/** Initialization method:
@param bkgWS -- shared pointer to the workspace which contains background
@param sourceWS -- shared pointer to the workspace to remove background from
@param emode -- energy conversion mode used during internal units conversion
(0 -- elastic, 1-direct, 2 indirect, as defined in Units conversion
@param pLog -- pointer to the logger class which would report errors
@param nThreads -- number of threads to be used for background removal
@param inPlace -- if the background removal occurs from the existing workspace
or target workspace has to be cloned.
*/
void BackgroundHelper::initialize(const API::MatrixWorkspace_const_sptr &bkgWS,
const API::MatrixWorkspace_sptr &sourceWS,
int emode, Kernel::Logger *pLog, int nThreads,
bool inPlace) {
m_bgWs = bkgWS;
m_wkWS = sourceWS;
m_Emode = emode;
m_pgLog = pLog;
m_inPlace = inPlace;
std::string bgUnits = bkgWS->getAxis(0)->unit()->unitID();
if (bgUnits != "TOF")
throw std::invalid_argument(" Background Workspace: " + bkgWS->getName() +
" should be in the units of TOF");
if (!(bkgWS->getNumberHistograms() == 1 ||
sourceWS->getNumberHistograms() == bkgWS->getNumberHistograms()))
throw std::invalid_argument(" Background Workspace: " + bkgWS->getName() +
" should have the same number of spectra as "
"source workspace or be a single histogram "
"workspace");
auto WSUnit = sourceWS->getAxis(0)->unit();
if (!WSUnit)
throw std::invalid_argument(" Source Workspace: " + sourceWS->getName() +
" should have units");
Geometry::IComponent_const_sptr source =
sourceWS->getInstrument()->getSource();
m_Sample = sourceWS->getInstrument()->getSample();
if ((!source) || (!m_Sample))
throw std::invalid_argument(
"Instrument on Source workspace:" + sourceWS->getName() +
"is not sufficiently defined: failed to get source and/or sample");
m_L1 = source->getDistance(*m_Sample);
// just in case.
this->deleteUnitsConverters();
// allocate the array of units converters to avoid units reallocation within a
// loop
m_WSUnit.assign(nThreads, NULL);
for (int i = 0; i < nThreads; i++) {
m_WSUnit[i] = WSUnit->clone();
}
m_singleValueBackground = false;
if (bkgWS->getNumberHistograms() == 0)
m_singleValueBackground = true;
const MantidVec &dataX = bkgWS->dataX(0);
const MantidVec &dataY = bkgWS->dataY(0);
// const MantidVec& dataE = bkgWS->dataE(0);
m_NBg = dataY[0];
m_dtBg = dataX[1] - dataX[0];
// m_ErrSq = dataE[0]*dataE[0]; // needs further clarification
m_Efix = this->getEi(sourceWS);
}
void SaveIsawDetCal::sizeBanks(std::string bankName, int &NCOLS, int &NROWS,
double &xsize, double &ysize) {
if (bankName.compare("None") == 0)
return;
boost::shared_ptr<const IComponent> parent =
inst->getComponentByName(bankName);
if (parent->type().compare("RectangularDetector") == 0) {
boost::shared_ptr<const RectangularDetector> RDet =
boost::dynamic_pointer_cast<const RectangularDetector>(parent);
NCOLS = RDet->xpixels();
NROWS = RDet->ypixels();
xsize = RDet->xsize();
ysize = RDet->ysize();
} else {
std::vector<Geometry::IComponent_const_sptr> children;
boost::shared_ptr<const Geometry::ICompAssembly> asmb =
boost::dynamic_pointer_cast<const Geometry::ICompAssembly>(parent);
asmb->getChildren(children, false);
if (children[0]->getName().compare("sixteenpack") == 0) {
asmb = boost::dynamic_pointer_cast<const Geometry::ICompAssembly>(
children[0]);
children.clear();
asmb->getChildren(children, false);
}
boost::shared_ptr<const Geometry::ICompAssembly> asmb2 =
boost::dynamic_pointer_cast<const Geometry::ICompAssembly>(children[0]);
std::vector<Geometry::IComponent_const_sptr> grandchildren;
asmb2->getChildren(grandchildren, false);
NROWS = static_cast<int>(grandchildren.size());
NCOLS = static_cast<int>(children.size());
Geometry::IComponent_const_sptr first = children[0];
Geometry::IComponent_const_sptr last = children[NCOLS - 1];
xsize = first->getDistance(*last);
first = grandchildren[0];
last = grandchildren[NROWS - 1];
ysize = first->getDistance(*last);
}
}
/** Execute the algorithm.
