/** Add workspace2 to workspace1 by adding spectrum.
*/
MatrixWorkspace_sptr
AlignAndFocusPowder::conjoinWorkspaces(API::MatrixWorkspace_sptr ws1,
API::MatrixWorkspace_sptr ws2,
size_t offset) {
// Get information from ws1: maximum spectrum number, and store original
// spectrum Nos
size_t nspec1 = ws1->getNumberHistograms();
specnum_t maxspecNo1 = 0;
std::vector<specnum_t> origspecNos;
for (size_t i = 0; i < nspec1; ++i) {
specnum_t tmpspecNo = ws1->getSpectrum(i).getSpectrumNo();
origspecNos.push_back(tmpspecNo);
if (tmpspecNo > maxspecNo1)
maxspecNo1 = tmpspecNo;
}
g_log.information() << "[DBx536] Max spectrum number of ws1 = " << maxspecNo1
<< ", Offset = " << offset << ".\n";
size_t nspec2 = ws2->getNumberHistograms();
// Conjoin 2 workspaces
Algorithm_sptr alg = this->createChildAlgorithm("AppendSpectra");
alg->initialize();
;
alg->setProperty("InputWorkspace1", ws1);
alg->setProperty("InputWorkspace2", ws2);
alg->setProperty("OutputWorkspace", ws1);
alg->setProperty("ValidateInputs", false);
alg->executeAsChildAlg();
API::MatrixWorkspace_sptr outws = alg->getProperty("OutputWorkspace");
// FIXED : Restore the original spectrum Nos to spectra from ws1
for (size_t i = 0; i < nspec1; ++i) {
specnum_t tmpspecNo = outws->getSpectrum(i).getSpectrumNo();
outws->getSpectrum(i).setSpectrumNo(origspecNos[i]);
g_log.information() << "[DBx540] Conjoined spectrum " << i
<< ": restore spectrum number to "
<< outws->getSpectrum(i).getSpectrumNo()
<< " from spectrum number = " << tmpspecNo << ".\n";
}
// Rename spectrum number
if (offset >= 1) {
for (size_t i = 0; i < nspec2; ++i) {
specnum_t newspecid = maxspecNo1 + static_cast<specnum_t>((i) + offset);
outws->getSpectrum(nspec1 + i).setSpectrumNo(newspecid);
// ISpectrum* spec = outws->getSpectrum(nspec1+i);
// if (spec)
// spec->setSpectrumNo(3);
}
}
return outws;
}
/** Sum all detector pixels except monitors and masked detectors
* @param WS :: The workspace containing the spectrum to sum
* @return A Workspace2D containing the sum
*/
API::MatrixWorkspace_sptr
CalculateTransmissionBeamSpreader::sumSpectra(API::MatrixWorkspace_sptr WS) {
Algorithm_sptr childAlg = createChildAlgorithm("SumSpectra");
childAlg->setProperty<MatrixWorkspace_sptr>("InputWorkspace", WS);
childAlg->setProperty<bool>("IncludeMonitors", false);
childAlg->executeAsChildAlg();
return childAlg->getProperty("OutputWorkspace");
}
/** Perform SortEvents on the output workspaces
* but only if they are EventWorkspaces.
*
* @param ws :: any Workspace. Does nothing if not EventWorkspace.
*/
void AlignAndFocusPowder::doSortEvents(Mantid::API::Workspace_sptr ws) {
EventWorkspace_sptr eventWS = boost::dynamic_pointer_cast<EventWorkspace>(ws);
if (!eventWS)
return;
Algorithm_sptr alg = this->createChildAlgorithm("SortEvents");
alg->setProperty("InputWorkspace", eventWS);
alg->setPropertyValue("SortBy", "X Value");
alg->executeAsChildAlg();
}
/** Perform SortEvents on the output workspaces (accumulation or output)
* but only if they are EventWorkspaces. This will help the GUI
* cope with redrawing.
