CompositeImage.java

package ij;
import ij.process.*;
import ij.gui.*;
import ij.plugin.*;
import ij.plugin.frame.*;
import ij.io.FileInfo;
import java.awt.*;
import java.awt.image.*;

public class CompositeImage extends ImagePlus {

	/** Display modes (note: TRANSPARENT mode has not yet been implemented) */
	public static final int COMPOSITE=1, COLOR=2, GRAYSCALE=3, TRANSPARENT=4;
	public static final int MAX_CHANNELS = 7;
	int[] rgbPixels;
	boolean newPixels;
	MemoryImageSource imageSource;
	Image awtImage;
	WritableRaster rgbRaster;
	SampleModel rgbSampleModel;
	BufferedImage rgbImage;
	ColorModel rgbCM;
	ImageProcessor[] cip;
	Color[] colors = {Color.red, Color.green, Color.blue, Color.white, Color.cyan, Color.magenta, Color.yellow};
	LUT[] lut;
	int currentChannel = -1;
	int previousChannel;
	int currentSlice = 1;
	int currentFrame = 1;
	boolean singleChannel;
	boolean[] active = new boolean[MAX_CHANNELS];
	int mode = COLOR;
	int bitDepth;
	double[] displayRanges;
	byte[][] channelLuts;
	boolean customLuts;
	boolean syncChannels;

	public CompositeImage(ImagePlus imp) {
		this(imp, COLOR);
	}
	
	public CompositeImage(ImagePlus imp, int mode) {
		if (mode<COMPOSITE || mode>GRAYSCALE)
			mode = COLOR;
		this.mode = mode;
		int channels = imp.getNChannels();
		bitDepth = getBitDepth();
		if (IJ.debugMode) IJ.log("CompositeImage: "+imp+" "+mode+" "+channels);
		ImageStack stack2;
		boolean isRGB = imp.getBitDepth()==24;
		if (isRGB) {
			if (imp.getImageStackSize()>1)
				throw new IllegalArgumentException("RGB stacks not supported");
			stack2 = getRGBStack(imp);
		} else
			stack2 = imp.getImageStack();
		int stackSize = stack2.getSize();
		if (channels==1 && isRGB)
			channels = 3;
		if (channels==1 && stackSize<=MAX_CHANNELS && !imp.dimensionsSet)
			channels = stackSize;
		if (channels<1 || (stackSize%channels)!=0)
			throw new IllegalArgumentException("stacksize not multiple of channels");
		if (mode==COMPOSITE && channels>MAX_CHANNELS)
			this.mode = COLOR;
		compositeImage = true;
		int z = imp.getNSlices();
		int t = imp.getNFrames();
		if (channels==stackSize || channels*z*t!=stackSize)
			setDimensions(channels, stackSize/channels, 1);
		else
			setDimensions(channels, z, t);
		setStack(imp.getTitle(), stack2);
		setCalibration(imp.getCalibration());
		FileInfo fi = imp.getOriginalFileInfo();
		if (fi!=null) {
			displayRanges = fi.displayRanges; 
			channelLuts = fi.channelLuts;
		}
		setFileInfo(fi);
		Object info = imp.getProperty("Info");
		if (info!=null)
			setProperty("Info", imp.getProperty("Info"));
		setProperties(imp.getPropertiesAsArray());		
		if (mode==COMPOSITE) {
			for (int i=0; i<MAX_CHANNELS; i++)
				active[i] = true;
		} else
			active[0] = true;
		//if (!(channels==3&&stackSize==3))
		setRoi(imp.getRoi());
		setOverlay(imp.getOverlay());
		if (channels!=stackSize)
			setOpenAsHyperStack(true);
	}

	@Override
	public Image getImage() {
		if (img==null)
			updateImage();
		return img;
	}
	
	public void updateChannelAndDraw() {
		if (!customLuts) singleChannel = true;
		updateAndDraw();
	}
	
	public void updateAllChannelsAndDraw() {
		if (mode!=COMPOSITE)
			updateChannelAndDraw();
		else {
			syncChannels = true;
			singleChannel = false;
			updateAndDraw();
		}
	}

	public ImageProcessor getChannelProcessor() {
		if (cip!=null && currentChannel!=-1)
			return cip[currentChannel];
		else
			return getProcessor();
	}

