \n";
g_log.information() << "Rotate (Y) = " << gsl_vector_get(s->x, 4) << " \n";
g_log.information() << "Rotate (Z) = " << gsl_vector_get(s->x, 5) << " \n";
Kernel::V3D CalCenter =
V3D(gsl_vector_get(s->x, 0) * 0.01, gsl_vector_get(s->x, 1) * 0.01,
gsl_vector_get(s->x, 2) * 0.01);
Kernel::V3D Center = detList[det]->getPos() + CalCenter;
int pixmax = detList[det]->xpixels() - 1;
int pixmid = (detList[det]->ypixels() - 1) / 2;
BoundingBox box;
detList[det]->getAtXY(pixmax, pixmid)->getBoundingBox(box);
double baseX = box.xMax();
double baseY = box.yMax();
double baseZ = box.zMax();
Kernel::V3D Base = V3D(baseX, baseY, baseZ) + CalCenter;
pixmid = (detList[det]->xpixels() - 1) / 2;
pixmax = detList[det]->ypixels() - 1;
detList[det]->getAtXY(pixmid, pixmax)->getBoundingBox(box);
double upX = box.xMax();
double upY = box.yMax();
double upZ = box.zMax();
Kernel::V3D Up = V3D(upX, upY, upZ) + CalCenter;
Base -= Center;
Up -= Center;
// Rotate around x
baseX = Base[0];
baseY = Base[1];
baseZ = Base[2];
double deg2rad = M_PI / 180.0;
double angle = gsl_vector_get(s->x, 3) * deg2rad;
Base = V3D(baseX, baseY * cos(angle) - baseZ * sin(angle),
baseY * sin(angle) + baseZ * cos(angle));
upX = Up[0];
upY = Up[1];
upZ = Up[2];
Up = V3D(upX, upY * cos(angle) - upZ * sin(angle),
upY * sin(angle) + upZ * cos(angle));
// Rotate around y
baseX = Base[0];
baseY = Base[1];
baseZ = Base[2];
angle = gsl_vector_get(s->x, 4) * deg2rad;
Base = V3D(baseZ * sin(angle) + baseX * cos(angle), baseY,
baseZ * cos(angle) - baseX * sin(angle));
upX = Up[0];
upY = Up[1];
upZ = Up[2];
Up = V3D(upZ * cos(angle) - upX * sin(angle), upY,
upZ * sin(angle) + upX * cos(angle));
// Rotate around z
baseX = Base[0];
baseY = Base[1];
baseZ = Base[2];
angle = gsl_vector_get(s->x, 5) * deg2rad;
Base = V3D(baseX * cos(angle) - baseY * sin(angle),
baseX * sin(angle) + baseY * cos(angle), baseZ);
upX = Up[0];
upY = Up[1];
upZ = Up[2];
Up = V3D(upX * cos(angle) - upY * sin(angle),
upX * sin(angle) + upY * cos(angle), upZ);
Base.normalize();
Up.normalize();
Center *= 100.0;
// << det+1 << " "
outfile << "5 " << detList[det]->getName().substr(4) << " "
<< detList[det]->xpixels() << " " << detList[det]->ypixels()
<< " " << 100.0 * detList[det]->xsize() << " "
<< 100.0 * detList[det]->ysize() << " "
<< "0.2000"
<< " " << Center.norm() << " ";
Center.write(outfile);
outfile << " ";
Base.write(outfile);
outfile << " ";
Up.write(outfile);
outfile << "\n";
// clean up dynamically allocated gsl stuff
gsl_vector_free(x);
gsl_vector_free(ss);
gsl_multimin_fminimizer_free(s);
// Remove the now-unneeded grouping workspace
AnalysisDataService::Instance().remove(groupWSName);
prog.report(detList[det]->getName());
}
// Closing
outfile.close();
}
/** Executes the algorithm
* @throw Exception::FileError If the grouping file cannot be opened or read
* successfully
* @throw runtime_error If unable to run one of the Child Algorithms
* successfully
*/
void AlignAndFocusPowder::exec() {
// retrieve the properties
m_inputW = getProperty("InputWorkspace");
m_inputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_inputW);
m_instName = m_inputW->getInstrument()->getName();
m_instName =
Kernel::ConfigService::Instance().getInstrument(m_instName).shortName();
std::string calFilename = getPropertyValue("CalFileName");
std::string groupFilename = getPropertyValue("GroupFilename");
m_calibrationWS = getProperty("CalibrationWorkspace");
m_maskWS = getProperty("MaskWorkspace");
m_groupWS = getProperty("GroupingWorkspace");
DataObjects::TableWorkspace_sptr maskBinTableWS = getProperty("MaskBinTable");
m_l1 = getProperty("PrimaryFlightPath");
specids = getProperty("SpectrumIDs");
l2s = getProperty("L2");
tths = getProperty("Polar");
phis = getProperty("Azimuthal");
m_params = getProperty("Params");
dspace = getProperty("DSpacing");
auto dmin = getVecPropertyFromPmOrSelf("DMin", m_dmins);
auto dmax = getVecPropertyFromPmOrSelf("DMax", m_dmaxs);
LRef = getProperty("UnwrapRef");
DIFCref = getProperty("LowResRef");
minwl = getProperty("CropWavelengthMin");
maxwl = getProperty("CropWavelengthMax");
if (maxwl == 0.)
