2023.05.15 (1.54e46; Spectrum Plot)

ij/ImageJ.java

@@ -79,7 +79,7 @@ public class ImageJ extends Frame implements ActionListener,
 
 	/** Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string. */
 	public static final String VERSION = "1.54e";
-	public static final String BUILD = "37";
+	public static final String BUILD = "46";
 	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/Menus.java

@@ -299,6 +299,7 @@ public static Menu getExamplesMenu(ActionListener listener) {
 		addExample(submenu, "Plot Styles", "Plot_Styles_.ijm");
 		addExample(submenu, "Random Data", "Random_Data_.ijm");
 		addExample(submenu, "Plot Results", "Plot_Results_.ijm");
+		addExample(submenu, "Plot With Spectrum", "Plot_With_Spectrum_.ijm");
 		submenu.addActionListener(listener);
 		menu.add(submenu);
 

ij/VirtualStack.java

@@ -107,10 +107,10 @@ public void addSlice(String sliceLabel, ImageProcessor ip, int n) {
 
 	/** Deletes the specified slice, where {@literal 1<=n<=nslices}. */
 	public void deleteSlice(int n) {
+		if (nSlices==0)
+			return;
 		if (n<1 || n>nSlices)
 			throw new IllegalArgumentException("Argument out of range: "+n);
-		if (nSlices<1)
-			return;
 		for (int i=n; i<nSlices; i++)
 			names[i-1] = names[i];
 		names[nSlices-1] = null;

ij/macro/Functions.java

@@ -8243,7 +8243,7 @@ static boolean isStringFunction(String name, int type) {
 				break;
 			case COLOR:
 				if (name.equals("foreground") || name.equals("background")
-				|| name.equals("toString"))
+				|| name.equals("toString") || name.equals("wavelengthToColor"))
 					isString = true;
 				break;
 		}
@@ -8340,6 +8340,9 @@ private Variable doColor() {
 		} else if (name.equals("getLut")) {
 			getLut();
 			return null;
+		} else if (name.equals("wavelengthToColor")) {
+			Color c = Colors.wavelengthToColor(getArg());
+			return new Variable(Colors.colorToString(c));
 		} else
 			interp.error("Unrecognized Color function");
 		return null;

ij/plugin/Colors.java

@@ -15,6 +15,9 @@ public class Colors implements PlugIn, ItemListener {
 	private static final String[] colors2 = {"Red","Green","Blue","Magenta","Cyan","Yellow","Orange","Black","White","Gray","lightGray","darkGray","Pink"};
 	private Choice fchoice, bchoice, schoice;
 	private Color fc2, bc2, sc2;
+	private static final double gamma = 0.8;
+	private static final double intensityMax = 255;
+
 
  	public void run(String arg) {
 		showDialog();
@@ -273,4 +276,52 @@ public static String[] getColors(String... moreColors) {
 			names.add(arg);
 		return (String[])names.toArray(new String[names.size()]);
 	}
+
+	/** Converts a wavelength (380-750 nm) to color.
+	 * Based on the wavelength_to_rgb.R program at
+	 * https://gist.github.com/friendly/67a7df339aa999e2bcfcfec88311abfc,
+	 * which in turn is based on a FORTRAN program at
+	 * http://www.physics.sfasu.edu/astro/color.html.
+	 * Thia method is used the the LutLoader class to 
+	 * generate the "Spectrum" LUT.
+	*/
+	public static Color wavelengthToColor(double wl) {
+		double R, G, B;
+		if (wl >= 380 & wl <= 440) {
+			double attenuation = 0.3 + 0.7 * (wl - 380) / (440 - 380);
+			R = Math.pow((-(wl - 440) / (440 - 380) * attenuation), gamma);
+			G = 0.0;
+			B = Math.pow((1.0 * attenuation), gamma);
+		} else if (wl >= 440 & wl <= 490) {
+			R = 0.0;
+			G = Math.pow(((wl - 440) / (490 - 440)), gamma);
+			B = 1.0;
+		} else if (wl >= 490 & wl <= 510) {
+			R = 0.0;
+			G = 1.0;
+			B = Math.pow((-(wl - 510) / (510 - 490)), gamma);
+		} else if (wl >= 510 & wl <= 580) {
+			R = Math.pow(((wl - 510) / (580 - 510)), gamma);
+			G = 1.0;
+			B = 0.0;
+		} else if (wl >= 580 & wl <= 645) {
+			R = 1.0;
+			G = Math.pow((-(wl - 645) / (645 - 580)), gamma);
+			B = 0.0;
+		} else if (wl >= 645 & wl <= 750) {
+			double attenuation = 0.3 + 0.7 * (750 - wl) / (750 - 645);
+			R = Math.pow((1.0 * attenuation), gamma);
+			G = 0.0;
+			B = 0.0;
+		} else {
+			R = 0.0;
+			G = 0.0;
+			B = 0.0;
+		}
+		R = Math.floor(R*255);
+		G = Math.floor(G*255);
+		B = Math.floor(B*255);
+		return new Color((int)R, (int)G, (int)B);
+	}
+
 }

