/**
* Called before any fit/simulation is started to allow caching of
* frequently used parameters
* @param workspace :: The MD that will be used for the fit
*/
void TobyFitResolutionModel::preprocess(
const API::IMDEventWorkspace_const_sptr &workspace) {
Kernel::Timer timer;
// Fill the observation cache
auto iterator = workspace->createIterator();
g_log.debug() << "Starting preprocessing loop\n";
do {
const size_t nevents = iterator->getNumEvents();
for (size_t i = 0; i < nevents; ++i) {
uint16_t innerRunIndex = iterator->getInnerRunIndex(i);
detid_t detID = iterator->getInnerDetectorID(i);
const auto key = std::make_pair(innerRunIndex, detID);
if (m_exptCache.find(key) == m_exptCache.end()) {
API::ExperimentInfo_const_sptr expt =
workspace->getExperimentInfo(innerRunIndex);
m_exptCache.insert(
std::make_pair(key, new CachedExperimentInfo(*expt, detID)));
}
}
} while (iterator->next());
g_log.debug() << "Done preprocessing loop:" << timer.elapsed()
<< " seconds\n";
delete iterator;
}
/** Get detectors' counts
* @brief GetSpiceDataRawCountsFromMD::getDetCounts
* @param mdws
* @param runnumber :: run number of the detectors having for exporting; -1 for
* all run numbers
* @param detid :: detector ID for the detectors for exporting; -1 for all
* detectors
* @param vecX :: x-values as 2theta position of detectors to be exported;
* @param vecY :: raw detector's counts
* @param formX :: flag to set up vecX
*/
void GetSpiceDataRawCountsFromMD::getDetCounts(
API::IMDEventWorkspace_const_sptr mdws, const int &runnumber,
const int &detid, std::vector<double> &vecX, std::vector<double> &vecY,
bool formX) {
// Get sample and source position
if (mdws->getNumExperimentInfo() == 0)
throw std::runtime_error(
"There is no ExperimentInfo object that has been set to "
"input MDEventWorkspace!");
V3D samplepos;
V3D sourcepos;
if (formX) {
ExperimentInfo_const_sptr expinfo = mdws->getExperimentInfo(0);
Geometry::IComponent_const_sptr sample =
expinfo->getInstrument()->getSample();
samplepos = sample->getPos();
g_log.debug() << "Sample position is " << samplepos.X() << ", "
<< samplepos.Y() << ", " << samplepos.Z() << "\n";
Geometry::IComponent_const_sptr source =
expinfo->getInstrument()->getSource();
sourcepos = source->getPos();
g_log.debug() << "Source position is " << sourcepos.X() << ","
<< sourcepos.Y() << ", " << sourcepos.Z() << "\n";
vecX.clear();
}
vecY.clear();
// Go through all events to find out their positions
IMDIterator *mditer = mdws->createIterator();
bool scancell = true;
size_t nextindex = 1;
while (scancell) {
// get the number of events of this cell
size_t numev2 = mditer->getNumEvents();
g_log.debug() << "MDWorkspace " << mdws->name() << " Cell " << nextindex - 1
<< ": Number of events = " << numev2
<< " Does NEXT cell exist = " << mditer->next() << "\n";
// loop over all the events in current cell
for (size_t iev = 0; iev < numev2; ++iev) {
// filter out the events with uninterrested run numbers and detid
// runnumber/detid < 0 indicates that all run number or all detectors will
// be taken
int thisrunnumber = mditer->getInnerRunIndex(iev);
if (runnumber >= 0 && thisrunnumber != runnumber)
continue;
int thisdetid = mditer->getInnerDetectorID(iev);
if (detid >= 0 && thisdetid != detid)
continue;
// get detector position for 2theta
if (formX) {
double tempx = mditer->getInnerPosition(iev, 0);
double tempy = mditer->getInnerPosition(iev, 1);
double tempz = mditer->getInnerPosition(iev, 2);
Kernel::V3D detpos(tempx, tempy, tempz);
Kernel::V3D v_det_sample = detpos - samplepos;
Kernel::V3D v_sample_src = samplepos - sourcepos;
double twotheta = v_det_sample.angle(v_sample_src) / M_PI * 180.;
vecX.push_back(twotheta);
}
// add new value to vecPair
double signal = mditer->getInnerSignal(iev);
vecY.push_back(signal);
} // ENDFOR (iev)
// Advance to next cell
if (mditer->next()) {
// advance to next cell
mditer->jumpTo(nextindex);
++nextindex;
} else {
// break the loop
scancell = false;
}
} // ENDOF(while)
delete (mditer);
return;
}
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);
}