Retire ImageJA

Relevant functionality of the ImageJA project has been rolled into the core ImageJ repository, which has been renamed from imagej1 to ImageJ, so ImageJA is no longer necessary. See: imagej/ImageJ#142
imagej · Jan 20, 2022 · 0084c55 · 0084c55
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diff --git a/_includes/layout/menu b/_includes/layout/menu
@@ -228,7 +228,6 @@
               <li><a href="/libs/imagej-ops">ImageJ Ops</a></li>
               <li><a href="/libs/imagej-common">ImageJ Common</a></li>
               <li><a href="/libs/imagej-legacy">ImageJ Legacy</a></li>
-              <li><a href="/libs/imageja">ImageJA</a></li>
               <li><a href="/libs/scijava">SciJava</a></li>
               <li><a href="/libs/scifio">SCIFIO</a></li>
 

diff --git a/_pages/contribute/index.md b/_pages/contribute/index.md
@@ -41,7 +41,7 @@ Changes to the original [ImageJ](/software/imagej) are made by {% include person
 
 Methods of getting the patch to Wayne include:
 
--   Submit a pull request on GitHub against {% include github org='imagej' repo='imagej1' label='the ImageJ repository' %}. Be aware that PRs will be reviewed and integrated by hand, not merged via the standard Git/GitHub workflow.
+-   Submit a pull request on GitHub against {% include github org='imagej' repo='ImageJ' label='the ImageJ repository' %}. Be aware that PRs will be reviewed and integrated by hand, not merged via the standard Git/GitHub workflow.
 -   Send the modified code in a [private mail to Wayne](mailto:rasband@gmail.com).
 
 The important part is that Wayne receive the code/patch, since he is the only one with the authority to merge it.

diff --git a/_pages/develop/ij1-plugins.md b/_pages/develop/ij1-plugins.md
@@ -115,7 +115,7 @@ The source of the various Fiji-related projects is spread over several source co
 
 ## The class *IJ*
 
-The class {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/IJ.java' label='ij.IJ' %} is a convenience class with many static functions. Two of them are particularly useful for debugging:
+The class {% include github org='imagej' repo='ImageJ' branch='master' path='ij/IJ.java' label='ij.IJ' %} is a convenience class with many static functions. Two of them are particularly useful for debugging:
 
 ```java
 // output into the Log window
@@ -127,7 +127,7 @@ IJ.showMessage("Hello, World!");
 
 ## The class *ImageJ*
 
-The class {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/ImageJ.java' label='ij.ImageJ' %} implements the main window of ImageJ / Fiji, and you can access it via *ij.IJ*'s static method *getInstance()*:
+The class {% include github org='imagej' repo='ImageJ' branch='master' path='ij/ImageJ.java' label='ij.ImageJ' %} implements the main window of ImageJ / Fiji, and you can access it via *ij.IJ*'s static method *getInstance()*:
 
 ```java
 // check if ImageJ is used interactively
@@ -139,7 +139,7 @@ Typically, all you do with that instance is to test whether ImageJ is used as a
 
