Merge remote-tracking branch 'upstream/master' into master

imjoy-team · Oct 28, 2020 · ba0a59c · ba0a59c
2 parents 105e497 + 4c8b596
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diff --git a/.travis.yml b/.travis.yml
@@ -1,5 +1,5 @@
 language: java
-jdk: openjdk8
+jdk: openjdk11
 branches:
   only:
   - master

diff --git a/README.md b/README.md
@@ -6,3 +6,11 @@ history of the [ImageJ 1.x](https://imagej.net/ImageJ1) project, with a proper
 without hassles.
 
 See the [ImageJA page](https://imagej.net/ImageJA) for details.
+
+## Editing this repository
+
+Because much of the content in this repository is generated automatically, depending on the type of change you want to make your edit should go in one of three places:
+
+* Source file content changes (e.g. bug fixes) should go to the [ImageJ1 repository](https://github.com/imagej/imagej1).
+* Source file *location* changes (e.g. moving a file to the correct package) go in the [IJ1-builds repository](https://github.com/imagej/ij1-builds).
+* Changes to the build structure (e.g. `pom.xml` updates) can be done directly in this repository.
diff --git a/pom.xml b/pom.xml
@@ -11,7 +11,7 @@
 
 	<groupId>net.imagej</groupId>
 	<artifactId>ij</artifactId>
-	<version>1.53e</version>
+	<version>1.53f</version>
 
 	<name>ImageJ</name>
 	<description>ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.</description>
@@ -90,6 +90,7 @@
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sonatype-oss-release</releaseProfiles>
+
 	</properties>
 
 	<dependencies>
@@ -106,6 +107,72 @@
 		</dependency>
 	</dependencies>
 
+	<build>
+		<plugins>
+			<plugin>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>default-compile</id>
+						<configuration>
+							<!-- compile everything to ensure module-info contains right entries -->
+							<!-- required when JAVA_HOME is JDK 8 or below -->
+							<jdkToolchain>
+								<version>9</version>
+							</jdkToolchain>
+							<!-- Exclude MacAdapter because it requires internal packages -->
+							<excludes>
+								<exclude>**/MacAdapter.java</exclude>
+							</excludes>
+							<release>9</release>
+						</configuration>
+					</execution>
+					<execution>
+						<id>complete-recompile</id>
+						<goals>
+							<goal>compile</goal>
+						</goals>
+						<!-- recompile everything for target VM except the module-info.java -->
+						<configuration>
+							<excludes>
+								<exclude>**/module-info.java</exclude>
+							</excludes>
+
+							<!-- Force recompilation. NB: This is the stupidest bug ever.
+								See https://issues.apache.org/jira/browse/MCOMPILER-209
+							-->
+							<useIncrementalCompilation>true</useIncrementalCompilation>
+						</configuration>
+					</execution>
+				</executions>
+				<!-- defaults for compile and testCompile -->
+				<configuration>
+					<!-- jdkToolchain required when JAVA_HOME is JDK 9 or above -->
+					<jdkToolchain>
+						<version>[1.6,8)</version>
+					</jdkToolchain>
+					<source>1.6</source>
+					<target>1.6</target>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-javadoc-plugin</artifactId>
+				<configuration>
+					<!-- Avoid failing due to IJ1 javadoc errors -->
+					<doclint>none</doclint>
+
+					<!-- Required to build with Java 11+
+					     See https://bugs.openjdk.java.net/browse/JDK-8212233
+					 -->
+					<source>8</source>
+					<links>
+						<link>https://imagej.nih.gov/ij/developer/api/</link>
+					</links>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+
 	<profiles>
 		<profile>
 			<id>javac</id>

diff --git a/release-notes.html b/release-notes.html
@@ -5,10 +5,76 @@
 </head>
 <body>
 
