import ij.*;
import ij.plugin.filter.PlugInFilter;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import java.awt.image.*;
import java.util.*;
import java.awt.event.*;
import ij.measure.*;
import ij.plugin.frame.*;
import ij.plugin.*;


/** This plugin isolates pixels in an RGB image or stack according to a range of Hue.
	Bob Dougherty  Some code borrowed from ThresholdAdjuster by Wayne Rasband.

	Version 0 5/12/2002.
	Version 1 5/13.  Filtered pixels set to foreground color.  Speed improved.
	Version 2 5/13.  Fixed a bug in setting the restore pixels that was causing problems with stacks.
					Explicitly get the foreground color from the toolbar in apply.
 */
/*	License:
	Copyright (c) 2002, 2005, OptiNav, Inc.
	All rights reserved.

	Redistribution and use in source and binary forms, with or without
	modification, are permitted provided that the following conditions
	are met:

		Redistributions of source code must retain the above copyright
	notice, this list of conditions and the following disclaimer.
		Redistributions in binary form must reproduce the above copyright
	notice, this list of conditions and the following disclaimer in the
	documentation and/or other materials provided with the distribution.
		Neither the name of OptiNav, Inc. nor the names of its contributors
	may be used to endorse or promote products derived from this software
	without specific prior written permission.

	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
	"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
	A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
public class Band_Pass2 implements PlugInFilter {

	ImagePlus imp;
	boolean canceled = false;
	int low = 0;
	int high = 255;

	public int setup(String arg, ImagePlus imp) {
		this.imp = imp;
		return DOES_RGB;
	}

	public void run(ImageProcessor ip) {

		BandAdjuster ba = new BandAdjuster();
 	}

	private void getBand() {
		GenericDialog gd = new GenericDialog("Band Selection", IJ.getInstance());
		gd.addNumericField("Lowest Hue to keep", low, 0);
		gd.addNumericField("Highest Hue to keep", high, 0);
		gd.showDialog();
		if (gd.wasCanceled()) {
			canceled = true;
		}
		low = (int)gd.getNextNumber();
		high = (int)gd.getNextNumber();
	}


/**  Selects pixels according to hue.  */
public class BandAdjuster extends PlugInFrame implements PlugIn, Measurements,
	ActionListener, AdjustmentListener, FocusListener {

	Frame instance;

	HuePlot plot = new HuePlot();

	int sliderRange = 256;

	Panel panel;
	Button  resetB, applyB, setB;
	Checkbox bandPass, bandStop;
	CheckboxGroup filterType;
	int previousImageID = -1;
	int previousSlice = -1;
	ImageJ ij;
	double minHue = 0;
	double maxHue = 255;
	Scrollbar minSlider, maxSlider;
	Label label1, label2;
	boolean done;
	boolean invertedLut;
	boolean blackAndWhite;
	int lutColor = ImageProcessor.RED_LUT;
	byte[] hSource,sSource,bSource;
	int[] fillMask,restore;
	ImagePlus imp;
	ImageProcessor ip;

	int numSlices ;
	ImageStack stack;
	int width,height,numPixels;

	Cursor wait, ok;

	public BandAdjuster() {
		super("Hue Band");
		if (instance!=null) {
			instance.toFront();
			return;
		}
		imp = WindowManager.getCurrentImage();
		if (imp==null) {
			IJ.beep();
			IJ.showStatus("No image");
			return;
		}

		WindowManager.addWindow(this);
		instance = this;
		IJ.register(PasteController.class);

		ij = IJ.getInstance();
		Font font = new Font("SansSerif", Font.PLAIN, 10);
		GridBagLayout gridbag = new GridBagLayout();
		GridBagConstraints c = new GridBagConstraints();
		setLayout(gridbag);

		wait = new Cursor(Cursor.WAIT_CURSOR);
		ok = new Cursor(Cursor.DEFAULT_CURSOR);

		// plot
		int y = 0;
		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 2;
		c.fill = c.BOTH;
		c.anchor = c.CENTER;
		c.insets = new Insets(10, 10, 0, 10);
		add(plot, c);

		// minHue slider
		minSlider = new Scrollbar(Scrollbar.HORIZONTAL, sliderRange/3, 1, 0, sliderRange);
		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 1;
		c.weightx = IJ.isMacintosh()?90:100;
		c.fill = c.HORIZONTAL;
		c.insets = new Insets(5, 10, 0, 0);
		add(minSlider, c);
		minSlider.addAdjustmentListener(this);
		minSlider.setUnitIncrement(1);

