int MaskPeaksWorkspace::findPixelID(std::string bankName, int col, int row) {
Geometry::Instrument_const_sptr Iptr = m_inputW->getInstrument();
boost::shared_ptr<const IComponent> parent =
Iptr->getComponentByName(bankName);
if (parent->type().compare("RectangularDetector") == 0) {
boost::shared_ptr<const RectangularDetector> RDet =
boost::dynamic_pointer_cast<const RectangularDetector>(parent);
boost::shared_ptr<Detector> pixel = RDet->getAtXY(col, row);
return pixel->getID();
} else {
std::string bankName0 = bankName;
// Only works for WISH
bankName0.erase(0, 4);
std::ostringstream pixelString;
pixelString << Iptr->getName() << "/" << bankName0 << "/" << bankName
<< "/tube" << std::setw(3) << std::setfill('0') << col
<< "/pixel" << std::setw(4) << std::setfill('0') << row;
boost::shared_ptr<const Geometry::IComponent> component =
Iptr->getComponentByName(pixelString.str());
boost::shared_ptr<const Detector> pixel =
boost::dynamic_pointer_cast<const Detector>(component);
return pixel->getID();
}
}
Peak PeakHKLErrors::createNewPeak(const Geometry::IPeak &peak_old,
Geometry::Instrument_sptr instrNew, double T0,
double L0) {
Geometry::Instrument_const_sptr inst = peak_old.getInstrument();
if (inst->getComponentID() != instrNew->getComponentID()) {
g_log.error("All peaks must have the same instrument");
throw std::invalid_argument("All peaks must have the same instrument");
}
double T = peak_old.getTOF() + T0;
int ID = peak_old.getDetectorID();
Kernel::V3D hkl = peak_old.getHKL();
// peak_old.setDetectorID(ID); //set det positions
Peak peak(instrNew, ID, peak_old.getWavelength(), hkl,
peak_old.getGoniometerMatrix());
Wavelength wl;
wl.initialize(L0, peak.getL2(), peak.getScattering(), 0,
peak_old.getInitialEnergy(), 0.0);
peak.setWavelength(wl.singleFromTOF(T));
peak.setIntensity(peak_old.getIntensity());
peak.setSigmaIntensity(peak_old.getSigmaIntensity());
peak.setRunNumber(peak_old.getRunNumber());
peak.setBinCount(peak_old.getBinCount());
//!!!peak.setDetectorID(ID);
return peak;
}
/**
* Apply any instrument adjustments from the file
* @param filename :: The file to take the positions
*/
void CreateSimulationWorkspace::adjustInstrument(const std::string &filename) {
// If requested update the instrument to positions in the raw file
const Geometry::ParameterMap &pmap = m_outputWS->instrumentParameters();
Geometry::Instrument_const_sptr instrument = m_outputWS->getInstrument();
boost::shared_ptr<Geometry::Parameter> updateDets =
pmap.get(instrument->getComponentID(), "det-pos-source");
if (!updateDets)
return; // No tag, use IDF
std::string value = updateDets->value<std::string>();
if (value.substr(0, 8) == "datafile") {
IAlgorithm_sptr updateInst =
createChildAlgorithm("UpdateInstrumentFromFile", 0.75, 1.0);
updateInst->setProperty<MatrixWorkspace_sptr>("Workspace", m_outputWS);
updateInst->setPropertyValue("Filename", filename);
if (value == "datafile-ignore-phi") {
updateInst->setProperty("IgnorePhi", true);
g_log.information("Detector positions in IDF updated with positions in "
"the data file except for the phi values");
} else {
g_log.information(
"Detector positions in IDF updated with positions in the data file");
}
// We want this to throw if it fails to warn the user that the information
// is not correct.
