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

Example 1 with ThresholdToSelection

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

the class Object3DFuzzy method createRoi.

@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 2 with ThresholdToSelection

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

the class Object3DLabel method createRoi.

/**
 * Constructor for the createRoi object
 *
 * @param z Description of the Parameter
 * @return Description of the Return Value
 */
@Deprecated
public Roi createRoi(int z) {
    // IJ.write("create roi " + z);
    int sx = labelImage.sizeX;
    int sy = labelImage.sizeY;
    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();
    return maskPlus.getRoi();
}

Example 3 with ThresholdToSelection

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

the class RoiEnlarger method shrink.

private static Roi shrink(Roi roi, int n) {
    Rectangle bounds = roi.getBounds();
    int width = bounds.width + 2;
    int height = bounds.height + 2;
    ImageProcessor ip = new ByteProcessor(width, height);
    roi.setLocation(1, 1);
    ip.setColor(255);
    ip.fill(roi);
    roi.setLocation(bounds.x, bounds.y);
    boolean bb = Prefs.blackBackground;
    Prefs.blackBackground = true;
    new EDM().toEDM(ip);
    Prefs.blackBackground = bb;
    ip.setThreshold(n + 1, 255, ImageProcessor.NO_LUT_UPDATE);
    Roi roi2 = (new ThresholdToSelection()).convert(ip);
    if (roi2 == null)
        return roi;
    Rectangle bounds2 = roi2.getBounds();
    if (bounds2.width <= 0 && bounds2.height <= 0)
        return roi;
    roi2.setLocation(bounds.x + bounds2.x - 1, bounds.y + bounds2.y - 1);
    return roi2;
}

Example 4 with ThresholdToSelection

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

the class RoiEnlarger method enlarge.

public static Roi enlarge(Roi roi, double pixels) {
    if (pixels == 0)
        return roi;
    int type = roi.getType();
    int n = (int) Math.round(pixels);
    if (type == Roi.RECTANGLE || type == Roi.OVAL)
        return enlargeRectOrOval(roi, n);
    if (n > 255)
        n = 255;
    if (n < 0)
        return shrink(roi, -n);
    Rectangle bounds = roi.getBounds();
    int width = bounds.width;
    int height = bounds.height;
    width += 2 * n + 2;
    height += 2 * n + 2;
    ImageProcessor ip = new ByteProcessor(width, height);
    ip.invert();
    roi.setLocation(n + 1, n + 1);
    ip.setColor(0);
    ip.fill(roi);
    roi.setLocation(bounds.x, bounds.y);
    boolean bb = Prefs.blackBackground;
    Prefs.blackBackground = true;
    new EDM().toEDM(ip);
    // new ImagePlus("ip", ip).show();
    Prefs.blackBackground = bb;
    ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE);
    Roi roi2 = (new ThresholdToSelection()).convert(ip);
    if (roi2 == null)
        return roi;
    roi2.setLocation(bounds.x - n, bounds.y - n);
    roi2.setStrokeColor(roi.getStrokeColor());
    if (roi.getStroke() != null)
        roi2.setStroke(roi.getStroke());
    return roi2;
}

Example 5 with ThresholdToSelection

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

the class RoiInterpolator method run.

public void run(String arg) {
    RoiManager roiman = RoiManager.getInstance();
    if (roiman == null || roiman.getCount() < 2) {
        IJ.error("RoiInterpolator", "Please populate the ROI Manager with at least two ROIs");
        return;
    }
    Roi[] rois = roiman.getRoisAsArray();
    int xmax = 0;
    int xmin = Integer.MAX_VALUE;
    int ymax = 0;
    int ymin = Integer.MAX_VALUE;
    int zmax = 1;
    int zmin = Integer.MAX_VALUE;
    ArrayList<Integer> templateSlices = new ArrayList<Integer>();
    for (Roi roi : rois) {
        int slice = roiman.getSliceNumber(roi.getName());
        if (!templateSlices.contains(new Integer(slice)))
            templateSlices.add(new Integer(slice));
        if (// ignore non-slice associated ROIs
        slice == 0)
            continue;
        zmin = Math.min(slice, zmin);
        zmax = Math.max(slice, zmax);
        Rectangle bounds = roi.getBounds();
        xmin = Math.min(xmin, bounds.x);
        ymin = Math.min(ymin, bounds.y);
        xmax = Math.max(xmax, bounds.x + bounds.width);
        ymax = Math.max(ymax, bounds.y + bounds.height);
    }
    if (templateSlices.size() < 2) {
        IJ.error("RoiInterpolator", "ROIs are all on the same slice, nothing to interpolate");
        return;
    }
    // create the binary stack
    final int stackW = xmax - xmin + 1;
    final int stackH = ymax - ymin + 1;
    final int nSlices = zmax - zmin + 1;
    ImageStack stack = new ImageStack(stackW, stackH);
    for (int s = 0; s < nSlices; s++) {
        ByteProcessor bp = new ByteProcessor(stackW, stackH);
        bp.setColor(255);
        for (Roi roi : rois) {
            int slice = roiman.getSliceNumber(roi.getName());
            if (slice == zmin + s) {
                Rectangle bounds = roi.getBounds();
                roi.setLocation(bounds.x - xmin, bounds.y - ymin);
                bp.setRoi(roi);
                if (roi.getType() == Roi.RECTANGLE)
                    bp.fill();
                else
                    bp.fill(roi);
            }
        }
        stack.addSlice("" + s, bp);
    }
    // do the binary interpolation
    BinaryInterpolator bi = new BinaryInterpolator();
    bi.run(stack);
    ImagePlus binary = new ImagePlus("interpolated", stack);
    // get the ROIs
    ThresholdToSelection ts = new ThresholdToSelection();
    ts.setup("", binary);
    for (int s = 0; s < nSlices; s++) {
        if (templateSlices.contains(new Integer(s + zmin)))
            continue;
        ImageProcessor bp = stack.getProcessor(s + 1);
        int threshold = 255;
        bp.setThreshold(threshold, threshold, ImageProcessor.NO_LUT_UPDATE);
        Roi roi = ts.convert(bp);
        roi.setPosition(s + zmin);
        Rectangle bounds = roi.getBounds();
        roi.setLocation(bounds.x + xmin, bounds.y + ymin);
        roiman.addRoi(roi);
    }
    for (Roi roi : rois) {
        Rectangle bounds = roi.getBounds();
        roi.setLocation(bounds.x + xmin, bounds.y + ymin);
    }
    roiman.runCommand("sort");
    IJ.showStatus("ROIs interpolated");
}