/**
* Calculate the twoTheta angle from the detector and sample locations.
* @return: twoTheta
*/
double SpecularReflectionAlgorithm::calculateTwoTheta() const {
MatrixWorkspace_sptr inWS = this->getProperty("InputWorkspace");
const std::string analysisMode = this->getProperty("AnalysisMode");
Instrument_const_sptr instrument = inWS->getInstrument();
IComponent_const_sptr detector =
this->getDetectorComponent(inWS, analysisMode == pointDetectorAnalysis);
IComponent_const_sptr sample = this->getSurfaceSampleComponent(instrument);
const V3D detSample = detector->getPos() - sample->getPos();
boost::shared_ptr<const ReferenceFrame> refFrame =
instrument->getReferenceFrame();
const double upoffset = refFrame->vecPointingUp().scalar_prod(detSample);
const double beamoffset =
refFrame->vecPointingAlongBeam().scalar_prod(detSample);
const double twoTheta = std::atan2(upoffset, beamoffset) * 180 / M_PI;
return twoTheta;
}
/** Get instrument geometry setup including L2 for each detector and L1
*/
void CreateLogTimeCorrection::getInstrumentSetup() {
// 1. Get sample position and source position
IComponent_const_sptr sample = m_instrument->getSample();
if (!sample) {
throw runtime_error("No sample has been set.");
}
V3D samplepos = sample->getPos();
IComponent_const_sptr source = m_instrument->getSource();
if (!source) {
throw runtime_error("No source has been set.");
}
V3D sourcepos = source->getPos();
m_L1 = sourcepos.distance(samplepos);
// 2. Get detector IDs
std::vector<detid_t> detids = m_instrument->getDetectorIDs(true);
for (auto &detid : detids) {
IDetector_const_sptr detector = m_instrument->getDetector(detid);
V3D detpos = detector->getPos();
double l2 = detpos.distance(samplepos);
m_l2map.emplace(detid, l2);
}
// 3. Output information
g_log.information() << "Sample position = " << samplepos << "; "
<< "Source position = " << sourcepos << ", L1 = " << m_L1
<< "; "
<< "Number of detector/pixels = " << detids.size()
<< ".\n";
}
/**
* Correct the position of the detectors based on the input theta value.
* @param toCorrect : Workspace to correct detector posisitions on.
* @param twoThetaInDeg : 2* Theta in degrees to use in correction calculations.
* @param sample : Pointer to the sample
* @param detector : Pointer to a given detector
*/
void SpecularReflectionPositionCorrect::correctPosition(
API::MatrixWorkspace_sptr toCorrect, const double &twoThetaInDeg,
IComponent_const_sptr sample, IComponent_const_sptr detector) {
auto instrument = toCorrect->getInstrument();
const V3D detectorPosition = detector->getPos();
const V3D samplePosition = sample->getPos();
const V3D sampleToDetector = detectorPosition - samplePosition;
auto referenceFrame = instrument->getReferenceFrame();
const double twoThetaInRad = twoThetaInDeg * (M_PI / 180.0);
double acrossOffset = 0;
double beamOffset = sampleToDetector.scalar_prod(
referenceFrame
->vecPointingAlongBeam()); // We just recalculate beam offset.
double upOffset =
(beamOffset *
std::tan(0.5 * twoThetaInRad)); // We only correct vertical position
// Apply the movements.
moveDetectors(toCorrect, detector, sample, upOffset, acrossOffset,
detector->getPos());
}
/**
* Execute the MoveInstrumentComponent on all (named) subcomponents
* @param toCorrect : Workspace to correct
* @param detector : Detector or DetectorGroup
* @param sample : Sample Component
* @param upOffset : Up offset to apply
* @param acrossOffset : Across offset to apply
* @param detectorPosition: Actual detector or detector group position.
*/
void SpecularReflectionPositionCorrect::moveDetectors(
API::MatrixWorkspace_sptr toCorrect, IComponent_const_sptr detector,
IComponent_const_sptr sample, const double &upOffset,
const double &acrossOffset, const V3D &detectorPosition) {
auto instrument = toCorrect->getInstrument();
const V3D samplePosition = sample->getPos();
auto referenceFrame = instrument->getReferenceFrame();
if (auto groupDetector = boost::dynamic_pointer_cast<const DetectorGroup>(
detector)) // Do we have a group of detectors
{
const std::vector<IDetector_const_sptr> detectors =
groupDetector->getDetectors();
const bool commonParent = hasCommonParent(detectors);
if (commonParent) {
/*
* Same parent component. So lets move that.
