/** Update the shape cache if necessary
* @param det :: a pointer to the detector to query
* @param detRadius :: An output parameter that contains the detector radius
* @param detAxis :: An output parameter that contains the detector axis vector
*/
void DetectorEfficiencyCor::getDetectorGeometry(const Geometry::IDetector_const_sptr & det, double & detRadius, V3D & detAxis)
{
boost::shared_ptr<const Object> shape_sptr = det->shape();
if(!shape_sptr->hasValidShape())
{
throw Exception::NotFoundError("Shape", "Detector has no shape");
}
std::map<const Geometry::Object *, std::pair<double, Kernel::V3D> >::const_iterator it =
m_shapeCache.find(shape_sptr.get());
if( it == m_shapeCache.end() )
{
double xDist = distToSurface( V3D(DIST_TO_UNIVERSE_EDGE, 0, 0), shape_sptr.get() );
double zDist = distToSurface( V3D(0, 0, DIST_TO_UNIVERSE_EDGE), shape_sptr.get() );
if ( std::abs(zDist - xDist) < 1e-8 )
{
detRadius = zDist/2.0;
detAxis = V3D(0,1,0);
// assume radi in z and x and the axis is in the y
PARALLEL_CRITICAL(deteff_shapecachea)
{
m_shapeCache.insert(std::pair<const Object *,std::pair<double, V3D> >(shape_sptr.get(), std::pair<double, V3D>(detRadius, detAxis)));
}
return;
}
/**
Non-member helper method to convert x y z enumeration directions into proper
3D vectors.
@param direction : direction marker
@return 3D vector
*/
V3D directionToVector(const PointingAlong &direction) {
Mantid::Kernel::V3D result;
if (direction == X) {
result = V3D(1, 0, 0);
} else if (direction == Y) {
result = V3D(0, 1, 0);
} else {
result = V3D(0, 0, 1);
}
return result;
}
/// Calculate the distances traversed by the neutrons within the sample
/// @param detector :: The detector we are working on
/// @param L2s :: A vector of the sample-detector distance for each segment of
/// the sample
void AbsorptionCorrection::calculateDistances(const IDetector &detector,
std::vector<double> &L2s) const {
V3D detectorPos(detector.getPos());
if (detector.nDets() > 1) {
// We need to make sure this is right for grouped detectors - should use
// average theta & phi
detectorPos.spherical(detectorPos.norm(),
detector.getTwoTheta(V3D(), V3D(0, 0, 1)) * 180.0 /
M_PI,
detector.getPhi() * 180.0 / M_PI);
}
for (size_t i = 0; i < m_numVolumeElements; ++i) {
// Create track for distance in cylinder between scattering point and
// detector
V3D direction = detectorPos - m_elementPositions[i];
direction.normalize();
Track outgoing(m_elementPositions[i], direction);
int temp = m_sampleObject->interceptSurface(outgoing);
/* Most of the time, the number of hits is 1. Sometime, we have more than
* one intersection due to
* arithmetic imprecision. If it is the case, then selecting the first
* intersection is valid.
* In principle, one could check the consistency of all distances if hits is
* larger than one by doing:
* Mantid::Geometry::Track::LType::const_iterator it=outgoing.begin();
* and looping until outgoing.end() checking the distances with it->Dist
*/
// Not hitting the cylinder from inside, usually means detector is badly
// defined,
// i.e, position is (0,0,0).
if (temp < 1) {
// FOR NOW AT LEAST, JUST IGNORE THIS ERROR AND USE A ZERO PATH LENGTH,
// WHICH I RECKON WILL MAKE A
// NEGLIGIBLE DIFFERENCE ANYWAY (ALWAYS SEEMS TO HAPPEN WITH ELEMENT RIGHT
// AT EDGE OF SAMPLE)
L2s[i] = 0.0;
// std::ostringstream message;
// message << "Problem with detector at " << detectorPos << " ID:" <<
// detector->getID() << '\n';
// message << "This usually means that this detector is defined inside the
// sample cylinder";
// g_log.error(message.str());
// throw std::runtime_error("Problem in
// AbsorptionCorrection::calculateDistances");
} else // The normal situation
{
L2s[i] = outgoing.cbegin()->distFromStart;
}
}
}
void jacTransform(MXD& J, const mtInput& input) const{
J.setZero();
const int& camID = input.CfP(ID_).camID_;
if(camID != outputCamID_){
input.updateMultiCameraExtrinsics(mpMultiCamera_);
const QPD qDC = input.qCM(outputCamID_)*input.qCM(camID).inverted(); // TODO: avoid double computation
const V3D CrCD = input.qCM(camID).rotate(V3D(input.MrMC(outputCamID_)-input.MrMC(camID)));
const V3D CrCP = input.dep(ID_).getDistance()*input.CfP(ID_).get_nor().getVec();
const V3D DrDP = qDC.rotate(V3D(CrCP-CrCD));
const double d_out = DrDP.norm();
const LWF::NormalVectorElement nor_out(DrDP); // TODO: test if Jacobian works, this new setting of vector is dangerous
const Eigen::Matrix<double,1,3> J_d_DrDP = nor_out.getVec().transpose();
const Eigen::Matrix<double,2,3> J_nor_DrDP = nor_out.getM().transpose()/d_out;
const Eigen::Matrix<double,3,3> J_DrDP_qDC = gSM(DrDP);
const Eigen::Matrix<double,3,3> J_DrDP_CrCP = MPD(qDC).matrix();
const Eigen::Matrix<double,3,3> J_DrDP_CrCD = -MPD(qDC).matrix();
const Eigen::Matrix<double,3,3> J_qDC_qDB = Eigen::Matrix3d::Identity();
const Eigen::Matrix<double,3,3> J_qDC_qCB = -MPD(qDC).matrix();
const Eigen::Matrix<double,3,3> J_CrCD_qCB = gSM(CrCD);
const Eigen::Matrix<double,3,3> J_CrCD_BrBC = -MPD(input.qCM(camID)).matrix();
const Eigen::Matrix<double,3,3> J_CrCD_BrBD = MPD(input.qCM(camID)).matrix();
const Eigen::Matrix<double,3,1> J_CrCP_d = input.CfP(ID_).get_nor().getVec()*input.dep(ID_).getDistanceDerivative();
