diff --git a/.classpath b/.classpath
index 373b83c7ad36b985d889e4699104d78f14456193..f31c84e7ce44c2258c6866e15c14dbcda6aa1406 100644
--- a/.classpath
+++ b/.classpath
@@ -1,10 +1,48 @@
<?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="lib" path="/Icy-App/plugins/adufour/ezplug/EzPlug.jar"/>
<classpathentry kind="lib" path="/Icy-App/plugins/adufour/blocks/Blocks.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
+ <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="ICY_JAR"/>
- <classpathentry kind="output" path="bin"/>
- <referencedentry kind="lib" path="D:/Stephane/Documents/dev/GIT/Icy-App/lib/scifio.jar" sourcepath="D:/Stephane/Documents/dev/GIT/bioformats"/>
+ <classpathentry kind="lib" path="F:/SDKs/Java/jdk1.8.0_241/lib/tools.jar"/>
+ <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
+ <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
+ <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
+ <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
+ <classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/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: org.bioimageanalysis.icy:icy-blocks:1.0.1"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-protocols:3.0.9"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-javadocparser:1.0.0"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: com.nativelibs4java:ochafik-util:0.12"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-ezplug:3.15.13"/>
+ <classpathentry kind="output" path="target/classes"/>
</classpath>
diff --git a/.gitignore b/.gitignore
index 88e283fbbe38edf75f524ead36b103a8eeb25e1a..18c1c4b324adf41df851fd5281471dcb9e2d0373 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,10 @@
-bin
-*.jar
+bin/
+target/
+.settings/
+pluginfile-sequence-blocks*.jar
+.idea/
+*.iml
+*.eml
+.project
+.classpath
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7c8b1fb42f70ad23b8a1d5ad9c6125d1d67acb2e
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,45 @@
+<?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>
+ <artifactId>pom-icy</artifactId>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <version>1.0.4</version>
+ </parent>
+
+ <artifactId>icy-sequence-blocks</artifactId>
+ <version>2.0.15</version>
+
+ <name>SequenceBlocks</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>
+ </properties>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>icy-kernel</artifactId>
+ <version>2.1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>icy-blocks</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ </dependencies>
+
+ <repositories>
+ <repository>
+ <id>icy</id>
+ <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ </repository>
+ </repositories>
+</project>
\ No newline at end of file
diff --git a/src/plugins/tprovoost/sequenceblocks/SequenceBlocks.java b/src/main/java/plugins/tprovoost/sequenceblocks/SequenceBlocks.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/SequenceBlocks.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/SequenceBlocks.java
diff --git a/src/plugins/tprovoost/sequenceblocks/add/AddOverlays.java b/src/main/java/plugins/tprovoost/sequenceblocks/add/AddOverlays.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/add/AddOverlays.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/add/AddOverlays.java
diff --git a/src/plugins/tprovoost/sequenceblocks/add/AddRois.java b/src/main/java/plugins/tprovoost/sequenceblocks/add/AddRois.java
similarity index 92%
rename from src/plugins/tprovoost/sequenceblocks/add/AddRois.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/add/AddRois.java
index d389298426610e460c616cc5bc049e11d4945a2c..cbf26c84a61aa965af654edd9d7f4973873a6d8e 100644
--- a/src/plugins/tprovoost/sequenceblocks/add/AddRois.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/add/AddRois.java
@@ -16,11 +16,9 @@ import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
/**
- * Block to add one or several {@link ROI} to a Sequence.
