ij.CompositeImage Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of ij Show documentation
Show all versions of ij Show documentation
ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.
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 (modeGRAYSCALE)
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"));
if (mode==COMPOSITE) {
for (int i=0; i0 && (stack2.getProcessor(1) instanceof ColorProcessor)) { // RGB?
cip = null;
lut = null;
return;
}
setupLuts(channels);
if (mode==COMPOSITE) {
cip = new ImageProcessor[channels];
for (int i=0; iMAX_CHANNELS?createLutFromColor(Color.white):null;
for (int i=0; istack2.getSize() || channels>MAX_CHANNELS)
return;
for (int i=0; inChannels) 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 (mode==COLOR)
ip.setColorModel(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=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; icip.length)
return;
for (int i=1; i=0; i--)
sb.copyBits(cip[i], 0, 0, Blitter. OR);
}
img = ip.createImage();
singleChannel = false;
}
*/
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);
}
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 (modeGRAYSCALE)
return;
if (mode==COMPOSITE && getNChannels()>MAX_CHANNELS)
mode = COLOR;
for (int i=0; ilut.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; iMAX_CHANNELS && getMode()==COMPOSITE)
setMode(COLOR);
setup(nChannels, getImageStack());
}
/* 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 && clut.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 © 2015 - 2025 Weber Informatics LLC | Privacy Policy