const Eigen::Matrix<double,3,2> J_CrCP_nor = input.dep(ID_).getDistance()*input.CfP(ID_).get_nor().getM();
J.template block<2,2>(mtOutput::template getId<mtOutput::_fea>(),mtInput::template getId<mtInput::_fea>(ID_)) = J_nor_DrDP*J_DrDP_CrCP*J_CrCP_nor;
J.template block<2,1>(mtOutput::template getId<mtOutput::_fea>(),mtInput::template getId<mtInput::_fea>(ID_)+2) = J_nor_DrDP*J_DrDP_CrCP*J_CrCP_d;
if(!ignoreDistanceOutput_){
J.template block<1,2>(mtOutput::template getId<mtOutput::_fea>()+2,mtInput::template getId<mtInput::_fea>(ID_)) = J_d_DrDP*J_DrDP_CrCP*J_CrCP_nor;
J.template block<1,1>(mtOutput::template getId<mtOutput::_fea>()+2,mtInput::template getId<mtInput::_fea>(ID_)+2) = J_d_DrDP*J_DrDP_CrCP*J_CrCP_d;
}
if(input.aux().doVECalibration_ && camID != outputCamID_){
J.template block<2,3>(mtOutput::template getId<mtOutput::_fea>(),mtInput::template getId<mtInput::_vea>(camID)) = J_nor_DrDP*(J_DrDP_qDC*J_qDC_qCB+J_DrDP_CrCD*J_CrCD_qCB);
J.template block<2,3>(mtOutput::template getId<mtOutput::_fea>(),mtInput::template getId<mtInput::_vea>(outputCamID_)) = J_nor_DrDP*J_DrDP_qDC*J_qDC_qDB;
J.template block<2,3>(mtOutput::template getId<mtOutput::_fea>(),mtInput::template getId<mtInput::_vep>(camID)) = J_nor_DrDP*J_DrDP_CrCD*J_CrCD_BrBC;
J.template block<2,3>(mtOutput::template getId<mtOutput::_fea>(),mtInput::template getId<mtInput::_vep>(outputCamID_)) = J_nor_DrDP*J_DrDP_CrCD*J_CrCD_BrBD;
if(!ignoreDistanceOutput_){
J.template block<1,3>(mtOutput::template getId<mtOutput::_fea>()+2,mtInput::template getId<mtInput::_vea>(camID)) = J_d_DrDP*(J_DrDP_qDC*J_qDC_qCB+J_DrDP_CrCD*J_CrCD_qCB);
J.template block<1,3>(mtOutput::template getId<mtOutput::_fea>()+2,mtInput::template getId<mtInput::_vea>(outputCamID_)) = J_d_DrDP*J_DrDP_qDC*J_qDC_qDB;
J.template block<1,3>(mtOutput::template getId<mtOutput::_fea>()+2,mtInput::template getId<mtInput::_vep>(camID)) = J_d_DrDP*J_DrDP_CrCD*J_CrCD_BrBC;
J.template block<1,3>(mtOutput::template getId<mtOutput::_fea>()+2,mtInput::template getId<mtInput::_vep>(outputCamID_)) = J_d_DrDP*J_DrDP_CrCD*J_CrCD_BrBD;
}
}
} else {
J.template block<2,2>(mtOutput::template getId<mtOutput::_fea>(),mtInput::template getId<mtInput::_fea>(ID_)) = Eigen::Matrix2d::Identity();
J.template block<1,1>(mtOutput::template getId<mtOutput::_fea>()+2,mtInput::template getId<mtInput::_fea>(ID_)+2) = Eigen::Matrix<double,1,1>::Identity();
}
}
void evalTransform(mtOutput& output, const mtInput& input) const{
input.updateMultiCameraExtrinsics(mpMultiCamera_);
mpMultiCamera_->transformFeature(outputCamID_,input.CfP(ID_),input.dep(ID_),output.c(),output.d());
if(input.CfP(ID_).trackWarping_ && input.CfP(ID_).com_warp_nor()){
const int& camID = input.CfP(ID_).camID_;
const QPD qDC = input.qCM(outputCamID_)*input.qCM(camID).inverted(); // TODO: avoid double computation
const V3D CrCD = input.qCM(camID).rotate(V3D(input.MrMC(outputCamID_)-input.MrMC(camID)));
const V3D CrCP = input.dep(ID_).getDistance()*input.CfP(ID_).get_nor().getVec();
const V3D DrDP = qDC.rotate(V3D(CrCP-CrCD));
const double d_out = DrDP.norm();
const LWF::NormalVectorElement nor_out(DrDP);
const Eigen::Matrix<double,2,3> J_nor_DrDP = nor_out.getM().transpose()/d_out;
const Eigen::Matrix<double,3,3> J_DrDP_CrCP = MPD(qDC).matrix();
const Eigen::Matrix<double,3,2> J_CrCP_nor = input.dep(ID_).getDistance()*input.CfP(ID_).get_nor().getM();
output.c().set_warp_nor(J_nor_DrDP*J_DrDP_CrCP*J_CrCP_nor*input.CfP(ID_).get_warp_nor());
}
}
/** Create or adjust "rot" parameter for a component
* Assumed that name either equals "rotx", "roty" or "rotz" otherwise this
* method will not add/modify "rot" parameter
* @param comp :: Component
* @param name :: Parameter name
* @param deg :: Parameter value in degrees
* @param pDescription :: a pointer (may be NULL) to a string, containing
* parameter's
* description. If provided, the contents of the string is copied to the
* parameter's
* memory
*/
void ParameterMap::addRotationParam(const IComponent *comp,
const std::string &name, const double deg,
const std::string *const pDescription) {
Parameter_sptr paramRotX = get(comp, rotx());
Parameter_sptr paramRotY = get(comp, roty());
Parameter_sptr paramRotZ = get(comp, rotz());
double rotX, rotY, rotZ;
if (paramRotX)
rotX = paramRotX->value<double>();
else
rotX = 0.0;
if (paramRotY)
rotY = paramRotY->value<double>();
else
rotY = 0.0;
if (paramRotZ)
rotZ = paramRotZ->value<double>();
else
rotZ = 0.0;
// adjust rotation
Quat quat;
if (name.compare(rotx()) == 0) {
addDouble(comp, rotx(), deg);
quat = Quat(deg, V3D(1, 0, 0)) * Quat(rotY, V3D(0, 1, 0)) *
Quat(rotZ, V3D(0, 0, 1));
} else if (name.compare(roty()) == 0) {
addDouble(comp, roty(), deg);
quat = Quat(rotX, V3D(1, 0, 0)) * Quat(deg, V3D(0, 1, 0)) *
Quat(rotZ, V3D(0, 0, 1));
} else if (name.compare(rotz()) == 0) {
addDouble(comp, rotz(), deg);
quat = Quat(rotX, V3D(1, 0, 0)) * Quat(rotY, V3D(0, 1, 0)) *
Quat(deg, V3D(0, 0, 1));
} else {
g_log.warning()
<< "addRotationParam() called with unrecognized coordinate symbol: "
<< name;
return;
}
// clear the position cache
clearPositionSensitiveCaches();
// finally add or update "pos" parameter
addQuat(comp, rot(), quat, pDescription);
}
/** Execute the algorithm.