+ * Block to add one or several {@link ROI} to a Sequence
*
- * class: plugins.tprovoost.sequenceblocks.add.AddRois
- *
- * @author Stephane Dallongeville
+ * @author Stephane
*/
public class AddRois extends Plugin implements SequenceBlock, PluginLibrary, PluginBundled
{
diff --git a/src/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertColor.java
diff --git a/src/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertStack.java
diff --git a/src/plugins/tprovoost/sequenceblocks/convert/ConvertType.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/convert/ConvertType.java
diff --git a/src/plugins/tprovoost/sequenceblocks/convert/Resize.java b/src/main/java/plugins/tprovoost/sequenceblocks/convert/Resize.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/convert/Resize.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/convert/Resize.java
diff --git a/src/plugins/tprovoost/sequenceblocks/creation/CombineChannels.java b/src/main/java/plugins/tprovoost/sequenceblocks/creation/CombineChannels.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/creation/CombineChannels.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/creation/CombineChannels.java
diff --git a/src/plugins/tprovoost/sequenceblocks/creation/CreateSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/creation/CreateSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/creation/CreateSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/creation/CreateSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/creation/DuplicateSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/extract/CropCZT.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropCZT.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/extract/CropCZT.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/extract/CropCZT.java
diff --git a/src/plugins/tprovoost/sequenceblocks/extract/CropSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/extract/CropSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractChannel.java
diff --git a/src/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractMultiChannels.java
diff --git a/src/plugins/tprovoost/sequenceblocks/extract/ExtractSlice.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractSlice.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/extract/ExtractSlice.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractSlice.java
diff --git a/src/plugins/tprovoost/sequenceblocks/extract/ExtractTime.java b/src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractTime.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/extract/ExtractTime.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/extract/ExtractTime.java
diff --git a/src/plugins/tprovoost/sequenceblocks/files/IsFileValid.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/IsFileValid.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/files/IsFileValid.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/files/IsFileValid.java
diff --git a/src/plugins/tprovoost/sequenceblocks/files/LoadMetadata.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadMetadata.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/files/LoadMetadata.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/files/LoadMetadata.java
diff --git a/src/plugins/tprovoost/sequenceblocks/files/LoadSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/files/LoadSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/files/LoadSubSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSubSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/files/LoadSubSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/files/LoadSubSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/files/SaveMetadata.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveMetadata.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/files/SaveMetadata.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/files/SaveMetadata.java
diff --git a/src/plugins/tprovoost/sequenceblocks/files/SaveSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/files/SaveSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/files/SaveSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/files/SaveSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/images/AddImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/AddImage.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/images/AddImage.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/images/AddImage.java
diff --git a/src/plugins/tprovoost/sequenceblocks/images/AsImageArray.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/AsImageArray.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/images/AsImageArray.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/images/AsImageArray.java
diff --git a/src/plugins/tprovoost/sequenceblocks/images/GetImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/GetImage.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/images/GetImage.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/images/GetImage.java
diff --git a/src/plugins/tprovoost/sequenceblocks/images/RemoveImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/RemoveImage.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/images/RemoveImage.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/images/RemoveImage.java
diff --git a/src/plugins/tprovoost/sequenceblocks/images/SetImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/images/SetImage.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/images/SetImage.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/images/SetImage.java
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/importer/PositionedSequenceFileImporter.java
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterClose.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterClose.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterClose.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterClose.java
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
similarity index 91%
rename from src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
index 7794f12ee8b40c846ca82ac3fb96fc0a7be69933..3720a15cafe134f661fc1b06283f41292e2f9546 100644
--- a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
@@ -38,11 +38,11 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
super();
importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
- series = new VarInteger("Series", -1);
+ series = new VarInteger("Series", 0);
resolution = new VarInteger("Resolution (0=full, 1=1/2, ..)", 0);
region = new VarROIArray("XY region (ROI)", null);
- zIndex = new VarInteger("Z (slice) index", -1);
- tIndex = new VarInteger("T (frame) index", -1);
+ zIndex = new VarInteger("Z (slice) index", 0);
+ tIndex = new VarInteger("T (frame) index", 0);
cIndex = new VarInteger("C (channel) index", -1);
image = new Var<IcyBufferedImage>("Image", IcyBufferedImage.class);
@@ -71,7 +71,7 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds()
: null;
- // undefined values ? use internal position if any defined
+ // default values ? use internal position if any defined
if ((s == 0) && (pi.s != -1))
s = pi.s;
if ((z == 0) && (pi.z != -1))
@@ -83,10 +83,6 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
