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Enabled module for loading ImgLib2 images
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This acts as a starting point for loading ImgLib2 disk cached images.
Most modules still don't support this.
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@sjcross
sjcross committed Nov 28, 2023
1 parent 23ca594 commit 387c5ff
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Showing 17 changed files with 425 additions and 124 deletions.
14 changes: 7 additions & 7 deletions .vscode/launch.json
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@@ -1,12 +1,12 @@
{
"configurations": [
// {
// "type": "java",
// "name": "MIA",
// "request": "launch",
// "mainClass": "io.github.mianalysis.mia.MIA",
// "projectName": "pom-mia"
// },
{
"type": "java",
"name": "MIA",
"request": "launch",
"mainClass": "io.github.mianalysis.mia.MIA",
"projectName": "pom-mia"
},
{
"type": "java",
"name": "MIA-main",
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120 changes: 80 additions & 40 deletions dependency-reduced-pom.xml
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Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>pom-scijava</artifactId>
<groupId>org.scijava</groupId>
<version>36.0.0</version>
<version>37.0.0</version>
<relativePath>pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>
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</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.scif</groupId>
<artifactId>scifio</artifactId>
<version>0.45.0</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>scifio-jai-imageio</artifactId>
<groupId>io.scif</groupId>
</exclusion>
<exclusion>
<artifactId>imagej-common</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2-cache</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.scif</groupId>
<artifactId>scifio-bf-compat</artifactId>
<version>4.1.1</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>formats-api</artifactId>
<groupId>ome</groupId>
</exclusion>
<exclusion>
<artifactId>scifio-ome-xml</artifactId>
<groupId>io.scif</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>bio-formats_plugins</artifactId>
<version>6.14.0</version>
<version>7.0.0</version>
<scope>provided</scope>
<exclusions>
<exclusion>
Expand All @@ -403,10 +447,6 @@
<artifactId>ome-xml</artifactId>
<groupId>org.openmicroscopy</groupId>
</exclusion>
<exclusion>
<artifactId>formats-api</artifactId>
<groupId>ome</groupId>
</exclusion>
<exclusion>
<artifactId>jgoodies-forms</artifactId>
<groupId>com.jgoodies</groupId>
Expand All @@ -415,12 +455,16 @@
<artifactId>ij</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>formats-api</artifactId>
<groupId>ome</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-bsd</artifactId>
<version>6.14.0</version>
<version>7.0.0</version>
<scope>provided</scope>
<exclusions>
<exclusion>
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<artifactId>ome-xml</artifactId>
<groupId>org.openmicroscopy</groupId>
</exclusion>
<exclusion>
<artifactId>formats-api</artifactId>
<groupId>ome</groupId>
</exclusion>
<exclusion>
<artifactId>jgoodies-forms</artifactId>
<groupId>com.jgoodies</groupId>
</exclusion>
<exclusion>
<artifactId>formats-api</artifactId>
<groupId>ome</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
<version>6.14.0</version>
<version>7.0.0</version>
<scope>provided</scope>
<exclusions>
<exclusion>
Expand All @@ -519,10 +563,6 @@
<artifactId>cdm-core</artifactId>
<groupId>edu.ucar</groupId>
</exclusion>
<exclusion>
<artifactId>JWlz</artifactId>
<groupId>woolz</groupId>
</exclusion>
<exclusion>
<artifactId>json</artifactId>
<groupId>org.json</groupId>
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<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej</artifactId>
<version>2.14.0</version>
<version>2.15.0</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>imagej-common</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>imagej-launcher</artifactId>
<groupId>net.imagej</groupId>
Expand All @@ -571,10 +607,6 @@
<artifactId>imagej-updater</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>scifio</artifactId>
<groupId>io.scif</groupId>
</exclusion>
<exclusion>
<artifactId>imagej-deprecated</artifactId>
<groupId>net.imagej</groupId>
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<artifactId>imagej-scripting</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>scifio-labeling</artifactId>
<groupId>io.scif</groupId>
</exclusion>
<exclusion>
<artifactId>scijava-io-http</artifactId>
<groupId>org.scijava</groupId>
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<artifactId>script-editor-scala</artifactId>
<groupId>org.scijava</groupId>
</exclusion>
<exclusion>
<artifactId>imagej-common</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
Expand All @@ -643,10 +683,6 @@
<version>1.0.1</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>imglib2</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2-roi</artifactId>
<groupId>net.imglib2</groupId>
Expand All @@ -660,17 +696,21 @@
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>imagej-common</artifactId>
<artifactId>imagej-deprecated</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>imagej-deprecated</artifactId>
<artifactId>imagej-updater</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>imagej-updater</artifactId>
<artifactId>imagej-common</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
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<artifactId>jama</artifactId>
<groupId>gov.nist.math</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2-roi</artifactId>
<groupId>net.imglib2</groupId>
Expand All @@ -723,6 +759,10 @@
<artifactId>imagej-common</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
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<artifactId>imglib2-algorithm</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
<exclusion>
<artifactId>ij</artifactId>
<groupId>net.imagej</groupId>
</exclusion>
<exclusion>
<artifactId>imglib2</artifactId>
<groupId>net.imglib2</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
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35 changes: 24 additions & 11 deletions pom.xml
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Expand Up @@ -6,13 +6,13 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>36.0.0</version>
<version>37.0.0</version>
<relativePath />
</parent>

