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oeway wants to merge 2,030 commits into master from move-dir

.github/workflows/build-imagej.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -22,9 +22,10 @@ jobs: @@
           - name: Compile ImageJ.JS
             run: bash compile-js.sh
           - uses: meeDamian/[email protected]
+            if: github.ref == 'refs/heads/master'
             with:
               token: ${{ secrets.GITHUB_TOKEN }}
-              tag: 1.53m
+              tag: 1.53o
               name: ImageJ.JS
               files: imagej-js-dist/
               allow_override: true

0 src/main/resources/IJ_Props.txt → IJ_Props.txt

File renamed without changes.

compile-js-dev.sh

-Original file line number
+Diff line change
@@ Expand Up / @@ -3,7 +3,7 @@ @@
     set -e
-    IJ_JAR="ij-1.53m.jar"
+    IJ_JAR="ij-1.53o.jar"
     DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
     mvn clean
@@ Expand Down @@

compile-js.sh

-Original file line number
+Diff line change
@@ Expand Up / @@ -25,7 +25,7 @@ cd imagej-js-dist @@
     # download ij153 from imagej.net
     export IJ1_VERSION=ij153
-    export IJ_JAR=ij-1.53m.jar
+    export IJ_JAR=ij-1.53o.jar
     curl http://wsr.imagej.net/distros/cross-platform/${IJ1_VERSION}.zip -LO
     unzip -q -o ${IJ1_VERSION}.zip
@@ Expand Down @@

0 src/main/java/ij/CommandListener.java → ij/CommandListener.java

File renamed without changes.

src/main/java/ij/CompositeImage.java → ij/CompositeImage.java

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -277,12 +277,25 @@ public synchronized void updateImage() {
  
    			rgbImage = null;

    		}

    		cip[currentChannel].setMinAndMax(ip.getMin(),ip.getMax());

    		int projectionMode = ImageProcessor.SUM_PROJECTION;

    		String prop = getProp("CompositeProjection");

    		if (prop!=null) {

    			if (prop.contains("Max")||prop.contains("max"))

    				projectionMode = ImageProcessor.MAX_PROJECTION;

    			if (prop.contains("Min")||prop.contains("min"))

    				projectionMode = ImageProcessor.MIN_PROJECTION;

    			if (prop.contains("Invert")||prop.contains("invert"))

    				projectionMode = ImageProcessor.INVERT_PROJECTION;

    		}

    		long t0 = IJ.debugMode?System.currentTimeMillis():0L;

    		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;

    				case 0: cip[0].updateComposite(rgbPixels, ImageProcessor.UPDATE_RED); break;

    				case 1: cip[1].updateComposite(rgbPixels, ImageProcessor.UPDATE_GREEN); break;

    				case 2: cip[2].updateComposite(rgbPixels, ImageProcessor.UPDATE_BLUE); break;

    			}

    		} else if (projectionMode==ImageProcessor.INVERT_PROJECTION){

    			makeInvertedComposite(active);

    		} else {

    			if (cip==null) return;

    			if (syncChannels) {

    @@ -296,20 +309,104 @@ public synchronized void updateImage() {
  
    				syncChannels = false;

    			}

    			if (active[0])

    				cip[0].updateComposite(rgbPixels, 4);

    			else

    				{for (int i=1; i<imageSize; i++) rgbPixels[i] = 0;}

    				cip[0].updateComposite(rgbPixels, ImageProcessor.SET_FIRST_CHANNEL);

    			else {

    				int fill = projectionMode==ImageProcessor.MIN_PROJECTION?0xffffff:0;

    				for (int i=1; i<imageSize; i++)

    					rgbPixels[i] = fill;

    			}

    			if (cip==null || nChannels>cip.length)

    				return;

    			for (int i=1; i<nChannels; i++)

    				if (active[i]) cip[i].updateComposite(rgbPixels, 5);

    				if (active[i]) cip[i].updateComposite(rgbPixels, projectionMode);