		// minHue slider label
		c.gridx = 1;
		c.gridwidth = 1;
		c.weightx = IJ.isMacintosh()?10:0;
		c.insets = new Insets(5, 0, 0, 10);
		label1 = new Label("       ", Label.RIGHT);
    	label1.setFont(font);
		add(label1, c);

		// maxHue slider
		maxSlider = new Scrollbar(Scrollbar.HORIZONTAL, sliderRange*2/3, 1, 0, sliderRange);
		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 1;
		c.weightx = 100;
		c.insets = new Insets(0, 10, 0, 0);
		add(maxSlider, c);
		maxSlider.addAdjustmentListener(this);
		maxSlider.setUnitIncrement(1);

		// maxHue slider label
		c.gridx = 1;
		c.gridwidth = 1;
		c.weightx = 0;
		c.insets = new Insets(0, 0, 0, 10);
		label2 = new Label("       ", Label.RIGHT);
    	label2.setFont(font);
		add(label2, c);

		// buttons
		panel = new Panel();
		//panel.setLayout(new GridLayout(2, 2, 0, 0));
		applyB = new Button("Apply");
		applyB.addActionListener(this);
		applyB.addKeyListener(ij);
		panel.add(applyB);

		resetB = new Button("Reset");
		resetB.addActionListener(this);
		resetB.addKeyListener(ij);
		panel.add(resetB);

		setB = new Button("Apply stack");
		setB.addActionListener(this);
		setB.addKeyListener(ij);
		panel.add(setB);

		//Checkboxes
		filterType = new CheckboxGroup();

		bandPass = new Checkbox("Pass");
		bandPass.setCheckboxGroup(filterType);
		//bandPass.addItemListener(this);
		panel.add(bandPass);

		bandStop = new Checkbox("Stop");
		bandStop.setCheckboxGroup(filterType);
		//bandStop.addItemListener(this);
		panel.add(bandStop);

		bandPass.setState(true);

		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 2;
		c.insets = new Insets(5, 5, 10, 5);
		add(panel, c);

 		addKeyListener(ij);  // ImageJ handles keyboard shortcuts
		pack();
		GUI.center(this);
		setVisible(true);

		ip = setup(imp);
		if (ip==null) {
			imp.unlock();
			IJ.beep();
			IJ.showStatus("RGB images cannot be thresolded");
			return;
		}
	}

	public void adjustmentValueChanged(AdjustmentEvent e) {
		if (!checkImage()){
			IJ.beep();
			IJ.showStatus("No Image");
			return;
		}
		if (e.getSource()==minSlider){
			double minValue = minSlider.getValue();
			adjustMinHue(minValue);
		} else {
			double maxValue = maxSlider.getValue();
			adjustMaxHue(maxValue);
		}
		updateLabels();
		updatePlot();
	}

	public void focusGained(FocusEvent e){
		if (!checkImage()){
			IJ.beep();
			IJ.showStatus("No Image");
		}
	}

	public void focusLost(FocusEvent e){}


	public void actionPerformed(ActionEvent e) {
		Button b = (Button)e.getSource();
		if (b==null) return;

		boolean imageThere = checkImage();

		if (imageThere){
			if (b==resetB){
				reset(imp,ip);
			} else if (b==applyB){
				apply(imp,ip);
			} else if (b==setB){
				applyStack();
			}
			updatePlot();
			updateLabels();
			imp.updateAndDraw();
		} else {
			IJ.beep();
			IJ.showStatus("No Image");
		}
	}
	private boolean checkImage(){
		imp = WindowManager.getCurrentImage();
		if (imp==null) {
			IJ.beep();
			IJ.showStatus("No image");
			return false;
		}
		ip = setup(imp);
		if (ip==null)
			return false;
		return true;
	}


	ImageProcessor setup(ImagePlus imp) {
		ImageProcessor ip;
		int type = imp.getType();
		if (type!=ImagePlus.COLOR_RGB)
			return null;
		ip = imp.getProcessor();
		int id = imp.getID();
		int slice = imp.getCurrentSlice();
		if ((id!=previousImageID)|(slice!=previousSlice) ) {

			numSlices = imp.getStackSize();
			stack = imp.getStack();
			width = stack.getWidth();
			height = stack.getHeight();
			numPixels = width*height;

			hSource = new byte[numPixels];
			sSource = new byte[numPixels];
			bSource = new byte[numPixels];


