/**
* Execute the algorithm.
*/
void LoadSassena::exec() {
// auto
// gws=boost::dynamic_pointer_cast<API::WorkspaceGroup>(getProperty("OutputWorkspace"));
// API::WorkspaceGroup_sptr gws=getProperty("OutputWorkspace");
API::Workspace_sptr ows = getProperty("OutputWorkspace");
API::WorkspaceGroup_sptr gws =
boost::dynamic_pointer_cast<API::WorkspaceGroup>(ows);
if (gws && API::AnalysisDataService::Instance().doesExist(gws->name())) {
// gws->deepRemoveAll(); // remove workspace members
API::AnalysisDataService::Instance().deepRemoveGroup(gws->name());
} else {
gws = boost::make_shared<API::WorkspaceGroup>();
setProperty("OutputWorkspace",
boost::dynamic_pointer_cast<API::Workspace>(gws));
}
// populate m_validSets
int nvalidSets = 4;
const char *validSets[] = {"fq", "fq0", "fq2", "fqt"};
for (int iSet = 0; iSet < nvalidSets; iSet++)
this->m_validSets.push_back(validSets[iSet]);
// open the HDF5 file for reading
m_filename = this->getPropertyValue("Filename");
hid_t h5file = H5Fopen(m_filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if (h5file < 0) {
this->g_log.error("Cannot open " + m_filename);
throw Kernel::Exception::FileError("Unable to open:", m_filename);
}
// find out the sassena version used
char cversion[16];
if (H5LTget_attribute_string(h5file, "/", "sassena_version", cversion) < 0) {
this->g_log.error("Unable to read Sassena version");
}
// const std::string version(cversion);
// determine which loader protocol to use based on the version
// to be done at a later time, maybe implement a Version class
std::vector<int> sorting_indexes;
const MantidVec qvmod = this->loadQvectors(h5file, gws, sorting_indexes);
// iterate over the valid sets
std::string setName;
for (std::vector<std::string>::const_iterator it = this->m_validSets.begin();
it != this->m_validSets.end(); ++it) {
setName = *it;
if (H5LTfind_dataset(h5file, setName.c_str()) == 1) {
if (setName == "fq" || setName == "fq0" || setName == "fq2")
this->loadFQ(h5file, gws, setName, qvmod, sorting_indexes);
else if (setName == "fqt")
this->loadFQT(h5file, gws, setName, qvmod, sorting_indexes);
} else
this->g_log.information("Dataset " + setName + " not present in file");
} // end of iterate over the valid sets
H5Fclose(h5file);
} // end of LoadSassena::exec()
/**
* Create the output workspace group.
* @param baseName :: The base name for the output workspace. Suffix "Workspace"
* will be added to it.
* @param function :: A function to calculate the values. Must be of the
* MultiDomainFunction type.
* @param domain :: Domain created earlier with this creator (unused)
* @param values :: Values created earlier with this creator (unused)
* @param outputWorkspacePropertyName :: Name for the property to hold the
* output workspace. If
* empty the property won't be created.
* @return A shared pointer to the created workspace.
*/
boost::shared_ptr<API::Workspace> MultiDomainCreator::createOutputWorkspace(
const std::string &baseName, API::IFunction_sptr function,
boost::shared_ptr<API::FunctionDomain> domain,
boost::shared_ptr<API::FunctionValues> values,
const std::string &outputWorkspacePropertyName) {
UNUSED_ARG(domain);
UNUSED_ARG(values);
auto mdFunction =
boost::dynamic_pointer_cast<API::MultiDomainFunction>(function);
if (!mdFunction) {
throw std::runtime_error("A MultiDomainFunction is expected to be used "
"with MultiDomainCreator.");
}
// split the function into independent parts
std::vector<API::IFunction_sptr> functions =
mdFunction->createEquivalentFunctions();
// there must be as many parts as there are domains
if (functions.size() != m_creators.size()) {
throw std::runtime_error("Number of functions and domains don't match");
}
API::WorkspaceGroup_sptr outWS =
API::WorkspaceGroup_sptr(new API::WorkspaceGroup());
for (size_t i = 0; i < functions.size(); ++i) {
std::string localName =
baseName + "Workspace_" + boost::lexical_cast<std::string>(i);
auto fun = functions[i];
auto creator = m_creators[i];
boost::shared_ptr<API::FunctionDomain> localDomain;
boost::shared_ptr<API::FunctionValues> localValues;
fun->setUpForFit();
