/**
* Creates a new data sink for the specified set of pixels.
*
* @param pixels The pixels set the data sink is for.
* @return See above.
*/
public static DataSink createDataSink(PixelsData pixels) {
if (pixels == null) throw new IllegalArgumentException("Pixels cannot be null.");
if (singleton.pixelsSource != null && singleton.pixelsSource.isSame(pixels.getId()))
return singleton.pixelsSource;
registry.getCacheService().clearAllCaches();
int size = getCacheSize();
if (size <= 0) size = 0;
singleton.pixelsSource = DataSink.makeNew(pixels, registry, size);
return singleton.pixelsSource;
}
/**
* Creates a new image with one channel from a source image.
*
* @param info The information about the data to handle.
*/
private void CreateNewImage(ConfigurationInfo info) throws Exception {
PixelsData pixels = image.getDefaultPixels();
int sizeZ = pixels.getSizeZ();
int sizeT = pixels.getSizeT();
int sizeC = pixels.getSizeC();
int sizeX = pixels.getSizeX();
int sizeY = pixels.getSizeY();
long pixelsId = pixels.getId();
if (sizeC <= 1) throw new Exception("The image must have at least 2 channels.");
RawPixelsStorePrx store = null;
// Create a new image.
Map<Integer, byte[]> map = new LinkedHashMap<Integer, byte[]>();
try {
store = connector.getRawPixelsStore();
store.setPixelsId(pixelsId, false);
for (int z = 0; z < sizeZ; z++) {
for (int t = 0; t < sizeT; t++) {
byte[] planeC1 = store.getPlane(z, 0, t);
byte[] planeC2 = store.getPlane(z, 1, t);
byte[] newPlane = new byte[planeC1.length];
for (int i = 0; i < planeC1.length; i++) {
newPlane[i] = (byte) ((planeC1[i] + planeC2[i]) / 2);
}
map.put(linearize(z, t, sizeZ), newPlane);
}
}
} catch (Exception e) {
throw new Exception("Cannot retrieve the plane", e);
} finally {
if (store != null) store.close();
}
// Now we are going to create the new image.
IPixelsPrx proxy = connector.getPixelsService();
List<IObject> l = proxy.getAllEnumerations(PixelsType.class.getName());
Iterator<IObject> i = l.iterator();
PixelsType type = null;
String original = pixels.getPixelType();
while (i.hasNext()) {
PixelsType o = (PixelsType) i.next();
String value = o.getValue().getValue();
if (value.equals(original)) {
type = o;
break;
}
}
if (type == null) throw new Exception("Pixels Type not valid.");
String name = "newImageFrom" + image.getId();
RLong idNew =
proxy.createImage(
sizeX,
sizeY,
sizeZ,
sizeT,
Arrays.asList(0),
type,
name,
"From Image ID: " + image.getId());
if (idNew == null) throw new Exception("New image could not be created.");
ImageData newImage = loadImage(idNew.getValue());
// link the new image and the dataset hosting the source image.
DatasetImageLink link = new DatasetImageLinkI();
link.setParent(new DatasetI(info.getDatasetId(), false));
link.setChild(new ImageI(newImage.getId(), false));
connector.getUpdateService().saveAndReturnObject(link);
// Write the data.
try {
store = connector.getRawPixelsStore();
store.setPixelsId(newImage.getDefaultPixels().getId(), false);
int index = 0;
for (int z = 0; z < sizeZ; z++) {
for (int t = 0; t < sizeT; t++) {
index = linearize(z, t, sizeZ);
store.setPlane(map.get(index), z, 0, t);
}
}
store.save();
System.err.println("image created");
} catch (Exception e) {
throw new Exception("Cannot set the plane", e);
} finally {
if (store != null) store.close();
}
}