    		}

    		if (IJ.debugMode) IJ.log(""+(System.currentTimeMillis()-t0));

    		createBufferedImage();

    		if (img==null && awtImage!=null)

    			img = awtImage;

    		singleChannel = false;

    	}

    	}		

    	// Creates multi-channel composite view with inverted LUTs

    	// https://forum.image.sc/t/multi-channel-composite-view-with-inverted-luts-in-imagej-fiji/61163

    	// Peter Haub, 12'2021

    	private void makeInvertedComposite(boolean[] chnActive) {

    		int bitDepth = getBitDepth();

    		int w = getWidth();

    		int h = getHeight();

    		int nChn = getNChannels();

    		int nChnActive = 0;

    		for (int c=0; c<nChn; c++){

    			if (chnActive[c])

    				nChnActive++;

    		}		

    		byte[][] in8 = null;

    		short[][] in16 = null;

    		float[][] in32 = null;

    		switch (bitDepth) {

    			case 8: in8=new byte[nChn][]; break;

    			case 16: in16=new short[nChn][]; break;

    			case 32: in32=new float[nChn][]; break;

    		}

    		double[] mins = new double[nChn];

    		double[] maxs = new double[nChn];

    		double[] scale = new double[nChn];		

    		LUT[] luts = getLuts();

    		for (int c=0; c<nChn; c++){

    			mins[c] = cip[c].getMin();

    			maxs[c] = cip[c].getMax();

    			scale[c] = (255.0 / (maxs[c] - mins[c]));			

    			switch (bitDepth) {

    				case 8: in8[c] = (byte[]) cip[c].getPixels(); break;

    				case 16: in16[c] = (short[]) cip[c].getPixels(); break;

    				case 32: in32[c] = (float[]) cip[c].getPixels(); break;

    			}

    		} 

    		int value;

    		int[] v = new int[nChn];

    		int[] r = new int[nChn]; int[] g = new int[nChn]; int[] b = new int[nChn];

    		int sumR, sumG, sumB;

    		int newR, newG, newB;

    		for (int idx=0; idx<w*h; idx++) {

    			for (int c=0; c<nChn; c++){

    				switch (bitDepth) {

    					case 8: v[c] = (int)Math.floor(((in8[c][idx]&0xff)-mins[c])*scale[c]); break;

    					case 16: v[c] = (int)Math.floor(((in16[c][idx]&0xffff)-mins[c])*scale[c]); break;

    					case 32: v[c] = (int)Math.floor((in32[c][idx]-mins[c])*scale[c]); break;

    				}

    				v[c] = Math.min(v[c], 255);

    				v[c] = Math.max(v[c], 0);

    				r[c] = luts[c].getRed(v[c]);

    				g[c] = luts[c].getGreen(v[c]);

    				b[c] = luts[c].getBlue(v[c]);                   

    			}

    			// Modify 'composite merge' condition here

    			sumR = sumG = sumB = 0;

    			for (int c=0; c<nChn; c++){

    				if (chnActive[c]){				

    					sumR += r[c];

    					sumG += g[c];

    					sumB += b[c];

    				}

    			}

    			newR = sumR - (nChnActive-1)*255;

    			newG = sumG - (nChnActive-1)*255;

    			newB = sumB - (nChnActive-1)*255;

    			newR = Math.max(newR, 0);

    			newG = Math.max(newG, 0);

    			newB = Math.max(newB, 0);

    			value = newR*256*256 + newG*256 + newB;

    			rgbPixels[idx] = value;

    		}   

        }

    	void createImage() {

    		if (imageSource==null) {

    			rgbCM = new DirectColorModel(32, 0xff0000, 0xff00, 0xff);

    @@ -412,8 +509,10 @@ public synchronized void setMode(int mode) {
  
    			return;

    		if (mode==COMPOSITE && getNChannels()>MAX_CHANNELS)

    			mode = COLOR;

    		for (int i=0; i<MAX_CHANNELS; i++)

    			active[i] = true;

    		if (!(mode==COMPOSITE && mode==this.mode)) {

    			for (int i=0; i<MAX_CHANNELS; i++)

    				active[i] = true;

