├── .gitignore
├── README.md
├── pom.xml
└── src
    └── main
        └── java
            └── com
                └── mycompany
                    └── imagej
                        └── GaussFiltering.java


/.gitignore:
--------------------------------------------------------------------------------
1 | /.classpath
2 | /.project
3 | /.settings/
4 | /target/
5 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | This is an example Maven project implementing an ImageJ2 command.
 2 | 
 3 | For an example Maven project implementing an **original ImageJ plugin**, see:
 4 |     https://github.com/imagej/example-legacy-plugin
 5 | 
 6 | It is intended as an ideal starting point to develop new ImageJ2 commands
 7 | in an IDE of your choice. You can even collaborate with developers using a
 8 | different IDE than you.
 9 | 
10 | * In [Eclipse](http://eclipse.org), for example, it is as simple as
11 |   _File › Import... › Existing Maven Project_.
12 | 
13 | * In [NetBeans](http://netbeans.org), it is even simpler:
14 |   _File › Open Project_.
15 | 
16 | * The same works in [IntelliJ](http://jetbrains.net).
17 | 
18 | * If [jEdit](http://jedit.org) is your preferred IDE, you will need the
19 |   [Maven Plugin](http://plugins.jedit.org/plugins/?MavenPlugin).
20 | 
21 | Die-hard command-line developers can use Maven directly by calling `mvn`
22 | in the project root.
23 | 
24 | However you build the project, in the end you will have the `.jar` file
25 | (called *artifact* in Maven speak) in the `target/` subdirectory.
26 | 
27 | To copy the artifact into the correct place, you can call
28 | `mvn -Dscijava.app.directory="/path/to/ImageJ2.app/"`.
29 | This will not only copy your artifact, but also all the dependencies.
30 | 
31 | Developing code in an IDE is convenient, especially for debugging.
32 | To that end, this project contains a `main` method which launches ImageJ2,
33 | loads an image and runs the command.
34 | 
35 | Since this project is intended as a starting point for your own
36 | developments, it is in the public domain.
37 | 
38 | How to use this project as a starting point
39 | ===========================================
40 | 
41 | 1. Visit [this link](https://github.com/imagej/example-imagej2-command/generate)
42 |    to create a new repository in your space using this one as a template.
43 | 
44 | 2. [Clone your new repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository).
45 | 
46 | 3. Edit the `pom.xml` file, fixing all the lines labeled `FIXME`.
47 | 
48 | 4. Remove the `GaussFiltering.java` file and add your own `.java` files
49 |    to `src/main/java/<package>/` (if you need supporting files such as icons
50 |    in the resulting `.jar` file, put them into `src/main/resources/`)
51 | 
52 | 5. Replace the contents of `README.md` with information about your project.
53 | 
54 | 6. Make your initial
55 |    [commit](https://docs.github.com/en/desktop/contributing-and-collaborating-using-github-desktop/making-changes-in-a-branch/committing-and-reviewing-changes-to-your-project) and
56 |    [push the results](https://docs.github.com/en/get-started/using-git/pushing-commits-to-a-remote-repository)!
57 | 
58 | ### Eclipse: To ensure that Maven copies the command to your ImageJ2 folder
59 | 
60 | 1. Go to _Run Configurations..._
61 | 2. Choose _Maven Build_
62 | 3. Add the following parameter:
63 |     - name: `scijava.app.directory`
64 |     - value: `/path/to/ImageJ2.app/`
65 | 
66 | This ensures that the final `.jar` file will also be copied
67 | into your ImageJ2 folder everytime you run the Maven build.