if ((rect == null) && (pi.xyRegion != null))
rect = pi.xyRegion;
- // still undefined ? --> set default value for series
- if (s == -1)
- s = 0;
-
try
{
image.setValue(imp.getImage(s, res, rect, z, t, c));
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetMetadata.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetMetadata.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetMetadata.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetMetadata.java
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetThumbnail.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetThumbnail.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetThumbnail.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetThumbnail.java
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetTileSize.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetTileSize.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetTileSize.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetTileSize.java
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
similarity index 93%
rename from src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
index 666f65cc710b68cabe97b37fd1ecaaf4b2c604b5..34c8ba2d6a387750d1b97aef4b1300a5f8c6dda8 100644
--- a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
@@ -43,7 +43,7 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
- series = new VarInteger("Series", -1);
+ series = new VarInteger("Series", 0);
resolution = new VarInteger("Resolution (0=full, 1=1/2, ..)", 0);
region = new VarROIArray("XY region (ROI)", null);
minZIndex = new VarInteger("Z min (slice)", -1);
@@ -80,8 +80,8 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds()
: null;
- // undefined values ? use internal position if any defined
- if ((s == -1) && (pi.s != -1))
+ // default values ? use internal position if any defined
+ if ((s == 0) && (pi.s != -1))
s = pi.s;
if ((minZ == -1) && (maxZ == -1) && (pi.z != -1))
{
@@ -93,14 +93,10 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
minT = pi.t;
maxT = pi.t;
}
- if ((c == -1) && (pi.c != -1))
+ if ((c == 0) && (pi.c != -1))
c = pi.c;
if ((rect == null) && (pi.xyRegion != null))
rect = pi.xyRegion;
-
- // still undefined ? --> set default value for series
- if (s == -1)
- s = 0;
try
{
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterOpen.java b/src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterOpen.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterOpen.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterOpen.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/CreateLinearColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/CreateLinearColormap.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/CreateLinearColormap.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/CreateLinearColormap.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/Dimensions.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/Dimensions.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/Dimensions.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/Dimensions.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/EzVarColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/EzVarColormap.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/EzVarColormap.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/EzVarColormap.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetChannelName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelName.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetChannelName.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelName.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetChannelsName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelsName.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetChannelsName.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetChannelsName.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormap.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetColormap.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormap.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetColormaps.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormaps.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetColormaps.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetColormaps.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetDataType.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetDataType.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetDataType.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetDataType.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetFileName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
similarity index 97%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
index 2bf3699ee50a8651b20df613489457db5bc6e286..477a91549d9c19cffc6ad3aa69f178a3ca2b3cc5 100644
--- a/src/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetFileName.java
@@ -42,7 +42,7 @@ public class GetFileName extends Plugin implements SequenceBlock, PluginBundled
result = FileUtil.getFileName(result);
// remove extension ?
if (!withExtension.getValue().booleanValue())
- result = FileUtil.setExtension(result, "");
+ FileUtil.setExtension(result, "");
filename.setValue(result);
}
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetMetaData.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetMetaData.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetMetaData.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetMetaData.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetName.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetName.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetName.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetOutputFilename.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetOutputFilename.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetOutputFilename.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetOutputFilename.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetResolution.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetResolution.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetResolution.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetResolution.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/GetRoisAsRegion.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/GetRoisAsRegion.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/GetRoisAsRegion.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/GetRoisAsRegion.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/ReadMetadata.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/ReadMetadata.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/ReadMetadata.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/ReadMetadata.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/SetChannelName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelName.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/SetChannelName.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelName.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/SetChannelsName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelsName.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/SetChannelsName.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/SetChannelsName.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/SetColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormap.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/SetColormap.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormap.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/SetColormaps.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormaps.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/SetColormaps.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/SetColormaps.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/SetName.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetName.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/SetName.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/SetName.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/SetResolution.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/SetResolution.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/infos/SetResolution.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/SetResolution.java