 ## The class *WindowManager*
 
-Use the class {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/WindowManager.java' label='ij.WindowManager' %} to access the ImageJ windows / images:
+Use the class {% include github org='imagej' repo='ImageJ' branch='master' path='ij/WindowManager.java' label='ij.WindowManager' %} to access the ImageJ windows / images:
 
 ```java
 // how many windows / images are active?
@@ -155,7 +155,7 @@ When implementing a filter plugin, you usually do not need to access *WindowMana
 
 ## The hierarchy of the classes representing an image
 
-All images are represented as instances of {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/ImagePlus.java' label='ij.ImagePlus' %}. This class wraps an {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/ImageStack.java' label='ij.ImageStack' %} of slices. Slices are data-type dependent instances of {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/process/ImageProcessor.java' label='ij.process.ImageProcessor' %}: {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/process/ByteProcessor.java' label='ij.process.ByteProcessor' %}, {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/process/ShortProcessor.java' label='ij.process.ShortProcessor' %}, {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/process/FloatProcessor.java' label='ij.process.FloatProcessor' %}, and {% include github org='imagej' repo='ImageJA' branch='master' path='src/main/java/ij/process/ColorProcessor.java' label='ij.process.ColorProcessor' %}. Or graphically:
+All images are represented as instances of {% include github org='imagej' repo='ImageJ' branch='master' path='ij/ImagePlus.java' label='ij.ImagePlus' %}. This class wraps an {% include github org='imagej' repo='ImageJ' branch='master' path='ij/ImageStack.java' label='ij.ImageStack' %} of slices. Slices are data-type dependent instances of {% include github org='imagej' repo='ImageJ' branch='master' path='ij/process/ImageProcessor.java' label='ij.process.ImageProcessor' %}: {% include github org='imagej' repo='ImageJ' branch='master' path='ij/process/ByteProcessor.java' label='ij.process.ByteProcessor' %}, {% include github org='imagej' repo='ImageJ' branch='master' path='ij/process/ShortProcessor.java' label='ij.process.ShortProcessor' %}, {% include github org='imagej' repo='ImageJ' branch='master' path='ij/process/FloatProcessor.java' label='ij.process.FloatProcessor' %}, and {% include github org='imagej' repo='ImageJ' branch='master' path='ij/process/ColorProcessor.java' label='ij.process.ColorProcessor' %}. Or graphically:
 
 <figure><img src="/media/image-class-hierarchy.png" title="Image_Class_Hierarchy.png" width="600" alt="Image_Class_Hierarchy.png" /><figcaption aria-hidden="true">Image_Class_Hierarchy.png</figcaption></figure>
 

diff --git a/_pages/develop/ij1-unit-tests.md b/_pages/develop/ij1-unit-tests.md
@@ -4,34 +4,19 @@ title: Unit tests for ImageJ
 project: /software/imagej
 ---
 
-There are a [substantial number of unit tests](/news/2011-10-07-unit-tests-for-imagej-1-45) to exercise [ImageJ](/software/imagej) functionality. You can find them in the {% include github org='imagej' repo='ij1-tests' label='ij1-tests repository' %}:
-
-```shell
-git clone git://github.com/imagej/ij1-tests
-```
-
-There is a [Travis](/develop/travis) job [here](https://travis-ci.com/imagej/ij1-tests) that automatically runs the tests with each new version of ImageJ.
+There are a [substantial number of unit tests](/news/2011-10-07-unit-tests-for-imagej-1-45) to exercise [ImageJ](/software/imagej) functionality. You can find them in the {% include github org='imagej' repo='ImageJ' label='ImageJ repository' %} in the `tests` directory.
 
 ### Running the tests
 
 If you wish to run the unit tests manually, you can do so from the command line:
 