<groupId>io.github.mianalysis</groupId>
<artifactId>mia</artifactId>
<version>1.4.8</version>
<version>1.4.8-SNAPSHOT</version>
<packaging>jar</packaging>
<name>MIA</name>
<url>https://github.com/mianalysis/mia</url>
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<mailingLists>
<mailingList>
<name>Image.sc Forum</name>
<archive>https://forum.image.sc/tag/modular-image-analysis</archive>
</mailingList>
<name>Image.sc Forum</name>
<archive>https://forum.image.sc/tag/modular-image-analysis</archive>
</mailingList>
</mailingLists>

<scm>
Expand All @@ -108,9 +108,9 @@
</scm>

<ciManagement>
<system>GitHub Actions</system>
<url>https://github.com/mianalysis/mia</url>
</ciManagement>
<system>GitHub Actions</system>
<url>https://github.com/mianalysis/mia</url>
</ciManagement>

<repositories>
<repository>
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<version>0.4.8</version>
</dependency>

<dependency>
<groupId>io.scif</groupId>
<artifactId>scifio</artifactId>
<scope>${scp}</scope>
</dependency>

<dependency>
<groupId>io.scif</groupId>
<artifactId>scifio-bf-compat</artifactId>
<scope>${scp}</scope>
</dependency>

<dependency>
<groupId>ome</groupId>
<artifactId>bio-formats_plugins</artifactId>
Expand Down Expand Up @@ -495,7 +507,7 @@
<includeScope>runtime</includeScope>

<excludeArtifactIds>
commons-codec,commons-collections4,commons-io,guava,ij,jama,javassist,junit,MorphoLibJ_,Skeletonize3D_,vecmath</excludeArtifactIds>
commons-codec,commons-collections4,commons-io,guava,ij,jama,javassist,junit,MorphoLibJ_,Skeletonize3D_,vecmath</excludeArtifactIds>

<outputDirectory>${project.build.directory}/jars/</outputDirectory>
<overWriteReleases>false</overWriteReleases>
Expand All @@ -516,7 +528,8 @@
<!-- Use the following to deploy -->
<!-- Manually delete "target" folder -->
<!-- mvn clean deploy -Dscp=provided -Dmaven.test.skip -->
<!-- CHECK GENERATED MIA JAR RUNS IN FIJI (sometimes it generates a larger jar which fails to run - maybe when "target" isn't deleted first)-->
<!-- CHECK GENERATED MIA JAR RUNS IN FIJI (sometimes it generates a larger jar which
fails to run - maybe when "target" isn't deleted first)-->
<!-- Release to Maven Central using following -->
<!-- mvn nexus-staging:release -->

Expand Down Expand Up @@ -596,4 +609,4 @@
</plugin>
</plugins>
</reporting>
</project>
</project>

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