diff --git a/src/plugins/tprovoost/sequenceblocks/infos/VarColormap.java b/src/main/java/plugins/tprovoost/sequenceblocks/infos/VarColormap.java
similarity index 97%
rename from src/plugins/tprovoost/sequenceblocks/infos/VarColormap.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/infos/VarColormap.java
index d1776836e52a74e0452f8cc35bfb7b1add7c1203..017f8b950f6b668f493e16b8085eebd77cd6913a 100644
--- a/src/plugins/tprovoost/sequenceblocks/infos/VarColormap.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/infos/VarColormap.java
@@ -50,7 +50,7 @@ public class VarColormap extends Var<IcyColorMap>
// create the var editor (combo box type here)
final ComboBox<IcyColorMap> result = new ComboBox<IcyColorMap>(this);
// get the editor component
- final JComboBox<?> combo = result.getEditorComponent();
+ final JComboBox combo = result.getEditorComponent();
// and set a specific renderer
combo.setRenderer(new ColormapComboBoxRenderer(combo));
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
similarity index 92%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
index 763ccaa66f8f588bbfdb8c9077948077494654e1..f227dcdf5f39c9831fca6562ccaf1e5788b66547 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceChannelBatch.java
@@ -17,10 +17,15 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
*/
public class SequenceChannelBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
- // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
+ // important to not initialize and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
+ public SequenceChannelBatch()
+ {
+ super();
+ }
+
@Override
public VarSequence getBatchSource()
{
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
similarity index 63%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
index 48ef8fb78bc0c06d0580986a67f365c3b701a6e0..782c76cf22a1fcc65214f96af01bd64148f79d4c 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
@@ -1,15 +1,11 @@
package plugins.tprovoost.sequenceblocks.loop;
-import java.util.List;
-
import icy.file.SequenceFileImporter;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
import plugins.adufour.blocks.lang.Batch;
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
-import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.Var;
-import plugins.adufour.vars.lang.VarInteger;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
@@ -21,10 +17,9 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
*/
public abstract class SequenceFileImporterBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
- // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
+ // important to not initialize and create them in getBatchSource() and getBatchElement()
protected Var<PositionedSequenceFileImporter> positionedImporter;
protected Var<PositionedSequenceFileImporter> element;
- protected VarInteger series;
// internal
protected int limit;
@@ -63,42 +58,8 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
if (imp.getOpened() == null)
throw new VarException(positionedImporter, "Importer is not opened !");
- // create new positioned importer for element initialization
- final PositionedSequenceFileImporter pi = new PositionedSequenceFileImporter(value);
-
- final int s = series.getValue().intValue();
-
- // defined series ? --> set series position
- if (s != -1)
- pi.s = s;
-
- // init element with a copy of current positioned importer (and eventually set serie position)
- element.setValue(pi);
- }
-
- @Override
- public void declareInput(VarList inputMap)
- {
- super.declareInput(inputMap);
-
- // lazy creation
- if (series == null)
- series = new VarInteger("Series", -1);
-
- inputMap.add("series", series);
- }
-
- @Override
- public void declareLoopVariables(List<Var<?>> loopVariables)
- {
- // need to be called after
- super.declareLoopVariables(loopVariables);
-
- // lazy creation
- if (series == null)
- series = new VarInteger("Series", -1);
-
- loopVariables.add(series);
+ // init element with a copy of current positioned importer
+ element.setValue(new PositionedSequenceFileImporter(value));
}
@Override
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
similarity index 91%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
index afc3b0405731be0aab4532d1fec43677f797bbe9..46640c56371c0c1eade6faae2c6d3a23d531ce35 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
@@ -17,8 +17,7 @@ public class SequenceFileImporterChannelBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- // can take position from element which should have been initialized here
- final PositionedSequenceFileImporter pi = element.getValue();
+ final PositionedSequenceFileImporter pi = positionedImporter.getValue();
try
{
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
similarity index 91%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
index ba8bf1066324d59de57918deaf474eb654dae72b..e91d5f4ff98aba478bb7aa82b97957726f288141 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
@@ -17,8 +17,7 @@ public class SequenceFileImporterFrameBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- // can take position from element which should have been initialized here
- final PositionedSequenceFileImporter pi = element.getValue();
+ final PositionedSequenceFileImporter pi = positionedImporter.getValue();
try
{
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
similarity index 94%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
index 05f05183d8836780a5e821f1701ded158786fcc3..0bbd8bb263a02730c16eb1c2aa4fac2fd7dad8cd 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
@@ -24,7 +24,6 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
*/
public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
{
- // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
protected VarROIArray rois;
protected VarInteger inputRoisResolution;
protected VarInteger inputRoisMargin;
@@ -35,8 +34,7 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- // can take position from element which should have been initialized here
- final PositionedSequenceFileImporter pi = element.getValue();
+ final PositionedSequenceFileImporter pi = positionedImporter.getValue();
// can iterate over XY dimension ?
