diff --git a/.gitignore b/.gitignore
index d054a8f0873988d37e7828bfd603990b5d79a970..fb538c4fbbe2731cd2e50862ffe5ebc399ca2450 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,8 @@
.settings/
target/
build/
+out/
*.iml
.classpath
.project
+**/.DS_Store
\ No newline at end of file
diff --git a/README.md b/README.md
index 3723ff80a7bce8d753eb34b72df72907260d9e7d..f8ed769c4233f7f69f4cdd3ad4e57b4e4aa38416 100644
--- a/README.md
+++ b/README.md
@@ -87,7 +87,7 @@ Just keep it as is.
By convention the Java package of Icy plugins takes the following form:
```java
-package plugins.authorname.pluginname
+package plugins.authorname.pluginname;
```
`authorname` should be a condensed version of your name. For instance the author Alexandre Dufour uses `adufour`. Jean-Yves Tinevez uses `tinevez` _etc_.
@@ -139,7 +139,7 @@ http://icy.bioimageanalysis.org
## Author(s)
-Amandine TOURNAY, Jean-Yves Tinevez, Stéphane Dallongeville
+Amandine TOURNAY, Jean-Yves Tinevez, Stéphane Dallongeville, Thomas MUSSET
## Additional information
diff --git a/pom.xml b/pom.xml
index 0fe5388137d7c050526c103603aaeb4cb25dbaad..e4f0badb3aa87c507ca2e9b2d30231500ffb3fe3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,19 +8,17 @@
<parent>
<artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
- <version>2.1.0</version>
+ <version>2.1.5</version>
</parent>
<!-- Project Information -->
<artifactId>plugin-template</artifactId>
- <version>1.0.3-SNAPSHOT</version>
-
- <packaging>jar</packaging>
+ <version>1.0.0-SNAPSHOT</version>
<name>A template for Icy plugins.</name>
<description>This repo serves as a template for you to implement new Icy plugins.</description>
- <url></url>
- <inceptionYear>2020</inceptionYear>
+ <url>https://www.example.org</url>
+ <inceptionYear>2023</inceptionYear>
<organization>
<name>MyOrganizationName</name>
@@ -55,21 +53,16 @@
<!-- Project properties -->
<properties>
-
+ <artifact-to-extract>JMathPlot,JMathIO,JMathArray</artifact-to-extract>
</properties>
- <!-- Project build configuration -->
- <build>
-
- </build>
-
<!-- List of project's dependencies -->
<dependencies>
<!-- The core of Icy -->
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>icy-kernel</artifactId>
- <version>2.1.4</version>
+ <version>2.4.3</version>
</dependency>
<!-- The EzPlug library, simplifies writing UI for Icy plugins. -->
@@ -78,6 +71,22 @@
<artifactId>ezplug</artifactId>
</dependency>
+ <!-- External libraries example -->
+ <dependency>
+ <groupId>com.github.yannrichet</groupId>
+ <artifactId>JMathPlot</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>com.github.yannrichet</groupId>
+ <artifactId>JMathIO</artifactId>
+ <version>1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>com.github.yannrichet</groupId>
+ <artifactId>JMathArray</artifactId>
+ <version>1.0</version>
+ </dependency>
</dependencies>
<!-- Icy Maven repository (to find parent POM) -->
@@ -88,15 +97,4 @@
<url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
</repository>
</repositories>
-
- <distributionManagement>
- <snapshotRepository>
- <id>server-id</id>
- <url>server's url</url>
- </snapshotRepository>
- <repository>
- <id>server-id</id>
- <url>server's url</url>
- </repository>
- </distributionManagement>
</project>
diff --git a/src/main/java/plugins/authorname/templateplugin/MyEzPlugIcyPlugin.java b/src/main/java/plugins/authorname/templateplugin/MyEzPlugIcyPlugin.java
index 8b91ed889767a3d9b6269f4b699ea58465f2733c..2931121e54e0a536d7bde5d1fc084d01f720ab09 100644
--- a/src/main/java/plugins/authorname/templateplugin/MyEzPlugIcyPlugin.java
+++ b/src/main/java/plugins/authorname/templateplugin/MyEzPlugIcyPlugin.java
