void LoadDNSSCD::updateProperties(API::Run &run,
std::map<std::string, T> &metadata,
std::string time) {
typename std::map<std::string, T>::iterator it = metadata.begin();
while (it != metadata.end()) {
TimeSeriesProperty<T> *timeSeries(nullptr);
std::string name(it->first);
std::string units;
// std::regex does not work for rhel7, thus boost
boost::regex reg("([-_a-zA-Z]+)\\[(.*)]");
boost::smatch match;
if (boost::regex_search(name, match, reg) && match.size() > 2) {
std::string new_name(match.str(1));
units.assign(match.str(2));
name = new_name;
}
if (run.hasProperty(name)) {
timeSeries = dynamic_cast<TimeSeriesProperty<T> *>(run.getLogData(name));
if (!timeSeries)
throw std::invalid_argument(
"Log '" + name +
"' already exists but the values are a different type.");
} else {
timeSeries = new TimeSeriesProperty<T>(name);
if (!units.empty())
timeSeries->setUnits(units);
run.addProperty(timeSeries);
}
timeSeries->addValue(time, it->second);
++it;
}
}
/**
* Get a value from one of a set of logs.
* @param run
* @param propName
* @return
*/
double PDDetermineCharacterizations::getLogValue(API::Run &run,
const std::string &propName) {
std::vector<std::string> names = getProperty(propName);
std::string label = "frequency";
if (propName == WL_PROP_NAME)
label = "wavelength";
std::unordered_set<std::string> validUnits;
if (propName == WL_PROP_NAME) {
validUnits.insert("Angstrom");
validUnits.insert("A");
} else {
validUnits.insert("Hz");
}
for (auto &name : names) {
if (run.hasProperty(name)) {
const std::string units = run.getProperty(name)->units();
if (validUnits.find(units) != validUnits.end()) {
double value = run.getLogAsSingleValue(name);
if (value == 0.) {
std::stringstream msg;
msg << "'" << name << "' has a mean value of zero " << units;
g_log.information(msg.str());
} else {
std::stringstream msg;
msg << "Found " << label << " in log '" << name
<< "' with mean value " << value << " " << units;
g_log.information(msg.str());
return value;
}
} else {
std::stringstream msg;
msg << "When looking at " << name << " log encountered unknown units '"
<< units << "' for " << label << ":" << units;
g_log.warning(msg.str());
}
}
}
g_log.warning("Failed to determine " + label);
return 0.;
}
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);
}
