/** 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());
}
}
/** This method loops through the response return_vector and saves the datasets details to a table workspace
* @param response :: const reference to response object
* @param outputws :: shred pointer to workspace
* @returns shared pointer to table workspace which stores the data
*/
void CICatHelper::saveDataSets(const ns1__getInvestigationIncludesResponse& response,API::ITableWorkspace_sptr& outputws)
{
//create table workspace
if (outputws->getColumnNames().empty())
{
outputws->addColumn("str","Name");//File name
outputws->addColumn("str","Status");
outputws->addColumn("str","Type");
outputws->addColumn("str","Description");
outputws->addColumn("long64","Sample Id");
}
try
{
std::vector<ns1__dataset*> datasetVec;
datasetVec.assign((response.return_)->datasetCollection.begin(),(response.return_)->datasetCollection.end());
std::vector<ns1__dataset*>::const_iterator dataset_citr;
for(dataset_citr=datasetVec.begin();dataset_citr!=datasetVec.end();++dataset_citr)
{
API::TableRow t = outputws->appendRow();
// DataSet Name
savetoTableWorkspace((*dataset_citr)->name,t);
// DataSet Status
savetoTableWorkspace((*dataset_citr)->datasetStatus,t);
//DataSet Type
savetoTableWorkspace((*dataset_citr)->datasetType,t);
//DataSet Type
savetoTableWorkspace((*dataset_citr)->description,t);
//DataSet Type
savetoTableWorkspace((*dataset_citr)->sampleId,t);
}
}
catch(std::runtime_error& )
{
throw;
}
//return outputws;
}
/** This method saves the search response( investigations )data to a table
* workspace
* @param response :: const reference to response object
* @param outputws :: shared pointer to output workspace
*/
void CICatHelper::saveSearchRessults(
const ns1__searchByAdvancedPaginationResponse &response,
API::ITableWorkspace_sptr &outputws) {
if (outputws->getColumnNames().empty()) {
outputws->addColumn("str", "Investigation id");
outputws->addColumn("str", "Facility");
outputws->addColumn("str", "Title");
outputws->addColumn("str", "Instrument");
outputws->addColumn("str", "Run range");
outputws->addColumn("str", "Start date");
outputws->addColumn("str", "End date");
outputws->addColumn("str", "SessionID");
}
saveInvestigations(response.return_, outputws);
}
/**
Read from the instrument file the dead wires and store the information in a TableWorkspace.
If asked, the dead wires are removed from the data set.
@param localWorkspace :: input raw data workspace, containing the information about the instrument
@param outputws :: input dead wire liste workspace
*/
void PoldiRemoveDeadWires::runExcludWires3
(
DataObjects::Workspace2D_sptr &localWorkspace,
API::ITableWorkspace_sptr &outputws
)
{
outputws->addColumn("int","DeadWires");
boost::shared_ptr<const Mantid::Geometry::IComponent> comp = localWorkspace->getInstrument()->getComponentByName("holder");
boost::shared_ptr<const Mantid::Geometry::ICompAssembly> bank = boost::dynamic_pointer_cast<const Mantid::Geometry::ICompAssembly>(comp);
if (bank)
{
// Get a vector of children (recursively)
std::vector<boost::shared_ptr<const Mantid::Geometry::IComponent> > children;
bank->getChildren(children, true);
std::vector<double> defaultDeadWires;
int ewLine = 0;
for (unsigned int it = 0; it < children.size(); ++it)
{
string wireName = children.at(it)->getName();
std::vector<boost::shared_ptr<const Mantid::Geometry::IComponent> > tyty =
localWorkspace.get()->getInstrument().get()->getAllComponentsWithName(wireName);
std::vector<double> tempWire = tyty[0]->getNumberParameter("excluded");
if(tempWire.size()>0) {
int val = (int)tempWire[0];
g_log.debug() << "_poldi : dead wires :" << val << std::endl;
defaultDeadWires.push_back(val);
for(unsigned int j=0; j<m_channelsPerSpectrum; j++) {
localWorkspace->maskBin(val-1,j,1);
}
ewLine++;
TableRow t = outputws->appendRow();
t << val ;
}
}
g_log.information() << "_poldi : dead wires set to 0 (nb:" << ewLine << ")" << std::endl;
setProperty("nbExcludedWires",ewLine);
} else {
g_log.information() << "_poldi : no dead wire removed" << std::endl;
}
}
/**
* Saves result from "getDataFiles" to workspace.
