/** Converts X axis to theta representation
* @param progress :: Progress indicator
* @param targetUnit :: Target conversion unit
* @param inputWS :: Input Workspace
* @param nHist :: Stores the number of histograms
*/
void ConvertSpectrumAxis2::createThetaMap(API::Progress &progress,
const std::string &targetUnit,
API::MatrixWorkspace_sptr &inputWS,
size_t nHist) {
// Set up binding to member funtion. Avoids condition as part of loop over
// nHistograms.
boost::function<double(const IDetector &)> thetaFunction;
if (targetUnit.compare("signed_theta") == 0 ||
targetUnit.compare("SignedTheta") == 0) {
thetaFunction =
boost::bind(&MatrixWorkspace::detectorSignedTwoTheta, inputWS, _1);
} else if (targetUnit == "theta" || targetUnit == "Theta") {
thetaFunction =
boost::bind(&MatrixWorkspace::detectorTwoTheta, inputWS, _1);
}
bool warningGiven = false;
for (size_t i = 0; i < nHist; ++i) {
try {
IDetector_const_sptr det = inputWS->getDetector(i);
// Invoke relevant member function.
m_indexMap.emplace(thetaFunction(*det) * rad2deg, i);
} catch (Exception::NotFoundError &) {
if (!warningGiven)
g_log.warning("The instrument definition is incomplete - spectra "
"dropped from output");
warningGiven = true;
}
progress.report("Converting to theta...");
}
}
void CalculateDIFC::calculate(API::Progress &progress,
API::MatrixWorkspace_sptr &outputWs,
DataObjects::OffsetsWorkspace_sptr &offsetsWS,
double l1, double beamlineNorm,
Kernel::V3D &beamline, Kernel::V3D &samplePos,
detid2det_map &allDetectors) {
SpecialWorkspace2D_sptr localWS =
boost::dynamic_pointer_cast<SpecialWorkspace2D>(outputWs);
// Now go through all
detid2det_map::const_iterator it = allDetectors.begin();
for (; it != allDetectors.end(); ++it) {
Geometry::IDetector_const_sptr det = it->second;
if ((!det->isMasked()) && (!det->isMonitor())) {
const detid_t detID = it->first;
double offset = 0.;
if (offsetsWS)
offset = offsetsWS->getValue(detID, 0.);
double difc = Geometry::Instrument::calcConversion(
l1, beamline, beamlineNorm, samplePos, det, offset);
difc = 1. / difc; // calcConversion gives 1/DIFC
localWS->setValue(detID, difc);
}
progress.report("Calculate DIFC");
}
}
/**
* Main work portion of algorithm. Calculates mean of standard deviation,
* ignoring
* the detectors marked as "bad", then determines if any of the detectors are
* "bad".
* @param progress :: progress indicator
* @param valid :: eventual output workspace, holding 0 for bad and 1 for good
* @param values :: stddeviations of each spectra (I think)
*/
void IdentifyNoisyDetectors::getStdDev(API::Progress &progress,
MatrixWorkspace_sptr valid,
MatrixWorkspace_sptr values) {
const int nhist = static_cast<int>(valid->getNumberHistograms());
int count = 0;
double mean = 0.0;
double mean2 = 0.0;
for (int i = 0; i < nhist; i++) {
if (valid->readY(i)[0] > 0) {
mean += values->readY(i)[0];
mean2 += std::pow(values->readY(i)[0], 2);
count++;
}
progress.report();
}
if (0 == count) {
// all values are zero, no need to loop
return;
}
mean = mean / count;
double stddev = sqrt((mean2 / count) - std::pow(mean, 2));
double upper = mean + 3 * stddev;
double lower = mean - 3 * stddev;
double min = mean * 0.0001;
for (int i = 0; i < nhist; i++) {
double value = values->readY(i)[0];
if (value > upper) {
valid->dataY(i)[0] = 0.0;
} else if (value < lower) {
valid->dataY(i)[0] = 0.0;
} else if (value < min) {
valid->dataY(i)[0] = 0.0;
}
progress.report("Calculating StdDev...");
}
}
/// Executes the algorithm for events
void UnaryOperation::execEvent() {
g_log.information("Processing event workspace");
const MatrixWorkspace_const_sptr matrixInputWS = getProperty(inputPropName());
// generate the output workspace pointer
API::MatrixWorkspace_sptr matrixOutputWS = getProperty(outputPropName());
if (matrixOutputWS != matrixInputWS) {
matrixOutputWS = matrixInputWS->clone();
setProperty(outputPropName(), matrixOutputWS);
}
auto outputWS = boost::dynamic_pointer_cast<EventWorkspace>(matrixOutputWS);
// Now fetch any properties defined by concrete algorithm
retrieveProperties();
int64_t numHistograms = static_cast<int64_t>(outputWS->getNumberHistograms());
API::Progress prog = API::Progress(this, 0.0, 1.0, numHistograms);
PARALLEL_FOR_IF(Kernel::threadSafe(*outputWS))
for (int64_t i = 0; i < numHistograms; ++i) {
PARALLEL_START_INTERUPT_REGION
// switch to weighted events if needed, and use the appropriate helper
// function
auto &evlist = outputWS->getSpectrum(i);
switch (evlist.getEventType()) {
case TOF:
// Switch to weights if needed.
