public ImagePlusLocalizablePlaneCursor(
final ImagePlusContainer<T, ?> container, final Image<T> image, final T type) {
super(container, image, type);
this.width = image.getDimension(0);
this.height = image.getDimension(1);
this.depth = image.getDimension(2);
}
public AbstractSortedGrayLevelIterator(final Image<T> image) {
this.image = image;
this.position = image.createPositionArray();
this.n = image.getNumPixels();
this.maxIdx = this.n - 1;
this.dimensions = image.getDimensions();
createInternalCursor();
this.sortedLinIdx = getLinearIndexArraySortedByGrayLevel();
reset();
}
/**
* Constructor
*
* @param image The intensity image to be labeled
* @param scale the minimum distance between maxima of objects. Less technically, this should be
* the diameter of the smallest object.
* @param sigma1 the standard deviation for the larger smoothing. The difference between sigma1
* and sigma2 should be roughly the width of the desired edge in the DoG image. A larger
* difference will obscure small, faint edges.
* @param sigma2 the standard deviation for the smaller smoothing. This should be on the order of
* the largest insignificant feature in the image.
* @param names - an iterator that generates names of type L for the labels. The iterator will
* waste the last name taken on the background label. You can use
* AllConnectedComponents.getIntegerNames() as your name generator if you don't care about
* names.
*/
public GradientWatershed(
Image<T> input, double[] scale, double[] sigma1, double[] sigma2, Iterator<L> names) {
this.input = input;
this.scale = scale;
this.sigma1 = sigma1;
this.sigma2 = sigma2;
structuringElement = AllConnectedComponents.getStructuringElement(input.getNumDimensions());
this.names = names;
labelingFactory =
new ImageFactory<LabelingType<L>>(new LabelingType<L>(), input.getContainerFactory());
}
protected <C extends Comparable<C> & Type<C>> C max(final Image<C> image) {
C max = image.createType();
// create a cursor for the image (the order does not matter)
Cursor<C> cursor = image.createCursor();
// initialize max with the first image value
max.set(cursor.next());
for (C type : cursor) {
if (type.compareTo(max) > 0) max.set(type);
}
return max;
}
public ContainerImpl(final ContainerFactory factory, int[] dim) {
this.numDimensions = dim.length;
this.numPixels = getNumPixels(dim);
this.dim = dim.clone();
this.factory = factory;
this.id = Image.createUniqueId();
}
protected void computeAdvanced(final long startPos, final long loopSize) {
final LocalizableByDimCursor<S> cursorIn = image.createLocalizableByDimCursor();
final LocalizableCursor<T> cursorOut = output.createLocalizableCursor();
// move to the starting position of the current thread
cursorOut.fwd(startPos);
// do as many pixels as wanted by this thread
for (long j = 0; j < loopSize; ++j) {
cursorOut.fwd();
cursorIn.setPosition(cursorOut);
converter.convert(cursorIn.getType(), cursorOut.getType());
}
cursorIn.close();
cursorOut.close();
}
/** Obtains planar access instance backing the given image, if any. */
@SuppressWarnings("unchecked")
public static PlanarAccess<ArrayDataAccess<?>> getPlanarAccess(Image<?> im) {
PlanarAccess<ArrayDataAccess<?>> planarAccess = null;
final Container<?> container = im.getContainer();
if (container instanceof PlanarAccess<?>) {
planarAccess = (PlanarAccess<ArrayDataAccess<?>>) container;
}
return planarAccess;
}
@Override
public boolean process() {
final long startTime = System.currentTimeMillis();
final long imageSize = image.getNumPixels();
final AtomicInteger ai = new AtomicInteger(0);
final Thread[] threads = SimpleMultiThreading.newThreads(getNumThreads());
final Vector<Chunk> threadChunks = SimpleMultiThreading.divideIntoChunks(imageSize, numThreads);
final boolean isCompatible =
image.getContainer().compareStorageContainerCompatibility(output.getContainer());
for (int ithread = 0; ithread < threads.length; ++ithread)