* @param response :: result response from the catalog.
* @param outputws :: shared pointer to datasets
*/
void ICat4Catalog::saveDataFiles(std::vector<xsd__anyType *> response,
API::ITableWorkspace_sptr &outputws) {
if (outputws->getColumnNames().empty()) {
// Add rows headers to the output workspace.
outputws->addColumn("str", "Name");
outputws->addColumn("str", "Location");
outputws->addColumn("str", "Create Time");
outputws->addColumn("long64", "Id");
outputws->addColumn("long64", "File size(bytes)");
outputws->addColumn("str", "File size");
outputws->addColumn("str", "Description");
}
std::vector<xsd__anyType *>::const_iterator iter;
for (iter = response.begin(); iter != response.end(); ++iter) {
ns1__datafile *datafile = dynamic_cast<ns1__datafile *>(*iter);
if (datafile) {
API::TableRow table = outputws->appendRow();
// Now add the relevant investigation data to the table.
savetoTableWorkspace(datafile->name, table);
savetoTableWorkspace(datafile->location, table);
std::string createDate =
formatDateTime(*datafile->createTime, "%Y-%m-%d %H:%M:%S");
savetoTableWorkspace(&createDate, table);
savetoTableWorkspace(datafile->id, table);
savetoTableWorkspace(datafile->fileSize, table);
std::string fileSize = bytesToString(*datafile->fileSize);
savetoTableWorkspace(&fileSize, table);
if (datafile->description)
savetoTableWorkspace(datafile->description, table);
} else {
throw std::runtime_error("ICat4Catalog::saveDataFiles expected a "
"datafile. Please contact the Mantid "
"development team.");
}
}
}
/**
* Loops through the response vector and saves the datasets details to a table
* workspace.
* @param response :: A vector containing the results of the search query.
* @param outputws :: Shared pointer to output workspace.
*/
void ICat4Catalog::saveDataSets(std::vector<xsd__anyType *> response,
API::ITableWorkspace_sptr &outputws) {
if (outputws->getColumnNames().empty()) {
// Add rows headers to the output workspace.
outputws->addColumn("long64", "ID");
outputws->addColumn("str", "Name");
outputws->addColumn("str", "Description");
outputws->addColumn("str", "Type");
outputws->addColumn("str", "Related investigation ID");
outputws->addColumn("size_t", "Number of datafiles");
}
std::string emptyCell;
for (auto &iter : response) {
ns1__dataset *dataset = dynamic_cast<ns1__dataset *>(iter);
if (dataset) {
API::TableRow table = outputws->appendRow();
savetoTableWorkspace(dataset->id, table);
savetoTableWorkspace(dataset->name, table);
if (dataset->description)
savetoTableWorkspace(dataset->description, table);
else
savetoTableWorkspace(&emptyCell, table);
if (dataset->type)
savetoTableWorkspace(dataset->type->name, table);
else
savetoTableWorkspace(&emptyCell, table);
if (dataset->investigation)
savetoTableWorkspace(dataset->investigation->name, table);
else
savetoTableWorkspace(&emptyCell, table);
size_t datafileCount = dataset->datafiles.size();
savetoTableWorkspace(&datafileCount, table);
} else {
throw std::runtime_error("ICat4Catalog::saveDataSets expected a dataset. "
"Please contact the Mantid development team.");
}
}
}
/**
* Load a table
*/
API::Workspace_sptr LoadNexusProcessed::loadTableEntry(NXEntry & entry)
{
API::ITableWorkspace_sptr workspace;
workspace = Mantid::API::WorkspaceFactory::Instance().createTable("TableWorkspace");
