/**
* Constructor. Creates a tree of GLActors. Each actor is responsible for displaying insrument components in 3D.
* Some of the components have "pick ID" assigned to them. Pick IDs can be uniquely converted to a RGB colour value
* which in turn can be used for picking the component from the screen.
* @param wsName :: Workspace name
* @param autoscaling :: True to start with autoscaling option on. If on the min and max of
* the colormap scale are defined by the min and max of the data.
* @param scaleMin :: Minimum value of the colormap scale. Used to assign detector colours. Ignored if autoscaling == true.
* @param scaleMax :: Maximum value of the colormap scale. Used to assign detector colours. Ignored if autoscaling == true.
*/
InstrumentActor::InstrumentActor(const QString &wsName, bool autoscaling, double scaleMin, double scaleMax):
m_workspace(AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(wsName.toStdString())),
m_ragged(true),
m_autoscaling(autoscaling),
m_defaultPos(),
m_maskedColor(100,100,100),
m_failedColor(200,200,200)
{
// settings
loadSettings();
auto sharedWorkspace = m_workspace.lock();
if (!sharedWorkspace)
throw std::logic_error("InstrumentActor passed a workspace that isn't a MatrixWorkspace");
// set up the color map
if (!m_currentColorMapFilename.isEmpty())
{
loadColorMap(m_currentColorMapFilename,false);
}
m_colorMap.changeScaleType(m_scaleType);
// set up data ranges and colours
setUpWorkspace(sharedWorkspace, scaleMin, scaleMax);
Instrument_const_sptr instrument = getInstrument();
// If the instrument is empty, maybe only having the sample and source
const int nelements = instrument->nelements();
if ( ( nelements == 0 ) ||
( nelements == 1 && ( instrument->getSource() || instrument->getSample() ) ) ||
( nelements == 2 && instrument->getSource() && instrument->getSample() )
)
{
QMessageBox::warning(NULL,"MantidPlot - Warning","This instrument appears to contain no detectors","OK");
}
// this adds actors for all instrument components to the scene and fills in m_detIDs
m_scene.addActor(new CompAssemblyActor(*this,instrument->getComponentID()));
setupPickColors();
if ( !m_showGuides )
{
// hide guide and other components
showGuides( m_showGuides );
}
}
void AnvredCorrection::scale_init(IDetector_const_sptr det, Instrument_const_sptr inst, int& bank, double& L2, double& depth, double& pathlength, std::string bankName)
{
bankName = det->getParent()->getParent()->getName();
std::string bankNameStr = bankName;
// Take out the "bank" part of the bank name and convert to an int
bankNameStr.erase(remove_if(bankNameStr.begin(), bankNameStr.end(), not1(std::ptr_fun (::isdigit))), bankNameStr.end());
Strings::convert(bankNameStr, bank);
IComponent_const_sptr sample = inst->getSample();
double cosA = inst->getComponentByName(bankName)->getDistance(*sample) / L2;
pathlength = depth / cosA;
}
void EstimatePDDetectorResolution::retrieveInstrumentParameters()
{
#if 0
// Call SolidAngle to get solid angles for all detectors
Algorithm_sptr calsolidangle = createChildAlgorithm("SolidAngle", -1, -1, true);
calsolidangle->initialize();
calsolidangle->setProperty("InputWorkspace", m_inputWS);
calsolidangle->execute();
if (!calsolidangle->isExecuted())
throw runtime_error("Unable to run solid angle. ");
m_solidangleWS = calsolidangle->getProperty("OutputWorkspace");
if (!m_solidangleWS)
throw runtime_error("Unable to get solid angle workspace from SolidAngle(). ");
size_t numspec = m_solidangleWS->getNumberHistograms();
for (size_t i = 0; i < numspec; ++i)
g_log.debug() << "[DB]: " << m_solidangleWS->readY(i)[0] << "\n";
#endif