*/
void EditInstrumentGeometry::exec() {
// Lots of things have to do with the input workspace
MatrixWorkspace_sptr workspace = getProperty("Workspace");
Geometry::Instrument_const_sptr originstrument = workspace->getInstrument();
// Get and check the primary flight path
double l1 = this->getProperty("PrimaryFlightPath");
if (isEmpty(l1)) {
// Use the original L1
if (!originstrument) {
std::string errmsg(
"It is not supported that L1 is not given, ",
"while there is no instrument associated to input workspace.");
g_log.error(errmsg);
throw std::runtime_error(errmsg);
}
Geometry::IComponent_const_sptr source = originstrument->getSource();
Geometry::IComponent_const_sptr sample = originstrument->getSample();
l1 = source->getDistance(*sample);
g_log.information() << "Retrieve L1 from input data workspace. \n";
}
g_log.information() << "Using L1 = " << l1 << "\n";
// Get spectra number in case they are in a funny order
std::vector<int32_t> specids = this->getProperty("SpectrumIDs");
if (specids.empty()) // they are using the order of the input workspace
{
size_t numHist = workspace->getNumberHistograms();
for (size_t i = 0; i < numHist; ++i) {
specids.push_back(workspace->getSpectrum(i).getSpectrumNo());
g_log.information() << "Add spectrum "
<< workspace->getSpectrum(i).getSpectrumNo() << ".\n";
}
}
// Get the detector ids - empsy means ignore it
const vector<int> vec_detids = getProperty("DetectorIDs");
const bool renameDetID(!vec_detids.empty());
// Get individual detector geometries ordered by input spectrum Numbers
const std::vector<double> l2s = this->getProperty("L2");
const std::vector<double> tths = this->getProperty("Polar");
std::vector<double> phis = this->getProperty("Azimuthal");
// empty list of L2 and 2-theta is not allowed
if (l2s.empty()) {
throw std::runtime_error("User must specify L2 for all spectra. ");
}
if (tths.empty()) {
throw std::runtime_error("User must specify 2theta for all spectra.");
}
// empty list of phi means that they are all zero
if (phis.empty()) {
phis.assign(l2s.size(), 0.);
}
// Validate
for (size_t ib = 0; ib < l2s.size(); ib++) {
g_log.information() << "Detector " << specids[ib] << " L2 = " << l2s[ib]
<< " 2Theta = " << tths[ib] << '\n';
if (specids[ib] < 0) {
// Invalid spectrum Number : less than 0.
stringstream errmsgss;
errmsgss << "Detector ID = " << specids[ib] << " cannot be less than 0.";
throw std::invalid_argument(errmsgss.str());
}
if (l2s[ib] <= 0.0) {
throw std::invalid_argument("L2 cannot be less or equal to 0");
}
}
// Keep original instrument and set the new instrument, if necessary
const auto spec2indexmap = workspace->getSpectrumToWorkspaceIndexMap();
// ??? Condition: spectrum has 1 and only 1 detector
size_t nspec = workspace->getNumberHistograms();
// Initialize another set of L2/2-theta/Phi/DetectorIDs vector ordered by
// workspace index
std::vector<double> storL2s(nspec, 0.);
std::vector<double> stor2Thetas(nspec, 0.);
std::vector<double> storPhis(nspec, 0.);
vector<int> storDetIDs(nspec, 0);
// Map the properties from spectrum Number to workspace index
for (size_t i = 0; i < specids.size(); i++) {
// Find spectrum's workspace index
auto it = spec2indexmap.find(specids[i]);
if (it == spec2indexmap.end()) {
stringstream errss;
errss << "Spectrum Number " << specids[i] << " is not found. "
<< "Instrument won't be edited for this spectrum. \n";
g_log.error(errss.str());
throw std::runtime_error(errss.str());
}
// Store and set value
size_t workspaceindex = it->second;
storL2s[workspaceindex] = l2s[i];
stor2Thetas[workspaceindex] = tths[i];
storPhis[workspaceindex] = phis[i];
if (renameDetID)
storDetIDs[workspaceindex] = vec_detids[i];
g_log.debug() << "workspace index = " << workspaceindex
<< " is for Spectrum " << specids[i] << '\n';
}
// Generate a new instrument
// Name of the new instrument
std::string name = std::string(getProperty("InstrumentName"));
if (name.empty()) {
// Use the original L1
if (!originstrument) {
std::string errmsg(
"It is not supported that InstrumentName is not given, ",
"while there is no instrument associated to input workspace.");
g_log.error(errmsg);
throw std::runtime_error(errmsg);
}
name = originstrument->getName();
}
// Create a new instrument from scratch any way.
