/**
* Return true if the two workspaces are compatible for this operation
* Virtual: will be overridden as needed.
* @param lhs :: left-hand workspace to check
* @param rhs :: right-hand workspace to check
* @return flag for the compatibility to the two workspaces
*/
bool BinaryOperation::checkCompatibility(const API::MatrixWorkspace_const_sptr lhs,const API::MatrixWorkspace_const_sptr rhs) const
{
Unit_const_sptr lhs_unit;
Unit_const_sptr rhs_unit;
if ( lhs->axes() && rhs->axes() ) // If one of these is a WorkspaceSingleValue then we don't want to check units match
{
lhs_unit = lhs->getAxis(0)->unit();
rhs_unit = rhs->getAxis(0)->unit();
}
const std::string lhs_unitID = ( lhs_unit ? lhs_unit->unitID() : "" );
const std::string rhs_unitID = ( rhs_unit ? rhs_unit->unitID() : "" );
// Check the workspaces have the same units and distribution flag
if ( lhs_unitID != rhs_unitID && lhs->blocksize() > 1 && rhs->blocksize() > 1 )
{
g_log.error("The two workspace are not compatible because they have different units on the X axis.");
return false;
}
// Check the size compatibility
if (!checkSizeCompatibility(lhs,rhs))
{
std::ostringstream ostr;
ostr<<"The sizes of the two workspaces " <<
"(" << lhs->getName() << ": " << lhs->getNumberHistograms() << " spectra, blocksize " << lhs->blocksize() << ")"
<< " and " <<
"(" << rhs->getName() << ": " << rhs->getNumberHistograms() << " spectra, blocksize " << rhs->blocksize() << ")"
<< " are not compatible for algorithm "<<this->name();
g_log.error() << ostr.str() << std::endl;
throw std::invalid_argument( ostr.str() );
}
return true;
}
/**
* Creates the output workspace for this algorithm
* @param inputWorkspace A parent workspace to initialize from.
* @return A pointer to the output workspace.
*/
API::MatrixWorkspace_sptr Transpose::createOutputWorkspace(
API::MatrixWorkspace_const_sptr inputWorkspace) {
Mantid::API::Axis *yAxis = getVerticalAxis(inputWorkspace);
const size_t oldNhist = inputWorkspace->getNumberHistograms();
const MantidVec &inX = inputWorkspace->readX(0);
const size_t oldYlength = inputWorkspace->blocksize();
const size_t oldVerticalAxislength = yAxis->length();
// The input Y axis may be binned so the new X data should be too
size_t newNhist(oldYlength), newXsize(oldVerticalAxislength),
newYsize(oldNhist);
MatrixWorkspace_sptr outputWorkspace = WorkspaceFactory::Instance().create(
inputWorkspace, newNhist, newXsize, newYsize);
// Create a new numeric axis for Y the same length as the old X array
// Values come from input X
API::NumericAxis *newYAxis(nullptr);
if (inputWorkspace->isHistogramData()) {
newYAxis = new API::BinEdgeAxis(inX);
} else {
newYAxis = new API::NumericAxis(inX);
}
newYAxis->unit() = inputWorkspace->getAxis(0)->unit();
outputWorkspace->getAxis(0)->unit() = inputWorkspace->getAxis(1)->unit();
outputWorkspace->replaceAxis(1, newYAxis);
setProperty("OutputWorkspace", outputWorkspace);
return outputWorkspace;
}
/**
* Return true if the two workspaces are compatible for this operation
* Virtual: will be overridden as needed.
* @param lhs :: left-hand workspace to check
* @param rhs :: right-hand workspace to check
* @return flag for the compatibility to the two workspaces
*/
bool BinaryOperation::checkCompatibility(
const API::MatrixWorkspace_const_sptr lhs,
const API::MatrixWorkspace_const_sptr rhs) const {
Unit_const_sptr lhs_unit;
Unit_const_sptr rhs_unit;
if (lhs->axes() && rhs->axes()) // If one of these is a WorkspaceSingleValue
// then we don't want to check units match
{
lhs_unit = lhs->getAxis(0)->unit();
rhs_unit = rhs->getAxis(0)->unit();
}
const std::string lhs_unitID = (lhs_unit ? lhs_unit->unitID() : "");
const std::string rhs_unitID = (rhs_unit ? rhs_unit->unitID() : "");
// Check the workspaces have the same units and distribution flag
if (lhs_unitID != rhs_unitID && lhs->blocksize() > 1 &&
rhs->blocksize() > 1) {
g_log.error("The two workspace are not compatible because they have "
"different units on the X axis.");
return false;
}
// Check the size compatibility
std::string checkSizeCompatibilityResult = checkSizeCompatibility(lhs, rhs);
if (!checkSizeCompatibilityResult.empty()) {
throw std::invalid_argument(checkSizeCompatibilityResult);
}
return true;
}
/**
* Creates the output workspace for this algorithm
* @param inputWorkspace A parent workspace to initialize from.