-<li> <u>1.53e  12 September 2020</u>
+<li> <u>1.53f  22 October 2020</u>
+<ul>
+<li> Thanks to Wei Ouyang, tool bar and image popup menus are
+now triggered by a long presses in addition to right clicks, This is needed
+because right clicks are not possible when
+<a href="https://ij.imjoy.io/">Image.JS</a>
+is running on Android and iOS devices.
+<li> Thanks to Wei Ouyang, added a popup menu to the
+magnifying glass tool icon.
+<li> Added a popup menu that is triggered when you right click or
+long press inside a selection.
+<li> Updated the built in toolbar "Dev" menu.
+<li> Thanks to Michael Schmid, the text in a text selection can now
+be edited in the <i>Edit&gt;Selection&gt;Properties</i>
+dialog.
+<li> Thanks to Stein Rorvik, the <i>File&gt;Import&gt;Image Sequence</i>
+dialog is used when drag and dropping a folder on the
+"ImageJ" window.
+<li> Thanks to Michael Schmid and Thomas Fischer, Undo works with
+overlays when translating and rotating images and the "Overlay only"
+checkbox is only shown in the Translate dialog when there
+is an overlay.
+<li> Thanks to Robert Haase, added the <i>Edit&gt;Options&gt;Fresh Start</i>
+command, which closes all images, empties the ROI Manager, clears the
+Results table and enables the "Black background" option. 
+<li> Thanks to Conner Phillips and Stein Rorvik, the <i>Reslice</i> command
+is faster on Windows when re-slicing from "Left" or "Right" and it
+uses an ordinary progress bar when run from a macro.
+<li> Thanks to Stein Rorvik, added an "Open as separate images" checkbox
+to the <i>File&gt;Import&gt;Image Sequence</i> dialog.
+<li> Thanks to Stein Rorvik, Added "Foreground..." and "Background..." entries
+to the new color picker tool popup menu.
+<li> Thanks to 'MIKEIII' and Dmitry Fedorov, added the Image.width, Image.height,
+Image.copy and Image.paste(x,y) macro functions DOCUMENT
+(<a href="http://wsr.imagej.net/macros/PasteDemo.txt">example</a>).
+<li> Thanks to Stein Rorvik, added the Array.filter(arr,str),
+Math.toRadians(degrees) and Math.toDegrees(radians) functions. DOCUMENT
+<li> Thanks to Nima Hojat, added the ResultsTable.addRow()
+method. For an example, run
+<i>Help&gt;Examples&gt;JavaScript&gt;Sine/Cosine Table</i>.
+<li> Thanks to Philippe Carl, fixed a bug that caused the
+RoiManager.getSelectedIndexes() method to sometimes not
+work as expected.
+<li> Thanks to Christian Tischer, fixed a bug that slowed saving of
+virtual stacks as TIFF stacks.
+<li> Thanks to Thomas Fischer, fixed a bug that caused the
+dynamic "Value" and "Count" values in HIstogram windows
+to sometimes not be displayed correctly.
+<li> Thanks to Gaurav Joshi, fixed a bug that caused the 
+Ctrl+F (Edit>Fill) keyboard shortcut on Windows, when
+used on a stack, to not display the "Proces Stack?" dialog.
+<li> Thanks to 'Quiroz-1', fixed a 1.53e regression that caused
+the imageCaculator() macro function do somethimes not
+work as expected.
+<li> Thanks to Pradeep Rajasekhar and Jan Eglinger, fixed a 1.52
+regression that caused the Analyze Skeleton plugin to output
+incorrect Results tables.
+<li> Thanks to 'tongtao', fixed a regression that caused the
+<i>Edit&gt;Copy to Image Info</i> command in the text
+editor to fail. 
+<li> Thanks to Stein Rorvik, fixed a 1.53c regression in the AVI Reader
+that caused it to throw a null pointer exception.
+<li> Thanks to Eric Perlman, fixed a 1.52 regresion that caused the
+IJ.getImage() method to sometimes display model error dialogs.
+</ul>
+
+<li> <u>1.53e  16 September 2020</u>
 <ul>
 <li> Thanks to Michael Schmid, the color picker tool has
-a new icon and a new right click drop down menu.
+a new icon and a right click drop down menu.
 <li> The "Black background" option is no longer
 saved in the preferences file. Add
 setOption("BlackBackground",true) to Edit>Options>Startup
@@ -17,7 +83,7 @@
 <i>Edit&gt;Selection&gt;Add to Manager</i> command.
 <li> Thanks to Michael Ellis, added a module-info.java file,
 used by the Java Module System, to the ImageJ source.
-<li> Thanks to 'mkhapp', added the RoiManager.selected macro DOCUMENT
+<li> Thanks to 'mkhapp', added the RoiManager.selected macro
 function, which returns the number of selected ROIs in the
 ROI Manager
 (<a href="http://wsr.imagej.net/macros/SetGroupDemo.txt">example</a>).
@@ -26,12 +92,12 @@
 of the Color Picker to be opened.
 <li> Thanks to 'Ben', fixed a bug that caused the Table.get()
 macro function to return strings instead of numbers.
-<li>Thanks to Fred Damen and Michael chmid, fixed a bug
+<li>Thanks to Fred Damen and Michael Schmid, fixed a bug
 that caused the run("Copy to System") macro function to
 sometimes copy the wrong image to the system clipboard.
 <li>Thanks to Fred Damen, fixed a bug that caused unreliable
 zooming of images with selections when using the arrow keys
-and shift or control.
+while holding the shift or control key down.
 <li>Thanks to Fred Damen, fixed a bug that caused the
 img3=ImageCalculator.run(img1,img2,operation) method
 to return null if the 'operation' string did not contain
@@ -42,7 +108,7 @@
 <li> Thanks to Robert Svoboda, fixed a 1.53d regression on
 Windows that could cause the getDirectory() macro function
 to throw an exception or crash ImageJ.
-<li> Thanks to Stein Rorvik, fixed a 1.53d regression that caused
+<li> Thanks to Stein Rorvik, fixed a 1.53d regression that could cause
 the run("Image Sequence...",options) macro function to fail.
 </ul>
 