threads[ithread] =
new Thread(
new Runnable() {
public void run() {
// Thread ID
final int myNumber = ai.getAndIncrement();
// get chunk of pixels to process
final Chunk myChunk = threadChunks.get(myNumber);
// check if all container types are comparable so that we can use simple iterators
// we assume transivity here
if (isCompatible) {
// we can simply use iterators
computeSimple(myChunk.getStartPosition(), myChunk.getLoopSize());
} else {
// we need a combination of Localizable and LocalizableByDim
computeAdvanced(myChunk.getStartPosition(), myChunk.getLoopSize());
}
}
});
SimpleMultiThreading.startAndJoin(threads);
processingTime = System.currentTimeMillis() - startTime;
return true;
}
@Override
public boolean checkInput() {
if (errorMessage.length() > 0) {
return false;
} else if (image == null) {
errorMessage = "ImageCalculator: [Image<S> image1] is null.";
return false;
} else if (output == null) {
errorMessage = "ImageCalculator: [Image<T> output] is null.";
return false;
} else if (converter == null) {
errorMessage = "ImageCalculator: [Converter<S,T>] is null.";
return false;
} else if (!image.getContainer().compareStorageContainerDimensions(output.getContainer())) {
errorMessage =
"ImageCalculator: Images have different dimensions, not supported:"
+ " Image: "
+ Util.printCoordinates(image.getDimensions())
+ " Output: "
+ Util.printCoordinates(output.getDimensions());
return false;
} else return true;
}
@Override
public boolean process() {
floatImage = null;
if (output == null) {
output = new Labeling<L>(labelingFactory, input.getDimensions(), null);
} else {
/*
* Initialize the output to all background
*/
LocalizableCursor<LabelingType<L>> c = output.createLocalizableCursor();
List<L> background = c.getType().intern(new ArrayList<L>());
for (LabelingType<L> t : c) {
t.setLabeling(background);
}
c.close();
}
/*
* Get the smoothed image.
*/
Image<FloatType> kernel =
FourierConvolution.createGaussianKernel(input.getContainerFactory(), scale);
FourierConvolution<FloatType, FloatType> convolution =
new FourierConvolution<FloatType, FloatType>(getFloatImage(), kernel);
if (!convolution.process()) return false;
Image<FloatType> smoothed = convolution.getResult();
/*
* Find the local maxima and label them individually.
*/
PickImagePeaks<FloatType> peakPicker = new PickImagePeaks<FloatType>(smoothed);
peakPicker.setSuppression(scale);
peakPicker.process();
Labeling<L> seeds = output.createNewLabeling();
LocalizableByDimCursor<LabelingType<L>> lc = seeds.createLocalizableByDimCursor();
LocalizableByDimCursor<FloatType> imageCursor = smoothed.createLocalizableByDimCursor();
int[] dimensions = input.getDimensions();
for (int[] peak : peakPicker.getPeakList()) {
if (!filterPeak(imageCursor, peak, dimensions, false)) continue;
lc.setPosition(peak);
lc.getType().setLabel(names.next());
}
imageCursor.close();
/*
* Find the local minima and label them all the same.
*/
List<L> background = lc.getType().intern(names.next());
Converter<FloatType, FloatType> invert =
new Converter<FloatType, FloatType>() {
@Override
public void convert(FloatType input, FloatType output) {
output.setReal(-input.getRealFloat());
}
};
ImageConverter<FloatType, FloatType> invSmoothed =
new ImageConverter<FloatType, FloatType>(smoothed, smoothed, invert);
invSmoothed.process();
peakPicker = new PickImagePeaks<FloatType>(smoothed);
peakPicker.setSuppression(scale);
peakPicker.process();
imageCursor = smoothed.createLocalizableByDimCursor();
for (int[] peak : peakPicker.getPeakList()) {
if (!filterPeak(imageCursor, peak, dimensions, true)) continue;
lc.setPosition(peak);
lc.getType().setLabeling(background);
}
lc.close();
imageCursor.close();
smoothed = null;
invSmoothed = null;
Image<FloatType> gradientImage = getGradientImage();
if (gradientImage == null) return false;
/*
* Run the seeded watershed on the image.