	synchronized void setup(int channels, ImageStack stack2) {
		if (stack2!=null && stack2.getSize()>0 && (stack2.getProcessor(1) instanceof ColorProcessor)) { // RGB?
			cip = null;
			lut = null;
			return;
		}
		setupLuts(channels);
		if (mode==COMPOSITE) {
			cip = new ImageProcessor[channels];
			for (int i=0; i<channels; ++i) {
				cip[i] = stack2.getProcessor(i+1);
				cip[i].setLut(lut[i]);
			}
			currentSlice = currentFrame = 1;
		}
	}

	void setupLuts(int channels) {
		if (ip==null)
			return;
		if (lut==null || lut.length<channels) {
			if (displayRanges!=null && channels!=displayRanges.length/2)
				displayRanges = null;
			if (displayRanges==null&&ip.getMin()==0.0&&ip.getMax()==0.0)
				ip.resetMinAndMax();
			lut = new LUT[channels];
			LUT lut2 = channels>MAX_CHANNELS?createLutFromColor(Color.white):null;
			for (int i=0; i<channels; ++i) {
				if (channelLuts!=null && i<channelLuts.length) {
					lut[i] = createLutFromBytes(channelLuts[i]);
					customLuts = true;
				} else if (i<MAX_CHANNELS)
					lut[i] = createLutFromColor(colors[i]);
				else
					lut[i] = (LUT)lut2.clone();
				if (displayRanges!=null) {
					lut[i].min = displayRanges[i*2];
					lut[i].max = displayRanges[i*2+1];
				} else {
					lut[i].min = ip.getMin();
					lut[i].max = ip.getMax();
				}
			}
			displayRanges = null;
		}
	}
	
	public void resetDisplayRanges() {
		int channels = getNChannels();
		if (lut==null)
			setupLuts(channels);
		ImageStack stack2 = getImageStack();
		if (lut==null || channels!=lut.length || channels>stack2.getSize() || channels>MAX_CHANNELS)
			return;
		for (int i=0; i<channels; ++i) {
			ImageProcessor ip2 = stack2.getProcessor(i+1);
			ip2.resetMinAndMax();
			lut[i].min = ip2.getMin();
			lut[i].max = ip2.getMax();
		}
	}

	public void updateAndDraw() {
		updateImage();
		if (win!=null)
			notifyListeners(UPDATED);
		draw();
	}

	public synchronized void updateImage() {
		int imageSize = width*height;
		int nChannels = getNChannels();
		int redValue, greenValue, blueValue;
		int ch = getChannel();
		
		//IJ.log("updateImage: "+ch+"/"+nChannels+" "+currentSlice+" "+currentFrame);
		if (ch>nChannels) ch = nChannels;
		boolean newChannel = false;
		if (ch-1!=currentChannel) {
			previousChannel = currentChannel;
			currentChannel = ch-1;
			newChannel = true;
		}

		ImageProcessor ip = getProcessor();
		if (mode!=COMPOSITE) {
			if (newChannel) {
				setupLuts(nChannels);
				LUT cm = lut[currentChannel];
				if (ip!=null && !(ip instanceof ColorProcessor)) {
					if (mode==COLOR)
						ip.setLut(cm);
					if (!(cm.min==0.0&&cm.max==0.0))
						ip.setMinAndMax(cm.min, cm.max);
				}
				if (!IJ.isMacro()) ContrastAdjuster.update();
				for (int i=0; i<MAX_CHANNELS; i++)
					active[i] = i==currentChannel?true:false;
				Channels.updateChannels();
			}
			if (ip!=null)
				img = ip.createImage();
			return;
		}

		if (nChannels==1) {
			cip = null;
			rgbPixels = null;
			awtImage = null;
			if (ip!=null)
				img = ip.createImage();
			return;
		}
	
		if (cip==null||cip[0].getWidth()!=width||cip[0].getHeight()!=height||getBitDepth()!=bitDepth) {
			setup(nChannels, getImageStack());
			rgbPixels = null;
			rgbSampleModel = null;
			if (currentChannel>=nChannels) {
				setSlice(1);
				currentChannel = 0;
				newChannel = true;
			}
			bitDepth = getBitDepth();
		}
		
		if (newChannel) {
			getProcessor().setMinAndMax(cip[currentChannel].getMin(), cip[currentChannel].getMax());
			if (!IJ.isMacro()) ContrastAdjuster.update();
		}
		//IJ.log(nChannels+" "+ch+" "+currentChannel+"  "+newChannel);
				
