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ReflectometryReductionOneAuto2.cpp
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ReflectometryReductionOneAuto2.cpp
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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source,
// Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidReflectometry/ReflectometryReductionOneAuto2.h"
#include "MantidAPI/BoostOptionalToAlgorithmProperty.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/RegexStrings.h"
#include "MantidKernel/Strings.h"
#include <boost/lexical_cast.hpp>
#include <boost/regex.hpp>
namespace Mantid {
namespace Reflectometry {
using namespace Mantid::API;
using namespace Mantid::Geometry;
using namespace Mantid::Kernel;
namespace { // anonymous
// Property names
namespace Prop {
static const std::string FLIPPERS{"Flippers"};
static const std::string POLARIZATION_ANALYSIS{"PolarizationAnalysis"};
} // namespace Prop
namespace CorrectionMethod {
static const std::string WILDES{"Wildes"};
static const std::string FREDRIKZE{"Fredrikze"};
// Map correction methods to which correction-option property name they use
static const std::map<std::string, std::string> OPTION_NAME{{CorrectionMethod::WILDES, Prop::FLIPPERS},
{CorrectionMethod::FREDRIKZE, Prop::POLARIZATION_ANALYSIS}};
void validate(const std::string &method) {
if (!CorrectionMethod::OPTION_NAME.count(method))
throw std::invalid_argument("Unsupported polarization correction method: " + method);
}
} // namespace CorrectionMethod
std::vector<std::string> workspaceNamesInGroup(std::string const &groupName) {
auto group = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(groupName);
return group->getNames();
}
std::string vectorToString(std::vector<std::string> const &vec) {
std::string result;
for (auto item : vec) {
if (!result.empty())
result += ",";
result += item;
}
return result;
}
void removeAllWorkspacesFromGroup(std::string const &groupName) {
auto group = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(groupName);
group->removeAll();
}
void removeWorkspacesFromADS(std::vector<std::string> const &workspaceNames) {
for (auto workspaceName : workspaceNames)
AnalysisDataService::Instance().remove(workspaceName);
}
} // namespace
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(ReflectometryReductionOneAuto2)
namespace {
std::string const OUTPUT_WORKSPACE_BINNED_DEFAULT_PREFIX("IvsQ_binned");
std::string const OUTPUT_WORKSPACE_DEFAULT_PREFIX("IvsQ");
std::string const OUTPUT_WORKSPACE_WAVELENGTH_DEFAULT_PREFIX("IvsLam");
} // namespace
//----------------------------------------------------------------------------------------------
/// Algorithm's name for identification. @see Algorithm::name
const std::string ReflectometryReductionOneAuto2::name() const { return "ReflectometryReductionOneAuto"; }
/// Algorithm's version for identification. @see Algorithm::version
int ReflectometryReductionOneAuto2::version() const { return 2; }
/// Algorithm's category for identification. @see Algorithm::category
const std::string ReflectometryReductionOneAuto2::category() const { return "Reflectometry\\ISIS"; }
/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
const std::string ReflectometryReductionOneAuto2::summary() const {
return "Reduces a single TOF/Lambda reflectometry run into a mod Q vs I/I0 "
"workspace attempting to pick instrument parameters for missing "
"properties";
}
/** Validate transmission runs
*
* @return :: result of the validation as a map
*/
std::map<std::string, std::string> ReflectometryReductionOneAuto2::validateInputs() {
std::map<std::string, std::string> results;
// Validate transmission runs only if our input workspace is a group
if (!checkGroups())
return results;
auto group = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(getPropertyValue("InputWorkspace"));
if (!group)
return results;
// First transmission run
const std::string firstStr = getPropertyValue("FirstTransmissionRun");
if (!firstStr.empty()) {
auto firstTransGroup = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(firstStr);
// If it is not a group, we don't need to validate its size
if (!firstTransGroup)
return results;
const bool polarizationCorrections = getPropertyValue("PolarizationAnalysis") != "None";
if (group->size() != firstTransGroup->size() && !polarizationCorrections) {
// If they are not the same size then we cannot associate a transmission
// group member with every input group member.
