@Test
public void loadLoaderFactoryMetaData() throws Exception {
IMetadata meta = LoaderFactory.getMetadata(testFileFolder + file, null);
assertEquals(meta.getMetaValue("MagicNumber"), "P5");
assertEquals(meta.getMetaValue("Width"), "1024");
assertEquals(meta.getMetaValue("Height"), "1024");
assertEquals(meta.getMetaValue("Maxval"), "65535");
}
private int getAmountOfWork(IConversionContext context) {
int c = 0;
String name = context.getDatasetNames().get(0);
int[] dd = null;
Map<Integer, String> sliceDimensions = context.getSliceDimensions();
for (String path : context.getFilePaths()) {
try {
IMetadata metadata = ServiceHolder.getLoaderService().getMetadata(path, null);
int[] s = metadata.getDataShapes().get(name);
if (s == null) {
try {
s =
ServiceHolder.getLoaderService()
.getData(path, null)
.getLazyDataset(name)
.getShape();
} catch (Exception e) {
logger.warn("Can't get shape to calculate work from");
}
}
Slice[] slices = Slicer.getSliceArrayFromSliceDimensions(sliceDimensions, s);
SliceND slice = new SliceND(s, slices);
int[] nShape = slice.getShape();
if (dd == null) {
dd = Slicer.getDataDimensions(s, context.getSliceDimensions());
Arrays.sort(dd);
}
int n = 1;
for (int i = 0; i < nShape.length; i++) {
if (Arrays.binarySearch(dd, i) < 0) n *= nShape[i];
}
c += n;
} catch (Exception e) {
logger.warn("cannot load metadata for {}, assuming one frame", path);
c++;
}
}
return c;
}
/**
* 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;
}