updateInst->execute();
}
}
/**
* Get position in space of a componentName
*/
V3D LoadILLSANS::getComponentPosition(const std::string &componentName) {
Geometry::Instrument_const_sptr instrument =
m_localWorkspace->getInstrument();
Geometry::IComponent_const_sptr component =
instrument->getComponentByName(componentName);
return component->getPos();
}
void LoadILLIndirect::moveComponent(const std::string &componentName,
double twoTheta, double offSet) {
try {
Geometry::Instrument_const_sptr instrument =
m_localWorkspace->getInstrument();
Geometry::IComponent_const_sptr component =
instrument->getComponentByName(componentName);
double r, theta, phi, newTheta, newR;
V3D oldPos = component->getPos();
oldPos.getSpherical(r, theta, phi);
newTheta = twoTheta;
newR = offSet;
V3D newPos;
newPos.spherical(newR, newTheta, phi);
// g_log.debug() << tube->getName() << " : t = " << theta << " ==> t = " <<
// newTheta << "\n";
Geometry::ParameterMap &pmap = m_localWorkspace->instrumentParameters();
Geometry::ComponentHelper::moveComponent(
*component, pmap, newPos, Geometry::ComponentHelper::Absolute);
} catch (Mantid::Kernel::Exception::NotFoundError &) {
throw std::runtime_error("Error when trying to move the " + componentName +
" : NotFoundError");
} catch (std::runtime_error &) {
throw std::runtime_error("Error when trying to move the " + componentName +
" : runtime_error");
}
}
/** Convert bank to detectors
* This routine has never been used. Dead code.
* @param singlebanks -- vector of string containing bank names
* @param detectors -- vector of detector-id-s belonging to these banks
*/
void LoadMask::bankToDetectors(const std::vector<std::string> &singlebanks,
std::vector<detid_t> &detectors) {
std::stringstream infoss;
infoss << "Bank IDs to be converted to detectors: \n";
for (auto &singlebank : singlebanks) {
infoss << "Bank: " << singlebank << '\n';
}
g_log.debug(infoss.str());
Geometry::Instrument_const_sptr minstrument = m_maskWS->getInstrument();
for (auto &singlebank : singlebanks) {
std::vector<Geometry::IDetector_const_sptr> idetectors;
minstrument->getDetectorsInBank(idetectors, singlebank);
g_log.debug() << "Bank: " << singlebank << " has " << idetectors.size()
<< " detectors\n";
// a) get information
size_t numdets = idetectors.size();
detid_t detid_first = idetectors.front()->getID();
detid_t detid_last = idetectors.back()->getID();
// b) set detectors
for (const auto &det : idetectors) {
detid_t detid = det->getID();
detectors.push_back(detid);
}
g_log.debug() << "Number of Detectors in Bank " << singlebank
<< " is: " << numdets << "\nRange From: " << detid_first
<< " To: " << detid_last << '\n';
} // ENDFOR
}
bool CentroidPeaks::edgePixel(std::string bankName, int col, int row,
int Edge) {
if (bankName.compare("None") == 0)
return false;
Geometry::Instrument_const_sptr Iptr = inWS->getInstrument();
boost::shared_ptr<const IComponent> parent =
Iptr->getComponentByName(bankName);
if (parent->type().compare("RectangularDetector") == 0) {
boost::shared_ptr<const RectangularDetector> RDet =
boost::dynamic_pointer_cast<const RectangularDetector>(parent);
return col < Edge || col >= (RDet->xpixels() - Edge) || row < Edge ||
row >= (RDet->ypixels() - Edge);
} 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);
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);
int NROWS = static_cast<int>(grandchildren.size());
int NCOLS = static_cast<int>(children.size());
// Wish pixels and tubes start at 1 not 0
return col - 1 < Edge || col - 1 >= (NCOLS - Edge) || row - 1 < Edge ||
row - 1 >= (NROWS - Edge);
}
return false;
}
double LoadHelper::getL1(const API::MatrixWorkspace_sptr& workspace)
{
Geometry::Instrument_const_sptr instrument = workspace->getInstrument();
Geometry::IComponent_const_sptr sample = instrument->getSample();
double l1 = instrument->getSource()->getDistance(*sample);
return l1;
}
/** Retrieves the detector postion for a given spectrum
* @param index :: The workspace index of the spectrum
* @param l1 :: Returns the source-sample distance
* @param l2 :: Returns the sample-detector distance
* @param twoTheta :: Returns the detector's scattering angle
*/
void RemoveBins::calculateDetectorPosition(const int& index, double& l1, double& l2, double& twoTheta)
{
// Get a pointer to the instrument contained in the workspace
Geometry::Instrument_const_sptr instrument = m_inputWorkspace->getInstrument();
// Get the distance between the source and the sample (assume in metres)
Geometry::IObjComponent_const_sptr sample = instrument->getSample();
// Check for valid instrument
if (sample == NULL)
{
throw Exception::InstrumentDefinitionError("Instrument not sufficiently defined: failed to get sample");
}
l1 = instrument->getSource()->getDistance(*sample);
Geometry::IDetector_const_sptr det = m_inputWorkspace->getDetector(index);
// Get the sample-detector distance for this detector (in metres)
if ( ! det->isMonitor() )
{
l2 = det->getDistance(*sample);
// The scattering angle for this detector (in radians).