*/
void CalculateUMatrix::exec()
{
double a=this->getProperty("a");
double b=this->getProperty("b");
double c=this->getProperty("c");
double alpha=this->getProperty("alpha");
double beta=this->getProperty("beta");
double gamma=this->getProperty("gamma");
OrientedLattice o(a,b,c,alpha,beta,gamma);
Matrix<double> B=o.getB();
double H,K,L;
PeaksWorkspace_sptr ws;
ws = boost::dynamic_pointer_cast<PeaksWorkspace>(AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
if (!ws) throw std::runtime_error("Problems reading the peaks workspace");
Matrix<double> Hi(4,4),Si(4,4),HS(4,4),zero(4,4);
for (int i=0;i<ws->getNumberPeaks();i++)
{
Peak p=ws->getPeaks()[i];
H=p.getH();
K=p.getK();
L=p.getL();
if(H*H+K*K+L*L>0)
{
V3D Qhkl=B*V3D(H,K,L);
Hi[0][0]=0.; Hi[0][1]=-Qhkl.X(); Hi[0][2]=-Qhkl.Y(); Hi[0][3]=-Qhkl.Z();
Hi[1][0]=Qhkl.X(); Hi[1][1]=0.; Hi[1][2]=Qhkl.Z(); Hi[1][3]=-Qhkl.Y();
Hi[2][0]=Qhkl.Y(); Hi[2][1]=-Qhkl.Z(); Hi[2][2]=0.; Hi[2][3]=Qhkl.X();
Hi[3][0]=Qhkl.Z(); Hi[3][1]=Qhkl.Y(); Hi[3][2]=-Qhkl.X(); Hi[3][3]=0.;
V3D Qgon=p.getQSampleFrame();
Si[0][0]=0.; Si[0][1]=-Qgon.X(); Si[0][2]=-Qgon.Y(); Si[0][3]=-Qgon.Z();
Si[1][0]=Qgon.X(); Si[1][1]=0.; Si[1][2]=-Qgon.Z(); Si[1][3]=Qgon.Y();
Si[2][0]=Qgon.Y(); Si[2][1]=Qgon.Z(); Si[2][2]=0.; Si[2][3]=-Qgon.X();
Si[3][0]=Qgon.Z(); Si[3][1]=-Qgon.Y(); Si[3][2]=Qgon.X(); Si[3][3]=0.;
HS+=(Hi*Si);
}
}
//check if HS is 0
if (HS==zero) throw std::invalid_argument("The peaks workspace is not indexed or something really bad happened");
Matrix<double> Eval;
Matrix<double> Diag;
HS.Diagonalise(Eval,Diag);
Eval.sortEigen(Diag);
Mantid::Kernel::Quat qR(Eval[0][0],Eval[1][0],Eval[2][0],Eval[3][0]);//the first column corresponds to the highest eigenvalue
DblMatrix U(qR.getRotation());
o.setU(U);
ws->mutableSample().setOrientedLattice(new OrientedLattice(o));
}
/** Get the position relative to the parent IComponent (absolute if no parent)
* This is calculated on-the-fly.
*
* @return position relative to the 0,0 point of the parent panel
*/
const Kernel::V3D RectangularDetectorPixel::getRelativePos() const {
// Calculate the x,y position
double x = m_panel->xstart() + double(m_col) * m_panel->xstep();
double y = m_panel->ystart() + double(m_row) * m_panel->ystep();
// The parent m_panel is always the unparametrized version,
// so the xstep() etc. returned are the UNSCALED one.
