double EstimateResolutionDiffraction::getWavelength() {
double wavelength = getProperty("Wavelength");
if (!isEmpty(wavelength)) {
return wavelength;
}
Property *cwlproperty = m_inputWS->run().getProperty("LambdaRequest");
if (!cwlproperty)
throw runtime_error(
"Unable to locate property LambdaRequest as central wavelength. ");
TimeSeriesProperty<double> *cwltimeseries =
dynamic_cast<TimeSeriesProperty<double> *>(cwlproperty);
if (!cwltimeseries)
throw runtime_error(
"LambdaReqeust is not a TimeSeriesProperty in double. ");
string unit = cwltimeseries->units();
if (unit.compare("Angstrom") != 0) {
throw runtime_error("Unit is not recognized: " + unit);
}
return cwltimeseries->timeAverageValue();
}
/** Try to load the "Veto_pulse" field in DASLogs
* and convert it to a sample log.
*
* @param file :: open nexus file at the DASLogs group
* @param workspace :: workspace to add to.
*/
void LoadNexusLogs::loadVetoPulses(
::NeXus::File &file,
boost::shared_ptr<API::MatrixWorkspace> workspace) const {
try {
file.openGroup("Veto_pulse", "NXgroup");
} catch (::NeXus::Exception &) {
// No group. This is common in older files
return;
}
file.openData("veto_pulse_time");
// Load the start date/time as ISO8601 string.
std::string start_time;
file.getAttr("start_time", start_time);
DateAndTime start(start_time);
// Read the offsets
std::vector<double> time_double;
file.getData(time_double);
// Fake values with zeroes.
std::vector<double> values(time_double.size(), 0.0);
TimeSeriesProperty<double> *tsp =
new TimeSeriesProperty<double>("veto_pulse_time");
tsp->create(start, time_double, values);
tsp->setUnits("");
// Add the log
workspace->mutableRun().addProperty(tsp);
file.closeData();
file.closeGroup();
}
void EstimatePDDetectorResolution::retrieveInstrumentParameters()
{
#if 0
// Call SolidAngle to get solid angles for all detectors
Algorithm_sptr calsolidangle = createChildAlgorithm("SolidAngle", -1, -1, true);
calsolidangle->initialize();
calsolidangle->setProperty("InputWorkspace", m_inputWS);
calsolidangle->execute();
if (!calsolidangle->isExecuted())
throw runtime_error("Unable to run solid angle. ");
m_solidangleWS = calsolidangle->getProperty("OutputWorkspace");
if (!m_solidangleWS)
throw runtime_error("Unable to get solid angle workspace from SolidAngle(). ");
size_t numspec = m_solidangleWS->getNumberHistograms();
for (size_t i = 0; i < numspec; ++i)
g_log.debug() << "[DB]: " << m_solidangleWS->readY(i)[0] << "\n";
#endif
// Calculate centre neutron velocity
Property* cwlproperty = m_inputWS->run().getProperty("LambdaRequest");
if (!cwlproperty)
throw runtime_error("Unable to locate property LambdaRequest as central wavelength. ");
TimeSeriesProperty<double>* cwltimeseries = dynamic_cast<TimeSeriesProperty<double>* >(cwlproperty);
if (!cwltimeseries)
throw runtime_error("LambdaReqeust is not a TimeSeriesProperty in double. ");
if (cwltimeseries->size() != 1)
throw runtime_error("LambdaRequest should contain 1 and only 1 entry. ");
double centrewavelength = cwltimeseries->nthValue(0);
string unit = cwltimeseries->units();
if (unit.compare("Angstrom") == 0)
centrewavelength *= 1.0E-10;
else
throw runtime_error("Unit is not recognized");
m_centreVelocity = PhysicalConstants::h/PhysicalConstants::NeutronMass/centrewavelength;
g_log.notice() << "Centre wavelength = " << centrewavelength << ", Centre neutron velocity = " << m_centreVelocity << "\n";
// Calcualte L1 sample to source
Instrument_const_sptr instrument = m_inputWS->getInstrument();
V3D samplepos = instrument->getSample()->getPos();
V3D sourcepos = instrument->getSource()->getPos();
m_L1 = samplepos.distance(sourcepos);
g_log.notice() << "L1 = " << m_L1 << "\n";
return;
}
/// Do the actual work of modifying the log in the workspace.