ij/plugin/LutLoader.java

@@ -227,9 +227,9 @@ int ice(byte[] reds, byte[] greens, byte[] blues) {
 	}
 
 	int spectrum(byte[] reds, byte[] greens, byte[] blues) {
-		Color c;
 		for (int i=0; i<256; i++) {
-			c = Color.getHSBColor(i/255f, 1f, 1f);
+			double wavelength = 380 + i*(700-380)/255.0;
+			Color c = Colors.wavelengthToColor(wavelength);
 			reds[i] = (byte)c.getRed();
 			greens[i] = (byte)c.getGreen();
 			blues[i] = (byte)c.getBlue();

ij/plugin/SubstackMaker.java

@@ -31,7 +31,6 @@ public class SubstackMaker implements PlugIn {
 	private static boolean staticNoCreate;
 	private boolean noCreate;
 	private boolean methodCall;
-	private boolean isFFMPEG;
 
 	public void run(String arg) {
 		ImagePlus imp = IJ.getImage();
@@ -40,16 +39,16 @@ public void run(String arg) {
 			return;
 		}
 		ImageStack stack = imp.getStack();
-		if (stack.isVirtual() && stack.getClass().getName().contains("ffmpeg")) {
-			// stacks opened with FFMPEG plugin do not support delete
-			isFFMPEG = true;
-		} 
+		int size1 = stack.size();
 		String userInput = showDialog();
 		if (userInput==null)
 			return;
 		ImagePlus imp2 = makeSubstack(imp, userInput);
 		if (imp2!=null && !noCreate)
 			imp2.show();
+		// stacks opened with FFMPEG and BioFormats plugins do not support slice delete
+		if (delete && stack.isVirtual() && stack.size()==size1)
+			IJ.log("This virtual stack does not support delete: "+stack.getClass().getName());
 	}
 
