Thresholder.java

package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.*;
import ij.plugin.frame.Recorder;
import ij.plugin.filter.PlugInFilter;
import java.awt.*;

public class Thresholder implements PlugIn, Measurements {
    
    private int slice;
    private double minThreshold;
    private double maxThreshold;
    boolean autoThreshold;
    boolean skipDialog;
    static boolean fill1 = true;
    static boolean fill2 = true;
    static boolean useBW = true;


    public void run(String arg) {
        skipDialog = arg.equals("skip");
        ImagePlus imp = IJ.getInstance().getImagePlus();
        if (imp==null)
            {IJ.noImage(); return;}
        //if (imp.getType()==ImagePlus.COLOR_RGB)
        //  {IJ.error("RGB images are not supported."); return;}
        Undo.reset();
        applyThreshold(imp);
    }

    void applyThreshold(ImagePlus imp) {
        if (!imp.lock())
            return;
        imp.killRoi();
        ImageProcessor ip = imp.getProcessor();
        double saveMinThreshold = ip.getMinThreshold();
        double saveMaxThreshold = ip.getMaxThreshold();
        double saveMin = ip.getMin();
        double saveMax = ip.getMax();
        if (ip instanceof ByteProcessor)
            {saveMin =0; saveMax = 255;}
        autoThreshold = saveMinThreshold==ImageProcessor.NO_THRESHOLD;
                    
        boolean useBlackAndWhite = true;
        if (skipDialog)
            fill1 = fill2 = useBlackAndWhite = true;
        else if (!autoThreshold) {
            GenericDialog gd = new GenericDialog("Apply Lut");
            gd.addCheckbox("Thresholded pixels to foreground color", fill1);
            gd.addCheckbox("Remaining pixels to background color", fill2);
            gd.addMessage("");
            gd.addCheckbox("Black foreground, white background", useBW);
            gd.showDialog();
            if (gd.wasCanceled())
                {imp.unlock(); return;}
            fill1 = gd.getNextBoolean();
            fill2 = gd.getNextBoolean();
            useBW = useBlackAndWhite = gd.getNextBoolean();
        } else
            fill1 = fill2 = true;

        if (!(imp.getType()==ImagePlus.GRAY8))
            convertToByte(imp);
        ip = imp.getProcessor();
        if (autoThreshold)
            autoThreshold(imp);
        else {
            if (Recorder.record)
                Recorder.record("setThreshold", (int)saveMinThreshold, (int)saveMaxThreshold);
            minThreshold = ((saveMinThreshold-saveMin)/(saveMax-saveMin))*255.0;
            maxThreshold = ((saveMaxThreshold-saveMin)/(saveMax-saveMin))*255.0;
        }

        int fcolor, bcolor;
        ip.resetThreshold();
        int savePixel = ip.getPixel(0,0);
        if (useBlackAndWhite)
            ip.setColor(Color.black);
        else
            ip.setColor(Toolbar.getForegroundColor());
        ip.drawPixel(0,0);
        fcolor = ip.getPixel(0,0);
        if (useBlackAndWhite)
            ip.setColor(Color.white);
        else
            ip.setColor(Toolbar.getBackgroundColor());
        ip.drawPixel(0,0);
        bcolor = ip.getPixel(0,0);
        ip.setColor(Toolbar.getForegroundColor());
        ip.putPixel(0,0,savePixel);

        int[] lut = new int[256];
        for (int i=0; i<256; i++) {
            if (i>=minThreshold && i<=maxThreshold)
                lut[i] = fill1?fcolor:(byte)i;
            else {
                lut[i] = fill2?bcolor:(byte)i;
            }
        }
        int result = IJ.setupDialog(imp, 0);
        ip.applyTable(lut);
        imp.updateAndDraw();
        imp.unlock();
    }

    void convertToByte(ImagePlus imp) {
        ImageProcessor ip = imp.getProcessor();
        imp.setProcessor(null, ip.convertToByte(true));
    }
    
    void autoThreshold(ImagePlus imp) {
        ImageStatistics stats = imp.getStatistics(MIN_MAX+MODE);
        ImageProcessor ip = imp.getProcessor();
        int threshold = ((ByteProcessor)ip).getAutoThreshold();
        if ((stats.max-stats.mode)<(stats.mode-stats.min)) {
            minThreshold = stats.min;
            maxThreshold = threshold;
        } else {
            minThreshold = threshold;
            maxThreshold = stats.max;
        }
    }

}