void ChangeLogTime::exec()
{
// check that a log was specified
string logname = this->getProperty("LogName");
if (logname.empty()) {
throw std::runtime_error("Failed to supply a LogName");
}
// everything will need an offset
double offset = this->getProperty("TimeOffset");
// make sure the log is in the input workspace
MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
Kernel::TimeSeriesProperty<double> * oldlog = dynamic_cast<Kernel::TimeSeriesProperty<double> *>( inputWS->run().getLogData(logname) );
if (!oldlog) {
stringstream msg;
msg << "InputWorkspace \'" << this->getPropertyValue("InputWorkspace")
<< "\' does not have LogName \'" << logname << "\'";
throw std::runtime_error(msg.str());
}
// Create the new log
TimeSeriesProperty<double>* newlog = new TimeSeriesProperty<double>(logname);
newlog->setUnits(oldlog->units());
int size = oldlog->realSize();
vector<double> values = oldlog->valuesAsVector();
vector<DateAndTime> times = oldlog->timesAsVector();
for (int i = 0; i < size; i++) {
newlog->addValue(times[i] + offset, values[i]);
}
// Just overwrite if the change is in place
MatrixWorkspace_sptr outputWS = getProperty("OutputWorkspace");
if (outputWS != inputWS)
{
IAlgorithm_sptr duplicate = createChildAlgorithm("CloneWorkspace");
duplicate->initialize();
duplicate->setProperty<Workspace_sptr>("InputWorkspace", boost::dynamic_pointer_cast<Workspace>(inputWS));
duplicate->execute();
Workspace_sptr temp = duplicate->getProperty("OutputWorkspace");
outputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(temp);
setProperty("OutputWorkspace", outputWS);
}
outputWS->mutableRun().addProperty(newlog, true);
}
/**
* Add a sample environment log for the proton chage (charge of the pulse in
*picoCoulombs)
* and set the scalar value (total proton charge, microAmps*hours, on the
*sample)
*
* @param workspace :: Event workspace to set the proton charge on
*/
void LoadEventPreNexus::setProtonCharge(
DataObjects::EventWorkspace_sptr &workspace) {
if (this->proton_charge.empty()) // nothing to do
return;
Run &run = workspace->mutableRun();
// Add the proton charge entries.
TimeSeriesProperty<double> *log =
new TimeSeriesProperty<double>("proton_charge");
log->setUnits("picoCoulombs");
// Add the time and associated charge to the log
log->addValues(this->pulsetimes, this->proton_charge);
/// TODO set the units for the log
run.addLogData(log);
double integ = run.integrateProtonCharge();
// run.setProtonCharge(this->proton_charge_tot); //This is now redundant
this->g_log.information() << "Total proton charge of " << integ
<< " microAmp*hours found by integrating.\n";
}
/**
* Check if the file is SNS text; load it if it is, return false otherwise.
* @return true if the file was a SNS style; false otherwise.
*/
bool LoadLog::LoadSNSText()
{
// Get the SNS-specific parameter
std::vector<std::string> names = getProperty("Names");
std::vector<std::string> units = getProperty("Units");
// Get the input workspace and retrieve run from workspace.
