/**
* Construct the volume encompassing the sample + any environment kit. The
* beam profile defines a bounding region for the sampling of the scattering
* position.
* @param sample A reference to a sample object that defines a valid shape
* & material
* @param activeRegion Restrict scattering point sampling to this region
*/
MCInteractionVolume::MCInteractionVolume(
const API::Sample &sample, const Geometry::BoundingBox &activeRegion)
: m_sample(sample.getShape()), m_env(nullptr),
m_activeRegion(activeRegion) {
if (!m_sample.hasValidShape()) {
throw std::invalid_argument(
"MCInteractionVolume() - Sample shape does not have a valid shape.");
}
try {
m_env = &sample.getEnvironment();
if (m_env->nelements() == 0) {
throw std::invalid_argument(
"MCInteractionVolume() - Sample enviroment has zero components.");
}
} catch (std::runtime_error &) {
// swallow this as no defined environment from getEnvironment
}
}
/// Create the sample object using the Geometry classes, or use the existing one
void AbsorptionCorrection::constructSample(API::Sample &sample) {
const std::string xmlstring = sampleXML();
if (xmlstring.empty()) {
// This means that we should use the shape already defined on the sample.
m_sampleObject = &sample.getShape();
// Check there is one, and fail if not
if (!m_sampleObject->hasValidShape()) {
const std::string mess(
"No shape has been defined for the sample in the input workspace");
g_log.error(mess);
throw std::invalid_argument(mess);
}
} else {
boost::shared_ptr<IObject> shape = ShapeFactory().createShape(xmlstring);
sample.setShape(shape);
m_sampleObject = &sample.getShape();
g_log.information("Successfully constructed the sample object");
}
}
/**
* Compute a region that defines how the beam illuminates the given sample/can
* @param sample A reference to a sample object holding its shape
* @return A BoundingBox defining the active region
*/
Geometry::BoundingBox
RectangularBeamProfile::defineActiveRegion(const API::Sample &sample) const {
auto sampleBox = sample.getShape().getBoundingBox();
try {
const auto &envBox = sample.getEnvironment().boundingBox();
sampleBox.grow(envBox);
} catch (std::runtime_error &) {
}
// In the beam direction use the maximum sample extent other wise restrict
// the active region to the width/height of beam
const auto &sampleMin(sampleBox.minPoint());
const auto &sampleMax(sampleBox.maxPoint());
V3D minPoint, maxPoint;
minPoint[m_horIdx] = m_min[m_horIdx];
maxPoint[m_horIdx] = m_min[m_horIdx] + m_width;
minPoint[m_upIdx] = m_min[m_upIdx];
maxPoint[m_upIdx] = m_min[m_upIdx] + m_height;
minPoint[m_beamIdx] = sampleMin[m_beamIdx];
maxPoint[m_beamIdx] = sampleMax[m_beamIdx];
return Geometry::BoundingBox(maxPoint.X(), maxPoint.Y(), maxPoint.Z(),
minPoint.X(), minPoint.Y(), minPoint.Z());
}
void vtkDataSetToNonOrthogonalDataSet::execute() {
// Downcast to a vtkUnstructuredGrid
vtkUnstructuredGrid *data = vtkUnstructuredGrid::SafeDownCast(m_dataSet);
if (NULL == data)
{
throw std::runtime_error("VTK dataset does not inherit from vtkPointSet");
}
// Get the workspace from the ADS
ADSWorkspaceProvider<API::IMDWorkspace> workspaceProvider;
API::Workspace_sptr ws = workspaceProvider.fetchWorkspace(m_wsName);
std::string wsType = ws->id();
Geometry::OrientedLattice oLatt;
std::vector<double> wMatArr;
Kernel::Matrix<coord_t> affMat;
// Have to cast since inherited class doesn't provide access to all info
if (boost::algorithm::find_first(wsType, "MDHistoWorkspace")) {
API::IMDHistoWorkspace_const_sptr infoWs =
boost::dynamic_pointer_cast<const API::IMDHistoWorkspace>(ws);
m_boundingBox[0] = infoWs->getDimension(0)->getMinimum();
m_boundingBox[1] = infoWs->getDimension(0)->getMaximum();
m_boundingBox[2] = infoWs->getDimension(1)->getMinimum();
m_boundingBox[3] = infoWs->getDimension(1)->getMaximum();
m_boundingBox[4] = infoWs->getDimension(2)->getMinimum();
m_boundingBox[5] = infoWs->getDimension(2)->getMaximum();
m_numDims = infoWs->getNumDims();
m_coordType = infoWs->getSpecialCoordinateSystem();
if (Kernel::HKL != m_coordType) {
throw std::invalid_argument(
"Cannot create non-orthogonal view for non-HKL coordinates");
}
const API::Sample sample = infoWs->getExperimentInfo(0)->sample();
if (!sample.hasOrientedLattice()) {
throw std::invalid_argument(
"OrientedLattice is not present on workspace");
}
oLatt = sample.getOrientedLattice();
const API::Run run = infoWs->getExperimentInfo(0)->run();
if (!run.hasProperty("W_MATRIX")) {
throw std::invalid_argument("W_MATRIX is not present on workspace");
}
wMatArr = run.getPropertyValueAsType<std::vector<double>>("W_MATRIX");
try {
API::CoordTransform const * transform = infoWs->getTransformToOriginal();
affMat = transform->makeAffineMatrix();
} catch (std::runtime_error &) {
// Create identity matrix of dimension+1
std::size_t nDims = infoWs->getNumDims() + 1;
Kernel::Matrix<coord_t> temp(nDims, nDims, true);
affMat = temp;
}
}
// This is only here to make the unit test run.
