Merge pull request #16 from clEsperanto/update-to-0.16.0

Update-to-0.16.9

rely on:
- clesperantoj-0.16.9
- pom-scijava-40.0.0

.gitignore

@@ -9,6 +9,7 @@ native/build
 /.idea/
 *.iml
 CLIJ*.txt
+*.app
 
 # temporary files
 *.log

demo/basic_demo.py

@@ -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()
 
 

pom.xml

@@ -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>
@@ -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>
@@ -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>

readme.md

@@ -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