results["FirstTransmissionRun"] = "FirstTransmissionRun group must be the "
"same size as the InputWorkspace group "
"when polarization analysis is 'None'.";
}
}
// The same for the second transmission run
const std::string secondStr = getPropertyValue("SecondTransmissionRun");
if (!secondStr.empty()) {
auto secondTransGroup = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(secondStr);
// If it is not a group, we don't need to validate its size
if (!secondTransGroup)
return results;
const bool polarizationCorrections = getPropertyValue("PolarizationAnalysis") != "None";
if (group->size() != secondTransGroup->size() && !polarizationCorrections) {
results["SecondTransmissionRun"] = "SecondTransmissionRun group must be the "
"same size as the InputWorkspace group "
"when polarization analysis is 'None'.";
}
}
return results;
}
std::string ReflectometryReductionOneAuto2::getRunNumberForWorkspaceGroup(const WorkspaceGroup_const_sptr &group) {
// Return the run number for the first child workspace
if (!group)
throw std::runtime_error("Invalid workspace group type");
if (group->getNumberOfEntries() < 1)
throw std::runtime_error("Cannot run algorithm on empty group");
auto childWs = group->getItem(0);
auto childMatrixWs = std::dynamic_pointer_cast<MatrixWorkspace>(childWs);
if (!childMatrixWs)
throw std::runtime_error("Child workspace is not a MatrixWorkspace");
return getRunNumber(*childMatrixWs);
}
// Get output workspace names from the user-specified properties, or default
// names if the properties were not specified
auto ReflectometryReductionOneAuto2::getOutputWorkspaceNames() -> WorkspaceNames {
WorkspaceNames result;
MatrixWorkspace_const_sptr matrixWs = getProperty("InputWorkspace");
std::string runNumber;
if (matrixWs) {
runNumber = getRunNumber(*matrixWs);
} else {
// Casting to WorkspaceGroup doesn't work - I think because InputWorkspace
// is declared as a MatrixWorkspace - so get it from the ADS instead
auto groupWs = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(getPropertyValue("InputWorkspace"));
runNumber = getRunNumberForWorkspaceGroup(groupWs);
}
if (isDefault("OutputWorkspaceBinned"))
result.iVsQBinned = OUTPUT_WORKSPACE_BINNED_DEFAULT_PREFIX + runNumber;
else
result.iVsQBinned = getPropertyValue("OutputWorkspaceBinned");
if (isDefault("OutputWorkspace"))
result.iVsQ = OUTPUT_WORKSPACE_DEFAULT_PREFIX + runNumber;
else
result.iVsQ = getPropertyValue("OutputWorkspace");
if (isDefault("OutputWorkspaceWavelength"))
result.iVsLam = OUTPUT_WORKSPACE_WAVELENGTH_DEFAULT_PREFIX + runNumber;
else
result.iVsLam = getPropertyValue("OutputWorkspaceWavelength");
return result;
}
// Set default names for output workspaces
void ReflectometryReductionOneAuto2::setDefaultOutputWorkspaceNames() {
bool const isDebug = getProperty("Debug");
auto outputNames = getOutputWorkspaceNames();
if (isDefault("OutputWorkspaceBinned")) {
setPropertyValue("OutputWorkspaceBinned", outputNames.iVsQBinned);
}
if (isDefault("OutputWorkspace")) {
setPropertyValue("OutputWorkspace", outputNames.iVsQ);
}
if (isDebug && isDefault("OutputWorkspaceWavelength")) {
setPropertyValue("OutputWorkspaceWavelength", outputNames.iVsLam);
}
}
/** Initialize the algorithm's properties.
*/
void ReflectometryReductionOneAuto2::init() {
// Input ws
declareProperty(std::make_unique<WorkspaceProperty<MatrixWorkspace>>("InputWorkspace", "", Direction::Input,
PropertyMode::Mandatory),
"Input run in TOF or wavelength");
// Reduction type
initReductionProperties();
// Analysis mode
const std::vector<std::string> analysisMode{"PointDetectorAnalysis", "MultiDetectorAnalysis"};
auto analysisModeValidator = std::make_shared<StringListValidator>(analysisMode);
declareProperty("AnalysisMode", analysisMode[0], analysisModeValidator,
"Analysis mode. This property is only used when "
"ProcessingInstructions is not set.",
Direction::Input);
// Processing instructions
declareProperty(std::make_unique<PropertyWithValue<std::string>>("ProcessingInstructions", "", Direction::Input),
"Grouping pattern of spectrum numbers to yield only the"
" detectors of interest. See GroupDetectors for syntax.");
// Theta
declareProperty("ThetaIn", Mantid::EMPTY_DBL(), "Angle in degrees", Direction::Input);
// ThetaLogName
declareProperty("ThetaLogName", "", "The name ThetaIn can be found in the run log as");
// Whether to correct detectors
declareProperty(std::make_unique<PropertyWithValue<bool>>("CorrectDetectors", true, Direction::Input),
"Moves detectors to twoTheta if ThetaIn or ThetaLogName is given");
// Detector position correction type
const std::vector<std::string> correctionType{"VerticalShift", "RotateAroundSample"};
auto correctionTypeValidator = std::make_shared<CompositeValidator>();
correctionTypeValidator->add(std::make_shared<MandatoryValidator<std::string>>());
correctionTypeValidator->add(std::make_shared<StringListValidator>(correctionType));
declareProperty("DetectorCorrectionType", correctionType[0], correctionTypeValidator,