*/
moveDetectors(toCorrect, detectors[0], sample, upOffset, acrossOffset,
detectorPosition); // Recursive call
} else {
/*
* We have to move individual components.
*/
for (size_t i = 0; i < detectors.size(); ++i) {
moveDetectors(toCorrect, detectors[i], sample, upOffset, acrossOffset,
detectorPosition); // Recursive call
}
}
} else {
auto moveComponentAlg =
this->createChildAlgorithm("MoveInstrumentComponent");
moveComponentAlg->initialize();
moveComponentAlg->setProperty("Workspace", toCorrect);
IComponent_const_sptr root = getParentComponent(detector);
const std::string componentName = root->getName();
moveComponentAlg->setProperty("ComponentName", componentName);
moveComponentAlg->setProperty("RelativePosition", false);
// Movements
moveComponentAlg->setProperty(
referenceFrame->pointingAlongBeamAxis(),
detectorPosition.scalar_prod(referenceFrame->vecPointingAlongBeam()));
moveComponentAlg->setProperty(referenceFrame->pointingHorizontalAxis(),
acrossOffset);
const double detectorVerticalPosition =
detectorPosition.scalar_prod(referenceFrame->vecPointingUp());
const double rootVerticalPosition =
root->getPos().scalar_prod(referenceFrame->vecPointingUp());
const double dm = rootVerticalPosition - detectorVerticalPosition;
moveComponentAlg->setProperty(
referenceFrame->pointingUpAxis(),
samplePosition.scalar_prod(referenceFrame->vecPointingUp()) + upOffset +
dm);
// Execute the movement.
moveComponentAlg->execute();
}
}
/** Creates or modifies the parameter map for the specified detector adding
* pressure and wall thickness information
* @param params :: these will be written to the detector paraments 3He(atm)=pressure) and wallT(m)=wall thickness
* @param change :: if the parameters are successfully changed they are stored here
* @throw NotFoundError if a pointer to the specified detector couldn't be retrieved
*/
void LoadDetectorInfo::setDetectorParams(const detectorInfo ¶ms, detectorInfo &change)
{
Geometry::IDetector_sptr det;
try
{
det = boost::const_pointer_cast<IDetector>(m_workspace->getInstrument()->baseInstrument()->getDetector(params.detID));
}
catch( std::runtime_error &e)
{
throw Exception::NotFoundError(e.what(), params.detID);
}
Geometry::ParameterMap &pmap = m_workspace->instrumentParameters();
// Set the detectors pressure.
pmap.addDouble(det->getComponentID(), "3He(atm)", params.pressure);
// Set the wall thickness
pmap.addDouble(det->getComponentID(), "wallT(m)", params.wallThick);
// If we have a l2, theta and phi. Update the postion if required
if( m_moveDets &&
params.l2 != DBL_MAX && params.theta != DBL_MAX && params.phi != DBL_MAX )
{
V3D newPos;
newPos.spherical(params.l2, params.theta, params.phi);
// The sample position may not be at 0,0,0
newPos += m_samplePos;
IComponent_const_sptr parent = det->getParent();
if (parent)
{
newPos -= parent->getPos();
Quat rot = parent->getRotation();
rot.inverse();
rot.rotate(newPos);
}
det->setPos(newPos);
}
// this operation has been successful if we are here, the following infomation is usefull for logging
change = params;
}
/**
* Cache frequently accessed values
* @param instrument : The instrument for this run
* @param detID : The det ID for this observation
*/
void CachedExperimentInfo::initCaches(
const Geometry::Instrument_const_sptr &instrument, const detid_t detID) {
// Throws if detector does not exist
// Takes into account possible detector mapping
IDetector_const_sptr det = m_exptInfo.getDetectorByID(detID);
// Instrument distances
boost::shared_ptr<const ReferenceFrame> refFrame =
instrument->getReferenceFrame();
m_beam = refFrame->pointingAlongBeam();
m_up = refFrame->pointingUp();
m_horiz = refFrame->pointingHorizontal();
IComponent_const_sptr source = instrument->getSource();
IComponent_const_sptr sample = instrument->getSample();
IComponent_const_sptr aperture =
instrument->getComponentByName("aperture", 1);
if (!aperture) {
throw std::invalid_argument(
"No component named \"aperture\" found in instrument.");
}
IObjComponent_const_sptr firstChopper = instrument->getChopperPoint(0);
const Kernel::V3D samplePos = sample->getPos();