evlist.switchTo(WEIGHTED);
/* no break */
// Fall through
case WEIGHTED:
unaryOperationEventHelper(evlist.getWeightedEvents());
break;
case WEIGHTED_NOTIME:
unaryOperationEventHelper(evlist.getWeightedEventsNoTime());
break;
}
prog.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
outputWS->clearMRU();
auto inputWS = boost::dynamic_pointer_cast<EventWorkspace>(matrixOutputWS);
if (inputWS->getNumberEvents() != outputWS->getNumberEvents()) {
g_log.information() << "Number of events has changed!!!\n";
}
}
/** Create the final output workspace after converting the X axis
* @returns the final output workspace
*
* @param progress :: Progress indicator
* @param targetUnit :: Target conversion unit
* @param inputWS :: Input workspace
* @param nHist :: Stores the number of histograms
*/
MatrixWorkspace_sptr ConvertSpectrumAxis2::createOutputWorkspace(
API::Progress &progress, const std::string &targetUnit,
API::MatrixWorkspace_sptr &inputWS, size_t nHist) {
// Create the output workspace. Can not re-use the input one because the
// spectra are re-ordered.
MatrixWorkspace_sptr outputWorkspace = WorkspaceFactory::Instance().create(
inputWS, m_indexMap.size(), inputWS->x(0).size(), inputWS->y(0).size());
// Now set up a new numeric axis holding the theta values corresponding to
// each spectrum.
auto const newAxis = new NumericAxis(m_indexMap.size());
outputWorkspace->replaceAxis(1, newAxis);
progress.setNumSteps(nHist + m_indexMap.size());
// Set the units of the axis.
if (targetUnit == "theta" || targetUnit == "Theta" ||
targetUnit == "signed_theta" || targetUnit == "SignedTheta") {
newAxis->unit() = boost::make_shared<Units::Degrees>();
} else if (targetUnit == "ElasticQ") {
newAxis->unit() = UnitFactory::Instance().create("MomentumTransfer");
} else if (targetUnit == "ElasticQSquared") {
newAxis->unit() = UnitFactory::Instance().create("QSquared");
}
std::multimap<double, size_t>::const_iterator it;
size_t currentIndex = 0;
for (it = m_indexMap.begin(); it != m_indexMap.end(); ++it) {
// Set the axis value.
newAxis->setValue(currentIndex, it->first);
// Copy over the data.
outputWorkspace->setHistogram(currentIndex, inputWS->histogram(it->second));
// We can keep the spectrum numbers etc.
outputWorkspace->getSpectrum(currentIndex)
.copyInfoFrom(inputWS->getSpectrum(it->second));
++currentIndex;
progress.report("Creating output workspace...");
}
return outputWorkspace;
}
/** Convert X axis to Elastic Q representation
* @param progress :: Progress indicator
* @param targetUnit :: Target conversion unit
* @param inputWS :: Input workspace
* @param nHist :: Stores the number of histograms
*/
void ConvertSpectrumAxis2::createElasticQMap(API::Progress &progress,
const std::string &targetUnit,
API::MatrixWorkspace_sptr &inputWS,
size_t nHist) {
IComponent_const_sptr source = inputWS->getInstrument()->getSource();
IComponent_const_sptr sample = inputWS->getInstrument()->getSample();
const std::string emodeStr = getProperty("EMode");
int emode = 0;
if (emodeStr == "Direct")
emode = 1;
else if (emodeStr == "Indirect")
emode = 2;
for (size_t i = 0; i < nHist; i++) {
IDetector_const_sptr detector = inputWS->getDetector(i);
double twoTheta(0.0), efixed(0.0);
if (!detector->isMonitor()) {
twoTheta = 0.5 * inputWS->detectorTwoTheta(*detector);
efixed = getEfixed(detector, inputWS, emode); // get efixed
} else {
twoTheta = 0.0;
efixed = DBL_MIN;
}
// Convert to MomentumTransfer
double elasticQInAngstroms = Kernel::UnitConversion::run(twoTheta, efixed);
if (targetUnit == "ElasticQ") {
m_indexMap.emplace(elasticQInAngstroms, i);
} else if (targetUnit == "ElasticQSquared") {
// The QSquared value.