*/
Watershed.seededWatershed(gradientImage, seeds, structuringElement, output);
return true;
}
protected ImageFactory<FloatType> getFloatFactory() {
if (floatFactory == null) {
floatFactory = new ImageFactory<FloatType>(new FloatType(), input.getContainerFactory());
}
return floatFactory;
}
@Override
public boolean checkInput() {
if (error_message.length() > 0) return false;
if (input == null) {
error_message = "The input image is null.";
return false;
}
if (scale == null) {
error_message = "The scale is null.";
return false;
}
if (sigma1 == null) {
error_message = "The first smoothing standard deviation (sigma1) is null.";
return false;
}
if (sigma2 == null) {
error_message = "The second smoothing standard deviation (sigma2) is null.";
return false;
}
if (structuringElement == null) {
error_message = "The structuring element is null.";
return false;
}
if (names == null) {
error_message = "The names iterator is null.";
}
if (!checkDimensions(scale)) {
error_message = "The dimensions of the scale do not match those of the image";
return false;
}
if (!checkDimensions(sigma1)) {
error_message = "The dimensions of sigma1 do not match those of the image";
return false;
}
if (!checkDimensions(sigma2)) {
error_message = "The dimensions of sigma2 do not match those of the image";
return false;
}
for (int[] coord : structuringElement) {
if (coord == null) {
error_message = "One of the coordinates of the structuring element is null.";
return false;
}
if (!checkDimensions(coord)) {
error_message =
"The dimensions of one of the coordinates of the structuring element does not match those of the image.";
return false;
}
}
if (wantsToQuantize && (numQuanta < 2)) {
error_message =
String.format(
"The number of quanta is %d, but must be at least 2 (and ideally > 20).", numQuanta);
return false;
}
for (int i = 0; i < sigma1.length; i++) {
if (sigma1[i] <= sigma2[i]) {
error_message =
String.format(
"All values of sigma1 should be greater than sigma2. For dimension %d, sigma1=%f, sigma2=%f",
i, sigma1[i], sigma2[i]);
return false;
}
}
if (output != null) {
int[] dimensions = output.getDimensions();
if (!checkDimensions(dimensions)) {
error_message = "The labeling container does not have the correct number of dimensions";
return false;
}
for (int i = 0; i < dimensions.length; i++) {
if (dimensions[i] != input.getDimension(i)) {
error_message =
String.format(
"The labeling container is not the same size as the image: dimension %d, labeling = %d, image = %d",
i, dimensions[i], input.getDimension(i));
return false;
}
}
}
return true;
}
protected boolean checkDimensions(double[] array) {
return array.length == input.getNumDimensions();
}
/**
* Fuse one slice/volume (one channel)
*
* @param output - same the type of the ImagePlus input
* @param input - FloatType, because of Interpolation that needs to be done
* @param transform - the transformation
*/
public static <T extends RealType<T>> void fuseChannel(
final Image<T> output,
final Image<FloatType> input,
final float[] offset,
final InvertibleCoordinateTransform transform,
final InterpolatorFactory<FloatType> factory) {
final int dims = output.getNumDimensions();
long imageSize = output.getDimension(0);
for (int d = 1; d < output.getNumDimensions(); ++d) imageSize *= output.getDimension(d);
// run multithreaded
final AtomicInteger ai = new AtomicInteger(0);
final Thread[] threads = SimpleMultiThreading.newThreads();
final Vector<Chunk> threadChunks =
SimpleMultiThreading.divideIntoChunks(imageSize, threads.length);
for (int ithread = 0; ithread < threads.length; ++ithread)
threads[ithread] =
new Thread(
new Runnable() {
public void run() {
