Java Code Examples for ij.plugin.frame.RoiManager#add()

@Override
public void run() {

    // Converters
    ImagePlusMatConverter ic = new ImagePlusMatConverter();
    opencv_core.Mat m = ic.convert(imp, Mat.class);
    MatListOvalRoiConverter cc = new MatListOvalRoiConverter();

    Mat gray = new Mat();
    opencv_imgproc.cvtColor(m, gray, opencv_imgproc.COLOR_BGR2GRAY);

    Mat circles = new Mat();
    opencv_imgproc.HoughCircles(gray, circles, opencv_imgproc.CV_HOUGH_GRADIENT, 1.2, 100);

    ArrayList<OvalRoi> or = new ArrayList<OvalRoi>();
    or = cc.convert(circles, or.getClass());

    RoiManager rm = new RoiManager();

    for (int i = 0; i < or.size(); i++) {
        rm.add(imp, or.get(i), i);
    }

}
 

@Override
public void run() {
    //Converters
    RectRoiConverter rc = new RectRoiConverter();
    opencv_core.Mat img2 = ImagePlusMatConverter.toMat(imp, 8); // also does RGB to Gray automatically

    // Detect the faces and store them as an array of rectangles
    opencv_core.RectVector rv = detectFaces(img2);

    // Add rectangles to ROI Manager
    RoiManager rm = new RoiManager();
    rm.setVisible(true);
    for (int i = 0; i < rv.size(); i++) {
        Roi r = rc.convert(rv.get(i), Roi.class);
        rm.add(imp, r, 0);
    }
    
    //Show all ROI
    rm.runCommand("Show All");

}
 

@Override
public void run() {
    // Get the ROI and check that it is a polygon
    PolygonRoi r = (PolygonRoi) imp.getRoi();

    if (r == null) {
        IJ.error("Select first a polygon ROI");
        return;
    }

    // Converter
    PolygonRoiMatConverter pc = new PolygonRoiMatConverter();
    MatPointRoiConverter mpc = new MatPointRoiConverter();

    Mat m = pc.convert(r, Mat.class);
    Mat convexHull = new Mat();
    opencv_imgproc.convexHull(m, convexHull);

    PolygonRoi pr = mpc.convert(convexHull, PolygonRoi.class);

    RoiManager rm = new RoiManager();
    rm.add(imp, r, 0);
    rm.add(imp, pr, 1);

}
 

@Override
  public void run() {
 
// Do line detection
ArrayList<Line> linesIJ = HoughLines(imp, min_length, step_line, min_theta, max_theta, step_theta);

// Add lines to RoiManager
      RoiManager rm = new RoiManager();
      rm.setVisible(true);

      for (int i = 0; i < linesIJ.size(); i++) {
          rm.add(imp, linesIJ.get(i), i);
       }
}
 

/**
 * Adds the specified paths to the list of ROI of the image plus.
 * 
 * @param target The ImagePlus that will be associated with ROIS
 * @param geodDiams the list of paths
 */
public void createPathRois(ImagePlus target, Map<Integer, GeodesicDiameter.Result> geodDiams)
{
	// get instance of ROI Manager
	RoiManager manager = RoiManager.getRoiManager();
	Calibration calib = target.getCalibration();
	
	// add each path to the ROI Manager
	int index = 0;
	for (GeodesicDiameter.Result result : geodDiams.values())
	{
	    manager.add(target, createPathRoi(result.path, calib), index++);
	}
}
 

@Override
public void run() {
    ImagePlus original = (ImagePlus) imp.clone();

    Roi r = imp.getRoi();

    if (r == null) {
        IJ.error("Select a rectangle first");
        return;
    }

    if (r.isArea() && (r.getType() == Roi.RECTANGLE)) {

        // Crop the selection to be the template
        IJ.run(imp, "Crop", "");

        //Converters
        ImagePlusMatConverter ic = new ImagePlusMatConverter();
        RectRoiConverter rc = new RectRoiConverter();

        // Convert the ImageJ images to OpenCV images
        opencv_core.Mat matching = ic.convert(original, Mat.class);
        opencv_core.Mat template = ic.convert(imp, Mat.class);

        opencv_core.Mat gray = new opencv_core.Mat();
        opencv_imgproc.cvtColor(matching, gray, opencv_imgproc.COLOR_BGR2GRAY);
        opencv_imgproc.cvtColor(template, template, opencv_imgproc.COLOR_BGR2GRAY);

        opencv_core.Mat results = new opencv_core.Mat();

        // Matching and normalisation
        matchTemplate(gray, template, results, TM_CCOEFF_NORMED);
        normalize(results, results, 0, 1, NORM_MINMAX, -1, new opencv_core.Mat());

        DoublePointer minVal = new DoublePointer();
        DoublePointer maxVal= new DoublePointer();
        opencv_core.Point minLoc = new opencv_core.Point();
        opencv_core.Point maxLoc = new opencv_core.Point();
        opencv_core.Point matchLoc;

        minMaxLoc(results, minVal, maxVal, minLoc, maxLoc, new opencv_core.Mat());

        ArrayList<opencv_core.Point> locations = obtainLocations(results, 0.99, template.cols(), template.rows());
        RoiManager rm = new RoiManager();
        rm.setVisible(true);

        opencv_core.Rect solution;
        Roi solutionIJ;
        opencv_core.Point p;
        for (int i = 0; i < locations.size(); i++) {
            p = locations.get(i);
            solution = new opencv_core.Rect(p.x(), p.y(), template.cols(), template.rows());
            solutionIJ = rc.convert(solution, Roi.class);
            rm.add(original, solutionIJ, i);

        }

        imp.changes = false;
        imp.close();
        original.show();

    } else {
        IJ.error("Select a rectangle");
    }
}
 

@Override
public void run() {
    
    // Converters
    ImagePlusMatConverter ic = new ImagePlusMatConverter();

    opencv_core.Mat m = ic.convert(imp,opencv_core.Mat.class);
    MatVectorListPolygonRoiConverter pc = new MatVectorListPolygonRoiConverter();
    
    
    opencv_core.Mat gray = new opencv_core.Mat();
    opencv_imgproc.cvtColor(m,gray,opencv_imgproc.COLOR_BGR2GRAY);
    
    MatVector contours = new opencv_core.MatVector();
    
    opencv_imgproc.findContours(gray,contours,opencv_imgproc.RETR_LIST,opencv_imgproc.CHAIN_APPROX_SIMPLE);
    
    ArrayList<PolygonRoi> contoursROI = new ArrayList<PolygonRoi>();
    contoursROI= pc.convert(contours,contoursROI.getClass());
    
     // Add rectangles to ROI Manager
    RoiManager rm = new RoiManager();
    rm.setVisible(true);
    for (PolygonRoi contoursROI1 : contoursROI) {
        rm.add(imp, contoursROI1, 0);
    }
    
    
    

}