// the log file(s) will be loaded into the run object of the workspace
const MatrixWorkspace_sptr localWorkspace = getProperty("Workspace");
// open log file
std::ifstream inLogFile(m_filename.c_str());
// Get the first line
std::string aLine;
if (!Mantid::Kernel::Strings::extractToEOL(inLogFile,aLine))
return false;
std::vector<double> cols;
bool ret = SNSTextFormatColumns(aLine, cols);
// Any error?
if (!ret || cols.size() < 2)
return false;
size_t numCols = static_cast<size_t>(cols.size()-1);
if (names.size() != numCols)
throw std::invalid_argument("The Names parameter should have one fewer entry as the number of columns in a SNS-style text log file.");
if ((!units.empty()) && (units.size() != numCols))
throw std::invalid_argument("The Units parameter should have either 0 entries or one fewer entry as the number of columns in a SNS-style text log file.");
// Ok, create all the logs
std::vector<TimeSeriesProperty<double>*> props;
for(size_t i=0; i < numCols; i++)
{
TimeSeriesProperty<double>* p = new TimeSeriesProperty<double>(names[i]);
if (units.size() == numCols)
p->setUnits(units[i]);
props.push_back(p);
}
// Go back to start
inLogFile.seekg(0);
while(Mantid::Kernel::Strings::extractToEOL(inLogFile,aLine))
{
if (aLine.size() == 0)
break;
if (SNSTextFormatColumns(aLine, cols))
{
if (cols.size() == numCols+1)
{
DateAndTime time(cols[0], 0.0);
for(size_t i=0; i<numCols; i++)
props[i]->addValue(time, cols[i+1]);
}
else
throw std::runtime_error("Inconsistent number of columns while reading SNS-style text file.");
}
else
throw std::runtime_error("Error while reading columns in SNS-style text file.");
}
// Now add all the full logs to the workspace
for(size_t i=0; i < numCols; i++)
{
std::string name = props[i]->name();
if (localWorkspace->mutableRun().hasProperty(name))
{
localWorkspace->mutableRun().removeLogData(name);
g_log.information() << "Log data named " << name << " already existed and was overwritten.\n";
}
localWorkspace->mutableRun().addLogData(props[i]);
}
return true;
}
/**
* Executes the algorithm
*/
void PlotAsymmetryByLogValue::exec()
{
m_forward_list = getProperty("ForwardSpectra");
m_backward_list = getProperty("BackwardSpectra");
m_autogroup = ( m_forward_list.size() == 0 && m_backward_list.size() == 0);
//double alpha = getProperty("Alpha");
std::string logName = getProperty("LogValue");
int red = getProperty("Red");
int green = getProperty("Green");
std::string stype = getProperty("Type");
m_int = stype == "Integral";
std::string firstFN = getProperty("FirstRun");
std::string lastFN = getProperty("LastRun");
std::string ext = firstFN.substr(firstFN.find_last_of("."));
firstFN.erase(firstFN.size()-4);
lastFN.erase(lastFN.size()-4);
std::string fnBase = firstFN;
size_t i = fnBase.size()-1;
while(isdigit(fnBase[i])) i--;
if (i == fnBase.size()-1)
{
g_log.error("File name must end with a number.");
throw Exception::FileError("File name must end with a number.",firstFN);
}
fnBase.erase(i+1);
firstFN.erase(0,fnBase.size());
lastFN.erase(0,fnBase.size());
size_t is = atoi(firstFN.c_str()); // starting run number
size_t ie = atoi(lastFN.c_str()); // last run number
int w = static_cast<int>(firstFN.size());
// The number of runs
size_t npoints = ie - is + 1;
// Create the 2D workspace for the output
int nplots = green != EMPTY_INT() ? 4 : 1;
MatrixWorkspace_sptr outWS = WorkspaceFactory::Instance().create("Workspace2D",
nplots, // the number of plots
npoints, // the number of data points on a plot
npoints // it's not a histogram