// Calculate centre neutron velocity
Property* cwlproperty = m_inputWS->run().getProperty("LambdaRequest");
if (!cwlproperty)
throw runtime_error("Unable to locate property LambdaRequest as central wavelength. ");
TimeSeriesProperty<double>* cwltimeseries = dynamic_cast<TimeSeriesProperty<double>* >(cwlproperty);
if (!cwltimeseries)
throw runtime_error("LambdaReqeust is not a TimeSeriesProperty in double. ");
if (cwltimeseries->size() != 1)
throw runtime_error("LambdaRequest should contain 1 and only 1 entry. ");
double centrewavelength = cwltimeseries->nthValue(0);
string unit = cwltimeseries->units();
if (unit.compare("Angstrom") == 0)
centrewavelength *= 1.0E-10;
else
throw runtime_error("Unit is not recognized");
m_centreVelocity = PhysicalConstants::h/PhysicalConstants::NeutronMass/centrewavelength;
g_log.notice() << "Centre wavelength = " << centrewavelength << ", Centre neutron velocity = " << m_centreVelocity << "\n";
// Calcualte L1 sample to source
Instrument_const_sptr instrument = m_inputWS->getInstrument();
V3D samplepos = instrument->getSample()->getPos();
V3D sourcepos = instrument->getSource()->getPos();
m_L1 = samplepos.distance(sourcepos);
g_log.notice() << "L1 = " << m_L1 << "\n";
return;
}
/** Method for updating m_waveLength.
* If size of m_waveLength is equal to number of data (for a new instance of
*this
* class this vector is empty initially) then don't recalculate it.
*
* @param xValues :: x values
* @param nData :: length of xValues
*/
void IkedaCarpenterPV::calWavelengthAtEachDataPoint(const double *xValues,
const size_t &nData) const {
// if wavelength vector already have the right size no need for resizing it
// further we make the assumption that no need to recalculate this vector if
// it already has the right size
if (m_waveLength.size() != nData) {
m_waveLength.resize(nData);
Mantid::Kernel::Unit_sptr wavelength =
Mantid::Kernel::UnitFactory::Instance().create("Wavelength");
for (size_t i = 0; i < nData; i++) {
m_waveLength[i] = xValues[i];
}
// note if a version of convertValue was added which allows a double* as
// first argument
// then could avoid copying above plus only have to resize m_wavelength when
// its size smaller than nData
API::MatrixWorkspace_const_sptr mws = getMatrixWorkspace();
if (mws) {
API::MatrixWorkspace_const_sptr mws = getMatrixWorkspace();
Instrument_const_sptr instrument = mws->getInstrument();
Geometry::IComponent_const_sptr sample = instrument->getSample();
if (sample != nullptr) {
convertValue(m_waveLength, wavelength, mws, m_workspaceIndex);
} else {
g_log.warning()
<< "No sample set for instrument in workspace.\n"
<< "Can't calculate wavelength in IkedaCarpenter.\n"
<< "Default all wavelengths to one.\n"
<< "Solution is to load appropriate instrument into workspace.\n";
for (size_t i = 0; i < nData; i++)
m_waveLength[i] = 1.0;
}
} else {
g_log.warning() << "Workspace not set.\n"
<< "Can't calculate wavelength in IkedaCarpenter.\n"
<< "Default all wavelengths to one.\n"
<< "Solution call setMatrixWorkspace() for function.\n";
for (size_t i = 0; i < nData; i++)
m_waveLength[i] = 1.0;
}
}
}
void EstimateResolutionDiffraction::retrieveInstrumentParameters() {
double centrewavelength = getWavelength();
g_log.notice() << "Centre wavelength = " << centrewavelength << " Angstrom\n";
if (centrewavelength > WAVELENGTH_MAX) {
throw runtime_error("unphysical wavelength used");
}
// Calculate centre neutron velocity
m_centreVelocity = WAVELENGTH_TO_VELOCITY / centrewavelength;
g_log.notice() << "Centre neutron velocity = " << m_centreVelocity << "\n";
// Calculate L1 sample to source