"When correcting detector positions, this determines whether detectors"
"should be shifted vertically or rotated around the sample position.",
Direction::Input);
setPropertySettings("DetectorCorrectionType",
std::make_unique<Kernel::EnabledWhenProperty>("CorrectDetectors", IS_EQUAL_TO, "1"));
// Wavelength limits
declareProperty("WavelengthMin", Mantid::EMPTY_DBL(), "Wavelength Min in angstroms", Direction::Input);
declareProperty("WavelengthMax", Mantid::EMPTY_DBL(), "Wavelength Max in angstroms", Direction::Input);
// Monitor properties
initMonitorProperties();
// Init properties for transmission normalization
initTransmissionProperties();
// Init properties for algorithmic corrections
initAlgorithmicProperties(true);
// Momentum transfer properties
initMomentumTransferProperties();
// Polarization correction
std::vector<std::string> propOptions = {"None", "PA", "PNR", "ParameterFile"};
declareProperty("PolarizationAnalysis", "None", std::make_shared<StringListValidator>(propOptions),
"Polarization analysis mode.");
declareProperty(std::make_unique<ArrayProperty<double>>("CPp", Direction::Input),
"Effective polarizing power of the polarizing system. "
"Expressed as a ratio 0 < Pp < 1");
declareProperty(std::make_unique<ArrayProperty<double>>("CAp", Direction::Input),
"Effective polarizing power of the analyzing system. "
"Expressed as a ratio 0 < Ap < 1");
declareProperty(std::make_unique<ArrayProperty<double>>("CRho", Direction::Input),
"Ratio of efficiencies of polarizer spin-down to polarizer "
"spin-up. This is characteristic of the polarizer flipper. "
"Values are constants for each term in a polynomial "
"expression.");
declareProperty(std::make_unique<ArrayProperty<double>>("CAlpha", Direction::Input),
"Ratio of efficiencies of analyzer spin-down to analyzer "
"spin-up. This is characteristic of the analyzer flipper. "
"Values are factors for each term in a polynomial "
"expression.");
setPropertyGroup("PolarizationAnalysis", "Polarization Corrections");
setPropertyGroup("CPp", "Polarization Corrections");
setPropertyGroup("CAp", "Polarization Corrections");
setPropertyGroup("CRho", "Polarization Corrections");
setPropertyGroup("CAlpha", "Polarization Corrections");
// Flood correction
propOptions = {"Workspace", "ParameterFile"};
declareProperty("FloodCorrection", "Workspace", std::make_shared<StringListValidator>(propOptions),
"The way to apply flood correction: "
"Workspace - use FloodWorkspace property to get the flood "
"workspace, ParameterFile - use parameters in the parameter "
"file to construct and apply flood correction workspace.");
declareProperty(std::make_unique<WorkspaceProperty<MatrixWorkspace>>("FloodWorkspace", "", Direction::Input,
PropertyMode::Optional),
"A flood workspace to apply; if empty and FloodCorrection is "
"'Workspace' then no correction is applied.");
// Init properties for diagnostics
initDebugProperties();
// Output workspace in Q
declareProperty(std::make_unique<WorkspaceProperty<MatrixWorkspace>>("OutputWorkspaceBinned", "", Direction::Output,
PropertyMode::Optional),
"Output workspace in Q (rebinned workspace)");
// Output workspace in Q (unbinned)
declareProperty(std::make_unique<WorkspaceProperty<MatrixWorkspace>>("OutputWorkspace", "", Direction::Output,
PropertyMode::Optional),
"Output workspace in Q (native binning)");
// Output workspace in wavelength
declareProperty(std::make_unique<WorkspaceProperty<MatrixWorkspace>>("OutputWorkspaceWavelength", "",
Direction::Output, PropertyMode::Optional),
"Output workspace in wavelength");
}
/** Execute the algorithm.
*/
void ReflectometryReductionOneAuto2::exec() {
applyFloodCorrections();
setDefaultOutputWorkspaceNames();
MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
auto instrument = inputWS->getInstrument();
auto alg = createChildAlgorithm("ReflectometryReductionOne");
alg->initialize();
// Mandatory properties
alg->setProperty("SummationType", getPropertyValue("SummationType"));
alg->setProperty("ReductionType", getPropertyValue("ReductionType"));
alg->setProperty("IncludePartialBins", getPropertyValue("IncludePartialBins"));
alg->setProperty("Diagnostics", getPropertyValue("Diagnostics"));
alg->setProperty("Debug", getPropertyValue("Debug"));
auto wavMin = checkForMandatoryInstrumentDefault<double>(this, "WavelengthMin", instrument, "LambdaMin");
alg->setProperty("WavelengthMin", wavMin);
auto wavMax = checkForMandatoryInstrumentDefault<double>(this, "WavelengthMax", instrument, "LambdaMax");
alg->setProperty("WavelengthMax", wavMax);
convertProcessingInstructions(instrument, inputWS);
alg->setProperty("ProcessingInstructions", m_processingInstructions);
// Now that we know the detectors of interest, we can move them if
// necessary (i.e. if theta is given). If not, we calculate theta from the
// current detector positions
bool correctDetectors = getProperty("CorrectDetectors");
double theta;