twoTheta = m_inputWorkspace->detectorTwoTheta(det);
}
else // If this is a monitor then make l1+l2 = source-detector distance and twoTheta=0
{
l2 = det->getDistance(*(instrument->getSource()));
l2 = l2 - l1;
twoTheta = 0.0;
}
g_log.debug() << "Detector for index " << index << " has L1+L2=" << l1+l2 << " & 2theta= " << twoTheta << std::endl;
return;
}
/** This function will check how to group spectra when calculating median
*
*
*/
std::vector<std::vector<size_t> > DetectorDiagnostic::makeMap(API::MatrixWorkspace_sptr countsWS)
{
std::multimap<Mantid::Geometry::ComponentID,size_t> mymap;
Geometry::Instrument_const_sptr instrument = countsWS->getInstrument();
if (m_parents==0)
{
return makeInstrumentMap(countsWS);
}
if (!instrument)
{
g_log.warning("Workspace has no instrument. LevelsUP is ignored");
return makeInstrumentMap(countsWS);
}
//check if not grouped. If grouped, it will throw
if ( countsWS->hasGroupedDetectors() )
{
throw std::runtime_error("Median detector test: not able to create detector to spectra map. Try with LevelUp=0.");
}
for(size_t i=0;i < countsWS->getNumberHistograms();i++)
{
detid_t d=(*((countsWS->getSpectrum(i))->getDetectorIDs().begin()));
std::vector<boost::shared_ptr<const Mantid::Geometry::IComponent> > anc=instrument->getDetector(d)->getAncestors();
//std::vector<boost::shared_ptr<const IComponent> > anc=(*(countsWS->getSpectrum(i)->getDetectorIDs().begin()))->getAncestors();
if (anc.size()<static_cast<size_t>(m_parents))
{
g_log.warning("Too many levels up. Will ignore LevelsUp");
m_parents=0;
return makeInstrumentMap(countsWS);
}
mymap.insert(std::pair<Mantid::Geometry::ComponentID,size_t>(anc[m_parents-1]->getComponentID(),i));
}
std::vector<std::vector<size_t> > speclist;
std::vector<size_t> speclistsingle;
std::multimap<Mantid::Geometry::ComponentID,size_t>::iterator m_it, s_it;
for (m_it = mymap.begin(); m_it != mymap.end(); m_it = s_it)
{
Mantid::Geometry::ComponentID theKey = (*m_it).first;
std::pair<std::multimap<Mantid::Geometry::ComponentID,size_t>::iterator,std::multimap<Mantid::Geometry::ComponentID,size_t>::iterator> keyRange = mymap.equal_range(theKey);
// Iterate over all map elements with key == theKey
speclistsingle.clear();
for (s_it = keyRange.first; s_it != keyRange.second; ++s_it)
{
speclistsingle.push_back( (*s_it).second );
}
speclist.push_back(speclistsingle);
}
return speclist;
}
// read the monitors list from the workspace and try to do it once for any
// particular ws;
bool MonIDPropChanger::monitorIdReader(
API::MatrixWorkspace_const_sptr inputWS) const {
// no workspace
if (!inputWS)
return false;
// no instrument
Geometry::Instrument_const_sptr pInstr = inputWS->getInstrument();
if (!pInstr)
return false;
std::vector<detid_t> mon = pInstr->getMonitors();
if (mon.empty()) {
if (iExistingAllowedValues.empty()) {
return false;
} else {
iExistingAllowedValues.clear();
return true;
}
}
// are these monitors really there?
// got the index of correspondent spectra.
std::vector<size_t> indexList = inputWS->getIndicesFromDetectorIDs(mon);
if (indexList.empty()) {
if (iExistingAllowedValues.empty()) {
return false;
} else {
iExistingAllowedValues.clear();
return true;
}
}
// index list can be less or equal to the mon list size (some monitors do not
// have spectra)
size_t mon_count =
(mon.size() < indexList.size()) ? mon.size() : indexList.size();
std::vector<int> allowed_values(mon_count);
for (size_t i = 0; i < mon_count; i++) {
allowed_values[i] = mon[i];
}
// are known values the same as the values we have just identified?
if (iExistingAllowedValues.size() != mon_count) {
iExistingAllowedValues.clear();
iExistingAllowedValues.assign(allowed_values.begin(), allowed_values.end());
return true;
}
// the monitor list has the same size as before. Is it equivalent to the
// existing one?