 ```shell
-cd ij1-tests
-mvn clean test
+git clone https://github.com/imagej/ImageJ
+cd ImageJ
+mvn test
 ```
 
 Or from Eclipse:
 
-1.  Import the `ij1-tests` project using {% include bc path='File | Import Existing Maven Projects'%} and choosing the `ij1-tests/pom.xml` file.
-2.  Right-click the `ij1-tests` project, {% include bc path='Run As | JUnit Test'%}.
-
-### Using a different version of ImageJ
-
-You can change which version of ImageJ is tested by overriding the `imagej1.version` property:
-
-```shell
-mvn -Dimagej1.version=1.48a clean test
-```
-
-Or whichever version you wish to use (of [those listed here](https://maven.scijava.org/content/groups/public/net/imagej/ij/)). The unit tests were created circa 1.44, and do not compile correctly with earlier versions of ImageJ.
+1.  Import the `ImageJ` project using {% include bc path='File | Import Existing Maven Projects' %} and choosing the `ImageJ/pom.xml` file.
+2.  Right-click the `ImageJ` project, {% include bc path='Run As | JUnit Test' %}.
diff --git a/_pages/develop/maven.md b/_pages/develop/maven.md
@@ -14,9 +14,9 @@ section: Extend:Development:Tools
 {% endcapture %}
 {% include img src='icons/maven' align='right' width=150 caption=maven-caption %}
 
-[ImageJ2](/software/imagej2), [Fiji](/software/fiji) and other [SciJava](/libs/scijava) projects use [Maven](https://maven.apache.org/) for their project infrastructure.
+[ImageJ](/software/imagej), [ImageJ2](/software/imagej2), [Fiji](/software/fiji), and other [SciJava](/libs/scijava)-based projects use [Maven](https://maven.apache.org/) for their project infrastructure.
 
-Maven artifacts are published to the [SciJava Maven repository](/develop/project-management#maven).
+Maven artifacts are published to [Maven Central](https://search.maven.org/) or to the [SciJava Maven repository](/develop/project-management#maven).
 
 # Why do we use Maven?
 

diff --git a/_pages/develop/source.md b/_pages/develop/source.md
@@ -7,15 +7,7 @@ section: Extend:Development
 
 The source code of the original [ImageJ](/software/imagej) is available at:
 
-{% include link-banner url='https://github.com/imagej/imagej1' %}
-
-And there is a version with clean [Git](/develop/git) history and release tags, with a [Maven](/develop/maven)-based build system, available at:
-
-{% include link-banner url='https://github.com/imagej/ImageJA' %}
-
-## ImageJ unit tests
-
-There are a substantial number of [unit tests to exercise ImageJ functionality](/develop/ij1-unit-tests).
+{% include link-banner url='https://github.com/imagej/ImageJ' %}
 
 # ImageJ2
 
@@ -37,7 +29,7 @@ All source code is on [GitHub](/develop/github).
 | ![](/media/icons/imagej2.png){:width="28"} | [ImageJ2](https://github.com/imagej)  | A general-purpose image processing application                  |
 | ![](/media/icons/imglib2.png){:width="28"} | [ImgLib2](https://github.com/imglib)  | Generic multi-dimensional data processing                       |
 | ![](/media/icons/scifio.png){:width="28"}  | [SCIFIO](https://github.com/scifio)   | Extensible image file I/O                                       |
-| ![](/media/icons/fiji.png){:width="28"}    | [Fiji](https://github.com/fiji)       | A "batteries-included" distribution of ImageJ                   |
+| ![](/media/icons/fiji.png){:width="28"}    | [Fiji](https://github.com/fiji)       | A "batteries-included" distribution of ImageJ and ImageJ2       |
 
 See the [Architecture](/develop/architecture) page for more information about the relationship between these projects.
 

diff --git a/_pages/learn/faq.md b/_pages/learn/faq.md
@@ -302,10 +302,10 @@ Here are several ways to do so:
     -   Using the search bar, locate your command, taking note of the Class column's value.
         -   E.g., if we type "make binary" we see that the class is `ij.plugin.Thresholder`.
     -   Open the relevant project in GitHub:
-        -   E.g., for "ij." classes, go to: https://github.com/imagej/ImageJA
+        -   E.g., for "ij." classes, go to: https://github.com/imagej/ImageJ
     -   Press the {% include key key='T' %} key, and type the name of the file you are looking for.
         -   In the example above, this is Thresholder.java.
-    -   You should end up with a hit like: https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/plugin/Thresholder.java.
+    -   You should end up with a hit like: https://github.com/imagej/ImageJ/blob/master/ij/plugin/Thresholder.java.
     -   This method requires that you know in which repository the code lives. However, you can combine it with **search.imagej.net** method above to figure out which repository, then load the code on GitHub, if desired.
 4.  **Using the "Open Source for Menu Item" command:**
     -   Run {% include bc path='Plugins | Scripting | Open Source for Menu Item' %}.