Instrument_const_sptr instrument = m_inputWS->getInstrument();
V3D samplepos = instrument->getSample()->getPos();
V3D sourcepos = instrument->getSource()->getPos();
m_L1 = samplepos.distance(sourcepos);
g_log.notice() << "L1 = " << m_L1 << "\n";
return;
}
void EstimateResolutionDiffraction::estimateDetectorResolution() {
Instrument_const_sptr instrument = m_inputWS->getInstrument();
V3D samplepos = instrument->getSample()->getPos();
size_t numspec = m_inputWS->getNumberHistograms();
double mintwotheta = 10000;
double maxtwotheta = 0;
double mint3 = 1;
double maxt3 = 0;
size_t count_nodetsize = 0;
for (size_t i = 0; i < numspec; ++i) {
// Get detector
IDetector_const_sptr det = m_inputWS->getDetector(i);
double detdim;
boost::shared_ptr<const Detector> realdet =
boost::dynamic_pointer_cast<const Detector>(det);
if (realdet) {
double dy = realdet->getHeight();
double dx = realdet->getWidth();
detdim = sqrt(dx * dx + dy * dy) * 0.5;
} else {
// Use detector dimension as 0 as no-information
detdim = 0;
++count_nodetsize;
}
// Get the distance from detector to source
V3D detpos = det->getPos();
double l2 = detpos.distance(samplepos);
if (l2 < 0)
throw runtime_error("L2 is negative");
// Calculate T
double centraltof = (m_L1 + l2) / m_centreVelocity;
// Angle
double twotheta = m_inputWS->detectorTwoTheta(det);
double theta = 0.5 * twotheta;
// double solidangle = m_solidangleWS->readY(i)[0];
double solidangle = det->solidAngle(samplepos);
double deltatheta = sqrt(solidangle);
// Resolution
double t1 = m_deltaT / centraltof;
double t2 = detdim / (m_L1 + l2);
double t3 = deltatheta * (cos(theta) / sin(theta));
double resolution = sqrt(t1 * t1 + t2 * t2 + t3 * t3);
m_outputWS->dataX(i)[0] = static_cast<double>(i);
m_outputWS->dataY(i)[0] = resolution;
if (twotheta > maxtwotheta)
maxtwotheta = twotheta;
else if (twotheta < mintwotheta)
mintwotheta = twotheta;
if (fabs(t3) < mint3)
mint3 = fabs(t3);
else if (fabs(t3) > maxt3)
maxt3 = fabs(t3);
g_log.debug() << det->type() << " " << i << "\t\t" << twotheta
<< "\t\tdT/T = " << t1 * t1 << "\t\tdL/L = " << t2
<< "\t\tdTheta*cotTheta = " << t3 << "\n";
}
g_log.notice() << "2theta range: " << mintwotheta << ", " << maxtwotheta
<< "\n";
g_log.notice() << "t3 range: " << mint3 << ", " << maxt3 << "\n";
g_log.notice() << "Number of detector having NO size information = "
<< count_nodetsize << "\n";
return;
}
/** Executes the algorithm
*
* @throw runtime_error Thrown if algorithm cannot execute
*/
void DiffractionEventCalibrateDetectors::exec() {
// Try to retrieve optional properties
const int maxIterations = getProperty("MaxIterations");
const double peakOpt = getProperty("LocationOfPeakToOptimize");
// Get the input workspace
EventWorkspace_sptr inputW = getProperty("InputWorkspace");
// retrieve the properties
const std::string rb_params = getProperty("Params");
// Get some stuff from the input workspace
Instrument_const_sptr inst = inputW->getInstrument();
// Build a list of Rectangular Detectors
std::vector<boost::shared_ptr<RectangularDetector>> detList;
// --------- Loading only one bank ----------------------------------
std::string onebank = getProperty("BankName");
bool doOneBank = (onebank != "");
for (int i = 0; i < inst->nelements(); i++) {
boost::shared_ptr<RectangularDetector> det;
boost::shared_ptr<ICompAssembly> assem;
boost::shared_ptr<ICompAssembly> assem2;
det = boost::dynamic_pointer_cast<RectangularDetector>((*inst)[i]);
if (det) {
if (det->getName().compare(onebank) == 0)
detList.push_back(det);
if (!doOneBank)
detList.push_back(det);
} else {
// Also, look in the first sub-level for RectangularDetectors (e.g. PG3).