if (m_map) {
// Apply the scaling factors
if (m_map->contains(m_panel, "scalex"))
x *= m_map->get(m_panel, "scalex")->value<double>();
if (m_map->contains(m_panel, "scaley"))
y *= m_map->get(m_panel, "scaley")->value<double>();
}
return V3D(x, y, 0);
}
std::vector<VMDBase<TYPE>>
VMDBase<TYPE>::makeVectorsOrthogonal(std::vector<VMDBase> &vectors) {
if (vectors.size() != 2)
throw std::runtime_error(
"VMDBase::makeVectorsOrthogonal(): Need 2 input vectors.");
if (vectors[0].getNumDims() != 3 || vectors[1].getNumDims() != 3)
throw std::runtime_error(
"VMDBase::makeVectorsOrthogonal(): Need 3D input vectors.");
std::vector<V3D> in, out;
for (size_t i = 0; i < vectors.size(); i++)
in.push_back(V3D(vectors[i][0], vectors[i][1], vectors[i][2]));
out = V3D::makeVectorsOrthogonal(in);
std::vector<VMDBase> retVal;
for (size_t i = 0; i < out.size(); i++)
retVal.push_back(VMDBase(out[i]));
return retVal;
}
/** Create or adjust "rot" parameter for a component
* Assumed that name either equals "rotx", "roty" or "rotz" otherwise this
* method will not add/modify "rot" parameter
* @param comp :: Component
* @param name :: Parameter name
* @param deg :: Parameter value in degrees
*/
void ParameterMap::addRotationParam(const IComponent* comp,const std::string& name, const double deg)
{
Parameter_sptr param = get(comp,"rot");
Quat quat;
Parameter_sptr paramRotX = get(comp,"rotx");
Parameter_sptr paramRotY = get(comp,"roty");
Parameter_sptr paramRotZ = get(comp,"rotz");
double rotX, rotY, rotZ;
if ( paramRotX )
rotX = paramRotX->value<double>();
else
rotX = 0.0;
if ( paramRotY )
rotY = paramRotY->value<double>();
else
rotY = 0.0;
if ( paramRotZ )
rotZ = paramRotZ->value<double>();
else
rotZ = 0.0;
// adjust rotation
if ( name.compare("rotx")==0 )
{
if (paramRotX)
paramRotX->set(deg);
else
addDouble(comp, "rotx", deg);
quat = Quat(deg,V3D(1,0,0))*Quat(rotY,V3D(0,1,0))*Quat(rotZ,V3D(0,0,1));
}
else if ( name.compare("roty")==0 )
{
if (paramRotY)
paramRotY->set(deg);
else
addDouble(comp, "roty", deg);
quat = Quat(rotX,V3D(1,0,0))*Quat(deg,V3D(0,1,0))*Quat(rotZ,V3D(0,0,1));
}
else if ( name.compare("rotz")==0 )
{
if (paramRotZ)
paramRotZ->set(deg);
else
addDouble(comp, "rotz", deg);
quat = Quat(rotX,V3D(1,0,0))*Quat(rotY,V3D(0,1,0))*Quat(deg,V3D(0,0,1));
}
else
{
g_log.warning() << "addRotationParam() called with unrecognised coordinate symbol: " << name;
return;
}
//clear the position cache
clearCache();
// finally add or update "pos" parameter
if (param)
param->set(quat);
else
addQuat(comp, "rot", quat);
}
if( it == m_shapeCache.end() )
{
double xDist = distToSurface( V3D(DIST_TO_UNIVERSE_EDGE, 0, 0), shape_sptr.get() );
double zDist = distToSurface( V3D(0, 0, DIST_TO_UNIVERSE_EDGE), shape_sptr.get() );
if ( std::abs(zDist - xDist) < 1e-8 )
{
detRadius = zDist/2.0;
detAxis = V3D(0,1,0);
// assume radi in z and x and the axis is in the y
PARALLEL_CRITICAL(deteff_shapecachea)
{
m_shapeCache.insert(std::pair<const Object *,std::pair<double, V3D> >(shape_sptr.get(), std::pair<double, V3D>(detRadius, detAxis)));
}
return;
}
double yDist = distToSurface( V3D(0, DIST_TO_UNIVERSE_EDGE, 0), shape_sptr.get() );
if ( std::abs(yDist - zDist) < 1e-8 )
{
detRadius = yDist/2.0;
detAxis = V3D(1,0,0);
// assume that y and z are radi of the cylinder's circular cross-section and the axis is perpendicular, in the x direction
PARALLEL_CRITICAL(deteff_shapecacheb)
{
m_shapeCache.insert(std::pair<const Object *,std::pair<double, V3D> >(shape_sptr.get(), std::pair<double, V3D>(detRadius, detAxis)));
}
return;
}
if ( std::abs(xDist - yDist) < 1e-8 )
{
detRadius = xDist/2.0;
/** Execute the algorithm.
*/
void CalculateUMatrix::exec()
{
double a=this->getProperty("a");
double b=this->getProperty("b");
double c=this->getProperty("c");
double alpha=this->getProperty("alpha");
double beta=this->getProperty("beta");
double gamma=this->getProperty("gamma");
OrientedLattice o(a,b,c,alpha,beta,gamma);
Matrix<double> B=o.getB();
double H,K,L;
PeaksWorkspace_sptr ws;
ws = AnalysisDataService::Instance().retrieveWS<PeaksWorkspace>(this->getProperty("PeaksWorkspace") );
if (!ws) throw std::runtime_error("Problems reading the peaks workspace");
size_t nIndexedpeaks=0;
bool found2nc=false;
V3D old(0,0,0);
Matrix<double> Hi(4,4),Si(4,4),HS(4,4),zero(4,4);
for (int i=0;i<ws->getNumberPeaks();i++)
{
Peak p=ws->getPeaks()[i];
H=p.getH();
K=p.getK();
L=p.getL();
if(H*H+K*K+L*L>0)
{
nIndexedpeaks++;
if (!found2nc)
{
if (nIndexedpeaks==1)
{
old=V3D(H,K,L);
}
else
{
if (!old.coLinear(V3D(0,0,0),V3D(H,K,L))) found2nc=true;
}
}
V3D Qhkl=B*V3D(H,K,L);
Hi[0][0]=0.; Hi[0][1]=-Qhkl.X(); Hi[0][2]=-Qhkl.Y(); Hi[0][3]=-Qhkl.Z();
Hi[1][0]=Qhkl.X(); Hi[1][1]=0.; Hi[1][2]=Qhkl.Z(); Hi[1][3]=-Qhkl.Y();
Hi[2][0]=Qhkl.Y(); Hi[2][1]=-Qhkl.Z(); Hi[2][2]=0.; Hi[2][3]=Qhkl.X();