creator->createDomain(localDomain, localValues);
creator->initFunction(fun);
auto ws = creator->createOutputWorkspace(localName, fun, localDomain,
localValues, "");
API::AnalysisDataService::Instance().addOrReplace(localName, ws);
outWS->addWorkspace(ws);
}
if (!outputWorkspacePropertyName.empty()) {
declareProperty(
new API::WorkspaceProperty<API::WorkspaceGroup>(
outputWorkspacePropertyName, "", Kernel::Direction::Output),
"Name of the output Workspace holding resulting simulated spectrum");
m_manager->setPropertyValue(outputWorkspacePropertyName,
baseName + "Workspaces");
m_manager->setProperty(outputWorkspacePropertyName, outWS);
}
return outWS;
}
/**
* Register a workspace in the Analysis Data Service and add it to the
* groupWorkspace
* @param gws pointer to WorkspaceGroup being filled
* @param wsName name of workspace to be added and registered
* @param ws pointer to workspace to be added and registered
* @param description
*/
void LoadSassena::registerWorkspace(API::WorkspaceGroup_sptr gws,
const std::string wsName,
DataObjects::Workspace2D_sptr ws,
const std::string &description) {
UNUSED_ARG(description);
API::AnalysisDataService::Instance().add(wsName, ws);
gws->addWorkspace(ws);
}
/** Fits each spectrum in the workspace to f(x) = A * sin( w * x + p)
* @param ws :: [input] The workspace to fit
* @param freq :: [input] Hint for the frequency (w)
* @param groupName :: [input] The name of the output workspace group
* @param resTab :: [output] Table workspace storing the asymmetries and phases
* @param resGroup :: [output] Workspace group storing the fitting results
*/
void CalMuonDetectorPhases::fitWorkspace(const API::MatrixWorkspace_sptr &ws,
double freq, std::string groupName,
API::ITableWorkspace_sptr &resTab,
API::WorkspaceGroup_sptr &resGroup) {
int nhist = static_cast<int>(ws->getNumberHistograms());
// Create the fitting function f(x) = A * sin ( w * x + p )
// The same function and initial parameters are used for each fit
std::string funcStr = createFittingFunction(freq, true);
// Set up results table
resTab->addColumn("int", "Spectrum number");
resTab->addColumn("double", "Asymmetry");
resTab->addColumn("double", "Phase");
// Loop through fitting all spectra individually
const static std::string success = "success";
for (int wsIndex = 0; wsIndex < nhist; wsIndex++) {
reportProgress(wsIndex, nhist);
auto fit = createChildAlgorithm("Fit");
fit->initialize();
fit->setPropertyValue("Function", funcStr);
fit->setProperty("InputWorkspace", ws);
fit->setProperty("WorkspaceIndex", wsIndex);
fit->setProperty("CreateOutput", true);
fit->setPropertyValue("Output", groupName);
fit->execute();
std::string status = fit->getProperty("OutputStatus");
if (!fit->isExecuted() || status != success) {
std::ostringstream error;
error << "Fit failed for spectrum at workspace index " << wsIndex;
error << ": " << status;
throw std::runtime_error(error.str());
}
API::MatrixWorkspace_sptr fitOut = fit->getProperty("OutputWorkspace");
resGroup->addWorkspace(fitOut);
API::ITableWorkspace_sptr tab = fit->getProperty("OutputParameters");
// Now we have our fitting results stored in tab
// but we need to extract the relevant information, i.e.
// the detector phases (parameter 'p') and asymmetries ('A')
const auto &spectrum = ws->getSpectrum(static_cast<size_t>(wsIndex));
extractDetectorInfo(tab, resTab, spectrum.getSpectrumNo());
}
}
void Load::loadMultipleFiles() {
// allFilenames contains "rows" of filenames. If the row has more than 1 file
// in it
// then that row is to be summed across each file in the row
const std::vector<std::vector<std::string>> allFilenames =
getProperty("Filename");
std::string outputWsName = getProperty("OutputWorkspace");
std::vector<std::string> wsNames(allFilenames.size());
std::transform(allFilenames.begin(), allFilenames.end(), wsNames.begin(),
generateWsNameFromFileNames);
auto wsName = wsNames.cbegin();
assert(allFilenames.size() == wsNames.size());
std::vector<API::Workspace_sptr> loadedWsList;
loadedWsList.reserve(allFilenames.size());
Workspace_sptr tempWs;
// Cycle through the filenames and wsNames.
