/**
* 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);
}
/** 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;
}
/**
* 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);
}
/*
* 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 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");
}
}
/**
* Updates from a more generic ascii file
* @param filename :: The input filename
*/
void UpdateInstrumentFromFile::updateFromAscii(const std::string & filename)
{
AsciiFileHeader header;
const bool isSpectrum = parseAsciiHeader(header);
Geometry::Instrument_const_sptr inst = m_workspace->getInstrument();
// Throws for multiple detectors
const spec2index_map specToIndex(m_workspace->getSpectrumToWorkspaceIndexMap());
std::ifstream datfile(filename.c_str(), std::ios_base::in);
const int skipNLines = getProperty("SkipFirstNLines");
std::string line;
int lineCount(0);
while(lineCount < skipNLines)
{
std::getline(datfile,line);
++lineCount;
}
std::vector<double> colValues(header.colCount - 1, 0.0);
while(std::getline(datfile,line))
{
boost::trim(line);
std::istringstream is(line);
// Column 0 should be ID/spectrum number
int32_t detOrSpec(-1000);
is >> detOrSpec;
// If first thing read is not a number then skip the line
if(is.fail())
{
g_log.debug() << "Skipping \"" << line << "\". Cannot interpret as list of numbers.\n";
continue;
}
Geometry::IDetector_const_sptr det;
try
{
if(isSpectrum)
{
auto it = specToIndex.find(detOrSpec);
if(it != specToIndex.end())
{
const size_t wsIndex = it->second;
det = m_workspace->getDetector(wsIndex);
}
else
{
g_log.debug() << "Skipping \"" << line << "\". Spectrum is not in workspace.\n";
continue;
}
}
else
{
det = inst->getDetector(detOrSpec);
}
}
catch(Kernel::Exception::NotFoundError&)
{
g_log.debug() << "Skipping \"" << line << "\". Spectrum in workspace but cannot find associated detector.\n";
continue;
}
// Special cases for detector r,t,p. Everything else is
// attached as an detector parameter
double R(0.0),theta(0.0), phi(0.0);
for(size_t i = 1; i < header.colCount; ++i)
{
double value(0.0);
is >> value;
if(i < header.colCount - 1 && is.eof())
{
//If stringstream is at EOF & we are not at the last column then
// there aren't enought columns in the file
throw std::runtime_error("UpdateInstrumentFromFile::updateFromAscii - "
"File contains fewer than expected number of columns, check AsciiHeader property.");
}
if(i == header.rColIdx) R = value;
else if(i == header.thetaColIdx) theta = value;
else if(i == header.phiColIdx) phi = value;
else if(header.detParCols.count(i) == 1)
{
Geometry::ParameterMap & pmap = m_workspace->instrumentParameters();
pmap.addDouble(det->getComponentID(), header.colToName[i],value);
}
}
// Check stream state. stringstream::EOF should have been reached, if not then there is still more to
// read and the file has more columns than the header indicated
if(!is.eof())
{
throw std::runtime_error("UpdateInstrumentFromFile::updateFromAscii - "
"File contains more than expected number of columns, check AsciiHeader property.");
}
// If not supplied use current values
double r,t,p;
det->getPos().getSpherical(r,t,p);
if(header.rColIdx == 0) R = r;
if(header.thetaColIdx == 0) theta = t;
if(header.phiColIdx == 0) phi = p;
setDetectorPosition(det, static_cast<float>(R), static_cast<float>(theta), static_cast<float>(phi));
}
}