* @return A pointer to the output workspace.
*/
API::MatrixWorkspace_sptr Transpose::createOutputWorkspace(
API::MatrixWorkspace_const_sptr inputWorkspace) {
Mantid::API::Axis *yAxis = getVerticalAxis(inputWorkspace);
const size_t oldNhist = inputWorkspace->getNumberHistograms();
const auto &inX = inputWorkspace->x(0);
const size_t oldYlength = inputWorkspace->blocksize();
const size_t oldVerticalAxislength = yAxis->length();
// The input Y axis may be binned so the new X data should be too
size_t newNhist(oldYlength), newXsize(oldVerticalAxislength),
newYsize(oldNhist);
MatrixWorkspace_sptr outputWorkspace = inputWorkspace->cloneEmpty();
outputWorkspace->initialize(newNhist, newXsize, newYsize);
outputWorkspace->setTitle(inputWorkspace->getTitle());
outputWorkspace->setComment(inputWorkspace->getComment());
outputWorkspace->copyExperimentInfoFrom(inputWorkspace.get());
outputWorkspace->setYUnit(inputWorkspace->YUnit());
outputWorkspace->setYUnitLabel(inputWorkspace->YUnitLabel());
outputWorkspace->setDistribution(inputWorkspace->isDistribution());
// Create a new numeric axis for Y the same length as the old X array
// Values come from input X
API::NumericAxis *newYAxis(nullptr);
if (inputWorkspace->isHistogramData()) {
newYAxis = new API::BinEdgeAxis(inX.rawData());
} else {
newYAxis = new API::NumericAxis(inX.rawData());
}
newYAxis->unit() = inputWorkspace->getAxis(0)->unit();
outputWorkspace->getAxis(0)->unit() = inputWorkspace->getAxis(1)->unit();
outputWorkspace->replaceAxis(1, newYAxis);
setProperty("OutputWorkspace", outputWorkspace);
return outputWorkspace;
}
// internal helper function which extract one or two axis from input matrix
// workspace;
void MDTransfNoQ::getAxes(API::MatrixWorkspace_const_sptr inWS,
API::NumericAxis *&pXAxis,
API::NumericAxis *&pYAxis) {
// get the X axis of input workspace, it has to be there; if not axis throws
// invalid index
pXAxis = dynamic_cast<API::NumericAxis *>(inWS->getAxis(0));
if (!pXAxis) {
std::string ERR =
"Can not retrieve X axis from the source workspace: " + inWS->getName();
throw(std::invalid_argument(ERR));
}
// get optional Y axis which can be used in NoQ-kind of algorithms
pYAxis = dynamic_cast<API::NumericAxis *>(inWS->getAxis(1));
}
/** Initialization method:
@param bkgWS -- shared pointer to the workspace which contains background
@param sourceWS -- shared pointer to the workspace to remove background from
@param emode -- energy conversion mode used during internal units conversion
(0 -- elastic, 1-direct, 2 indirect, as defined in Units conversion
@param pLog -- pointer to the logger class which would report errors
@param nThreads -- number of threads to be used for background removal
@param inPlace -- if the background removal occurs from the existing workspace
or target workspace has to be cloned.
*/
void BackgroundHelper::initialize(const API::MatrixWorkspace_const_sptr &bkgWS,
const API::MatrixWorkspace_sptr &sourceWS,
int emode, Kernel::Logger *pLog, int nThreads,
bool inPlace) {
m_bgWs = bkgWS;
m_wkWS = sourceWS;
m_Emode = emode;
m_pgLog = pLog;
m_inPlace = inPlace;
std::string bgUnits = bkgWS->getAxis(0)->unit()->unitID();
if (bgUnits != "TOF")
throw std::invalid_argument(" Background Workspace: " + bkgWS->getName() +
" should be in the units of TOF");
if (!(bkgWS->getNumberHistograms() == 1 ||
sourceWS->getNumberHistograms() == bkgWS->getNumberHistograms()))
throw std::invalid_argument(" Background Workspace: " + bkgWS->getName() +
" should have the same number of spectra as "
"source workspace or be a single histogram "
"workspace");
auto WSUnit = sourceWS->getAxis(0)->unit();
if (!WSUnit)
throw std::invalid_argument(" Source Workspace: " + sourceWS->getName() +
" should have units");
Geometry::IComponent_const_sptr source =
sourceWS->getInstrument()->getSource();
m_Sample = sourceWS->getInstrument()->getSample();
if ((!source) || (!m_Sample))
throw std::invalid_argument(
"Instrument on Source workspace:" + sourceWS->getName() +
"is not sufficiently defined: failed to get source and/or sample");
m_L1 = source->getDistance(*m_Sample);
// just in case.