bool values_redefined = false;
for (size_t i = 0; i < mon_count; i++) {
if (iExistingAllowedValues[i] != allowed_values[i]) {
values_redefined = true;
iExistingAllowedValues[i] = allowed_values[i];
}
}
return values_redefined;
}
double LoadHelper::getL2(const API::MatrixWorkspace_sptr& workspace, int detId)
{
// Get a pointer to the instrument contained in the workspace
Geometry::Instrument_const_sptr instrument = workspace->getInstrument();
// Get the distance between the source and the sample (assume in metres)
Geometry::IComponent_const_sptr sample = instrument->getSample();
// Get the sample-detector distance for this detector (in metres)
double l2 = workspace->getDetector(detId)->getPos().distance(sample->getPos());
return l2;
}
// read the monitors list from the workspace and try to do it once for any
// particular ws;
bool MonIDPropChanger::monitorIdReader(
MatrixWorkspace_const_sptr inputWS) const {
// no workspace
if (!inputWS)
return false;
// no instrument
Geometry::Instrument_const_sptr pInstr = inputWS->getInstrument();
if (!pInstr)
return false;
// are these monitors really there?
std::vector<detid_t> monitorIDList = pInstr->getMonitors();
{
const auto &specInfo = inputWS->spectrumInfo();
std::set<detid_t> idsInWorkspace;
size_t i = 0;
// Loop over spectra, but finish early if we find everything
while (i < specInfo.size() &&
idsInWorkspace.size() < monitorIDList.size()) {
if (specInfo.isMonitor(i))
idsInWorkspace.insert(specInfo.detector(i).getID());
++i;
}
monitorIDList =
std::vector<detid_t>(idsInWorkspace.begin(), idsInWorkspace.end());
}
if (monitorIDList.empty()) {
if (iExistingAllowedValues.empty()) {
return false;
} else {
iExistingAllowedValues.clear();
return true;
}
}
// are known values the same as the values we have just identified?
if (iExistingAllowedValues.size() != monitorIDList.size()) {
iExistingAllowedValues.clear();
iExistingAllowedValues.assign(monitorIDList.begin(), monitorIDList.end());
return true;
}
// the monitor list has the same size as before. Is it equivalent to the
// existing one?
bool values_redefined = false;
for (size_t i = 0; i < monitorIDList.size(); i++) {
if (iExistingAllowedValues[i] != monitorIDList[i]) {
values_redefined = true;
iExistingAllowedValues[i] = monitorIDList[i];
}
}
return values_redefined;
}
/**
* Setup a detector cache for randomly picking IDs from the first
* instrument in the ExperimentInfo list.
* @param ws :: The input workspace
*/
void FakeMDEventData::setupDetectorCache(const API::IMDEventWorkspace &ws) {
try {
Geometry::Instrument_const_sptr inst =
ws.getExperimentInfo(0)->getInstrument();
m_detIDs = inst->getDetectorIDs(true); // true=skip monitors
size_t max = m_detIDs.size() - 1;
m_uniformDist = boost::uniform_int<size_t>(0, max); // Includes max
} catch (std::invalid_argument &) {
g_log.information("Cannot retrieve instrument from input workspace, "
"detector information will be garbage.");
}
}
V3D LoadHelper::getComponentPosition(API::MatrixWorkspace_sptr ws, const std::string &componentName)
{
try
{
Geometry::Instrument_const_sptr instrument = ws->getInstrument();
Geometry::IComponent_const_sptr component = instrument->getComponentByName(componentName);
V3D pos = component->getPos();
return pos;
} catch (Mantid::Kernel::Exception::NotFoundError&)
{
throw std::runtime_error("Error when trying to move the " + componentName + " : NotFoundError");
}
}
/** Extract a component's detectors and return it within detectors array
* It is a generalized version of bankToDetectors()
*
* @param componentnames -- vector of component names to process
* @param detectors -- vector of detector ids, which belongs to components
*provided as input.
