/**
* 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;
}
/** 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);
}