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 void run(String arg0) {
// get list of image stacks
final int[] idList = WindowManager.getIDList();
if (idList == null || idList.length < 2) {
IJ.error("You need at least two open images.");
return;
}
final String[] imgList = new String[idList.length];
for (int i = 0; i < idList.length; ++i)
imgList[i] = WindowManager.getImage(idList[i]).getTitle();
if (defaultImg1 >= imgList.length || defaultImg2 >= imgList.length) {
defaultImg1 = 0;
defaultImg2 = 1;
}
/** The first dialog for choosing the images */
final GenericDialog gd = new GenericDialog("Descriptor based registration");
gd.addChoice("First_image (to register)", imgList, imgList[defaultImg1]);
gd.addChoice("Second_image (reference)", imgList, imgList[defaultImg2]);
if (lastModel1 != null) gd.addCheckbox("Reapply last model", defaultReApply);
gd.addMessage(
"Warning: if images are of RGB or 8-bit color they will be converted to hyperstacks.");
gd.addMessage(
"Please note that the SPIM Registration is based on a publication.\n"
+ "If you use it successfully for your research please be so kind to cite our work:\n"
+ "Preibisch et al., Nature Methods (2010), 7(6):418-419\n");
MultiLineLabel text = (MultiLineLabel) gd.getMessage();
Bead_Registration.addHyperLinkListener(text, paperURL);
gd.showDialog();
if (gd.wasCanceled()) return;
ImagePlus imp1 = WindowManager.getImage(idList[defaultImg1 = gd.getNextChoiceIndex()]);
ImagePlus imp2 = WindowManager.getImage(idList[defaultImg2 = gd.getNextChoiceIndex()]);
boolean reApply = false;
if (lastModel1 != null) {
reApply = gd.getNextBoolean();
defaultReApply = reApply;
}
// if one of the images is rgb or 8-bit color convert them to hyperstack
imp1 = Hyperstack_rearranger.convertToHyperStack(imp1);
imp2 = Hyperstack_rearranger.convertToHyperStack(imp2);
// test if the images are compatible
String error = testRegistrationCompatibility(imp1, imp2);
if (error != null) {
IJ.log(error);
return;
}
// get the parameters
final int dimensionality;
if (imp1.getNSlices() > 1) dimensionality = 3;
else dimensionality = 2;
if (imp1.getNFrames() > 1 || imp2.getNFrames() > 2)
IJ.log(
"WARNING: Images have more than one timepoint, same model as the first timepoint will be applied to all timepoints.");
if (imp1.getNFrames() != imp2.getNFrames())
IJ.log(
"CRITICAL: Images do not have the same amount of timepoints. Will use the number of timepoints of the smaller series.");
// reapply?
if (reApply) {
if (dimensionality < lastDimensionality) {
IJ.log(
"Cannot reapply, cannot apply a "
+ lastModel1.getClass().getSimpleName()
+ " to "
+ dimensionality
+ " data.");
defaultReApply = false;
return;
} else if (dimensionality > lastDimensionality) {
IJ.log(
"WARNING: applying a "
+ lastModel1.getClass().getSimpleName()
+ " to "
+ dimensionality
+ " data.");
}
// just fuse
final DescriptorParameters params = new DescriptorParameters();
params.dimensionality = dimensionality;
params.reApply = true;
params.fuse = 0;
params.setPointsRois = false;
Matching.descriptorBasedRegistration(imp1, imp2, params);
return;
}
// open a second dialog and query the other parameters
final DescriptorParameters params = getParameters(imp1, imp2, dimensionality);
if (params == null) return;
// compute the actual matching
Matching.descriptorBasedRegistration(imp1, imp2, params);
}
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;
}
}