// Thread ID
final int myNumber = ai.getAndIncrement();
// get chunk of pixels to process
final Chunk myChunk = threadChunks.get(myNumber);
final long startPos = myChunk.getStartPosition();
final long loopSize = myChunk.getLoopSize();
final LocalizableCursor<T> out = output.createLocalizableCursor();
final Interpolator<FloatType> in = input.createInterpolator(factory);
final float[] tmp = new float[input.getNumDimensions()];
try {
// move to the starting position of the current thread
out.fwd(startPos);
// do as many pixels as wanted by this thread
for (long j = 0; j < loopSize; ++j) {
out.fwd();
for (int d = 0; d < dims; ++d) tmp[d] = out.getPosition(d) + offset[d];
transform.applyInverseInPlace(tmp);
in.setPosition(tmp);
out.getType().setReal(in.getType().get());
}
} catch (NoninvertibleModelException e) {
IJ.log("Cannot invert model, qutting.");
return;
}
}
});
SimpleMultiThreading.startAndJoin(threads);
/*
final LocalizableCursor<T> out = output.createLocalizableCursor();
final Interpolator<FloatType> in = input.createInterpolator( factory );
final float[] tmp = new float[ input.getNumDimensions() ];
try
{
while ( out.hasNext() )
{
out.fwd();
for ( int d = 0; d < dims; ++d )
tmp[ d ] = out.getPosition( d ) + offset[ d ];
transform.applyInverseInPlace( tmp );
in.setPosition( tmp );
out.getType().setReal( in.getType().get() );
}
}
catch (NoninvertibleModelException e)
{
IJ.log( "Cannot invert model, qutting." );
return;
}
*/
}
public ImageConverter(
final Image<S> image, final ImageFactory<T> factory, final Converter<S, T> converter) {
this(image, createImageFromFactory(factory, image.getDimensions()), converter);
}
public SortedGrayLevelIteratorFactory(Image<T> image) {
isArrayContainer = Array.class.isInstance(image.getContainer());
}
@Override
public void getDimensions(int[] position) {
image.getDimensions(position);
}
@Override
public int[] getPosition() {
int[] position = image.createPositionArray();
getPosition(position);
return position;
}
public static <T extends RealType<T>> CompositeImage createOverlay(
final T targetType,
final ArrayList<ImagePlus> images,
final ArrayList<InvertibleBoundable> models,
final int dimensionality,
final int timepoint,
final InterpolatorFactory<FloatType> factory) {
final int numImages = images.size();
// the size of the new image
final int[] size = new int[dimensionality];
// the offset relative to the output image which starts with its local coordinates (0,0,0)
final float[] offset = new float[dimensionality];
// estimate the boundaries of the output image and the offset for fusion (negative coordinates
// after transform have to be shifted to 0,0,0)
estimateBounds(offset, size, images, models, dimensionality);
// for output
final ImageFactory<T> f = new ImageFactory<T>(targetType, new ImagePlusContainerFactory());
// the composite
final ImageStack stack = new ImageStack(size[0], size[1]);
int numChannels = 0;
// loop over all images
for (int i = 0; i < images.size(); ++i) {
final ImagePlus imp = images.get(i);
// loop over all channels
for (int c = 1; c <= imp.getNChannels(); ++c) {
final Image<T> out = f.createImage(size);
fuseChannel(
out,
ImageJFunctions.convertFloat(Hyperstack_rearranger.getImageChunk(imp, c, timepoint)),
offset,
models.get(i + (timepoint - 1) * numImages),
factory);
try {
final ImagePlus outImp = ((ImagePlusContainer<?, ?>) out.getContainer()).getImagePlus();
for (int z = 1; z <= out.getDimension(2); ++z)
stack.addSlice(imp.getTitle(), outImp.getStack().getProcessor(z));
} catch (ImgLibException e) {
IJ.log("Output image has no ImageJ type: " + e);
}
// count all channels
++numChannels;
}
}
// convertXYZCT ...