const Kernel::V3D beamDir = samplePos - source->getPos();
// Cache
m_twoTheta = det->getTwoTheta(samplePos, beamDir);
m_phi = det->getPhi();
m_modToChop = firstChopper->getDistance(*source);
m_apertureToChop = firstChopper->getDistance(*aperture);
m_chopToSample = sample->getDistance(*firstChopper);
m_sampleToDet = det->getDistance(*sample);
// Aperture
Geometry::BoundingBox apertureBox;
aperture->getBoundingBox(apertureBox);
if (apertureBox.isNull()) {
throw std::invalid_argument("CachedExperimentInfo::initCaches - Aperture "
"has no bounding box, cannot sample from it");
}
m_apertureSize.first = apertureBox.maxPoint()[0] - apertureBox.minPoint()[0];
m_apertureSize.second = apertureBox.maxPoint()[1] - apertureBox.minPoint()[1];
// Sample volume
const API::Sample &sampleDescription = m_exptInfo.sample();
const Geometry::Object &shape = sampleDescription.getShape();
m_sampleWidths = shape.getBoundingBox().width();
// Detector volume
// Make sure it encompasses all possible detectors
det->getBoundingBox(m_detBox);
if (m_detBox.isNull()) {
throw std::invalid_argument("CachedExperimentInfo::initCaches - Detector "
"has no bounding box, cannot sample from it. "
"ID:" +
boost::lexical_cast<std::string>(det->getID()));
}
const double rad2deg = 180. / M_PI;
const double thetaInDegs = twoTheta() * rad2deg;
const double phiInDegs = phi() * rad2deg;
m_gonimeter = new Goniometer;
m_gonimeter->makeUniversalGoniometer();
m_gonimeter->setRotationAngle("phi", thetaInDegs);
m_gonimeter->setRotationAngle("chi", phiInDegs);
m_sampleToDetMatrix =
m_exptInfo.sample().getOrientedLattice().getU() * m_gonimeter->getR();
// EFixed
m_efixed = m_exptInfo.getEFixed(det);
}
void SofQWCentre::exec() {
using namespace Geometry;
MatrixWorkspace_const_sptr inputWorkspace = getProperty("InputWorkspace");
// Do the full check for common binning
if (!WorkspaceHelpers::commonBoundaries(*inputWorkspace)) {
g_log.error(
"The input workspace must have common binning across all spectra");
throw std::invalid_argument(
"The input workspace must have common binning across all spectra");
}
std::vector<double> verticalAxis;
MatrixWorkspace_sptr outputWorkspace = setUpOutputWorkspace(
inputWorkspace, getProperty("QAxisBinning"), verticalAxis);
setProperty("OutputWorkspace", outputWorkspace);
// Holds the spectrum-detector mapping
std::vector<specnum_t> specNumberMapping;
std::vector<detid_t> detIDMapping;
m_EmodeProperties.initCachedValues(*inputWorkspace, this);
int emode = m_EmodeProperties.m_emode;
// Get a pointer to the instrument contained in the workspace
Instrument_const_sptr instrument = inputWorkspace->getInstrument();
// Get the distance between the source and the sample (assume in metres)
IComponent_const_sptr source = instrument->getSource();
IComponent_const_sptr sample = instrument->getSample();
V3D beamDir = sample->getPos() - source->getPos();
beamDir.normalize();
try {
double l1 = source->getDistance(*sample);
g_log.debug() << "Source-sample distance: " << l1 << '\n';
} catch (Exception::NotFoundError &) {
g_log.error("Unable to calculate source-sample distance");
throw Exception::InstrumentDefinitionError(
"Unable to calculate source-sample distance",
inputWorkspace->getTitle());
}
// Conversion constant for E->k. k(A^-1) = sqrt(energyToK*E(meV))
const double energyToK = 8.0 * M_PI * M_PI * PhysicalConstants::NeutronMass *
PhysicalConstants::meV * 1e-20 /
(PhysicalConstants::h * PhysicalConstants::h);
// Loop over input workspace bins, reassigning data to correct bin in output
// qw workspace
const size_t numHists = inputWorkspace->getNumberHistograms();
const size_t numBins = inputWorkspace->blocksize();
Progress prog(this, 0.0, 1.0, numHists);
for (int64_t i = 0; i < int64_t(numHists); ++i) {
try {
// Now get the detector object for this histogram
IDetector_const_sptr spectrumDet = inputWorkspace->getDetector(i);
if (spectrumDet->isMonitor())
continue;
const double efixed = m_EmodeProperties.getEFixed(*spectrumDet);
// For inelastic scattering the simple relationship q=4*pi*sinTheta/lambda