68 | 


--------------------------------------------------------------------------------
/pom.xml:
--------------------------------------------------------------------------------
  1 | <?xml version="1.0" encoding="UTF-8"?>
  2 | <project xmlns="http://maven.apache.org/POM/4.0.0"
  3 | 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  4 | 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
  5 | 		http://maven.apache.org/xsd/maven-4.0.0.xsd">
  6 | 	<modelVersion>4.0.0</modelVersion>
  7 | 
  8 | 	<parent>
  9 | 		<groupId>org.scijava</groupId>
 10 | 		<artifactId>pom-scijava</artifactId>
 11 | 		<version>31.1.0</version>
 12 | 		<relativePath />
 13 | 	</parent>
 14 | 
 15 | 	<groupId>com.mycompany</groupId>        <!-- FIXME: Your organization groupId here -->
 16 | 	<artifactId>GaussFiltering</artifactId> <!-- FIXME: Your project artifactId here   -->
 17 | 	<version>0.1.0-SNAPSHOT</version>
 18 | 
 19 | 	<name>Gauss Filtering</name>                                               <!-- FIXME: Your project name here          -->
 20 | 	<description>A Maven project implementing an ImageJ command.</description> <!-- FIXME: Your project description here   -->
 21 | 	<url>https://mycompany.com/imagej/gauss-filtering/</url>                   <!-- FIXME: Your project website here       -->
 22 | 	<inceptionYear>2017</inceptionYear>                                        <!-- FIXME: Your project starting year here -->
 23 | 	<organization>
 24 | 		<name>My Company</name>           <!-- FIXME: Your organization name here    -->
 25 | 		<url>https://mycompany.com/</url> <!-- FIXME: Your organization website here -->
 26 | 	</organization>
 27 | 	<licenses>
 28 | 		<license>                         <!-- FIXME: Your license here -->
 29 | 			<name>CC0</name>
 30 | 			<url>https://creativecommons.org/publicdomain/zero/1.0/</url>
 31 | 			<distribution>repo</distribution>
 32 | 		</license>
 33 | 	</licenses>
 34 | 
 35 | 	<developers>
 36 | 		<!-- See https://imagej.net/Team -->
 37 | 		<developer>
 38 | 			<id>octocat</id>                                          <!-- FIXME: Your GitHub handle here -->
 39 | 			<name>Noma Onomatopoeia</name>                            <!-- FIXME: Your name here          -->
 40 | 			<url>https://mycompany.com/people/noma-onomatopoeia</url> <!-- FIXME: Your website here       -->
 41 | 			<roles>
 42 | 				<role>founder</role>
 43 | 				<role>lead</role>
 44 | 				<role>developer</role>
 45 | 				<role>debugger</role>
 46 | 				<role>reviewer</role>
 47 | 				<role>support</role>
 48 | 				<role>maintainer</role>
 49 | 			</roles>
 50 | 		</developer>
 51 | 	</developers>
 52 | 	<contributors>
 53 | 		<contributor>
 54 | 			<name>None</name>
 55 | 		</contributor>
 56 | 	</contributors>
 57 | 
 58 | 	<mailingLists>
 59 | 		<mailingList>
 60 | 			<name>Image.sc Forum</name>
 61 | 			<archive>https://forum.image.sc/tag/imagej</archive>
 62 | 		</mailingList>
 63 | 	</mailingLists>
 64 | 
 65 | 	<scm>
 66 | 		<connection>scm:git:https://github.com/imagej/example-imagej2-command</connection>
 67 | 		<developerConnection>scm:git:git@github.com:imagej/example-imagej2-command</developerConnection>
 68 | 		<tag>HEAD</tag>
 69 | 		<url>https://github.com/imagej/example-imagej2-command</url>
 70 | 	</scm>
 71 | 	<issueManagement>
 72 | 		<system>GitHub Issues</system>
 73 | 		<url>https://github.com/imagej/example-imagej2-command/issues</url>
 74 | 	</issueManagement>
 75 | 	<ciManagement>
 76 | 		<system>None</system>
 77 | 	</ciManagement>
 78 | 
 79 | 	<properties>
 80 | 		<package-name>com.mycompany.imagej</package-name>                   <!-- FIXME: Your project package prefix here -->
 81 | 		<main-class>com.mycompany.imagej.GaussFiltering</main-class>        <!-- FIXME: Your project main class here, or delete for none -->
 82 | 		<license.licenseName>cc0</license.licenseName>                      <!-- FIXME: Your license-maven-plugin license code here -->
 83 | 		<license.copyrightOwners>My Company, Inc.</license.copyrightOwners> <!-- FIXME: Your organization legal entity name here -->
 84 | 	</properties>
 85 | 
 86 | 	<repositories>
 87 | 		<repository>
 88 | 			<id>scijava.public</id>
 89 | 			<url>https://maven.scijava.org/content/groups/public</url>
 90 | 		</repository>
 91 | 	</repositories>
 92 | 
 93 | 	<dependencies>
 94 | 		<dependency>
 95 | 			<groupId>net.imagej</groupId>
 96 | 			<artifactId>imagej</artifactId>
 97 | 		</dependency>
 98 | 	</dependencies>
 99 | </project>
100 | 


--------------------------------------------------------------------------------
/src/main/java/com/mycompany/imagej/GaussFiltering.java:
--------------------------------------------------------------------------------
  1 | /*
  2 |  * To the extent possible under law, the ImageJ developers have waived
  3 |  * all copyright and related or neighboring rights to this tutorial code.