		if (getSlice()!=currentSlice || getFrame()!=currentFrame) {
			currentSlice = getSlice();
			currentFrame = getFrame();
			int position = getStackIndex(1, currentSlice, currentFrame);
			if (cip==null) return;
			for (int i=0; i<nChannels; ++i)
				cip[i].setPixels(getImageStack().getProcessor(position+i).getPixels());
		}

		if (rgbPixels == null) {
			rgbPixels = new int[imageSize];
			newPixels = true;
			imageSource = null;
			rgbRaster = null;
			rgbImage = null;
		}
		cip[currentChannel].setMinAndMax(ip.getMin(),ip.getMax());
		if (singleChannel && nChannels<=3) {
			switch (currentChannel) {
				case 0: cip[0].updateComposite(rgbPixels, 1); break;
				case 1: cip[1].updateComposite(rgbPixels, 2); break;
				case 2: cip[2].updateComposite(rgbPixels, 3); break;
			}
		} else {
			if (cip==null) return;
			if (syncChannels) {
				ImageProcessor ip2 = getProcessor();
				double min=ip2.getMin(), max=ip2.getMax();
				for (int i=0; i<nChannels; i++) {
					cip[i].setMinAndMax(min, max);
					lut[i].min = min;
					lut[i].max = max;
				}
				syncChannels = false;
			}
			if (active[0])
				cip[0].updateComposite(rgbPixels, 4);
			else
				{for (int i=1; i<imageSize; i++) rgbPixels[i] = 0;}
			if (cip==null || nChannels>cip.length)
				return;
			for (int i=1; i<nChannels; i++)
				if (active[i]) cip[i].updateComposite(rgbPixels, 5);
		}
		createBufferedImage();
		if (img==null && awtImage!=null)
			img = awtImage;
		singleChannel = false;
	}
		
	void createImage() {
		if (imageSource==null) {
			rgbCM = new DirectColorModel(32, 0xff0000, 0xff00, 0xff);
			imageSource = new MemoryImageSource(width, height, rgbCM, rgbPixels, 0, width);
			imageSource.setAnimated(true);
			imageSource.setFullBufferUpdates(true);
			awtImage = Toolkit.getDefaultToolkit().createImage(imageSource);
			newPixels = false;
		} else if (newPixels){
			imageSource.newPixels(rgbPixels, rgbCM, 0, width);
			newPixels = false;
		} else
			imageSource.newPixels();	
	}

	void createBufferedImage() {
		if (rgbSampleModel==null)
			rgbSampleModel = getRGBSampleModel();
		if (rgbRaster==null) {
			DataBuffer dataBuffer = new DataBufferInt(rgbPixels, width*height, 0);
			rgbRaster = Raster.createWritableRaster(rgbSampleModel, dataBuffer, null);
		}
		if (rgbImage==null)
			rgbImage = new BufferedImage(rgbCM, rgbRaster, false, null);
		awtImage = rgbImage;
	}

	SampleModel getRGBSampleModel() {
		rgbCM = new DirectColorModel(24, 0xff0000, 0xff00, 0xff);
		WritableRaster wr = rgbCM.createCompatibleWritableRaster(1, 1);
		SampleModel sampleModel = wr.getSampleModel();
		sampleModel = sampleModel.createCompatibleSampleModel(width, height);
		return sampleModel;
	}

	ImageStack getRGBStack(ImagePlus imp) {
		ImageProcessor ip = imp.getProcessor();
		int w = ip.getWidth();
		int h = ip.getHeight();
		int size = w*h;
		byte[] r = new byte[size];
		byte[] g = new byte[size];
		byte[] b = new byte[size];
		((ColorProcessor)ip).getRGB(r, g, b);
		ImageStack stack = new ImageStack(w, h);
		stack.addSlice("Red", r);	
		stack.addSlice("Green", g);	
		stack.addSlice("Blue", b);
		stack.setColorModel(ip.getDefaultColorModel());
		return stack;
	}

	public LUT createLutFromColor(Color color) {
		return LUT.createLutFromColor(color);
	}
	
	LUT createLutFromBytes(byte[] bytes) {
		if (bytes==null || bytes.length!=768)
			return createLutFromColor(Color.white);
		byte[] r = new byte[256];
		byte[] g = new byte[256];
		byte[] b = new byte[256];
		for (int i=0; i<256; i++) r[i] = bytes[i];
		for (int i=0; i<256; i++) g[i] = bytes[256+i];
		for (int i=0; i<256; i++) b[i] = bytes[512+i];
		return new LUT(r, g, b);
	}