maxwl = EMPTY_DBL(); // python can only specify 0 for unused
tmin = getProperty("TMin");
tmax = getProperty("TMax");
m_preserveEvents = getProperty("PreserveEvents");
m_resampleX = getProperty("ResampleX");
// determine some bits about d-space and binning
if (m_resampleX != 0) {
m_params.clear(); // ignore the normal rebin parameters
} else if (m_params.size() == 1) {
if (dmax > 0.)
dspace = true;
else
dspace = false;
}
if (dspace) {
if (m_params.size() == 1 && dmax > 0) {
double step = m_params[0];
m_params.clear();
if (step > 0 || dmin > 0) {
m_params.push_back(dmin);
m_params.push_back(step);
m_params.push_back(dmax);
g_log.information() << "d-Spacing Binning: " << m_params[0] << " "
<< m_params[1] << " " << m_params[2] << "\n";
}
}
} else {
if (m_params.size() == 1 && tmax > 0) {
double step = m_params[0];
if (step > 0 || tmin > 0) {
m_params[0] = tmin;
m_params.push_back(step);
m_params.push_back(tmax);
g_log.information() << "TOF Binning: " << m_params[0] << " "
<< m_params[1] << " " << m_params[2] << "\n";
}
}
}
xmin = 0.;
xmax = 0.;
if (tmin > 0.) {
xmin = tmin;
}
if (tmax > 0.) {
xmax = tmax;
}
if (!dspace && m_params.size() == 3) {
xmin = m_params[0];
xmax = m_params[2];
}
// Low resolution
int lowresoffset = getProperty("LowResSpectrumOffset");
if (lowresoffset < 0) {
m_processLowResTOF = false;
} else {
m_processLowResTOF = true;
m_lowResSpecOffset = static_cast<size_t>(lowresoffset);
}
loadCalFile(calFilename, groupFilename);
// Now setup the output workspace
m_outputW = getProperty("OutputWorkspace");
if (m_inputEW) {
if (m_outputW != m_inputW) {
m_outputEW = m_inputEW->clone();
}
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
} else {
if (m_outputW != m_inputW) {
m_outputW = WorkspaceFactory::Instance().create(m_inputW);
}
}
if (m_processLowResTOF) {
if (!m_inputEW) {
throw std::runtime_error(
"Input workspace is not EventWorkspace. It is not supported now.");
} else {
// Make a brand new EventWorkspace
m_lowResEW = boost::dynamic_pointer_cast<EventWorkspace>(
WorkspaceFactory::Instance().create(
"EventWorkspace", m_inputEW->getNumberHistograms(), 2, 1));
// Cast to the matrixOutputWS and save it
m_lowResW = boost::dynamic_pointer_cast<MatrixWorkspace>(m_lowResEW);
// m_lowResW->setName(lowreswsname);
}
}
// set up a progress bar with the "correct" number of steps
m_progress = new Progress(this, 0., 1., 22);
if (m_inputEW) {
double tolerance = getProperty("CompressTolerance");
if (tolerance > 0.) {
g_log.information() << "running CompressEvents(Tolerance=" << tolerance
<< ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr compressAlg = createChildAlgorithm("CompressEvents");
compressAlg->setProperty("InputWorkspace", m_outputEW);
compressAlg->setProperty("OutputWorkspace", m_outputEW);
compressAlg->setProperty("OutputWorkspace", m_outputEW);
compressAlg->setProperty("Tolerance", tolerance);
compressAlg->executeAsChildAlg();
m_outputEW = compressAlg->getProperty("OutputWorkspace");
m_outputW = boost::dynamic_pointer_cast<MatrixWorkspace>(m_outputEW);
} else {
g_log.information() << "Not compressing event list\n";
doSortEvents(m_outputW); // still sort to help some thing out
}
}
m_progress->report();
if (xmin > 0. || xmax > 0.) {
double tempmin;
double tempmax;
m_outputW->getXMinMax(tempmin, tempmax);
g_log.information() << "running CropWorkspace(TOFmin=" << xmin
<< ", TOFmax=" << xmax << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr cropAlg = createChildAlgorithm("CropWorkspace");