*/
void LoadMask::componentToDetectors(
const std::vector<std::string> &componentnames,
std::vector<detid_t> &detectors) {
Geometry::Instrument_const_sptr minstrument = m_maskWS->getInstrument();
for (auto &componentname : componentnames) {
g_log.debug() << "Component name = " << componentname << '\n';
// a) get component
Geometry::IComponent_const_sptr component =
minstrument->getComponentByName(componentname);
if (component)
g_log.debug() << "Component ID = " << component->getComponentID() << '\n';
else {
// A non-exiting component. Ignore
g_log.warning() << "Component " << componentname << " does not exist!\n";
continue;
}
// b) component -> component assembly --> children (more than detectors)
boost::shared_ptr<const Geometry::ICompAssembly> asmb =
boost::dynamic_pointer_cast<const Geometry::ICompAssembly>(component);
std::vector<Geometry::IComponent_const_sptr> children;
asmb->getChildren(children, true);
g_log.debug() << "Number of Children = " << children.size() << '\n';
size_t numdets(0);
detid_t id_min(std::numeric_limits<Mantid::detid_t>::max());
detid_t id_max(0);
for (const auto &child : children) {
// c) convert component to detector
Geometry::IDetector_const_sptr det =
boost::dynamic_pointer_cast<const Geometry::IDetector>(child);
if (det) {
detid_t detid = det->getID();
detectors.push_back(detid);
numdets++;
if (detid < id_min)
id_min = detid;
if (detid > id_max)
id_max = detid;
}
}
g_log.debug() << "Number of Detectors in Children = " << numdets
<< " Range = " << id_min << ", " << id_max << '\n';
} // for component
}
/**
* Mask the outlier values to get a better median value.
* @param medianvec The median value calculated from the current counts.
* @param countsWS The counts workspace. Any outliers will be masked here.
* @param indexmap Index map.
* @returns The number failed.
*/
int MedianDetectorTest::maskOutliers(const std::vector<double> medianvec, API::MatrixWorkspace_sptr countsWS,std::vector<std::vector<size_t> > indexmap)
{
// Fractions of the median
const double out_lo = getProperty("LowOutlier");
const double out_hi = getProperty("HighOutlier");
int numFailed(0);
bool checkForMask = false;
Geometry::Instrument_const_sptr instrument = countsWS->getInstrument();
if (instrument != NULL)
{
checkForMask = ((instrument->getSource() != NULL) && (instrument->getSample() != NULL));
}
for (size_t i=0; i<indexmap.size(); ++i)
{
std::vector<size_t> hists=indexmap.at(i);
double median=medianvec.at(i);
PARALLEL_FOR1(countsWS)
for(int j = 0; j < static_cast<int>(hists.size()); ++j)
{
const double value = countsWS->readY(hists.at(j))[0];
if ((value == 0.) && checkForMask)
{
const std::set<detid_t>& detids = countsWS->getSpectrum(hists.at(j))->getDetectorIDs();
if (instrument->isDetectorMasked(detids))
{
numFailed -= 1; // it was already masked
}
}
if( (value < out_lo*median) && (value > 0.0) )
{
countsWS->maskWorkspaceIndex(hists.at(j));
PARALLEL_ATOMIC
++numFailed;
}
else if( value > out_hi*median )
{
countsWS->maskWorkspaceIndex(hists.at(j));
PARALLEL_ATOMIC
++numFailed;
}
}
PARALLEL_CHECK_INTERUPT_REGION
}
return numFailed;
}
/**
* Creates a new parameterized instrument for which the parameter values can be changed
*
* @param Peaks - a PeaksWorkspace used to get the original instrument. The instrument from the 0th peak is
* the one that is used.
*
* NOTE: All the peaks in the PeaksWorkspace must use the same instrument.