if ((pi.xyRegion == null) && (rois.getValue() != null))
@@ -116,8 +114,6 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
@Override
public void declareLoopVariables(List<Var<?>> loopVariables)
{
- super.declareLoopVariables(loopVariables);
-
// lazy creation
if (rois == null)
rois = new VarROIArray("XY regions (ROIs)");
@@ -129,6 +125,8 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
loopVariables.add(rois);
loopVariables.add(inputRoisResolution);
loopVariables.add(inputRoisMargin);
+
+ super.declareLoopVariables(loopVariables);
}
@Override
diff --git a/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
new file mode 100644
index 0000000000000000000000000000000000000000..255c14ceb98dbccc3ec8b09e5a4db47f420a240f
--- /dev/null
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
@@ -0,0 +1,48 @@
+package plugins.tprovoost.sequenceblocks.loop;
+
+import icy.file.SequenceFileImporter;
+import icy.sequence.MetaDataUtil;
+import plugins.adufour.vars.util.VarException;
+import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
+
+/**
+ * Simple batch loop to iterate over all series from the specified opened {@link SequenceFileImporter} object.
+ *
+ * @author Stephane
+ */
+public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
+{
+ @Override
+ public void initializeLoop()
+ {
+ super.initializeLoop();
+
+ final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+
+ try
+ {
+ // force series iteration as by default series is set to 0
+ limit = MetaDataUtil.getNumSeries(pi.getMetadata());
+ }
+ catch (Exception e)
+ {
+ throw new VarException(element,
+ "Error while initializing SequenceFileImporter series batch: " + e.getMessage());
+ }
+ }
+
+ @Override
+ public void beforeIteration()
+ {
+ // set current position S
+ element.getValue().s = getIterationCounter().getValue().intValue();
+ // force element changed event so loop get correctly executed
+ element.valueChanged(element, element.getValue(), element.getValue());
+ }
+
+ @Override
+ public boolean isStopConditionReached()
+ {
+ return getIterationCounter().getValue().intValue() >= limit;
+ }
+}
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
similarity index 91%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
index 93a5514285f7563ec343e5d173322757dc65f535..061b76de2ce25f577b22617ab6d0e5ec2b1049a7 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
@@ -17,8 +17,7 @@ public class SequenceFileImporterSliceBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- // can take position from element which should have been initialized here
- final PositionedSequenceFileImporter pi = element.getValue();
+ final PositionedSequenceFileImporter pi = positionedImporter.getValue();
try
{
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
similarity index 68%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
index 57d3af77dfe12a277bbc5710fe1efe70b8fcbdf8..5386fb6de960654e2274d0f96aebebc51482b1a6 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
@@ -6,10 +6,7 @@ import java.util.List;
import icy.file.SequenceFileImporter;
import icy.image.ImageUtil;
import icy.sequence.MetaDataUtil;
-import plugins.adufour.blocks.util.VarList;
-import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarInteger;
-import plugins.adufour.vars.lang.VarROIArray;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
@@ -20,19 +17,25 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
*/
public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
{
- // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
- protected VarInteger tileW;
- protected VarInteger tileH;
+ protected final VarInteger tileW;
+ protected final VarInteger tileH;
protected List<Rectangle> tiles;
+ public SequenceFileImporterTileBatch()
+ {
+ super();
+
+ tileW = new VarInteger("Tile width (-1 = auto)", 0);
+ tileH = new VarInteger("Tile height (-1 = auto)", 0);
+ }
+
@Override
public void initializeLoop()
{
super.initializeLoop();
- // can take position from element which should have been initialized here
- final PositionedSequenceFileImporter pi = element.getValue();
+ final PositionedSequenceFileImporter pi = positionedImporter.getValue();
// can iterate over XY dimension ?