@@ -1,8 +1,22 @@
-package plugins.authorname.templateplugin;
-
-import java.lang.reflect.InvocationTargetException;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import javax.swing.SwingUtilities;
+package plugins.authorname.templateplugin;
import icy.file.Loader;
import icy.gui.dialog.MessageDialog;
@@ -11,76 +25,75 @@ import icy.main.Icy;
import icy.plugin.PluginLauncher;
import icy.plugin.PluginLoader;
import icy.sequence.Sequence;
+import icy.system.IcyExceptionHandler;
import icy.system.thread.ThreadUtil;
import plugins.adufour.ezplug.EzButton;
import plugins.adufour.ezplug.EzPlug;
import plugins.adufour.ezplug.EzVarBoolean;
import plugins.adufour.ezplug.EzVarInteger;
-public class MyEzPlugIcyPlugin extends EzPlug
-{
-
- private final EzVarInteger age = new EzVarInteger( "Your age", 30, 10, 100, 1 );
-
- private final EzVarBoolean yummy = new EzVarBoolean( "Like chocolate?", true );
-
- private final EzButton button = new EzButton( "Load an show an image now", l -> loadAndShow() );
-
- @Override
- protected void initialize()
- {
- // Add elements in order of appearance.
- addEzComponent( age );
- addEzComponent( yummy );
- addEzComponent( button );
- }
-
- @Override
- public void clean()
- {
- // Nothing to do
- }
-
- @Override
- protected void execute()
- {
- final String str = "This plugin start button does not do anything useful.\n "
- + "You say you are " + age.getValue() + " years old and you "
- + (yummy.getValue() ? "like" : "don't like" )
- + " chocolate.";
- MessageDialog.showDialog( str );
- }
-
- private void loadAndShow()
- {
- final String imagePath = "samples/Cont1.lsm";
-
- // Load in a separate thread.
- ThreadUtil.bgRun(() -> {
-
- final Sequence sequence = Loader.loadSequence( imagePath, 0, true );
-
- // Display the images.
- try
- {
- SwingUtilities.invokeAndWait( () -> new Viewer( sequence ));
- }
- catch ( InvocationTargetException | InterruptedException e )
- {
- e.printStackTrace();
- }
- });
- }
-
- public static void main( final String[] args )
- {
- // Launch the application.
- Icy.main( args );
-
- /*
- * Programmatically launch a plugin, as if the user had clicked its
- * button.
- */
- PluginLauncher.start( PluginLoader.getPlugin( MyEzPlugIcyPlugin.class.getName() ) );
- }
+import javax.swing.*;
+import java.lang.reflect.InvocationTargetException;
+
+public class MyEzPlugIcyPlugin extends EzPlug {
+
+ private final EzVarInteger age = new EzVarInteger("Your age", 30, 10, 100, 1);
+
+ private final EzVarBoolean yummy = new EzVarBoolean("Like chocolate?", true);
+
+ private final EzButton button = new EzButton("Load an show an image now", l -> loadAndShow());
+
+ @Override
+ protected void initialize() {
+ // Add elements in order of appearance.
+ addEzComponent(age);
+ addEzComponent(yummy);
+ addEzComponent(button);
+ }
+
+ @Override
+ public void clean() {
+ // Nothing to do
+ }
+
+ @Override
+ protected void execute() {
+ final String str = "This plugin start button does not do anything useful.\n "
+ + "You say you are " + age.getValue() + " years old and you "
+ + (yummy.getValue() ? "like" : "don't like")
+ + " chocolate.";
+ MessageDialog.showDialog(str);
+ }
+
+ private void loadAndShow() {
+ final String imagePath = "samples/Cont1.lsm";
+
+ // Load in a separate thread.
+ ThreadUtil.bgRun(() -> {
+
+ final Sequence sequence = Loader.loadSequence(imagePath, 0, true);
+
+ // Display the images.
+ try {
+ SwingUtilities.invokeAndWait(() -> new Viewer(sequence));
+ }
+ catch (final InvocationTargetException | InterruptedException e) {
+ IcyExceptionHandler.showErrorMessage(e, true);
+ }
+ });
+ }
+
+ /**
+ * Only for test purpose.