*/
boost::shared_ptr<Geometry::Instrument> PeakHKLErrors::getNewInstrument( PeaksWorkspace_sptr Peaks )const
{
Geometry::Instrument_const_sptr instSave = Peaks->getPeak( 0 ).getInstrument();
boost::shared_ptr<Geometry::ParameterMap> pmap( new Geometry::ParameterMap() );
boost::shared_ptr<const Geometry::ParameterMap> pmapSv = instSave->getParameterMap();
if ( !instSave )
{
g_log.error( " Peaks workspace does not have an instrument" );
throw std::invalid_argument( " Not all peaks have an instrument" );
}
boost::shared_ptr<Geometry::Instrument> instChange( new Geometry::Instrument() );
if ( !instSave->isParametrized() )
{
boost::shared_ptr<Geometry::Instrument> instClone( instSave->clone() );
boost::shared_ptr<Geometry::Instrument> Pinsta( new Geometry::Instrument( instSave, pmap ) );
instChange = Pinsta;
}
else //catch(... )
{
boost::shared_ptr<Geometry::Instrument> P1( new Geometry::Instrument( instSave->baseInstrument(),
pmap ) );
instChange = P1;
}
if ( !instChange )
{
g_log.error( "Cannot 'clone' instrument" );
throw std::logic_error( "Cannot clone instrument" );
}
//------------------"clone" orig instruments pmap -------------------
cLone( pmap, instSave, pmapSv );
IComponent_const_sptr sample = instChange->getSample();
V3D sampPos = sample->getRelativePos();
V3D sampOffsets( getParameter( "SampleXOffset" ), getParameter( "SampleYOffset" ), getParameter( "SampleZOffset" ) );
pmap->addPositionCoordinate( sample.get(), std::string("x"), sampPos.X() + sampOffsets.X() );
pmap->addPositionCoordinate( sample.get(), std::string("y"), sampPos.Y() + sampOffsets.Y() );
pmap->addPositionCoordinate( sample.get(), std::string("z"), sampPos.Z() + sampOffsets.Z() );
return instChange;
}
/** Check whether workspace has a non-trivial instrument
* (1) There is an instrument associated with
* (2) Number of detectors is larger than 0
*/
bool MaskWorkspace::hasInstrument()
{
bool hasinst;
Geometry::Instrument_const_sptr inst = this->getInstrument();
if (inst)
{
if (inst->getNumberDetectors() > 0)
hasinst = true;
else
hasinst = false;
}
else hasinst = false;
return hasinst;
}
/** Convert bank to detectors
*/
void LoadMask::bankToDetectors(std::vector<std::string> singlebanks,
std::vector<int32_t> &detectors,
std::vector<int32_t> &detectorpairslow,
std::vector<int32_t> &detectorpairsup) {
std::stringstream infoss;
infoss << "Bank IDs to be converted to detectors: " << endl;
for (auto &singlebank : singlebanks) {
infoss << "Bank: " << singlebank << std::endl;
}
g_log.debug(infoss.str());
Geometry::Instrument_const_sptr minstrument = m_maskWS->getInstrument();
for (auto &singlebank : singlebanks) {
std::vector<Geometry::IDetector_const_sptr> idetectors;
minstrument->getDetectorsInBank(idetectors, singlebank);
g_log.debug() << "Bank: " << singlebank << " has " << idetectors.size()
<< " detectors" << std::endl;
// a) get information
size_t numdets = idetectors.size();
detid_t detid_first = idetectors[0]->getID();
detid_t detid_last = idetectors[idetectors.size() - 1]->getID();
// b) set detectors
if (detid_first + int32_t(numdets) == detid_last + 1 && false) {
// TODO This save-time method is not used at this stage
g_log.information() << "Using Range of Detectors" << std::endl;
detectorpairslow.push_back(detid_first);
detectorpairsup.push_back(detid_last);
} else {
g_log.debug() << "Apply 1 by 1 "
<< "DetID: " << detid_first << ", " << detid_last
<< std::endl;
for (const auto &det : idetectors) {
int32_t detid = det->getID();
detectors.push_back(detid);
}
} // if-else
} // ENDFOR
return;
}
/** Gets the primary flightpath (L1)
* @return L1
* @throw Kernel::Exception::InstrumentDefinitionError if L1 is not available
*/
double UnwrapMonitor::getPrimaryFlightpath() const {
// Get a pointer to the instrument contained in the input workspace
Geometry::Instrument_const_sptr instrument = m_inputWS->getInstrument();
// Get the distance between the source and the sample
Geometry::IComponent_const_sptr sample = instrument->getSample();
double L1;
try {
L1 = instrument->getSource()->getDistance(*sample);
g_log.debug() << "Source-sample distance (in metres): " << L1 << std::endl;
} catch (Exception::NotFoundError &) {
g_log.error("Unable to calculate source-sample distance");
throw Exception::InstrumentDefinitionError(
"Unable to calculate source-sample distance", m_inputWS->getTitle());
}
return L1;
}
/**
* Set the absolute detector position of a detector
* @param instrument :: The instrument that contains the defined detector
* @param detID :: Detector ID
* @param pos :: new position of Dectector
* @param sameParent :: true if detector has same parent as previous detector set here.