for (auto filenames = allFilenames.cbegin(); filenames != allFilenames.cend();
++filenames, ++wsName) {
auto filename = filenames->cbegin();
Workspace_sptr sumWS = loadFileToWs(*filename, *wsName);
++filename;
for (; filename != filenames->cend(); ++filename) {
tempWs = loadFileToWs(*filename, "__@loadsum_temp@");
sumWS = plusWs(sumWS, tempWs);
}
API::WorkspaceGroup_sptr group =
boost::dynamic_pointer_cast<WorkspaceGroup>(sumWS);
if (group) {
std::vector<std::string> childWsNames = group->getNames();
auto childWsName = childWsNames.begin();
size_t count = 1;
for (; childWsName != childWsNames.end(); ++childWsName, ++count) {
Workspace_sptr childWs = group->getItem(*childWsName);
const std::string childName =
group->getName() + "_" + std::to_string(count);
API::AnalysisDataService::Instance().addOrReplace(childName, childWs);
// childWs->setName(group->getName() + "_" +
// boost::lexical_cast<std::string>(count));
}
}
// Add the sum to the list of loaded workspace names.
loadedWsList.push_back(sumWS);
}
// If we only have one loaded ws, set it as the output.
if (loadedWsList.size() == 1) {
setProperty("OutputWorkspace", loadedWsList[0]);
AnalysisDataService::Instance().rename(loadedWsList[0]->getName(),
outputWsName);
}
// Else we have multiple loaded workspaces - group them and set the group as
// output.
else {
API::WorkspaceGroup_sptr group = groupWsList(loadedWsList);
setProperty("OutputWorkspace", group);
std::vector<std::string> childWsNames = group->getNames();
size_t count = 1;
for (auto &childWsName : childWsNames) {
if (childWsName == outputWsName) {
Mantid::API::Workspace_sptr child = group->getItem(childWsName);
// child->setName(child->getName() + "_" +
// boost::lexical_cast<std::string>(count));
const std::string childName =
child->getName() + "_" + std::to_string(count);
API::AnalysisDataService::Instance().addOrReplace(childName, child);
count++;
}
}
childWsNames = group->getNames();
count = 1;
for (auto &childWsName : childWsNames) {
Workspace_sptr childWs = group->getItem(childWsName);
std::string outWsPropName = "OutputWorkspace_" + std::to_string(count);
++count;
declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
outWsPropName, childWsName, Direction::Output));
setProperty(outWsPropName, childWs);
}
}
// Clean up.
if (tempWs) {
Algorithm_sptr alg =
AlgorithmManager::Instance().createUnmanaged("DeleteWorkspace");
alg->initialize();
alg->setChild(true);
alg->setProperty("Workspace", tempWs);
alg->execute();
}
}
/** Fits each spectrum in the workspace to f(x) = A * sin( w * x + p)
* @param ws :: [input] The workspace to fit
* @param freq :: [input] Hint for the frequency (w)
* @param groupName :: [input] The name of the output workspace group
* @param resTab :: [output] Table workspace storing the asymmetries and phases
* @param resGroup :: [output] Workspace group storing the fitting results
*/
void CalMuonDetectorPhases::fitWorkspace(const API::MatrixWorkspace_sptr &ws,
double freq, std::string groupName,
API::ITableWorkspace_sptr resTab,
API::WorkspaceGroup_sptr &resGroup) {
int nhist = static_cast<int>(ws->getNumberHistograms());
// Create the fitting function f(x) = A * sin ( w * x + p )
// The same function and initial parameters are used for each fit
std::string funcStr = createFittingFunction(freq, true);
// Set up results table
resTab->addColumn("int", "Spectrum number");
resTab->addColumn("double", "Asymmetry");
resTab->addColumn("double", "Phase");
const auto &indexInfo = ws->indexInfo();
// Loop through fitting all spectra individually
const static std::string success = "success";
for (int wsIndex = 0; wsIndex < nhist; wsIndex++) {
reportProgress(wsIndex, nhist);
const auto &yValues = ws->y(wsIndex);
auto emptySpectrum = std::all_of(yValues.begin(), yValues.end(),
[](double value) { return value == 0.; });