this->deleteUnitsConverters();
// allocate the array of units converters to avoid units reallocation within a
// loop
m_WSUnit.assign(nThreads, NULL);
for (int i = 0; i < nThreads; i++) {
m_WSUnit[i] = WSUnit->clone();
}
m_singleValueBackground = false;
if (bkgWS->getNumberHistograms() == 0)
m_singleValueBackground = true;
const MantidVec &dataX = bkgWS->dataX(0);
const MantidVec &dataY = bkgWS->dataY(0);
// const MantidVec& dataE = bkgWS->dataE(0);
m_NBg = dataY[0];
m_dtBg = dataX[1] - dataX[0];
// m_ErrSq = dataE[0]*dataE[0]; // needs further clarification
m_Efix = this->getEi(sourceWS);
}
/** Checks that the two input workspace have common binning & size, the same instrument & unit.
* Also calls the checkForOverlap method.
* @param ws1 :: The first input workspace
* @param ws2 :: The second input workspace
* @throw std::invalid_argument If the workspaces are not compatible
*/
void ConjoinWorkspaces::validateInputs(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2) const
{
// This is the full check for common binning
if ( !WorkspaceHelpers::commonBoundaries(ws1) || !WorkspaceHelpers::commonBoundaries(ws2) )
{
g_log.error("Both input workspaces must have common binning for all their spectra");
throw std::invalid_argument("Both input workspaces must have common binning for all their spectra");
}
if ( ws1->getInstrument()->getName() != ws2->getInstrument()->getName() )
{
const std::string message("The input workspaces are not compatible because they come from different instruments");
g_log.error(message);
throw std::invalid_argument(message);
}
Unit_const_sptr ws1_unit = ws1->getAxis(0)->unit();
Unit_const_sptr ws2_unit = ws2->getAxis(0)->unit();
const std::string ws1_unitID = ( ws1_unit ? ws1_unit->unitID() : "" );
const std::string ws2_unitID = ( ws2_unit ? ws2_unit->unitID() : "" );
if ( ws1_unitID != ws2_unitID )
{
const std::string message("The input workspaces are not compatible because they have different units on the X axis");
g_log.error(message);
throw std::invalid_argument(message);
}
if ( ws1->isDistribution() != ws2->isDistribution() )
{
const std::string message("The input workspaces have inconsistent distribution flags");
g_log.error(message);
throw std::invalid_argument(message);
}
if ( !WorkspaceHelpers::matchingBins(ws1,ws2,true) )
{
const std::string message("The input workspaces are not compatible because they have different binning");
g_log.error(message);
throw std::invalid_argument(message);
}
this->checkForOverlap(ws1,ws2, true);
}
/** Remove peaks from a input workspace
*/
Workspace2D_sptr
RemovePeaks::removePeaks(API::MatrixWorkspace_const_sptr dataws, int wsindex,
double numfwhm) {
// Check
if (m_vecPeakCentre.empty())
throw runtime_error("RemovePeaks has not been setup yet. ");
// Initialize vectors
const MantidVec &vecX = dataws->readX(wsindex);
const MantidVec &vecY = dataws->readY(wsindex);
const MantidVec &vecE = dataws->readE(wsindex);
size_t sizex = vecX.size();
vector<bool> vec_useX(sizex, true);
// Exclude regions
size_t numbkgdpoints =
excludePeaks(vecX, vec_useX, m_vecPeakCentre, m_vecPeakFWHM, numfwhm);
size_t numbkgdpointsy = numbkgdpoints;
size_t sizey = vecY.size();
if (sizex > sizey)
--numbkgdpointsy;
// Construct output workspace
Workspace2D_sptr outws = boost::dynamic_pointer_cast<Workspace2D>(
WorkspaceFactory::Instance().create("Workspace2D", 1, numbkgdpoints,
numbkgdpointsy));
outws->getAxis(0)->setUnit(dataws->getAxis(0)->unit()->unitID());
MantidVec &outX = outws->dataX(0);
MantidVec &outY = outws->dataY(0);
MantidVec &outE = outws->dataE(0);
size_t index = 0;
for (size_t i = 0; i < sizex; ++i) {
if (vec_useX[i]) {
if (index >= numbkgdpoints)