    		}

    		if (this.mode!=COMPOSITE && mode==COMPOSITE)

    			img = null;

    		this.mode = mode;

0 src/main/java/ij/Executer.java → ij/Executer.java

File renamed without changes.

src/main/java/ij/IJ.java → ij/IJ.java

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1520,8 +1520,17 @@ public static void setThreshold(ImagePlus img, double lowerThreshold, double upp
  
    		setRawThreshold(img, lowerThreshold, upperThreshold, displayMode);

    	}

    	/** This is a version of setThreshold() that uses raw (uncalibrated)

    	 * values in the range 0-255 for 8-bit images and 0-65535 for 16-bit

    	 * images and the "Red" LUT display mode.

    	*/

    	public static void setRawThreshold(ImagePlus img, double lowerThreshold, double upperThreshold) {

    		setRawThreshold(img, lowerThreshold, upperThreshold, null);

    	}

    	/** This is a version of setThreshold() that always uses raw (uncalibrated) values

    		 in the range 0-255 for 8-bit images and 0-65535 for 16-bit images. */

    	 * in the range 0-255 for 8-bit images and 0-65535 for 16-bit images.

    	*/

    	public static void setRawThreshold(ImagePlus img, double lowerThreshold, double upperThreshold, String displayMode) {

    		int mode = ImageProcessor.RED_LUT;

    		if (displayMode!=null) {

    @@ -1895,8 +1904,9 @@ else if (build.length()==1)
  
    		"home" ("user.home"), "downloads", "startup",  "imagej" (ImageJ directory),

    		"plugins", "macros", "luts", "temp", "current", "default",

    		"image" (directory active image was loaded from), "file" 

    		(directory most recently used to open or save a file) or "cwd"

    		(current working directory), otherwise displays a dialog and

    		(directory most recently used to open or save a file), "cwd"

    		(current working directory) or "preferences" (location of

    		"IJ_Prefs.txt" file), otherwise displays a dialog and

    		returns the path to the directory selected by the user. Returns

    		null if the specified directory is not found or the user cancels the

    		dialog box. Also aborts the macro if the user cancels the

    @@ -1924,6 +1934,8 @@ else if (title2.equals("imagej"))
  
    			dir = Prefs.getImageJDir();

    		else if (title2.equals("current") || title2.equals("default"))

    			dir = OpenDialog.getDefaultDirectory();

    		else if (title2.equals("preferences"))

    			dir = Prefs.getPrefsDir();

    		else if (title2.equals("temp")) {

    			dir = System.getProperty("java.io.tmpdir");

    			if (isMacintosh()) dir = "/tmp/";

    @@ -2151,7 +2163,7 @@ public static void saveAs(String format, String path) {
  
    	public static byte[] saveAsBytes(ImagePlus imp, String format) {

    		String tmp = "/files/tmp";

    		String title = imp.getTitle();

    		tmp = saveAs(imp, format, tmp);

    		saveAs(imp, format, tmp);

    		// recover the title

    		imp.setTitle(title);

    		byte[] bytes = openAsBytes(tmp);

    @@ -2192,9 +2204,9 @@ public static PlugInFrame createPlugInFrame(String title, int x, int y, int widt
  
    	/* Saves the specified image. The format argument must be "tiff",  

    		"jpeg", "gif", "zip", "raw", "avi", "bmp", "fits", "pgm", "png", 

    		"text image", "lut", "selection" or "xy Coordinates". */

     	public static String saveAs(ImagePlus imp, String format, String path) {

     	public static void saveAs(ImagePlus imp, String format, String path) {

    		if (format==null)

    			return null;

    			return;

    		if (path!=null && path.length()==0)

    			path = null;

    		format = format.toLowerCase(Locale.US);

    @@ -2203,15 +2215,15 @@ public static String saveAs(ImagePlus imp, String format, String path) {
  
    			roi2.endPaste();

    		if (format.indexOf("tif")!=-1) {

    			saveAsTiff(imp, path);

    			return path;

    			return;

    		} else if (format.indexOf("jpeg")!=-1 || format.indexOf("jpg")!=-1) {

    			path = updateExtension(path, ".jpg");