*
* @param ws :: any Workspace. Does nothing if not EventWorkspace.
*/
void LoadLiveData::doSortEvents(Mantid::API::Workspace_sptr ws) {
EventWorkspace_sptr eventWS = boost::dynamic_pointer_cast<EventWorkspace>(ws);
if (!eventWS)
return;
CPUTimer tim;
Algorithm_sptr alg = this->createChildAlgorithm("SortEvents");
alg->setProperty("InputWorkspace", eventWS);
alg->setPropertyValue("SortBy", "X Value");
alg->executeAsChildAlg();
g_log.debug() << tim << " to perform SortEvents on " << ws->name() << '\n';
}
/** Extracts a single spectrum from a Workspace2D into a new workspaces. Uses
* CropWorkspace to do this.
* @param WS :: The workspace containing the spectrum to extract
* @param index :: The workspace index of the spectrum to extract
* @return A Workspace2D containing the extracted spectrum
*/
API::MatrixWorkspace_sptr
CalculateTransmissionBeamSpreader::extractSpectrum(API::MatrixWorkspace_sptr WS,
const size_t index) {
// Check that given spectra are monitors
if (!WS->getDetector(index)->isMonitor()) {
g_log.information(
"The Incident Beam Monitor UDET provided is not marked as a monitor");
}
Algorithm_sptr childAlg =
createChildAlgorithm("ExtractSingleSpectrum", 0.0, 0.4);
childAlg->setProperty<MatrixWorkspace_sptr>("InputWorkspace", WS);
childAlg->setProperty<int>("WorkspaceIndex", static_cast<int>(index));
childAlg->executeAsChildAlg();
return childAlg->getProperty("OutputWorkspace");
}
/** Get a pointer to an instrument in one of 3 ways: InputWorkspace,
* InstrumentName, InstrumentFilename
* @param alg :: algorithm from which to get the property values.
* */
Geometry::Instrument_const_sptr
LoadCalFile::getInstrument3Ways(Algorithm *alg) {
MatrixWorkspace_sptr inWS = alg->getProperty("InputWorkspace");
std::string InstrumentName = alg->getPropertyValue("InstrumentName");
std::string InstrumentFilename = alg->getPropertyValue("InstrumentFilename");
// Some validation
int numParams = 0;
if (inWS)
numParams++;
if (!InstrumentName.empty())
numParams++;
if (!InstrumentFilename.empty())
numParams++;
if (numParams > 1)
throw std::invalid_argument("You must specify exactly ONE way to get an "
"instrument (workspace, instrument name, or "
"IDF file). You specified more than one.");
if (numParams == 0)
throw std::invalid_argument("You must specify exactly ONE way to get an "
"instrument (workspace, instrument name, or "
"IDF file). You specified none.");
// ---------- Get the instrument one of 3 ways ---------------------------
Instrument_const_sptr inst;
if (inWS) {
inst = inWS->getInstrument();
} else {
Algorithm_sptr childAlg =
alg->createChildAlgorithm("LoadInstrument", 0.0, 0.2);
MatrixWorkspace_sptr tempWS = boost::make_shared<Workspace2D>();
childAlg->setProperty<MatrixWorkspace_sptr>("Workspace", tempWS);
childAlg->setPropertyValue("Filename", InstrumentFilename);
childAlg->setPropertyValue("InstrumentName", InstrumentName);
childAlg->setProperty("RewriteSpectraMap",
Mantid::Kernel::OptionalBool(false));
childAlg->executeAsChildAlg();
inst = tempWS->getInstrument();
}
return inst;
}
/** Uses 'Linear' as a ChildAlgorithm to fit the log of the exponential curve
* expected for the transmission.