double elasticQSquaredInAngstroms =
elasticQInAngstroms * elasticQInAngstroms;
m_indexMap.emplace(elasticQSquaredInAngstroms, i);
}
progress.report("Converting to Elastic Q...");
}
}
/** Execute the algorithm.
*/
void LoadNXSPE::exec() {
std::string filename = getProperty("Filename");
// quicly check if it's really nxspe
try {
::NeXus::File file(filename);
std::string mainEntry = (*(file.getEntries().begin())).first;
file.openGroup(mainEntry, "NXentry");
file.openData("definition");
if (identiferConfidence(file.getStrData()) < 1) {
throw std::invalid_argument("Not NXSPE");
}
file.close();
} catch (...) {
throw std::invalid_argument("Not NeXus or not NXSPE");
}
// Load the data
::NeXus::File file(filename);
std::string mainEntry = (*(file.getEntries().begin())).first;
file.openGroup(mainEntry, "NXentry");
file.openGroup("NXSPE_info", "NXcollection");
std::map<std::string, std::string> entries = file.getEntries();
std::vector<double> temporary;
double fixed_energy, psi = 0.;
if (!entries.count("fixed_energy")) {
throw std::invalid_argument("fixed_energy field was not found");
}
file.openData("fixed_energy");
file.getData(temporary);
fixed_energy = temporary.at(0);
file.closeData();
if (entries.count("psi")) {
file.openData("psi");
file.getData(temporary);
psi = temporary.at(0);
file.closeData();
}
int kikfscaling = 0;
if (entries.count("ki_over_kf_scaling")) {
file.openData("ki_over_kf_scaling");
std::vector<int> temporaryint;
file.getData(temporaryint);
kikfscaling = temporaryint.at(0);
file.closeData();
}
file.closeGroup(); // NXSPE_Info
file.openGroup("data", "NXdata");
entries = file.getEntries();
if (!entries.count("data")) {
throw std::invalid_argument("data field was not found");
}
file.openData("data");
::NeXus::Info info = file.getInfo();
std::size_t numSpectra = static_cast<std::size_t>(info.dims.at(0));
std::size_t numBins = static_cast<std::size_t>(info.dims.at(1));
std::vector<double> data;
file.getData(data);
file.closeData();
if (!entries.count("error")) {
throw std::invalid_argument("error field was not found");
}
file.openData("error");
std::vector<double> error;
file.getData(error);
file.closeData();
if (!entries.count("energy")) {
throw std::invalid_argument("energy field was not found");
}
file.openData("energy");
std::vector<double> energies;
file.getData(energies);
file.closeData();
if (!entries.count("azimuthal")) {
throw std::invalid_argument("azimuthal field was not found");
}
file.openData("azimuthal");
std::vector<double> azimuthal;
file.getData(azimuthal);
file.closeData();
if (!entries.count("azimuthal_width")) {
throw std::invalid_argument("azimuthal_width field was not found");
}
file.openData("azimuthal_width");
std::vector<double> azimuthal_width;
file.getData(azimuthal_width);
file.closeData();
if (!entries.count("polar")) {
throw std::invalid_argument("polar field was not found");
}
file.openData("polar");
std::vector<double> polar;
file.getData(polar);
file.closeData();
if (!entries.count("polar_width")) {
throw std::invalid_argument("polar_width field was not found");
}
file.openData("polar_width");
std::vector<double> polar_width;
file.getData(polar_width);
file.closeData();
// distance might not have been saved in all NXSPE files
std::vector<double> distance;
if (entries.count("distance")) {
file.openData("distance");
file.getData(distance);
file.closeData();
}
file.closeGroup(); // data group
file.closeGroup(); // Main entry
file.close();
// check if dimensions of the vectors are correct
if ((error.size() != data.size()) || (azimuthal.size() != numSpectra) ||
(azimuthal_width.size() != numSpectra) || (polar.size() != numSpectra) ||