if (boost::algorithm::find_first(wsType, "MDEventWorkspace")) {
API::IMDEventWorkspace_const_sptr infoWs =
boost::dynamic_pointer_cast<const API::IMDEventWorkspace>(ws);
m_numDims = infoWs->getNumDims();
m_coordType = infoWs->getSpecialCoordinateSystem();
if (Kernel::HKL != m_coordType) {
throw std::invalid_argument(
"Cannot create non-orthogonal view for non-HKL coordinates");
}
const API::Sample sample = infoWs->getExperimentInfo(0)->sample();
if (!sample.hasOrientedLattice()) {
throw std::invalid_argument(
"OrientedLattice is not present on workspace");
}
oLatt = sample.getOrientedLattice();
const API::Run run = infoWs->getExperimentInfo(0)->run();
if (!run.hasProperty("W_MATRIX")) {
throw std::invalid_argument("W_MATRIX is not present on workspace");
}
wMatArr = run.getPropertyValueAsType<std::vector<double>>("W_MATRIX");
try {
API::CoordTransform const *transform = infoWs->getTransformToOriginal();
affMat = transform->makeAffineMatrix();
} catch (std::runtime_error &) {
// Create identity matrix of dimension+1
std::size_t nDims = infoWs->getNumDims() + 1;
Kernel::Matrix<coord_t> temp(nDims, nDims, true);
affMat = temp;
}
}
Kernel::DblMatrix wTrans(wMatArr);
this->createSkewInformation(oLatt, wTrans, affMat);
// Get the original points
vtkPoints *points = data->GetPoints();
double outPoint[3];
vtkPoints *newPoints = vtkPoints::New();
newPoints->Allocate(points->GetNumberOfPoints());
/// Put together the skew matrix for use
double skew[9];
// Create from the internal skew matrix
std::size_t index = 0;
for (std::size_t i = 0; i < m_skewMat.numRows(); i++) {
for (std::size_t j = 0; j < m_skewMat.numCols(); j++) {
skew[index] = m_skewMat[i][j];
index++;
}
}
for (int i = 0; i < points->GetNumberOfPoints(); i++) {
double *inPoint = points->GetPoint(i);
vtkMatrix3x3::MultiplyPoint(skew, inPoint, outPoint);
newPoints->InsertNextPoint(outPoint);
}
data->SetPoints(newPoints);
this->updateMetaData(data);
}
void vtkDataSetToNonOrthogonalDataSet::execute() {
// Downcast to a vtkPointSet
vtkPointSet *data = vtkPointSet::SafeDownCast(m_dataSet);
if (NULL == data) {
throw std::runtime_error("VTK dataset does not inherit from vtkPointSet");
}
// Get the workspace from the ADS
ADSWorkspaceProvider<API::IMDWorkspace> workspaceProvider;
API::Workspace_sptr ws = workspaceProvider.fetchWorkspace(m_wsName);
std::string wsType = ws->id();
Geometry::OrientedLattice oLatt;
std::vector<double> wMatArr;
Kernel::Matrix<coord_t> affMat;
// Have to cast since inherited class doesn't provide access to all info
if (boost::algorithm::find_first(wsType, "MDHistoWorkspace")) {
API::IMDHistoWorkspace_const_sptr infoWs =
boost::dynamic_pointer_cast<const API::IMDHistoWorkspace>(ws);
m_boundingBox[0] = infoWs->getXDimension()->getMinimum();
m_boundingBox[1] = infoWs->getXDimension()->getMaximum();
m_boundingBox[2] = infoWs->getYDimension()->getMinimum();
m_boundingBox[3] = infoWs->getYDimension()->getMaximum();
m_boundingBox[4] = infoWs->getZDimension()->getMinimum();
m_boundingBox[5] = infoWs->getZDimension()->getMaximum();
m_numDims = infoWs->getNumDims();
m_coordType = infoWs->getSpecialCoordinateSystem();
if (Kernel::HKL != m_coordType) {
throw std::invalid_argument(
"Cannot create non-orthogonal view for non-HKL coordinates");
}
const API::Sample sample = infoWs->getExperimentInfo(0)->sample();
if (!sample.hasOrientedLattice()) {
throw std::invalid_argument(
"OrientedLattice is not present on workspace");
}
oLatt = sample.getOrientedLattice();
const API::Run run = infoWs->getExperimentInfo(0)->run();
if (!run.hasProperty("W_MATRIX")) {
throw std::invalid_argument("W_MATRIX is not present on workspace");
}
wMatArr = run.getPropertyValueAsType<std::vector<double>>("W_MATRIX");
try {
API::CoordTransform const *transform = infoWs->getTransformToOriginal();
affMat = transform->makeAffineMatrix();
} catch (std::runtime_error &) {
// Create identity matrix of dimension+1
std::size_t nDims = infoWs->getNumDims() + 1;
Kernel::Matrix<coord_t> temp(nDims, nDims, true);
affMat = temp;
}
}
// This is only here to make the unit test run.
