/** Executes the algorithm
* @throw Exception::FileError If the calibration file cannot be opened and
* read successfully
* @throw Exception::InstrumentDefinitionError If unable to obtain the
* source-sample distance
*/
void AlignDetectors::exec() {
// Get the input workspace
MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
this->getCalibrationWS(inputWS);
// Initialise the progress reporting object
m_numberOfSpectra = static_cast<int64_t>(inputWS->getNumberHistograms());
API::MatrixWorkspace_sptr outputWS = getProperty("OutputWorkspace");
// If input and output workspaces are not the same, create a new workspace for
// the output
if (outputWS != inputWS) {
outputWS = inputWS->clone();
setProperty("OutputWorkspace", outputWS);
}
// Set the final unit that our output workspace will have
setXAxisUnits(outputWS);
ConversionFactors converter = ConversionFactors(m_calibrationWS);
Progress progress(this, 0.0, 1.0, m_numberOfSpectra);
auto eventW = boost::dynamic_pointer_cast<EventWorkspace>(outputWS);
if (eventW) {
align(converter, progress, *eventW);
} else {
align(converter, progress, *outputWS);
}
}
void SANSSolidAngleCorrection::execEvent() {
MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
// generate the output workspace pointer
MatrixWorkspace_sptr outputWS = getProperty("OutputWorkspace");
if (outputWS != inputWS) {
outputWS = inputWS->clone();
setProperty("OutputWorkspace", outputWS);
}
auto outputEventWS = boost::dynamic_pointer_cast<EventWorkspace>(outputWS);
const int numberOfSpectra =
static_cast<int>(outputEventWS->getNumberHistograms());
Progress progress(this, 0.0, 1.0, numberOfSpectra);
progress.report("Solid Angle Correction");
PARALLEL_FOR1(outputEventWS)
for (int i = 0; i < numberOfSpectra; i++) {
PARALLEL_START_INTERUPT_REGION
IDetector_const_sptr det;
try {
det = outputEventWS->getDetector(i);
} catch (Exception::NotFoundError &) {
g_log.warning() << "Workspace index " << i
<< " has no detector assigned to it - discarding\n";
// Catch if no detector. Next line tests whether this happened - test
// placed
// outside here because Mac Intel compiler doesn't like 'continue' in a
// catch
// in an openmp block.
}
if (!det)
continue;
// Skip if we have a monitor or if the detector is masked.
if (det->isMonitor() || det->isMasked())
continue;
// Compute solid angle correction factor
const bool is_tube = getProperty("DetectorTubes");
const double tanTheta = tan(outputEventWS->detectorTwoTheta(*det));
const double theta_term = sqrt(tanTheta * tanTheta + 1.0);
double corr;
if (is_tube) {
const double tanAlpha = tan(getYTubeAngle(det, inputWS));
const double alpha_term = sqrt(tanAlpha * tanAlpha + 1.0);
corr = alpha_term * theta_term * theta_term;
} else {
corr = theta_term * theta_term * theta_term;
}
EventList &el = outputEventWS->getSpectrum(i);
el *= corr;
progress.report("Solid Angle Correction");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
setProperty("OutputMessage", "Solid angle correction applied");
}
/**
* This performs a similar operation to divide, but is a separate algorithm so
*that the correct spectra are used in the case of detector scans. This
*currently does not support event workspaces properly, but should be made to in
*the future.
*
* @param inputWorkspace The workspace with the spectra to divide by the monitor
* @param outputWorkspace The resulting workspace
*/
void NormaliseToMonitor::performHistogramDivision(
const MatrixWorkspace_sptr &inputWorkspace,
MatrixWorkspace_sptr &outputWorkspace) {
if (outputWorkspace != inputWorkspace)
outputWorkspace = inputWorkspace->clone();
size_t monitorWorkspaceIndex = 0;
Progress prog(this, 0.0, 1.0, m_workspaceIndexes.size());
const auto &specInfo = inputWorkspace->spectrumInfo();
for (const auto workspaceIndex : m_workspaceIndexes) {
// Errors propagated according to
// http://docs.mantidproject.org/nightly/concepts/ErrorPropagation.html#error-propagation
// This is similar to that in MantidAlgorithms::Divide
prog.report("Performing normalisation");
size_t timeIndex = 0;
if (m_scanInput)
timeIndex = specInfo.spectrumDefinition(workspaceIndex)[0].second;
const auto newYFactor =
1.0 / m_monitor->histogram(monitorWorkspaceIndex).y()[0];
const auto divisorError =
m_monitor->histogram(monitorWorkspaceIndex).e()[0];
const double yErrorFactor = pow(divisorError * newYFactor, 2);
monitorWorkspaceIndex++;
PARALLEL_FOR_IF(Kernel::threadSafe(*outputWorkspace))
for (int64_t i = 0; i < int64_t(outputWorkspace->getNumberHistograms());
++i) {
PARALLEL_START_INTERUPT_REGION
const auto &specDef = specInfo.spectrumDefinition(i);
if (!spectrumDefinitionsMatchTimeIndex(specDef, timeIndex))
continue;
auto hist = outputWorkspace->histogram(i);
auto &yValues = hist.mutableY();
auto &eValues = hist.mutableE();
for (size_t j = 0; j < yValues.size(); ++j) {
eValues[j] = newYFactor * sqrt(eValues[j] * eValues[j] +
yValues[j] * yValues[j] * yErrorFactor);
yValues[j] *= newYFactor;
}
outputWorkspace->setHistogram(i, hist);
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
}
}
/**
* Utility function to add the given workspace to the ADS if debugging is
* enabled.