Hi[3][0]=Qhkl.Z(); Hi[3][1]=Qhkl.Y(); Hi[3][2]=-Qhkl.X(); Hi[3][3]=0.;
V3D Qgon=p.getQSampleFrame();
Si[0][0]=0.; Si[0][1]=-Qgon.X(); Si[0][2]=-Qgon.Y(); Si[0][3]=-Qgon.Z();
Si[1][0]=Qgon.X(); Si[1][1]=0.; Si[1][2]=-Qgon.Z(); Si[1][3]=Qgon.Y();
Si[2][0]=Qgon.Y(); Si[2][1]=Qgon.Z(); Si[2][2]=0.; Si[2][3]=-Qgon.X();
Si[3][0]=Qgon.Z(); Si[3][1]=-Qgon.Y(); Si[3][2]=Qgon.X(); Si[3][3]=0.;
HS+=(Hi*Si);
}
}
//check if enough peaks are indexed or if HS is 0
if ((nIndexedpeaks<2) || (found2nc==false)) throw std::invalid_argument("Less then two non-colinear peaks indexed");
if (HS==zero) throw std::invalid_argument("Something really bad happened");
Matrix<double> Eval;
Matrix<double> Diag;
HS.Diagonalise(Eval,Diag);
Eval.sortEigen(Diag);
Mantid::Kernel::Quat qR(Eval[0][0],Eval[1][0],Eval[2][0],Eval[3][0]);//the first column corresponds to the highest eigenvalue
DblMatrix U(qR.getRotation());
o.setU(U);
ws->mutableSample().setOrientedLattice(new OrientedLattice(o));
}
void addFullInstrumentToWorkspace(MatrixWorkspace &workspace,
bool includeMonitors, bool startYNegative,
const std::string &instrumentName) {
auto instrument = boost::make_shared<Instrument>(instrumentName);
instrument->setReferenceFrame(
boost::make_shared<ReferenceFrame>(Y, Z, Right, ""));
workspace.setInstrument(instrument);
const double pixelRadius(0.05);
Object_sptr pixelShape = ComponentCreationHelper::createCappedCylinder(
pixelRadius, 0.02, V3D(0.0, 0.0, 0.0), V3D(0., 1.0, 0.), "tube");
const double detZPos(5.0);
// Careful! Do not use size_t or auto, the unisgned will break the -=2 below.
int ndets = static_cast<int>(workspace.getNumberHistograms());
if (includeMonitors)
ndets -= 2;
for (int i = 0; i < ndets; ++i) {
std::ostringstream lexer;
lexer << "pixel-" << i << ")";
Detector *physicalPixel =
new Detector(lexer.str(), workspace.getAxis(1)->spectraNo(i),
pixelShape, instrument.get());
int ycount(i);
if (startYNegative)
ycount -= 1;
const double ypos = ycount * 2.0 * pixelRadius;
physicalPixel->setPos(0.0, ypos, detZPos);
instrument->add(physicalPixel);
instrument->markAsDetector(physicalPixel);
workspace.getSpectrum(i).setDetectorID(physicalPixel->getID());
}
// Monitors last
if (includeMonitors) // These occupy the last 2 spectra
{
Detector *monitor1 =
new Detector("mon1", workspace.getAxis(1)->spectraNo(ndets),
Object_sptr(), instrument.get());
monitor1->setPos(0.0, 0.0, -9.0);
instrument->add(monitor1);
instrument->markAsMonitor(monitor1);
workspace.getSpectrum(ndets).setDetectorID(ndets + 1);
Detector *monitor2 =
new Detector("mon2", workspace.getAxis(1)->spectraNo(ndets) + 1,
Object_sptr(), instrument.get());
monitor2->setPos(0.0, 0.0, -2.0);
instrument->add(monitor2);
instrument->markAsMonitor(monitor2);
workspace.getSpectrum(ndets + 1).setDetectorID(ndets + 2);
}
// Define a source and sample position
// Define a source component
ObjComponent *source = new ObjComponent(
"moderator",
ComponentCreationHelper::createSphere(0.1, V3D(0, 0, 0), "1"),
instrument.get());
source->setPos(V3D(0.0, 0.0, -20.0));
instrument->add(source);
instrument->markAsSource(source);
// Define a sample as a simple sphere
ObjComponent *sample = new ObjComponent(
"samplePos",
ComponentCreationHelper::createSphere(0.1, V3D(0, 0, 0), "1"),
instrument.get());
instrument->setPos(0.0, 0.0, 0.0);
instrument->add(sample);
instrument->markAsSamplePos(sample);
// chopper position
Component *chop_pos = new Component("chopper-position",
Kernel::V3D(0, 0, -10), instrument.get());
instrument->add(chop_pos);
}
/**
* Construct a PoldiPeakCollection from a Poldi2DFunction
*
* This method performs the opposite operation of
*getFunctionFromPeakCollection.
* It takes a function, checks if it's of the proper type and turns the
* information into a PoldiPeakCollection.
*
* @param Poldi2DFunction with one PoldiSpectrumDomainFunction per peak
* @return PoldiPeakCollection containing peaks with normalized intensities
*/
PoldiPeakCollection_sptr PoldiFitPeaks2D::getPeakCollectionFromFunction(
const IFunction_sptr &fitFunction) {
Poldi2DFunction_sptr poldi2DFunction =
boost::dynamic_pointer_cast<Poldi2DFunction>(fitFunction);
if (!poldi2DFunction) {
throw std::invalid_argument(
"Cannot process function that is not a Poldi2DFunction.");
}
PoldiPeakCollection_sptr normalizedPeaks =
boost::make_shared<PoldiPeakCollection>(PoldiPeakCollection::Integral);
boost::shared_ptr<const Kernel::DblMatrix> covarianceMatrix =
poldi2DFunction->getCovarianceMatrix();
size_t offset = 0;
for (size_t i = 0; i < poldi2DFunction->nFunctions(); ++i) {
boost::shared_ptr<PoldiSpectrumPawleyFunction> poldiPawleyFunction =
boost::dynamic_pointer_cast<PoldiSpectrumPawleyFunction>(
poldi2DFunction->getFunction(i));
// If it's a Pawley function, there are several peaks in one function.