if (boost::algorithm::find_first(wsType, "MDEventWorkspace")) {
API::IMDEventWorkspace_const_sptr infoWs =
boost::dynamic_pointer_cast<const API::IMDEventWorkspace>(ws);
m_boundingBox[0] = infoWs->getXDimension()->getMinimum();
m_boundingBox[1] = infoWs->getXDimension()->getMaximum();
m_boundingBox[2] = infoWs->getYDimension()->getMinimum();
m_boundingBox[3] = infoWs->getYDimension()->getMaximum();
m_boundingBox[4] = infoWs->getZDimension()->getMinimum();
m_boundingBox[5] = infoWs->getZDimension()->getMaximum();
m_numDims = infoWs->getNumDims();
m_coordType = infoWs->getSpecialCoordinateSystem();
if (Kernel::HKL != m_coordType) {
throw std::invalid_argument(
"Cannot create non-orthogonal view for non-HKL coordinates");
}
const API::Sample sample = infoWs->getExperimentInfo(0)->sample();
if (!sample.hasOrientedLattice()) {
throw std::invalid_argument(
"OrientedLattice is not present on workspace");
}
oLatt = sample.getOrientedLattice();
const API::Run run = infoWs->getExperimentInfo(0)->run();
if (!run.hasProperty("W_MATRIX")) {
throw std::invalid_argument("W_MATRIX is not present on workspace");
}
wMatArr = run.getPropertyValueAsType<std::vector<double>>("W_MATRIX");
try {
API::CoordTransform const *transform = infoWs->getTransformToOriginal();
affMat = transform->makeAffineMatrix();
} catch (std::runtime_error &) {
// Create identity matrix of dimension+1
std::size_t nDims = infoWs->getNumDims() + 1;
Kernel::Matrix<coord_t> temp(nDims, nDims, true);
affMat = temp;
}
}
Kernel::DblMatrix wTrans(wMatArr);
this->createSkewInformation(oLatt, wTrans, affMat);
/// Put together the skew matrix for use
Mantid::coord_t skew[9];
// Create from the internal skew matrix
std::size_t index = 0;
for (std::size_t i = 0; i < m_skewMat.numRows(); i++) {
for (std::size_t j = 0; j < m_skewMat.numCols(); j++) {
skew[index] = static_cast<Mantid::coord_t>(m_skewMat[i][j]);
index++;
}
}
// Get the original points
vtkFloatArray *points =
vtkFloatArray::SafeDownCast(data->GetPoints()->GetData());
if (points == NULL) {
throw std::runtime_error("Failed to cast vtkDataArray to vtkFloatArray.");
} else if (points->GetNumberOfComponents() != 3) {
throw std::runtime_error("points array must have 3 components.");
}
float *end = points->GetPointer(points->GetNumberOfTuples() * 3);
for (float *it = points->GetPointer(0); it < end; std::advance(it, 3)) {
float v1 = it[0];
float v2 = it[1];
float v3 = it[2];
it[0] = v1 * skew[0] + v2 * skew[1] + v3 * skew[2];
it[1] = v1 * skew[3] + v2 * skew[4] + v3 * skew[5];
it[2] = v1 * skew[6] + v2 * skew[7] + v3 * skew[8];
}
this->updateMetaData(data);
}