diff --git a/.classpath b/.classpath index 03f7b32eab652ef4d5a2f884ac0c38af8e587292..171a694cea8c23f901ab103c620d82ad484e3667 100644 --- a/.classpath +++ b/.classpath @@ -1,11 +1,41 @@ <?xml version="1.0" encoding="UTF-8"?> <classpath> - <classpathentry kind="src" path="src"/> + <classpathentry kind="src" path="src/main/java"/> + <classpathentry kind="src" path="src/main/resources"/> + <classpathentry kind="src" path="src/test/java"/> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/> <classpathentry kind="var" path="MM_HOME/plugins/Micro-Manager/MMCoreJ.jar" sourcepath="/MM_SOURCES"/> <classpathentry kind="var" path="MM_HOME/plugins/Micro-Manager/MMJ_.jar" sourcepath="/GIT/micro-manager"/> <classpathentry kind="var" path="ICY_JAR"/> - <classpathentry kind="output" path="bin"/> - <referencedentry kind="lib" path="D:/Stephane/Documents/dev/GIT/Icy-App/lib/swingx-all.jar" sourcepath="D:/Stephane/workspace/Libraries/SwingX"/> - <referencedentry kind="lib" path="D:/Stephane/Documents/dev/GIT/Icy-App/lib/bioformats.jar" sourcepath="/bioformats"/> + <classpathentry kind="lib" path="F:/SDKs/Java/jdk1.8.0_241/lib/tools.jar"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-kernel:2.1.0"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.sf.ehcache:ehcache:2.10.6"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.slf4j:slf4j-api:1.7.25"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-bioformats:6.3.1"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-insubstantial:7.3.7"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-vtk:6.3.0.1"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.imagej:ij:1.52q"/> + <classpathentry kind="lib" path="D:/SDKs/Java/jdk1.8.0_241/lib/tools.jar"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: javax.media:jai-core:1.1.3"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: javax.media:jai-codec:1.1.3"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all:2.1.5-01"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-linux-amd64:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-linux-i586:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-macosx-universal:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-windows-amd64:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-windows-i586:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt:2.1.5-01"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-linux-amd64:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-linux-i586:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-macosx-universal:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-windows-amd64:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-windows-i586:2.1.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.javassist:javassist:3.22.0-GA"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.sourceforge.jexcelapi:jxl:2.6.12"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: log4j:log4j:1.2.14"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.swinglabs.swingx:swingx-all:1.6.5-1"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: joda-time:joda-time:2.10.5"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.micromanager:MMCoreJ:1.4.22"/> + <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.micromanager:MMJ_:1.4.22"/> + <classpathentry kind="output" path="target/classes"/> </classpath> diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..9a247eb5b94db0b24a64b97b329e7bc33b5dcfe2 --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +.idea/ +workspace/ +build/ +target/ +*.iml +*.eml \ No newline at end of file diff --git a/pom.xml b/pom.xml new file mode 100644 index 0000000000000000000000000000000000000000..c526a8b5532bf2cba4463812d98b5db5d1e7db4b --- /dev/null +++ b/pom.xml @@ -0,0 +1,90 @@ +<?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> + + <groupId>org.bioimageanalysis.icy</groupId> + <artifactId>icy-micromanager</artifactId> + <version>1.0.3</version> + + <name>MicroManager for Icy</name> + + <properties> + <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> + <jdk.version>1.8</jdk.version> + + <maven.compiler.source>1.8</maven.compiler.source> + <maven.compiler.target>1.8</maven.compiler.target> + + <outputJar>${project.build.outputDirectory}/../plugin</outputJar> + </properties> + + <build> + <finalName>${project.artifactId}</finalName> + + <plugins> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-jar-plugin</artifactId> + <version>3.1.2</version> + <configuration> + <outputDirectory>${outputJar}</outputDirectory> + <archive> + <manifest> + <addClasspath>true</addClasspath> + <mainClass>plugins.tprovoost.Microscopy.MicroManagerForIcy.MicromanagerPlugin</mainClass> + </manifest> + </archive> + </configuration> + </plugin> + </plugins> + </build> + + <dependencies> + <dependency> + <groupId>org.bioimageanalysis.icy</groupId> + <artifactId>icy-kernel</artifactId> + <version>2.1.0</version> + </dependency> + <dependency> + <groupId>joda-time</groupId> + <artifactId>joda-time</artifactId> + <version>2.10.5</version> + </dependency> + <dependency> + <groupId>org.micromanager</groupId> + <artifactId>MMCoreJ</artifactId> + <version>1.4.22</version> + </dependency> + <dependency> + <groupId>org.micromanager</groupId> + <artifactId>MMJ_</artifactId> + <version>1.4.22</version> + </dependency> + </dependencies> + + <repositories> + <repository> + <id>icy</id> + <url>https://icy-nexus.pasteur.fr/repository/Icy/</url> + </repository> + <repository> + <id>imagej-release</id> + <url>http://maven.imagej.net/content/repositories/public/</url> + </repository> + </repositories> + + <distributionManagement> + <snapshotRepository> + <id>icy-dev</id> + <name>icy-dev</name> + <url>https://icy-nexus-dev.pasteur.cloud/repository/icy-core/</url> + </snapshotRepository> + <repository> + <id>icy-prod</id> + <name>icy-prod</name> + <url>https://icy-nexus.pasteur.fr/repository/icy-core/</url> + </repository> + </distributionManagement> +</project> \ No newline at end of file diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/MicroManager.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionHandler.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionHandler.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionHandler.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionHandler.