[ImageJ-devel] plugin dev in elcipse

[Mark Hiner]

Hi Dan,

>its not obvious for an elclipse noob like me.

No worries. I definitely found the instructions confusing as well (which is
why for a long time I'd just build and copy the jars).

>what would a main class look like for running the coloc plugin straight
from ellipse

Coloc 2 already has a dependency on fiji-lib, so you just need a class with
two things:

1. import fiji.Debug;

2. a main method like this:
    public static void main(String[] args) {
        Debug.run(null, null);
    }

You can just put that method in Coloc_2.java, for example, and run it in
Eclipse. It should start up an ImageJ instance with Coloc_2 installed
properly.

>i dont see any place where the coloc .jar is biult and saved? Where should
the built .jar be located by default?

If you build it as a Maven project Eclipse should create the .jars[1]. Also
all ImageJ/Fiji projects can be built from the command line[2] by using
mvn. In either case the output jar is in the /target subdirectory, per
Maven convention.

Let us know if you run into any more problems or if any of this is unclear!

Best,
Mark

[1]
http://stackoverflow.com/questions/12993504/my-maven-java-project-in-eclipse-doesnt-generate-jar-file
[2] http://imagej.net/Developing_ImageJ_on_the_command_line#Build_the_source

On Thu, Jul 9, 2015 at 3:40 AM, Daniel White <dan at chalkie.org.uk> wrote:

> Hi Mark, Hi Tom
> I seem to be having trouble getting the colocalization analysis plugins
> top build, this is in Eclipse mars.
>
> I imported the maven project, and imageJ runs fine from eclipse, but i
> dont see any place where the coloc .jar is biult and saved? Where should
> the built .jar be located by default?
>
> what would a main class look like for running the coloc plugin straight
> from ellipse, without having to copy a .jar into another fiji ?
>
> maybe i am missing something at
> http://imagej.net/Developing_Fiji_in_Eclipse#Running_and_Debugging
> its not obvious for an elclipse noob like me.
>
> cheers
>
> D
>
>
>
> On 25 June 2015 at 19:39, Mark Hiner <hiner at wisc.edu> wrote:
>
>> Hi Daniel,
>>
>> >The Fiji.sc docs describe how to do a plugin in the script editor,
>> >or how to develop imageJ itself in eclipse,
>> >but not how to get one of the external Fiji plugins, like coloc
>> analysis,
>> >and then run Fiji with my hacked plugin code running from eclipse????
>>
>> This process is described in the Developing Fiji in Eclipse tutorial[1] -
>> which I just updated with a bit more information.
>>
>> >i can run imageJ from there by highlighting the ij jar and doing run as
>> java application
>>
>> If you are running ij.jar from the Maven dependencies of
>> Colocalisation_Analysis, then Eclipse is likely just literally executing
>> the jar without anything else on the classpath. Using Debug.run will give
>> you an ImageJ with your plugin loaded properly.
>>
>> Also, if you don't want to make a temporary main method, you can always
>> build the .jar for your plugin and put it into an existing Fiji
>> installation.
>>
>> Hope that helps.
>>
>> Best,
>> Mark
>>
>> [1] http://imagej.net/Developing_Fiji_in_Eclipse#Running_and_Debugging
>>
>>
>> On Thu, Jun 25, 2015 at 7:32 AM, Daniel White <dan at chalkie.org.uk> wrote:
>>
>>> Hi All,
>>>
>>> I'm setting up my plugin dev environment (win7 x64), by reading the docs
>>> on the fiji.sc pages.
>>> I got eclipse installed, new JDK installed and seen by eclipse,
>>> Colocalization_Analysis plugin cloned from github using github for
>>> windows
>>> I imported the plugin as described with the import maven project gadget
>>> in eclipse,
>>> and it got the dependencies as jars apparently.
>>>
>>> So i can run imageJ from there by highlighting the ij jar and doing run
>>> as java application,
>>> but the coloc_2 plugin doesnt appear in the Analyze menu??????
>>>
>>> The Fiji.sc docs describe how to do a plugin in the script editor,
>>> or how to develop imageJ itself in eclipse,
>>> but not how to get one of the external Fiji plugins, like coloc
>>> analysis,
>>> and then run Fiji with my hacked plugin code running from eclipse????
>>>
>>> Can I help fix the docs so noobs like me can get started easier,
>>> and in the process get myself up and running with a little help from on
>>> of you folks please?
>>>
>>> cheers
>>>
>>> Dan White
>>>
>>> _______________________________________________
>>> ImageJ-devel mailing list
>>> ImageJ-devel at imagej.net
>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>
>>>
>>
>
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