Thanks Mark!
I found the jar!
Hiding in plain sight in the correct place.i just expected to see it also
from eclipse.... But you don't. Noob error
I will try the main method way too to see if it's easier or more
comfortable.
I can also update the wiki so this makes sense to a clueless noob like
myself.
Cheers
D
On Thursday, July 9, 2015, Mark Hiner <hi...@wisc.edu> wrote:
> 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 <d...@chalkie.org.uk
> <javascript:_e(%7B%7D,'cvml','d...@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 <hi...@wisc.edu
>> <javascript:_e(%7B%7D,'cvml','hi...@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 <d...@chalkie.org.uk
>>> <javascript:_e(%7B%7D,'cvml','d...@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@imagej.net
>>>> <javascript:_e(%7B%7D,'cvml','ImageJ-devel@imagej.net');>
>>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>>
>>>>
>>>
>>
>
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