001/*******************************************************************************
002 * This software is provided as a supplement to the authors' textbooks on digital
003 * image processing published by Springer-Verlag in various languages and editions.
004 * Permission to use and distribute this software is granted under the BSD 2-Clause
005 * "Simplified" License (see http://opensource.org/licenses/BSD-2-Clause).
006 * Copyright (c) 2006-2023 Wilhelm Burger, Mark J. Burge. All rights reserved.
007 * Visit https://imagingbook.com for additional details.
008 ******************************************************************************/
009package Ch08_Binary_Regions;
010
011import ij.IJ;
012import ij.ImagePlus;
013import ij.gui.GenericDialog;
014import ij.plugin.filter.PlugInFilter;
015import ij.process.ByteProcessor;
016import ij.process.ImageProcessor;
017import imagingbook.common.geometry.basic.Pnt2d;
018import imagingbook.common.geometry.moments.FlusserMoments;
019import imagingbook.common.ij.DialogUtils;
020import imagingbook.common.ij.overlay.ColoredStroke;
021import imagingbook.common.ij.overlay.ShapeOverlayAdapter;
022import imagingbook.common.regions.BinaryRegion;
023import imagingbook.common.regions.BinaryRegionSegmentation;
024import imagingbook.common.regions.Contour;
025import imagingbook.common.regions.RegionContourSegmentation;
026import imagingbook.core.jdoc.JavaDocHelp;
027import imagingbook.sampleimages.kimia.KimiaCollage;
028
029import java.awt.Color;
030import java.awt.Font;
031import java.util.Comparator;
032import java.util.List;
033
034import static imagingbook.common.ij.IjUtils.noCurrentImage;
035
036/**
037 * <p>
038 * This ImageJ plugin calculates and lists the 11 scale and rotation invariant Flusser moments for the binary regions
039 * contained in the given image. See Sec. 8.6.5 of [1] for additional details. The plugin expects a binary image (with 0
040 * background and non-zero foreground). A sample image is automatically loaded if no other image is currently open.
041 * </p>
042 * <p>
043 * [1] W. Burger, M.J. Burge, <em>Digital Image Processing &ndash; An Algorithmic Introduction</em>, 3rd ed, Springer
044 * (2022).
045 * </p>
046 *
047 * @author WB
048 * @version 2022/12/28
049 */
050public class Flusser_Moments_From_Binary_Regions implements PlugInFilter, JavaDocHelp {
051
052    private static int MIN_REGION_SIZE = 100;
053    private static int MAX_REGION_COUNT = 30;
054    private static boolean MARK_OUTER_CONTOURS = true;
055
056    private static final Font MarkerFont = new Font(Font.SANS_SERIF, Font.BOLD, 12);
057    private static final Color MarkerColor = Color.blue;
058
059    private ImagePlus im;
060
061    /**
062     * Constructor, asks to open a predefined sample image if no other image is currently open.
063     */
064    public Flusser_Moments_From_Binary_Regions() {
065        if (noCurrentImage()) {
066            DialogUtils.askForSampleImage(KimiaCollage.ShapeCollage1);  // Kimia216.bird02
067        }
068    }
069
070    public int setup(String arg0, ImagePlus im) {
071        this.im = im;
072        return DOES_8G + DOES_8C;
073    }
074
075    public void run(ImageProcessor ip) {
076        if (!runDialog())
077            return;
078
079        BinaryRegionSegmentation segmenter = new RegionContourSegmentation((ByteProcessor) ip);
080        List<BinaryRegion> regions = segmenter.getRegions(true);
081        if (regions.isEmpty()) {
082            IJ.log("No regions found!");
083            return;
084        }
085
086        IJ.log("Regions found: " + regions.size());
087        regions.sort(Comparator.comparingDouble(r -> r.getCenter().getY()));    // sort regions by Y-coordinates
088
089        ShapeOverlayAdapter ola = new ShapeOverlayAdapter();
090        ola.setStroke(new ColoredStroke(0.5, Color.green));
091        ola.setFont(MarkerFont);
092        ola.setTextColor(MarkerColor);
093        int i = 0;
094        for (BinaryRegion r : regions) {
095            if (r.getSize() >= MIN_REGION_SIZE) {
096                IJ.log("Region " + i + ", size = " + r.getSize());
097                Contour oc = r.getOuterContour();
098                ola.addShape(oc.getPolygonPath());
099                Pnt2d c = r.getCenter();
100                ola.addText(c.getX(), c.getY(), "R" + i);
101                double[] moments = new FlusserMoments(r).getInvariantMoments();
102                print(moments);
103                i++;
104                if (i > MAX_REGION_COUNT)
105                    break;
106            }
107        }
108        im.setOverlay(ola.getOverlay());
109    }
110
111    private void print(double[] moments) {
112        for (int i = 0; i < moments.length; i++) {
113            IJ.log("   p" + (i+1) + " = " + moments[i]);
114        }
115    }
116
117    // ------------------------------------------------------
118
119    private boolean runDialog() {
120        GenericDialog gd = new GenericDialog(this.getClass().getSimpleName());
121        gd.addHelp(getJavaDocUrl());
122        if (im.isInvertedLut()) {
123            gd.setInsets(0, 0, 0);
124            gd.addMessage("NOTE: Image has inverted LUT (0 = white)!");
125        }
126        gd.addNumericField("Minimum region size (pixels)", MIN_REGION_SIZE);
127        gd.addNumericField("Maximum region count", MAX_REGION_COUNT);
128        gd.addCheckbox("Mark outer contours", MARK_OUTER_CONTOURS);
129
130        gd.showDialog();
131        if (gd.wasCanceled()) {
132            return false;
133        }
134
135        MIN_REGION_SIZE = (int) gd.getNextNumber();
136        MAX_REGION_COUNT = (int) gd.getNextNumber();
137        MARK_OUTER_CONTOURS = gd.getNextBoolean();
138        return true;
139    }
140
141}