	/** Returns the color used to display the image subtitle and "B&C" histogram. */
	public Color getChannelColor() {
		if (lut==null || mode==GRAYSCALE)
			return Color.black;
		IndexColorModel cm = lut[getChannelIndex()];
		if (cm==null)
			return Color.black;
		int index = cm.getMapSize() - 1;
		int r = cm.getRed(index);
		int g = cm.getGreen(index);
		int b = cm.getBlue(index);
		//IJ.log(index+" "+r+" "+g+" "+b);
		if (r<100 || g<100 || b<100)
			return new Color(r, g, b);
		else
			return Color.black;
	}

	public ImageProcessor getProcessor(int channel) {
		if (cip==null || channel>cip.length)
			return null;
		else
			return cip[channel-1];
	}

	public boolean[] getActiveChannels() {
		return active;
	}
	
	public synchronized void setMode(int mode) {
		if (mode<COMPOSITE || mode>GRAYSCALE)
			return;
		if (mode==COMPOSITE && getNChannels()>MAX_CHANNELS)
			mode = COLOR;
		for (int i=0; i<MAX_CHANNELS; i++)
			active[i] = true;
		if (this.mode!=COMPOSITE && mode==COMPOSITE)
			img = null;
		this.mode = mode;
		if (mode==COLOR || mode==GRAYSCALE) {
			if (cip!=null) {
				for (int i=0; i<cip.length; i++) {
					if (cip[i]!=null) cip[i].setPixels(null);
					cip[i] = null;
				}
			}
			cip = null;
			rgbPixels = null;
			awtImage = null;
			currentChannel = -1;
		}
		if (mode==GRAYSCALE || mode==TRANSPARENT)
			ip.setColorModel(ip.getDefaultColorModel());
		Channels.updateChannels();
	}

	public int getMode() {
		return mode;
	}
	
	public String getModeAsString() {
		switch (mode) {
			case COMPOSITE: return "composite";
			case COLOR: return "color";
			case GRAYSCALE: return "grayscale";
		}
		return "";
	}
	
	/* Returns the LUT used by the specified channel. */
	public LUT getChannelLut(int channel) {
		int channels = getNChannels();
		if (lut==null) setupLuts(channels);
		if (channel<1 || channel>lut.length)
			throw new IllegalArgumentException("Channel out of range: "+channel);
		return lut[channel-1];
	}
	
	/* Returns the LUT used by the current channel. */
	public LUT getChannelLut() {
		int c = getChannelIndex();
		return lut[c];
	}
	
	/* Returns a copy of this image's channel LUTs as an array. */
	public LUT[] getLuts() {
		int channels = getNChannels();
		if (lut==null)
			setupLuts(channels);
		LUT[] luts = new LUT[channels];
		for (int i=0; i<channels; i++) {
			if (i<lut.length)
				luts[i] = (LUT)lut[i].clone();
			else
				luts[i] = (LUT)lut[0].clone();
		}
		return luts;
	}

	/* Sets the channel LUTs with clones of the LUTs in 'luts'. */
	public void setLuts(LUT[] luts) {
		int channels = getNChannels();
		if (lut==null) setupLuts(channels);
		if (luts==null || luts.length<channels)
			throw new IllegalArgumentException("Lut array is null or too small");
		for (int i=0; i<channels; i++)
			setChannelLut(luts[i], i+1);
	}
	
	/** Copies the LUTs and display mode of 'imp' to this image. Does
		nothing if 'imp' is not a CompositeImage or 'imp' and this
		image do not have the same number of channels. */
	public synchronized void copyLuts(ImagePlus imp) {
		int channels = getNChannels();
		if (!imp.isComposite() || imp.getNChannels()!=channels)
			return;
		CompositeImage ci = (CompositeImage)imp;
		LUT[] luts = ci.getLuts();
		if (luts!=null && luts.length==channels) {
			lut = luts;
			cip = null;
		}
		int mode2 = ci.getMode();
		setMode(mode2);
		if (mode2==COMPOSITE) {
			boolean[] active2 = ci.getActiveChannels();
			for (int i=0; i<MAX_CHANNELS; i++)
				active[i] = active2[i];
		}
		if (ci.hasCustomLuts())
			customLuts = true;
	}

