2024.06.28 (1.54k8; RoiManager select)

imagej · Jun 28, 2024 · 8799326 · 8799326
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diff --git a/functions.html b/functions.html
@@ -14,7 +14,7 @@
 <font color="#224488">
 
 <a name="Top"></a>
-<p class=navbar> <a href="https://imagej.nih.gov/ij/">home</a> | <a href="https://imagej.nih.gov/ij/download.html">download</a> | <a href="https://imagej.nih.gov/ij/developer/index.html">resources</a></p>
+<p class=navbar> <a href="https://imagej.net/ij/">home</a> | <a href="https://imagej.net/ij/download.html">download</a> | <a href="https://imagej.net/ij/developer/index.html">resources</a></p>
 <h1>Built-in Macro Functions</h1>
 
 </font>
@@ -5463,9 +5463,9 @@ <h1>Built-in Macro Functions</h1>
 
 </blockquote>
 
-<p class=navbar> <a href="#Top">top</a> | <a href="https://imagej.nih.gov/ij/index.html">home</a></p>
+<p class=navbar> <a href="#Top">top</a> | <a href="https://imagej.net/ij/index.html">home</a></p>
 
-<small>Last updated 2024-06-12</small>
+<small>Last updated 2024-06-17</small>
 
 </body>
 </html>
diff --git a/ij/CommandListener.java b/ij/CommandListener.java
@@ -2,7 +2,7 @@
 
 	/** Plugins that implement this interface are notified when ImageJ
 		is about to run a menu command. There is an example plugin at
-		http://imagej.nih.gov/ij/plugins/download/misc/Command_Listener.java
+		http://imagej.net/ij/plugins/download/misc/Command_Listener.java
 	*/
 	public interface CommandListener {
 

diff --git a/ij/IJ.java b/ij/IJ.java
@@ -42,7 +42,7 @@ public class IJ {
 	public static final int COMPOSITE=1, COLOR=2, GRAYSCALE=3;
 
 	/** @deprecated */
-	public static final String URL = "http://imagej.nih.gov/ij";
+	public static final String URL = "http://imagej.net/ij";
 
 	/** ImageJ website */
 	public static final String URL2 = "http://imagej.net/ij";
@@ -534,7 +534,7 @@ public static void showStatus(String message, String options) {
 	* @deprecated
 	* replaced by IJ.log(), ResultsTable.setResult() and TextWindow.append().
 	* There are examples at
-	*   http://imagej.nih.gov/ij/plugins/sine-cosine.html
+	*   http://imagej.net/ij/plugins/sine-cosine.html
 	*/
 	public static void write(String s) {
 		if (textPanel==null && ij!=null)
@@ -799,7 +799,7 @@ public static void showMessage(String msg) {
 	/** Displays a message in a dialog box with the specified title.
 		Displays HTML formatted text if 'msg' starts with "<html>".
 		There are examples at
-		"http://imagej.nih.gov/ij/macros/HtmlDialogDemo.txt".
+		"http://imagej.net/ij/macros/HtmlDialogDemo.txt".
 		Writes to the Java console if ImageJ is not present. */
 	public static void showMessage(String title, String msg) {
 		if (ij!=null) {

diff --git a/ij/ImageJ.java b/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 = "1.54k";
-	public static final String BUILD = "3";
+	public static final String BUILD = "8";
 	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);

diff --git a/ij/gui/GenericDialog.java b/ij/gui/GenericDialog.java
@@ -627,7 +627,7 @@ public void addCheckboxGroup(int rows, int columns, String[] labels, boolean[] d
 	* @param labels			the labels
 	* @param defaultValues	the initial states
 	* @param headings	the column headings
-	* Example: http://imagej.nih.gov/ij/plugins/multi-column-dialog/index.html
+	* Example: http://imagej.net/ij/plugins/multi-column-dialog/index.html
 	*/
 	public void addCheckboxGroup(int rows, int columns, String[] labels, boolean[] defaultValues, String[] headings) {
 		Panel panel = new Panel();
@@ -1903,7 +1903,7 @@ public void windowClosing(WindowEvent e) {
 	/** Adds a "Help" button that opens the specified URL in the default browser.
 		With v1.46b or later, displays an HTML formatted message if
 		'url' starts with "<html>". There is an example at
-		http://imagej.nih.gov/ij/macros/js/DialogWithHelp.js
+		http://imagej.net/ij/macros/js/DialogWithHelp.js
 		If url is an empty String, pressing the "Help" button does nothing except
 	calling the DialogListeners (if any). See also: setHelpLabel.
 	*/

diff --git a/ij/gui/ProfilePlot.java b/ij/gui/ProfilePlot.java
@@ -8,7 +8,7 @@
 import ij.measure.*;
 import ij.plugin.Straightener;
 
