protected OperationData process(IDataset input, IMonitor monitor) throws OperationException {
double d = (2 * Math.PI) / model.getqValue();
double p = (2 * Math.PI) / (model.getqValue() + model.getqDelta());
double m = (2 * Math.PI) / (model.getqValue() - model.getqDelta());
IDiffractionMetadata dm = getFirstDiffractionMetadata(input);
if (dm == null) throw new OperationException(this, "No calibration information!");
IParametricROI[] inOut = new IParametricROI[2];
IParametricROI conic =
(IParametricROI)
DSpacing.conicFromDSpacing(
dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), d);
inOut[0] =
(IParametricROI)
DSpacing.conicFromDSpacing(
dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), m);
inOut[1] =
(IParametricROI)
DSpacing.conicFromDSpacing(
dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), p);
PolylineROI points =
PeakFittingEllipseFinder.findPointsOnConic(
DatasetUtils.convertToDataset(input), null, conic, inOut, 256, null);
double rms = -1;
double[] semi = new double[2];
double[] point = new double[2];
double ang = 0;
if (points != null && points.getNumberOfPoints() < 3) {
EllipticalFitROI efroi = PowderRingsUtils.fitAndTrimOutliers(null, points, 2, false);
rms = efroi.getRMS();
semi = efroi.getSemiAxes();
point = efroi.getPoint();
ang = efroi.getAngleDegrees();
}
Dataset r = DatasetFactory.createFromObject(new double[] {rms});
r.setName("rms");
Dataset ax = DatasetFactory.createFromObject(semi);
ax.setName("semi-axes");
Dataset po = DatasetFactory.createFromObject(point);
po.setName("centre");
Dataset a = DatasetFactory.createFromObject(new double[] {ang});
a.setName("angle");
return new OperationData(input, new Serializable[] {r, ax, po, a});
}
@Override
protected OperationData process(IDataset input, IMonitor monitor) {
double theta = 0;
try {
theta = ScanMetadata.getTheta(input);
} catch (Exception e) {
}
NormalDistribution beamfootprint =
new NormalDistribution(
0, (1e-3 * model.getBeamHeight() / 2 * Math.sqrt(2 * Math.log(2) - 0.5)));
double areaCorrection =
2
* (beamfootprint.cumulativeProbability(
(model.getFootprint()
* Math.sin((theta + model.getAngularFudgeFactor()) * Math.PI / 180))));
Dataset output = DatasetUtils.cast(input, Dataset.FLOAT64);
output = Maths.multiply(input, areaCorrection);
Dataset outputSum =
DatasetFactory.createFromObject((DatasetUtils.cast(output, Dataset.FLOAT64)).sum());
return new OperationData(output, outputSum);
}
private void populateDataBasedFunctions(
final Map<String, Serializable> data, IFunction function) {
if (function instanceof CompositeFunction) {
CompositeFunction compositeFunction = (CompositeFunction) function;
for (IFunction func : compositeFunction.getFunctions()) {
populateDataBasedFunctions(data, func);
}
}
if (function instanceof IDataBasedFunction) {
IDataBasedFunction dbFunction = (IDataBasedFunction) function;
String sdName = seedDataName.getExpression();
String sdAxis = seedAxisName.getExpression();
Dataset seedDataset = DatasetFactory.createFromObject(data.get(sdName)).clone();
Dataset seedAxisDataset = DatasetFactory.createFromObject(data.get(sdAxis)).clone();
dbFunction.setData(seedAxisDataset, seedDataset);
}
}
@Override
protected DataMessageComponent getTransformedMessage(List<DataMessageComponent> cache)
throws DataMessageException {
// get the data out of the message, name of the item should be specified
final Map<String, Serializable> data = MessageUtils.getList(cache);
Map<String, AFunction> functions;
try {
functions = MessageUtils.getFunctions(cache);
} catch (Exception e) {
throw new DataMessageException(
"Could not parse the Funcitons comming into the FunctionToDatsetActor", null, e);
}
// prepare the output message
DataMessageComponent result = MessageUtils.copy(cache);
// get the required datasets
String dataset = datasetName.getExpression();
String xAxis = xAxisName.getExpression();
String functionString = functionName.getExpression();
// Get the actual objects
Dataset xAxisDS = DatasetFactory.createFromObject(data.get(xAxis)).clone();
AFunction function = functions.get(functionString);
populateDataBasedFunctions(data, function);
// process the data
// TODO Add Null Protection here.
DoubleDataset createdDS = function.calculateValues(xAxisDS);
createdDS.setName(dataset);
// Add it to the result
result.addList(createdDS.getName(), createdDS);
return result;
}
@Test
public void testWriteNX() {
String filename = "/tmp/sample.nxs";
NexusFileBuilder builder = new DefaultNexusFileBuilder(filename);
NXsample nxample = sample.getNXsample(builder);
int nCompo = sample.getPhases().size();
assertEquals("NX name incorrect", sample.getName(), nxample.getNameScalar());
assertEquals(
"NX description incorrect",
sample.getName() + ", " + sample.getComposition() + ", " + sample.getShapeName(),
nxample.getDescriptionScalar());
assertEquals(
"NX component names incorrect",
DatasetFactory.createFromList(
sample.getPhases().stream().map(a -> a.getName()).collect(Collectors.toList())),
nxample.getComponent());
assertEquals(
"NX component formulae incorrect",
DatasetFactory.createFromObject(
sample
.getPhases()
.stream()
.map(a -> a.getComposition().getHallNotation(false))
.collect(Collectors.toList()),
nCompo,
1),
nxample.getChemical_formula());
assertEquals(
"NX formula weight incorrect",
DatasetFactory.createFromList(
sample
.getPhases()
.stream()
.map(a -> a.getComposition().getFormulaMass())
.collect(Collectors.toList())),
nxample.getDataset("chemical_formula_weight"));
// unit cell parameters...
assertEquals(
"NX unit cell volume incorrect",
DatasetFactory.createFromList(
sample
.getPhases()
.stream()
.map(a -> a.getUnitCellVolume())
.collect(Collectors.toList())),
nxample.getUnit_cell_volume());
assertEquals(
"NX unit cell class incorrect",
DatasetFactory.createFromList(
sample
.getPhases()
.stream()
.map(a -> a.getCrystalSystem().getName())
.collect(Collectors.toList())),
nxample.getUnit_cell_class());
assertEquals(
"NX unit cell space group incorrect",
DatasetFactory.createFromList(
sample
.getPhases()
.stream()
.map(a -> a.getSpaceGroup().getNumber() + ": " + a.getSpaceGroup().getName())
.collect(Collectors.toList())),
nxample.getUnit_cell_group());
assertEquals(
"NX theoretical densities incorrect",
DatasetFactory.createFromList(
sample.getPhases().stream().map(a -> a.getDensity()).collect(Collectors.toList())),
nxample.getDataset("theoretical_density"));
}