NXData nx_tw = entry.openNXData("table_workspace");
std::vector<double> values;
bool hasNumberOfRowBeenSet = false;
//int numberOfRows = 0;
int columnNumber = 1;
do
{
std::string str = "column_" + boost::lexical_cast<std::string>(columnNumber);
NXInfo info = nx_tw.getDataSetInfo(str.c_str());
if (info.stat == NX_ERROR)
{
break;
}
if ( info.type == NX_FLOAT64 )
{
NXDouble nxDouble = nx_tw.openNXDouble(str.c_str());
std::string columnTitle = nxDouble.attributes("name");
if (!columnTitle.empty())
{
workspace->addColumn("double", columnTitle);
nxDouble.load();
int length = nxDouble.dim0();
if ( !hasNumberOfRowBeenSet )
{
workspace->setRowCount(length);
hasNumberOfRowBeenSet = true;
}
for (int i = 0; i < length; i++)
workspace->cell<double>(i,columnNumber-1) = *(nxDouble() + i);
}
}
else if ( info.type == NX_CHAR )
{
NXChar data = nx_tw.openNXChar(str.c_str());
std::string columnTitle = data.attributes("name");
if (!columnTitle.empty())
{
workspace->addColumn("str", columnTitle);
int nRows = info.dims[0];
if ( !hasNumberOfRowBeenSet )
{
workspace->setRowCount(nRows);
hasNumberOfRowBeenSet = true;
}
int maxStr = info.dims[1];
std::string fromCrap(maxStr,' ');
data.load();
for (int iR = 0; iR < nRows; iR++)
{
for (int i = 0; i < maxStr; i++)
fromCrap[i] = *(data()+i+maxStr*iR);
workspace->cell<std::string>(iR,columnNumber-1) = fromCrap;
}
}
}
columnNumber++;
} while ( 1 );
return boost::static_pointer_cast<API::Workspace>(workspace);
}
/**
* This method loops through the response return_vector and saves the datafile
* details to a table workspace
* @param response :: const reference to response object
* @param outputws :: shared pointer to table workspace which stores the data
*/
void CICatHelper::saveInvestigationIncludesResponse(
const ns1__getInvestigationIncludesResponse &response,
API::ITableWorkspace_sptr &outputws) {
if (outputws->getColumnNames().empty()) {
outputws->addColumn("str", "Name");
outputws->addColumn("str", "Location");
outputws->addColumn("str", "Create Time");
outputws->addColumn("long64", "Id");
outputws->addColumn("long64", "File size(bytes)");
outputws->addColumn("str", "File size");
outputws->addColumn("str", "Description");
}
try {
std::vector<ns1__dataset *> datasetVec;
datasetVec.assign((response.return_)->datasetCollection.begin(),
(response.return_)->datasetCollection.end());
if (datasetVec.empty()) {
throw std::runtime_error("No data files exists in the ICAT database for "
"the selected investigation");
}
std::vector<ns1__dataset *>::const_iterator dataset_citr;
for (dataset_citr = datasetVec.begin(); dataset_citr != datasetVec.end();
++dataset_citr) {
std::vector<ns1__datafile *> datafileVec;
datafileVec.assign((*dataset_citr)->datafileCollection.begin(),
(*dataset_citr)->datafileCollection.end());
if (datafileVec.empty()) {
throw std::runtime_error("No data files exists in the ICAT database "
"for the selected investigation ");
}
std::vector<ns1__datafile *>::const_iterator datafile_citr;
for (datafile_citr = datafileVec.begin();
datafile_citr != datafileVec.end(); ++datafile_citr) {
API::TableRow t = outputws->appendRow();
// File Name
savetoTableWorkspace((*datafile_citr)->name, t);
savetoTableWorkspace((*datafile_citr)->location, t);
// File creation Time.