*
* @param ws [in] : the workspace to add to the ADS
* @param wsName [in] : the name to output the workspace as
* @param wsSuffix [in] : a suffix to apply to the wsName
* @param debug [in] : true if the workspace should be added to the ADS (the
* function does nothing if this is false)
* @param step [inout] : the current step number, which is added to the wsSuffix
* and is incremented after the workspace is output
*/
void ReflectometryReductionOne2::outputDebugWorkspace(
MatrixWorkspace_sptr ws, const std::string &wsName,
const std::string &wsSuffix, const bool debug, int &step) {
// Nothing to do if debug is not enabled
if (debug) {
// Clone the workspace because otherwise we can end up outputting the same
// workspace twice with different names, which is confusing.
MatrixWorkspace_sptr cloneWS = ws->clone();
AnalysisDataService::Instance().addOrReplace(
wsName + "_" + std::to_string(step) + wsSuffix, cloneWS);
++step;
}
}
/** Convert a workspace to Q
*
* @param inputWS : The input workspace (in wavelength) to convert to Q
* @return : output workspace in Q
*/
MatrixWorkspace_sptr
ReflectometryReductionOne2::convertToQ(MatrixWorkspace_sptr inputWS) {
bool const moreThanOneDetector = inputWS->getDetector(0)->nDets() > 1;
bool const shouldCorrectAngle =
!(*getProperty("ThetaIn")).isDefault() && !summingInQ();
if (shouldCorrectAngle && moreThanOneDetector) {
if (inputWS->getNumberHistograms() > 1) {
throw std::invalid_argument(
"Expected a single group in "
"ProcessingInstructions to be able to "
"perform angle correction, found " +
std::to_string(inputWS->getNumberHistograms()));
}
MatrixWorkspace_sptr IvsQ = inputWS->clone();
auto &XOut0 = IvsQ->mutableX(0);
const auto &XIn0 = inputWS->x(0);
double const theta = getProperty("ThetaIn");
double const factor = 4.0 * M_PI * sin(theta * M_PI / 180.0);
std::transform(XIn0.rbegin(), XIn0.rend(), XOut0.begin(),
[factor](double x) { return factor / x; });
auto &Y0 = IvsQ->mutableY(0);
auto &E0 = IvsQ->mutableE(0);
std::reverse(Y0.begin(), Y0.end());
std::reverse(E0.begin(), E0.end());
IvsQ->getAxis(0)->unit() =
UnitFactory::Instance().create("MomentumTransfer");
return IvsQ;
} else {
auto convertUnits = this->createChildAlgorithm("ConvertUnits");
convertUnits->initialize();
convertUnits->setProperty("InputWorkspace", inputWS);
convertUnits->setProperty("Target", "MomentumTransfer");
convertUnits->setProperty("AlignBins", false);
convertUnits->execute();
MatrixWorkspace_sptr IvsQ = convertUnits->getProperty("OutputWorkspace");
return IvsQ;
}
}
/** Carries out the bin-by-bin normalization
* @param inputWorkspace The input workspace
* @param outputWorkspace The result workspace
*/
void NormaliseToMonitor::normaliseBinByBin(
const MatrixWorkspace_sptr &inputWorkspace,
MatrixWorkspace_sptr &outputWorkspace) {
EventWorkspace_sptr inputEvent =
boost::dynamic_pointer_cast<EventWorkspace>(inputWorkspace);
// Only create output workspace if different to input one
if (outputWorkspace != inputWorkspace) {
if (inputEvent) {
outputWorkspace = inputWorkspace->clone();
} else
outputWorkspace = create<MatrixWorkspace>(*inputWorkspace);
}
auto outputEvent =
boost::dynamic_pointer_cast<EventWorkspace>(outputWorkspace);
const auto &inputSpecInfo = inputWorkspace->spectrumInfo();
const auto &monitorSpecInfo = m_monitor->spectrumInfo();