throw runtime_error("Programming logic error (1)");
outX[index] = vecX[i];
++index;
}
}
index = 0;
for (size_t i = 0; i < sizey; ++i) {
if (vec_useX[i]) {
if (index >= numbkgdpointsy)
throw runtime_error("Programming logic error (2)");
outY[index] = vecY[i];
outE[index] = vecE[i];
++index;
}
}
return outws;
}
/** Checks that the axes of the input workspaces match and creates the output
* workspace if necessary
* @param w1 :: The first input workspace
* @param w2 :: The second input workspace
* @param out :: Pointer to the output workspace
*/
void PointByPointVCorrection::check_validity(
API::MatrixWorkspace_const_sptr &w1, API::MatrixWorkspace_const_sptr &w2,
API::MatrixWorkspace_sptr &out) {
// First check that the instrument matches for both input workspaces
if (w1->getInstrument()->getName() != w2->getInstrument()->getName()) {
g_log.error("The input workspaces have different instrument definitions");
throw std::runtime_error(
"The input workspaces have different instrument definitions");
}
// Check that the two workspaces are the same size
if (w1->size() != w2->size()) {
g_log.error("The input workspaces are not the same size");
throw std::runtime_error("The input workspaces are not the same size");
}
// Now check that the bins match
if (!WorkspaceHelpers::matchingBins(*w1, *w2)) {
g_log.error("The input workspaces have different binning");
throw std::runtime_error("The input workspaces have different binning");
}
const Mantid::API::Axis *const axis1 = w1->getAxis(1);
const Mantid::API::Axis *const axis2 = w2->getAxis(1);
if (!((*axis1) == (*axis2))) // Spectra axis are different, so division does
// not make any sense
{
g_log.error(
"The two workspaces InputW1 and InputW2 have different spectra list");
throw std::runtime_error(
"The two workspaces InputW1 and InputW2 have different spectra list");
}
if (out != w1 && out != w2) // Create a new workspace only if it is different
// from of the input ones.
{
out = API::WorkspaceFactory::Instance().create(w1);
setProperty("OutputWorkspace", out);
} else if (out == w2) {
g_log.warning("Any masking in the output workspaces will be taken from the "
"vanadium workspace (InputW2)");
}
}
/** Initialise the member variables
* @param inputWS The input workspace
*/
void ConvertUnits::setupMemberVariables(const API::MatrixWorkspace_const_sptr inputWS)
{
m_numberOfSpectra = inputWS->getNumberHistograms();
// In the context of this algorithm, we treat things as a distribution if the flag is set
// AND the data are not dimensionless
m_distribution = inputWS->isDistribution() && !inputWS->YUnit().empty();
//Check if its an event workspace
m_inputEvents = ( boost::dynamic_pointer_cast<const EventWorkspace>(inputWS) != NULL );
m_inputUnit = inputWS->getAxis(0)->unit();
const std::string targetUnit = getPropertyValue("Target");
m_outputUnit = UnitFactory::Instance().create(targetUnit);
}
/** returns the units, the input ws is actually in as they coinside with input
* units for this class */
const std::string
MDTransfNoQ::inputUnitID(Kernel::DeltaEMode::Type mode,
API::MatrixWorkspace_const_sptr inWS) const {
UNUSED_ARG(mode);
API::NumericAxis *pXAxis;
// get the X axis of input workspace, it has to be there; if not axis throws
// invalid index
pXAxis = dynamic_cast<API::NumericAxis *>(inWS->getAxis(0));
if (!pXAxis) {
std::string ERR =
"Can not retrieve X axis from the source workspace: " + inWS->getName();
throw(std::invalid_argument(ERR));
}
return pXAxis->unit()->unitID();
}
/** Checks that the input workspace and table have compatible dimensions
* @return a map where: Key = string name of the the property; Value = string
* describing the problem with the property.