			//restore = (int[])ip.getPixelsCopy(); //This runs into trouble sometimes, so do it the long way:
			int[] temp = (int[])ip.getPixels();
			restore = new int[numPixels];
			for (int i = 0; i < numPixels; i++)restore[i] = temp[i];

			fillMask = new int[numPixels];

			//Get hue, saturation and brightness of the RGB image.
			ColorProcessor cp = (ColorProcessor)ip;

			IJ.showStatus("Bandpass: gathering data");

			setCursor(wait);

			cp.getHSB(hSource,sSource,bSource);
			IJ.showStatus("done");
			this.setCursor(ok);

			//Create a spectrum ColorModel for the Hue histogram plot.
			Color c;
			byte[] reds = new byte[256];
			byte[] greens = new byte[256];
			byte[] blues = new byte[256];
			for (int i=0; i<256; i++) {
				c = Color.getHSBColor(i/255f, 1f, 1f);
				reds[i] = (byte)c.getRed();
				greens[i] = (byte)c.getGreen();
				blues[i] = (byte)c.getBlue();
			}
			ColorModel cm = new IndexColorModel(8, 256, reds, greens, blues);

			//Make an image with just the hue from the RGB image and the spectrum LUT.
			//This is just for a histogram for the plot.  Do not show it.
			//ByteProcessor bpHue = new ByteProcessor(width,height,h,cm);
			ByteProcessor bpHue = new ByteProcessor(width,height,hSource,cm);
			ImagePlus impHue = new ImagePlus("Hue",bpHue);
			//impHue.show();
			plot.setHistogram(impHue);

			updateLabels();
			updatePlot();
			updateScrollBars();
			imp.updateAndDraw();
		}
	 	previousImageID = id;
	 	previousSlice = slice;
	 	return ip;
	}

	void updatePlot() {
		plot.minHue = minHue;
		plot.maxHue = maxHue;
		plot.repaint();
	}

	void updateLabels() {
		label1.setText(""+((int)minHue));
		label2.setText(""+((int)maxHue));
	}

	void updateScrollBars() {
		minSlider.setValue((int)minHue);
		maxSlider.setValue((int)maxHue);
	}

	/** Restore image outside non-rectangular roi. */
  	/*void doMasking(ImagePlus imp, ImageProcessor ip) {
		int[] mask = imp.getMask();
		if (mask!=null)
			ip.reset(mask);
	}*/

	void adjustMinHue(double value) {
		if (IJ.altKeyDown()) {
			double width = maxHue-minHue;
			if (width<1.0) width = 1.0;
			minHue = value;
			maxHue = minHue+width;
			if ((minHue+width)>255) {
				minHue = 255-width;
				maxHue = minHue+width;
				minSlider.setValue((int)minHue);
			}
			maxSlider.setValue((int)maxHue);
			//scaleUpAndSet(ip, minHue, maxHue);
			return;
		}
		minHue = value;
		if (maxHue<minHue) {
			maxHue = minHue;
			maxSlider.setValue((int)maxHue);
		}
		//scaleUpAndSet(ip, minHue, maxHue);
	}

	void adjustMaxHue(double cvalue) {
		maxHue = cvalue;
		if (minHue>maxHue) {
			minHue = maxHue;
			minSlider.setValue((int)minHue);
		}
		//scaleUpAndSet(ip, minHue, maxHue);
	}

	void apply(ImagePlus imp, ImageProcessor ip) {
		this.setCursor(wait);
		IJ.showStatus("Bandpassing slice "+previousSlice);


