Examples with Patch ini.trakem2.display.Patch used on opensource projects

Example 6 with Patch

use of ini.trakem2.display.Patch in project TrakEM2 by trakem2.

the class PatchStack method invertLookupTable.

public void invertLookupTable() {
    Loader loader = patch[currentSlice - 1].getProject().getLoader();
    ImagePlus imp = loader.fetchImagePlus(patch[currentSlice - 1]);
    imp.getProcessor().invert();
    Display.repaint(patch[currentSlice - 1].getLayer(), patch[currentSlice - 1], 0);
    // TODO if the database updates are too much, then one could put a "save" button somewhere that shows as "unsaved" (red?) when there are unsaved changes.
    patch[currentSlice - 1].updateInDatabase("tiff_working");
    // just saved
    imp.changes = false;
}

Example 7 with Patch

use of ini.trakem2.display.Patch in project TrakEM2 by trakem2.

the class PatchStack method createColor256Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createColor256Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    Loader loader = patch[0].getProject().getLoader();
    // the montage, in RGB
    patch[0].getProject().getLoader().releaseToFit(4 * patch.length * width * height);
    final ColorProcessor montage = new ColorProcessor(width * patch.length, height);
    for (int i = 0; i < patch.length; i++) {
        montage.insert(this.stack.getProcessor(i + 1), i * width, 0);
    }
    final MedianCut mc = new MedianCut(montage);
    loader.releaseToFit(patch.length * width * height);
    ImageProcessor m2 = mc.convertToByte(256);
    final ImageStack st = new ImageStack(width, height);
    for (int i = 0; i < patch.length; i++) {
        m2.setRoi(i * width, 0, width, height);
        loader.releaseToFit(width * height);
        st.addSlice(null, m2.crop());
    }
    ImagePlus imp = new ImagePlus("color256", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}

Example 8 with Patch

use of ini.trakem2.display.Patch in project TrakEM2 by trakem2.

the class PatchStack method createGray8Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createGray8Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    // compute minimum bounding box
    ImageStack st = new ImageStack(width, height);
    Loader loader = patch[0].getProject().getLoader();
    for (int i = 1; i < patch.length; i++) {
        loader.releaseToFit(width * height);
        st.addSlice(Integer.toString(i), this.stack.getProcessor(i).convertToByte(true));
    }
    ImagePlus imp = new ImagePlus("byte", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}

Example 9 with Patch

use of ini.trakem2.display.Patch in project TrakEM2 by trakem2.

the class Blending method blendLayerWise.

public static final void blendLayerWise(final List<Layer> layers, final boolean respect_current_mask, final Filter<Patch> filter) {
    for (final Layer layer : layers) {
        final List<Patch> patches = layer.getAll(Patch.class);
        final Set<Patch> s = new HashSet<Patch>();
        if (null == filter) {
            s.addAll(patches);
        } else {
            for (final Iterator<Patch> it = patches.iterator(); it.hasNext(); ) {
                final Patch p = it.next();
                if (filter.accept(p))
                    s.add(p);
            }
        }
        blendPatches(s, respect_current_mask);
    }
}

Example 10 with Patch

use of ini.trakem2.display.Patch in project TrakEM2 by trakem2.

the class Blending method blendPatches.

public static final void blendPatches(final Set<Patch> patches, final boolean respect_current_mask) {
    ExecutorService exe = null;
    try {
        if (null == patches || patches.size() < 2)
            return;
        final Layer layer = patches.iterator().next().getLayer();
        for (final Patch p : patches) {
            if (null != p.getCoordinateTransform()) {
                Utils.log("CANNOT blend: at least one image has a coordinate transform.\nBlending of coordinate-transformed images will be enabled in the near future.");
                return;
            }
            if (p.getLayer() != layer) {
                Utils.log("CANNOT blend: all images must belong to the same layer!\n  Otherwise the overlap cannot be computed.");
                return;
            }
        }
        final HashMap<Patch, TransformMesh> meshes = new HashMap<Patch, TransformMesh>();
        for (final Patch p : patches) {
            meshes.put(p, null == p.getCoordinateTransform() ? null : new TransformMesh(p.getCoordinateTransform(), p.getMeshResolution(), p.getOWidth(), p.getOHeight()));
        }
        exe = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
        final List<Future<?>> futures = Collections.synchronizedList(new ArrayList<Future<?>>());
        final List<Future<?>> futures2 = Collections.synchronizedList(new ArrayList<Future<?>>());
        // Cache the indices that determine overlap order within the layer
        final HashMap<Patch, Integer> indices = new HashMap<Patch, Integer>();
        int i = 0;
        for (final Displayable d : layer.getDisplayables()) {
            if (d.getClass() == Patch.class && patches.contains((Patch) d)) {
                indices.put((Patch) d, i);
            }
            i += 1;
        }
        for (final Patch p : patches) {
            if (Thread.currentThread().isInterrupted())
                break;
            futures.add(exe.submit(new Runnable() {

                @Override
                public void run() {
                    final int pLayerIndex = indices.get(p);
                    final Set<Patch> overlapping = new HashSet<Patch>();
                    for (final Patch op : patches) {
                        if (indices.get(op) < pLayerIndex)
                            overlapping.add(op);
                    }
                    if (setBlendingMask(p, overlapping, meshes, respect_current_mask)) {
                        futures2.add(p.updateMipMaps());
                    }
                }
            }, null));
        }
        // join all:
        Utils.waitIfAlive(futures, false);
        Utils.waitIfAlive(futures2, false);
    } catch (final Exception e) {
        IJError.print(e);
    } finally {
        if (null != exe)
            exe.shutdown();
        Display.repaint();
    }
}