@Test
public void testStackedFile() throws ScanFileHolderException {
ILazyDataset image =
new TIFFImageLoader(TestFileFolder + "untitled1020.TIF").loadFile().getLazyDataset(0);
Assert.assertArrayEquals("Shape not equal", new int[] {3, 2048, 2048}, image.getShape());
IDataset d = image.getSlice(new Slice(1));
Assert.assertArrayEquals("Shape not equal", new int[] {1, 2048, 2048}, d.getShape());
Assert.assertEquals("Type is int32", Integer.class, d.elementClass());
d = image.getSlice(new Slice(1, 3), new Slice(1));
Assert.assertArrayEquals("Shape not equal", new int[] {2, 1, 2048}, d.getShape());
Assert.assertEquals("Type is int32", Integer.class, d.elementClass());
d = image.getSlice(new Slice(1, 3), new Slice(null, null, 4), new Slice(2, 25));
Assert.assertArrayEquals("Shape not equal", new int[] {2, 512, 23}, d.getShape());
Assert.assertEquals("Type is int32", Integer.class, d.elementClass());
}
@Override
public StringDatasetBase setSlice(final Object obj, final IndexIterator siter) {
if (obj instanceof IDataset) {
final IDataset ds = (IDataset) obj;
final int[] oshape = ds.getShape();
if (!areShapesCompatible(siter.getShape(), oshape)) {
throw new IllegalArgumentException(
String.format(
"Input dataset is not compatible with slice: %s cf %s",
Arrays.toString(oshape), Arrays.toString(siter.getShape())));
}
if (ds instanceof Dataset) {
final Dataset ads = (Dataset) ds;
final IndexIterator oiter = ads.getIterator();
while (siter.hasNext() && oiter.hasNext())
data[siter.index] = ads.getStringAbs(oiter.index); // GET_ELEMENT_WITH_CAST
} else {
final IndexIterator oiter = new PositionIterator(oshape);
final int[] pos = oiter.getPos();
while (siter.hasNext() && oiter.hasNext())
data[siter.index] = ds.getString(pos); // PRIM_TYPE
}
} else {
try {
String v = obj.toString(); // PRIM_TYPE // FROM_OBJECT
while (siter.hasNext()) data[siter.index] = v;
} catch (IllegalArgumentException e) {
throw new IllegalArgumentException("Object for setting slice is not a dataset or number");
}
}
setDirty();
return this;
}
@Override
public List<Dataset> integrate(IDataset dataset) {
// Generate radial and azimuthal look-up arrays as required
// TODO test shape of axis array
if (radialArray == null) {
generateRadialArray(dataset.getShape(), false);
}
if (azimuthalArray == null) {
generateMinMaxAzimuthalArray(
qSpace.getDetectorProperties().getBeamCentreCoords(), dataset.getShape());
}
Dataset mt = mask;
if (mask != null && !Arrays.equals(mask.getShape(), dataset.getShape()))
throw new IllegalArgumentException("Mask shape does not match dataset shape");
List<Dataset> result = new ArrayList<Dataset>();
if (binEdges == null) {
binEdges = calculateBins(radialArray, mt, radialRange, nbins);
binsChi = calculateBins(azimuthalArray, mt, azimuthalRange, nBinsChi);
}
final double[] edgesQ = binEdges.getData();
final double loQ = edgesQ[0];
final double hiQ = edgesQ[nbins];
final double spanQ = (hiQ - loQ) / nbins;
final double[] edgesChi = binsChi.getData();
final double loChi = edgesChi[0];
final double hiChi = edgesChi[nBinsChi];
final double spanChi = (hiChi - loChi) / nBinsChi;
FloatDataset histo = new FloatDataset(nBinsChi, nbins);
FloatDataset intensity = new FloatDataset(nBinsChi, nbins);
// final double[] h = histo.getData();
// final double[] in = intensity.getData();
// if (spanQ <= 0) {
// h[0] = ds.getSize();
// result.add(histo);
// result.add(bins);
// continue;
// }
Dataset a = DatasetUtils.convertToDataset(radialArray[0]);
Dataset b = DatasetUtils.convertToDataset(dataset);
// PositionIterator iter = b.getPositionIterator();
//
// int[] pos = iter.getPos();
// int[] posStop = pos.clone();
IndexIterator iter = a.getIterator();
while (iter.hasNext()) {
// posStop[0] = pos[0]+2;
// posStop[1] = pos[1]+2;
// Dataset qrange = a.getSlice(pos, posStop, null);
// Dataset chirange = azimuthalArray.getSlice(pos, posStop, null);
if (mt != null && !mt.getElementBooleanAbs(iter.index)) continue;
final double qMax = radialArray[1].getElementDoubleAbs(iter.index);
final double qMin = radialArray[0].getElementDoubleAbs(iter.index);
final double chiMax = azimuthalArray[1].getElementDoubleAbs(iter.index);
final double chiMin = azimuthalArray[0].getElementDoubleAbs(iter.index);
final double sig = b.getElementDoubleAbs(iter.index);
if (qMax < loQ || qMin > hiQ) {
continue;
}
if (chiMax < loChi || chiMin > hiChi) {
continue;
}
// losing something here? is flooring (int cast best?)
double minBinExactQ = (qMin - loQ) / spanQ;
double maxBinExactQ = (qMax - loQ) / spanQ;
int minBinQ = (int) minBinExactQ;
int maxBinQ = (int) maxBinExactQ;
double minBinExactChi = (chiMin - loChi) / spanChi;
double maxBinExactChi = (chiMax - loChi) / spanChi;
int minBinChi = (int) minBinExactChi;
int maxBinChi = (int) maxBinExactChi;
// FIXME potentially may need to deal with azimuthal arrays with discontinuities (+180/-180
// degress etc)
double iPerPixel = 1 / ((maxBinExactQ - minBinExactQ) * (maxBinExactChi - minBinExactChi));
double minFracQ = 1 - (minBinExactQ - minBinQ);
double maxFracQ = maxBinExactQ - maxBinQ;
double minFracChi = 1 - (minBinExactChi - minBinChi);
double maxFracChi = maxBinExactChi - maxBinChi;
for (int i = minBinQ; i <= maxBinQ; i++) {
if (i < 0 || i >= binEdges.getSize() - 1) continue;
for (int j = minBinChi; j <= maxBinChi; j++) {
if (j < 0 || j >= binsChi.getSize() - 1) continue;
int[] setPos = new int[] {j, i};
double val = histo.get(setPos);
double modify = 1;
if (i == minBinQ && minBinQ != maxBinQ) modify *= minFracQ;
if (i == maxBinQ && minBinQ != maxBinQ) modify *= maxFracQ;
if (i == minBinChi && minBinChi != maxBinChi) modify *= minFracChi;
if (i == maxBinChi && minBinChi != maxBinChi) modify *= maxFracChi;
histo.set(val + iPerPixel * modify, setPos);
double inVal = intensity.get(setPos);
intensity.set(inVal + sig * iPerPixel * modify, setPos);
}
}
}
processAndAddToResult(intensity, histo, result, radialRange, dataset.getName());
return result;
}
/**
* 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;
}