if (!getPointerToProperty("ThetaIn")->isDefault()) {
theta = getProperty("ThetaIn");
} else if (!getPropertyValue("ThetaLogName").empty()) {
theta = getThetaFromLogs(inputWS, getPropertyValue("ThetaLogName"));
} else {
// Calculate theta from detector positions
theta = calculateTheta(inputWS);
// Never correct detector positions if ThetaIn or ThetaLogName is not
// specified
correctDetectors = false;
}
// Pass theta to the child algorithm
alg->setProperty("ThetaIn", theta);
if (correctDetectors) {
inputWS = correctDetectorPositions(inputWS, 2 * theta);
}
// Optional properties
alg->setPropertyValue("TransmissionProcessingInstructions", getPropertyValue("TransmissionProcessingInstructions"));
populateMonitorProperties(alg, instrument);
alg->setPropertyValue("NormalizeByIntegratedMonitors", getPropertyValue("NormalizeByIntegratedMonitors"));
bool transRunsFound = populateTransmissionProperties(alg);
if (!transRunsFound)
populateAlgorithmicCorrectionProperties(alg, instrument);
alg->setProperty("InputWorkspace", inputWS);
alg->execute();
// Set the unbinned output workspace in Q, cropped to the min/max q
MatrixWorkspace_sptr IvsQ = alg->getProperty("OutputWorkspace");
auto const params = getRebinParams(IvsQ, theta);
auto IvsQC = IvsQ;
if (!(params.qMinIsDefault() && params.qMaxIsDefault()))
IvsQC = cropQ(IvsQ, params);
setProperty("OutputWorkspace", IvsQC);
// Set the binned output workspace in Q
if (params.hasQStep()) {
MatrixWorkspace_sptr IvsQB = rebinAndScale(IvsQ, params);
setProperty("OutputWorkspaceBinned", IvsQB);
} else {
g_log.error("NRCalculateSlitResolution failed. Workspace in Q will not be "
"rebinned. Please provide dQ/Q.");
setProperty("OutputWorkspaceBinned", IvsQC);
}
// Set the output workspace in wavelength, if debug outputs are enabled
bool const isDebug = getProperty("Debug");
if (isDebug || isChild()) {
MatrixWorkspace_sptr IvsLam = alg->getProperty("OutputWorkspaceWavelength");
setProperty("OutputWorkspaceWavelength", IvsLam);
}
// Set other properties so they can be updated in the Reflectometry interface
setProperty("ThetaIn", theta);
setProperty("MomentumTransferMin", params.qMin());
setProperty("MomentumTransferMax", params.qMax());
if (params.hasQStep())
setProperty("MomentumTransferStep", -params.qStep());
if (getPointerToProperty("ScaleFactor")->isDefault())
setProperty("ScaleFactor", 1.0);
}
/** Returns the detectors of interest, specified via processing instructions.
* Note that this returns the names of the parent detectors of the first and
* last spectrum indices in the processing instructions. It is assumed that all
* the interim detectors have the same parent.
*
* @param inputWS :: the input workspace
* @return :: the names of the detectors of interest
*/
std::vector<std::string> ReflectometryReductionOneAuto2::getDetectorNames(const MatrixWorkspace_sptr &inputWS) {
std::vector<std::string> wsIndices;
boost::split(wsIndices, m_processingInstructionsWorkspaceIndex, boost::is_any_of(":,-+"));
// vector of comopnents
std::vector<std::string> detectors;
try {
for (const auto &wsIndex : wsIndices) {
auto index = boost::lexical_cast<size_t>(wsIndex);
auto detector = inputWS->getDetector(index);
auto parent = detector->getParent();
if (parent) {
auto parentType = parent->type();
auto detectorName = (parentType == "Instrument") ? detector->getName() : parent->getName();
detectors.emplace_back(detectorName);
}
}
} catch (boost::bad_lexical_cast &) {
throw std::runtime_error("Invalid processing instructions: " + m_processingInstructionsWorkspaceIndex);
}
return detectors;
}
/** Correct an instrument component by shifting it vertically or
* rotating it around the sample.
*
* @param inputWS :: the input workspace
* @param twoTheta :: the angle to move detectors to
* @return :: the corrected workspace
*/
MatrixWorkspace_sptr ReflectometryReductionOneAuto2::correctDetectorPositions(MatrixWorkspace_sptr inputWS,
const double twoTheta) {
auto detectorsOfInterest = getDetectorNames(inputWS);
// Detectors of interest may be empty. This happens for instance when we input
// a workspace that was previously reduced using this algorithm. In this case,
// we shouldn't correct the detector positions
if (detectorsOfInterest.empty())
return inputWS;
const std::set<std::string> detectorSet(detectorsOfInterest.begin(), detectorsOfInterest.end());
const std::string correctionType = getProperty("DetectorCorrectionType");
MatrixWorkspace_sptr corrected = inputWS;
for (const auto &detector : detectorSet) {
auto alg = createChildAlgorithm("SpecularReflectionPositionCorrect");
alg->setProperty("InputWorkspace", corrected);
alg->setProperty("TwoTheta", twoTheta);
alg->setProperty("DetectorCorrectionType", correctionType);
alg->setProperty("DetectorComponentName", detector);
alg->execute();
corrected = alg->getProperty("OutputWorkspace");
}
return corrected;
}
/** Calculate the theta value of the detector of interest specified via