if (poldiPawleyFunction) {
IPawleyFunction_sptr pawleyFunction =
poldiPawleyFunction->getPawleyFunction();
if (pawleyFunction) {
CompositeFunction_sptr decoratedFunction =
boost::dynamic_pointer_cast<CompositeFunction>(
pawleyFunction->getDecoratedFunction());
offset = decoratedFunction->getFunction(0)->nParams();
for (size_t j = 0; j < pawleyFunction->getPeakCount(); ++j) {
IPeakFunction_sptr profileFunction =
pawleyFunction->getPeakFunction(j);
size_t nLocalParams = profileFunction->nParams();
boost::shared_ptr<Kernel::DblMatrix> localCov =
getLocalCovarianceMatrix(covarianceMatrix, offset, nLocalParams);
profileFunction->setCovarianceMatrix(localCov);
// Increment offset for next function
offset += nLocalParams;
V3D peakHKL = pawleyFunction->getPeakHKL(j);
PoldiPeak_sptr peak =
getPeakFromPeakFunction(profileFunction, peakHKL);
normalizedPeaks->addPeak(peak);
}
}
break;
}
// Otherwise, it's just one peak in this function.
boost::shared_ptr<PoldiSpectrumDomainFunction> peakFunction =
boost::dynamic_pointer_cast<PoldiSpectrumDomainFunction>(
poldi2DFunction->getFunction(i));
if (peakFunction) {
IPeakFunction_sptr profileFunction =
boost::dynamic_pointer_cast<IPeakFunction>(
peakFunction->getProfileFunction());
// Get local covariance matrix
size_t nLocalParams = profileFunction->nParams();
boost::shared_ptr<Kernel::DblMatrix> localCov =
getLocalCovarianceMatrix(covarianceMatrix, offset, nLocalParams);
profileFunction->setCovarianceMatrix(localCov);
// Increment offset for next function
offset += nLocalParams;
PoldiPeak_sptr peak =
getPeakFromPeakFunction(profileFunction, V3D(0, 0, 0));
normalizedPeaks->addPeak(peak);
}
}
return normalizedPeaks;
}
void SANSDirectBeamScaling::exec()
{
MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace");
const double beamRadius = getProperty("BeamRadius");
const double attTrans = getProperty("AttenuatorTransmission");
const double attTransErr = getProperty("AttenuatorTransmissionError");
// Extract the required spectra into separate workspaces
std::vector<detid_t> udet;
std::vector<size_t> index;
udet.push_back(getProperty("BeamMonitor"));
// Convert UDETs to workspace indices
inputWS->getIndicesFromDetectorIDs(udet,index);
if (index.size() < 1)
{
g_log.debug() << "inputWS->getIndicesFromDetectorIDs() returned empty\n";
throw std::invalid_argument("Could not find the incident beam monitor spectra\n");
}
const int64_t numHists = inputWS->getNumberHistograms();
Progress progress(this,0.0,1.0,numHists);
// Number of X bins
const int64_t xLength = inputWS->readY(0).size();
// Monitor counts
double monitor = 0.0;
const MantidVec& MonIn = inputWS->readY(index[0]);
for (int64_t j = 0; j < xLength; j++)
monitor += MonIn[j];
const V3D sourcePos = inputWS->getInstrument()->getSource()->getPos();
double counts = 0.0;
double error = 0.0;
int nPixels = 0;
// Sample-detector distance for the contributing pixels
double sdd = 0.0;
for (int64_t i = 0; i < int64_t(numHists); ++i)
{
IDetector_const_sptr det;
try {
det = inputWS->getDetector(i);
} catch (Exception::NotFoundError&) {
g_log.warning() << "Spectrum index " << i << " has no detector assigned to it - discarding" << std::endl;
continue;
}
// Skip if we have a monitor or if the detector is masked.
if ( det->isMonitor() || det->isMasked() ) continue;
const MantidVec& YIn = inputWS->readY(i);
const MantidVec& EIn = inputWS->readE(i);
// Sum up all the counts
V3D pos = det->getPos() - V3D(sourcePos.X(), sourcePos.Y(), 0.0);
const double pixelDistance = pos.Z();
pos.setZ(0.0);
if (pos.norm() <= beamRadius) {
// Correct data for all X bins
for (int64_t j = 0; j < xLength; j++)
{
counts += YIn[j];
error += EIn[j]*EIn[j];
}
nPixels += 1;
sdd += pixelDistance;
}
progress.report("Absolute Scaling");
}
// Get the average SDD for the counted pixels, and transform to mm.
sdd = sdd/nPixels*1000.0;
error = std::sqrt(error);
// Transform from m to mm
double sourceAperture = getProperty("SourceApertureRadius");
sourceAperture *= 1000.0;
// Transform from m to mm
double sampleAperture = getProperty("SampleApertureRadius");
sampleAperture *= 1000.0;
//TODO: replace this by some meaningful value
const double KCG2FluxPerMon_SUGAR = 1.0;
// Solid angle correction scale in 1/(cm^2)/steradian
double solidAngleCorrScale = sdd/(M_PI*sourceAperture*sampleAperture);
solidAngleCorrScale = solidAngleCorrScale*solidAngleCorrScale*100.0;
// Scaling factor in n/(monitor count)/(cm^2)/steradian
double scale = counts/monitor*solidAngleCorrScale/KCG2FluxPerMon_SUGAR;
double scaleErr = std::abs(error/monitor)*solidAngleCorrScale/KCG2FluxPerMon_SUGAR;
scaleErr = std::abs(scale/attTrans)*sqrt( (scaleErr/scale)*(scaleErr/scale) +(attTransErr/attTrans)*(attTransErr/attTrans) );
scale /= attTrans;
std::vector<double> output;
output.push_back(scale);
output.push_back(scaleErr);
setProperty("ScaleFactor", output);
}
/** 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();
}
/**
* 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;
}
/**
* Cross product
*/
V3D V2D::cross_prod(const V2D &other) const {
return V3D(0.0, 0.0, m_x * other.m_y - m_y * other.m_x);
}
/** method to cacluate the detectors parameters and add them to the detectors
*averages
*@param det -- reference to the Mantid Detector
*@param Observer -- sample position or the centre of the polar system of
*coordinates to calculate detector's parameters.
