Examples with ThresholdToSelection ij.plugin.filter.ThresholdToSelection used on opensource projects

Example 6 with ThresholdToSelection

use of ij.plugin.filter.ThresholdToSelection in project imagej1 by imagej.

the class BinaryInterpolator method run.

public void run(ImagePlus image, Roi[] rois) {
    w = image.getWidth();
    h = image.getHeight();
    ImageStack stack = new ImageStack(w, h);
    int firstIndex = -1, lastIndex = -1;
    for (int i = 1; i < rois.length; i++) {
        if (rois[i] != null) {
            firstIndex = (firstIndex == -1) ? i : firstIndex;
            lastIndex = i;
        }
    }
    if (firstIndex == -1) {
        IJ.error("There must be at least one selection in order to interpolate.");
        return;
    }
    for (int i = firstIndex; i <= lastIndex; i++) {
        ByteProcessor bp = new ByteProcessor(w, h);
        if (rois[i] != null) {
            bp.copyBits(rois[i].getMask(), rois[i].getBounds().x, rois[i].getBounds().y, ij.process.Blitter.ADD);
        }
        stack.addSlice("", bp);
    }
    run(stack);
    ImagePlus roiImage = new ImagePlus("bla", stack);
    ThresholdToSelection ts = new ThresholdToSelection();
    ts.setup("", roiImage);
    for (int i = firstIndex; i <= lastIndex; i++) {
        ImageProcessor bp = stack.getProcessor(1);
        stack.deleteSlice(1);
        int threshold = 255;
        bp.setThreshold(threshold, threshold, ImageProcessor.NO_LUT_UPDATE);
        ts.run(bp);
        rois[i] = roiImage.getRoi();
    }
}

Example 7 with ThresholdToSelection

use of ij.plugin.filter.ThresholdToSelection in project TrakEM2 by trakem2.

the class AreaUtils method manyToManyInterpolation.

public static final Area[] manyToManyInterpolation(final Area a1, final Area a2, final int nInterpolates) throws InterruptedException, ExecutionException {
    final Rectangle b = a1.getBounds();
    b.add(a2.getBounds());
    final AffineTransform translate = new AffineTransform(1, 0, 0, 1, -b.x, -b.y);
    final ShapeList<BitType> shapeList1 = new ShapeListCached<BitType>(new int[] { b.width, b.height }, new BitType(false), 32);
    shapeList1.addShape(a1.createTransformedArea(translate), new BitType(true), new int[] { 0 });
    final Image<BitType> img1 = new Image<BitType>(shapeList1, shapeList1.getBackground(), "ShapeListContainer");
    final ShapeList<BitType> shapeList2 = new ShapeListCached<BitType>(new int[] { b.width, b.height }, new BitType(false), 32);
    shapeList2.addShape(a2.createTransformedArea(translate), new BitType(true), new int[] { 0 });
    final Image<BitType> img2 = new Image<BitType>(shapeList2, shapeList2.getBackground(), "ShapeListContainer");
    final float inc = 1.0f / (nInterpolates + 1);
    final BinaryInterpolation2D interpol = new BinaryInterpolation2D(img1, img2, inc);
    if (!interpol.checkInput()) {
        System.out.println("Error: " + interpol.getErrorMessage());
        return null;
    }
    final Area[] as = new Area[nInterpolates];
    final AffineTransform back = new AffineTransform(1, 0, 0, 1, b.x, b.y);
    // TODO parallelize, which needs the means to call process() in parallel too--currently it cannot,
    // the result would get overwritten.
    final ExecutorService exec = Executors.newFixedThreadPool(Math.min(nInterpolates, Runtime.getRuntime().availableProcessors()));
    final ArrayList<Future<Area>> fus = new ArrayList<Future<Area>>();
    try {
        for (int i = 1; i <= nInterpolates; i++) {
            final float weight = 1 - inc * i;
            fus.add(exec.submit(new Callable<Area>() {