*/
std::map<std::string, std::string> PhaseQuadMuon::validateInputs() {
std::map<std::string, std::string> result;
// Check that input ws and table ws have compatible dimensions
API::MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace");
API::ITableWorkspace_const_sptr tabWS = getProperty("PhaseTable");
if (!inputWS) {
result["InputWorkspace"] = "InputWorkspace is of Incorrect type. Please "
"provide a MatrixWorkspace as the "
"InputWorkspace";
return result;
}
size_t nspec = inputWS->getNumberHistograms();
size_t ndet = tabWS->rowCount();
if (tabWS->columnCount() == 0) {
result["PhaseTable"] = "Please provide a non-empty PhaseTable.";
}
if (nspec != ndet) {
result["PhaseTable"] = "PhaseTable must have one row per spectrum";
}
// PhaseTable should have three columns: (detector, asymmetry, phase)
if (tabWS->columnCount() != 3) {
result["PhaseTable"] = "PhaseTable must have three columns";
}
// Check units, should be microseconds
Unit_const_sptr unit = inputWS->getAxis(0)->unit();
if ((unit->caption() != "Time") || (unit->label().ascii() != "microsecond")) {
result["InputWorkspace"] = "InputWorkspace units must be microseconds";
}
return result;
}
/** Get groupings from XML file
* @param fname :: the full path name of the file to open
* @param workspace :: a pointer to the input workspace, used to get spectra indexes from numbers
* @param unUsedSpec :: the list of spectra indexes that have been included in a group (so far)
* @throw FileError if there's any problem with the file or its format
*/
void GroupDetectors2::processXMLFile(std::string fname,
API::MatrixWorkspace_const_sptr workspace, std::vector<int64_t> &unUsedSpec)
{
// 1. Get maps for spectrum ID and detector ID
spec2index_map specs2index;
const SpectraAxis* axis = dynamic_cast<const SpectraAxis*>(workspace->getAxis(1));
if (axis)
{
axis->getSpectraIndexMap(specs2index);
}
detid2index_map* detIdToWiMap = workspace->getDetectorIDToWorkspaceIndexMap(false);
// 2. Load XML file
DataHandling::LoadGroupXMLFile loader;
loader.setDefaultStartingGroupID(0);
loader.loadXMLFile(fname);
std::map<int, std::vector<detid_t> > mGroupDetectorsMap = loader.getGroupDetectorsMap();
std::map<int, std::vector<int> > mGroupSpectraMap = loader.getGroupSpectraMap();
// 3. Build m_GroupSpecInds
std::map<int, std::vector<detid_t> >::iterator dit;
for (dit = mGroupDetectorsMap.begin(); dit != mGroupDetectorsMap.end(); ++ dit)
{
int groupid = dit->first;
std::vector<size_t> tempv;
m_GroupSpecInds.insert(std::make_pair(groupid, tempv));
}
// 4. Detector IDs
for (dit = mGroupDetectorsMap.begin(); dit != mGroupDetectorsMap.end(); ++ dit)
{
int groupid = dit->first;
std::vector<detid_t> detids = dit->second;
storage_map::iterator sit;
sit = m_GroupSpecInds.find(groupid);
if (sit == m_GroupSpecInds.end())
continue;
std::vector<size_t>& wsindexes = sit->second;
for (size_t i = 0; i < detids.size(); i++)
{
detid_t detid = detids[i];
detid2index_map::iterator ind =detIdToWiMap->find(detid);
if ( ind != detIdToWiMap->end() )
{
size_t wsid = ind->second;
wsindexes.push_back(wsid);
if ( unUsedSpec[wsid] != ( 1000 - INT_MAX ) )
{
unUsedSpec[wsid] = ( 1000 - INT_MAX );
}
}
else
{
g_log.error() << "Detector with ID " << detid << " is not found in instrument " << std::endl;
}
} // for index
} // for group
// 5. Spectrum IDs
std::map<int, std::vector<int> >::iterator pit;
for (pit = mGroupSpectraMap.begin(); pit != mGroupSpectraMap.end(); ++pit)
{
int groupid = pit->first;
std::vector<int> spectra = pit->second;
storage_map::iterator sit;
sit = m_GroupSpecInds.find(groupid);
if (sit == m_GroupSpecInds.end())
continue;
std::vector<size_t>& wsindexes = sit->second;
for (size_t i = 0; i < spectra.size(); i++)
{
int specid = spectra[i];
spec2index_map::iterator ind = specs2index.find(specid);
if ( ind != specs2index.end() )
{
size_t wsid = ind->second;
wsindexes.push_back(wsid);
if ( unUsedSpec[wsid] != ( 1000 - INT_MAX ) )
{
unUsedSpec[wsid] = ( 1000 - INT_MAX );
}
}
else
{
g_log.error() << "Spectrum with ID " << specid<< " is not found in instrument " << std::endl;
}
} // for index
} // for group
return;
}
/** Read the spectra numbers in from the input file (the file format is in the
* source file "GroupDetectors2.h" and make an array of spectra indexes to group
* @param fname :: the full path name of the file to open
* @param workspace :: a pointer to the input workspace, used to get spectra indexes from numbers
* @param unUsedSpec :: the list of spectra indexes that have been included in a group (so far)
* @throw FileError if there's any problem with the file or its format
*/
void GroupDetectors2::processFile(std::string fname,
API::MatrixWorkspace_const_sptr workspace, std::vector<int64_t> &unUsedSpec)
{
// tring to open the file the user told us exists, skip down 20 lines to find out what happens if we can read from it
g_log.debug() << "Opening input file ... " << fname;
std::ifstream File(fname.c_str(), std::ios::in);
std::string firstLine;
std::getline( File, firstLine );
// for error reporting keep a count of where we are reading in the file
size_t lineNum = 1;
if (File.fail())
{
g_log.debug() << " file state failbit set after read attempt\n";
throw Exception::FileError("Couldn't read file", fname);
}
g_log.debug() << " success opening input file " << fname << std::endl;
progress(m_FracCompl += OPENINGFILE);
// check for a (user) cancel message
interruption_point();
// allow spectra number to spectra index look ups
spec2index_map specs2index;
const SpectraAxis* axis = dynamic_cast<const SpectraAxis*>(workspace->getAxis(1));
if (axis)
{
axis->getSpectraIndexMap(specs2index);
}
try
{
// we don't use the total number of groups report at the top of the file but we'll tell them later if there is a problem with it for their diagnostic purposes
int totalNumberOfGroups = readInt(firstLine);
// Reading file now ...