cropAlg->setProperty("InputWorkspace", m_outputW);
cropAlg->setProperty("OutputWorkspace", m_outputW);
if ((xmin > 0.) && (xmin > tempmin))
cropAlg->setProperty("Xmin", xmin);
if ((xmax > 0.) && (xmax < tempmax))
cropAlg->setProperty("Xmax", xmax);
cropAlg->executeAsChildAlg();
m_outputW = cropAlg->getProperty("OutputWorkspace");
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
}
m_progress->report();
// filter the input events if appropriate
double removePromptPulseWidth = getProperty("RemovePromptPulseWidth");
if (removePromptPulseWidth > 0.) {
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if (m_outputEW->getNumberEvents() > 0) {
g_log.information() << "running RemovePromptPulse(Width="
<< removePromptPulseWidth << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr filterPAlg =
createChildAlgorithm("RemovePromptPulse");
filterPAlg->setProperty("InputWorkspace", m_outputW);
filterPAlg->setProperty("OutputWorkspace", m_outputW);
filterPAlg->setProperty("Width", removePromptPulseWidth);
filterPAlg->executeAsChildAlg();
m_outputW = filterPAlg->getProperty("OutputWorkspace");
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
} else {
g_log.information("skipping RemovePromptPulse on empty EventWorkspace");
}
}
m_progress->report();
if (maskBinTableWS) {
g_log.information() << "running MaskBinsFromTable started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr alg = createChildAlgorithm("MaskBinsFromTable");
alg->setProperty("InputWorkspace", m_outputW);
alg->setProperty("OutputWorkspace", m_outputW);
alg->setProperty("MaskingInformation", maskBinTableWS);
alg->executeAsChildAlg();
m_outputW = alg->getProperty("OutputWorkspace");
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
}
m_progress->report();
if (m_maskWS) {
g_log.information() << "running MaskDetectors started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr maskAlg = createChildAlgorithm("MaskDetectors");
maskAlg->setProperty("Workspace", m_outputW);
maskAlg->setProperty("MaskedWorkspace", m_maskWS);
maskAlg->executeAsChildAlg();
Workspace_sptr tmpW = maskAlg->getProperty("Workspace");
m_outputW = boost::dynamic_pointer_cast<MatrixWorkspace>(tmpW);
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
}
m_progress->report();
if (!dspace)
m_outputW = rebin(m_outputW);
m_progress->report();
if (m_calibrationWS) {
g_log.information() << "running AlignDetectors started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr alignAlg = createChildAlgorithm("AlignDetectors");
alignAlg->setProperty("InputWorkspace", m_outputW);
alignAlg->setProperty("OutputWorkspace", m_outputW);
alignAlg->setProperty("CalibrationWorkspace", m_calibrationWS);
alignAlg->executeAsChildAlg();
m_outputW = alignAlg->getProperty("OutputWorkspace");
} else {
m_outputW = convertUnits(m_outputW, "dSpacing");
}
m_progress->report();
if (LRef > 0. || minwl > 0. || DIFCref > 0. || (!isEmpty(maxwl))) {
m_outputW = convertUnits(m_outputW, "TOF");
}
m_progress->report();
// Beyond this point, low resolution TOF workspace is considered.
if (LRef > 0.) {
g_log.information() << "running UnwrapSNS(LRef=" << LRef << ",Tmin=" << tmin
<< ",Tmax=" << tmax << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr removeAlg = createChildAlgorithm("UnwrapSNS");
removeAlg->setProperty("InputWorkspace", m_outputW);
removeAlg->setProperty("OutputWorkspace", m_outputW);
removeAlg->setProperty("LRef", LRef);
if (tmin > 0.)