-/** Creates a density profile plot of a rectangular selection or line selection. */
+/** Creates a density profile plot of a line or rectangular selection. */
 public class ProfilePlot {
 
 	static final int MIN_WIDTH = 350;
@@ -30,12 +30,22 @@ public class ProfilePlot {
 	public ProfilePlot() {
 	}
 
+	/** Based on the current line or rectangular selection,
+	 * creates a profile plot that can be retrieved using
+	 * the getPlot() method.
+	*/
 	public ProfilePlot(ImagePlus imp) {
 		this(imp, false);
 	}
 
-	public ProfilePlot(ImagePlus imp, boolean averageHorizontally) {
+	/** Based on the current rectangular selection,
+	 * creates profile plot, which is a vertical if
+	 * verticalPlot is 'true'. Use the getPlot() method
+	 * to retrieve the plot.
+	*/
+	public ProfilePlot(ImagePlus imp, boolean verticalPlot) {
 		this.imp = imp;
+		boolean averageHorizontally = verticalPlot;
 		Roi roi = imp.getRoi();
 		if (roi==null) {
 			IJ.error("Profile Plot", "Selection required.");
@@ -104,6 +114,7 @@ public void createWindow() {
 			plot.show();
 	}
 
+	/** Returns the profile plot as a Plot object. */
 	public Plot getPlot() {
 		if (profile==null)
 			return null;
@@ -283,22 +294,6 @@ public static double[] getColumnAverageProfile(Rectangle rect, ImageProcessor ip
 		return values2;
 	}
 
-	/*
-	double[] getIrregularProfile(Roi roi, ImageProcessor ip, Calibration cal) {
-		boolean interpolate = PlotWindow.interpolate;
-		FloatPolygon p = roi.getFloatPolygon();
-		float[][] xyPoints = ((PolygonRoi)roi).getEquidistantPoints(p.xpoints, p.ypoints, p.npoints, 1.0, imp);
-		float[] xPoints = xyPoints[0];
-		float[] yPoints = xyPoints[1];
-		double[] values = new double[xPoints.length];
-		for (int i=0; i<xPoints.length; i++)
-			values[i] = interpolate ?
-				ip.getInterpolatedValue(xPoints[i], yPoints[i]) :
-				ip.getPixelValue((int)Math.round(xPoints[i]), (int)Math.round(yPoints[i]));
-		return values;
-	}
-	*/
-
 	double[] getWideLineProfile(ImagePlus imp, int lineWidth) {
 		Roi roi = imp.getRoi();
 		if (roi == null) return null;	//roi may have changed asynchronously

diff --git a/ij/gui/TextRoi.java b/ij/gui/TextRoi.java
@@ -117,7 +117,7 @@ public TextRoi(int x, int y, String text, Font font, Color color) {
 		super(x, y, 1, 1);
 		if (font==null) font = new Font(name, style, size);
 		this.font = font;
-		IJ.error("TextRoi", "API has changed. See updated example at\nhttp://imagej.nih.gov/ij/macros/js/TextOverlay.js");
+		IJ.error("TextRoi", "API has changed. See updated example at\nhttp://imagej.net/ij/macros/js/TextOverlay.js");
 	}
 
 	public TextRoi(int x, int y, ImagePlus imp) {

diff --git a/ij/gui/Toolbar.java b/ij/gui/Toolbar.java
@@ -1738,7 +1738,7 @@ public void mouseMoved(MouseEvent e) {
 
 	/** Adds a tool to the toolbar. The 'toolTip' string is displayed in the status bar
 		 when the mouse is over the tool icon. The 'toolTip' string may include icon 
-		(http://imagej.nih.gov/ij/developer/macro/macros.html#tools).
+		(http://imagej.net/ij/developer/macro/macros.html#tools).
 		Returns the tool ID, or -1 if all tool slots are in use. */
 	public int addTool(String toolTip) {
 		int index = toolTip.indexOf('-');

diff --git a/ij/io/FileOpener.java b/ij/io/FileOpener.java
@@ -48,9 +48,10 @@ public FileOpener(FileInfo fi) {
 