const auto specLength = inputWorkspace->blocksize();
for (auto &workspaceIndex : m_workspaceIndexes) {
// Get hold of the monitor spectrum
const auto &monX = m_monitor->binEdges(workspaceIndex);
auto monY = m_monitor->counts(workspaceIndex);
auto monE = m_monitor->countStandardDeviations(workspaceIndex);
size_t timeIndex = 0;
if (m_scanInput)
timeIndex = monitorSpecInfo.spectrumDefinition(workspaceIndex)[0].second;
// Calculate the overall normalization just the once if bins are all
// matching
if (m_commonBins)
this->normalisationFactor(monX, monY, monE);
const size_t numHists = inputWorkspace->getNumberHistograms();
// Flag set when a division by 0 is found
bool hasZeroDivision = false;
Progress prog(this, 0.0, 1.0, numHists);
// Loop over spectra
PARALLEL_FOR_IF(
Kernel::threadSafe(*inputWorkspace, *outputWorkspace, *m_monitor))
for (int64_t i = 0; i < int64_t(numHists); ++i) {
PARALLEL_START_INTERUPT_REGION
prog.report();
const auto &specDef = inputSpecInfo.spectrumDefinition(i);
if (!spectrumDefinitionsMatchTimeIndex(specDef, timeIndex))
continue;
const auto &X = inputWorkspace->binEdges(i);
// If not rebinning, just point to our monitor spectra, otherwise create
// new vectors
auto Y = (m_commonBins ? monY : Counts(specLength));
auto E = (m_commonBins ? monE : CountStandardDeviations(specLength));
if (!m_commonBins) {
// ConvertUnits can give X vectors of all zeros - skip these, they
// cause
// problems
if (X.back() == 0.0 && X.front() == 0.0)
continue;
// Rebin the monitor spectrum to match the binning of the current data
// spectrum
VectorHelper::rebinHistogram(
monX.rawData(), monY.mutableRawData(), monE.mutableRawData(),
X.rawData(), Y.mutableRawData(), E.mutableRawData(), false);
// Recalculate the overall normalization factor
this->normalisationFactor(X, Y, E);
}
if (inputEvent) {
// --- EventWorkspace ---
EventList &outEL = outputEvent->getSpectrum(i);
outEL.divide(X.rawData(), Y.mutableRawData(), E.mutableRawData());
} else {
// --- Workspace2D ---
auto &YOut = outputWorkspace->mutableY(i);
auto &EOut = outputWorkspace->mutableE(i);
const auto &inY = inputWorkspace->y(i);
const auto &inE = inputWorkspace->e(i);
outputWorkspace->setSharedX(i, inputWorkspace->sharedX(i));
// The code below comes more or less straight out of Divide.cpp
for (size_t k = 0; k < specLength; ++k) {
// Get the input Y's
const double leftY = inY[k];
const double rightY = Y[k];
if (rightY == 0.0) {
hasZeroDivision = true;
}
// Calculate result and store in local variable to avoid overwriting
// original data if output workspace is same as one of the input
// ones
const double newY = leftY / rightY;
if (fabs(rightY) > 1.0e-12 && fabs(newY) > 1.0e-12) {
const double lhsFactor = (inE[k] < 1.0e-12 || fabs(leftY) < 1.0e-12)
? 0.0
: pow((inE[k] / leftY), 2);
const double rhsFactor =
E[k] < 1.0e-12 ? 0.0 : pow((E[k] / rightY), 2);
EOut[k] = std::abs(newY) * sqrt(lhsFactor + rhsFactor);
}
// Now store the result
YOut[k] = newY;
} // end Workspace2D case
} // end loop over current spectrum
PARALLEL_END_INTERUPT_REGION
} // end loop over spectra
PARALLEL_CHECK_INTERUPT_REGION
if (hasZeroDivision) {
g_log.warning() << "Division by zero in some of the bins.\n";
}
if (inputEvent)
outputEvent->clearMRU();
}
}
/** Execute the algorithm.