removeAlg->setProperty("Tmin", tmin);
if (tmax > tmin)
removeAlg->setProperty("Tmax", tmax);
removeAlg->executeAsChildAlg();
m_outputW = removeAlg->getProperty("OutputWorkspace");
}
m_progress->report();
if (minwl > 0. || (!isEmpty(maxwl))) { // just crop the worksapce
// turn off the low res stuff
m_processLowResTOF = false;
EventWorkspace_sptr ews =
boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if (ews)
g_log.information() << "Number of events = " << ews->getNumberEvents()
<< ". ";
g_log.information("\n");
m_outputW = convertUnits(m_outputW, "Wavelength");
g_log.information() << "running CropWorkspace(WavelengthMin=" << minwl;
if (!isEmpty(maxwl))
g_log.information() << ", WavelengthMax=" << maxwl;
g_log.information() << ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr removeAlg = createChildAlgorithm("CropWorkspace");
removeAlg->setProperty("InputWorkspace", m_outputW);
removeAlg->setProperty("OutputWorkspace", m_outputW);
removeAlg->setProperty("XMin", minwl);
removeAlg->setProperty("XMax", maxwl);
removeAlg->executeAsChildAlg();
m_outputW = removeAlg->getProperty("OutputWorkspace");
if (ews)
g_log.information() << "Number of events = " << ews->getNumberEvents()
<< ".\n";
} else if (DIFCref > 0.) {
g_log.information() << "running RemoveLowResTof(RefDIFC=" << DIFCref
<< ",K=3.22) started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
EventWorkspace_sptr ews =
boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if (ews)
g_log.information() << "Number of events = " << ews->getNumberEvents()
<< ". ";
g_log.information("\n");
API::IAlgorithm_sptr removeAlg = createChildAlgorithm("RemoveLowResTOF");
removeAlg->setProperty("InputWorkspace", m_outputW);
removeAlg->setProperty("OutputWorkspace", m_outputW);
removeAlg->setProperty("ReferenceDIFC", DIFCref);
removeAlg->setProperty("K", 3.22);
if (tmin > 0.)
removeAlg->setProperty("Tmin", tmin);
if (m_processLowResTOF)
removeAlg->setProperty("LowResTOFWorkspace", m_lowResW);
removeAlg->executeAsChildAlg();
m_outputW = removeAlg->getProperty("OutputWorkspace");
if (m_processLowResTOF)
m_lowResW = removeAlg->getProperty("LowResTOFWorkspace");
}
m_progress->report();
EventWorkspace_sptr ews =
boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if (ews) {
size_t numhighevents = ews->getNumberEvents();
if (m_processLowResTOF) {
EventWorkspace_sptr lowes =
boost::dynamic_pointer_cast<EventWorkspace>(m_lowResW);
size_t numlowevents = lowes->getNumberEvents();
g_log.information() << "Number of high TOF events = " << numhighevents
<< "; "
<< "Number of low TOF events = " << numlowevents
<< ".\n";
}
}
m_progress->report();
// Convert units
if (LRef > 0. || minwl > 0. || DIFCref > 0. || (!isEmpty(maxwl))) {
m_outputW = convertUnits(m_outputW, "dSpacing");
if (m_processLowResTOF)
m_lowResW = convertUnits(m_lowResW, "dSpacing");
}
m_progress->report();
if (dspace) {
m_outputW = rebin(m_outputW);
if (m_processLowResTOF)
m_lowResW = rebin(m_lowResW);
}
m_progress->report();
doSortEvents(m_outputW);
if (m_processLowResTOF)
doSortEvents(m_lowResW);
m_progress->report();
// Diffraction focus
m_outputW = diffractionFocus(m_outputW);
if (m_processLowResTOF)
m_lowResW = diffractionFocus(m_lowResW);
m_progress->report();
doSortEvents(m_outputW);
if (m_processLowResTOF)
doSortEvents(m_lowResW);
m_progress->report();
// this next call should probably be in for rebin as well
// but it changes the system tests
if (dspace && m_resampleX != 0) {
m_outputW = rebin(m_outputW);
if (m_processLowResTOF)
m_lowResW = rebin(m_lowResW);
}
m_progress->report();
// edit the instrument geometry
if (m_groupWS &&
(m_l1 > 0 || !tths.empty() || !l2s.empty() || !phis.empty())) {
size_t numreg = m_outputW->getNumberHistograms();
try {
// set up the vectors for doing everything
auto specidsSplit = splitVectors(specids, numreg, "specids");
auto tthsSplit = splitVectors(tths, numreg, "two-theta");
auto l2sSplit = splitVectors(l2s, numreg, "L2");
auto phisSplit = splitVectors(phis, numreg, "phi");
// Edit instrument
m_outputW = editInstrument(m_outputW, tthsSplit.reg, specidsSplit.reg,
l2sSplit.reg, phisSplit.reg);
if (m_processLowResTOF) {
m_lowResW = editInstrument(m_lowResW, tthsSplit.low, specidsSplit.low,
l2sSplit.low, phisSplit.low);
}