*/
void ApplyCalibration::setDetectorPosition(const Geometry::Instrument_const_sptr & instrument, int detID, V3D pos, bool /*sameParent*/ )
{
Geometry::IDetector_const_sptr det = instrument->getDetector(detID);
// Then find the corresponding relative position
boost::shared_ptr<const Geometry::IComponent> parent = det->getParent();
if (parent)
{
pos -= parent->getPos();
Quat rot = parent->getRelativeRot();
rot.inverse();
rot.rotate(pos);
}
boost::shared_ptr<const Geometry::IComponent>grandparent = parent->getParent();
if (grandparent)
{
Quat rot = grandparent->getRelativeRot();
rot.inverse();
rot.rotate(pos);
boost::shared_ptr<const Geometry::IComponent>greatgrandparent = grandparent->getParent();
if (greatgrandparent) {
Quat rot2 = greatgrandparent->getRelativeRot();
rot2.inverse();
rot2.rotate(pos);
}
}
// Add a parameter for the new position
m_pmap->addV3D(det.get(), "pos", pos);
}
/*
* Define edges for each instrument by masking. For CORELLI, tubes 1 and 16, and
*pixels 0 and 255.
* Get Q in the lab frame for every peak, call it C
* For every point on the edge, the trajectory in reciprocal space is a straight
*line, going through O=V3D(0,0,0).
* Calculate a point at a fixed momentum, say k=1. Q in the lab frame
*E=V3D(-k*sin(tt)*cos(ph),-k*sin(tt)*sin(ph),k-k*cos(ph)).
* Normalize E to 1: E=E*(1./E.norm())
*
* @param inst: instrument
*/
void IntegrateEllipsoids::calculateE1(Geometry::Instrument_const_sptr inst) {
std::vector<detid_t> detectorIDs = inst->getDetectorIDs();
for (auto &detectorID : detectorIDs) {
Mantid::Geometry::IDetector_const_sptr det = inst->getDetector(detectorID);
if (det->isMonitor())
continue; // skip monitor
if (!det->isMasked())
continue; // edge is masked so don't check if not masked
double tt1 = det->getTwoTheta(V3D(0, 0, 0), V3D(0, 0, 1)); // two theta
double ph1 = det->getPhi(); // phi
V3D E1 = V3D(-std::sin(tt1) * std::cos(ph1), -std::sin(tt1) * std::sin(ph1),
1. - std::cos(tt1)); // end of trajectory
E1 = E1 * (1. / E1.norm()); // normalize
E1Vec.push_back(E1);
}
}
/**
* Set the absolute detector position of a detector
* @param instrument :: The instrument that contains the defined detector
* @param detID :: Detector ID
* @param pos :: new position of Dectector
* @param sameParent :: true if detector has same parent as previous detector set here.
*/
void ApplyCalibration::setDetectorPosition(const Geometry::Instrument_const_sptr & instrument, int detID, V3D pos, bool /*sameParent*/ )
{
IComponent_const_sptr det =instrument->getDetector(detID); ;
// Do the move
using namespace Geometry::ComponentHelper;
TransformType positionType = Absolute;
// TransformType positionType = Relative;
Geometry::ComponentHelper::moveComponent(*det, *m_pmap, pos, positionType);
}
/**
* Set the detector positions given the r,theta and phi.
* @param detID :: A vector of detector IDs
* @param l2 :: A vector of l2 distances
* @param theta :: A vector of theta distances
* @param phi :: A vector of phi values
*/
void UpdateInstrumentFromFile::setDetectorPositions(const std::vector<int32_t> & detID, const std::vector<float> & l2,
const std::vector<float> & theta, const std::vector<float> & phi)
{
Geometry::Instrument_const_sptr inst = m_workspace->getInstrument();
const int numDetector = static_cast<int>(detID.size());
g_log.information() << "Setting new positions for " << numDetector << " detectors\n";
for (int i = 0; i < numDetector; ++i)
{
try
{
Geometry::IDetector_const_sptr det = inst->getDetector(detID[i]);
setDetectorPosition(det, l2[i], theta[i], phi[i]);
}
catch (Kernel::Exception::NotFoundError&)
{
continue;
}
progress(static_cast<double>(i)/numDetector,"Updating Detector Positions from File");
}
}
/**
@param ws Name of workspace containing peaks
@param bankName Name of bank containing peak
@param col Column number containing peak
@param row Row number containing peak
@param Edge Number of edge points for each bank
@return True if peak is on edge
*/
bool OptimizeLatticeForCellType::edgePixel(PeaksWorkspace_sptr ws,
std::string bankName, int col,
int row, int Edge) {
if (bankName.compare("None") == 0)
return false;
