ij.plugin.RGBStackConverter Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of ij Show documentation
ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.
The newest version!
package ij.plugin;
import java.awt.*;
import ij.*;
import ij.process.*;
import ij.gui.*;

/** Converts a 2 or 3 slice stack, or a hyperstack, to RGB. */
public class RGBStackConverter implements PlugIn, DialogListener {
	private int channels1, slices1, frames1;
	private int slices2, frames2;
	private int width, height;
	private double imageSize;
	private static boolean staticKeep = true;
	private boolean keep;
	private ImagePlus image;
	
	public void run(String arg) {
		ImagePlus imp = image;
		if (imp==null)
			imp = IJ.getImage();
		if (!IJ.isMacro()) keep = staticKeep;
		CompositeImage cimg = imp.isComposite()?(CompositeImage)imp:null;
		int size = imp.getStackSize();
		if ((size<2||size>3) && cimg==null) {
			IJ.error("A 2 or 3 image stack, or a HyperStack, required");
			return;
		}
		int type = imp.getType();
		if (cimg==null && !(type==ImagePlus.GRAY8 || type==ImagePlus.GRAY16)) {
			IJ.error("8-bit or 16-bit grayscale stack required");
			return;
		}
		if (!imp.lock())
			return;
		Undo.reset();
		String title = imp.getTitle()+" (RGB)";
		if (cimg!=null)
			compositeToRGB(cimg, title);
		else if (type==ImagePlus.GRAY16) {
			sixteenBitsToRGB(imp);
		} else {
			ImagePlus imp2 = imp.createImagePlus();
			imp2.setStack(title, imp.getStack());
	 		ImageConverter ic = new ImageConverter(imp2);
			ic.convertRGBStackToRGB();
			imp2.show();
		}
		imp.unlock();
	}
	
	/** Converts the specified multi-channel (composite) image to RGB. */
	public static void convertToRGB(ImagePlus imp) {
		if (!imp.isComposite())
			throw new IllegalArgumentException("Multi-channel image required");
		RGBStackConverter converter = new RGBStackConverter();
		ImageWindow win = imp.getWindow();
		Point location = null;
		if (win!=null) {
			location = win.getLocation();
			imp.hide();
		}
		converter.image = imp;
		converter.run("");
		if (win!=null) {
			ImageWindow.setNextLocation(location);
			imp.show();
		}
	}
	
	void compositeToRGB(CompositeImage imp, String title) {
		int channels = imp.getNChannels();
		int slices = imp.getNSlices();
		int frames = imp.getNFrames();
		int images = channels*slices*frames;
		if (channels==images) {
			compositeImageToRGB(imp, title);
			return;
		}
		width = imp.getWidth();
		height = imp.getHeight();
		imageSize = width*height*4.0/(1024.0*1024.0);
		channels1 = imp.getNChannels();
		slices1 = slices2 = imp.getNSlices();
		frames1 = frames2 = imp.getNFrames();
		int c1 = imp.getChannel();
		int z1 = imp.getSlice();
		int t2 = imp.getFrame();
		if (image!=null) {
			slices2 = slices1;
			frames2 = frames1;
			keep = false;
		} else {
			if (!showDialog())
				return;
		}
		//IJ.log("HyperStackReducer-2: "+keep+" "+channels2+" "+slices2+" "+frames2);
		String title2 = keep?WindowManager.getUniqueName(imp.getTitle()):imp.getTitle();
		ImagePlus imp2 = imp.createHyperStack(title2, 1, slices2, frames2, 24);
		convertHyperstack(imp, imp2);
		if (imp.getWindow()==null && !keep) {
			imp.setImage(imp2);
			imp.setOverlay(imp2.getOverlay());
			return;
		}
		imp2.setOpenAsHyperStack(slices2>1||frames2>1);
		Object info = imp.getProperty("Info");
		if (info!=null) imp2.setProperty("Info", info);		
		imp2.setProperties(imp.getPropertiesAsArray());
		imp2.show();
		if (!keep) {
			imp.changes = false;
			imp.close();
		}
		if (imp2.getWindow()!=null)
			IJ.selectWindow(imp2.getID());
	}

	public void convertHyperstack(ImagePlus imp, ImagePlus imp2) {
		int slices = imp2.getNSlices();
		int frames = imp2.getNFrames();
		int c1 = imp.getChannel();
		int z1 = imp.getSlice();
		int t1 = imp.getFrame();
		int i = 1;
		int c = 1;
		ImageStack stack = imp.getStack();
		ImageStack stack2 = imp2.getStack();
		imp.setPositionWithoutUpdate(c1, 1, 1);
		ImageProcessor ip = imp.getProcessor();
		double min = ip.getMin();
		double max = ip.getMax();
		boolean hsbStack = imp.getProp("HSB_Stack")!=null;
		for (int z=1; z<=slices; z++) {
			if (slices==1) z = z1;
			for (int t=1; t<=frames; t++) {
				//IJ.showProgress(i++, n);
				if (frames==1) t = t1;
				//ip = stack.getProcessor(n1);
				imp.setPositionWithoutUpdate(c1, z, t);
				boolean isHSB = hsbStack && imp.getNChannels()==3;
				int n2 = imp2.getStackIndex(c1, z, t);
				if (isHSB) {
					ImagePlus hsbImp = new Duplicator().run(imp, 1, 3, z, z, t, t);
					ImageConverter ic = new ImageConverter(hsbImp);
					ic.convertHSBToRGB();
					stack2.setPixels(hsbImp.getProcessor().getPixels(), n2);				
				} else {
					Image img = imp.getImage();
					stack2.setPixels((new ColorProcessor(img)).getPixels(), n2);				
				}
			}
		}
		imp.setPosition(c1, z1, t1);
		imp2.resetStack();
		imp2.setPosition(1, 1, 1);
		