} catch (std::runtime_error &e) {
g_log.warning("Not editing instrument geometry:");
g_log.warning(e.what());
}
}
m_progress->report();
// Conjoin 2 workspaces if there is low resolution
if (m_processLowResTOF) {
m_outputW = conjoinWorkspaces(m_outputW, m_lowResW, m_lowResSpecOffset);
}
m_progress->report();
// Convert units to TOF
m_outputW = convertUnits(m_outputW, "TOF");
m_progress->report();
// compress again if appropriate
double tolerance = getProperty("CompressTolerance");
m_outputEW = boost::dynamic_pointer_cast<EventWorkspace>(m_outputW);
if ((m_outputEW) && (tolerance > 0.)) {
g_log.information() << "running CompressEvents(Tolerance=" << tolerance
<< ") started at "
<< Kernel::DateAndTime::getCurrentTime() << "\n";
API::IAlgorithm_sptr compressAlg = createChildAlgorithm("CompressEvents");
compressAlg->setProperty("InputWorkspace", m_outputEW);
compressAlg->setProperty("OutputWorkspace", m_outputEW);
compressAlg->setProperty("OutputWorkspace", m_outputEW);
compressAlg->setProperty("Tolerance", tolerance);
compressAlg->executeAsChildAlg();
m_outputEW = compressAlg->getProperty("OutputWorkspace");
m_outputW = boost::dynamic_pointer_cast<MatrixWorkspace>(m_outputEW);
}
m_progress->report();
if ((!m_params.empty()) && (m_params.size() != 1)) {
m_params.erase(m_params.begin());
m_params.pop_back();
}
if (!m_dmins.empty())
m_dmins.clear();
if (!m_dmaxs.empty())
m_dmaxs.clear();
m_outputW = rebin(m_outputW);
m_progress->report();
// return the output workspace
setProperty("OutputWorkspace", m_outputW);
}
/** Execute the algorithm */
void LoadEventPreNexus::exec() {
// Check 'chunk' properties are valid, if set
const int chunks = getProperty("TotalChunks");
if (!isEmpty(chunks) && int(getProperty("ChunkNumber")) > chunks) {
throw std::out_of_range("ChunkNumber cannot be larger than TotalChunks");
}
prog = new Progress(this, 0.0, 1.0, 100);
// what spectra (pixel ID's) to load
this->spectra_list = this->getProperty(PID_PARAM);
// the event file is needed in case the pulseid fileanme is empty
string event_filename = this->getPropertyValue(EVENT_PARAM);
string pulseid_filename = this->getPropertyValue(PULSEID_PARAM);
bool throwError = true;
if (pulseid_filename.empty()) {
pulseid_filename = generatePulseidName(event_filename);
if (!pulseid_filename.empty()) {
if (Poco::File(pulseid_filename).exists()) {
this->g_log.information() << "Found pulseid file " << pulseid_filename
<< std::endl;
throwError = false;
} else {
pulseid_filename = "";
}
}
}
prog->report("Loading Pulse ID file");
this->readPulseidFile(pulseid_filename, throwError);
this->openEventFile(event_filename);
prog->report("Creating output workspace");
// prep the output workspace
EventWorkspace_sptr localWorkspace =
EventWorkspace_sptr(new EventWorkspace());
// Make sure to initialize.
// We can use dummy numbers for arguments, for event workspace it doesn't
// matter
localWorkspace->initialize(1, 1, 1);
// Set the units
localWorkspace->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
localWorkspace->setYUnit("Counts");
// TODO localWorkspace->setTitle(title);
// Add the run_start property
// Use the first pulse as the run_start time.
if (this->num_pulses > 0) {
// add the start of the run as a ISO8601 date/time string. The start = the
// first pulse.
// (this is used in LoadInstrument to find the right instrument file to
// use).
localWorkspace->mutableRun().addProperty(
"run_start", pulsetimes[0].toISO8601String(), true);
}
// determine the run number and add it to the run object
localWorkspace->mutableRun().addProperty("run_number",
getRunnumber(event_filename));
// Get the instrument!
prog->report("Loading Instrument");
this->runLoadInstrument(event_filename, localWorkspace);
// load the mapping file
prog->report("Loading Mapping File");
string mapping_filename = this->getPropertyValue(MAP_PARAM);
if (mapping_filename.empty()) {
mapping_filename = generateMappingfileName(localWorkspace);
if (!mapping_filename.empty())
this->g_log.information() << "Found mapping file \"" << mapping_filename
<< "\"" << std::endl;
}
this->loadPixelMap(mapping_filename);
// Process the events into pixels
this->procEvents(localWorkspace);
// Save output
this->setProperty<IEventWorkspace_sptr>(OUT_PARAM, localWorkspace);
// Cleanup
delete prog;
}