if (emptySpectrum) {
g_log.warning("Spectrum " + std::to_string(wsIndex) + " is empty");
TableWorkspace_sptr tab = boost::make_shared<TableWorkspace>();
tab->addColumn("str", "Name");
tab->addColumn("double", "Value");
tab->addColumn("double", "Error");
for (int j = 0; j < 4; j++) {
API::TableRow row = tab->appendRow();
if (j == PHASE_ROW) {
row << "dummy" << 0.0 << 0.0;
} else {
row << "dummy" << ASYMM_ERROR << 0.0;
}
}
extractDetectorInfo(*tab, *resTab, indexInfo.spectrumNumber(wsIndex));
} else {
auto fit = createChildAlgorithm("Fit");
fit->initialize();
fit->setPropertyValue("Function", funcStr);
fit->setProperty("InputWorkspace", ws);
fit->setProperty("WorkspaceIndex", wsIndex);
fit->setProperty("CreateOutput", true);
fit->setPropertyValue("Output", groupName);
fit->execute();
std::string status = fit->getProperty("OutputStatus");
if (!fit->isExecuted()) {
std::ostringstream error;
error << "Fit failed for spectrum at workspace index " << wsIndex;
error << ": " << status;
throw std::runtime_error(error.str());
} else if (status != success) {
g_log.warning("Fit failed for spectrum at workspace index " +
std::to_string(wsIndex) + ": " + status);
}
API::MatrixWorkspace_sptr fitOut = fit->getProperty("OutputWorkspace");
resGroup->addWorkspace(fitOut);
API::ITableWorkspace_sptr tab = fit->getProperty("OutputParameters");
// Now we have our fitting results stored in tab
// but we need to extract the relevant information, i.e.
// the detector phases (parameter 'p') and asymmetries ('A')
extractDetectorInfo(*tab, *resTab, indexInfo.spectrumNumber(wsIndex));
}
}
}
/// Create a list of input workspace names
std::vector<PlotPeakByLogValue::InputData> PlotPeakByLogValue::makeNames()const
{
std::vector<InputData> nameList;
std::string inputList = getPropertyValue("Input");
int default_wi = getProperty("WorkspaceIndex");
int default_spec = getProperty("Spectrum");
double start = 0;
double end = 0;
typedef Poco::StringTokenizer tokenizer;
tokenizer names(inputList, ";", tokenizer::TOK_IGNORE_EMPTY | tokenizer::TOK_TRIM);
for (tokenizer::Iterator it = names.begin(); it != names.end(); ++it)
{
tokenizer params(*it, ",", tokenizer::TOK_TRIM);
std::string name = params[0];
int wi = default_wi;
int spec = default_spec;
if (params.count() > 1)
{
std::string index = params[1]; // spectrum or workspace index with a prefix
if (index.size() > 2 && index.substr(0,2) == "sp")
{// spectrum number
spec = boost::lexical_cast<int>(index.substr(2));
wi = -1; // undefined yet
}
else if (index.size() > 1 && index[0] == 'i')
{// workspace index
wi = boost::lexical_cast<int>(index.substr(1));
spec = -1; // undefined yet
}
else if (index.size() > 0 && index[0] == 'v')
{
if (index.size() > 1)
{// there is some text after 'v'
tokenizer range(index.substr(1), ":", tokenizer::TOK_IGNORE_EMPTY | tokenizer::TOK_TRIM);
if (range.count() < 1)
{
wi = -2; // means use the whole range
}
else if (range.count() == 1)
{
start = boost::lexical_cast<double>(range[0]);
end = start;
wi = -1;
spec = -1;
}
else if (range.count() > 1)
{
start = boost::lexical_cast<double>(range[0]);
end = boost::lexical_cast<double>(range[1]);
if (start > end) std::swap(start,end);
wi = -1;
spec = -1;
}
}
else
{
wi = -2;
}
}
else
{// error
//throw std::invalid_argument("Malformed spectrum identifier ("+index+"). "
// "It must be either \"sp\" followed by a number for a spectrum number or"
// "\"i\" followed by a number for a workspace index.");
wi = default_wi;
}
}
int period = (params.count() > 2)? boost::lexical_cast<int>(params[2]) : 1;
if (API::AnalysisDataService::Instance().doesExist(name))
{
API::Workspace_sptr ws = API::AnalysisDataService::Instance().retrieve(name);
API::WorkspaceGroup_sptr wsg = boost::dynamic_pointer_cast<API::WorkspaceGroup>(ws);
if (wsg)
{
