initial version

.gitignore

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+/.idea/
+*.iml

license.txt

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+Robert Haase, Max Planck Institute for Molecular Cell Biology
+and Genetics, Dresden
+
+Knowledge is free. Thus, the code and text in this repository is public domain. However:
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+POSSIBILITY OF SUCH DAMAGE.

pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+		http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>org.scijava</groupId>
+		<artifactId>pom-scijava</artifactId>
+		<version>27.0.1</version>
+		<relativePath />
+	</parent>
+
+	<groupId>net.haesleinhuepf</groupId>
+	<artifactId>extend-macro-autocomplete</artifactId>
+	<version>0.1.0</version>
+
+	<name>extend-macro-autocomplete</name>
+	<description>extend-macro-autocomplete</description>
+	<url>https://github.com/haesleinhuepf/extend-macro-autocompletion</url>
+	<inceptionYear>2019</inceptionYear>
+	<organization>
+		<name>MPI CBG</name>
+		<url>http://www.mpi-cbg.de</url>
+	</organization>
+	<licenses>
+		<license>
+			<name>public domain</name>
+			<distribution>repo</distribution>
+		</license>
+	</licenses>
+
+	<developers>
+		<developer>
+			<id>haesleinhuepf</id>
+			<name>Robert Haase</name>
+			<url>https://haesleinhuepf.net</url>
+			<organization>MPI CBG</organization>
+			<roles>
+				<role>founder</role>
+				<role>lead</role>
+				<role>developer</role>
+				<role>debugger</role>
+				<role>reviewer</role>
+				<role>support</role>
+				<role>maintainer</role>
+			</roles>
+		</developer>
+	</developers>
+	<contributors>
+		<contributor>
+			<name>none</name>
+		</contributor>
+	</contributors>
+
+	<mailingLists>
+		<mailingList>
+			<name>ImageSc Forum</name>
+			<archive>http://image.sc/</archive>
+		</mailingList>
+	</mailingLists>
+
+	<scm>
+		<connection>scm:git:git://github.com/haesleinhuepf/extend-macro-autocompletion</connection>
+        <developerConnection>scm:git:git@github.com/haesleinhuepf/extend-macro-autocompletion</developerConnection>
+        <tag>HEAD</tag>
+		<url>https://github.com/haesleinhuepf/extend-macro-autocompletion</url>
+	</scm>
+	<issueManagement>
+		<system>GitHub Issues</system>
+		<url>https://github.com/haesleinhuepf/extend-macro-autocompletion/issues</url>
+	</issueManagement>
+	<ciManagement>
+		<system>None</system>
+	</ciManagement>
+
+	<properties>
+		<package-name>net.haesleinhuepf</package-name>
+		<license.licenseName>bsd_3</license.licenseName>
+		<license.copyrightOwners>Robert Haase, MPI CBG</license.copyrightOwners>
+		<scijava.app.directory>C:/programs/fiji-win64/Fiji.app/</scijava.app.directory>
+	</properties>
+
+	<dependencies>
+		<!-- ImageJ dependencies -->
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>ij</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>imagej-legacy</artifactId>
+		</dependency>
+
+		<!-- SciJava dependencies -->
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>scijava-common</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>script-editor</artifactId>
+		</dependency>
+
+		<!-- Third party dependencies -->
+		<dependency>
+			<groupId>com.fifesoft</groupId>
+			<artifactId>languagesupport</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.fifesoft</groupId>
+			<artifactId>rsyntaxtextarea</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.fifesoft</groupId>
+			<artifactId>autocomplete</artifactId>
+		</dependency>
+
+		<!-- Test scope dependencies -->
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+
+	<repositories>
+		<repository>
+			<id>sonatype</id>
+			<url>http://oss.sonatype.org/content/groups/public</url>
+		</repository>
+		<repository>
+			<id>imagej.releases</id>
+			<url>
+				http://maven.imagej.net/content/repositories/releases
+			</url>
+		</repository>
+		<repository>
+			<id>imagej.snapshots</id>
+			<url>
+				http://maven.imagej.net/content/repositories/snapshots
+			</url>
+		</repository>
+	</repositories>
+
+</project>

