INSTALL

Setup instructions for this Maven project
==========================================

Maven in Eclipse
-----------------

You need to enable Maven support within Eclipse.
To this end please ensure that you have the following add-ons installed:

 m2e Maven support for Eclipse, you can install the plugin via "Help" -> "Install New Software..." 

 Apt-Support for Maven (m2e-apt), for installation choose
 "Window" -> "Preferences" -> "Maven" -> "Discovery" -> "Open Catalog" and search for "m2e";

 after installing the add-on annotation processing for Maven needs to be enabled explicitly:
 go to "Window" -> "Preferences" -> "Maven" -> "Annotation Processing" 
 and select "Automatically configure JDT APT"


Setting up the project
-----------------------

1. Extract the zip archive to a folder of your choice.

2. Run Eclipse.
   Select 'File' -> 'Import...' from the menubar.
   The select 'Maven', subsequently 'Existing Maven Projects' and click 'Next'.

   If you do not see a menu entry for Maven, not all of the plugins required are installed. 
   To fix this please refer to subsection B.1.

   In the next window use the "Browse..." button to select the directory to which you extracted the zip archive.
   Please select the folder containing the 'pom.xml' file.
   If anything is ok Eclipse will then let you select the MiToBo demo project.

   Press the 'Finish' button.
   
   The project is then going to be imported into the workspace and will soon appear 
   in the project explorer under the name 'mitobo-demo-project'. 

   Attention! Do not delete the folder to which the zip archive was extracted until the Eclipse project is removed!
   	      And if you delete the Eclipse project from your workspace make sure that the resources are not deleted,
 	      otherwise your files are lost.

3. Your own class files should be placed in the source folder 'src/main/java' of the project. 
   All operators located there and properly annotated will automatically be indexed and appear in the operator
   runner's menu for operator selection.


Using the new operator in rhizoTrak
------------------------------------

You need to package a jar file with your new operator.

The easiest way is to run "mvn package" on command-line in the root directory of your project.

Then copy the generated jar file to be found in the "targets" folder to the "jars" folder of
your local Fiji installation and restart Fiji.
When running rhizoTrak the operator should appear in its segmentation operator list.