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/core/AcquisitionResult.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/AcquisitionListener.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/event/LiveListener.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java similarity index 98% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java index 515fa46517be0a7bc0a3643049625980754db954..85dcc8bdc9359cf369e29badf32ad8c2f619c3fe 100644 --- a/src/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java +++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AboutPanel.java @@ -49,7 +49,7 @@ public class AboutPanel extends JPanel "<html><body>" + "<h2>About</h2><p>Micro-Manager for Icy is being developed by Stephane Dallongeville, Irsath Nguyen and Thomas Provoost." + "<br/>Copyright 2016, Institut Pasteur</p><br/>" - + "<p>This plugin is based on Micro-Manager© " + MMVersion.VERSION_STRING + + "<p>This plugin is based on Micro-Manager? " + MMVersion.VERSION_STRING + " which is developed under the following license:<br/>" + "<i>This software is distributed free of charge in the hope that it will be<br/>" + "useful, but WITHOUT ANY WARRANTY; without even the implied<br/>" diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/AcquisitionInfoPanel.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ActionsPanel.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/CameraSettingsPanel.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/ChannelTable.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ChannelTable.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/ChannelTable.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ChannelTable.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/ConfigurationPanel.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LiveSettingsPanel.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadFrame.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/LoadingFrame.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadingFrame.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/LoadingFrame.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/LoadingFrame.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MMMainFrame.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/MainPanel.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/OptionsPanel.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/OptionsPanel.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/OptionsPanel.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/OptionsPanel.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/gui/PluginsToolbar.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/patch/MMPatcher.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMPatcher.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/patch/MMPatcher.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMPatcher.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/patch/MMStudioMethods.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/FrameUtils.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/tools/ImageGetter.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/ImageGetter.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/tools/ImageGetter.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/ImageGetter.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/MMUtils.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java similarity index 98% rename from src/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java index 1896ee1adf38f701685a1e1cd505fe9e960eabad..5c4c129ed190a05341d544dc32878cf37f50858b 100644 --- a/src/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java +++ b/src/main/java/plugins/tprovoost/Microscopy/MicroManager/tools/StageMover.java @@ -377,7 +377,7 @@ public class StageMover * Moves the stage on the Z-Axis. Wait for movement. * * @param position - * Z position (in µm) + * Z position (in ?m) * @throws Exception */ public static void moveZAbsolute(double position) throws Exception @@ -390,7 +390,7 @@ public class StageMover * <b>You should wait for the microscope if you are planning to capture image after this call</b> * * @param position - * Z position (in µm) + * Z position (in ?m) * @param wait * wait for device to process command. Note that you can use {@link #waitZMoving()} to ensure Z stage * complete the movement. @@ -474,7 +474,7 @@ public class StageMover * <b>Relative move may not be accurate !</b> * * @param movement - * : movement (in µm) + * : movement (in ?m) * @throws Exception */ public static void moveZRelative(double movement) throws Exception @@ -488,7 +488,7 @@ public class StageMover * <b>You should wait for the microscope if you are planning to capture image after this call</b> * * @param movement - * Z movement (in µm) + * Z movement (in ?m) * @param wait * wait for device to process command. Note that you can use {@link #waitZMoving()} to ensure Z stage * complete the movement. @@ -525,9 +525,9 @@ public class StageMover * <b>Relative move may not be accurate !</b> * * @param movX - * movement on X-Axis (in µm) + * movement on X-Axis (in ?m) * @param movY - * movement on Y-Axis (in µm) + * movement on Y-Axis (in ?m) * @throws Exception */ public static void moveXYRelative(double movX, double movY) throws Exception @@ -541,9 +541,9 @@ public class StageMover * <b>You should wait for the microscope if you are planning to capture image after this call</b> * * @param movX - * movement on X-Axis (in µm) + * movement on X-Axis (in ?m) * @param movY - * movement on Y-Axis (in µm) + * movement on Y-Axis (in ?m) * @param wait * wait for device to process command. Note that you can use {@link #waitXYMoving()} to ensure XY stage * complete the movement. diff --git a/src/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.java diff --git a/src/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java b/src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java similarity index 100% rename from src/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java rename to src/main/java/plugins/tprovoost/Microscopy/MicroManagerForIcy/MicroscopePlugin.java diff --git a/res/image/menu_tip.jpg b/src/main/resources/image/menu_tip.jpg similarity index 100% rename from res/image/menu_tip.jpg rename to src/main/resources/image/menu_tip.jpg