// We are not doing a full recursive search since that will be very long
// for lots of pixels.
assem = boost::dynamic_pointer_cast<ICompAssembly>((*inst)[i]);
if (assem) {
for (int j = 0; j < assem->nelements(); j++) {
det = boost::dynamic_pointer_cast<RectangularDetector>((*assem)[j]);
if (det) {
if (det->getName().compare(onebank) == 0)
detList.push_back(det);
if (!doOneBank)
detList.push_back(det);
} else {
// Also, look in the second sub-level for RectangularDetectors (e.g.
// PG3).
// We are not doing a full recursive search since that will be very
// long for lots of pixels.
assem2 = boost::dynamic_pointer_cast<ICompAssembly>((*assem)[j]);
if (assem2) {
for (int k = 0; k < assem2->nelements(); k++) {
det = boost::dynamic_pointer_cast<RectangularDetector>(
(*assem2)[k]);
if (det) {
if (det->getName().compare(onebank) == 0)
detList.push_back(det);
if (!doOneBank)
detList.push_back(det);
}
}
}
}
}
}
}
}
// set-up minimizer
std::string inname = getProperty("InputWorkspace");
std::string outname = inname + "2"; // getProperty("OutputWorkspace");
IAlgorithm_sptr algS = createChildAlgorithm("SortEvents");
algS->setProperty("InputWorkspace", inputW);
algS->setPropertyValue("SortBy", "X Value");
algS->executeAsChildAlg();
// Write DetCal File
std::string filename = getProperty("DetCalFilename");
std::fstream outfile;
outfile.open(filename.c_str(), std::ios::out);
if (detList.size() > 1) {
outfile << "#\n";
outfile << "# Mantid Optimized .DetCal file for SNAP with TWO detector "
"panels\n";
outfile << "# Old Panel, nominal size and distance at -90 degrees.\n";
outfile << "# New Panel, nominal size and distance at +90 degrees.\n";
outfile << "#\n";
outfile << "# Lengths are in centimeters.\n";
outfile << "# Base and up give directions of unit vectors for a local\n";
outfile << "# x,y coordinate system on the face of the detector.\n";
outfile << "#\n";
outfile << "# " << DateAndTime::getCurrentTime().toFormattedString("%c")
<< "\n";
outfile << "#\n";
outfile << "6 L1 T0_SHIFT\n";
IComponent_const_sptr source = inst->getSource();
IComponent_const_sptr sample = inst->getSample();
outfile << "7 " << source->getDistance(*sample) * 100 << " 0\n";
outfile << "4 DETNUM NROWS NCOLS WIDTH HEIGHT DEPTH DETD "
"CenterX CenterY CenterZ BaseX BaseY BaseZ "
"UpX UpY UpZ\n";
}
Progress prog(this, 0.0, 1.0, detList.size());
for (int det = 0; det < static_cast<int>(detList.size()); det++) {
std::string par[6];
par[0] = detList[det]->getName();
par[1] = inname;
par[2] = outname;
std::ostringstream strpeakOpt;
strpeakOpt << peakOpt;
par[3] = strpeakOpt.str();
par[4] = rb_params;
// --- Create a GroupingWorkspace for this detector name ------
CPUTimer tim;
IAlgorithm_sptr alg2 =
AlgorithmFactory::Instance().create("CreateGroupingWorkspace", 1);
alg2->initialize();
alg2->setProperty("InputWorkspace", inputW);
alg2->setPropertyValue("GroupNames", detList[det]->getName());
std::string groupWSName = "group_" + detList[det]->getName();
alg2->setPropertyValue("OutputWorkspace", groupWSName);
alg2->executeAsChildAlg();
par[5] = groupWSName;
std::cout << tim << " to CreateGroupingWorkspace\n";
const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex;
gsl_multimin_fminimizer *s = nullptr;
gsl_vector *ss, *x;
