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Update-to-0.16.0 #16

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merged 7 commits into from
Jan 9, 2025
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Update-to-0.16.0 #16

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8ccb43f
improve demo test
StRigaud Dec 18, 2024
c77ea73
update code
StRigaud Dec 18, 2024
7f937b2
update pom
StRigaud Dec 18, 2024
655b4d6
update pom
StRigaud Jan 9, 2025
85aaa46
update readme
StRigaud Jan 9, 2025
9d3f553
update pom
StRigaud Jan 9, 2025
128a4e3
use clesperantoj release 0.16.9
StRigaud Jan 9, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -9,6 +9,7 @@ native/build
/.idea/
*.iml
CLIJ*.txt
*.app

# temporary files
*.log
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6 changes: 4 additions & 2 deletions demo/basic_demo.py
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Expand Up @@ -9,9 +9,11 @@

gpu_image = cle.push(imp)

gpu_result = cle.gaussian_blur(gpu_image, None, 5, 5, 5)
blurred = cle.gaussian_blur(gpu_image, None, 1, 1, 1)
binary = cle.threshold_otsu(blurred, None)
labelled = cle.connected_component_labeling(binary, None, "box")

imp_res = cle.pull(gpu_result)
imp_res = cle.pull(labelled)
imp_res.show()


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24 changes: 15 additions & 9 deletions pom.xml
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Expand Up @@ -8,13 +8,13 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>38.0.1</version>
<version>40.0.0</version>
<relativePath />
</parent>

<groupId>net.clesperanto</groupId>
<artifactId>clij3_</artifactId>
<version>0.0.1-SNAPSHOT</version>
<artifactId>clij3</artifactId>
<version>0.16.9-SNAPSHOT</version>

<name>clij3</name>
<description>clij3</description>
Expand Down Expand Up @@ -86,9 +86,9 @@
<package-name>net.clesperanto</package-name>
<license.licenseName>bsd_3</license.licenseName>
<license.copyrightOwners>Robert Haase, Stéphane Rigaud, Institut Pasteur Paris, DFG Cluster of Excellence "Physice of Life" TU Dresden</license.copyrightOwners>
<!-- <scijava.app.directory>/home/strigaud/Libraries/Fiji.app</scijava.app.directory>
<scijava.app.directory>/home/rhaase/programs/fiji/Fiji.app/</scijava.app.directory>
<scijava.app.directory>/Applications/Fiji.app/</scijava.app.directory> -->
<scijava.app.directory>/data/clesperanto/clij3/Fiji_deploy.app</scijava.app.directory>
<!-- <scijava.app.directory>/Users/strigaud/Libraries/fiji_clij/Fiji.app</scijava.app.directory> -->
<!-- <scijava.app.directory>/home/rhaase/programs/fiji/Fiji.app/</scijava.app.directory> -->
</properties>

<dependencies>
Expand Down Expand Up @@ -121,17 +121,23 @@
<scope>test</scope>
</dependency>

<!-- add imglib2 dependecy -->
<!-- add imglib2 dependency -->
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2</artifactId>
<version>7.0.2</version>
</dependency>

<!-- add javacpp dependency -->
<dependency>
<groupId>org.bytedeco</groupId>
<artifactId>javacpp</artifactId>
</dependency>

<!-- clesperantoJ dependency -->
<dependency>
<groupId>net.clesperanto</groupId>
<artifactId>clesperantoj</artifactId>
<version>0.0.1-SNAPSHOT</version>
<version>0.16.9</version>
</dependency>

</dependencies>
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16 changes: 10 additions & 6 deletions readme.md
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@@ -1,18 +1,22 @@
# CLIJ3

This is under construction. Anyway...
clij3 plugin to use clesperanto in the Fiji framework.

This plugin is still in development, feedback are very welcomed!

![img.png](demo/screenshot.png)

## Installation instructions
## Plugin Installation

Download, build, and run `mvn install` from [clesperantoj-prototype](https://github.com/clEsperanto/clesperantoj_prototype).
Download the latest release using the update site `https://imagej.net/clij3` through the Fiji update site system.

Afterwards open this project in your IDE and run the `main` function in `net.clesperanto.CLIJ3`.
## Build and Installation

## Installation to Fiji
Clone, and build the project using maven: `mvn install`.

Configure the path where your Fiji is installed [here](https://github.com/clEsperanto/clij3/blob/95560c3e8a2173e65d1f56c827cf42787ad03a96/pom.xml#L71) and run `mvn install` from this directory. Afterwards, you can execute example scripts like [this one](https://github.com/clEsperanto/clij3/blob/95560c3e8a2173e65d1f56c827cf42787ad03a96/demo/basic_demo.py) in your Fiji.
Configure the `pom` file to specify the path to your local Fiji ([here](https://github.com/clEsperanto/clij3/blob/95560c3e8a2173e65d1f56c827cf42787ad03a96/pom.xml#L71))
Run `mvn install` to install the plugin to your Fiji.
Afterwards, you can execute example scripts like [this one](https://github.com/clEsperanto/clij3/blob/95560c3e8a2173e65d1f56c827cf42787ad03a96/demo/basic_demo.py) in your Fiji.

## Acknowledgements

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