*/
void AvrgDetector::addDetInfo(const Geometry::IDetector &det,
const Kernel::V3D &Observer) {
m_nComponents++;
Kernel::V3D detPos = det.getPos();
Kernel::V3D toDet = (detPos - Observer);
double dist2Det, Polar, Azimut, ringPolar, ringAzim;
// identify the detector' position in the beam coordinate system:
toDet.getSpherical(dist2Det, Polar, Azimut);
if (m_nComponents <= 1) {
m_FlightPathSum = dist2Det;
m_PolarSum = Polar;
m_AzimutSum = Azimut;
m_AzimBase = Polar;
m_PolarBase = Azimut;
ringPolar = Polar;
ringAzim = Azimut;
} else {
ringPolar = nearAngle(m_AzimBase, Polar);
ringAzim = nearAngle(m_PolarBase, Azimut);
m_FlightPathSum += dist2Det;
m_PolarSum += ringPolar;
m_AzimutSum += ringAzim;
}
// centre of the azimuthal ring (the ring detectors form around the beam)
Kernel::V3D ringCentre(0, 0, toDet.Z());
// Get the bounding box
Geometry::BoundingBox bbox;
std::vector<Kernel::V3D> coord(3);
// ez along beamline, which is always oz;
Kernel::V3D er(0, 1, 0), ez(0, 0, 1);
if (dist2Det != 0.0)
er = toDet / dist2Det; // direction to the detector
// tangential to the ring and anticlockwise.
Kernel::V3D e_tg = er.cross_prod(ez);
if (e_tg.nullVector(1e-12)) {
e_tg = V3D(1., 0., 0.);
} else {
e_tg.normalize();
}
// make orthogonal -- projections are calculated in this coordinate system
ez = e_tg.cross_prod(er);
coord[0] = er; // new X
coord[1] = ez; // new y
coord[2] = e_tg; // new z
bbox.setBoxAlignment(ringCentre, coord);
det.getBoundingBox(bbox);
// linear extensions of the bounding box orientied tangentially to the equal
// scattering angle circle
double azimMin = bbox.zMin();
double azimMax = bbox.zMax();
double polarMin = bbox.yMin(); // bounding box has been rotated according to
// coord above, so z is along e_tg
double polarMax = bbox.yMax();
if (m_useSphericalSizes) {
if (dist2Det == 0)
dist2Det = 1;
// convert to angular units
double polarHalfSize =
rad2deg * atan2(0.5 * (polarMax - polarMin), dist2Det);
double azimHalfSize = rad2deg * atan2(0.5 * (azimMax - azimMin), dist2Det);
polarMin = ringPolar - polarHalfSize;
polarMax = ringPolar + polarHalfSize;
azimMin = ringAzim - azimHalfSize;
azimMax = ringAzim + azimHalfSize;
}
if (m_AzimMin > azimMin)
m_AzimMin = azimMin;
if (m_AzimMax < azimMax)
m_AzimMax = azimMax;
if (m_PolarMin > polarMin)
m_PolarMin = polarMin;
if (m_PolarMax < polarMax)
m_PolarMax = polarMax;
}
void AnvredCorrection::execEvent()
{
const int64_t numHists = static_cast<int64_t>(m_inputWS->getNumberHistograms());
std::string unitStr = m_inputWS->getAxis(0)->unit()->unitID();
//Create a new outputworkspace with not much in it
DataObjects::EventWorkspace_sptr correctionFactors;
correctionFactors = boost::dynamic_pointer_cast<EventWorkspace>(
API::WorkspaceFactory::Instance().create("EventWorkspace",numHists,2,1) );
correctionFactors->sortAll(TOF_SORT, NULL);
//Copy required stuff from it
API::WorkspaceFactory::Instance().initializeFromParent(m_inputWS, correctionFactors, true);
bool inPlace = (this->getPropertyValue("InputWorkspace") == this->getPropertyValue("OutputWorkspace"));
if (inPlace)
g_log.debug("Correcting EventWorkspace in-place.");
// If sample not at origin, shift cached positions.
const V3D samplePos = m_inputWS->getInstrument()->getSample()->getPos();
const V3D pos = m_inputWS->getInstrument()->getSource()->getPos()-samplePos;
double L1 = pos.norm();
Progress prog(this,0.0,1.0,numHists);
// Loop over the spectra
PARALLEL_FOR2(eventW,correctionFactors)
for (int64_t i = 0; i < int64_t(numHists); ++i)
{
PARALLEL_START_INTERUPT_REGION
// Copy over bin boundaries
const MantidVec& X = eventW->readX(i);
correctionFactors->dataX(i) = X;
// Get detector position
IDetector_const_sptr det;
try
{
det = eventW->getDetector(i);
} catch (Exception::NotFoundError&)
{
// Catch if no detector. Next line tests whether this happened - test placed
// outside here because Mac Intel compiler doesn't like 'continue' in a catch
// in an openmp block.
}
// If no detector found, skip onto the next spectrum
if ( !det ) continue;
// This is the scattered beam direction
Instrument_const_sptr inst = eventW->getInstrument();
V3D dir = det->getPos() - samplePos;
double L2 = dir.norm();
// Two-theta = polar angle = scattering angle = between +Z vector and the scattered beam
double scattering = dir.angle( V3D(0.0, 0.0, 1.0) );
EventList el = eventW->getEventList(i);
el.switchTo(WEIGHTED_NOTIME);
std::vector<WeightedEventNoTime> events = el.getWeightedEventsNoTime();
std::vector<WeightedEventNoTime>::iterator itev;
std::vector<WeightedEventNoTime>::iterator itev_end = events.end();
Mantid::Kernel::Units::Wavelength wl;
std::vector<double> timeflight;
// multiplying an event list by a scalar value
for (itev = events.begin(); itev != itev_end; itev++)
{
timeflight.push_back(itev->tof());
if (unitStr.compare("TOF") == 0)
wl.fromTOF(timeflight, timeflight, L1, L2, scattering, 0, 0, 0);
double value = this->getEventWeight(timeflight[0], scattering);
timeflight.clear();
itev->m_errorSquared = static_cast<float>(itev->m_errorSquared * value*value);
itev->m_weight *= static_cast<float>(value);
}
correctionFactors->getOrAddEventList(i) +=events;
std::set<detid_t>& dets = eventW->getEventList(i).getDetectorIDs();
std::set<detid_t>::iterator j;
for (j = dets.begin(); j != dets.end(); ++j)
correctionFactors->getOrAddEventList(i).addDetectorID(*j);
// When focussing in place, you can clear out old memory from the input one!
if (inPlace)
{
eventW->getEventList(i).clear();
Mantid::API::MemoryManager::Instance().releaseFreeMemory();
}
prog.report();
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
correctionFactors->doneAddingEventLists();
setProperty("OutputWorkspace", boost::dynamic_pointer_cast<MatrixWorkspace>(correctionFactors));
// Now do some cleaning-up since destructor may not be called immediately
this->cleanup();
}
/** Executes the algorithm.
