From c4e9281264f0ef1067e6bda5cc132f5e8f1b5171 Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Sun, 7 Jul 2024 00:48:58 +0200
Subject: [PATCH] updated pom to v2.0.0-a.1, fix classes accordingly to new
architecture, added icon, updated .gitignore
---
.gitignore | 41 +++-
StackRotation.jar | Bin 4275 -> 0 bytes
export.jardesc | 16 --
pom.xml | 52 +----
.../spop/rotation3D/StackRotation.class | Bin 4632 -> 0 bytes
.../spop/rotation3D/StackRotation.java | 209 +++++++++---------
src/main/resources/stack-rotation.png | Bin 0 -> 5004 bytes
7 files changed, 148 insertions(+), 170 deletions(-)
delete mode 100644 StackRotation.jar
delete mode 100644 export.jardesc
delete mode 100644 src/main/java/plugins/spop/rotation3D/StackRotation.class
create mode 100644 src/main/resources/stack-rotation.png
diff --git a/.gitignore b/.gitignore
index 3d47f98..57f16fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,41 @@
-.idea/
+/build*
+/workspace
+setting.xml
+release/
target/
-.settings/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
+.classpath
+.factorypath
.project
-.classpath
\ No newline at end of file
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/StackRotation.jar b/StackRotation.jar
deleted file mode 100644
index a18d426e7d854c66773851fa79c5c553782d1ead..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/export.jardesc b/export.jardesc
deleted file mode 100644
index 7f140a2..0000000
--- a/export.jardesc
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
-<jardesc>
- <jar path="Stack Rotation/StackRotation.jar"/>
- <options buildIfNeeded="true" compress="true" descriptionLocation="/Stack Rotation/export.jardesc" exportErrors="false" exportWarnings="true" includeDirectoryEntries="true" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
- <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
- <selectedProjects/>
- <manifest generateManifest="true" manifestLocation="/Icy-Updater/META-INF/MANIFEST.MF" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
- <sealing sealJar="false">
- <packagesToSeal/>
- <packagesToUnSeal/>
- </sealing>
- </manifest>
- <selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
- <javaElement handleIdentifier="=Stack Rotation/src"/>
- </selectedElements>
-</jardesc>
diff --git a/pom.xml b/pom.xml
index 0f93d48..b3da942 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,20 +6,17 @@
<!-- Inherited Icy Parent POM -->
<parent>
- <artifactId>pom-icy</artifactId>
+ <artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
- <version>2.0.0</version>
- </parent>
+ <version>3.0.0-a.1</version>
+ </parent>
<!-- Project Information -->
<artifactId>stack-rotation</artifactId>
- <version>1.2.1</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0-a.1</version>
<name>Stack Rotation</name>
- <description>Rotate the 3D stack from Front view to Right view or from Front view to Top view. </description>
- <url></url>
+ <description>Rotate the 3D stack from Front view to Right view or from Front view to Top view.</description>
<inceptionYear>2020</inceptionYear>
<organization>
@@ -53,55 +50,22 @@
</developer>
</developers>
- <!-- Project properties -->
- <properties>
-
- </properties>
-
- <profiles>
- <profile>
- <id>icy-plugin</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- </profile>
- </profiles>
-
- <!-- List of project's dependencies -->
<dependencies>
- <!-- The core of Icy -->
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-kernel</artifactId>
- <version>${icy-kernel.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>blockvars</artifactId>
- <version>${blockvars.version}</version>
+ <artifactId>ezplug</artifactId>
</dependency>
-
- <!-- The EzPlug library, simplifies writing UI for Icy plugins. -->
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>ezplug</artifactId>
- <version>${ezplug.version}</version>
+ <artifactId>protocols</artifactId>
</dependency>
-
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-bioformats</artifactId>
- <version>${icy-bioformats.version}</version>
- </dependency>
</dependencies>
<!-- Icy Maven repository (to find parent POM) -->
<repositories>
<repository>
<id>icy</id>
- <name>Icy's Nexus</name>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/spop/rotation3D/StackRotation.class b/src/main/java/plugins/spop/rotation3D/StackRotation.class
deleted file mode 100644
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diff --git a/src/main/java/plugins/spop/rotation3D/StackRotation.java b/src/main/java/plugins/spop/rotation3D/StackRotation.java
index 95aa806..2bf56eb 100644
--- a/src/main/java/plugins/spop/rotation3D/StackRotation.java
+++ b/src/main/java/plugins/spop/rotation3D/StackRotation.java
@@ -1,168 +1,163 @@
+/*
+ * Copyright (c) 2010-2024. 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/>.