* processing instructions
*
* @param inputWS :: the input workspace
* @return :: the angle of the detector (only the first detector is considered)
*/
double ReflectometryReductionOneAuto2::calculateTheta(const MatrixWorkspace_sptr &inputWS) {
const auto detectorsOfInterest = getDetectorNames(inputWS);
// Detectors of interest may be empty. This happens for instance when we input
// a workspace that was previously reduced using this algorithm. In this case,
// we can't calculate theta
if (detectorsOfInterest.empty())
return 0.0;
auto alg = createChildAlgorithm("SpecularReflectionCalculateTheta");
alg->setProperty("InputWorkspace", inputWS);
alg->setProperty("DetectorComponentName", detectorsOfInterest[0]);
alg->execute();
const double theta = alg->getProperty("TwoTheta");
// Take a factor of 0.5 of the detector position, which is expected to be at
// 2 * theta
return theta * 0.5;
}
/** Set algorithmic correction properties
*
* @param alg :: ReflectometryReductionOne algorithm
* @param instrument :: The instrument attached to the workspace
*/
void ReflectometryReductionOneAuto2::populateAlgorithmicCorrectionProperties(const IAlgorithm_sptr &alg,
const Instrument_const_sptr &instrument) {
// With algorithmic corrections, monitors should not be integrated, see below
const std::string correctionAlgorithm = getProperty("CorrectionAlgorithm");
if (correctionAlgorithm == "PolynomialCorrection") {
alg->setProperty("NormalizeByIntegratedMonitors", false);
alg->setProperty("CorrectionAlgorithm", "PolynomialCorrection");
alg->setPropertyValue("Polynomial", getPropertyValue("Polynomial"));
} else if (correctionAlgorithm == "ExponentialCorrection") {
alg->setProperty("NormalizeByIntegratedMonitors", false);
alg->setProperty("CorrectionAlgorithm", "ExponentialCorrection");
alg->setProperty("C0", getPropertyValue("C0"));
alg->setProperty("C1", getPropertyValue("C1"));
} else if (correctionAlgorithm == "AutoDetect") {
// Figure out what to do from the instrument
try {
const auto corrVec = instrument->getStringParameter("correction");
if (corrVec.empty()) {
throw std::runtime_error("Could not find parameter 'correction' in "
"parameter file. Cannot auto detect the type of "
"correction.");
}
const std::string correctionStr = corrVec[0];
if (correctionStr == "polynomial") {
const auto polyVec = instrument->getStringParameter("polystring");
if (polyVec.empty())
throw std::runtime_error("Could not find parameter 'polystring' in "
"parameter file. Cannot apply polynomial "
"correction.");
alg->setProperty("CorrectionAlgorithm", "PolynomialCorrection");
alg->setProperty("Polynomial", polyVec[0]);
} else if (correctionStr == "exponential") {
const auto c0Vec = instrument->getStringParameter("C0");
if (c0Vec.empty())
throw std::runtime_error("Could not find parameter 'C0' in parameter "
"file. Cannot apply exponential correction.");
const auto c1Vec = instrument->getStringParameter("C1");
if (c1Vec.empty())
throw std::runtime_error("Could not find parameter 'C1' in parameter "
"file. Cannot apply exponential correction.");
alg->setProperty("C0", c0Vec[0]);
alg->setProperty("C1", c1Vec[0]);
}
alg->setProperty("NormalizeByIntegratedMonitors", false);
} catch (std::runtime_error &e) {
g_log.error() << e.what() << ". Polynomial correction will not be performed.";
alg->setProperty("CorrectionAlgorithm", "None");
}
} else {
alg->setProperty("CorrectionAlgorithm", "None");
}
}
auto ReflectometryReductionOneAuto2::getRebinParams(const MatrixWorkspace_sptr &inputWS, const double theta)
-> RebinParams {
bool qMinIsDefault = true, qMaxIsDefault = true;
auto const qMin = getPropertyOrDefault("MomentumTransferMin", inputWS->x(0).front(), qMinIsDefault);
auto const qMax = getPropertyOrDefault("MomentumTransferMax", inputWS->x(0).back(), qMaxIsDefault);
return RebinParams(qMin, qMinIsDefault, qMax, qMaxIsDefault, getQStep(inputWS, theta));
}
/** Get the binning step the final output workspace in Q
*
* @param inputWS :: the workspace in Q
* @param theta :: the angle of this run
* @return :: the rebin step in Q, or none if it could not be found
*/
boost::optional<double> ReflectometryReductionOneAuto2::getQStep(const MatrixWorkspace_sptr &inputWS,
const double theta) {
Property *qStepProp = getProperty("MomentumTransferStep");
double qstep;
if (!qStepProp->isDefault()) {
qstep = getProperty("MomentumTransferStep");
qstep = -qstep;
} else {
if (theta == 0.0) {
throw std::runtime_error("Theta determined from the detector positions is "
"0.0. Please provide a value for theta manually "
"or correct the detector position before running "
"this algorithm.");
}
auto calcRes = createChildAlgorithm("NRCalculateSlitResolution");
calcRes->setProperty("Workspace", inputWS);
calcRes->setProperty("TwoTheta", 2 * theta);
calcRes->execute();
if (!calcRes->isExecuted()) {
return boost::none;
}
qstep = calcRes->getProperty("Resolution");
qstep = -qstep;
}
return qstep;
}
/** Rebin and scale a workspace in Q.