 	/** Opens the image and returns it has an ImagePlus object. */
 	public ImagePlus openImage() {
-		Recorder.suspendRecording();
+		boolean headless = GraphicsEnvironment.isHeadless();
+		if (!headless) Recorder.suspendRecording();
 		ImagePlus imp = open(false);
-		Recorder.resumeRecording();
+		if (!headless) Recorder.resumeRecording();
 		return imp;
 	}
 

diff --git a/ij/plugin/ChannelArranger.java b/ij/plugin/ChannelArranger.java
@@ -83,7 +83,7 @@ public void run(String arg) {
 		The following example opens the FluorescentCells sample  
 		image and reverses the order of the channels.
 		<pre>
-		ImagePlus img = IJ.openImage("http://imagej.nih.gov/ij/images/FluorescentCells.zip");
+		ImagePlus img = IJ.openImage("http://imagej.net/ij/images/FluorescentCells.zip");
 		int[] order = {3,2,1};
 		ImagePlus img2 = ChannelArranger.run(img, order);
 		img2.setDisplayMode(IJ.COLOR);

diff --git a/ij/plugin/Duplicator.java b/ij/plugin/Duplicator.java
@@ -85,16 +85,18 @@ else if (duplicateStack || imp.getStackSize()==1) {
 			imp2 = crop(imp);
 			recordCrop(imp);
 		}
-		if (ignoreSelection && roi!=null)
+		if (ignoreSelection && roi!=null) {
 			imp.setRoi(roi);
+			imp2.setRoi((Roi)roi.clone());
+		}
 		Calibration cal = imp2.getCalibration();
 		if (roi!=null && (cal.xOrigin!=0.0||cal.yOrigin!=0.0)) {
 			cal.xOrigin -= roi.getBounds().x;
 			cal.yOrigin -= roi.getBounds().y;
 		}	
 		imp2.setTitle(newTitle);
 		imp2.setProp("UniqueName","true");
-		if (roi!=null && roi.isArea() && roi.getType()!=Roi.RECTANGLE) {
+		if (roi!=null && !ignoreSelection && roi.isArea() && roi.getType()!=Roi.RECTANGLE) {
 			Roi roi2 = cropRoi(imp, roi);
 			if (roi2==null)
 				return;

diff --git a/ij/plugin/FFT.java b/ij/plugin/FFT.java
@@ -14,7 +14,7 @@
 This class implements the FFT, Inverse FFT and Redisplay Power Spectrum commands 
 in the Process/FFT submenu. It is based on Arlo Reeves'	 
 Pascal implementation of the Fast Hartley Transform from NIH Image 
-(http://imagej.nih.gov/ij/docs/ImageFFT/). 
+(http://imagej.net/ij/docs/ImageFFT/). 
 The Fast Hartley Transform was restricted by U.S. Patent No. 4,646,256, but was placed 
 in the public domain by Stanford University in 1995 and is now freely available.
 

diff --git a/ij/plugin/ImageCalculator.java b/ij/plugin/ImageCalculator.java
@@ -10,8 +10,8 @@
 /** This plugin implements the Process/Image Calculator command.
 <pre>
    // test script
-   imp1 = IJ.openImage("http://imagej.nih.gov/ij/images/boats.gif")
-   imp2 = IJ.openImage("http://imagej.nih.gov/ij/images/bridge.gif")
+   imp1 = IJ.openImage("http://imagej.net/ij/images/boats.gif")
+   imp2 = IJ.openImage("http://imagej.net/ij/images/bridge.gif")
    imp3 = ImageCalculator.run(imp1, imp2, "add create 32-bit");
    imp3.show();
 </pre>