gsl_multimin_function minex_func;
// finally do the fitting
int nopt = 6;
int iter = 0;
int status = 0;
/* Starting point */
x = gsl_vector_alloc(nopt);
gsl_vector_set(x, 0, 0.0);
gsl_vector_set(x, 1, 0.0);
gsl_vector_set(x, 2, 0.0);
gsl_vector_set(x, 3, 0.0);
gsl_vector_set(x, 4, 0.0);
gsl_vector_set(x, 5, 0.0);
/* Set initial step sizes to 0.1 */
ss = gsl_vector_alloc(nopt);
gsl_vector_set_all(ss, 0.1);
/* Initialize method and iterate */
minex_func.n = nopt;
minex_func.f = &Mantid::Algorithms::gsl_costFunction;
minex_func.params = ∥
s = gsl_multimin_fminimizer_alloc(T, nopt);
gsl_multimin_fminimizer_set(s, &minex_func, x, ss);
do {
iter++;
status = gsl_multimin_fminimizer_iterate(s);
if (status)
break;
double size = gsl_multimin_fminimizer_size(s);
status = gsl_multimin_test_size(size, 1e-2);
} while (status == GSL_CONTINUE && iter < maxIterations &&
s->fval != -0.000);
// Output summary to log file
if (s->fval != -0.000)
movedetector(gsl_vector_get(s->x, 0), gsl_vector_get(s->x, 1),
gsl_vector_get(s->x, 2), gsl_vector_get(s->x, 3),
gsl_vector_get(s->x, 4), gsl_vector_get(s->x, 5), par[0],
getProperty("InputWorkspace"));
else {
gsl_vector_set(s->x, 0, 0.0);
gsl_vector_set(s->x, 1, 0.0);
gsl_vector_set(s->x, 2, 0.0);
gsl_vector_set(s->x, 3, 0.0);
gsl_vector_set(s->x, 4, 0.0);
gsl_vector_set(s->x, 5, 0.0);
}
std::string reportOfDiffractionEventCalibrateDetectors =
gsl_strerror(status);
if (s->fval == -0.000)
reportOfDiffractionEventCalibrateDetectors = "No events";
g_log.information() << "Detector = " << det << "\n"
<< "Method used = "
<< "Simplex"
<< "\n"
<< "Iteration = " << iter << "\n"
<< "Status = "
<< reportOfDiffractionEventCalibrateDetectors << "\n"
<< "Minimize PeakLoc-" << peakOpt << " = " << s->fval
<< "\n";
// Move in cm for small shifts
g_log.information() << "Move (X) = " << gsl_vector_get(s->x, 0) * 0.01
<< " \n";
g_log.information() << "Move (Y) = " << gsl_vector_get(s->x, 1) * 0.01
<< " \n";
g_log.information() << "Move (Z) = " << gsl_vector_get(s->x, 2) * 0.01
<< " \n";
g_log.information() << "Rotate (X) = " << gsl_vector_get(s->x, 3) << " \n";
g_log.information() << "Rotate (Y) = " << gsl_vector_get(s->x, 4) << " \n";
g_log.information() << "Rotate (Z) = " << gsl_vector_get(s->x, 5) << " \n";
Kernel::V3D CalCenter =
V3D(gsl_vector_get(s->x, 0) * 0.01, gsl_vector_get(s->x, 1) * 0.01,
gsl_vector_get(s->x, 2) * 0.01);
Kernel::V3D Center = detList[det]->getPos() + CalCenter;
int pixmax = detList[det]->xpixels() - 1;
int pixmid = (detList[det]->ypixels() - 1) / 2;
BoundingBox box;
detList[det]->getAtXY(pixmax, pixmid)->getBoundingBox(box);
double baseX = box.xMax();
double baseY = box.yMax();
double baseZ = box.zMax();
Kernel::V3D Base = V3D(baseX, baseY, baseZ) + CalCenter;
pixmid = (detList[det]->xpixels() - 1) / 2;
pixmax = detList[det]->ypixels() - 1;
detList[det]->getAtXY(pixmid, pixmax)->getBoundingBox(box);
double upX = box.xMax();
double upY = box.yMax();
double upZ = box.zMax();
Kernel::V3D Up = V3D(upX, upY, upZ) + CalCenter;
Base -= Center;
Up -= Center;
// Rotate around x
baseX = Base[0];
baseY = Base[1];
baseZ = Base[2];
double deg2rad = M_PI / 180.0;
double angle = gsl_vector_get(s->x, 3) * deg2rad;
Base = V3D(baseX, baseY * cos(angle) - baseZ * sin(angle),
baseY * sin(angle) + baseZ * cos(angle));