+ */
+ public static void main(final String[] args) {
+ // Launch the application.
+ Icy.main(args);
+
+ /*
+ * Programmatically launch a plugin, as if the user had clicked its
+ * button.
+ */
+ PluginLauncher.start(PluginLoader.getPlugin(MyEzPlugIcyPlugin.class.getName()));
+ }
}
diff --git a/src/main/java/plugins/authorname/templateplugin/MyIcyPlugin.java b/src/main/java/plugins/authorname/templateplugin/MyIcyPlugin.java
index 58c05df0eb1905d6d3463a110481b0c0b47eb0b8..393657a84e216999ca9e8b1cf41558104f60516e 100644
--- a/src/main/java/plugins/authorname/templateplugin/MyIcyPlugin.java
+++ b/src/main/java/plugins/authorname/templateplugin/MyIcyPlugin.java
@@ -1,8 +1,22 @@
-package plugins.authorname.templateplugin;
-
-import java.lang.reflect.InvocationTargetException;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import javax.swing.SwingUtilities;
+package plugins.authorname.templateplugin;
import icy.file.Loader;
import icy.gui.dialog.MessageDialog;
@@ -14,6 +28,9 @@ import icy.sequence.Sequence;
import icy.sequence.SequenceUtil;
import icy.system.thread.ThreadUtil;
+import javax.swing.*;
+import java.lang.reflect.InvocationTargetException;
+
/**
* A simple plugin demonstration.
* <p>
@@ -22,123 +39,112 @@ import icy.system.thread.ThreadUtil;
* <p>
* This is toy that shows how to make a plugin that can be launched from Icy and
* that will MODIFY an image.
- *
- * @author Jean-Yves Tinevez
*
+ * @author Jean-Yves Tinevez
*/
-public class MyIcyPlugin extends PluginActionable
-{
-
- /*
- * The run() method is called when the user presses the plugin button.
- */
-
- @Override
- public void run()
- {
- /*
- * We are in the Event Dispatch Thread (EDT) right now. It is a good
- * idea to jump into another thread so that the processing of our plugin
- * does not prevent the EDT to deal with the user-interface.
- */
-
- ThreadUtil.bgRun(() -> {
-
- /*
- * We are are not the EDT anymore. Now we can do heavy-lifting
- * operations and the Icy UI won't be blocked.
- */
-
- final Sequence sequence = getActiveSequence();
-
- // Check if a sequence is opened.
- if ( sequence == null )
- {
- MessageDialog.showDialog( "This plugin needs an opened sequence." );
- return;
- }
-
- final int width = sequence.getSizeX();
- final int height = sequence.getSizeY();
- final int nChannel = sequence.getSizeC();
-
- // Iterate over all the planes of the image, through C and Z.
- for ( final IcyBufferedImage plane : sequence.getAllImage() )
- {
- try
- {
- /*
- * We put the pixel edit between a beginUpdate() and an
- * endUpdate (all in a try/finally block), so that we
- * only display the display (which takes time) once the
- * edits of a plane are over.
- *
- * We could also have chosen to put the beginUpdate()
- * before editing the sequence to have only one display
- * update.
- */
-
- plane.beginUpdate();
-
- /*
- * We pedestriantly iterate pixel by pixel and recopy
- * the value of the every 7th pixel on the 2 that
- * follows.
- */
-
- for ( int c = 0; c < nChannel; c++ )
- {
- for ( int y = 0; y < height; y++ )
- {
- double val = 0;
- for ( int x = 0; x < width; x++ )
- {
- if ( x % 7 == 0 )
- val = plane.getData( x, y, c );
-
- plane.setData( x, y, c, val );
- }
- }
- }
- }
- finally
- {
- plane.endUpdate();
- }
- }
- });
- }
-
- /*
- * We use a main method to make this class runnable from your favorite IDE.
- * If you run this class, it will simply starts Icy. Your preferences won't
- * be there however, and it will be a naked" icy.
- *
- * Custom plugins with no extra configuration will show up in the "Plugins"
- * ribbons, under the "Other Plugins" button. This plugin button gets
- * automatically placed in the "authorname" menu. This is why by convention
- * Icy plugins have a package that always starts with "plugins.authorname".