    			JpegWriter.save(imp, path, FileSaver.getJpegQuality());

    			return path;

    			return;

    		} else if (format.indexOf("gif")!=-1) {

    			path = updateExtension(path, ".gif");

    			GifWriter.save(imp, path);

    			return path;

    			return;

    		} else if (format.indexOf("text image")!=-1) {

    			path = updateExtension(path, ".txt");

    			format = "Text Image...";

    @@ -2261,7 +2273,6 @@ public static String saveAs(ImagePlus imp, String format, String path) {
  
    			else

    				run(imp, format, "save="+path);

    		}

    		return path;

    	}

    	/** Saves the specified image in TIFF format. Displays a file save dialog

0 src/main/java/ij/IJEventListener.java → ij/IJEventListener.java

File renamed without changes.

src/main/java/ij/ImageJ.java → ij/ImageJ.java

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -79,8 +79,8 @@ public class ImageJ extends Frame implements ActionListener,
  
    	MouseListener, KeyListener, WindowListener, ItemListener, Runnable {

    	/** Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string. */

    	public static final String VERSION = "1.53m";

    	public static final String BUILD = ""; //41

    	public static final String VERSION = "1.53o";

    	public static final String BUILD = ""; //70

    	public static Color backgroundColor = new Color(237,237,237);

    	/** SansSerif, 12-point, plain font. */

    	public static final Font SansSerif12 = new Font("SansSerif", Font.PLAIN, 12);

    @@ -96,6 +96,9 @@ public class ImageJ extends Frame implements ActionListener,
  
    	/** Run embedded and invisible in another application. */

    	public static final int NO_SHOW = 2;

    	/** Run as the ImageJ application. */

    	public static final int IMAGEJ_APP = 3;

    	/** Run ImageJ in debug mode. */

    	public static final int DEBUG = 256;

    @@ -145,6 +148,10 @@ public ImageJ(java.applet.Applet applet, int mode) {
  
    		if ((mode&DEBUG)!=0)

    			IJ.setDebugMode(true);

    		mode = mode & 255;

    		boolean useExceptionHandler = false;

    		if (mode==IMAGEJ_APP) {

    			mode = STANDALONE;

    		}

    		if (IJ.debugMode) IJ.log("ImageJ starting in debug mode: "+mode);

    		embedded = applet==null && (mode==EMBEDDED||mode==NO_SHOW);

    		this.applet = applet;

    @@ -226,7 +233,7 @@ public ImageJ(java.applet.Applet applet, int mode) {
  
    		} 

    		if (applet==null)

    			IJ.runPlugIn("ij.plugin.DragAndDrop", "");

    		if (!getTitle().contains("Fiji")) {

    		if (!getTitle().contains("Fiji") && useExceptionHandler) {

    			Thread.setDefaultUncaughtExceptionHandler(new ExceptionHandler());

    			System.setProperty("sun.awt.exception.handler",ExceptionHandler.class.getName());

    		}

    @@ -712,7 +719,7 @@ public void savePreferences(Properties prefs) {
  
    	public static void main(String args[]) {

    		boolean noGUI = false;

    		int mode = STANDALONE;

    		int mode = IMAGEJ_APP;

    		arguments = args;

    		int nArgs = args!=null?args.length:0;

    		boolean commandLine = false;

    @@ -741,7 +748,7 @@ else if (delta>0 && DEFAULT_PORT+delta<65536)
  
    			} 

    		}

      		// If existing ImageJ instance, pass arguments to it and quit.

      		boolean passArgs = mode==STANDALONE && !noGUI;

      		boolean passArgs = (mode==IMAGEJ_APP||mode==STANDALONE) && !noGUI;

    		if (IJ.isMacOSX() && !commandLine)

    			passArgs = false;

    		if (passArgs && isRunning(args))

0 src/main/java/ij/ImageJApplet.java → ij/ImageJApplet.java

File renamed without changes.

0 src/main/java/ij/ImageListener.java → ij/ImageListener.java

File renamed without changes.

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