+ */
+
package plugins.spop.rotation3D;
-import icy.image.IcyBufferedImage;
-import icy.sequence.Sequence;
-import icy.type.collection.array.Array1DUtil;
-import icy.util.OMEUtil;
+import org.bioimageanalysis.icy.common.collection.array.Array1DUtil;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.OMEUtil;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.ezplug.EzPlug;
import plugins.adufour.ezplug.EzVarSequence;
import plugins.adufour.ezplug.EzVarText;
-public class StackRotation extends EzPlug implements Block
-{
-
- EzVarSequence input = new EzVarSequence("Input");
- EzVarText type = new EzVarText("Type", new String[] { "FrontToRight", "FrontToTop" }, false);
+@IcyPluginName("Stack Rotation")
+@IcyPluginIcon(path = "/stack-rotation.png")
+public class StackRotation extends EzPlug implements Block {
+ EzVarSequence input = new EzVarSequence("Input");
+ EzVarText type = new EzVarText("Type", new String[]{"FrontToRight", "FrontToTop"}, false);
// VarSequence output = new VarSequence("Output", false);
-
+
EzVarSequence output = new EzVarSequence("Output");
-
+
@Override
- public void initialize()
- {
- // TODO Auto-generated method stub
+ public void initialize() {
super.addEzComponent(input);
super.addEzComponent(type);
// super.addOutput(output);
super.setTimeDisplay(true);
-
+
}
-
+
@Override
- public void execute()
- {
-
- Sequence sequence = input.getValue(true);
+ public void execute() {
+ final Sequence sequence = input.getValue(true);
Sequence seq_out = new Sequence(OMEUtil.createOMEXMLMetadata(sequence.getOMEXMLMetadata()));
- if (type.getValue().equalsIgnoreCase("FrontToRight"))
- {
+ if (type.getValue().equalsIgnoreCase("FrontToRight")) {
seq_out = FrontToRight(sequence);
seq_out.setName("FrontToRight");
}
- if (type.getValue().equalsIgnoreCase("FrontToTop"))
- {
+ if (type.getValue().equalsIgnoreCase("FrontToTop")) {
seq_out = FrontToTop(sequence);
seq_out.setName("FrontToTop");
-
+
}
-
+
if (getUI() != null) addSequence(seq_out);
output.setValue(seq_out);
-
}
-
- public static Sequence FrontToRight(Sequence sequence)
- {
-
- int z = 0;
-
- Sequence seq = new Sequence();
-
- int dim_x = sequence.getSizeX();
- int dim_y = sequence.getSizeY();
- int dim_z = sequence.getSizeZ();
- int dim_t = sequence.getSizeT();
- int dim_c = sequence.getSizeC();
- double[][] tab = new double[dim_z][dim_x * dim_y];
- double[][][] tab_r = new double[dim_c][dim_x][dim_y * dim_z];
-
- for (int t = 0; t < dim_t; t++)
- {
- for (int c = 0; c < dim_c; c++)
- {
- for (z = 0; z < dim_z; z++)
- {
+
+ public static @NotNull Sequence FrontToRight(final @NotNull Sequence sequence) {
+ int z; // = 0;
+
+ final Sequence seq = new Sequence();
+
+ final int dim_x = sequence.getSizeX();
+ final int dim_y = sequence.getSizeY();
+ final int dim_z = sequence.getSizeZ();
+ final int dim_t = sequence.getSizeT();
+ final int dim_c = sequence.getSizeC();
+ final double[][] tab = new double[dim_z][dim_x * dim_y];
+ final double[][][] tab_r = new double[dim_c][dim_x][dim_y * dim_z];
+
+ for (int t = 0; t < dim_t; t++) {
+ for (int c = 0; c < dim_c; c++) {
+ for (z = 0; z < dim_z; z++) {
tab[z] = Array1DUtil.arrayToDoubleArray(sequence.getDataXY(t, z, c), false);
}
for (z = 0; z < dim_z; z++)
for (int y = 0; y < dim_y; y++)