		//Added by Marcel Boeglin 2013.09.26
		Overlay overlay = imp.getOverlay();
		if (overlay!=null) {
			int firstC = c1, lastC = c1, firstZ = z1, lastZ = z1, firstT = t1, lastT = t1;
			if (imp.isComposite() && ((CompositeImage)imp).getMode()==IJ.COMPOSITE) {
				firstC = 1;
				lastC = imp.getNChannels();
			}
			if (slices2>1) {firstZ = 1; lastZ = slices2;}
			if (frames2>1) {firstT = 1; lastT = frames2;}
			Overlay overlay2 = overlay.duplicate();
			if (slices2>1 && frames2>1)
				overlay2.crop(firstC, lastC, firstZ, lastZ, firstT, lastT);//imp2 is hyperstack : ROI's hypercoordinates are conserved but only those with C = 1 are displayed
			else
				overlay2.crop(c1, c1, firstZ, lastZ, firstT, lastT); //simple stack
			imp2.setOverlay(overlay2);
		}
	}

	void compositeImageToRGB(CompositeImage imp, String title) {
		if (imp.getMode()==IJ.COMPOSITE) {
			ImagePlus imp2 = imp.createImagePlus();
			imp.updateImage();
			imp2.setProcessor(title, new ColorProcessor(imp.getImage()));
			//Added by Marcel Boeglin 2013.09.26
			Overlay overlay = imp.getOverlay();
			Overlay overlay2 = null;
			if (overlay!=null) {
				overlay2 = overlay.duplicate();
				overlay2.crop(1, imp.getNChannels());
				imp2.setOverlay(overlay2);
			}
			if (image!=null && imp.getWindow()==null) {
				imp.setImage(imp2);
				imp.setOverlay(overlay2);
			} else
				imp2.show();
			return;
		}
		ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
		int c = imp.getChannel();
		int n = imp.getNChannels();
		for (int i=1; i<=n; i++) {
			imp.setPositionWithoutUpdate(i, 1, 1);
			stack.addSlice(null, new ColorProcessor(imp.getImage()));
		}
		imp.setPosition(c, 1, 1);
		ImagePlus imp2 = imp.createImagePlus();
		imp2.setStack(title, stack);
		Object info = imp.getProperty("Info");
		if (info!=null) imp2.setProperty("Info", info);		
		imp2.setProperties(imp.getPropertiesAsArray());
		Overlay overlay = imp.getOverlay();
		Overlay overlay2 = null;
		if (overlay!=null) {
			overlay2 = overlay.duplicate();
			overlay2.crop(1, imp.getNChannels());
			imp2.setOverlay(overlay2);
		}
		if (image!=null && imp.getWindow()==null) {
			imp.setImage(imp2);
			imp.setOverlay(overlay2);
		} else {
			imp2.show();
			imp2.setSlice(c);
		}
	}

	void sixteenBitsToRGB(ImagePlus imp) {
		Roi roi = imp.getRoi();
		int width, height;
		Rectangle r;
		if (roi!=null) {
			r = roi.getBounds();
			width = r.width;
			height = r.height;
		} else
			r = new Rectangle(0,0,imp.getWidth(),imp.getHeight());
		ImageProcessor ip;
		ImageStack stack1 = imp.getStack();
		ImageStack stack2 = new ImageStack(r.width, r.height);
		for (int i=1; i<=stack1.getSize(); i++) {
			ip = stack1.getProcessor(i);
			ip.setRoi(r);
			ImageProcessor ip2 = ip.crop();
			ip2 = ip2.convertToByte(true);
			stack2.addSlice(null, ip2);
		}
		ImagePlus imp2 = imp.createImagePlus();
		imp2.setStack(imp.getTitle()+" (RGB)", stack2);
	 	ImageConverter ic = new ImageConverter(imp2);
		ic.convertRGBStackToRGB();
		imp2.show();
	}
	
	boolean showDialog() {
		GenericDialog gd = new GenericDialog("Convert to RGB");
		gd.setInsets(10, 20, 5);
		gd.addMessage("Create RGB image with:");
		gd.setInsets(0, 35, 0);
		if (slices1!=1) gd.addCheckbox("Slices ("+slices1+")", true);
		gd.setInsets(0, 35, 0);
		if (frames1!=1) gd.addCheckbox("Frames ("+frames1+")", true);
		gd.setInsets(5, 20, 0);
		gd.addMessage(getNewDimensions()+"      ");
		gd.setInsets(15, 20, 0);
		gd.addCheckbox("Keep source", keep);
		gd.addDialogListener(this);
		gd.showDialog();
		if (gd.wasCanceled())
			return false;
		else
			return true;
	}

	public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
		if (IJ.isMacOSX()) IJ.wait(100);
		if (slices1!=1) slices2 = gd.getNextBoolean()?slices1:1;
		if (frames1!=1) frames2 = gd.getNextBoolean()?frames1:1;
		keep = gd.getNextBoolean();
		if (!IJ.isMacro()) staticKeep = keep;
		((Label)gd.getMessage()).setText(getNewDimensions());
		return true;
	}
	
	String getNewDimensions() {
		String s1 = slices2>1?"x"+slices2:"";
		String s2 = frames2>1?"x"+frames2:"";
		String s = width+"x"+height+s1+s2;
		s += " ("+(int)Math.round(imageSize*slices2*frames2)+"MB)";
		return(s);
	}

	
}