(polar_width.size() != numSpectra) ||
((energies.size() != numBins) && (energies.size() != numBins + 1))) {
throw std::invalid_argument(
"incompatible sizes of fields in the NXSPE file");
}
MatrixWorkspace_sptr outputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(
WorkspaceFactory::Instance().create("Workspace2D", numSpectra,
energies.size(), numBins));
// Need to get hold of the parameter map
outputWS->getAxis(0)->unit() = UnitFactory::Instance().create("DeltaE");
outputWS->setYUnit("SpectraNumber");
// add logs
outputWS->mutableRun().addLogData(
new PropertyWithValue<double>("Ei", fixed_energy));
outputWS->mutableRun().addLogData(new PropertyWithValue<double>("psi", psi));
outputWS->mutableRun().addLogData(new PropertyWithValue<std::string>(
"ki_over_kf_scaling", kikfscaling == 1 ? "true" : "false"));
// Set Goniometer
Geometry::Goniometer gm;
gm.pushAxis("psi", 0, 1, 0, psi);
outputWS->mutableRun().setGoniometer(gm, true);
// generate instrument
Geometry::Instrument_sptr instrument(new Geometry::Instrument("NXSPE"));
outputWS->setInstrument(instrument);
Geometry::ObjComponent *source = new Geometry::ObjComponent("source");
source->setPos(0.0, 0.0, -10.0);
instrument->add(source);
instrument->markAsSource(source);
Geometry::ObjComponent *sample = new Geometry::ObjComponent("sample");
instrument->add(sample);
instrument->markAsSamplePos(sample);
Geometry::Object_const_sptr cuboid(
createCuboid(0.1, 0.1, 0.1)); // FIXME: memory hog on rendering. Also,
// make each detector separate size
for (std::size_t i = 0; i < numSpectra; ++i) {
double r = 1.0;
if (!distance.empty()) {
r = distance.at(i);
}
Kernel::V3D pos;
pos.spherical(r, polar.at(i), azimuthal.at(i));
Geometry::Detector *det =
new Geometry::Detector("pixel", static_cast<int>(i + 1), sample);
det->setPos(pos);
det->setShape(cuboid);
instrument->add(det);
instrument->markAsDetector(det);
}
Geometry::ParameterMap &pmap = outputWS->instrumentParameters();
std::vector<double>::iterator itdata = data.begin(), iterror = error.begin(),
itdataend, iterrorend;
API::Progress prog = API::Progress(this, 0.0, 0.9, numSpectra);
for (std::size_t i = 0; i < numSpectra; ++i) {
itdataend = itdata + numBins;
iterrorend = iterror + numBins;
outputWS->dataX(i) = energies;
if ((!boost::math::isfinite(*itdata)) || (*itdata <= -1e10)) // masked bin
{
outputWS->dataY(i) = std::vector<double>(numBins, 0);
outputWS->dataE(i) = std::vector<double>(numBins, 0);
pmap.addBool(outputWS->getDetector(i)->getComponentID(), "masked", true);
} else {
outputWS->dataY(i) = std::vector<double>(itdata, itdataend);
outputWS->dataE(i) = std::vector<double>(iterror, iterrorend);
}
itdata = (itdataend);
iterror = (iterrorend);
prog.report();
}
setProperty("OutputWorkspace", outputWS);
}
/// Executes the algorithm for events
void UnaryOperation::execEvent() {
g_log.information("Processing event workspace");
const MatrixWorkspace_const_sptr matrixInputWS =
this->getProperty(inputPropName());
EventWorkspace_const_sptr inputWS =
boost::dynamic_pointer_cast<const EventWorkspace>(matrixInputWS);
// generate the output workspace pointer
API::MatrixWorkspace_sptr matrixOutputWS =
this->getProperty(outputPropName());
EventWorkspace_sptr outputWS;
if (matrixOutputWS == matrixInputWS) {
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(matrixOutputWS);
} else {
// Make a brand new EventWorkspace
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create(
"EventWorkspace", inputWS->getNumberHistograms(), 2, 1));
// Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS,
false);
// You need to copy over the data as well.