 	/**
@@ -62,11 +61,11 @@ public void run(String arg) {
 	public static ImagePlus run(ImagePlus imp, String rangeOrList) {
 		SubstackMaker sm = new SubstackMaker();
 		sm.delete = rangeOrList.contains("delete ");
-		sm.noCreate = rangeOrList.contains("do ");
+		sm.noCreate = rangeOrList.contains("do_not ");
 		if (sm.delete)
 			rangeOrList = rangeOrList.replace("delete ","");
 		if (sm.noCreate) {
-			rangeOrList = rangeOrList.replace("do ","");
+			rangeOrList = rangeOrList.replace("do_not ","");
 			sm.delete = true;
 		}
 		sm.methodCall = true;
@@ -132,6 +131,7 @@ public ImagePlus makeSubstack(ImagePlus imp, String userInput) {
 				imp2 = stackList(imp, count, numList, stackTitle);
 			}
 		} catch (Exception e) {
+			IJ.showProgress(1,1);
 			IJ.error("Substack Maker", "Invalid input string:  \n \n  \""+userInput+"\"");
 		}
 		if (hasFrames && imp2!=null)
@@ -154,32 +154,24 @@ String showDialog() {
 		gd.setInsets(10,45,0);
 		gd.addMessage("Enter a range (e.g. 2-14), a range with increment\n(e.g. 1-100-2) or a list (e.g. 7,9,25,27)", null, Color.darkGray);
 		gd.addStringField("Slices:", "", 40);
-		if (!isFFMPEG) {
-			gd.addCheckbox("Delete slices from original stack", delete);
-			gd.addCheckbox("Do not create substack", noCreate);
-		} else
-			gd.addMessage("FFMPEG plugin does not support virtual stack delete");
+		gd.addCheckbox("Delete slices from original stack", delete);
+		gd.addCheckbox("Do_not create substack", noCreate);
 		gd.showDialog();
 		if (gd.wasCanceled())
 			return null;
 		else {
 			String userInput = gd.getNextString();
-			if (isFFMPEG) {
-				staticDelete = delete = false;
-				staticNoCreate = noCreate = false;
-			} else {
-				delete = gd.getNextBoolean();
-				noCreate = gd.getNextBoolean();
-				if (noCreate)
-					staticDelete = delete = true;
-			}
+			delete = gd.getNextBoolean();
+			noCreate = gd.getNextBoolean();
+			if (noCreate)
+				staticDelete = delete = true;
 			if (!isMacro) {
 				staticDelete = delete;
 				staticNoCreate = noCreate;
 			}
 			options = "";
+			if (noCreate) options = "do_not "+options;
 			if (delete) options = "delete "+options;
-			if (noCreate) options = "do "+options;
 			Recorder.recordCall("SubstackMaker.run(imp, \""+options+userInput+"\");");
 			return userInput;
 		}
@@ -194,16 +186,17 @@ ImagePlus stackList(ImagePlus imp, int count, int[] numList, String stackTitle)
 		double max = imp.getDisplayRangeMax();
 		Roi roi = imp.getRoi();
 		boolean dup = imp.getWindow()!=null && !delete;
-		if (noCreate) dup=false;
 		for (int i=0, j=0; i<count; i++) {
 			int currSlice = numList[i]-j;
-			ImageProcessor ip2 = stack.getProcessor(currSlice);
-			ip2.setRoi(roi);
-			if (!methodCall || !delete)
-				ip2 = ip2.crop();
-			if (stack2==null)
-				stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
-			stack2.addSlice(stack.getSliceLabel(currSlice), dup?ip2.duplicate():ip2);
+			if (!noCreate) {
+				ImageProcessor ip2 = stack.getProcessor(currSlice);
+				ip2.setRoi(roi);
+				if (!methodCall || !delete)
+					ip2 = ip2.crop();
+				if (stack2==null)
+					stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
+				stack2.addSlice(stack.getSliceLabel(currSlice), dup?ip2.duplicate():ip2);
+			}
 			if (delete) {
 				stack.deleteSlice(currSlice);
 				j++;
@@ -217,6 +210,8 @@ ImagePlus stackList(ImagePlus imp, int count, int[] numList, String stackTitle)
 			if (swin!=null)
 				swin.updateSliceSelector();
 		}
+		if (stack2==null)
+			return null;
 		ImagePlus impSubstack = imp.createImagePlus();
 		impSubstack.setStack(stackTitle, stack2);
 		if (virtualStack)
@@ -234,16 +229,17 @@ ImagePlus stackRange(ImagePlus imp, int first, int last, int inc, String title)
 		Roi roi = imp.getRoi();
 		boolean showProgress = stack.size()>400 || stack.isVirtual();
 		boolean dup = imp.getWindow()!=null && !delete;
-		if (noCreate) dup=false;
 		for (int i= first, j=0; i<= last; i+=inc) {
 			if (showProgress) IJ.showProgress(i,last);
 			int currSlice = i-j;
-			ImageProcessor ip2 = stack.getProcessor(currSlice);
-			ip2.setRoi(roi);
-			ip2 = ip2.crop();
-			if (stack2==null)
-				stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
-			stack2.addSlice(stack.getSliceLabel(currSlice), dup?ip2.duplicate():ip2);
+			if (!noCreate) {
+				ImageProcessor ip2 = stack.getProcessor(currSlice);
+				ip2.setRoi(roi);
+				ip2 = ip2.crop();
+				if (stack2==null)
+					stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
+				stack2.addSlice(stack.getSliceLabel(currSlice), dup?ip2.duplicate():ip2);
+			}
 			if (delete) {
 				stack.deleteSlice(currSlice);
 				j++;
@@ -257,6 +253,8 @@ ImagePlus stackRange(ImagePlus imp, int first, int last, int inc, String title)
 			if (swin!=null)
 				swin.updateSliceSelector();
 		}
+		if (stack2==null)
+			return null;
 		ImagePlus substack = imp.createImagePlus();
 		substack.setStack(title, stack2);
 		substack.setCalibration(imp.getCalibration());

release-notes.html

@@ -5,8 +5,11 @@
 </head>
 <body>
 
-<li> <u>1.54e37  11 May 2023</u>
+<li> <u>1.54e46  15 May 2023</u>
 <ul>
+<li> Thanks to Jerome Mutterer, added the
+<i>Help&gt;Examples&gt;Plots&gt;Plot with Spectrum</i>
+example macro.
 <li> Thanks to Jerome Mutterer, selections can now be both
 filled and outlined.  For an example, use the new
 <i>Help&gt;Examples&gt;Macro&gt;Easter Eggs</i>
@@ -27,6 +30,9 @@
 command works with composite selections with holes.
 <li> Thanks to Philippe Carl and Michael Schmid, added the
 Plot.eneableLive() macro function.
+<li> Thanks to Jerome Mutterer, added the Color.wavelengthToColor()
+macro function and the Colors.wavelengthToColor() method,
+which is now used to generate the "Spectrum" LUT.
 <li> Thanks to Michael Schmid, fixed issue with thresholding of 16-bit
 and float images with inverting LUTs.
 <li> Thanks to 'Jossie', fixed problem with <i>Image&gt;Color&gt;Make Composite</i>