- for (int x = 0; x < dim_x; x++)
- {
+ for (int x = 0; x < dim_x; x++) {
tab_r[c][x][y * dim_z + z] = tab[z][y * dim_x + x];
}
}
-
- for (z = 0; z < dim_x; z++)
- {
- IcyBufferedImage Icy = new IcyBufferedImage(dim_z, dim_y, dim_c, sequence.getDataType());
+
+ for (z = 0; z < dim_x; z++) {
+ final IcyBufferedImage Icy = new IcyBufferedImage(dim_z, dim_y, dim_c, sequence.getDataType());
for (int c = 0; c < dim_c; c++)
Icy.setDataXY(c, tab_r[c][z]);
seq.setImage(t, z, Icy);
}
}
-
+
System.gc();
return seq;
-
}
-
- public static Sequence FrontToTop(Sequence sequence)
- {
-
- int z = 0;
-
- Sequence seq = new Sequence();
-
- int dim_x = sequence.getSizeX();
- int dim_y = sequence.getSizeY();
- int dim_z = sequence.getSizeZ();
- int dim_t = sequence.getSizeT();
- int dim_c = sequence.getSizeC();
- double[][] tab = new double[dim_z][dim_x * dim_y];
- double[][][] tab_r = new double[dim_c][dim_y][dim_x * dim_z];
-
- for (int t = 0; t < dim_t; t++)
- {
- for (int c = 0; c < dim_c; c++)
- {
- for (z = 0; z < dim_z; z++)
- {
+
+ public static @NotNull Sequence FrontToTop(final @NotNull Sequence sequence) {
+ int z; // = 0;
+
+ final Sequence seq = new Sequence();
+
+ final int dim_x = sequence.getSizeX();
+ final int dim_y = sequence.getSizeY();
+ final int dim_z = sequence.getSizeZ();
+ final int dim_t = sequence.getSizeT();
+ final int dim_c = sequence.getSizeC();
+ final double[][] tab = new double[dim_z][dim_x * dim_y];
+ final double[][][] tab_r = new double[dim_c][dim_y][dim_x * dim_z];
+
+ for (int t = 0; t < dim_t; t++) {
+ for (int c = 0; c < dim_c; c++) {
+ for (z = 0; z < dim_z; z++) {
tab[z] = Array1DUtil.arrayToDoubleArray(sequence.getDataXY(t, z, c), false);
}
for (z = 0; z < dim_z; z++)
for (int y = 0; y < dim_y; y++)
- for (int x = 0; x < dim_x; x++)
- {
- tab_r[c][y][z * dim_x + x] = tab[z][y * dim_x + x];
- }
+ if (dim_x >= 0) System.arraycopy(
+ tab[z],
+ y * dim_x, // + 0,
+ tab_r[c][y],
+ z * dim_x, // + 0,
+ dim_x);
}
-
- for (z = 0; z < dim_y; z++)
- {
- IcyBufferedImage Icy = new IcyBufferedImage(dim_x, dim_z, dim_c, sequence.getDataType());
+
+ for (z = 0; z < dim_y; z++) {
+ final IcyBufferedImage Icy = new IcyBufferedImage(dim_x, dim_z, dim_c, sequence.getDataType());
for (int c = 0; c < dim_c; c++)
Icy.setDataXY(c, tab_r[c][z]);
seq.setImage(t, z, Icy);
}
}
-
+
System.gc();
-
+
return seq;
-
+
}
-
- public void clean()
- {
+
+ @Override
+ public void clean() {
}
-
+
@Override
- public void declareInput(VarList inputMap)
- {
- // TODO Auto-generated method stub
- inputMap.add(input.getVariable());
- inputMap.add(type.getVariable());
-
+ public void declareInput(final @NotNull VarList inputMap) {
+ inputMap.add("input", input.getVariable());
+ inputMap.add("type", type.getVariable());
}
-
+
@Override
- public void declareOutput(VarList outputMap)
- {
- // TODO Auto-generated method stub
- outputMap.add(output.getVariable());
-
+ public void declareOutput(final @NotNull VarList outputMap) {
+ outputMap.add("output", output.getVariable());
}
-
}
diff --git a/src/main/resources/stack-rotation.png b/src/main/resources/stack-rotation.png
new file mode 100644
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--
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