* @param WS :: The single-spectrum workspace to fit
* @return A workspace containing the fit
*/
API::MatrixWorkspace_sptr
CalculateTransmissionBeamSpreader::fitToData(API::MatrixWorkspace_sptr WS) {
g_log.information("Fitting the experimental transmission curve");
Algorithm_sptr childAlg = createChildAlgorithm("Linear", 0.6, 1.0);
childAlg->setProperty<MatrixWorkspace_sptr>("InputWorkspace", WS);
const double lambdaMin = getProperty("MinWavelength");
const double lambdaMax = getProperty("MaxWavelength");
childAlg->setProperty<double>("StartX", lambdaMin);
childAlg->setProperty<double>("EndX", lambdaMax);
childAlg->executeAsChildAlg();
std::string fitStatus = childAlg->getProperty("FitStatus");
if (fitStatus != "success") {
g_log.error("Unable to successfully fit the data: " + fitStatus);
throw std::runtime_error("Unable to successfully fit the data");
}
// Only get to here if successful
MatrixWorkspace_sptr result = childAlg->getProperty("OutputWorkspace");
if (logFit) {
// Need to transform back to 'unlogged'
double b = childAlg->getProperty("FitIntercept");
double m = childAlg->getProperty("FitSlope");
b = std::pow(10, b);
m = std::pow(10, m);
const MantidVec &X = result->readX(0);
MantidVec &Y = result->dataY(0);
MantidVec &E = result->dataE(0);
for (size_t i = 0; i < Y.size(); ++i) {
Y[i] = b * (std::pow(m, 0.5 * (X[i] + X[i + 1])));
E[i] = std::abs(E[i] * Y[i]);
}
}
return result;
}
/**
* Determine the instrument from the various input parameters.
*
* @return The correct instrument.
*/
Instrument_const_sptr CreateChunkingFromInstrument::getInstrument() {
// try the input workspace
MatrixWorkspace_sptr inWS = getProperty(PARAM_IN_WKSP);
if (inWS) {
return inWS->getInstrument();
}
// temporary workspace to hang everything else off of
MatrixWorkspace_sptr tempWS(new Workspace2D());
// name of the instrument
string instName = getPropertyValue(PARAM_INST_NAME);
// see if there is an input file
string filename = getPropertyValue(PARAM_IN_FILE);
if (!filename.empty()) {
string top_entry_name("entry"); // TODO make more flexible
// get the instrument name from the filename
size_t n = filename.rfind('/');
if (n != std::string::npos) {
std::string temp = filename.substr(n + 1, filename.size() - n - 1);
n = temp.find('_');
if (n != std::string::npos && n > 0) {
instName = temp.substr(0, n);
}
}
// read information from the nexus file itself
try {
NeXus::File nxsfile(filename);
// get the run start time
string start_time;
nxsfile.openGroup(top_entry_name, "NXentry");
nxsfile.readData("start_time", start_time);
tempWS->mutableRun().addProperty(
"run_start", DateAndTime(start_time).toISO8601String(), true);
// get the instrument name
nxsfile.openGroup("instrument", "NXinstrument");
nxsfile.readData("name", instName);
nxsfile.closeGroup();
// Test if IDF exists in file, move on quickly if not
nxsfile.openPath("instrument/instrument_xml");
nxsfile.close();
IAlgorithm_sptr loadInst =
createChildAlgorithm("LoadIDFFromNexus", 0.0, 0.2);
// Now execute the Child Algorithm. Catch and log any error, but don't
// stop.