std::string *creationtime = nullptr;
if ((*datafile_citr)->datafileCreateTime != nullptr) {
time_t crtime = *(*datafile_citr)->datafileCreateTime;
char temp[25];
strftime(temp, 25, "%Y-%b-%d %H:%M:%S", localtime(&crtime));
std::string ftime(temp);
creationtime = new std::string;
creationtime->assign(ftime);
}
savetoTableWorkspace(creationtime, t);
if (creationtime)
delete creationtime;
//
savetoTableWorkspace((*datafile_citr)->id, t);
LONG64 fileSize =
boost::lexical_cast<LONG64>(*(*datafile_citr)->fileSize);
savetoTableWorkspace(&fileSize, t);
savetoTableWorkspace((*datafile_citr)->description, t);
}
}
} catch (std::runtime_error &) {
throw;
}
}
/** 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));
}
}
}
/**
* Calculates the EISF if the fit includes a Delta function
* @param tableWs - The TableWorkspace to append the EISF calculation to
*/
void ConvolutionFitSequential::calculateEISF(
API::ITableWorkspace_sptr &tableWs) {
// Get height data from parameter table
const auto columns = tableWs->getColumnNames();
const auto height = searchForFitParams("Height", columns).at(0);
const auto heightErr = searchForFitParams("Height_Err", columns).at(0);
auto heightY = tableWs->getColumn(height)->numeric_fill<>();
auto heightE = tableWs->getColumn(heightErr)->numeric_fill<>();
// Get amplitude column names
const auto ampNames = searchForFitParams("Amplitude", columns);
const auto ampErrorNames = searchForFitParams("Amplitude_Err", columns);
// For each lorentzian, calculate EISF
size_t maxSize = ampNames.size();
if (ampErrorNames.size() > maxSize) {
maxSize = ampErrorNames.size();
}
for (size_t i = 0; i < maxSize; i++) {
// Get amplitude from column in table workspace
const auto ampName = ampNames.at(i);
auto ampY = tableWs->getColumn(ampName)->numeric_fill<>();
const auto ampErrorName = ampErrorNames.at(i);
auto ampErr = tableWs->getColumn(ampErrorName)->numeric_fill<>();
// Calculate EISF and EISF error
// total = heightY + ampY
auto total = cloneVector(heightY);
std::transform(total.begin(), total.end(), ampY.begin(), total.begin(),
std::plus<double>());
// eisfY = heightY / total
auto eisfY = cloneVector(heightY);
std::transform(eisfY.begin(), eisfY.end(), total.begin(), eisfY.begin(),
std::divides<double>());
// heightE squared
auto heightESq = cloneVector(heightE);
heightESq = squareVector(heightESq);
// ampErr squared
auto ampErrSq = cloneVector(ampErr);
ampErrSq = squareVector(ampErrSq);
// totalErr = heightE squared + ampErr squared
auto totalErr = cloneVector(heightESq);
std::transform(totalErr.begin(), totalErr.end(), ampErrSq.begin(),
totalErr.begin(), std::plus<double>());
// heightY squared
auto heightYSq = cloneVector(heightY);
heightYSq = squareVector(heightYSq);
// total Squared
auto totalSq = cloneVector(total);
totalSq = squareVector(totalSq);
// errOverTotalSq = totalErr / total squared
auto errOverTotalSq = cloneVector(totalErr);
std::transform(errOverTotalSq.begin(), errOverTotalSq.end(),
totalSq.begin(), errOverTotalSq.begin(),
std::divides<double>());
// heightESqOverYSq = heightESq / heightYSq
auto heightESqOverYSq = cloneVector(heightESq);
std::transform(heightESqOverYSq.begin(), heightESqOverYSq.end(),
heightYSq.begin(), heightESqOverYSq.begin(),
std::divides<double>());
// sqrtESqOverYSq = squareRoot( heightESqOverYSq )
auto sqrtESqOverYSq = cloneVector(heightESqOverYSq);
std::transform(sqrtESqOverYSq.begin(), sqrtESqOverYSq.end(),
sqrtESqOverYSq.begin(),
static_cast<double (*)(double)>(sqrt));
// eisfYSumRoot = eisfY * sqrtESqOverYSq
auto eisfYSumRoot = cloneVector(eisfY);
std::transform(eisfYSumRoot.begin(), eisfYSumRoot.end(),
