2024.12.17 (1.54n4; Combine and Straighten)

Author: rasband

ij/ImageJ.java

@@ -78,8 +78,8 @@ 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 = "1.54m";
-	public static final String BUILD = ""; //37
+	public static final String VERSION = "1.54n";
+	public static final String BUILD = "4";
 	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);

ij/plugin/StackCombiner.java

@@ -2,6 +2,7 @@
 import ij.*;
 import ij.process.*;
 import ij.gui.*;
+import ij.io.FileInfo;
 import java.awt.*;
 
 /**
@@ -24,14 +25,25 @@ public void run(String arg) {
 			error();
 			return;
 		}
+		imp1.setDisplayMode(IJ.COLOR);
+		imp2.setDisplayMode(IJ.COLOR);
+		if (LUT.LutsDiffer(imp1,imp2)) {
+			RGBStackConverter.convertToRGB(imp1);
+			RGBStackConverter.convertToRGB(imp2);
+		}
 		int[] dim1 = imp1.getDimensions();
 		int[] dim2 = imp2.getDimensions();
+		boolean isHyperStack1 = imp1.isHyperStack() || imp1.isComposite();
+		boolean isHyperStack2 = imp2.isHyperStack() || imp2.isComposite();
 		if (imp1.isHyperStack() || imp2.isHyperStack()) {
 			if (dim1[2]!=dim2[2] || dim1[3]!=dim2[3] || dim1[4]!=dim2[4]) {
 				IJ.error("StackCombiner", "Hyperstacks must have identical CZT dimensions");	
 				return;
 			}
 		}
+		LUT[] luts = null;
+		if (imp1.isComposite())
+			luts = imp1.getLuts();
 		ImageStack stack1 = imp1.getStack();
 		ImageStack stack2 = imp2.getStack();
 		ImageStack stack3 = vertical?combineVertically(stack1, stack2):combineHorizontally(stack1, stack2);
@@ -41,16 +53,19 @@ public void run(String arg) {
 		imp2.close();
 		ImagePlus imp3 = imp1.createImagePlus();
 		imp3.setStack(stack3);
-		if (imp1.isHyperStack())
+		if (isHyperStack1)
 			imp3.setDimensions(dim1[2],dim1[3],dim1[4]);
 		if (imp1.isComposite()) {
 			imp3 = new CompositeImage(imp3, imp1.getCompositeMode());
 			imp3.setDimensions(dim1[2],dim1[3],dim1[4]);
+			if (luts!=null)
+				((CompositeImage)imp3).setLuts(luts);
+			((CompositeImage)imp3).resetDisplayRanges();
 		}
 		imp3.setTitle("Combined Stacks");
 		imp3.show();
 	}
-	
+		
 	public ImageStack combineHorizontally(ImageStack stack1, ImageStack stack2) {
 		int d1 = stack1.getSize();
 		int d2 = stack2.getSize();

ij/plugin/Straightener.java

@@ -25,7 +25,10 @@ public void run(String arg) {
 		int width = (int)Math.round(roi.getStrokeWidth());
 		boolean isMacro = IJ.macroRunning() && Macro.getOptions()!=null;
 		int stackSize = imp.getStackSize();
-		if (stackSize==1) processStack = false;
+		if (stackSize==1)
+			processStack = false;
+		if (imp.isComposite())
+			processStack = true;
 		String newTitle = WindowManager.getUniqueName(imp.getTitle());
 		if (width<=1 || isMacro || stackSize>1) {
 			if (width<=1) width = 20;
@@ -49,8 +52,21 @@ public void run(String arg) {
 		ImageProcessor ip2 = null;
 		ImagePlus imp2 = null;
 		if (processStack) {
+			boolean compositeMode = imp.isComposite() && imp.getDisplayMode()==IJ.COMPOSITE;
+			if (compositeMode)
+				imp.setDisplayMode(IJ.COLOR);
 			ImageStack stack2 = straightenStack(imp, roi, width);
 			imp2 = new ImagePlus(newTitle, stack2);
+			if (compositeMode)
+				imp.setDisplayMode(IJ.COMPOSITE);
+			if (imp.isComposite()) {
+				ImageConverter.setDoScaling(false);
+				if (imp.getBitDepth()==8)
+					new StackConverter(imp2).convertToGray8();
+				else if (imp.getBitDepth()==16)
+					new StackConverter(imp2).convertToGray16();
+				ImageConverter.setDoScaling(true);
+			}
 		} else {
 			ip2 = straighten(imp, roi, width);
 			imp2 = new ImagePlus(newTitle, ip2);
@@ -61,7 +77,14 @@ public void run(String arg) {
 		Calibration cal = imp.getCalibration();
 		if (cal.pixelWidth==cal.pixelHeight)
 			imp2.setCalibration(cal);
-		imp2.show();
+		if (imp.isComposite()) {
+			LUT[] luts = imp.getLuts();
+			CompositeImage cImp = new CompositeImage(imp2);
+			cImp.setLuts(luts);
+			cImp.setDisplayMode(imp.getDisplayMode());
+			cImp.show();
+		} else
+			imp2.show();
 	}
 
 	public ImageProcessor straighten(ImagePlus imp, Roi roi, int width) {

ij/process/LUT.java

@@ -1,5 +1,5 @@
 package ij.process;
-import ij.IJ;
+import ij.*;
 import ij.plugin.Colors;
 import java.awt.image.*;
 import java.awt.Color;
@@ -107,5 +107,32 @@ public  String toString() {
 		return "rgb[0]="+Colors.colorToString(new Color(getRGB(0)))+", rgb[255]="
 			+Colors.colorToString(new Color(getRGB(255)))+", min="+IJ.d2s(min,4)+", max="+IJ.d2s(max,4);
 	}
+	
+	/** Returns 'true' if the LUTs of these two images differ. */
+	public static boolean LutsDiffer(ImagePlus imp1, ImagePlus imp2) {
+		if (!imp1.isComposite() || !imp2.isComposite())
+			return false;
+		LUT[] luts1 = ((CompositeImage)imp1).getLuts();
+		LUT[] luts2 = ((CompositeImage)imp2).getLuts();
+		if (luts1==null || luts2==null)
+			return false;
+		if (luts1.length!=luts2.length)
+			return true;
+		for (int i=0; i<luts1.length; i++) {
+			if (luts1[i].min!=luts2[i].min)
+				return true;
+			if (luts1[i].max!=luts2[i].max)
+				return true;
+			byte[] bytes1 = luts1[i].getBytes();
+			byte[] bytes2 = luts2[i].getBytes();
+			if (bytes1.length!=bytes2.length)
+				return true;
+			for (int j=0; j<bytes1.length; j++) {
+				if (bytes1[j]!=bytes2[j])
+					return true;
+			}
+		}
+		return false;
+	}
 
 }

release-notes.html

@@ -6,6 +6,14 @@
 <body>
 
 
+<li> <u>1.54n4  17 December 2024</u>
+<ul>
+<li> Thanks to Christophe Leterrier, fixed bugs with how
+the <i>Image&gt;Stacks&gt;Tools&gt;Combine</i> and
+<i>Edit&gt;Selection&gt;Straighten</i> commands handle
+multi-channel images.
+</ul>
+
 <li> <u>1.54m  5 December 2024</u>
 <ul>
 <li> Thanks to Michael Cammer, the <i>Orthogonal Views</i> command