upX = Up[0];
upY = Up[1];
upZ = Up[2];
Up = V3D(upX, upY * cos(angle) - upZ * sin(angle),
upY * sin(angle) + upZ * cos(angle));
// Rotate around y
baseX = Base[0];
baseY = Base[1];
baseZ = Base[2];
angle = gsl_vector_get(s->x, 4) * deg2rad;
Base = V3D(baseZ * sin(angle) + baseX * cos(angle), baseY,
baseZ * cos(angle) - baseX * sin(angle));
upX = Up[0];
upY = Up[1];
upZ = Up[2];
Up = V3D(upZ * cos(angle) - upX * sin(angle), upY,
upZ * sin(angle) + upX * cos(angle));
// Rotate around z
baseX = Base[0];
baseY = Base[1];
baseZ = Base[2];
angle = gsl_vector_get(s->x, 5) * deg2rad;
Base = V3D(baseX * cos(angle) - baseY * sin(angle),
baseX * sin(angle) + baseY * cos(angle), baseZ);
upX = Up[0];
upY = Up[1];
upZ = Up[2];
Up = V3D(upX * cos(angle) - upY * sin(angle),
upX * sin(angle) + upY * cos(angle), upZ);
Base.normalize();
Up.normalize();
Center *= 100.0;
// << det+1 << " "
outfile << "5 " << detList[det]->getName().substr(4) << " "
<< detList[det]->xpixels() << " " << detList[det]->ypixels()
<< " " << 100.0 * detList[det]->xsize() << " "
<< 100.0 * detList[det]->ysize() << " "
<< "0.2000"
<< " " << Center.norm() << " ";
Center.write(outfile);
outfile << " ";
Base.write(outfile);
outfile << " ";
Up.write(outfile);
outfile << "\n";
// clean up dynamically allocated gsl stuff
gsl_vector_free(x);
gsl_vector_free(ss);
gsl_multimin_fminimizer_free(s);
// Remove the now-unneeded grouping workspace
AnalysisDataService::Instance().remove(groupWSName);
prog.report(detList[det]->getName());
}
// Closing
outfile.close();
}
/** Execute the algorithm.
*/
void SaveIsawPeaks::exec()
{
// Section header
std::string header = "2 SEQN H K L COL ROW CHAN L2 2_THETA AZ WL D IPK INTI SIGI RFLG";
std::string filename = getPropertyValue("Filename");
PeaksWorkspace_sptr ws = getProperty("InputWorkspace");
std::vector<Peak> peaks = ws->getPeaks();
// We must sort the peaks first by run, then bank #, and save the list of workspace indices of it
typedef std::map<int, std::vector<size_t> > bankMap_t;
typedef std::map<int, bankMap_t> runMap_t;
std::set<int> uniqueBanks;
runMap_t runMap;
for (size_t i=0; i < peaks.size(); ++i)
{
Peak & p = peaks[i];
int run = p.getRunNumber();
int bank = 0;
std::string bankName = p.getBankName();
if (bankName.size() <= 4)
{
g_log.information() << "Could not interpret bank number of peak " << i << "(" << bankName << ")\n";
continue;
}
// Take out the "bank" part of the bank name and convert to an int
bankName = bankName.substr(4, bankName.size()-4);
Strings::convert(bankName, bank);
// Save in the map
runMap[run][bank].push_back(i);
// Track unique bank numbers
uniqueBanks.insert(bank);
}
Instrument_const_sptr inst = ws->getInstrument();
if (!inst) throw std::runtime_error("No instrument in PeaksWorkspace. Cannot save peaks file.");
double l1; V3D beamline; double beamline_norm; V3D samplePos;
inst->getInstrumentParameters(l1, beamline, beamline_norm, samplePos);
std::ofstream out;
bool append = getProperty("AppendFile");
if (append)
{
out.open( filename.c_str(), std::ios::app);
}
else
{
out.open( filename.c_str());
out << "Version: 2.0 Facility: SNS " ;
out << " Instrument: " << inst->getName() << " Date: " ;
//TODO: The experiment date might be more useful than the instrument date.