// does not hold. In order to
// be completely general we must calculate the momentum transfer by
// calculating the incident and final
// wave vectors and then use |q| = sqrt[(ki - kf)*(ki - kf)]
DetectorGroup_const_sptr detGroup =
boost::dynamic_pointer_cast<const DetectorGroup>(spectrumDet);
std::vector<IDetector_const_sptr> detectors;
if (detGroup) {
detectors = detGroup->getDetectors();
} else {
detectors.push_back(spectrumDet);
}
const size_t numDets = detectors.size();
// cache to reduce number of static casts
const double numDets_d = static_cast<double>(numDets);
const auto &Y = inputWorkspace->y(i);
const auto &E = inputWorkspace->e(i);
const auto &X = inputWorkspace->x(i);
// Loop over the detectors and for each bin calculate Q
for (size_t idet = 0; idet < numDets; ++idet) {
IDetector_const_sptr det = detectors[idet];
// Calculate kf vector direction and then Q for each energy bin
V3D scatterDir = (det->getPos() - sample->getPos());
scatterDir.normalize();
for (size_t j = 0; j < numBins; ++j) {
const double deltaE = 0.5 * (X[j] + X[j + 1]);
// Compute ki and kf wave vectors and therefore q = ki - kf
double ei(0.0), ef(0.0);
if (emode == 1) {
ei = efixed;
ef = efixed - deltaE;
if (ef < 0) {
std::string mess =
"Energy transfer requested in Direct mode exceeds incident "
"energy.\n Found for det ID: " +
std::to_string(idet) + " bin No " + std::to_string(j) +
" with Ei=" + boost::lexical_cast<std::string>(efixed) +
" and energy transfer: " +
boost::lexical_cast<std::string>(deltaE);
throw std::runtime_error(mess);
}
} else {
ei = efixed + deltaE;
ef = efixed;
if (ef < 0) {
std::string mess =
"Incident energy of a neutron is negative. Are you trying to "
"process Direct data in Indirect mode?\n Found for det ID: " +
std::to_string(idet) + " bin No " + std::to_string(j) +
" with efied=" + boost::lexical_cast<std::string>(efixed) +
" and energy transfer: " +
boost::lexical_cast<std::string>(deltaE);
throw std::runtime_error(mess);
}
}
if (ei < 0)
throw std::runtime_error(
"Negative incident energy. Check binning.");
const V3D ki = beamDir * sqrt(energyToK * ei);
const V3D kf = scatterDir * (sqrt(energyToK * (ef)));
const double q = (ki - kf).norm();
// Test whether it's in range of the Q axis
if (q < verticalAxis.front() || q > verticalAxis.back())
continue;
// Find which q bin this point lies in
const MantidVec::difference_type qIndex =
std::upper_bound(verticalAxis.begin(), verticalAxis.end(), q) -
verticalAxis.begin() - 1;
// Add this spectra-detector pair to the mapping
specNumberMapping.push_back(
outputWorkspace->getSpectrum(qIndex).getSpectrumNo());
detIDMapping.push_back(det->getID());
// And add the data and it's error to that bin, taking into account
// the number of detectors contributing to this bin
outputWorkspace->mutableY(qIndex)[j] += Y[j] / numDets_d;
// Standard error on the average
outputWorkspace->mutableE(qIndex)[j] =
sqrt((pow(outputWorkspace->e(qIndex)[j], 2) + pow(E[j], 2)) /
numDets_d);
}
}
} catch (Exception::NotFoundError &) {
// Get to here if exception thrown when calculating distance to detector
// Presumably, if we get to here the spectrum will be all zeroes anyway
// (from conversion to E)
continue;
}
prog.report();
}
// If the input workspace was a distribution, need to divide by q bin width
if (inputWorkspace->isDistribution())
this->makeDistribution(outputWorkspace, verticalAxis);
// Set the output spectrum-detector mapping
SpectrumDetectorMapping outputDetectorMap(specNumberMapping, detIDMapping);
outputWorkspace->updateSpectraUsing(outputDetectorMap);
// Replace any NaNs in outputWorkspace with zeroes
if (this->getProperty("ReplaceNaNs")) {
auto replaceNans = this->createChildAlgorithm("ReplaceSpecialValues");
replaceNans->setChild(true);
replaceNans->initialize();
replaceNans->setProperty("InputWorkspace", outputWorkspace);
replaceNans->setProperty("OutputWorkspace", outputWorkspace);
replaceNans->setProperty("NaNValue", 0.0);
replaceNans->setProperty("InfinityValue", 0.0);
replaceNans->setProperty("BigNumberThreshold", DBL_MAX);
replaceNans->execute();
}
}