);
TextAxis* tAxis = new TextAxis(nplots);
if (nplots == 1)
{
tAxis->setLabel(0,"Asymmetry");
}
else
{
tAxis->setLabel(0,"Red-Green");
tAxis->setLabel(1,"Red");
tAxis->setLabel(2,"Green");
tAxis->setLabel(3,"Red+Green");
}
outWS->replaceAxis(1,tAxis);
Progress progress(this,0,1,ie-is+2);
for(size_t i=is; i<=ie; i++)
{
std::ostringstream fn,fnn;
fnn << std::setw(w) << std::setfill('0') << i ;
fn << fnBase << fnn.str() << ext;
// Load a muon nexus file with auto_group set to true
IAlgorithm_sptr loadNexus = createChildAlgorithm("LoadMuonNexus");
loadNexus->setPropertyValue("Filename", fn.str());
loadNexus->setPropertyValue("OutputWorkspace","tmp"+fnn.str());
if (m_autogroup)
loadNexus->setPropertyValue("AutoGroup","1");
loadNexus->execute();
std::string wsProp = "OutputWorkspace";
DataObjects::Workspace2D_sptr ws_red;
DataObjects::Workspace2D_sptr ws_green;
// Run through the periods of the loaded file and do calculations on the selected ones
Workspace_sptr tmp = loadNexus->getProperty(wsProp);
WorkspaceGroup_sptr wsGroup = boost::dynamic_pointer_cast<WorkspaceGroup>(tmp);
if (!wsGroup)
{
ws_red = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(tmp);
TimeSeriesProperty<double>* logp =
dynamic_cast<TimeSeriesProperty<double>*>(ws_red->run().getLogData(logName));
if (!logp)
{
throw std::invalid_argument("Log "+logName+" does not exist or not a double type");
}
double Y,E;
calcIntAsymmetry(ws_red,Y,E);
outWS->dataY(0)[i-is] = Y;
outWS->dataX(0)[i-is] = logp->lastValue();
outWS->dataE(0)[i-is] = E;
}
else
{
for( int period = 1; period <= wsGroup->getNumberOfEntries(); ++period )
{
std::stringstream suffix;
suffix << period;
wsProp = "OutputWorkspace_" + suffix.str();// form the property name for higher periods
// Do only one period
if (green == EMPTY_INT() && period == red)
{
Workspace_sptr tmpff = loadNexus->getProperty(wsProp);
ws_red = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(tmpff);
TimeSeriesProperty<double>* logp =
dynamic_cast<TimeSeriesProperty<double>*>(ws_red->run().getLogData(logName));
if (!logp)
{
throw std::invalid_argument("Log "+logName+" does not exist or not a double type");
}
double Y,E;
calcIntAsymmetry(ws_red,Y,E);
outWS->dataY(0)[i-is] = Y;
outWS->dataX(0)[i-is] = logp->lastValue();
outWS->dataE(0)[i-is] = E;
}
else // red & green
{
if (period == red)
{
Workspace_sptr temp = loadNexus->getProperty(wsProp);
ws_red = boost::dynamic_pointer_cast<Workspace2D>(temp);
}
if (period == green)
{
Workspace_sptr temp = loadNexus->getProperty(wsProp);
ws_green = boost::dynamic_pointer_cast<Workspace2D>(temp);
}
}
}
// red & green claculation
if (green != EMPTY_INT())
{
if (!ws_red || !ws_green)
throw std::invalid_argument("Red or green period is out of range");
TimeSeriesProperty<double>* logp =
dynamic_cast<TimeSeriesProperty<double>*>(ws_red->run().getLogData(logName));
if (!logp)
{
throw std::invalid_argument("Log "+logName+" does not exist or not a double type");
}
double Y,E;
double Y1,E1;
calcIntAsymmetry(ws_red,Y,E);
calcIntAsymmetry(ws_green,Y1,E1);
outWS->dataY(1)[i-is] = Y;
outWS->dataX(1)[i-is] = logp->lastValue();
outWS->dataE(1)[i-is] = E;
outWS->dataY(2)[i-is] = Y1;
outWS->dataX(2)[i-is] = logp->lastValue();
outWS->dataE(2)[i-is] = E1;
outWS->dataY(3)[i-is] = Y + Y1;
outWS->dataX(3)[i-is] = logp->lastValue();
outWS->dataE(3)[i-is] = sqrt(E*E+E1*E1);
// move to last for safety since some grouping takes place in the
// calcIntAsymmetry call below
calcIntAsymmetry(ws_red,ws_green,Y,E);
