FBIWP1_IPDM/README.md at master · France-Bio-Imaging-Data/FBIWP1_IPDM

What is Metro for?

Metro is a collection of Icy's plugin (Blocks). It gives you full access to bio-images stored those were stored in your OpenImadis or Omero remote servers. It also provides some tools to feed, populate metadata for your images and display meta information for analysis interacting with all plugins available in Icy.

As Metro runs over Icy's protocols at the end you would design your complete solution for metrology.

Version 0.0.1 (beta)

How do I get set up?

** For eclipse developers:

Go to File -> Import -> Git (Project from git)
Clone the project https://yourusername@bitbucket.org/fbiwp1/metro.git (master)
Right click over "metro" project. (Configure->Convert to Maven project)
Right click over « metro » project Properties->Tick Icy plugin (Icy Plugin Nature)
Run this from eclipse as you usually do in your Icy’s plugins (D)
Have fun

** For console developers:

Install maven version 3 or superior
clone the project: (git clone https://yourusername@bitbucket.org/fbiwp1/metro.git)
Enter to the project folder
to clean execute: mvn clean
to compile execute: mvn compile
to create a jar execute: mvn package
to create code coverage report execute: mvn cobertura:cobertura
you will find your jar file in target/ folder
Have fun

** No developers can find the plugin over Icy’s site (Not yet available)

How to run in headless mode ?

Go to the Icy folder.
execute : java -jar icy.jar -hl -x plugins.ofuica.metro.Metro
could be OpenImadis or Omero
image id
could be: psf_profiler

Executing protocol file

Go to icy folder
execute : java -jar icy.jar -hl -x plugins.adufour.protocols.Protocol protocol=<path_to_proto> psf_id= image_id=
(e.g) java -jar ./icy.jar -hl -x plugins.adufour.protocols.Protocols protocol=./benchmark.protocol psf_id=11844 image_id=11866
So benchmark protocol will execute.

Publisher

Using a terminal software, go to the metro's application folder publisher/apps/IcyProtocol
Then execute the command javac *.java. You will find a dot class generated file.

Executing the publisher on a computer or cluster

In your computer:

Using terminal software
Go to metro's application folder and publisher.
run ./run-compute.bat

In a cluster:

You will need copy all the publisher's folder to the cluster location.
Compile using your app javac *.java
Run ./run-compute.bat (It is necessary specify some parameters depending of the needs.)
Go to the OpenImadis web interface and execute the process for an image.