                @Override
                public Area call() throws Exception {
                    final Image<BitType> imb = interpol.process(weight);
                    final ImagePlus imp = ImageJFunctions.copyToImagePlus(imb, ImagePlus.GRAY8);
                    // BitType gets copied to 0 and 255 in 8-bit ByteProcessor
                    final ThresholdToSelection ts = new ThresholdToSelection();
                    ts.setup("", imp);
                    final ImageProcessor ip = imp.getProcessor();
                    ip.setThreshold(1, 255, ImageProcessor.NO_LUT_UPDATE);
                    ts.run(ip);
                    final Roi roi = imp.getRoi();
                    return null == roi ? new Area() : M.getArea(roi).createTransformedArea(back);
                }
            }));
        }
        int i = 0;
        for (final Future<Area> fu : fus) {
            as[i++] = fu.get();
        }
    } catch (final Throwable t) {
        IJError.print(t);
    } finally {
        exec.shutdown();
    }
    return as;
}

Example 8 with ThresholdToSelection

use of ij.plugin.filter.ThresholdToSelection in project mcib3d-core by mcib3d.

the class Object3DVoxels method createRoi.

/**
 * @param z Description of the Parameter
 * @return Description of the Return Value
 * @deprecated use Object3D-IJUtils
 * Constructor for the createRoi object
 */
@Override
public Roi createRoi(int z) {
    // IJ.write("create roi " + z);
    int sx = this.getXmax() - this.getXmin() + 1;
    int sy = this.getYmax() - this.getYmin() + 1;
    ByteProcessor mask = new ByteProcessor(sx, sy);
    // object black on white
    // mask.invert();
    draw(mask, z, 255);
    ImagePlus maskPlus = new ImagePlus("mask " + z, mask);
    // maskPlus.show();
    // IJ.run("Create Selection");
    ThresholdToSelection tts = new ThresholdToSelection();
    tts.setup("", maskPlus);
    tts.run(mask);
    maskPlus.updateAndDraw();
    // IJ.write("sel=" + maskPlus.getRoi());
    // maskPlus.hide();
    Roi roi = maskPlus.getRoi();
    Rectangle rect = roi.getBounds();
    rect.x += this.getXmin();
    rect.y += this.getYmin();
    return roi;
}

Example 9 with ThresholdToSelection

use of ij.plugin.filter.ThresholdToSelection in project mcib3d-core by mcib3d.

the class Object3D_IJUtils method createRoi.

public static Roi createRoi(Object3D object3D, int z) {
    // IJ.write("create roi " + z);
    int sx = object3D.getXmax() - object3D.getXmin() + 1;
    int sy = object3D.getYmax() - object3D.getYmin() + 1;
    ByteProcessor mask = new ByteProcessor(sx, sy);
    // object black on white
    // mask.invert();
    draw(object3D, mask, z, 255);
    ImagePlus maskPlus = new ImagePlus("mask " + z, mask);
    // maskPlus.show();
    // IJ.run("Create Selection");
    ThresholdToSelection tts = new ThresholdToSelection();
    tts.setup("", maskPlus);
    tts.run(mask);
    maskPlus.updateAndDraw();
    // IJ.write("sel=" + maskPlus.getRoi());
    // maskPlus.hide();
    Roi roi = maskPlus.getRoi();
    Rectangle rect = roi.getBounds();
    rect.x += object3D.getXmin();
    rect.y += object3D.getYmin();
    return roi;
}

Example 10 with ThresholdToSelection

use of ij.plugin.filter.ThresholdToSelection in project TrakEM2 by trakem2.

the class Patch method getArea.