readme.md

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+# ImageJ macro extensions and extending auto completion in Fijis script editor
+Since we introduced auto-completion in Fijis script editor, some developers asked me 
+how they can make their tools discoverable by auto-completion users. 
+This article explains how to achieve this. I'm providing a [fully functional example](https://github.com/haesleinhuepf/extend-macro-autocompletion) as 
+this might be a better starting point for developers.
+
+## Starting point a SciJava Fiji plugin
+As a starting point we assume to have a [maven](https://maven.apache.org/) project with a 
+[pom.xml](http://github.com/haesleinhuepf/extend) file 
+
+
+
+
+

src/main/java/net/haesleinhuepf/fiji/macro/MyMacroAutoCompletionExtension.java

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+package net.haesleinhuepf.fiji.macro;
+
+import net.haesleinhuepf.fiji.plugins.MyPlugins;
+import net.imagej.legacy.plugin.MacroExtensionAutoCompletionPlugin;
+import org.fife.ui.autocomplete.BasicCompletion;
+import org.fife.ui.autocomplete.CompletionProvider;
+import org.scijava.plugin.Plugin;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * MyMacroAutoCompletionExtension
+ *
+ * This class communicates with Fijis script editor. It hands over a list of potential commands
+ * which appear in the auto-completion pulldown.
+ *
+ * Author haesleinhuepf
+ *        August 2019
+ */
+@Plugin(type = MacroExtensionAutoCompletionPlugin.class)
+public class MyMacroAutoCompletionExtension implements MacroExtensionAutoCompletionPlugin {
+    @Override
+    public List<BasicCompletion> getCompletions(CompletionProvider completionProvider) {
+        ArrayList<BasicCompletion> completions = new ArrayList<BasicCompletion>();
+
+        MyMacroExtensionDescriptor[] pluginList = MyPlugins.list;
+
+        // go through plugins and provide an auto-complete entry for each
+        for (MyMacroExtensionDescriptor plugin : pluginList) {
+            String commandName = "Ext.MyLib_" + plugin.getClass().getSimpleName();
+            completions.add(new BasicCompletion(completionProvider, commandName, null, plugin.description()));
+        }
+
+
+
+        return completions;
+    }
+}

src/main/java/net/haesleinhuepf/fiji/macro/MyMacroExtensionDescriptor.java

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+package net.haesleinhuepf.fiji.macro;
+
+/**
+ * This is a suggested interface all macro extending plugins should implement.
+ * Change it according to your needs.
+ *
+ * @author haesleinhuepf
+ *         August 2019
+ */
+public interface MyMacroExtensionDescriptor {
+    void runFromMacro(Object[] parameters);
+    int[] parameterTypes();
+    String description();
+    String parameters();
+}