// For now, this allows the proper instrument to be loaded back after saving.
Kernel::DateAndTime expDate = inst->getValidFromDate() + 1.0;
out << expDate.to_ISO8601_string() << std::endl;
out << "6 L1 T0_SHIFT" << std::endl;
out << "7 "<< std::setw( 10 ) ;
out << std::setprecision( 4 ) << std::fixed << ( l1*100 ) ;
out << std::setw( 12 ) << std::setprecision( 3 ) << std::fixed ;
// Time offset of 0.00 for now
out << "0.000" << std::endl;
// ============================== Save .detcal info =========================================
if (true)
{
out << "4 DETNUM NROWS NCOLS WIDTH HEIGHT DEPTH DETD CenterX CenterY CenterZ BaseX BaseY BaseZ UpX UpY UpZ"
<< std::endl;
// Here would save each detector...
std::set<int>::iterator it;
for (it = uniqueBanks.begin(); it != uniqueBanks.end(); it++)
{
// Build up the bank name
int bank = *it;
std::ostringstream mess;
mess << "bank" << bank;
std::string bankName = mess.str();
// Retrieve it
RectangularDetector_const_sptr det = boost::dynamic_pointer_cast<const RectangularDetector>(inst->getComponentByName(bankName));
if (det)
{
// Center of the detector
V3D center = det->getPos();
// Distance to center of detector
double detd = (center - inst->getSample()->getPos()).norm();
// Base unit vector (along the horizontal, X axis)
V3D base = det->getAtXY(det->xpixels()-1,0)->getPos() - det->getAtXY(0,0)->getPos();
base.normalize();
// Up unit vector (along the vertical, Y axis)
V3D up = det->getAtXY(0,det->ypixels()-1)->getPos() - det->getAtXY(0,0)->getPos();
up.normalize();
// Write the line
out << "5 "
<< std::setw(6) << std::right << bank << " "
<< std::setw(6) << std::right << det->xpixels() << " "
<< std::setw(6) << std::right << det->ypixels() << " "
<< std::setw(7) << std::right << std::fixed << std::setprecision(4) << 100.0*det->xsize() << " "
<< std::setw(7) << std::right << std::fixed << std::setprecision(4) << 100.0*det->ysize() << " "
<< " 0.2000 "
<< std::setw(6) << std::right << std::fixed << std::setprecision(2) << 100.0*detd << " "
<< std::setw(9) << std::right << std::fixed << std::setprecision(4) << 100.0*center.X() << " "
<< std::setw(9) << std::right << std::fixed << std::setprecision(4) << 100.0*center.Y() << " "
<< std::setw(9) << std::right << std::fixed << std::setprecision(4) << 100.0*center.Z() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << base.X() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << base.Y() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << base.Z() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << up.X() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << up.Y() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << up.Z() << " "
<< std::endl;
}
}
}
}
// ============================== Save all Peaks =========================================
// Sequence number
int seqNum = 1;
// Go in order of run numbers
runMap_t::iterator runMap_it;
for (runMap_it = runMap.begin(); runMap_it != runMap.end(); runMap_it++)
{
// Start of a new run
int run = runMap_it->first;
bankMap_t & bankMap = runMap_it->second;
bankMap_t::iterator bankMap_it;
for (bankMap_it = bankMap.begin(); bankMap_it != bankMap.end(); bankMap_it++)
{
// Start of a new bank.