try {
loadInst->setPropertyValue("Filename", filename);
loadInst->setProperty<MatrixWorkspace_sptr>("Workspace", tempWS);
loadInst->setPropertyValue("InstrumentParentPath", top_entry_name);
loadInst->execute();
} catch (std::invalid_argument &) {
g_log.error("Invalid argument to LoadIDFFromNexus Child Algorithm ");
} catch (std::runtime_error &) {
g_log.debug("No instrument definition found in " + filename + " at " +
top_entry_name + "/instrument");
}
if (loadInst->isExecuted())
return tempWS->getInstrument();
else
g_log.information("No IDF loaded from Nexus file.");
} catch (::NeXus::Exception &) {
g_log.information("No instrument definition found in " + filename +
" at " + top_entry_name + "/instrument");
}
}
// run LoadInstrument if other methods have not run
string instFilename = getPropertyValue(PARAM_INST_FILE);
Algorithm_sptr childAlg = createChildAlgorithm("LoadInstrument", 0.0, 0.2);
childAlg->setProperty<MatrixWorkspace_sptr>("Workspace", tempWS);
childAlg->setPropertyValue("Filename", instFilename);
childAlg->setPropertyValue("InstrumentName", instName);
childAlg->executeAsChildAlg();
return tempWS->getInstrument();
}
/*
Executes the underlying algorithm to create the MVP model.
@param factory : visualisation factory to use.
@param loadingProgressUpdate : Handler for GUI updates while algorithm
progresses.
@param drawingProgressUpdate : Handler for GUI updates while
vtkDataSetFactory::create occurs.
*/
vtkSmartPointer<vtkDataSet>
EventNexusLoadingPresenter::execute(vtkDataSetFactory *factory,
ProgressAction &loadingProgressUpdate,
ProgressAction &drawingProgressUpdate) {
using namespace Mantid::API;
using namespace Mantid::Geometry;
this->m_view->getLoadInMemory(); // TODO, nexus reader algorithm currently has
// no use of this.
if (this->shouldLoad()) {
Poco::NObserver<ProgressAction,
Mantid::API::Algorithm::ProgressNotification>
observer(loadingProgressUpdate, &ProgressAction::handler);
AnalysisDataService::Instance().remove("MD_EVENT_WS_ID");
Algorithm_sptr loadAlg =
AlgorithmManager::Instance().createUnmanaged("LoadEventNexus");
loadAlg->initialize();
loadAlg->setChild(true);
loadAlg->setPropertyValue("Filename", this->m_filename);
loadAlg->setPropertyValue("OutputWorkspace", "temp_ws");
loadAlg->addObserver(observer);
loadAlg->executeAsChildAlg();
loadAlg->removeObserver(observer);
Workspace_sptr temp = loadAlg->getProperty("OutputWorkspace");
IEventWorkspace_sptr tempWS =
boost::dynamic_pointer_cast<IEventWorkspace>(temp);
Algorithm_sptr convertAlg = AlgorithmManager::Instance().createUnmanaged(
"ConvertToDiffractionMDWorkspace", 1);
convertAlg->initialize();
convertAlg->setChild(true);
convertAlg->setProperty("InputWorkspace", tempWS);
convertAlg->setProperty<bool>("ClearInputWorkspace", false);
convertAlg->setProperty<bool>("LorentzCorrection", true);
convertAlg->setPropertyValue("OutputWorkspace", "converted_ws");
convertAlg->addObserver(observer);
convertAlg->executeAsChildAlg();
convertAlg->removeObserver(observer);
IMDEventWorkspace_sptr outWS = convertAlg->getProperty("OutputWorkspace");
AnalysisDataService::Instance().addOrReplace("MD_EVENT_WS_ID", outWS);
}
Workspace_sptr result =
AnalysisDataService::Instance().retrieve("MD_EVENT_WS_ID");
Mantid::API::IMDEventWorkspace_sptr eventWs =
boost::dynamic_pointer_cast<Mantid::API::IMDEventWorkspace>(result);
m_wsTypeName = eventWs->id();
factory->setRecursionDepth(this->m_view->getRecursionDepth());
auto visualDataSet = factory->oneStepCreate(
eventWs, drawingProgressUpdate); // HACK: progressUpdate should be
// argument for drawing!
this->extractMetadata(*eventWs);
this->appendMetadata(visualDataSet, eventWs->getName());
return visualDataSet;
}
/**
* Set MDFrames for workspaces from legacy files
* @param ws:: poitner to the workspace which needs to be corrected
*/
void LoadMD::setMDFrameOnWorkspaceFromLegacyFile(API::IMDWorkspace_sptr ws) {
g_log.information()
<< "LoadMD: Encountered a legacy file which has a mismatch between "
"its MDFrames and its Special Coordinate System. "
"Attempting to convert MDFrames.\n";
auto numberOfDimensions = ws->getNumDims();
// Select an MDFrame based on the special coordinates.