diff --git a/_pages/learn/flavors.md b/_pages/learn/flavors.md
@@ -29,8 +29,6 @@ There are a many different derivatives of ImageJ with very similar names, and so
     </tr>
     <tr>
       <td><img src="/media/icons/imagej.png" width="64"/></td>
-      <td><a href="/software/imagej">ImageJ</a></td>
-      <td>{% include person id='rasband' %}</td>
       <td>The original version of ImageJ which has been in development since 1997.
         It has a strong, established user base, with thousands of plugins and
         macros for performing a wide variety of tasks. Sometimes referred to as
@@ -67,23 +65,17 @@ There are a many different derivatives of ImageJ with very similar names, and so
       <td><a href="/people/dscho#a-short-story-about-fiji">Dec. 2007</a></td>
       <td>Active</td>
     </tr>
-    <tr>
-      <td><img src="/media/icons/imagej.png" width="64"/></td>
-      <td><a href="/libs/imageja">ImageJA</a></td>
-      <td><a href="/people">{% include person id='rasband' %} (author); ImageJ2 team (maintainers)</a></td>
-      <td>ImageJA is a project that provides a clean <a href="/develop/git">Git</a>
-        history of the original ImageJ, with a proper 'pom.xml' file so that it
-        can be used with Maven without hassles.<br><br>It is what ImageJ2's
-        legacy support uses at its core.</td>
-      <td>Jul. 2005</td>
-      <td>Active</td>
-    </tr>
     <tr>
       <td><img src="https://ij.imjoy.io/assets/icons/chrome/chrome-installprocess-128-128.png" width="64"/></td>
       <td><a href="/software/imagej-js">ImageJ.JS</a></td>
       <td>{% include person id='oeway' %}</td>
-      <td>ImageJ.JS is a web version of <a href="/libs/imageja">ImageJA</a> that runs in the browser without installation,
-      compiled from Java to JavaScript using the <a href="https://leaningtech.com/cheerpj/">Cheerpj compiler</a> and integrated with the <a href="/software/imjoy">ImJoy</a> plugin system. It's accessible from <a href="https://ij.imjoy.io">https://ij.imjoy.io</a> and also support mobile devices and tablets.
+      <td>ImageJ.JS is a web version of ImageJ that runs in the browser without
+        installation, compiled from Java to JavaScript using the
+        <a href="https://leaningtech.com/cheerpj/">Cheerpj compiler</a> and
+        integrated with the <a href="/software/imjoy">ImJoy</a> plugin system.
+        It's accessible from
+        <a href="https://ij.imjoy.io">https://ij.imjoy.io</a>
+        and also supports mobile devices and tablets.
       </td>
       <td>2020</td>
       <td>Active</td>
@@ -158,6 +150,18 @@ There are a many different derivatives of ImageJ with very similar names, and so
       <td>2005</td>
       <td>Defunct<br>(Last update:<br>Dec. 2009)</td>
     </tr>
+    <tr>
+      <td><img src="/media/icons/imagej.png" width="64"/></td>
+      <td><a href="/libs/imageja">ImageJA</a></td>
+      <td><a href="/people">{% include person id='rasband' %} (author); ImageJ2 team (maintainers)</a></td>
+      <td>ImageJA was a project that provided a clean <a href="/develop/git">Git</a>
+        history of the original ImageJ, with a proper <code>pom.xml</code> file
+        so that it could be used with Maven without hassles. The ImageJ project
+        has since been updated to deploy releases to Maven Central directly,
+        without the need for the ImageJA project as an intermediate.</td>
+      <td>Jul. 2005</td>
+      <td>Superseded by ImageJ</td>
+    </tr>
     <tr>
       <td></td>
       <td><a href="/software/imagejx">ImageJX</a></td>

diff --git a/_pages/learn/launcher.md b/_pages/learn/launcher.md
@@ -41,7 +41,7 @@ The launcher can do all kinds of things, like:
 -   Control the [Updater](/plugins/updater) from the command line
 -   Open images: `./ImageJ-<platform> example.jpg`
 -   Call Jython scripts: `./ImageJ-<platform> example.py` (also works for JRuby scripts when they have an `.rb` extension, for Beanshell scripts with `.bsh` extension, `.clj` for Clojure and `.js` for Javascript)
--   Call the Jython interpreter: `./ImageJ-<platform> --jython` (the classpath will be the same as when calling ImageJA), and likewise `--jruby`, `--bsh` and `--js` for the respective language's command-line interpreters
+-   Call the Jython interpreter: `./ImageJ-<platform> --jython` (the classpath will be the same as when calling ImageJ), and likewise `--jruby`, `--bsh` and `--js` for the respective language's command-line interpreters
 -   Run ImageJ with the system Java instead of its own one: `./ImageJ-<platform> --system`. But beware: this might fail since some plugins need at least Java 1.5, and the 3D viewer needs Java3D.
 -   Show the java command line instead of running ImageJ: `./ImageJ-<platform> --dry-run`
 -   Compile a Java class: `./ImageJ-<platform> --javac example.java`