while ( totalNumberOfGroups == EMPTY_LINE )
{
if ( ! File ) throw Exception::FileError("The input file doesn't appear to contain any data", fname);
std::getline( File, firstLine ), lineNum ++;
totalNumberOfGroups = readInt(firstLine);
}
readFile(specs2index, File, lineNum, unUsedSpec);
if ( m_GroupSpecInds.size() != static_cast<size_t>(totalNumberOfGroups) )
{
g_log.warning() << "The input file header states there are " << totalNumberOfGroups << " but the file contains " << m_GroupSpecInds.size() << " groups\n";
}
}
// add some more info to the error messages, including the line number, to help users correct their files. These problems should cause the algorithm to stop
catch (std::invalid_argument &e)
{
g_log.debug() << "Exception thrown: " << e.what() << std::endl;
File.close();
std::string error(e.what() + std::string(" near line number ") + boost::lexical_cast<std::string>(lineNum));
if (File.fail())
{
error = "Input output error while reading file ";
}
throw Exception::FileError(error, fname);
}
catch (boost::bad_lexical_cast &e)
{
g_log.debug() << "Exception thrown: " << e.what() << std::endl;
File.close();
std::string error(std::string("Problem reading integer value \"") + e.what() + std::string("\" near line number ") + boost::lexical_cast<std::string>(lineNum));
if (File.fail())
{
error = "Input output error while reading file ";
}
throw Exception::FileError(error, fname);
}
File.close();
g_log.debug() << "Closed file " << fname << " after reading in " << m_GroupSpecInds.size() << " groups\n";
m_FracCompl += fileReadProg( m_GroupSpecInds.size(), specs2index.size() );
return;
}
/** Checks that the input workspace and table have compatible dimensions
* @return a map where: Key = string name of the the property; Value = string
* describing the problem with the property.
*/
std::map<std::string, std::string> PhaseQuadMuon::validateInputs() {
std::map<std::string, std::string> result;
// Check that input ws and table ws have compatible dimensions
API::MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace");
API::ITableWorkspace_const_sptr tabWS = getProperty("PhaseTable");
if (!inputWS) {
result["InputWorkspace"] = "InputWorkspace is of Incorrect type. Please "
"provide a MatrixWorkspace as the "
"InputWorkspace";
return result;
}
size_t nspec = inputWS->getNumberHistograms();
size_t ndet = tabWS->rowCount();
if (tabWS->columnCount() == 0) {
result["PhaseTable"] = "Please provide a non-empty PhaseTable.";
}
if (nspec != ndet) {
result["PhaseTable"] = "PhaseTable must have one row per spectrum";
}
// PhaseTable should have three columns: (detector, asymmetry, phase)
if (tabWS->columnCount() != 3) {
result["PhaseTable"] = "PhaseTable must have three columns";
}
auto names = tabWS->getColumnNames();
for (auto &name : names) {
std::transform(name.begin(), name.end(), name.begin(), ::tolower);
}
int phaseCount = 0;
int asymmetryCount = 0;
for (const std::string &name : names) {
for (const std::string &goodName : phaseNames) {
if (name == goodName) {
phaseCount += 1;
}
}
for (const std::string &goodName : asymmNames) {
if (name == goodName) {
asymmetryCount += 1;
}
}
}
if (phaseCount == 0) {
result["PhaseTable"] = "PhaseTable needs phases column";
}
if (asymmetryCount == 0) {
result["PhaseTable"] = "PhaseTable needs a asymmetry/asymm/asym column";
}
if (phaseCount > 1) {
result["PhaseTable"] =
"PhaseTable has " + std::to_string(phaseCount) + " phase columns";
}
if (asymmetryCount > 1) {
result["PhaseTable"] = "PhaseTable has " + std::to_string(asymmetryCount) +
" asymmetry/asymm/asym columns";
}
// Check units, should be microseconds
Unit_const_sptr unit = inputWS->getAxis(0)->unit();
if ((unit->caption() != "Time") || (unit->label().ascii() != "microsecond")) {
result["InputWorkspace"] = "InputWorkspace units must be microseconds";
}
return result;
}
/** Write out a MatrixWorkspace's data as a 2D matrix.
