/**
* Returns the input vertical
* @param workspace :: A pointer to a workspace
* @return An axis pointer for the vertical axis of the input workspace
*/
API::Axis *
Transpose::getVerticalAxis(API::MatrixWorkspace_const_sptr workspace) const {
API::Axis *yAxis;
try {
yAxis = workspace->getAxis(1);
} catch (Kernel::Exception::IndexError &) {
throw std::invalid_argument("Axis(1) not found on input workspace.");
}
// Can't put text in dataX
if (yAxis->isText()) {
throw std::invalid_argument(
"Axis(1) is a text axis. Transpose is unable to cope with text axes.");
}
return yAxis;
}
/** Get a workspace identified by an InputData structure.
* @param data :: InputData with name and either spec or i fields defined.
* @return InputData structure with the ws field set if everything was OK.
*/
PlotPeakByLogValue::InputData PlotPeakByLogValue::getWorkspace(const InputData& data)
{
InputData out(data);
if (API::AnalysisDataService::Instance().doesExist(data.name))
{
DataObjects::Workspace2D_sptr ws = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
API::AnalysisDataService::Instance().retrieve(data.name));
if (ws)
{
out.ws = ws;
}
else
{
return data;
}
}
else
{
std::ifstream fil(data.name.c_str());
if (!fil)
{
g_log.warning() << "File "<<data.name<<" does not exist\n";
return data;
}
fil.close();
std::string::size_type i = data.name.find_last_of('.');
if (i == std::string::npos)
{
g_log.warning() << "Cannot open file "<<data.name<<"\n";
return data;
}
std::string ext = data.name.substr(i);
try
{
API::IAlgorithm_sptr load = createSubAlgorithm("Load");
load->initialize();
load->setPropertyValue("FileName",data.name);
load->execute();
if (load->isExecuted())
{
API::Workspace_sptr rws = load->getProperty("OutputWorkspace");
if (rws)
{
DataObjects::Workspace2D_sptr ws = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(rws);
if (ws)
{
out.ws = ws;
}
else
{
API::WorkspaceGroup_sptr gws = boost::dynamic_pointer_cast<API::WorkspaceGroup>(rws);
if (gws)
{
std::vector<std::string> wsNames = gws->getNames();
std::string propName = "OUTPUTWORKSPACE_" + boost::lexical_cast<std::string>(data.period);
if (load->existsProperty(propName))
{
Workspace_sptr rws1 = load->getProperty(propName);
out.ws = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(rws1);
}
}
}
}
}
}
catch(std::exception& e)
{
g_log.error(e.what());
return data;
}
}
if (!out.ws) return data;
API::Axis* axis = out.ws->getAxis(1);
if (axis->isSpectra())
{// spectra axis
if (out.spec < 0)
{
if (out.i >= 0)
{
out.spec = axis->spectraNo(out.i);
}
else
{// i < 0 && spec < 0 => use start and end
for(size_t i=0;i<axis->length();++i)
{
double s = double(axis->spectraNo(i));
if (s >= out.start && s <= out.end)
{
out.indx.push_back(static_cast<int>(i));
}
}
}
}
else
{
for(size_t i=0;i<axis->length();++i)
{
int j = axis->spectraNo(i);
if (j == out.spec)
{
out.i = static_cast<int>(i);
break;
}
}
}
if (out.i < 0 && out.indx.empty())
{
return data;
}
}
else
{// numeric axis
out.spec = -1;
if (out.i >= 0)
{
out.indx.clear();
}
else
{
if (out.i < -1)
{
out.start = (*axis)(0);
out.end = (*axis)(axis->length()-1);
}
for(size_t i=0;i<axis->length();++i)
{
double s = (*axis)(i);
if (s >= out.start && s <= out.end)
{
out.indx.push_back(static_cast<int>(i));
}
}
}
}
return out;
}
/** 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 sub-algorithms successfully
*/
void DiffractionFocussing::exec()
{
// retrieve the properties
std::string groupingFileName=getProperty("GroupingFileName");
// Get the input workspace
MatrixWorkspace_sptr inputW = getProperty("InputWorkspace");
bool dist = inputW->isDistribution();