// Note that for None, we select a General Coordinate System,
// unless the name is "Unknown frame"
std::string selectedFrame;
switch (m_coordSystem) {
case Mantid::Kernel::QLab:
selectedFrame = Mantid::Geometry::QLab::QLabName;
break;
case Mantid::Kernel::QSample:
selectedFrame = Mantid::Geometry::QSample::QSampleName;
break;
case Mantid::Kernel::HKL:
selectedFrame = Mantid::Geometry::HKL::HKLName;
break;
default:
selectedFrame = Mantid::Geometry::GeneralFrame::GeneralFrameName;
}
// Get the old frames just in case something goes wrong. In this case we
// reset the frames.
std::vector<std::string> oldFrames(
numberOfDimensions, Mantid::Geometry::GeneralFrame::GeneralFrameName);
for (size_t index = 0; index < numberOfDimensions; ++index) {
oldFrames[index] = ws->getDimension(index)->getMDFrame().name();
}
// We want to set only up to the first three dimensions to the selected Frame;
// Everything else will be set to a General Frame
std::vector<std::string> framesToSet(
numberOfDimensions, Mantid::Geometry::GeneralFrame::GeneralFrameName);
auto fillUpTo = numberOfDimensions > 3 ? 3 : numberOfDimensions;
std::fill_n(framesToSet.begin(), fillUpTo, selectedFrame);
try {
// Set the MDFrames for each axes
Algorithm_sptr setMDFrameAlg = this->createChildAlgorithm("SetMDFrame");
int axesCounter = 0;
for (auto &frame : framesToSet) {
setMDFrameAlg->setProperty("InputWorkspace", ws);
setMDFrameAlg->setProperty("MDFrame", frame);
setMDFrameAlg->setProperty("Axes", std::vector<int>(1, axesCounter));
++axesCounter;
setMDFrameAlg->executeAsChildAlg();
}
} catch (...) {
g_log.warning() << "LoadMD: An issue occured while trying to correct "
"MDFrames. Trying to revert to original.\n";
// Revert to the old frames.
Algorithm_sptr setMDFrameAlg = this->createChildAlgorithm("SetMDFrame");
int axesCounter = 0;
for (auto &oldFrame : oldFrames) {
setMDFrameAlg->setProperty("InputWorkspace", ws);
setMDFrameAlg->setProperty("MDFrame", oldFrame);
setMDFrameAlg->setProperty("Axes", std::vector<int>(1, axesCounter));
++axesCounter;
setMDFrameAlg->executeAsChildAlg();
}
}
}
/** Execute the algorithm.