/**
 * Returns an Area in world coords representing the inside of this Patch. The fully alpha pixels are considered outside.
 */
@Override
public Area getArea() {
    CoordinateTransform ct = null;
    if (hasAlphaMask()) {
        // Read the mask as a ROI for the 0 pixels only and apply the AffineTransform to it:
        ImageProcessor alpha_mask = getAlphaMask();
        if (null == alpha_mask) {
            Utils.log2("Could not retrieve alpha mask for " + this);
        } else {
            if (hasCoordinateTransform()) {
                // must transform it
                ct = getCoordinateTransform();
                final TransformMesh mesh = new TransformMesh(ct, meshResolution, o_width, o_height);
                final TransformMeshMapping mapping = new TransformMeshMapping(mesh);
                // Without interpolation
                alpha_mask = mapping.createMappedImage(alpha_mask);
            // Keep in mind the affine of the Patch already contains the translation specified by the mesh bounds.
            }
            // Threshold all non-zero areas of the mask:
            alpha_mask.setThreshold(1, 255, ImageProcessor.NO_LUT_UPDATE);
            final ImagePlus imp = new ImagePlus("", alpha_mask);
            // TODO replace by our much faster method that scans by line, in AmiraImporter
            final ThresholdToSelection tts = new ThresholdToSelection();
            tts.setup("", imp);
            tts.run(alpha_mask);
            final Roi roi = imp.getRoi();
            if (null == roi) {
                // All pixels in the alpha mask have a value of zero
                return new Area();
            }
            return M.getArea(roi).createTransformedArea(this.at);
        }
    }
    // No alpha mask, or error in retrieving it:
    final int[] x = new int[o_width + o_width + o_height + o_height];
    final int[] y = new int[x.length];
    int next = 0;
    // Top edge:
    for (int i = 0; i <= o_width; i++, next++) {
        // len: o_width + 1
        x[next] = i;
        y[next] = 0;
    }
    // Right edge:
    for (int i = 1; i <= o_height; i++, next++) {
        // len: o_height
        x[next] = o_width;
        y[next] = i;
    }
    // bottom edge:
    for (int i = o_width - 1; i > -1; i--, next++) {
        // len: o_width
        x[next] = i;
        y[next] = o_height;
    }
    // left edge:
    for (int i = o_height - 1; i > 0; i--, next++) {
        // len: o_height -1
        x[next] = 0;
        y[next] = i;
    }
    if (hasCoordinateTransform() && null == ct)
        ct = getCoordinateTransform();
    if (null != ct) {
        final CoordinateTransformList<CoordinateTransform> t = new CoordinateTransformList<CoordinateTransform>();
        t.add(ct);
        final TransformMesh mesh = new TransformMesh(ct, meshResolution, o_width, o_height);
        final Rectangle box = mesh.getBoundingBox();
        final AffineTransform aff = new AffineTransform(this.at);
        // Must correct for the inverse of the mesh translation, because the affine also includes the translation.
        aff.translate(-box.x, -box.y);
        final AffineModel2D affm = new AffineModel2D();
        affm.set(aff);
        t.add(affm);
        /*
			 * WORKS FINE, but for points that fall outside the mesh, they don't get transformed!
			// Do it like Patch does it to generate the mipmap, with a mesh (and all the imprecisions of a mesh):
			final CoordinateTransformList t = new CoordinateTransformList();
			final TransformMesh mesh = new TransformMesh(this.ct, meshResolution, o_width, o_height);
			final AffineTransform aff = new AffineTransform(this.at);
			t.add(mesh);
			final AffineModel2D affm = new AffineModel2D();
			affm.set(aff);
			t.add(affm);
			*/
        final double[] f = new double[] { x[0], y[0] };
        t.applyInPlace(f);
        final Path2D.Float path = new Path2D.Float(Path2D.Float.WIND_EVEN_ODD, x.length + 1);
        path.moveTo(f[0], f[1]);
        for (int i = 1; i < x.length; i++) {
            f[0] = x[i];
            f[1] = y[i];
            t.applyInPlace(f);
            path.lineTo(f[0], f[1]);
        }
        // line to last call to moveTo
        path.closePath();
        return new Area(path);
    } else {
        return new Area(new Polygon(x, y, x.length)).createTransformedArea(this.at);
    }
}