- */
-
- public static void main( final String[] args ) throws InvocationTargetException, InterruptedException
- {
- // Launch the application.
- Icy.main( args );
-
- // Load an image.
- final String imagePath = "samples/Cont1.lsm";
- final Sequence sequence = Loader.loadSequence( imagePath, 0, true );
-
- // Copy it so that we work on a copy.
- final Sequence copy = SequenceUtil.getCopy( sequence );
-
- // Display the images.
- SwingUtilities.invokeAndWait( () -> {
- new Viewer( sequence );
- new Viewer( copy );
- } );
-
- // Run the plugin on the last active image (the copy).
- new MyIcyPlugin().run();
- }
+public class MyIcyPlugin extends PluginActionable {
+
+ /*
+ * The run() method is called when the user presses the plugin button.
+ */
+ @Override
+ public void run() {
+ /*
+ * We are in the Event Dispatch Thread (EDT) right now. It is a good
+ * idea to jump into another thread so that the processing of our plugin
+ * does not prevent the EDT to deal with the user-interface.
+ */
+
+ ThreadUtil.bgRun(() -> {
+
+ /*
+ * We are not the EDT anymore. Now we can do heavy-lifting
+ * operations and the Icy UI won't be blocked.
+ */
+
+ final Sequence sequence = getActiveSequence();
+
+ // Check if a sequence is opened.
+ if (sequence == null) {
+ MessageDialog.showDialog("This plugin needs an opened sequence.");
+ return;
+ }
+
+ final int width = sequence.getSizeX();
+ final int height = sequence.getSizeY();
+ final int nChannel = sequence.getSizeC();
+
+ // Iterate over all the planes of the image, through C and Z.
+ for (final IcyBufferedImage plane : sequence.getAllImage()) {
+ try {
+ /*
+ * We put the pixel edit between a beginUpdate() and an
+ * endUpdate (all in a try/finally block), so that we
+ * only display the display (which takes time) once the
+ * edits of a plane are over.
+ *
+ * We could also have chosen to put the beginUpdate()
+ * before editing the sequence to have only one display
+ * update.
+ */
+
+ plane.beginUpdate();
+
+ /*
+ * We pedestriantly iterate pixel by pixel and recopy
+ * the value of the every 7th pixel on the 2 that
+ * follows.
+ */
+
+ for (int c = 0; c < nChannel; c++) {
+ for (int y = 0; y < height; y++) {
+ double val = 0;
+ for (int x = 0; x < width; x++) {
+ if (x % 7 == 0)
+ val = plane.getData(x, y, c);
+
+ plane.setData(x, y, c, val);
+ }
+ }
+ }
+ }
+ finally {
+ plane.endUpdate();
+ }
+ }
+ });
+ }
+
+ /**
+ * We use a main method to make this class runnable from your favorite IDE.
+ * If you run this class, it will simply starts Icy. Your preferences won't
+ * be there however, and it will be a naked" icy.
+ * <p>
+ * Custom plugins with no extra configuration will show up in the "Plugins"
+ * ribbons, under the "Other Plugins" button. This plugin button gets
+ * automatically placed in the "authorname" menu. This is why by convention
+ * Icy plugins have a package that always starts with "plugins.authorname".
+ * <p>
+ * Only for test purpose.
+ */
+ public static void main(final String[] args) throws InvocationTargetException, InterruptedException {
+ // Launch the application.
+ Icy.main(args);
+
+ // Load an image.
+ final String imagePath = "samples/Cont1.lsm";
+ final Sequence sequence = Loader.loadSequence(imagePath, 0, true);
+
+ // Copy it so that we work on a copy.
+ final Sequence copy = SequenceUtil.getCopy(sequence);
+
+ // Display the images.
+ SwingUtilities.invokeAndWait(() -> {
+ new Viewer(sequence);
+ new Viewer(copy);
+ });
+
+ // Run the plugin on the last active image (the copy).
+ new MyIcyPlugin().run();
+ }
}
diff --git a/src/main/resources/plugins/authorname/templateplugin/add_resources_here.txt b/src/main/resources/plugins/authorname/templateplugin/add_resources_here.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391