outputWS->copyDataFrom((*inputWS));
// Cast to the matrixOutputWS and save it
matrixOutputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(outputWS);
this->setProperty("OutputWorkspace", matrixOutputWS);
}
// Now fetch any properties defined by concrete algorithm
retrieveProperties();
int64_t numHistograms = static_cast<int64_t>(inputWS->getNumberHistograms());
API::Progress prog = API::Progress(this, 0.0, 1.0, numHistograms);
PARALLEL_FOR1(outputWS)
for (int64_t i = 0; i < numHistograms; ++i) {
PARALLEL_START_INTERUPT_REGION
// switch to weighted events if needed, and use the appropriate helper
// function
EventList *evlist = outputWS->getEventListPtr(i);
switch (evlist->getEventType()) {
case TOF:
// Switch to weights if needed.
evlist->switchTo(WEIGHTED);
/* no break */
// Fall through
case WEIGHTED:
unaryOperationEventHelper(evlist->getWeightedEvents());
break;
case WEIGHTED_NOTIME:
unaryOperationEventHelper(evlist->getWeightedEventsNoTime());
break;
}
prog.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
outputWS->clearMRU();
if (inputWS->getNumberEvents() != outputWS->getNumberEvents()) {
g_log.information() << "Number of events has changed!!!" << std::endl;
}
}
void CorrectKiKf::execEvent()
{
g_log.information("Processing event workspace");
const MatrixWorkspace_const_sptr matrixInputWS = this->getProperty("InputWorkspace");
EventWorkspace_const_sptr inputWS= boost::dynamic_pointer_cast<const EventWorkspace>(matrixInputWS);
// generate the output workspace pointer
API::MatrixWorkspace_sptr matrixOutputWS = this->getProperty("OutputWorkspace");
EventWorkspace_sptr outputWS;
if (matrixOutputWS == matrixInputWS)
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(matrixOutputWS);
else
{
//Make a brand new EventWorkspace
outputWS = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace", inputWS->getNumberHistograms(), 2, 1));
//Copy geometry over.
API::WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS, false);
//You need to copy over the data as well.
outputWS->copyDataFrom( (*inputWS) );
//Cast to the matrixOutputWS and save it
matrixOutputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(outputWS);
this->setProperty("OutputWorkspace", matrixOutputWS);
}
const std::string emodeStr = getProperty("EMode");
double efixedProp = getProperty("EFixed"),efixed;
if( efixedProp == EMPTY_DBL() )
{
if (emodeStr == "Direct")
{
// Check if it has been store on the run object for this workspace
if( this->inputWS->run().hasProperty("Ei"))
{
Kernel::Property* eiprop = this->inputWS->run().getProperty("Ei");
efixedProp = boost::lexical_cast<double>(eiprop->value());
g_log.debug() << "Using stored Ei value " << efixedProp << "\n";
}
else
{
throw std::invalid_argument("No Ei value has been set or stored within the run information.");
}
}
else
{
// If not specified, will try to get Ef from the parameter file for indirect geometry,
// but it will be done for each spectrum separately, in case of different analyzer crystals
}
}
// Get the parameter map
const ParameterMap& pmap = outputWS->constInstrumentParameters();
int64_t numHistograms = static_cast<int64_t>(inputWS->getNumberHistograms());
API::Progress prog = API::Progress(this, 0.0, 1.0, numHistograms);
PARALLEL_FOR1(outputWS)
for (int64_t i=0; i < numHistograms; ++i)
{
PARALLEL_START_INTERUPT_REGION
double Efi = 0;
// Now get the detector object for this histogram to check if monitor
// or to get Ef for indirect geometry
if (emodeStr == "Indirect")
{
if ( efixedProp != EMPTY_DBL()) Efi = efixedProp;
else try
{
IDetector_const_sptr det = inputWS->getDetector(i);
if (!det->isMonitor())
{
try
{
Parameter_sptr par = pmap.getRecursive(det.get(),"Efixed");
if (par)
{
Efi = par->value<double>();
g_log.debug() << "Detector: " << det->getID() << " EFixed: " << Efi << "\n";
}
}
catch (std::runtime_error&) { /* Throws if a DetectorGroup, use single provided value */ }
}
}
catch(std::runtime_error&) { g_log.information() << "Workspace Index " << i << ": cannot find detector" << "\n"; }
}
if (emodeStr == "Indirect") efixed=Efi;
else efixed=efixedProp;
//Do the correction
EventList *evlist=outputWS->getEventListPtr(i);
switch (evlist->getEventType())
{
case TOF:
//Switch to weights if needed.