*/
void ResampleX::exec() {
// generically having access to the input workspace is a good idea
MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
MatrixWorkspace_sptr outputWS = getProperty("OutputWorkspace");
bool inPlace = (inputWS == outputWS); // Rebinning in-place
m_isDistribution = inputWS->isDistribution();
m_isHistogram = inputWS->isHistogramData();
const int numSpectra = static_cast<int>(inputWS->getNumberHistograms());
// the easy parameters
m_useLogBinning = getProperty("LogBinning");
m_numBins = getProperty("NumberBins");
m_preserveEvents = getProperty("PreserveEvents");
// determine the xmin/xmax for the workspace
vector<double> xmins = getProperty("XMin");
vector<double> xmaxs = getProperty("XMax");
string error = determineXMinMax(inputWS, xmins, xmaxs);
if (!error.empty())
throw std::runtime_error(error);
bool common_limits = true;
{
double xmin_common = xmins[0];
double xmax_common = xmaxs[0];
for (size_t i = 1; i < xmins.size(); ++i) {
if (xmins[i] != xmin_common) {
common_limits = false;
break;
}
if (xmaxs[i] != xmax_common) {
common_limits = false;
break;
}
}
}
if (common_limits) {
g_log.debug() << "Common limits between all spectra\n";
} else {
g_log.debug() << "Does not have common limits between all spectra\n";
}
// start doing actual work
EventWorkspace_const_sptr inputEventWS =
boost::dynamic_pointer_cast<const EventWorkspace>(inputWS);
if (inputEventWS != nullptr) {
if (m_preserveEvents) {
if (inPlace) {
g_log.debug() << "Rebinning event workspace in place\n";
} else {
g_log.debug() << "Rebinning event workspace out of place\n";
outputWS = inputWS->clone();
}
auto outputEventWS =
boost::dynamic_pointer_cast<EventWorkspace>(outputWS);
if (common_limits) {
// get the delta from the first since they are all the same
BinEdges xValues(0);
const double delta = this->determineBinning(xValues.mutableRawData(),
xmins[0], xmaxs[0]);
g_log.debug() << "delta = " << delta << "\n";
outputEventWS->setAllX(xValues);
} else {
// initialize progress reporting.
Progress prog(this, 0.0, 1.0, numSpectra);
// do the rebinning
PARALLEL_FOR_IF(Kernel::threadSafe(*inputEventWS, *outputWS))
for (int wkspIndex = 0; wkspIndex < numSpectra; ++wkspIndex) {
PARALLEL_START_INTERUPT_REGION
BinEdges xValues(0);
const double delta = this->determineBinning(
xValues.mutableRawData(), xmins[wkspIndex], xmaxs[wkspIndex]);
g_log.debug() << "delta[wkspindex=" << wkspIndex << "] = " << delta
<< " xmin=" << xmins[wkspIndex]
<< " xmax=" << xmaxs[wkspIndex] << "\n";
outputEventWS->setHistogram(wkspIndex, xValues);
prog.report(name()); // Report progress
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
}
} // end if (m_preserveEvents)
else // event workspace -> matrix workspace
{
//--------- Different output, OR you're inplace but not preserving Events
g_log.information() << "Creating a Workspace2D from the EventWorkspace "
<< inputEventWS->getName() << ".\n";
outputWS = create<DataObjects::Workspace2D>(
*inputWS, numSpectra, HistogramData::BinEdges(m_numBins + 1));
// Initialize progress reporting.
Progress prog(this, 0.0, 1.0, numSpectra);
// Go through all the histograms and set the data
PARALLEL_FOR_IF(Kernel::threadSafe(*inputEventWS, *outputWS))
for (int wkspIndex = 0; wkspIndex < numSpectra; ++wkspIndex) {
PARALLEL_START_INTERUPT_REGION
// Set the X axis for each output histogram
MantidVec xValues;
const double delta =
this->determineBinning(xValues, xmins[wkspIndex], xmaxs[wkspIndex]);
g_log.debug() << "delta[wkspindex=" << wkspIndex << "] = " << delta
<< "\n";
outputWS->setBinEdges(wkspIndex, xValues);
// Get a const event list reference. inputEventWS->dataY() doesn't work.
const EventList &el = inputEventWS->getSpectrum(wkspIndex);
MantidVec y_data, e_data;
// The EventList takes care of histogramming.
el.generateHistogram(xValues, y_data, e_data);
// Copy the data over.
outputWS->mutableY(wkspIndex) = std::move(y_data);
outputWS->mutableE(wkspIndex) = std::move(e_data);
// Report progress
prog.report(name());
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Copy all the axes
for (int i = 1; i < inputWS->axes(); i++) {
outputWS->replaceAxis(i, inputWS->getAxis(i)->clone(outputWS.get()));
outputWS->getAxis(i)->unit() = inputWS->getAxis(i)->unit();
}
// Copy the units over too.
for (int i = 0; i < outputWS->axes(); ++i) {
outputWS->getAxis(i)->unit() = inputWS->getAxis(i)->unit();
}
outputWS->setYUnit(inputEventWS->YUnit());
outputWS->setYUnitLabel(inputEventWS->YUnitLabel());
}
// Assign it to the output workspace property
setProperty("OutputWorkspace", outputWS);
return;
} else // (inputeventWS != NULL)
