/**************************************
*	Gel_converter.java class to invert b&w images, reduce the size and 
*	fix brightness/contrast for printing.
*
*	@author Jimmy Burnette, June 6, 2002 Finished June 14, 2002
*	@version 1.0
*	Please use, hack, and re-distribute for free. May not be used in fee based programs.
*		
*	Partially based on Inverter_.java plugin, ContrastAdjuster.java, and Scaler.java
*		 from Wayne Rasband
*			--	converts RGB to 8 Bit gray
*			--	inverts
*			--	AutoAdjusts brightness and contrast
*			--	despeckle
*			--	scale (user determines scaling factor)
*				-- user chooses image in new window or not.
*
*/



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

public class Gel_converter implements PlugInFilter {
	static final int AUTO_THRESHOLD = 5000;
	double scaleWidth = 0.0;
	double scaleHeight = 0.0;

    public int setup(String arg, ImagePlus imp) {
        if (arg.equals("about"))
            {showAbout(); return DONE;}
        return DOES_ALL;
    }
    
	private ImagePlus imp;
	
    public void run(ImageProcessor ip) {
    	imp = WindowManager.getCurrentImage();
        
    	if (ip instanceof ByteProcessor) {
    		invert8BitImage(ip);
    		IJ.showStatus ("Image inverted");
    		autoAdjust(ip, imp);
    		IJ.showStatus ("Brightness/Contrast adjusted");
    		IJ.showStatus ("Despeckling . . . ");
    		ip.medianFilter();		//despeckle filter.
    		IJ.showStatus ("Despeckled");
    		scale (ip, imp);
       		IJ.showMessage ("Conversion complete.");    		
    		
		}
    	else {
    		ImageConverter ic = new ImageConverter (imp);
    		ic.convertToGray8();
    		imp.repaintWindow();
    		ip = ip.convertToByte(true);
    		invert8BitImage(ip);
    		IJ.showStatus ("Image inverted");
    		autoAdjust(ip, imp);
    		IJ.showStatus ("Brightness/Contrast adjusted");
    		IJ.showStatus ("Despeckling . . . ");
    		ip.medianFilter();		//despeckle filter.
    		IJ.showStatus ("Despeckled");
    		scale (ip, imp);
       		IJ.showMessage ("Conversion complete.");    		

    	}
    		
     }     
     
	//from Inverter_.java    
    public void invert8BitImage(ImageProcessor ip) {
        byte[] pixels = (byte[])ip.getPixels();
        int width = ip.getWidth();
        Rectangle r = ip.getRoi();
        int offset, i;
        for (int y=r.y; y<(r.y+r.height); y++) {
            offset = y*width;
            for (int x=r.x; x<(r.x+r.width); x++) {
                i = offset + x;
                pixels[i] = (byte)(255-pixels[i]);
            }
        }
        imp.setProcessor ("Converted", ip);
        imp.repaintWindow();
    }
    
    public void showAbout() {
    	IJ.showMessage ("About Gel Converter . . .", 
    	"Gel Conveter takes a RGB image and converts it to 8 grays, \n" +
    	"inverts the image, auto adjusts the brightness/contrast, \n" +
    	"despeckles, and scales it, perfect for printing. \n" +
    	"Gel Converter was written to go along with images taken \n" +
    	"from a Kodak DC290 camera."
    	);
    }
    /** Get the scale factor and show scaled image in seperate window. Hacked from 
    *ij.plugin.filter.Scaler
    */
    public void scale (ImageProcessor ip, ImagePlus imp) {
    	boolean newWindow = true;
    	GenericDialog gd = new GenericDialog("Set scale factor", IJ.getInstance());
    	gd.addMessage ("Enter scale factor (5-100%). 20% works well for printing.");
    	gd.addNumericField ("Width: ", 20, 1);
    	gd.addNumericField ("Height: ", 20, 1);
    	gd.addMessage ("Select CANCEL for no scale.");
    	gd.addCheckbox ("Show in new window?", newWindow);
    	gd.showDialog();
    	if (gd.wasCanceled()) {
			//no scale
			IJ.showStatus ("Scale cancelled");
			return;
		}
		
		scaleWidth = (gd.getNextNumber () / 100);
		scaleHeight = (gd.getNextNumber () / 100);
		newWindow = gd.getNextBoolean();
		if (!newWindow) {
			ip.scale(scaleWidth, scaleHeight);
			imp.setProcessor ("Converted", ip);
       		imp.repaintWindow();
		} else {
			ImagePlus ipl2 = imp.createImagePlus();
			int newWidth = (int)(ip.getWidth() * scaleWidth);
			int newHeight = (int)(ip.getHeight() * scaleHeight);
			ipl2.setProcessor("Scaled", ip.resize(newWidth, newHeight));
			ipl2.show();
			ipl2.trimProcessor();
			imp.trimProcessor();
			ipl2.changes = true;		//force user to decide to save or not
		}
		IJ.showStatus ("Scaled");
    
    }
    
    /** 
    *autoAdjust() hacked from IJ.pluginFrame.ContrastAdjuster from main IJ package.
    *
    */
    void autoAdjust (ImageProcessor ip, ImagePlus imp) {
    	boolean RGBImage = false;
    	int autoThreshold = 0;
    	double min,max;
        if (RGBImage)
            ip.reset();
        Calibration cal = imp.getCalibration();
        imp.setCalibration(null);
        ImageStatistics stats = imp.getStatistics(); // get uncalibrated stats
        imp.setCalibration(cal);
        int[] histogram = stats.histogram;
        if (autoThreshold<10)
            autoThreshold = AUTO_THRESHOLD;
        else
            autoThreshold /= 2;
        int threshold = stats.pixelCount/autoThreshold;
        int i = -1;
        boolean found = false;
        do {
            i++;
            found = histogram[i] > threshold;
        } while (!found && i<255);
        int hmin = i;
        i = 256;
        do {
            i--;
            found = histogram[i] > threshold;
        } while (!found && i>0);
        int hmax = i;
        if (hmax>=hmin) {
            imp.killRoi();
            min = stats.histMin+hmin*stats.binSize;
            max = stats.histMin+hmax*stats.binSize;
            if (min==max)
                {min=stats.min; max=stats.max;}
            ip.setMinAndMax(min, max);
        } else {
            //reset(imp, ip);
            return;
        }
        Roi roi = imp.getRoi();
        if (roi!=null) {
            int[] mask = roi.getMask();
            if (mask!=null)
                ip.reset(mask);
        }
        imp.setProcessor ("Converted", ip);
       	imp.repaintWindow();
    }



} //closes class Gel_converter