src/main/java/net/haesleinhuepf/fiji/macro/MyMacroExtensions.java

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+package net.haesleinhuepf.fiji.macro;
+
+import ij.macro.Functions;
+import ij.macro.ExtensionDescriptor;
+import ij.macro.MacroExtension;
+import net.haesleinhuepf.fiji.plugins.MyPlugins;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+
+/**
+ * MyMacroExtensions
+ *
+ * This class communicates with ImageJs macro interpreter. It hands over a list of commands
+ * (of type ExtensionDescriptor) to the macro interpreter which will be accepted as valid
+ * commands. Furthermore, it's called when one of the commands is executed.
+ *
+ *
+ * @author haesleinhuepf
+ *         August 2019
+ */
+@Plugin(type = Command.class, menuPath = "Plugins>My Macro Extensions")
+public class MyMacroExtensions implements MacroExtension, Command {
+    @Override
+    public String handleExtension(String name, Object[] args) {
+        MyMacroExtensionDescriptor[] pluginList = MyPlugins.list;
+
+        // go through plugin list an check if we know the called plugin
+        for (MyMacroExtensionDescriptor plugin : pluginList) {
+            String command = MyPlugins.macroExtensionPrefix + plugin.getClass().getSimpleName();
+
+            // if name matches exactly
+            if (command.compareTo(name) == 0) {
+                // call the plugin
+                plugin.runFromMacro(args);
+                break;
+            }
+        }
+        return null;
+    }
+
+    @Override
+    public ExtensionDescriptor[] getExtensionFunctions() {
+        MyMacroExtensionDescriptor[] pluginList = MyPlugins.list;
+
+        ExtensionDescriptor[] result = new ExtensionDescriptor[pluginList.length];
+
+        int i = 0;
+        // formulate a list of ExtensionDescriptors describing all command this class can handle
+        for (MyMacroExtensionDescriptor plugin : pluginList) {
+            String call = MyPlugins.macroExtensionPrefix + plugin.getClass().getSimpleName() + "(" + plugin.parameters() + ")";
+            result[i] = new ExtensionDescriptor(call, plugin.parameterTypes(), this);
+            i++;
+        }
+
+        // hand over the list to ImageJs macro interpreter
+        return result;
+    }
+
+    @Override
+    public void run() {
+        // Activate this class as handler for macro extensions
+        Functions.registerExtensions(this);
+    }
+}

src/main/java/net/haesleinhuepf/fiji/plugins/MyPluginAdd.java

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+package net.haesleinhuepf.fiji.plugins;
+
+
+import ij.ImagePlus;
+import ij.WindowManager;
+import ij.macro.MacroExtension;
+import net.haesleinhuepf.fiji.macro.MyMacroExtensionDescriptor;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+/**
+ * A fancy plugin which adds a given number to all pixels of an image.
+ *
+ * @author haesleinhuepf
+ *         August 2019
+ */
+@Plugin(type = Command.class, menuPath = "Plugins>My Plugin Add")
+public class MyPluginAdd implements Command, MyMacroExtensionDescriptor {
+    /**
+     * This is the actual algorithm. It adds a number to any pixel of the image
+     *
+     * @param imp input image
+     * @param scalar number to add
+     */
+    private void actualAlgorithm(ImagePlus imp, double scalar) {
+        imp.getProcessor().add(scalar);
+    }
+
+    // --------------------------------------------------------------------------------------
+    // these are implementations allowing MyMacroExtensions building autocompletion and
+    // calling the right command
+
+    // called by MyMacroExtensions in case the command is called from macro
+    @Override
+    public void runFromMacro(Object[] parameters) {
+        // We get an array of objects from the Macro interpeter.
+        // We need to convert/cast it to what we need
+        ImagePlus imp = WindowManager.getImage((String)parameters[0]);
+        double scalar = Double.parseDouble((String)parameters[1]);
+
+        // call the actual algorithm
+        actualAlgorithm(imp, scalar);
+    }
+
+    /**
+     * We need to define a list of parameter types
+     * @return int arry with parameter types as defined in the MacroExtension class.
+     */
+    @Override
+    public int[] parameterTypes() {
+        return new int[] {MacroExtension.ARG_STRING, MacroExtension.ARG_NUMBER};
+    }
+
+    /**
+     * We should provide a user readable list of parameters
+     * @return list of parameters
+     */
+    @Override
+    public String parameters() {
+        return "imageTitle, number";
+    }
+
+    /**
+     * We should define a description for users.
+     * @return algorithm/parameter description
+     */
+    @Override
+    public String description() {
+        return "Hey folks, just enter an image and a number.\n\n :-)";
+    }
+
+
+    // --------------------------------------------------------------------------------------
+    // This is the definition of parameters to allow SciJava building a
+    // dialog for us in case the user clicks the menu
+    @Parameter
+    ImagePlus input;
+
+    @Parameter
+    Double scalar;
+
+    // called by SciJava on menu click
+    @Override
+    public void run() {
+        actualAlgorithm(input, scalar);
+    }
+}