evlist->switchTo(WEIGHTED);
/* no break */
// Fall through
case WEIGHTED:
correctKiKfEventHelper(evlist->getWeightedEvents(), efixed,emodeStr);
break;
case WEIGHTED_NOTIME:
correctKiKfEventHelper(evlist->getWeightedEventsNoTime(), efixed,emodeStr);
break;
}
prog.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
outputWS->clearMRU();
if (inputWS->getNumberEvents( ) != outputWS->getNumberEvents( ))
{
g_log.information() <<"Ef <= 0 or Ei <= 0 for "<<inputWS->getNumberEvents( )-outputWS->getNumberEvents( )<<" events, out of "<<inputWS->getNumberEvents( )<<std::endl;
if ( efixedProp == EMPTY_DBL()) g_log.information()<<"Try to set fixed energy"<<std::endl ;
}
}
/**
* Create an test instrument with n panels of rectangular detectors,
*pixels*pixels in size,
* a source and spherical sample shape.
*
* Banks' lower-left corner is at position (0,0,5*banknum) and they go up to
*(pixels*0.008, pixels*0.008, Z)
* Pixels are 4 mm wide.
*
* @param progress :: progress indicator
* @param num_banks :: number of rectangular banks to create
* @param pixels :: number of pixels in each direction.
* @param pixelSpacing :: padding between pixels
* @param bankDistanceFromSample :: Distance of first bank from sample (defaults
*to 5.0m)
* @param sourceSampleDistance :: The distance from the source to the sample
* @returns A shared pointer to the generated instrument
*/
Instrument_sptr CreateSampleWorkspace::createTestInstrumentRectangular(
API::Progress &progress, int num_banks, int pixels, double pixelSpacing,
const double bankDistanceFromSample, const double sourceSampleDistance) {
boost::shared_ptr<Instrument> testInst(new Instrument("basic_rect"));
// The instrument is going to be set up with z as the beam axis and y as the
// vertical axis.
testInst->setReferenceFrame(
boost::shared_ptr<ReferenceFrame>(new ReferenceFrame(Y, Z, Left, "")));
const double cylRadius(pixelSpacing / 2);
const double cylHeight(0.0002);
// One object
Object_sptr pixelShape = createCappedCylinder(
cylRadius, cylHeight, V3D(0.0, -cylHeight / 2.0, 0.0), V3D(0., 1.0, 0.),
"pixel-shape");
for (int banknum = 1; banknum <= num_banks; banknum++) {
// Make a new bank
std::ostringstream bankname;
bankname << "bank" << banknum;
RectangularDetector *bank = new RectangularDetector(bankname.str());
bank->initialize(pixelShape, pixels, 0.0, pixelSpacing, pixels, 0.0,
pixelSpacing, banknum * pixels * pixels, true, pixels);
// Mark them all as detectors
for (int x = 0; x < pixels; x++)
for (int y = 0; y < pixels; y++) {
boost::shared_ptr<Detector> detector = bank->getAtXY(x, y);
if (detector)
// Mark it as a detector (add to the instrument cache)
testInst->markAsDetector(detector.get());
}
testInst->add(bank);
// Set the bank along the z-axis of the instrument. (beam direction).
bank->setPos(V3D(0.0, 0.0, bankDistanceFromSample * banknum));
progress.report();
}
// Define a source component
ObjComponent *source =
new ObjComponent("moderator", Object_sptr(new Object), testInst.get());
source->setPos(V3D(0.0, 0.0, -sourceSampleDistance));
testInst->add(source);
testInst->markAsSource(source);
// Add chopper
ObjComponent *chopper = new ObjComponent(
"chopper-position", Object_sptr(new Object), testInst.get());
chopper->setPos(V3D(0.0, 0.0, -0.25 * sourceSampleDistance));
testInst->add(chopper);
// Define a sample as a simple sphere
Object_sptr sampleSphere =
createSphere(0.001, V3D(0.0, 0.0, 0.0), "sample-shape");
ObjComponent *sample =
new ObjComponent("sample", sampleSphere, testInst.get());
testInst->setPos(0.0, 0.0, 0.0);
testInst->add(sample);
testInst->markAsSamplePos(sample);
return testInst;
}