Shape Shape::createShape(
ShapeType type,
float size /* = 1.0f */,
float texturing /* = 2.0f */,
int resolution /* = 16 */,
float width /* = 0.0f */,
float height /* = 0.0f */,
float depth /* = 0.0f */)
{
this->setSize(size);
this->setResolution(resolution);
switch (type)
{
case SPHERE:
this->setVertices(createSphere(size, resolution, true));
break;
case PYRAMID:
this->setVertices(createPyramid(size, texturing));
break;
case TETRAHEDRON:
this->setVertices(createTetrahedron(size, texturing));
break;
case CUBOID:
this->setVertices(createCuboid(size, width, height, depth, texturing));
break;
default:
break;
}
this->setMesh(Mesh(this->m_vertices, this->m_vertices.size()));
return *(this);
}
/** Execute the algorithm.
*/
void LoadNXSPE::exec() {
std::string filename = getProperty("Filename");
// quicly check if it's really nxspe
try {
::NeXus::File file(filename);
std::string mainEntry = (*(file.getEntries().begin())).first;
file.openGroup(mainEntry, "NXentry");
file.openData("definition");
if (identiferConfidence(file.getStrData()) < 1) {
throw std::invalid_argument("Not NXSPE");
}
file.close();
} catch (...) {
throw std::invalid_argument("Not NeXus or not NXSPE");
}
// Load the data
::NeXus::File file(filename);
std::string mainEntry = (*(file.getEntries().begin())).first;
file.openGroup(mainEntry, "NXentry");
file.openGroup("NXSPE_info", "NXcollection");
std::map<std::string, std::string> entries = file.getEntries();
std::vector<double> temporary;
double fixed_energy, psi = 0.;
if (!entries.count("fixed_energy")) {
throw std::invalid_argument("fixed_energy field was not found");
}
file.openData("fixed_energy");
file.getData(temporary);
fixed_energy = temporary.at(0);
file.closeData();
if (entries.count("psi")) {
file.openData("psi");
file.getData(temporary);
psi = temporary.at(0);
file.closeData();
}
int kikfscaling = 0;
if (entries.count("ki_over_kf_scaling")) {
file.openData("ki_over_kf_scaling");
std::vector<int> temporaryint;
file.getData(temporaryint);
kikfscaling = temporaryint.at(0);
file.closeData();
}
file.closeGroup(); // NXSPE_Info
file.openGroup("data", "NXdata");
entries = file.getEntries();
if (!entries.count("data")) {
throw std::invalid_argument("data field was not found");
}
file.openData("data");
::NeXus::Info info = file.getInfo();
std::size_t numSpectra = static_cast<std::size_t>(info.dims.at(0));
std::size_t numBins = static_cast<std::size_t>(info.dims.at(1));
std::vector<double> data;
file.getData(data);
file.closeData();
if (!entries.count("error")) {
throw std::invalid_argument("error field was not found");
}
file.openData("error");
std::vector<double> error;
file.getData(error);
file.closeData();
if (!entries.count("energy")) {
throw std::invalid_argument("energy field was not found");
}
file.openData("energy");
std::vector<double> energies;
file.getData(energies);
file.closeData();
if (!entries.count("azimuthal")) {
throw std::invalid_argument("azimuthal field was not found");
}
file.openData("azimuthal");
std::vector<double> azimuthal;
file.getData(azimuthal);
file.closeData();
if (!entries.count("azimuthal_width")) {
throw std::invalid_argument("azimuthal_width field was not found");
}
file.openData("azimuthal_width");
std::vector<double> azimuthal_width;
file.getData(azimuthal_width);
file.closeData();
if (!entries.count("polar")) {
throw std::invalid_argument("polar field was not found");
}
file.openData("polar");
std::vector<double> polar;
file.getData(polar);