*
* @param inputWS :: the workspace in Q
* @param params :: A vector containing the three rebin parameters (min, step
* and max)
* @return :: the output workspace
*/
MatrixWorkspace_sptr ReflectometryReductionOneAuto2::rebinAndScale(const MatrixWorkspace_sptr &inputWS,
RebinParams const ¶ms) {
// Rebin
auto algRebin = createChildAlgorithm("Rebin");
algRebin->initialize();
algRebin->setProperty("InputWorkspace", inputWS);
algRebin->setProperty("OutputWorkspace", inputWS);
algRebin->setProperty("Params", params.asVector());
algRebin->execute();
MatrixWorkspace_sptr IvsQ = algRebin->getProperty("OutputWorkspace");
// Scale (optional)
Property *scaleProp = getProperty("ScaleFactor");
if (!scaleProp->isDefault()) {
double scaleFactor = getProperty("ScaleFactor");
auto algScale = createChildAlgorithm("Scale");
algScale->initialize();
algScale->setProperty("InputWorkspace", IvsQ);
algScale->setProperty("OutputWorkspace", IvsQ);
algScale->setProperty("Factor", 1.0 / scaleFactor);
algScale->execute();
IvsQ = algScale->getProperty("OutputWorkspace");
}
return IvsQ;
}
MatrixWorkspace_sptr ReflectometryReductionOneAuto2::cropQ(const MatrixWorkspace_sptr &inputWS,
RebinParams const ¶ms) {
auto algCrop = createChildAlgorithm("CropWorkspace");
algCrop->initialize();
algCrop->setProperty("InputWorkspace", inputWS);
algCrop->setProperty("OutputWorkspace", inputWS);
if (!params.qMinIsDefault())
algCrop->setProperty("XMin", params.qMin());
if (!params.qMaxIsDefault())
algCrop->setProperty("XMax", params.qMax());
algCrop->execute();
MatrixWorkspace_sptr IvsQ = algCrop->getProperty("OutputWorkspace");
return IvsQ;
}
/**
* @brief Get the Property Or return a default given value
*
* @param propertyName : the name of the property to get
* @param defaultValue : the default value to use if the property is not set
* @param isDefault [out] : true if the default value was used
*/
double ReflectometryReductionOneAuto2::getPropertyOrDefault(const std::string &propertyName, const double defaultValue,
bool &isDefault) {
Property *property = getProperty(propertyName);
isDefault = property->isDefault();
if (isDefault)
return defaultValue;
else
return getProperty(propertyName);
}
/** Check if input workspace is a group
*/
bool ReflectometryReductionOneAuto2::checkGroups() {
const std::string wsName = getPropertyValue("InputWorkspace");
try {
auto ws = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(wsName);
if (ws)
return true;
} catch (...) {
}
return false;
}
void ReflectometryReductionOneAuto2::setOutputWorkspaces(WorkspaceNames const &outputGroupNames,
std::vector<std::string> &IvsLamGroup,
std::vector<std::string> &IvsQBinnedGroup,
std::vector<std::string> &IvsQGroup) {
// Group the IvsQ and IvsLam workspaces
Algorithm_sptr groupAlg = createChildAlgorithm("GroupWorkspaces");
groupAlg->setChild(false);
groupAlg->setRethrows(true);
if (!IvsLamGroup.empty()) {
groupAlg->setProperty("InputWorkspaces", IvsLamGroup);
groupAlg->setProperty("OutputWorkspace", outputGroupNames.iVsLam);
groupAlg->execute();
}
groupAlg->setProperty("InputWorkspaces", IvsQBinnedGroup);
groupAlg->setProperty("OutputWorkspace", outputGroupNames.iVsQBinned);
groupAlg->execute();
groupAlg->setProperty("InputWorkspaces", IvsQGroup);
groupAlg->setProperty("OutputWorkspace", outputGroupNames.iVsQ);
groupAlg->execute();
setPropertyValue("OutputWorkspace", outputGroupNames.iVsQ);
setPropertyValue("OutputWorkspaceBinned", outputGroupNames.iVsQBinned);
setPropertyValue("OutputWorkspaceWavelength", outputGroupNames.iVsLam);
}
/** Process groups. Groups are processed differently depending on transmission
* runs and polarization analysis. If transmission run is a matrix workspace,
* it will be applied to each of the members in the input workspace group. If
* transmission run is a workspace group, the behaviour is different depending
* on polarization analysis. If polarization analysis is off (i.e.
* 'PolarizationAnalysis' is set to 'None') each item in the transmission
* group is associated with the corresponding item in the input workspace
* group. If polarization analysis is on (i.e. 'PolarizationAnalysis' is 'PA'
* or 'PNR') items in the transmission group will be summed to produce a
* matrix workspace that will be applied to each of the items in the input
* workspace group. See documentation of this algorithm for more details.