* Use writeNexusProcessedDataEvent if writing an EventWorkspace.
*/
int NexusFileIO::writeNexusProcessedData2D( const API::MatrixWorkspace_const_sptr& localworkspace,
const bool& uniformSpectra, const std::vector<int>& spec,
const char * group_name, bool write2Ddata) const
{
NXstatus status;
//write data entry
status=NXmakegroup(fileID,group_name,"NXdata");
if(status==NX_ERROR)
return(2);
NXopengroup(fileID,group_name,"NXdata");
// write workspace data
const size_t nHist=localworkspace->getNumberHistograms();
if(nHist<1)
return(2);
const size_t nSpectBins=localworkspace->readY(0).size();
const size_t nSpect=spec.size();
int dims_array[2] = { static_cast<int>(nSpect),static_cast<int>(nSpectBins) };
// Set the axis labels and values
Mantid::API::Axis *xAxis=localworkspace->getAxis(0);
Mantid::API::Axis *sAxis=localworkspace->getAxis(1);
std::string xLabel,sLabel;
if ( xAxis->isSpectra() ) xLabel = "spectraNumber";
else
{
if ( xAxis->unit() ) xLabel = xAxis->unit()->unitID();
else xLabel = "unknown";
}
if ( sAxis->isSpectra() ) sLabel = "spectraNumber";
else
{
if ( sAxis->unit() ) sLabel = sAxis->unit()->unitID();
else sLabel = "unknown";
}
// Get the values on the vertical axis
std::vector<double> axis2;
if (nSpect < nHist)
for (size_t i=0;i<nSpect;i++)
axis2.push_back((*sAxis)(spec[i]));
else
for (size_t i=0;i<sAxis->length();i++)
axis2.push_back((*sAxis)(i));
int start[2]={0,0};
int asize[2]={1,dims_array[1]};
// -------------- Actually write the 2D data ----------------------------
if (write2Ddata)
{
std::string name="values";
NXcompmakedata(fileID, name.c_str(), NX_FLOAT64, 2, dims_array,m_nexuscompression,asize);
NXopendata(fileID, name.c_str());
for(size_t i=0;i<nSpect;i++)
{
int s = spec[i];
NXputslab(fileID, reinterpret_cast<void*>(const_cast<double*>(&(localworkspace->readY(s)[0]))),start,asize);
start[0]++;
}
if(m_progress != 0) m_progress->reportIncrement(1, "Writing data");
int signal=1;
NXputattr (fileID, "signal", &signal, 1, NX_INT32);
// More properties
const std::string axesNames="axis2,axis1";
NXputattr (fileID, "axes", reinterpret_cast<void*>(const_cast<char*>(axesNames.c_str())), static_cast<int>(axesNames.size()), NX_CHAR);
std::string yUnits=localworkspace->YUnit();
std::string yUnitLabel=localworkspace->YUnitLabel();
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>(yUnits.c_str())), static_cast<int>(yUnits.size()), NX_CHAR);
NXputattr (fileID, "unit_label", reinterpret_cast<void*>(const_cast<char*>(yUnitLabel.c_str())), static_cast<int>(yUnitLabel.size()), NX_CHAR);
NXclosedata(fileID);
// error
name="errors";
NXcompmakedata(fileID, name.c_str(), NX_FLOAT64, 2, dims_array,m_nexuscompression,asize);
NXopendata(fileID, name.c_str());
start[0]=0;
for(size_t i=0;i<nSpect;i++)
{
int s = spec[i];
NXputslab(fileID, reinterpret_cast<void*>(const_cast<double*>(&(localworkspace->readE(s)[0]))),start,asize);
start[0]++;
}
if(m_progress != 0) m_progress->reportIncrement(1, "Writing data");
// Fractional area for RebinnedOutput
if (localworkspace->id() == "RebinnedOutput")
{
RebinnedOutput_const_sptr rebin_workspace = boost::dynamic_pointer_cast<const RebinnedOutput>(localworkspace);
name="frac_area";
NXcompmakedata(fileID, name.c_str(), NX_FLOAT64, 2,
dims_array,m_nexuscompression,asize);
NXopendata(fileID, name.c_str());
start[0]=0;
for(size_t i=0;i<nSpect;i++)
{
int s = spec[i];
NXputslab(fileID, reinterpret_cast<void*>(const_cast<double*>(&(rebin_workspace->readF(s)[0]))),