	int getChannelIndex() {
		int channels = getNChannels();
		if (lut==null) setupLuts(channels);
		int index = getChannel()-1;
		return index;
	}
	
	public void reset() {
		int nChannels = getNChannels();
		if (nChannels>MAX_CHANNELS && getMode()==COMPOSITE)
			setMode(COLOR);
		setup(nChannels, getImageStack());
	}
	
	public void completeReset() {
		cip = null;
		lut = null;
	}
	
	/* Sets the LUT of the current channel. */
	public void setChannelLut(LUT table) {
		int c = getChannelIndex();
		double min = lut[c].min;
		double max = lut[c].max;
		lut[c] = table;
		lut[c].min = min;
		lut[c].max = max;
		if (mode==COMPOSITE && cip!=null && c<cip.length) {
			cip[c].setColorModel(lut[c] );
			imageSource = null;
			newPixels = true;
			img = null;
		}
		currentChannel = -1;
		getProcessor().setLut(table);
		customLuts = true;
		if (!IJ.isMacro()) ContrastAdjuster.update();
	}
	
	/* Sets the LUT of the specified channel using a clone of 'table'. */
	public synchronized void setChannelLut(LUT table, int channel) {
		int channels = getNChannels();
		if (lut==null) setupLuts(channels);
		if (channel<1 || channel>lut.length)
			throw new IllegalArgumentException("Channel out of range");
		lut[channel-1] = (LUT)table.clone();
		if (getWindow()!=null && channel==getChannel())
			getProcessor().setLut(lut[channel-1]);
		if (cip!=null && cip.length>=channel && cip[channel-1]!=null)
			cip[channel-1].setLut(lut[channel-1]);
		else
			cip = null;
		customLuts = true;
	}

	/* Sets the IndexColorModel of the current channel. */
	public void setChannelColorModel(IndexColorModel cm) {
		setChannelLut(new LUT(cm,0.0,0.0));
	}
	
	public void setDisplayRange(double min, double max) {
		ip.setMinAndMax(min, max);
		int c = getChannelIndex();
		lut[c].min = min;
		lut[c].max = max;
		if (getWindow()==null && cip!=null && c<cip.length)
			cip[c].setLut(lut[c]);
	}

	public double getDisplayRangeMin() {
		if (lut!=null)
			return lut[getChannelIndex()].min;
		else
			return 0.0;
	}

	public double getDisplayRangeMax() {
		if (lut!=null)
			return lut[getChannelIndex()].max;
		else
			return 255.0;
	}

	public void resetDisplayRange() {
		if (getType()==GRAY16 && getDefault16bitRange()!=0) {
			int defaultRange = getDefault16bitRange();
			for (int i=1; i<=getNChannels(); i++) {
				LUT lut = getChannelLut(i);
				lut.min = 0;
				lut.max = Math.pow(2,defaultRange)-1;
				if (getWindow()!=null)
					setChannelLut(lut, i);
			}
		} else {
			ip.resetMinAndMax();
			int c = getChannelIndex();
			lut[c].min = ip.getMin();
			lut[c].max = ip.getMax();
		}
	}
	
	public boolean hasCustomLuts() {
		return customLuts && mode!=GRAYSCALE;
	}
	
	public void close() {
		super.close();
		rgbPixels = null;
		imageSource = null;
		awtImage = null;
		rgbRaster = null;
		rgbSampleModel = null;
		rgbImage = null;
		rgbCM = null;
		if (cip!=null) {
			for (int i=0; i<cip.length; i++)
				cip[i] = null;
			cip = null;
		}
		if (lut!=null) {
			for (int i=0; i<lut.length; i++)
				lut[i] = null;
			lut = null;
		}
		if (channelLuts!=null) {
			for (int i=0; i<channelLuts.length; i++)
				channelLuts[i] = null;
			channelLuts = null;
		}
	}

	/** Deprecated */
	public synchronized void setChannelsUpdated() {
		if (cip!=null) {
			for (int i=0; i<cip.length; i++) {
				if (cip[i]!=null) cip[i].setPixels(null);
				cip[i] = null;
			}
		}
		cip = null;
		lut = null;
		img = null;
		currentChannel = -1;
		previousChannel = 0;
		currentSlice = currentFrame = 1;
		singleChannel = false;
		rgbPixels = null;
		awtImage = null;
		channelLuts = null;
		boolean[] active = new boolean[MAX_CHANNELS];
	}

}