*/
bool ReflectometryReductionOneAuto2::processGroups() {
// this algorithm effectively behaves as MultiPeriodGroupAlgorithm
m_usingBaseProcessGroups = true;
// Get our input workspace group
auto group = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(getPropertyValue("InputWorkspace"));
// Get the output workspace names
auto const output = getOutputWorkspaceNames();
// Create a copy of ourselves
Algorithm_sptr alg = createChildAlgorithm(name(), -1, -1, isLogging(), version());
alg->setChild(false);
alg->setRethrows(true);
// Copy all the non-workspace properties over
const std::vector<Property *> props = getProperties();
for (auto &prop : props) {
if (prop) {
auto *wsProp = dynamic_cast<IWorkspaceProperty *>(prop);
if (!wsProp)
alg->setPropertyValue(prop->name(), prop->value());
}
}
const bool polarizationAnalysisOn = getPropertyValue("PolarizationAnalysis") != "None";
// Check if the transmission runs are groups or not
const std::string firstTrans = getPropertyValue("FirstTransmissionRun");
WorkspaceGroup_sptr firstTransG;
MatrixWorkspace_sptr firstTransSum;
if (!firstTrans.empty()) {
auto firstTransWS = AnalysisDataService::Instance().retrieveWS<Workspace>(firstTrans);
firstTransG = std::dynamic_pointer_cast<WorkspaceGroup>(firstTransWS);
if (!firstTransG) {
alg->setProperty("FirstTransmissionRun", firstTrans);
} else {
g_log.information("A group has been passed as the first transmission run "
"so the first run only is being used");
alg->setProperty("FirstTransmissionRun", firstTransG->getItem(0));
}
}
const std::string secondTrans = getPropertyValue("SecondTransmissionRun");
WorkspaceGroup_sptr secondTransG;
MatrixWorkspace_sptr secondTransSum;
if (!secondTrans.empty()) {
auto secondTransWS = AnalysisDataService::Instance().retrieveWS<Workspace>(secondTrans);
secondTransG = std::dynamic_pointer_cast<WorkspaceGroup>(secondTransWS);
if (!secondTransG) {
alg->setProperty("SecondTransmissionRun", secondTrans);
} else {
g_log.information("A group has been passed as the second transmission "
"run so the first run only is being used");
alg->setProperty("secondTransmissionRun", secondTransG->getItem(0));
}
}
std::vector<std::string> IvsQBinnedGroup, IvsQGroup, IvsLamGroup;
std::string runNumber = getRunNumberForWorkspaceGroup(group);
// Execute algorithm over each group member
for (size_t i = 0; i < group->size(); ++i) {
auto inputName = group->getItem(i)->getName();
auto outputNames = getOutputNamesForGroups(inputName, runNumber, i);
const std::string IvsQName = outputNames.iVsQ;
const std::string IvsQBinnedName = outputNames.iVsQBinned;
const std::string IvsLamName = outputNames.iVsLam;
alg->setProperty("InputWorkspace", inputName);
alg->setProperty("Debug", true);
alg->setProperty("OutputWorkspace", IvsQName);
alg->setProperty("OutputWorkspaceBinned", IvsQBinnedName);
alg->setProperty("OutputWorkspaceWavelength", IvsLamName);
if (!isDefault("FloodWorkspace")) {
MatrixWorkspace_sptr flood = getProperty("FloodWorkspace");
alg->setProperty("FloodWorkspace", flood);
}
alg->execute();
IvsQGroup.emplace_back(IvsQName);
IvsQBinnedGroup.emplace_back(IvsQBinnedName);
if (AnalysisDataService::Instance().doesExist(IvsLamName)) {
IvsLamGroup.emplace_back(IvsLamName);
}
}
// Group the IvsQ and IvsLam workspaces
Algorithm_sptr groupAlg = createChildAlgorithm("GroupWorkspaces");
groupAlg->setChild(false);
groupAlg->setRethrows(true);
if (!IvsLamGroup.empty()) {
groupAlg->setProperty("InputWorkspaces", IvsLamGroup);
groupAlg->setProperty("OutputWorkspace", output.iVsLam);
groupAlg->execute();
}
groupAlg->setProperty("InputWorkspaces", IvsQBinnedGroup);
groupAlg->setProperty("OutputWorkspace", output.iVsQBinned);
groupAlg->execute();
groupAlg->setProperty("InputWorkspaces", IvsQGroup);
groupAlg->setProperty("OutputWorkspace", output.iVsQ);
groupAlg->execute();
// Set other properties so they can be updated in the Reflectometry interface
setPropertyValue("ThetaIn", alg->getPropertyValue("ThetaIn"));
setPropertyValue("MomentumTransferMin", alg->getPropertyValue("MomentumTransferMin"));
setPropertyValue("MomentumTransferMax", alg->getPropertyValue("MomentumTransferMax"));
setPropertyValue("MomentumTransferStep", alg->getPropertyValue("MomentumTransferStep"));
setPropertyValue("ScaleFactor", alg->getPropertyValue("ScaleFactor"));
setOutputWorkspaces(output, IvsLamGroup, IvsQBinnedGroup, IvsQGroup);
if (!polarizationAnalysisOn) {
// No polarization analysis. Reduction stops here
return true;
}
applyPolarizationCorrection(output.iVsLam);