auto instrument = boost::make_shared<Geometry::Instrument>(name);
if (!bool(instrument)) {
stringstream errss;
errss << "Trying to use a Parametrized Instrument as an Instrument.";
g_log.error(errss.str());
throw std::runtime_error(errss.str());
}
// Set up source and sample information
Geometry::ObjComponent *samplepos =
new Geometry::ObjComponent("Sample", instrument.get());
instrument->add(samplepos);
instrument->markAsSamplePos(samplepos);
samplepos->setPos(0.0, 0.0, 0.0);
Geometry::ObjComponent *source =
new Geometry::ObjComponent("Source", instrument.get());
instrument->add(source);
instrument->markAsSource(source);
source->setPos(0.0, 0.0, -1.0 * l1);
// Add/copy detector information
auto indexInfo = workspace->indexInfo();
std::vector<detid_t> detIDs;
for (size_t i = 0; i < workspace->getNumberHistograms(); i++) {
// Create a new detector.
// (Instrument will take ownership of pointer so no need to delete.)
detid_t newdetid;
if (renameDetID)
newdetid = storDetIDs[i];
else
newdetid = detid_t(i) + 100;
Geometry::Detector *detector =
new Geometry::Detector("det", newdetid, samplepos);
// Set up new detector parameters related to new instrument
double l2 = storL2s[i];
double tth = stor2Thetas[i];
double phi = storPhis[i];
Kernel::V3D pos;
pos.spherical(l2, tth, phi);
detector->setPos(pos);
// Add new detector to spectrum and instrument
// Good and do some debug output
g_log.debug() << "Orignal spectrum " << indexInfo.spectrumNumber(i)
<< "has " << indexInfo.detectorIDs(i).size()
<< " detectors. \n";
detIDs.push_back(newdetid);
instrument->add(detector);
instrument->markAsDetector(detector);
} // ENDFOR workspace index
indexInfo.setDetectorIDs(std::move(detIDs));
workspace->setIndexInfo(indexInfo);
// Add the new instrument
workspace->setInstrument(instrument);
}
/** method does preliminary calculations of the detectors positions to convert
results into k-dE space ;
and places the results into static cash to be used in subsequent calls to this
algorithm */
void PreprocessDetectorsToMD::processDetectorsPositions(
const API::MatrixWorkspace_const_sptr &inputWS,
DataObjects::TableWorkspace_sptr &targWS) {
g_log.information()
<< "Preprocessing detector locations in a target reciprocal space\n";
//
Geometry::Instrument_const_sptr instrument = inputWS->getInstrument();
// this->pBaseInstr = instrument->baseInstrument();
//
Geometry::IComponent_const_sptr source = instrument->getSource();
Geometry::IComponent_const_sptr sample = instrument->getSample();
if ((!source) || (!sample)) {
g_log.error() << " Instrument is not fully defined. Can not identify "
"source or sample\n";
throw Kernel::Exception::InstrumentDefinitionError(
"Instrument not sufficiently defined: failed to get source and/or "
"sample");
}
// L1
try {
double L1 = source->getDistance(*sample);
targWS->logs()->addProperty<double>("L1", L1, true);
g_log.debug() << "Source-sample distance: " << L1 << '\n';
} catch (Kernel::Exception::NotFoundError &) {
throw Kernel::Exception::InstrumentDefinitionError(
"Unable to calculate source-sample distance for workspace",
inputWS->getTitle());
}
// Instrument name
std::string InstrName = instrument->getName();
targWS->logs()->addProperty<std::string>(
"InstrumentName", InstrName,
true); // "The name which should unique identify current instrument");
targWS->logs()->addProperty<bool>("FakeDetectors", false, true);
// get access to the workspace memory
auto &sp2detMap = targWS->getColVector<size_t>("spec2detMap");
auto &detId = targWS->getColVector<int32_t>("DetectorID");
auto &detIDMap = targWS->getColVector<size_t>("detIDMap");
auto &L2 = targWS->getColVector<double>("L2");
auto &TwoTheta = targWS->getColVector<double>("TwoTheta");
auto &Azimuthal = targWS->getColVector<double>("Azimuthal");
auto &detDir = targWS->getColVector<Kernel::V3D>("DetDirections");
// Efixed; do we need one and does one exist?