outWS->dataY(0)[i-is] = Y;
outWS->dataX(0)[i-is] = logp->lastValue();
outWS->dataE(0)[i-is] = E;
}
else if (!ws_red)
throw std::invalid_argument("Red period is out of range");
}
progress.report();
}
outWS->getAxis(0)->title() = logName;
outWS->setYUnitLabel("Asymmetry");
// Assign the result to the output workspace property
setProperty("OutputWorkspace", outWS);
}
/**
* Executes the algorithm
*/
void PlotPeakByLogValue::exec()
{
// Create a list of the input workspace
const std::vector<InputData> wsNames = makeNames();
std::string fun = getPropertyValue("Function");
//int wi = getProperty("WorkspaceIndex");
std::string logName = getProperty("LogValue");
bool sequential = getPropertyValue("FitType") == "Sequential";
bool isDataName = false; // if true first output column is of type string and is the data source name
ITableWorkspace_sptr result = WorkspaceFactory::Instance().createTable("TableWorkspace");
if (logName == "SourceName")
{
result->addColumn("str","Source name");
isDataName = true;
}
else if (logName.empty())
{
result->addColumn("double","axis-1");
}
else
{
result->addColumn("double",logName);
}
// Create an instance of the fitting function to obtain the names of fitting parameters
IFitFunction* ifun = FunctionFactory::Instance().createInitialized(fun);
if (!ifun)
{
throw std::invalid_argument("Fitting function failed to initialize");
}
for(size_t iPar=0;iPar<ifun->nParams();++iPar)
{
result->addColumn("double",ifun->parameterName(iPar));
result->addColumn("double",ifun->parameterName(iPar)+"_Err");
}
result->addColumn("double","Chi_squared");
delete ifun;
setProperty("OutputWorkspace",result);
double dProg = 1./static_cast<double>(wsNames.size());
double Prog = 0.;
for(int i=0;i<static_cast<int>(wsNames.size());++i)
{
InputData data = getWorkspace(wsNames[i]);
if (!data.ws)
{
g_log.warning() << "Cannot access workspace " << wsNames[i].name << '\n';
continue;
}
if (data.i < 0 && data.indx.empty())
{
g_log.warning() << "Zero spectra selected for fitting in workspace " << wsNames[i].name << '\n';
continue;
}
int j,jend;
if (data.i >= 0)
{
j = data.i;
jend = j + 1;
}
else
{// no need to check data.indx.empty()
j = data.indx.front();
jend = data.indx.back() + 1;
}
dProg /= abs(jend - j);
for(;j < jend;++j)
{
// Find the log value: it is either a log-file value or simply the workspace number
double logValue;
if (logName.empty())
{
API::Axis* axis = data.ws->getAxis(1);
logValue = (*axis)(j);
}
else if (logName != "SourceName")
{
Kernel::Property* prop = data.ws->run().getLogData(logName);
if (!prop)
{
throw std::invalid_argument("Log value "+logName+" does not exist");
}
TimeSeriesProperty<double>* logp =
dynamic_cast<TimeSeriesProperty<double>*>(prop);
logValue = logp->lastValue();
}
std::string resFun = fun;
std::vector<double> errors;
double chi2;
try
{
// Fit the function
API::IAlgorithm_sptr fit = createSubAlgorithm("Fit");
fit->initialize();
fit->setProperty("InputWorkspace",data.ws);
//fit->setPropertyValue("InputWorkspace",data.ws->getName());
fit->setProperty("WorkspaceIndex",j);
fit->setPropertyValue("Function",fun);
fit->setPropertyValue("StartX",getPropertyValue("StartX"));
fit->setPropertyValue("EndX",getPropertyValue("EndX"));
fit->setPropertyValue("Minimizer",getPropertyValue("Minimizer"));
fit->setPropertyValue("CostFunction",getPropertyValue("CostFunction"));
fit->execute();
resFun = fit->getPropertyValue("Function");
errors = fit->getProperty("Errors");
chi2 = fit->getProperty("OutputChi2overDoF");
}
catch(...)