std::vector<std::string> wsNames = wsg->getNames();
for(std::vector<std::string>::iterator i=wsNames.begin();i!=wsNames.end();++i)
{
nameList.push_back(InputData(*i,wi,-1,period,start,end));
}
continue;
}
}
nameList.push_back(InputData(name,wi,spec,period,start,end));
}
return nameList;
}
/** 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;
}
/// Execute the algorithm
void SassenaFFT::exec()
{
const std::string gwsName = this->getPropertyValue("InputWorkspace");
API::WorkspaceGroup_sptr gws = this->getProperty("InputWorkspace");
const std::string ftqReName = gwsName + "_fqt.Re";
const std::string ftqImName = gwsName + "_fqt.Im";
// Make sure the intermediate structure factor is there
if(!gws->contains(ftqReName) )
{
const std::string errMessg = "workspace "+gwsName+" does not contain an intermediate structure factor";
this->g_log.error(errMessg);
throw Kernel::Exception::NotFoundError("group workspace does not contain",ftqReName);
}
// Retrieve the real and imaginary parts of the intermediate scattering function
DataObjects::Workspace2D_sptr fqtRe = boost::dynamic_pointer_cast<DataObjects::Workspace2D>( gws->getItem( ftqReName ) );
DataObjects::Workspace2D_sptr fqtIm = boost::dynamic_pointer_cast<DataObjects::Workspace2D>( gws->getItem( ftqImName ) );
// Calculate the FFT for all spectra, retaining only the real part since F(q,-t) = F*(q,t)
int part=3; // extract the real part of the transform, assuming I(Q,t) is real
const std::string sqwName = gwsName + "_sqw";
API::IAlgorithm_sptr fft = this->createChildAlgorithm("ExtractFFTSpectrum");
fft->setProperty<DataObjects::Workspace2D_sptr>("InputWorkspace", fqtRe);
if( !this->getProperty("FFTonlyRealPart") )
{
part=0; // extract the real part of the transform, assuming I(Q,t) is complex
fft->setProperty<DataObjects::Workspace2D_sptr>("InputImagWorkspace", fqtIm);
}
fft->setPropertyValue("OutputWorkspace", sqwName );
fft->setProperty<int>("FFTPart",part); // extract the real part
fft->executeAsChildAlg();
API::MatrixWorkspace_sptr sqw0 = fft->getProperty("OutputWorkspace");
DataObjects::Workspace2D_sptr sqw = boost::dynamic_pointer_cast<DataObjects::Workspace2D>( sqw0 );
API::AnalysisDataService::Instance().addOrReplace( sqwName, sqw );
// Transform the X-axis to appropriate dimensions
// We assume the units of the intermediate scattering function are in picoseconds
// The resulting frequency unit is in mili-eV, thus use m_ps2meV
API::IAlgorithm_sptr scaleX = this->createChildAlgorithm("ScaleX");
scaleX->setProperty<DataObjects::Workspace2D_sptr>("InputWorkspace",sqw);
scaleX->setProperty<double>("Factor", m_ps2meV);
scaleX->setProperty<DataObjects::Workspace2D_sptr>("OutputWorkspace", sqw);
scaleX->executeAsChildAlg();
//Do we apply the detailed balance condition exp(E/(2*kT)) ?
if( this->getProperty("DetailedBalance") )
{
double T = this->getProperty("Temp");
// The ExponentialCorrection algorithm assumes the form C0*exp(-C1*x). Note the explicit minus in the exponent
API::IAlgorithm_sptr ec = this->createChildAlgorithm("ExponentialCorrection");
ec->setProperty<DataObjects::Workspace2D_sptr>("InputWorkspace", sqw);
ec->setProperty<DataObjects::Workspace2D_sptr>("OutputWorkspace", sqw);
ec->setProperty<double>("C0",1.0);
ec->setProperty<double>("C1",-1.0/(2.0*T*m_T2ueV)); // Temperature in units of ueV
ec->setPropertyValue("Operation","Multiply");
ec->executeAsChildAlg();
}
// Set the Energy unit for the X-axis
sqw->getAxis(0)->unit() = Kernel::UnitFactory::Instance().create("DeltaE");
// Add to group workspace, except if we are replacing the workspace. In this case, the group workspace
// is already notified of the changes by the analysis data service.
if(!gws->contains(sqwName))
{
gws->add( sqwName );
}
else
{
this->g_log.information("Workspace "+sqwName+" replaced with new contents");
}
}