// Polarization correction may have changed the number of workspaces in the
// groups
IvsLamGroup.clear();
IvsQBinnedGroup.clear();
IvsQGroup.clear();
// Now we've overwritten the IvsLam workspaces, we'll need to recalculate
// the IvsQ ones
alg->setProperty("FirstTransmissionRun", "");
alg->setProperty("SecondTransmissionRun", "");
alg->setProperty("CorrectionAlgorithm", "None");
auto outputIvsLamNames = workspaceNamesInGroup(output.iVsLam);
for (size_t i = 0; i < outputIvsLamNames.size(); ++i) {
auto inputName = group->getItem(i)->getName();
auto outputNames = getOutputNamesForGroups(inputName, runNumber, i);
const std::string IvsQName = outputNames.iVsQ;
const std::string IvsQBinnedName = outputNames.iVsQBinned;
const std::string IvsLamName = outputIvsLamNames[i];
// Find the spectrum processing instructions for ws index 0
auto currentWorkspace =
std::dynamic_pointer_cast<MatrixWorkspace>(AnalysisDataService::Instance().retrieve(outputIvsLamNames[i]));
auto newProcInst = convertToSpectrumNumber("0", currentWorkspace);
alg->setProperty("ProcessingInstructions", newProcInst);
alg->setProperty("InputWorkspace", IvsLamName);
alg->setProperty("OutputWorkspace", IvsQName);
alg->setProperty("OutputWorkspaceBinned", IvsQBinnedName);
alg->setProperty("OutputWorkspaceWavelength", IvsLamName);
alg->execute();
IvsQBinnedGroup.emplace_back(IvsQBinnedName);
IvsQGroup.emplace_back(IvsQName);
if (AnalysisDataService::Instance().doesExist(IvsLamName)) {
IvsLamGroup.emplace_back(IvsLamName);
}
}
setOutputWorkspaces(output, IvsLamGroup, IvsQBinnedGroup, IvsQGroup);
return true;
}
/** Get the output workspace names for a workspace in a group.
* If an input workspace has been passed with the format
* TOF_<runNumber>_<otherInfo> then the output workspaces will be of the same
* format otherwise they are numbered according to the wsGroupNumber
*/
auto ReflectometryReductionOneAuto2::getOutputNamesForGroups(const std::string &inputName, const std::string &runNumber,
const size_t wsGroupNumber) -> WorkspaceNames {
auto const output = getOutputWorkspaceNames();
std::string informativeName = "TOF" + runNumber + "_";
WorkspaceNames outputNames;
if ((informativeName.length() < inputName.length()) &&
(equal(informativeName.begin(), informativeName.end(), inputName.begin()))) {
auto informativeTest = inputName.substr(informativeName.length());
outputNames.iVsQ = output.iVsQ + "_" + informativeTest;
outputNames.iVsQBinned = output.iVsQBinned + "_" + informativeTest;
outputNames.iVsLam = output.iVsLam + "_" + informativeTest;
} else {
outputNames.iVsQ = output.iVsQ + "_" + std::to_string(wsGroupNumber + 1);
outputNames.iVsQBinned = output.iVsQBinned + "_" + std::to_string(wsGroupNumber + 1);
outputNames.iVsLam = output.iVsLam + "_" + std::to_string(wsGroupNumber + 1);
}
return outputNames;
}
/** Construct a polarization efficiencies workspace based on values of input
* properties.
*/
std::tuple<API::MatrixWorkspace_sptr, std::string, std::string>
ReflectometryReductionOneAuto2::getPolarizationEfficiencies() {
auto groupIvsLam =
AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(getPropertyValue("OutputWorkspaceWavelength"));
std::string const paMethod = getPropertyValue("PolarizationAnalysis");
Workspace_sptr workspace = groupIvsLam->getItem(0);
MatrixWorkspace_sptr efficiencies;
std::string correctionMethod;
std::string correctionOption;
if (paMethod == "ParameterFile") {
auto effAlg = createChildAlgorithm("ExtractPolarizationEfficiencies");
effAlg->setProperty("InputWorkspace", workspace);
effAlg->execute();
efficiencies = effAlg->getProperty("OutputWorkspace");
correctionMethod = effAlg->getPropertyValue("CorrectionMethod");
correctionOption = effAlg->getPropertyValue("CorrectionOption");
} else {
auto effAlg = createChildAlgorithm("CreatePolarizationEfficiencies");
effAlg->setProperty("InputWorkspace", workspace);
if (!isDefault("CPp")) {
effAlg->setProperty("Pp", getPropertyValue("CPp"));
}
if (!isDefault("CRho")) {
effAlg->setProperty("Rho", getPropertyValue("CRho"));
}
if (!isDefault("CAp")) {
effAlg->setProperty("Ap", getPropertyValue("CAp"));
}
if (!isDefault("CAlpha")) {
effAlg->setProperty("Alpha", getPropertyValue("CAlpha"));
}
effAlg->execute();
efficiencies = effAlg->getProperty("OutputWorkspace");
correctionMethod = "Fredrikze";
correctionOption = paMethod;
}
return std::make_tuple(efficiencies, correctionMethod, correctionOption);
}
/**
* Apply a polarization correction to workspaces in lambda.
* @param outputIvsLam :: Name of a workspace group to apply the correction