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});
}
/**
* Fetch diffraction metadata, doesn't add it to the IDataset
*
* @param image
* @param altPath alternative for file path if metadata is null or does not hold it
* @param service
* @param statusText returned message (can be null)
* @return diffraction metadata
*/
public static IDiffractionMetadata getDiffractionMetadata(
IDataset image, String altPath, ILoaderService service, String[] statusText) {
// Now always returns IDiffractionMetadata to prevent creation of a new
// metadata object after listeners have been added to the old metadata
// TODO improve this section- it's pretty horrible
IDiffractionMetadata lockedMeta = service.getLockedDiffractionMetaData();
if (image == null) return lockedMeta;
int[] shape = image.getShape();
IMetadata mdImage = null;
try {
mdImage = image.getMetadata();
} catch (Exception e1) {
// do nothing
}
if (lockedMeta != null) {
if (mdImage instanceof IDiffractionMetadata) {
IDiffractionMetadata dmd = (IDiffractionMetadata) mdImage;
if (!dmd.getDiffractionCrystalEnvironment()
.equals(lockedMeta.getDiffractionCrystalEnvironment())
|| !dmd.getDetector2DProperties().equals(lockedMeta.getDetector2DProperties())) {
try {
DiffractionMetadataUtils.copyNewOverOld(lockedMeta, (IDiffractionMetadata) mdImage);
} catch (IllegalArgumentException e) {
if (statusText != null)
statusText[0] = "Locked metadata does not match image dimensions!";
}
}
} else {
// TODO what if the image is rotated?
if (shape[0] == lockedMeta.getDetector2DProperties().getPx()
&& shape[1] == lockedMeta.getDetector2DProperties().getPy()) {
} else {
IDiffractionMetadata clone = lockedMeta.clone();
clone.getDetector2DProperties().setPx(shape[0]);
clone.getDetector2DProperties().setPy(shape[1]);
if (statusText != null)
statusText[0] = "Locked metadata does not match image dimensions!";
}
}
if (statusText != null && statusText[0] == null) {
statusText[0] = "Metadata loaded from locked version";
}
return lockedMeta;
}
// If not see if the trace has diffraction meta data
if (mdImage instanceof IDiffractionMetadata) {
if (statusText != null && statusText[0] == null) {
statusText[0] = "Metadata loaded from image";
}
return (IDiffractionMetadata) mdImage;
}
// Try and get the filename here, it will help later on
String filePath = mdImage == null ? null : mdImage.getFilePath();
if (filePath == null) {
filePath = altPath;
}
if (filePath != null) {
// see if we can read diffraction info from nexus files
NexusDiffractionMetaCreator ndmc = new NexusDiffractionMetaCreator(filePath);
IDiffractionMetadata difMet = ndmc.getDiffractionMetadataFromNexus(shape);
if (difMet != null) {
// TODO comment out
// image.setMetadata(difMet);
if (statusText != null && statusText[0] == null) {
if (ndmc.isCompleteRead()) {
statusText[0] = "Metadata completely loaded from nexus tree";
return difMet;
} else if (ndmc.isPartialRead()) {
statusText[0] = "Required metadata loaded from nexus tree";
return difMet;
} else if (ndmc.anyValuesRead())
statusText[0] = "Incomplete metadata in nexus tree, loading from preferences";
else statusText[0] = "No metadata in nexus tree, metadata loaded from preferences";
}
}
}
// if it is null try and get it from the loader service
if (mdImage == null && filePath != null) {
IMetadata md = null;
try {
md = service.getMetadata(filePath, null);
} catch (Exception e) {
logger.error("Cannot read meta data from part", e);
}
// If it is there and diffraction data return it
if (md instanceof IDiffractionMetadata) {
if (statusText != null && statusText[0] == null) {
statusText[0] = "Metadata loaded from file";
}
return (IDiffractionMetadata) md;
}
}
// if there is no meta or is not nexus or IDiff create default IDiff and put it in the dataset
mdImage = DiffractionDefaultMetadata.getDiffractionMetadata(filePath, shape);
// image.setMetadata(mdImage);
if (statusText != null && statusText[0] == null) {
statusText[0] = "No metadata found. Values loaded from preferences:";
}
return (IDiffractionMetadata) mdImage;
}