double Efi = targWS->getLogs()->getPropertyValueAsType<double>("Ei");
float *pEfixedArray(nullptr);
const Geometry::ParameterMap &pmap = inputWS->constInstrumentParameters();
if (m_getEFixed)
pEfixedArray = targWS->getColDataArray<float>("eFixed");
// check if one needs to generate masked detectors column.
int *pMasksArray(nullptr);
if (m_getIsMasked)
pMasksArray = targWS->getColDataArray<int>("detMask");
//// progress message appearance
size_t div = 100;
size_t nHist = targWS->rowCount();
Mantid::API::Progress theProgress(this, 0, 1, nHist);
//// Loop over the spectra
uint32_t liveDetectorsCount(0);
const auto &spectrumInfo = inputWS->spectrumInfo();
for (size_t i = 0; i < nHist; i++) {
sp2detMap[i] = std::numeric_limits<uint64_t>::quiet_NaN();
detId[i] = std::numeric_limits<int32_t>::quiet_NaN();
detIDMap[i] = std::numeric_limits<uint64_t>::quiet_NaN();
L2[i] = std::numeric_limits<double>::quiet_NaN();
TwoTheta[i] = std::numeric_limits<double>::quiet_NaN();
Azimuthal[i] = std::numeric_limits<double>::quiet_NaN();
// detMask[i] = true;
if (!spectrumInfo.hasDetectors(i) || spectrumInfo.isMonitor(i))
continue;
// if masked detectors state is not used, masked detectors just ignored;
bool maskDetector = spectrumInfo.isMasked(i);
if (m_getIsMasked)
*(pMasksArray + liveDetectorsCount) = maskDetector ? 1 : 0;
else if (maskDetector)
continue;
const auto &spDet = spectrumInfo.detector(i);
// calculate the requested values;
sp2detMap[i] = liveDetectorsCount;
detId[liveDetectorsCount] = int32_t(spDet.getID());
detIDMap[liveDetectorsCount] = i;
L2[liveDetectorsCount] = spectrumInfo.l2(i);
double polar = spectrumInfo.twoTheta(i);
double azim = spDet.getPhi();
TwoTheta[liveDetectorsCount] = polar;
Azimuthal[liveDetectorsCount] = azim;
double sPhi = sin(polar);
double ez = cos(polar);
double ex = sPhi * cos(azim);
double ey = sPhi * sin(azim);
detDir[liveDetectorsCount].setX(ex);
detDir[liveDetectorsCount].setY(ey);
detDir[liveDetectorsCount].setZ(ez);
// double sinTheta=sin(0.5*polar);
// this->SinThetaSq[liveDetectorsCount] = sinTheta*sinTheta;
// specific code which should work and makes sense
// for indirect instrument but may be deployed on any code with Ei property
// defined;
if (pEfixedArray) {
try {
Geometry::Parameter_sptr par = pmap.getRecursive(&spDet, "eFixed");
if (par)
Efi = par->value<double>();
} catch (std::runtime_error &) {
}
// set efixed for each existing detector
*(pEfixedArray + liveDetectorsCount) = static_cast<float>(Efi);
}
liveDetectorsCount++;
if (i % div == 0)
theProgress.report(i, "Preprocessing detectors");
}
targWS->logs()->addProperty<uint32_t>("ActualDetectorsNum",
liveDetectorsCount, true);
theProgress.report();
g_log.information() << "Finished preprocessing detector locations. Found: "
<< liveDetectorsCount << " detectors out of: " << nHist
<< " histograms\n";
}