sqrtESqOverYSq.begin(), eisfYSumRoot.begin(),
std::multiplies<double>());
// eisfErr = eisfYSumRoot + errOverTotalSq
auto eisfErr = cloneVector(eisfYSumRoot);
std::transform(eisfErr.begin(), eisfErr.end(), errOverTotalSq.begin(),
eisfErr.begin(), std::plus<double>());
// Append the calculated values to the table workspace
auto columnName =
ampName.substr(0, (ampName.size() - std::string("Amplitude").size()));
columnName += "EISF";
auto errorColumnName = ampErrorName.substr(
0, (ampErrorName.size() - std::string("Amplitude_Err").size()));
errorColumnName += "EISF_Err";
tableWs->addColumn("double", columnName);
tableWs->addColumn("double", errorColumnName);
size_t maxEisf = eisfY.size();
if (eisfErr.size() > maxEisf) {
maxEisf = eisfErr.size();
}
Column_sptr col = tableWs->getColumn(columnName);
Column_sptr errCol = tableWs->getColumn(errorColumnName);
for (size_t j = 0; j < maxEisf; j++) {
col->cell<double>(j) = eisfY.at(j);
errCol->cell<double>(j) = eisfErr.at(j);
}
}
}
/**
* Saves investigations to a table workspace.
* @param response :: A vector containing the results of the search query.
* @param outputws :: Shared pointer to output workspace.
*/
void ICat4Catalog::saveInvestigations(std::vector<xsd__anyType *> response,
API::ITableWorkspace_sptr &outputws) {
if (outputws->getColumnNames().empty()) {
// Add rows headers to the output workspace.
outputws->addColumn("long64", "DatabaseID");
outputws->addColumn("str", "InvestigationID");
outputws->addColumn("str", "Facility");
outputws->addColumn("str", "Title");
outputws->addColumn("str", "Instrument");
outputws->addColumn("str", "Run range");
outputws->addColumn("str", "Start date");
outputws->addColumn("str", "End date");
outputws->addColumn("str", "SessionID");
}
// Add data to each row in the output workspace.
std::vector<xsd__anyType *>::const_iterator iter;
for (iter = response.begin(); iter != response.end(); ++iter) {
// Cast from xsd__anyType to subclass (xsd__string).
ns1__investigation *investigation =
dynamic_cast<ns1__investigation *>(*iter);
if (investigation) {
API::TableRow table = outputws->appendRow();
// Used to insert an empty string into the cell if value does not exist.
std::string emptyCell;
// Now add the relevant investigation data to the table (They always
// exist).
savetoTableWorkspace(investigation->id, table);
savetoTableWorkspace(investigation->name, table);
savetoTableWorkspace(investigation->facility->name, table);
savetoTableWorkspace(investigation->title, table);
savetoTableWorkspace(
investigation->investigationInstruments.at(0)->instrument->name,
table);
// Verify that the run parameters vector exist prior to doing anything.
// Since some investigations may not have run parameters.
if (!investigation->parameters.empty()) {
savetoTableWorkspace(investigation->parameters[0]->stringValue, table);
} else {
savetoTableWorkspace(&emptyCell, table);
}
// Again, we need to check first if start and end date exist prior to
// insertion.
if (investigation->startDate) {
std::string startDate =
formatDateTime(*investigation->startDate, "%Y-%m-%d");
savetoTableWorkspace(&startDate, table);
} else {
savetoTableWorkspace(&emptyCell, table);
}
if (investigation->endDate) {
std::string endDate =
formatDateTime(*investigation->endDate, "%Y-%m-%d");
savetoTableWorkspace(&endDate, table);
} else {
savetoTableWorkspace(&emptyCell, table);
}
std::string sessionID = m_session->getSessionId();
savetoTableWorkspace(&sessionID, table);
} else {
throw std::runtime_error("ICat4Catalog::saveInvestigations expected an "
"investigation. Please contact the Mantid "
"development team.");
}
}
}