diff --git a/src/main/java/ij/IJ.java b/src/main/java/ij/IJ.java
@@ -140,20 +140,21 @@ public static void setDebugMode(boolean b) {
 		LogStream.redirectSystem(debugMode);
 	}
 
-	/** Runs the macro contained in the string <code>macro</code>.
-		Returns any string value returned by the macro, null if the macro
-		does not return a value, or "[aborted]" if the macro was aborted
-		due to an error. The equivalent macro function is eval(). */
+	/** Runs the macro contained in the string <code>macro</code>
+		on the current thread. Returns any string value returned by
+		the macro, null if the macro does not return a value, or
+		"[aborted]" if the macro was aborted due to an error. The
+		equivalent macro function is eval(). */
 	public static String runMacro(String macro) {
 		return runMacro(macro, "");
 	}
 
-	/** Runs the macro contained in the string <code>macro</code>.
-		The optional string argument can be retrieved in the
-		called macro using the getArgument() macro function. 
-		Returns any string value returned by the macro, null if the macro
-		does not return a value, or "[aborted]" if the macro was aborted
-		due to an error.  */
+	/** Runs the macro contained in the string <code>macro</code>
+		on the current thread. The optional string argument can be
+		retrieved in the called macro using the getArgument() macro
+		function. Returns any string value returned by the macro, null
+		if the macro does not return a value, or "[aborted]" if the
+		macro was aborted due to an error.  */
 	public static String runMacro(String macro, String arg) {
 		if(EventQueue.isDispatchThread()){
 			Macro_Runner mr = new Macro_Runner();

diff --git a/src/main/java/ij/ImageJ.java b/src/main/java/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 = "1.53e";
-	public static final String BUILD = "";  //23
+	public static final String VERSION = "1.53f";
+	public static final String BUILD = "51";
 	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);
@@ -549,7 +549,7 @@ else if (roi!=null) {
 
 		if (cmd!=null && !cmd.equals("")) {
 			commandName = cmd;
-			if (cmd.equals("Fill")||cmd.equals("Draw"))
+			if (!control && !meta && (cmd.equals("Fill")||cmd.equals("Draw")))
 				hotkey = true;
 			if (cmd.charAt(0)==MacroInstaller.commandPrefix)
 				MacroInstaller.runMacroShortcut(cmd);

diff --git a/src/main/java/ij/ImagePlus.java b/src/main/java/ij/ImagePlus.java
@@ -2804,7 +2804,7 @@ public void paste() {
 			cr = cRoi.getBounds();
 		if (cr==null)
 			cr = new Rectangle(0, 0, w, h);
-		if (r==null || (cr.width!=r.width || cr.height!=r.height)) {
+		if (r==null || Math.abs(cr.width-r.width)>10 || Math.abs(cr.height-r.height)>10) {
 			// Create a new roi centered on visible part of image, or centered on image if clipboard is >= image
 			ImageCanvas ic = win!=null?ic = win.getCanvas():null;
 			Rectangle srcRect = ic!=null?ic.getSrcRect():new Rectangle(0,0,width,height);
@@ -2841,12 +2841,30 @@ public void paste() {
 		}
 		changes = true;
     }
-
-	/** Returns the internal clipboard or null if the internal clipboard is empty. */
-	public static ImagePlus getClipboard() {
-		return clipboard;
+
+    /** Inserts the contents of the internal clipboard at the
+    	specified location, without updating the display. */
+	 public void paste(int x, int y) {
+		if (clipboard==null)
+			return;
+		Roi roi = clipboard.getRoi();
+		boolean nonRect = roi!=null && roi.getType()!=Roi.RECTANGLE;
+		if (nonRect)
+			ip.snapshot();
+		ip.insert(clipboard.getProcessor(), x, y);
+		if (nonRect) {
+			ImageProcessor mask = roi.getMask();
+			ip.setRoi(x, y, mask.getWidth(), mask.getHeight());
+			ip.setMask(mask);
+			ip.reset(ip.getMask());
+		}
 	}
 
+    /** Returns the internal clipboard or null if the internal clipboard is empty. */
+    public static ImagePlus getClipboard() {
+        return clipboard;
+    }
+
 	/** Clears the internal clipboard. */
 	public static void resetClipboard() {
 		clipboard = null;