//do this first to check that a valid file is available before doing any work
std::multimap<int64_t,int64_t> detectorGroups;// <group, UDET>
if (!readGroupingFile(groupingFileName, detectorGroups))
{
throw Exception::FileError("Error reading .cal file",groupingFileName);
}
//Convert to d-spacing units
API::MatrixWorkspace_sptr tmpW = convertUnitsToDSpacing(inputW);
//Rebin to a common set of bins
RebinWorkspace(tmpW);
std::set<int64_t> groupNumbers;
for(std::multimap<int64_t,int64_t>::const_iterator d = detectorGroups.begin();d!=detectorGroups.end();d++)
{
if (groupNumbers.find(d->first) == groupNumbers.end())
{
groupNumbers.insert(d->first);
}
}
int iprogress = 0;
int iprogress_count = static_cast<int>(groupNumbers.size());
int iprogress_step = iprogress_count / 100;
if (iprogress_step == 0) iprogress_step = 1;
std::vector<int64_t> resultIndeces;
for(std::set<int64_t>::const_iterator g = groupNumbers.begin();g!=groupNumbers.end();g++)
{
if (iprogress++ % iprogress_step == 0)
{
progress(0.68 + double(iprogress)/iprogress_count/3);
}
std::multimap<int64_t,int64_t>::const_iterator from = detectorGroups.lower_bound(*g);
std::multimap<int64_t,int64_t>::const_iterator to = detectorGroups.upper_bound(*g);
std::vector<detid_t> detectorList;
for(std::multimap<int64_t,int64_t>::const_iterator d = from;d!=to;d++)
detectorList.push_back(static_cast<detid_t>(d->second));
// Want version 1 of GroupDetectors here
API::IAlgorithm_sptr childAlg = createSubAlgorithm("GroupDetectors",-1.0,-1.0,true,1);
childAlg->setProperty("Workspace", tmpW);
childAlg->setProperty< std::vector<detid_t> >("DetectorList",detectorList);
childAlg->executeAsSubAlg();
try
{
// get the index of the combined spectrum
int ri = childAlg->getProperty("ResultIndex");
if (ri >= 0)
{
resultIndeces.push_back(ri);
}
}
catch(...)
{
throw std::runtime_error("Unable to get Properties from GroupDetectors sub-algorithm");
}
}
// Discard left-over spectra, but print warning message giving number discarded
int discarded = 0;
const int64_t oldHistNumber = tmpW->getNumberHistograms();
API::Axis *spectraAxis = tmpW->getAxis(1);
for(int64_t i=0; i < oldHistNumber; i++)
if ( spectraAxis->spectraNo(i) >= 0 && find(resultIndeces.begin(),resultIndeces.end(),i) == resultIndeces.end())
{
++discarded;
}
g_log.warning() << "Discarded " << discarded << " spectra that were not assigned to any group" << std::endl;
// Running GroupDetectors leads to a load of redundant spectra
// Create a new workspace that's the right size for the meaningful spectra and copy them in
int64_t newSize = tmpW->blocksize();
API::MatrixWorkspace_sptr outputW = API::WorkspaceFactory::Instance().create(tmpW,resultIndeces.size(),newSize+1,newSize);
// Copy units
outputW->getAxis(0)->unit() = tmpW->getAxis(0)->unit();
outputW->getAxis(1)->unit() = tmpW->getAxis(1)->unit();
API::Axis *spectraAxisNew = outputW->getAxis(1);
for(int64_t hist=0; hist < static_cast<int64_t>(resultIndeces.size()); hist++)
{
int64_t i = resultIndeces[hist];
double spNo = static_cast<double>(spectraAxis->spectraNo(i));
MantidVec &tmpE = tmpW->dataE(i);
MantidVec &outE = outputW->dataE(hist);
MantidVec &tmpY = tmpW->dataY(i);
MantidVec &outY = outputW->dataY(hist);
MantidVec &tmpX = tmpW->dataX(i);
MantidVec &outX = outputW->dataX(hist);
outE.assign(tmpE.begin(),tmpE.end());
outY.assign(tmpY.begin(),tmpY.end());
outX.assign(tmpX.begin(),tmpX.end());
spectraAxisNew->setValue(hist,spNo);
spectraAxis->setValue(i,-1);
}
progress(1.);
outputW->isDistribution(dist);
// Assign it to the output workspace property
setProperty("OutputWorkspace",outputW);
return;
}