file.closeData();
if (!entries.count("polar_width")) {
throw std::invalid_argument("polar_width field was not found");
}
file.openData("polar_width");
std::vector<double> polar_width;
file.getData(polar_width);
file.closeData();
// distance might not have been saved in all NXSPE files
std::vector<double> distance;
if (entries.count("distance")) {
file.openData("distance");
file.getData(distance);
file.closeData();
}
file.closeGroup(); // data group
file.closeGroup(); // Main entry
file.close();
// check if dimensions of the vectors are correct
if ((error.size() != data.size()) || (azimuthal.size() != numSpectra) ||
(azimuthal_width.size() != numSpectra) || (polar.size() != numSpectra) ||
(polar_width.size() != numSpectra) ||
((energies.size() != numBins) && (energies.size() != numBins + 1))) {
throw std::invalid_argument(
"incompatible sizes of fields in the NXSPE file");
}
MatrixWorkspace_sptr outputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(
WorkspaceFactory::Instance().create("Workspace2D", numSpectra,
energies.size(), numBins));
// Need to get hold of the parameter map
outputWS->getAxis(0)->unit() = UnitFactory::Instance().create("DeltaE");
outputWS->setYUnit("SpectraNumber");
// add logs
outputWS->mutableRun().addLogData(
new PropertyWithValue<double>("Ei", fixed_energy));
outputWS->mutableRun().addLogData(new PropertyWithValue<double>("psi", psi));
outputWS->mutableRun().addLogData(new PropertyWithValue<std::string>(
"ki_over_kf_scaling", kikfscaling == 1 ? "true" : "false"));
// Set Goniometer
Geometry::Goniometer gm;
gm.pushAxis("psi", 0, 1, 0, psi);
outputWS->mutableRun().setGoniometer(gm, true);
// generate instrument
Geometry::Instrument_sptr instrument(new Geometry::Instrument("NXSPE"));
outputWS->setInstrument(instrument);
Geometry::ObjComponent *source = new Geometry::ObjComponent("source");
source->setPos(0.0, 0.0, -10.0);
instrument->add(source);
instrument->markAsSource(source);
Geometry::ObjComponent *sample = new Geometry::ObjComponent("sample");
instrument->add(sample);
instrument->markAsSamplePos(sample);
Geometry::Object_const_sptr cuboid(
createCuboid(0.1, 0.1, 0.1)); // FIXME: memory hog on rendering. Also,
// make each detector separate size
for (std::size_t i = 0; i < numSpectra; ++i) {
double r = 1.0;
if (!distance.empty()) {
r = distance.at(i);
}
Kernel::V3D pos;
pos.spherical(r, polar.at(i), azimuthal.at(i));
Geometry::Detector *det =
new Geometry::Detector("pixel", static_cast<int>(i + 1), sample);
det->setPos(pos);
det->setShape(cuboid);
instrument->add(det);
instrument->markAsDetector(det);
}
Geometry::ParameterMap &pmap = outputWS->instrumentParameters();
std::vector<double>::iterator itdata = data.begin(), iterror = error.begin(),
itdataend, iterrorend;
API::Progress prog = API::Progress(this, 0.0, 0.9, numSpectra);
for (std::size_t i = 0; i < numSpectra; ++i) {
itdataend = itdata + numBins;
iterrorend = iterror + numBins;
outputWS->dataX(i) = energies;
if ((!boost::math::isfinite(*itdata)) || (*itdata <= -1e10)) // masked bin
{
outputWS->dataY(i) = std::vector<double>(numBins, 0);
outputWS->dataE(i) = std::vector<double>(numBins, 0);
pmap.addBool(outputWS->getDetector(i)->getComponentID(), "masked", true);
} else {
outputWS->dataY(i) = std::vector<double>(itdata, itdataend);
outputWS->dataE(i) = std::vector<double>(iterror, iterrorend);
}
itdata = (itdataend);
iterror = (iterrorend);
prog.report();
}
setProperty("OutputWorkspace", outputWS);
}