if (pi.xyRegion == null)
@@ -60,7 +63,7 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
}
catch (Exception e)
{
- throw new VarException(element,
+ throw new VarException(positionedImporter,
"Error while initializing SequenceFileImporter tile batch: " + e.getMessage());
}
@@ -85,37 +88,6 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
else
limit = 1;
}
-
- @Override
- public void declareInput(VarList inputMap)
- {
- super.declareInput(inputMap);
-
- // lazy creation
- if (tileW == null)
- tileW = new VarInteger("Tile width (-1 = auto)", -1);
- if (tileH == null)
- tileH = new VarInteger("Tile height (-1 = auto)", -1);
-
- inputMap.add("tileWidht", tileW);
- inputMap.add("tileHeight", tileH);
- }
-
- @Override
- public void declareLoopVariables(List<Var<?>> loopVariables)
- {
- // need to be called after
- super.declareLoopVariables(loopVariables);
-
- // lazy creation
- if (tileW == null)
- tileW = new VarInteger("Tile width (-1 = auto)", -1);
- if (tileH == null)
- tileH = new VarInteger("Tile height (-1 = auto)", -1);
-
- loopVariables.add(tileW);
- loopVariables.add(tileH);
- }
@Override
public void beforeIteration()
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
similarity index 91%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
index 0737a24c90b4b4c36ab9692f875098398f82614f..d06b0a6c91a7b520f7eb72e5bdeb9e26a14cf6e2 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceFrameBatch.java
@@ -16,7 +16,7 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
*/
public class SequenceFrameBatch extends Batch implements PluginLibrary, PluginBundled
{
- // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
+ // important to not initialize and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
@@ -40,7 +40,7 @@ public class SequenceFrameBatch extends Batch implements PluginLibrary, PluginBu
{
// initialize element if needed
if (element == null)
- element = new VarSequence("Frame Sequence", null);
+ element = new VarSequence("Channel Sequence", null);
return element;
}
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
similarity index 70%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
index 4612efc37d930d0a0944c51631c5f7b009bf7ac3..548ba91b6ad96f97bda809d1c73ab7538d72fd88 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceRegionBatch.java
@@ -4,7 +4,6 @@ import java.util.List;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
-import icy.roi.ROI;
import icy.sequence.Sequence;
import icy.sequence.SequenceUtil;
import plugins.adufour.blocks.lang.Batch;
@@ -23,55 +22,36 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
*/
public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
- // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
+ // important to not initialize and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
- protected VarROIArray rois;
- protected VarROIArray currentRoi;
+ protected final VarROIArray rois;
public SequenceRegionBatch()
{
super();
- }
-
- @Override
- public VarROIArray getBatchSource()
- {
- if (rois == null)
- rois = new VarROIArray("ROI(s)");
-
- return rois;
- }
-
- @Override
- public VarSequence getBatchElement()
- {
- if (element == null)
- element = new VarSequence("Region Sequence", null);
- return element;
+ rois = new VarROIArray("ROI(s)");
}
@Override
- public void declareInput(VarList inputMap)
+ public VarSequence getBatchSource()
{
- super.declareInput(inputMap);
-
+ // initialize variable if needed
if (inputSequence == null)
inputSequence = new VarSequence("Sequence", null);
- inputMap.add(inputSequence.getName(), inputSequence);
+ return inputSequence;
}
@Override
- public void declareOutput(VarList outputMap)
+ public VarSequence getBatchElement()
{
- super.declareOutput(outputMap);
-
- if (currentRoi == null)
- currentRoi = new VarROIArray("Current ROI");
+ // initialize element if needed
+ if (element == null)
+ element = new VarSequence("Channel Sequence", null);
- outputMap.add(currentRoi.getName(), currentRoi);
+ return element;
}
@Override
@@ -90,10 +70,8 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
public void beforeIteration()
{
// set result in element
- final ROI roi = rois.getValue()[getIterationCounter().getValue().intValue()];
-
- element.setValue(SequenceUtil.getSubSequence(inputSequence.getValue(), roi));
- currentRoi.setValue(new ROI[] {roi});
+ element.setValue(SequenceUtil.getSubSequence(inputSequence.getValue(),
+ rois.getValue()[getIterationCounter().getValue().intValue()]));
}
@Override
@@ -102,12 +80,20 @@ public class SequenceRegionBatch extends Batch implements SequenceBlock, PluginL
return getIterationCounter().getValue().intValue() >= rois.getValue().length;
}
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ inputMap.add("ROIs", rois);
+ }
+
@Override
public void declareLoopVariables(List<Var<?>> loopVariables)
{
super.declareLoopVariables(loopVariables);
- loopVariables.add(inputSequence);
- loopVariables.add(currentRoi);
+
+ loopVariables.add(rois);
}
@Override
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
similarity index 91%
rename from src/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