  4 |  *
  5 |  * See the CC0 1.0 Universal license for details:
  6 |  *     http://creativecommons.org/publicdomain/zero/1.0/
  7 |  */
  8 | 
  9 | package com.mycompany.imagej;
 10 | 
 11 | import net.imagej.Dataset;
 12 | import net.imagej.ImageJ;
 13 | import net.imagej.ops.OpService;
 14 | import net.imglib2.RandomAccessibleInterval;
 15 | import net.imglib2.img.Img;
 16 | import net.imglib2.type.numeric.RealType;
 17 | import org.scijava.command.Command;
 18 | import org.scijava.plugin.Parameter;
 19 | import org.scijava.plugin.Plugin;
 20 | import org.scijava.ui.UIService;
 21 | 
 22 | import java.io.File;
 23 | import java.util.ArrayList;
 24 | import java.util.List;
 25 | 
 26 | /**
 27 |  * This example illustrates how to create an ImageJ {@link Command} plugin.
 28 |  * <p>
 29 |  * The code here is a simple Gaussian blur using ImageJ Ops.
 30 |  * </p>
 31 |  * <p>
 32 |  * You should replace the parameter fields with your own inputs and outputs,
 33 |  * and replace the {@link run} method implementation with your own logic.
 34 |  * </p>
 35 |  */
 36 | @Plugin(type = Command.class, menuPath = "Plugins>Gauss Filtering")
 37 | public class GaussFiltering<T extends RealType<T>> implements Command {
 38 |     //
 39 |     // Feel free to add more parameters here...
 40 |     //
 41 | 
 42 |     @Parameter
 43 |     private Dataset currentData;
 44 | 
 45 |     @Parameter
 46 |     private UIService uiService;
 47 | 
 48 |     @Parameter
 49 |     private OpService opService;
 50 | 
 51 |     @Override
 52 |     public void run() {
 53 |         final Img<T> image = (Img<T>)currentData.getImgPlus();
 54 | 
 55 |         //
 56 |         // Enter image processing code here ...
 57 |         // The following is just a Gauss filtering example
 58 |         //
 59 |         final double[] sigmas = {1.0, 3.0, 5.0};
 60 | 
 61 |         List<RandomAccessibleInterval<T>> results = new ArrayList<>();
 62 | 
 63 |         for (double sigma : sigmas) {
 64 |             results.add(opService.filter().gauss(image, sigma));
 65 |         }
 66 | 
 67 |         // display result
 68 |         for (RandomAccessibleInterval<T> elem : results) {
 69 |             uiService.show(elem);
 70 |         }
 71 |     }
 72 | 
 73 |     /**
 74 |      * This main function serves for development purposes.
 75 |      * It allows you to run the plugin immediately out of
 76 |      * your integrated development environment (IDE).
 77 |      *
 78 |      * @param args whatever, it's ignored
 79 |      * @throws Exception
 80 |      */
 81 |     public static void main(final String... args) throws Exception {
 82 |         // create the ImageJ application context with all available services
 83 |         final ImageJ ij = new ImageJ();
 84 |         ij.ui().showUI();
 85 | 
 86 |         // ask the user for a file to open
 87 |         final File file = ij.ui().chooseFile(null, "open");
 88 | 
 89 |         if (file != null) {
 90 |             // load the dataset
 91 |             final Dataset dataset = ij.scifio().datasetIO().open(file.getPath());
 92 | 
 93 |             // show the image
 94 |             ij.ui().show(dataset);
 95 | 
 96 |             // invoke the plugin
 97 |             ij.command().run(GaussFiltering.class, true);
 98 |         }
 99 |     }
100 | 
101 | }
102 | 


--------------------------------------------------------------------------------