Fiji_OpenCV.java Source code

Introduction

Here is the source code for Fiji_OpenCV.java

Source

/*
 * To the extent possible under law, the Fiji developers have waived
 * all copyright and related or neighboring rights to this tutorial code.
 *
 * See the CC0 1.0 Universal license for details:
 *     http://creativecommons.org/publicdomain/zero/1.0/
 */

import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.plugin.filter.PlugInFilter;
import ij.process.ImageProcessor;
import ij.process.ColorProcessor;

import org.opencv.core.Core;
import org.opencv.core.Mat;
import org.opencv.core.CvType;
import org.opencv.core.Scalar;
import org.opencv.core.MatOfRect;
import org.opencv.core.Point;
import org.opencv.core.Rect;
import org.opencv.objdetect.CascadeClassifier;

/**
 * Fiji-OpenCV
 * 
 * OpenCV Bindings for Fiji
 * 
 * @author The Fiji Team
 */
public class Fiji_OpenCV implements PlugInFilter {
    protected ImagePlus imp;
    protected ImageProcessor ip;

    // image property members
    private int width;
    private int height;

    /**
     * @see ij.plugin.filter.PlugInFilter#setup(java.lang.String, ij.ImagePlus)
     */

    @Override
    public int setup(String arg, ImagePlus imp) {
        if (arg.equals("about")) {
            showAbout();
            return DONE;
        }

        this.imp = imp;
        return DOES_RGB;
    }

    /**
     * @see ij.plugin.filter.PlugInFilter#run(String arg)
     */

    @Override
    public void run(ImageProcessor ip) {
        nu.pattern.OpenCV.loadShared();
        IJ.log("Welcome to OpenCV " + Core.VERSION);

        this.ip = ip;
        // get width and height
        width = ip.getWidth();
        height = ip.getHeight();

        process(ip);
    }

    public void showAbout() {
        IJ.showMessage("Fiji-OpenCV", "OpenCV Bindings for Fiji");
    }

    /**
     * Process an image.
     * 
     * Please provide this method even if {@link ij.plugin.filter.PlugInFilter}
     * does require it; the method
     * {@link ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)} can
     * only handle 2-dimensional data.
     * 
     * If your plugin does not change the pixels in-place, make this method
     * return the results and change the
     * {@link #setup(java.lang.String, ij.ImagePlus)} method to return also the
     * <i>DOES_NOTHING</i> flag.
     * 
     * @param image
     *            the image (possible multi-dimensional)
     */
    public void process(ImagePlus image) {
        // slice numbers start with 1 for historical reasons
        for (int i = 1; i <= image.getStackSize(); i++)
            process(image.getStack().getProcessor(i));
    }

    // Select processing method depending on image type
    public void process(ImageProcessor ip) {
        int type = this.imp.getType();
        if (type == ImagePlus.COLOR_RGB)
            process((int[]) ip.getPixels());
        else {
            throw new RuntimeException("not supported");
        }
    }

    // processing of COLOR_RGB images
    public void process(int[] pixels) {
        int channels = 3;
        byte[] buf = new byte[pixels.length * channels];
        for (int i = 0; i < pixels.length; i++) {
            buf[i * channels] = (byte) (0x000000ff & (pixels[i]));
            buf[i * channels + 1] = (byte) (0x000000ff & (pixels[i] >>> 8));
            buf[i * channels + 2] = (byte) (0x000000ff & (pixels[i] >>> 16));
        }

        Mat image = new Mat(width, height, CvType.CV_8UC3);
        image.put(0, 0, buf);

        // Create a face detector from the cascade file in the resources
        // directory.
        CascadeClassifier faceDetector = new CascadeClassifier(
                getClass().getResource("/opencv/data/haarcascades/haarcascade_frontalface_alt2.xml").getPath());

        // Detect faces in the image.
        // MatOfRect is a special container class for Rect.
        MatOfRect faceDetections = new MatOfRect();
        faceDetector.detectMultiScale(image, faceDetections);

        System.out.println(String.format("Detected %s faces", faceDetections.toArray().length));

        // Draw a bounding box around each face.
        for (Rect rect : faceDetections.toArray()) {
            Core.rectangle(image, new Point(rect.x, rect.y), new Point(rect.x + rect.width, rect.y + rect.height),
                    new Scalar(0, 255, 0));
        }

        image.get(0, 0, buf);
        for (int i = 0; i < pixels.length; i++) {
            pixels[i] = 0x80000000 + ((int) (buf[i * channels + 2]) << 16) + ((int) (buf[i * channels + 1]) << 8)
                    + ((int) (buf[i * channels + 0]));
        }
        this.ip = new ColorProcessor(width, height, pixels);
    }

    /**
     * Main method for debugging.
     * 
     * For debugging, it is convenient to have a method that starts ImageJ,
     * loads an image and calls the plugin, e.g. after setting breakpoints.
     * 
     * @param args
     *            unused
     */
    public static void main(String[] args) {
        // set the plugins.dir property to make the plugin appear in the Plugins
        // menu
        Class<?> clazz = Fiji_OpenCV.class;
        String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
        String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
        System.setProperty("plugins.dir", pluginsDir);

        // start ImageJ
        new ImageJ();

        // open the Lena sample
        ImagePlus image = IJ.openImage("http://imagej.net/images/lena.jpg");
        image.show();

        // run the plugin
        IJ.runPlugIn(clazz.getName(), "");
    }
}