index e8c2003095f9ea416acb141df9c53a3fed7ed56d..d1bc6897915d2fb04e82c3327e30e83da2c8b802 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
+++ b/src/main/java/plugins/tprovoost/sequenceblocks/loop/SequenceSliceBatch.java
@@ -17,7 +17,7 @@ import plugins.tprovoost.sequenceblocks.SequenceBlocks;
*/
public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
- // important to not initialize here (even with null) and create them in getBatchSource() and getBatchElement()
+ // important to not initialize and create them in getBatchSource() and getBatchElement()
protected VarSequence inputSequence;
protected VarSequence element;
@@ -36,7 +36,7 @@ public class SequenceSliceBatch extends Batch implements SequenceBlock, PluginLi
{
// initialize element if needed
if (element == null)
- element = new VarSequence("Slice Sequence", null);
+ element = new VarSequence("Channel Sequence", null);
return element;
}
diff --git a/src/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/op/AdditiveFillSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/op/FillInnerSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java b/src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/op/FillOuterSequence.java
diff --git a/src/plugins/tprovoost/sequenceblocks/remove/RemoveAllRois.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveAllRois.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/remove/RemoveAllRois.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveAllRois.java
diff --git a/src/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveChannel.java
diff --git a/src/plugins/tprovoost/sequenceblocks/remove/RemoveFrame.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveFrame.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/remove/RemoveFrame.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveFrame.java
diff --git a/src/plugins/tprovoost/sequenceblocks/remove/RemoveOverlays.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveOverlays.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/remove/RemoveOverlays.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveOverlays.java
diff --git a/src/plugins/tprovoost/sequenceblocks/remove/RemoveRois.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveRois.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/remove/RemoveRois.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveRois.java
diff --git a/src/plugins/tprovoost/sequenceblocks/remove/RemoveSlice.java b/src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveSlice.java
similarity index 100%
rename from src/plugins/tprovoost/sequenceblocks/remove/RemoveSlice.java
rename to src/main/java/plugins/tprovoost/sequenceblocks/remove/RemoveSlice.java
diff --git a/res/SequenceBlocks.xml b/src/main/resources/SequenceBlocks.xml
similarity index 100%
rename from res/SequenceBlocks.xml
rename to src/main/resources/SequenceBlocks.xml
diff --git a/res/SequenceBlocks_icon.png b/src/main/resources/SequenceBlocks_icon.png
similarity index 100%
rename from res/SequenceBlocks_icon.png
rename to src/main/resources/SequenceBlocks_icon.png
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
deleted file mode 100644
index ffb8e57b7eec5d8a0c220be797cf52e763cae911..0000000000000000000000000000000000000000
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
+++ /dev/null
@@ -1,77 +0,0 @@
-package plugins.tprovoost.sequenceblocks.loop;
-
-import java.util.List;
-
-import icy.file.SequenceFileImporter;
-import icy.sequence.MetaDataUtil;
-import plugins.adufour.blocks.util.VarList;
-import plugins.adufour.vars.lang.Var;
-import plugins.adufour.vars.util.VarException;
-import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
-
-/**
- * Simple batch loop to iterate over all series from the specified opened {@link SequenceFileImporter} object.
- *
- * @author Stephane
- */
-public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
-{
- @Override
- public void initializeLoop()
- {
- super.initializeLoop();
-
- // can take position from element which should have been initialized here
- final PositionedSequenceFileImporter pi = element.getValue();
-
- try
- {
- // can iterate over S dimension ?
- if (pi.s == -1)
- limit = MetaDataUtil.getNumSeries(pi.getMetadata());
- else
- limit = 1;
- }
- catch (Exception e)
- {
- throw new VarException(element,
- "Error while initializing SequenceFileImporter series batch: " + e.getMessage());
- }
- }
-
- @Override
- public void declareInput(VarList inputMap)
- {
- super.declareInput(inputMap);
-
- // we don't want it here
- inputMap.remove(series);
- }
-
- @Override
- public void declareLoopVariables(List<Var<?>> loopVariables)
- {
- super.declareLoopVariables(loopVariables);
-
- // we don't want it here
- loopVariables.remove(series);
- }
-
- @Override
- public void beforeIteration()
- {
- // set current position S
- if (positionedImporter.getValue().s == -1)
- {
- element.getValue().s = getIterationCounter().getValue().intValue();
- // force element changed event so loop get correctly executed
- element.valueChanged(element, element.getValue(), element.getValue());
- }
- }
-
- @Override
- public boolean isStopConditionReached()
- {
- return getIterationCounter().getValue().intValue() >= limit;
- }
-}