int bank = bankMap_it->first;
std::vector<size_t> & ids = bankMap_it->second;
if (ids.size() > 0)
{
// Write the bank header
out << "0 NRUN DETNUM CHI PHI OMEGA MONCNT" << std::endl;
out << "1" << std::setw( 5 ) << run << std::setw( 7 ) <<
std::right << bank;
// Determine goniometer angles by calculating from the goniometer matrix of a peak in the list
Goniometer gon(peaks[ids[0]].getGoniometerMatrix());
std::vector<double> angles = gon.getEulerAngles("yzy");
double phi = angles[2];
double chi = angles[1];
double omega = angles[0];
out << std::setw( 7 ) << std::fixed << std::setprecision( 2 ) << chi << " ";
out << std::setw( 7 ) << std::fixed << std::setprecision( 2 ) << phi << " ";
out << std::setw( 7 ) << std::fixed << std::setprecision( 2 ) << omega << " ";
out << std::setw( 7 ) << (int)( 0 ) << std::endl;
out << header << std::endl;
// Go through each peak at this run / bank
for (size_t i=0; i < ids.size(); i++)
{
size_t wi = ids[i];
Peak & p = peaks[wi];
// Sequence (run) number
out << "3" << std::setw( 7 ) << seqNum;
// HKL is flipped by -1 due to different q convention in ISAW vs mantid.
out << std::setw( 5 ) << Utils::round(-p.getH())
<< std::setw( 5 ) << Utils::round(-p.getK())
<< std::setw( 5 ) << Utils::round(-p.getL());
// Row/column
out << std::setw( 8 ) << std::fixed << std::setprecision( 2 )
<< static_cast<double>(p.getCol()) << " ";
out << std::setw( 8 ) << std::fixed << std::setprecision( 2 )
<< static_cast<double>(p.getRow()) << " ";
out << std::setw( 8 ) << std::fixed << std::setprecision( 0 )
<< p.getTOF() << " ";
out << std::setw( 9 ) << std::fixed << std::setprecision( 3 )
<< (p.getL2()*100.0) << " ";
// This is the scattered beam direction
V3D dir = p.getDetPos() - inst->getSample()->getPos();
double scattering, azimuth;
// Two-theta = polar angle = scattering angle = between +Z vector and the scattered beam
scattering = dir.angle( V3D(0.0, 0.0, 1.0) );
// "Azimuthal" angle: project the beam onto the XY plane, and measure the angle between that and the +X axis (right-handed)
azimuth = atan2( dir.Y(), dir.X() );
out << std::setw( 9 ) << std::fixed << std::setprecision( 5 )
<< scattering << " "; //two-theta scattering
out << std::setw( 9 ) << std::fixed << std::setprecision( 5 )
<< azimuth << " ";
out << std::setw( 10 ) << std::fixed << std::setprecision( 6 )
<< p.getWavelength() << " ";
out << std::setw( 9 ) << std::fixed << std::setprecision( 4 )
<< p.getDSpacing() << " ";
out << std::setw( 8 ) << std::fixed << int(p.getBinCount()) << std::setw( 10 ) << " "
<< std::fixed << std::setprecision( 2 ) << p.getIntensity() << " ";
out << std::setw( 7 ) << std::fixed << std::setprecision( 2 )
<< p.getSigmaIntensity() << " ";
int thisReflag = 310;
out << std::setw( 5 ) << thisReflag;
out << std::endl;
// Count the sequence
seqNum++;
}
}
}
}
out.flush();
out.close();
// //REMOVE:
// std::string line;
// std::ifstream myfile (filename.c_str());
// if (myfile.is_open())
// {
// while ( myfile.good() )
// {
// getline (myfile,line);
// std::cout << line << std::endl;
// }
// myfile.close();
// }
}
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();
}
}