		//Make sure the ip is up to speed on the toolbar foreground color.
		java.awt.Color col = Toolbar.getForegroundColor();
		ip.setColor(col);

		int fill = ip.BLACK;
		int keep = 0;

		if (bandPass.getState()){
			for (int j = 0; j < numPixels; j++){
				int hue = hSource[j]&0xff;
				if ((hue < minHue)||(hue > maxHue)){
					fillMask[j] = fill;
				} else {
					fillMask[j] = keep;
				}
			}
		} else { //stop band
			for (int j = 0; j < numPixels; j++){
				int hue = hSource[j]&0xff;
				if ((hue >= minHue)&&(hue <= maxHue)){
					fillMask[j] = fill;
				} else {
					fillMask[j] = keep;
				}
			}
		}
		ip.fill(fillMask);
		this.setCursor(ok);
		IJ.showStatus("done");
	}
	void applyStack() {
		double minKeep = minHue;
		double maxKeep = maxHue;
		for (int i = 1; i <= numSlices; i++){
			imp.setSlice(i);
			if (!checkImage()){
				IJ.beep();
				IJ.showStatus("No Image");
				return;
			}
			minHue = minKeep;
			maxHue = maxKeep;
			apply(imp,ip);
		}
	}
	void reset(ImagePlus imp, ImageProcessor ip) {
		//Assign the pixels of ip to the data in the restore array, while
		//taking care to not give the address the restore array to the
		//image processor.
		int[] pixels = (int[])ip.getPixels();
		for (int i = 0; i < numPixels; i++)pixels[i] = restore[i];
	}

    public void windowClosing(WindowEvent e) {
		super.windowClosing(e);
		instance = null;
		done = true;
	}

} // HueAdjuster class


class HuePlot extends Canvas implements Measurements, MouseListener {

	final int WIDTH = 256, HEIGHT=64;
	double minHue = 0;
	double maxHue = 255;
	int[] histogram;
	Color[] hColors;
	int hmax;
	Image os;
	Graphics osg;

	public HuePlot() {
		addMouseListener(this);
		setSize(WIDTH+1, HEIGHT+1);
	}

	void setHistogram(ImagePlus imp) {
		ImageProcessor ip = imp.getProcessor();
		ImageStatistics stats = ImageStatistics.getStatistics(ip, AREA+MODE, null);
		int maxCount2 = 0;
		histogram = stats.histogram;
		for (int i = 0; i < stats.nBins; i++)
		if ((histogram[i] > maxCount2) && (i != stats.mode))
			maxCount2 = histogram[i];
		hmax = stats.maxCount;
		if ((hmax>(maxCount2 * 2)) && (maxCount2 != 0)) {
			hmax = (int)(maxCount2 * 1.5);
			histogram[stats.mode] = hmax;
        	}
		os = null;

   		ColorModel cm = ip.getColorModel();
		if (!(cm instanceof IndexColorModel))
			return;
		IndexColorModel icm = (IndexColorModel)cm;
		int mapSize = icm.getMapSize();
		if (mapSize!=256)
			return;
		byte[] r = new byte[256];
		byte[] g = new byte[256];
		byte[] b = new byte[256];
		icm.getReds(r);
		icm.getGreens(g);
		icm.getBlues(b);
		hColors = new Color[256];
		for (int i=0; i<256; i++)
			hColors[i] = new Color(r[i]&255, g[i]&255, b[i]&255);
	}

	public void update(Graphics g) {
		paint(g);
	}

	public void paint(Graphics g) {
		if (histogram!=null) {
			if (os==null) {
				os = createImage(WIDTH,HEIGHT);
				osg = os.getGraphics();
				osg.setColor(Color.white);
				osg.fillRect(0, 0, WIDTH, HEIGHT);
				osg.setColor(Color.gray);
				for (int i = 0; i < WIDTH; i++) {
					if (hColors!=null) osg.setColor(hColors[i]);
					osg.drawLine(i, HEIGHT, i, HEIGHT - ((int)(HEIGHT * histogram[i])/hmax));
				}
				osg.dispose();
			}
			g.drawImage(os, 0, 0, this);
		} else {
			g.setColor(Color.white);
			g.fillRect(0, 0, WIDTH, HEIGHT);
		}
		g.setColor(Color.black);
 		g.drawRect(0, 0, WIDTH, HEIGHT);
 		//g.setColor(Color.red);
 		g.drawRect((int)minHue, 1, (int)(maxHue-minHue), HEIGHT);
     }

	public void mousePressed(MouseEvent e) {}
	public void mouseReleased(MouseEvent e) {}
	public void mouseExited(MouseEvent e) {}
	public void mouseClicked(MouseEvent e) {}
	public void mouseEntered(MouseEvent e) {}

} // HuePlot class

} //Band_Pass2 class