*/
void CreateGroupingWorkspace::exec() {
MatrixWorkspace_sptr inWS = getProperty("InputWorkspace");
std::string InstrumentName = getPropertyValue("InstrumentName");
std::string InstrumentFilename = getPropertyValue("InstrumentFilename");
std::string OldCalFilename = getPropertyValue("OldCalFilename");
std::string GroupNames = getPropertyValue("GroupNames");
std::string grouping = getPropertyValue("GroupDetectorsBy");
int numGroups = getProperty("FixedGroupCount");
std::string componentName = getPropertyValue("ComponentName");
// Some validation
int numParams = 0;
if (inWS)
numParams++;
if (!InstrumentName.empty())
numParams++;
if (!InstrumentFilename.empty())
numParams++;
if (numParams > 1)
throw std::invalid_argument("You must specify exactly ONE way to get an "
"instrument (workspace, instrument name, or "
"IDF file). You specified more than one.");
if (numParams == 0)
throw std::invalid_argument("You must specify exactly ONE way to get an "
"instrument (workspace, instrument name, or "
"IDF file). You specified none.");
if (!OldCalFilename.empty() && !GroupNames.empty())
throw std::invalid_argument("You must specify either to use the "
"OldCalFilename parameter OR GroupNames but "
"not both!");
bool sortnames = false;
// ---------- Get the instrument one of 3 ways ---------------------------
Instrument_const_sptr inst;
if (inWS) {
inst = inWS->getInstrument();
} else {
Algorithm_sptr childAlg = createChildAlgorithm("LoadInstrument", 0.0, 0.2);
MatrixWorkspace_sptr tempWS = boost::make_shared<Workspace2D>();
childAlg->setProperty<MatrixWorkspace_sptr>("Workspace", tempWS);
childAlg->setPropertyValue("Filename", InstrumentFilename);
childAlg->setProperty("RewriteSpectraMap",
Mantid::Kernel::OptionalBool(true));
childAlg->setPropertyValue("InstrumentName", InstrumentName);
childAlg->executeAsChildAlg();
inst = tempWS->getInstrument();
}
if (GroupNames.empty() && OldCalFilename.empty()) {
if (grouping.compare("All") == 0) {
GroupNames = inst->getName();
} else if (inst->getName().compare("SNAP") == 0 &&
grouping.compare("Group") == 0) {
GroupNames = "East,West";
} else {
sortnames = true;
GroupNames = "";
int maxRecurseDepth = this->getProperty("MaxRecursionDepth");
// cppcheck-suppress syntaxError
PRAGMA_OMP(parallel for schedule(dynamic, 1) )
for (int num = 0; num < 300; ++num) {
PARALLEL_START_INTERUPT_REGION
std::ostringstream mess;
mess << grouping << num;
IComponent_const_sptr comp =
inst->getComponentByName(mess.str(), maxRecurseDepth);
PARALLEL_CRITICAL(GroupNames)
if (comp)
GroupNames += mess.str() + ",";
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
}
}
// --------------------------- Create the output --------------------------
auto outWS = boost::make_shared<GroupingWorkspace>(inst);
this->setProperty("OutputWorkspace", outWS);
// This will get the grouping
std::map<detid_t, int> detIDtoGroup;
Progress prog(this, 0.2, 1.0, outWS->getNumberHistograms());
// Make the grouping one of three ways:
if (!GroupNames.empty())
detIDtoGroup = makeGroupingByNames(GroupNames, inst, prog, sortnames);
else if (!OldCalFilename.empty())
detIDtoGroup = readGroupingFile(OldCalFilename, prog);
else if ((numGroups > 0) && !componentName.empty())
detIDtoGroup =
makeGroupingByNumGroups(componentName, numGroups, inst, prog);
g_log.information() << detIDtoGroup.size()
<< " entries in the detectorID-to-group map.\n";
setProperty("NumberGroupedSpectraResult",
static_cast<int>(detIDtoGroup.size()));
if (detIDtoGroup.empty()) {
g_log.warning() << "Creating empty group workspace\n";
setProperty("NumberGroupsResult", static_cast<int>(0));
} else {
size_t numNotFound = 0;
// Make the groups, if any
std::map<detid_t, int>::const_iterator it_end = detIDtoGroup.end();
std::map<detid_t, int>::const_iterator it;
std::unordered_set<int> groupCount;
for (it = detIDtoGroup.begin(); it != it_end; ++it) {
int detID = it->first;
int group = it->second;
groupCount.insert(group);
try {
outWS->setValue(detID, double(group));
} catch (std::invalid_argument &) {
numNotFound++;
}
}
setProperty("NumberGroupsResult", static_cast<int>(groupCount.size()));
if (numNotFound > 0)
g_log.warning() << numNotFound << " detector IDs (out of "
<< detIDtoGroup.size()
<< ") were not found in the instrument\n.";
}
}