start, asize);
start[0]++;
}
if(m_progress != 0) m_progress->reportIncrement(1, "Writing data");
}
NXclosedata(fileID);
}
// write X data, as single array or all values if "ragged"
if(uniformSpectra)
{
dims_array[0]=static_cast<int>(localworkspace->readX(0).size());
NXmakedata(fileID, "axis1", NX_FLOAT64, 1, dims_array);
NXopendata(fileID, "axis1");
NXputdata(fileID, reinterpret_cast<void*>(const_cast<double*>(&(localworkspace->readX(0)[0]))));
}
else
{
dims_array[0]=static_cast<int>(nSpect);
dims_array[1]=static_cast<int>(localworkspace->readX(0).size());
NXmakedata(fileID, "axis1", NX_FLOAT64, 2, dims_array);
NXopendata(fileID, "axis1");
start[0]=0; asize[1]=dims_array[1];
for(size_t i=0;i<nSpect;i++)
{
NXputslab(fileID, reinterpret_cast<void*>(const_cast<double*>(&(localworkspace->readX(i)[0]))),start,asize);
start[0]++;
}
}
std::string dist=(localworkspace->isDistribution()) ? "1" : "0";
NXputattr(fileID, "distribution", reinterpret_cast<void*>(const_cast<char*>(dist.c_str())), 2, NX_CHAR);
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>(xLabel.c_str())), static_cast<int>(xLabel.size()), NX_CHAR);
auto label = boost::dynamic_pointer_cast<Mantid::Kernel::Units::Label>(xAxis->unit());
if(label)
{
NXputattr (fileID, "caption", reinterpret_cast<void*>(const_cast<char*>(label->caption().c_str())), static_cast<int>(label->caption().size()), NX_CHAR);
auto unitLbl = label->label();
NXputattr (fileID, "label", reinterpret_cast<void*>(const_cast<char*>(unitLbl.ascii().c_str())), static_cast<int>(unitLbl.ascii().size()), NX_CHAR);
}
NXclosedata(fileID);
if ( ! sAxis->isText() )
{
// write axis2, maybe just spectra number
dims_array[0]=static_cast<int>(axis2.size());
NXmakedata(fileID, "axis2", NX_FLOAT64, 1, dims_array);
NXopendata(fileID, "axis2");
NXputdata(fileID, (void*)&(axis2[0]));
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>(sLabel.c_str())), static_cast<int>(sLabel.size()), NX_CHAR);
auto label = boost::dynamic_pointer_cast<Mantid::Kernel::Units::Label>(sAxis->unit());
if(label)
{
NXputattr (fileID, "caption", reinterpret_cast<void*>(const_cast<char*>(label->caption().c_str())), static_cast<int>(label->caption().size()), NX_CHAR);
auto unitLbl = label->label();
NXputattr (fileID, "label", reinterpret_cast<void*>(const_cast<char*>(unitLbl.ascii().c_str())), static_cast<int>(unitLbl.ascii().size()), NX_CHAR);
}
NXclosedata(fileID);
}
else
{
std::string textAxis;
for ( size_t i = 0; i < sAxis->length(); i ++ )
{
std::string label = sAxis->label(i);
textAxis += label + "\n";
}
dims_array[0] = static_cast<int>(textAxis.size());
NXmakedata(fileID, "axis2", NX_CHAR, 2, dims_array);
NXopendata(fileID, "axis2");
NXputdata(fileID, reinterpret_cast<void*>(const_cast<char*>(textAxis.c_str())));
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>("TextAxis")), 8, NX_CHAR);
auto label = boost::dynamic_pointer_cast<Mantid::Kernel::Units::Label>(sAxis->unit());
if(label)
{
NXputattr (fileID, "caption", reinterpret_cast<void*>(const_cast<char*>(label->caption().c_str())), static_cast<int>(label->caption().size()), NX_CHAR);
auto unitLbl = label->label();
NXputattr (fileID, "label", reinterpret_cast<void*>(const_cast<char*>(unitLbl.ascii().c_str())), static_cast<int>(unitLbl.ascii().size()), NX_CHAR);
}
NXclosedata(fileID);
}
writeNexusBinMasking(localworkspace);
status=NXclosegroup(fileID);
return((status==NX_ERROR)?3:0);
}