diff --git a/ij/plugin/Macro_Runner.java b/ij/plugin/Macro_Runner.java
@@ -287,7 +287,7 @@ private static String runScript(Object plugin, String script, String arg) {
 	/** Runs a BeanShell script on the current thread, passing a string argument, 
 		which the script can retrieve using the getArgument() function. Returns,
 		as a string, the last expression evaluated by the script.
-		Uses the plugin at http://imagej.nih.gov/ij/plugins/bsh/
+		Uses the plugin at http://imagej.net/ij/plugins/bsh/
 		to run the script.
 	*/
 	public static String runBeanShell(String script, String arg) {
@@ -309,7 +309,7 @@ public static String runBeanShell(String script, String arg) {
 		which the script can retrieve using the getArgument() function. Returns,
 		as a string, the value of the variable 'result'. For example, a Python script  
 		containing the line "result=123" will return the string "123".
-		Uses the plugin at http://imagej.nih.gov/ij/plugins/jython/
+		Uses the plugin at http://imagej.net/ij/plugins/jython/
 		to run the script.
 	*/
 	public static String runPython(String script, String arg) {

diff --git a/ij/plugin/ZProjector.java b/ij/plugin/ZProjector.java
@@ -72,7 +72,7 @@ public static ImagePlus run(ImagePlus imp, String method) {
 	/** Performs projection using the specified method and stack range, and returns
 		 the result, where 'method' is "avg", "min", "max", "sum", "sd" or "median".
 		Add " all" to 'method' to project all hyperstack time points. <br>
-		Example: http://imagej.nih.gov/ij/macros/js/ProjectionDemo.js
+		Example: http://imagej.net/ij/macros/js/ProjectionDemo.js
 	*/
 	 public static ImagePlus run(ImagePlus imp, String method, int startSlice, int stopSlice) {
     	ZProjector zp = new ZProjector(imp);

diff --git a/ij/plugin/filter/Benchmark.java b/ij/plugin/filter/Benchmark.java
@@ -7,7 +7,7 @@
 /** Implements the Plugins/Utilities/Run Benchmark command when
 	the current image is 512x512 and RGB. Results and additional
 	benchmarks are available at<br> 
-	"http://imagej.nih.gov/ij/plugins/benchmarks.html". */
+	"http://imagej.net/ij/plugins/benchmarks.html". */
 public class Benchmark implements PlugInFilter{
 
 	String arg;

diff --git a/ij/plugin/filter/FFTFilter.java b/ij/plugin/filter/FFTFilter.java
@@ -9,7 +9,7 @@
 
 /** 
 This class implements the Process/FFT/Bandpass Filter command. It is based on 
-Joachim Walter's FFT Filter plugin at "http://imagej.nih.gov/ij/plugins/fft-filter.html".
+Joachim Walter's FFT Filter plugin at "http://imagej.net/ij/plugins/fft-filter.html".
 2001/10/29: First Version (JW)
 2003/02/06: 1st bugfix (works in macros/plugins, works on stacks, overwrites image(=>filter)) (JW)
 2003/07/03: integrated into ImageJ, added "Display Filter" option (WSR)

diff --git a/ij/plugin/filter/MaximumFinder.java b/ij/plugin/filter/MaximumFinder.java
@@ -249,7 +249,7 @@ public void run(ImageProcessor ip) {
 
     /** Finds the image maxima and returns them as a Polygon, where
      * poly.npoints is the number of maxima. There is an example at<br>
-     * http://imagej.nih.gov/ij/macros/js/FindMaxima.js.
+     * http://imagej.net/ij/macros/js/FindMaxima.js.
      * @param ip             The input image
      * @param tolerance      Height tolerance: maxima are accepted only if protruding more than this value
      *                       from the ridge to a higher maximum

diff --git a/ij/plugin/filter/ParticleAnalyzer.java b/ij/plugin/filter/ParticleAnalyzer.java
@@ -1194,7 +1194,7 @@ public static void setLineWidth(int width) {
 
 	/** Sets the RoiManager to be used by the next ParticleAnalyzer 
 		instance. There is a JavaScript example at
-		http://imagej.nih.gov/ij/macros/js/HiddenRoiManager.js
+		http://imagej.net/ij/macros/js/HiddenRoiManager.js
 	*/
 	public static void setRoiManager(RoiManager manager) {
 		staticRoiManager = manager;

diff --git a/ij/plugin/frame/Editor.java b/ij/plugin/frame/Editor.java
@@ -614,7 +614,7 @@ public void evaluateScript(String ext) {
 			plugin = "bsh";
 			url = "/plugins/bsh/BeanShell.jar";
 		} else {
-			// download Jython from http://imagej.nih.gov/ij/plugins/jython/
+			// download Jython from http://imagej.net/ij/plugins/jython/
 			plugin = "Jython";
 			url = "/plugins/jython/Jython.jar";
 		}