ImagePlus result =
new ImagePlus(
"overlay " + images.get(0).getTitle() + " ... " + images.get(numImages - 1).getTitle(),
stack);
// numchannels, z-slices, timepoints (but right now the order is still XYZCT)
if (dimensionality == 3) {
result.setDimensions(size[2], numChannels, 1);
result = OverlayFusion.switchZCinXYCZT(result);
} else {
result.setDimensions(numChannels, 1, 1);
}
return new CompositeImage(result, CompositeImage.COMPOSITE);
}
@Override
public int[] createPositionArray() {
return image.createPositionArray();
}
@Override
public boolean process() {
// 0. Prepare new dimensions
int downSamplingFactor = settings.downSamplingFactor;
int[] dimensions = new int[img.getNumDimensions()];
int[] dsarr = new int[img.getNumDimensions()];
float[] dwnCalibration = new float[img.getNumDimensions()];
for (int i = 0; i < 2; i++) {
dimensions[i] = img.getDimension(i) / downSamplingFactor;
dsarr[i] = downSamplingFactor;
dwnCalibration[i] = calibration[i] * downSamplingFactor;
}
if (img.getNumDimensions() > 2) {
// 3D
float zratio = calibration[2] / calibration[0]; // Z spacing is how much bigger
int zdownsampling = (int) (downSamplingFactor / zratio); // temper z downsampling
zdownsampling = Math.max(1, zdownsampling); // but at least 1
dimensions[2] = img.getDimension(2) / zdownsampling;
dsarr[2] = zdownsampling;
dwnCalibration[2] = calibration[2] * zdownsampling;
}
// 1. Downsample the image
Image<T> downsampled = img.createNewImage(dimensions);
LocalizableCursor<T> dwnCursor = downsampled.createLocalizableCursor();
LocalizableByDimCursor<T> srcCursor = img.createLocalizableByDimCursor();
int[] pos = dwnCursor.createPositionArray();
while (dwnCursor.hasNext()) {
dwnCursor.fwd();
dwnCursor.getPosition(pos);
// Scale up position
for (int i = 0; i < pos.length; i++) {
pos[i] = pos[i] * dsarr[i];
}
// Pass it to source cursor
srcCursor.setPosition(pos);
// Copy pixel data
dwnCursor.getType().set(srcCursor.getType());
}
dwnCursor.close();
srcCursor.close();
// 2. Segment downsampled image
// 2.1. Create settings object
LogSegmenterSettings logSettings = new LogSegmenterSettings();
logSettings.expectedRadius = settings.expectedRadius;
logSettings.threshold = settings.threshold;
logSettings.doSubPixelLocalization = true;
;
logSettings.useMedianFilter = settings.useMedianFilter;
// 2.2 Instantiate segmenter
LogSegmenter<T> segmenter = new LogSegmenter<T>();
segmenter.setTarget(downsampled, dwnCalibration, logSettings);
// 2.3 Execute segmentation
if (!segmenter.checkInput() || !segmenter.process()) {
errorMessage = BASE_ERROR_MESSAGE + segmenter.getErrorMessage();
return false;
}
// 3. Benefits
spots = segmenter.getResult();
return true;
}
@Override
public int getNumDimensions() {
return image.getNumDimensions();
}
/**
* Return a difference of gaussian image that measures the gradient at a scale defined by the two
* sigmas of the gaussians.
*
* @param image
* @param sigma1
* @param sigma2
* @return
*/
public Image<FloatType> getGradientImage() {
/*
* Create the DoG kernel.
*/
double[][] kernels1d1 = new double[input.getNumDimensions()][];
double[][] kernels1d2 = new double[input.getNumDimensions()][];
int[] kernelDimensions = input.createPositionArray();
int[] offset = input.createPositionArray();
for (int i = 0; i < kernels1d1.length; i++) {
kernels1d1[i] = Util.createGaussianKernel1DDouble(sigma1[i], true);
kernels1d2[i] = Util.createGaussianKernel1DDouble(sigma2[i], true);
kernelDimensions[i] = kernels1d1[i].length;
offset[i] = (kernels1d1[i].length - kernels1d2[i].length) / 2;
}
Image<FloatType> kernel = getFloatFactory().createImage(kernelDimensions);
LocalizableCursor<FloatType> kc = kernel.createLocalizableCursor();
int[] position = input.createPositionArray();
for (FloatType t : kc) {
kc.getPosition(position);
double value1 = 1;
double value2 = 1;
for (int i = 0; i < kernels1d1.length; i++) {
value1 *= kernels1d1[i][position[i]];
int position2 = position[i] - offset[i];
if ((position2 >= 0) && (position2 < kernels1d2[i].length)) {
value2 *= kernels1d2[i][position2];
} else {
value2 = 0;
}
}
t.setReal(value1 - value2);
}
kc.close();
/*
* Apply the kernel to the image.