Geometry::Instrument_const_sptr Iptr = ws->getInstrument();
boost::shared_ptr<const IComponent> parent =
Iptr->getComponentByName(bankName);
if (parent->type().compare("RectangularDetector") == 0) {
boost::shared_ptr<const RectangularDetector> RDet =
boost::dynamic_pointer_cast<const RectangularDetector>(parent);
return col < Edge || col >= (RDet->xpixels() - Edge) || row < Edge ||
row >= (RDet->ypixels() - Edge);
} 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);
int startI = 1;
if (children[0]->getName() == "sixteenpack") {
startI = 0;
parent = children[0];
children.clear();
boost::shared_ptr<const Geometry::ICompAssembly> asmb =
boost::dynamic_pointer_cast<const Geometry::ICompAssembly>(parent);
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);
int NROWS = static_cast<int>(grandchildren.size());
int NCOLS = static_cast<int>(children.size());
// Wish pixels and tubes start at 1 not 0
return col - startI < Edge || col - startI >= (NCOLS - Edge) ||
row - startI < Edge || row - startI >= (NROWS - Edge);
}
return false;
}
/**
* Init variables caches
* @param :: Workspace pointer
*/
void SofQW2::initCachedValues(API::MatrixWorkspace_const_sptr workspace)
{
m_progress->report("Initializing caches");
// Retrieve the emode & efixed properties
const std::string emode = getProperty("EMode");
// Convert back to an integer representation
m_emode = 0;
if (emode == "Direct") m_emode=1;
else if (emode == "Indirect") m_emode = 2;
m_efixed = getProperty("EFixed");
// Conversion constant for E->k. k(A^-1) = sqrt(energyToK*E(meV))
m_EtoK = 8.0*M_PI*M_PI*PhysicalConstants::NeutronMass*PhysicalConstants::meV*1e-20 /
(PhysicalConstants::h*PhysicalConstants::h);
// Get a pointer to the instrument contained in the workspace
Geometry::Instrument_const_sptr instrument = workspace->getInstrument();
// Get the distance between the source and the sample (assume in metres)
Geometry::IObjComponent_const_sptr source = instrument->getSource();
Geometry::IObjComponent_const_sptr sample = instrument->getSample();
m_samplePos = sample->getPos();
m_beamDir = m_samplePos - source->getPos();
m_beamDir.normalize();
// Is the instrument set up correctly
double l1(0.0);
try
{
l1 = source->getDistance(*sample);
g_log.debug() << "Source-sample distance: " << l1 << std::endl;
}
catch (Exception::NotFoundError &)
{
throw Exception::InstrumentDefinitionError("Unable to calculate source-sample distance",
workspace->getTitle());
}
// Index Q cache
initQCache(workspace);
}
void LoadHelper::rotateComponent(API::MatrixWorkspace_sptr ws, const std::string &componentName,
const Kernel::Quat & rot)
{
try
{
Geometry::Instrument_const_sptr instrument = ws->getInstrument();
Geometry::IComponent_const_sptr component = instrument->getComponentByName(componentName);
//g_log.debug() << tube->getName() << " : t = " << theta << " ==> t = " << newTheta << "\n";
Geometry::ParameterMap& pmap = ws->instrumentParameters();
Geometry::ComponentHelper::rotateComponent(*component, pmap, rot,
Geometry::ComponentHelper::Absolute);
} catch (Mantid::Kernel::Exception::NotFoundError&)
{
throw std::runtime_error("Error when trying to move the " + componentName + " : NotFoundError");
} catch (std::runtime_error &)
{
throw std::runtime_error("Error when trying to move the " + componentName + " : runtime_error");
}
}
void PoldiBasicChopper::loadConfiguration(
Geometry::Instrument_const_sptr poldiInstrument) {
Geometry::ICompAssembly_const_sptr chopperGroup =
boost::dynamic_pointer_cast<const Geometry::ICompAssembly>(
poldiInstrument->getComponentByName(std::string("chopper")));
size_t numberOfSlits = chopperGroup->nelements();
std::vector<double> slitPositions(numberOfSlits);
for (size_t i = 0; i < numberOfSlits; ++i) {
slitPositions[i] =
chopperGroup->getChild(static_cast<const int>(i))->getPos().X();
}
double distance = chopperGroup->getPos().norm() * 1000.0;
double t0 = chopperGroup->getNumberParameter("t0").front();
double t0const = chopperGroup->getNumberParameter("t0_const").front();
initializeFixedParameters(slitPositions, distance, t0, t0const);
}
/** 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);
}