FloodTracker3D.java

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package theba.trackers;

import javax.swing.JOptionPane;

import theba.core.ImageFunctions;
import theba.core.Stack;
import theba.core.Tracker;
import theba.core.gui.ThebaGUI;
import theba.core.math.Point3D;


public class FloodTracker3D extends Tracker {

        public FloodTracker3D(ThebaGUI f) {
                super(f);
        }

        @Override
        public void setup() {
                Runnable lumenAction = new Runnable() {
                        public void run() {
                                track();
                        }
                };
                control.addMenuItem("Label regions", lumenAction);
        }

        @Override
        public void track() {
                Stack input = control.getStack();
                String min = JOptionPane.showInputDialog(
                                "Set minimum region size in voxels", "100");
                if (min == null)
                        return;
                long totalSize = 0;
                int removeCount = 0;
                int count = 0;
                short id = 255;
                for (int z = 0; z < input.getDepth(); z++) {
                        for (int y = 0; y < input.getHeight(); y++) {
                                for (int x = 0; x < input.getWidth(); x++) {
                                        short val = input.getVoxelUnchecked(x, y, z);
                                        if (val == 0xff) {
                                                id++;
                                                long size = ImageFunctions.floodFill3D(input, x, y, z,
                                                                id);
                                                totalSize += size;
                                                if (size < 100) {
                                                        ImageFunctions.delete3D(input, x, y, z);
                                                        id--;
                                                        removeCount++;
                                                } else {
                                                        count++;
                                                }
                                        }
                                }
                        }
                        StringBuffer total = new StringBuffer();
                        total.append("Regions found : " + (count) + "\n");
                        total.append("Removed: " + removeCount + "\n");
                        total.append("Avgsize : " + (totalSize / (count)) + "\n");
                        control.showResults(total, "Results");
                        control.setProgress(z);
                }

                control.updateImage();
        }

        @Override
        public void mouseClicked(Point3D point3D) {
                // pass
        }

        @Override
        public void stop() {
                // pass
        }

        @Override
        public void reset() {
                // pass
        }
}