*/
FourierConvolution<FloatType, FloatType> convolution =
new FourierConvolution<FloatType, FloatType>(getFloatImage(), kernel);
if (!convolution.process()) return null;
Image<FloatType> result = convolution.getResult();
/*
* Quantize the image.
*/
ComputeMinMax<FloatType> computeMinMax = new ComputeMinMax<FloatType>(result);
computeMinMax.process();
final float min = computeMinMax.getMin().get();
final float max = computeMinMax.getMax().get();
if (max == min) return result;
ImageConverter<FloatType, FloatType> quantizer =
new ImageConverter<FloatType, FloatType>(
result,
result.getImageFactory(),
new Converter<FloatType, FloatType>() {
@Override
public void convert(FloatType input, FloatType output) {
float value = (input.get() - min) / (max - min);
value = Math.round(value * 100);
output.set(value);
}
});
quantizer.process();
return quantizer.getResult();
}
/**
* Reads in an imglib {@link Image} from the given initialized {@link IFormatReader}, using the
* given {@link ImageFactory}.
*/
public <T extends RealType<T>> Image<T> openImage(IFormatReader r, ImageFactory<T> imageFactory)
throws FormatException, IOException {
final String[] dimTypes = getDimTypes(r);
final int[] dimLengths = getDimLengths(r);
// TEMP - make suffix out of dimension types, until imglib supports them
final String id = r.getCurrentFile();
final File idFile = new File(id);
String name = idFile.exists() ? idFile.getName() : id;
name = encodeName(name, dimTypes);
// create image object
final Image<T> img = imageFactory.createImage(dimLengths, name);
// set calibration of the image
img.setCalibration(getCalibration(r, dimLengths));
// TODO - create better container types; either:
// 1) an array container type using one byte array per plane
// 2) as #1, but with an IFormatReader reference reading planes on demand
// 3) as PlanarContainer, but with an IFormatReader reference
// reading planes on demand
// PlanarContainer is useful for efficient access to pixels in ImageJ
// (e.g., getPixels)
// #1 is useful for efficient Bio-Formats import, and useful for tools
// needing byte arrays (e.g., BufferedImage Java3D texturing by reference)
// #2 is useful for efficient memory use for tools wanting matching
// primitive arrays (e.g., virtual stacks in ImageJ)
// #3 is useful for efficient memory use
// get container
final PlanarAccess<?> planarAccess = getPlanarAccess(img);
final T inputType = makeType(r.getPixelType());
final T outputType = imageFactory.createType();
final boolean compatibleTypes = outputType.getClass().isAssignableFrom(inputType.getClass());
final long startTime = System.currentTimeMillis();
// populate planes
final int planeCount = r.getImageCount();
if (planarAccess == null || !compatibleTypes) {
// use cursor to populate planes
// NB: This solution is general and works regardless of container,
// but at the expense of performance both now and later.