{
g_log.error("Error in Fit subalgorithm");
throw;
}
if (sequential)
{
fun = resFun;
}
// Extract the fitted parameters and put them into the result table
TableRow row = result->appendRow();
if (isDataName)
{
row << wsNames[i].name;
}
else
{
row << logValue;
}
ifun = FunctionFactory::Instance().createInitialized(resFun);
for(size_t iPar=0;iPar<ifun->nParams();++iPar)
{
row << ifun->getParameter(iPar) << errors[iPar];
}
row << chi2;
delete ifun;
Prog += dProg;
progress(Prog);
interruption_point();
} // for(;j < jend;++j)
}
}
/** Execute the algorithm.
*/
void LoadDNSSCD::exec() {
MultipleFileProperty *multiFileProp =
dynamic_cast<MultipleFileProperty *>(getPointerToProperty("Filenames"));
if (!multiFileProp) {
throw std::logic_error(
"Filenames property must have MultipleFileProperty type.");
}
std::vector<std::string> filenames =
VectorHelper::flattenVector(multiFileProp->operator()());
if (filenames.empty())
throw std::invalid_argument("Must specify at least one filename.");
// set type of normalization
std::string normtype = getProperty("Normalization");
if (normtype == "monitor") {
m_normtype = "Monitor";
m_normfactor = 1.0;
} else {
m_normtype = "Timer";
m_normfactor = 0.0; // error for time should be 0
}
g_log.notice() << "The normalization workspace will contain " << m_normtype
<< ".\n";
ExperimentInfo_sptr expinfo = boost::make_shared<ExperimentInfo>();
API::Run &run = expinfo->mutableRun();
for (auto fname : filenames) {
std::map<std::string, std::string> str_metadata;
std::map<std::string, double> num_metadata;
try {
read_data(fname, str_metadata, num_metadata);
// if no stop_time, take file_save_time
std::string time(str_metadata["stop_time"]);
if (time.empty()) {
g_log.warning()
<< "stop_time is empty! File save time will be used instead."
<< std::endl;
time = str_metadata["file_save_time"];
}
updateProperties<std::string>(run, str_metadata, time);
updateProperties<double>(run, num_metadata, time);
} catch (...) {
g_log.warning() << "Failed to read file " << fname;
g_log.warning() << ". This file will be ignored. " << std::endl;
g_log.debug() << boost::current_exception_diagnostic_information()
<< std::endl;
}
}
if (m_data.empty())
throw std::runtime_error(
"No valid DNS files have been provided. Nothing to load.");
m_OutWS = MDEventFactory::CreateMDWorkspace(m_nDims, "MDEvent");
m_OutWS->addExperimentInfo(expinfo);
// load huber angles from a table workspace if given
ITableWorkspace_sptr huberWS = getProperty("LoadHuberFrom");
if (huberWS) {
g_log.notice() << "Huber angles will be loaded from " << huberWS->getName()
<< std::endl;
loadHuber(huberWS);
}
// get wavelength
TimeSeriesProperty<double> *wlprop =
dynamic_cast<TimeSeriesProperty<double> *>(
expinfo->run().getProperty("Lambda"));
// assume, that lambda is in nm
double wavelength =
wlprop->minValue() * 10.0; // needed to estimate extents => minValue
run.addProperty("wavelength", wavelength);
run.getProperty("wavelength")->setUnits("Angstrom");
fillOutputWorkspace(wavelength);
std::string saveHuberTableWS = getProperty("SaveHuberTo");
if (!saveHuberTableWS.empty()) {
Mantid::API::ITableWorkspace_sptr huber_table = saveHuber();
setProperty("SaveHuberTo", huber_table);
}
setProperty("OutputWorkspace", m_OutWS);
}