*
* @throw std::runtime_error Thrown with Workspace problems
*/
void RotateInstrumentComponent::exec()
{
// Get the workspace
MatrixWorkspace_sptr WS = getProperty("Workspace");
const std::string ComponentName = getProperty("ComponentName");
const int DetID = getProperty("DetectorID");
const double X = getProperty("X");
const double Y = getProperty("Y");
const double Z = getProperty("Z");
const double angle = getProperty("Angle");
const bool RelativeRotation = getProperty("RelativeRotation");
if (X + Y + Z == 0.0) throw std::invalid_argument("The rotation axis must not be a zero vector");
Instrument_const_sptr inst = WS->getInstrument();
IComponent_const_sptr comp;
// Find the component to move
if (DetID != -1)
{
comp = inst->getDetector(DetID);
if (comp == 0)
{
std::ostringstream mess;
mess<<"Detector with ID "<<DetID<<" was not found.";
g_log.error(mess.str());
throw std::runtime_error(mess.str());
}
}
else if (!ComponentName.empty())
{
comp = inst->getComponentByName(ComponentName);
if (comp == 0)
{
std::ostringstream mess;
mess<<"Component with name "<<ComponentName<<" was not found.";
g_log.error(mess.str());
throw std::runtime_error(mess.str());
}
}
else
{
g_log.error("DetectorID or ComponentName must be given.");
throw std::invalid_argument("DetectorID or ComponentName must be given.");
}
// First set new relative or absolute rotation
Quat Rot;
if (RelativeRotation)
{
Quat Rot0 = comp->getRelativeRot();
Rot = Rot0 * Quat(angle,V3D(X,Y,Z));
}
else
{
Rot = Quat(angle,V3D(X,Y,Z));
// Then find the corresponding relative position
boost::shared_ptr<const IComponent> parent = comp->getParent();
if (parent)
{
Quat rot0 = parent->getRelativeRot();
rot0.inverse();
Rot = Rot * rot0;
}
}
//Need to get the address to the base instrument component
Geometry::ParameterMap& pmap = WS->instrumentParameters();
// Add a parameter for the new rotation
pmap.addQuat(comp.get(), "rot", Rot);
return;
}
/** Execute the algorithm.
*/
void FindUBUsingIndexedPeaks::exec()
{
PeaksWorkspace_sptr ws;
ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
if (!ws)
{
throw std::runtime_error("Could not read the peaks workspace");
}
std::vector<Peak> peaks = ws->getPeaks();
size_t n_peaks = ws->getNumberPeaks();
std::vector<V3D> q_vectors;
std::vector<V3D> hkl_vectors;
q_vectors.reserve( n_peaks );
hkl_vectors.reserve( n_peaks );
size_t indexed_count = 0;
for ( size_t i = 0; i < n_peaks; i++ )
{
V3D hkl( peaks[i].getH(), peaks[i].getK(), peaks[i].getL() ); // ##### KEEP
if ( IndexingUtils::ValidIndex( hkl, 1.0 ) ) // use tolerance == 1 to
// just check for (0,0,0)
{
q_vectors.push_back( peaks[i].getQSampleFrame() );
V3D miller_ind( round(hkl[0]), round(hkl[1]), round(hkl[2]) );
hkl_vectors.push_back( V3D(miller_ind) );
indexed_count++;
}
}
if ( indexed_count < 3 )
{
throw std::runtime_error(
"At least three linearly independent indexed peaks are needed.");
}
Matrix<double> UB(3,3,false);
double error = IndexingUtils::Optimize_UB( UB, hkl_vectors, q_vectors );
std::cout << "Error = " << error << std::endl;
std::cout << "UB = " << UB << std::endl;
if ( ! IndexingUtils::CheckUB( UB ) ) // UB not found correctly
{
g_log.notice( std::string(
"Found Invalid UB...peaks used might not be linearly independent") );
g_log.notice( std::string(
"UB NOT SAVED.") );
}
else // tell user how many would be indexed
{ // from the full list of peaks, and
q_vectors.clear(); // save the UB in the sample
q_vectors.reserve( n_peaks );
for ( size_t i = 0; i < n_peaks; i++ )
{
q_vectors.push_back( peaks[i].getQSampleFrame() );
}
double tolerance = 0.1;
int num_indexed = IndexingUtils::NumberIndexed(UB, q_vectors, tolerance);
char logInfo[200];
sprintf( logInfo,
std::string("New UB will index %1d Peaks out of %1d with tolerance %5.3f").c_str(),
num_indexed, n_peaks, tolerance);
g_log.notice( std::string(logInfo) );
OrientedLattice o_lattice;
o_lattice.setUB( UB );
double calc_a = o_lattice.a();
double calc_b = o_lattice.b();
double calc_c = o_lattice.c();
double calc_alpha = o_lattice.alpha();
double calc_beta = o_lattice.beta();
double calc_gamma = o_lattice.gamma();
// Show the modified lattice parameters
sprintf( logInfo,
std::string("Lattice Parameters: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f").c_str(),
calc_a, calc_b, calc_c, calc_alpha, calc_beta, calc_gamma);
g_log.notice( std::string(logInfo) );
ws->mutableSample().setOrientedLattice( new OrientedLattice(o_lattice) );
}
}