final LocalizablePlaneCursor<T> cursor = img.createLocalizablePlaneCursor();
byte[] plane = null;
for (int no = 0; no < planeCount; no++) {
notifyListeners(
new StatusEvent(no, planeCount, "Reading plane " + (no + 1) + "/" + planeCount));
if (plane == null) plane = r.openBytes(no);
else r.openBytes(no, plane);
populatePlane(r, no, plane, cursor);
}
cursor.close();
} else {
// populate the values directly using PlanarAccess interface;
// e.g., to a PlanarContainer
byte[] plane = null;
for (int no = 0; no < planeCount; no++) {
notifyListeners(
new StatusEvent(no, planeCount, "Reading plane " + (no + 1) + "/" + planeCount));
if (plane == null) plane = r.openBytes(no);
else r.openBytes(no, plane);
populatePlane(r, no, plane, planarAccess);
}
}
r.close();
final long endTime = System.currentTimeMillis();
final float time = (endTime - startTime) / 1000f;
notifyListeners(
new StatusEvent(
planeCount, planeCount, id + ": read " + planeCount + " planes in " + time + "s"));
return img;
}
public static <T extends RealType<T>> ImagePlus createReRegisteredSeries(
final T targetType,
final ImagePlus imp,
final ArrayList<InvertibleBoundable> models,
final int dimensionality,
final String directory) {
final int numImages = imp.getNFrames();
// the size of the new image
final int[] size = new int[dimensionality];
// the offset relative to the output image which starts with its local coordinates (0,0,0)
final float[] offset = new float[dimensionality];
final int[][] imgSizes = new int[numImages][dimensionality];
for (int i = 0; i < numImages; ++i) {
imgSizes[i][0] = imp.getWidth();
imgSizes[i][1] = imp.getHeight();
if (dimensionality == 3) imgSizes[i][2] = imp.getNSlices();
}
// estimate the boundaries of the output image and the offset for fusion (negative coordinates
// after transform have to be shifted to 0,0,0)
estimateBounds(offset, size, imgSizes, models, dimensionality);
// use the same size as the first image, this is a little bit ad-hoc
if (useSizeOfFirstImage) {
for (int d = 0; d < dimensionality; ++d) {
size[d] = imgSizes[0][d];
offset[d] = 0;
}
}
// for output
final ImageFactory<T> f = new ImageFactory<T>(targetType, new ImagePlusContainerFactory());
// the composite
final ImageStack stack = new ImageStack(size[0], size[1]);
for (int t = 1; t <= numImages; ++t) {
for (int c = 1; c <= imp.getNChannels(); ++c) {
final Image<T> out = f.createImage(size);
if (useNearestNeighborInterpolation)
fuseChannel(
out,
ImageJFunctions.convertFloat(Hyperstack_rearranger.getImageChunk(imp, c, t)),
offset,
models.get(t - 1),
new NearestNeighborInterpolatorFactory<FloatType>(
new OutOfBoundsStrategyValueFactory<FloatType>()));
else
fuseChannel(
out,
ImageJFunctions.convertFloat(Hyperstack_rearranger.getImageChunk(imp, c, t)),
offset,
models.get(t - 1),
new LinearInterpolatorFactory<FloatType>(
new OutOfBoundsStrategyValueFactory<FloatType>()));
try {
final ImagePlus outImp = ((ImagePlusContainer<?, ?>) out.getContainer()).getImagePlus();
if (directory == null) {
// fuse
for (int z = 1; z <= out.getDimension(2); ++z)
stack.addSlice(imp.getTitle(), outImp.getStack().getProcessor(z));
} else {
// write to disk
for (int z = 1; z <= out.getDimension(2); ++z) {
final ImagePlus tmp =
new ImagePlus(
"img_t"
+ lz(t, numImages)
+ "_z"
+ lz(z, out.getDimension(2))
+ "_c"
+ lz(c, imp.getNChannels()),
outImp.getStack().getProcessor(z));
final FileSaver fs = new FileSaver(tmp);
fs.saveAsTiff(new File(directory, tmp.getTitle()).getAbsolutePath());
tmp.close();
}
out.close();
outImp.close();
}
} catch (ImgLibException e) {
IJ.log("Output image has no ImageJ type: " + e);
}
}
}
if (directory != null) return null;
// convertXYZCT ...
ImagePlus result = new ImagePlus("registered " + imp.getTitle(), stack);
// numchannels, z-slices, timepoints (but right now the order is still XYZCT)
if (dimensionality == 3) {
result.setDimensions(size[2], imp.getNChannels(), imp.getNFrames());
result = OverlayFusion.switchZCinXYCZT(result);
return new CompositeImage(result, CompositeImage.COMPOSITE);
} else {
// IJ.log( "ch: " + imp.getNChannels() );
// IJ.log( "slices: " + imp.getNSlices() );
// IJ.log( "frames: " + imp.getNFrames() );
result.setDimensions(imp.getNChannels(), 1, imp.getNFrames());
if (imp.getNChannels() > 1) return new CompositeImage(result, CompositeImage.COMPOSITE);
else return result;
}
}
@Override
public Container<T> getStorageContainer() {
return image.getContainer();
}