Re: Using results from plugins in scripts

Posted by Marcello DiStasio on Nov 02, 2013; 1:54am
URL: http://imagej.273.s1.nabble.com/Using-results-from-plugins-in-scripts-tp5005391p5005427.html

A further question about developing a plugin:  I am trying to edit this
java plugin so that it can be called from a Jython script.

Where should I place the *.java/*.class/*.jar file in the Fiji directory so
that it can be imported into my Jython script?  Do I need to specify a
particular package/namespace in my java code?

Thanks!
-Marcello


On Fri, Nov 1, 2013 at 12:52 PM, Marcello DiStasio <[hidden email]>wrote:

> Thanks Curtis!  I will take a crack at refactoring the java code into the
> recommended run and exec methods and if it works I'll file a pull request.
> -Marcello
> On Oct 31, 2013 2:57 PM, "Curtis Rueden" <[hidden email]> wrote:
>
>> Hi Marcello,
>>
>> > What I want is access to one (or all) of these result images in my
>> > calling script.  Is there a way (in Jython) to 'drill down' into the
>> > plugin in order to get the ImagePlus objects for these results?
>>
>> Let's look at the source code for Colour_Deconvolution:
>>
>> https://github.com/fiji/fiji/blob/master/src-plugins/Colour_Deconvolution/src/main/java/Colour_Deconvolution.java
>>
>> You can see that all work is done in the run(String) method and three
>> ImagePlus objects are created and shown at the end. There is no recourse.
>> The plugin would need to be refactored to split the work into helper
>> methods which return the ImagePlus objects without showing them. Then you
>> could call that Java API from Jython to use it as a library.
>>
>> I encourage you to make these changes and then file a pull request on
>> GitHub so that we can improve the plugin in the core Fiji distribution.
>> See:
>> https://help.github.com/articles/using-pull-requests
>>
>> Regards,
>> Curtis
>>
>>
>> On Wed, Oct 30, 2013 at 5:17 PM, Marcello DiStasio <[hidden email]
>> >wrote:
>>
>> > Hello ImageJ list, and apologies if this isn't the appropriate venue for
>> > this question, but I have been unable to come up with an obvious answer
>> > elsewhere.
>> >
>> > I want to use a plugin (one that is a standard plugin bundled with Fiji
>> as
>> > a *.jar in the ./Fiji.app/plugins directory -- specifically
>> > 'Colour_Deconvolution') as part of an image processing pipeline that I
>> am
>> > writing using Jython.  I am able to run the command as recorded by the
>> > Macro Recorder using the IJ.run method:
>> >
>> > IJ.run(imp, "Colour Deconvolution", "vectors=H&E")
>> >
>> > The problem is that this method returns nothing to the calling script.
>>  The
>> > method runs the command in Fiji, and 3 result images are generated and
>> > shown.  What I want is access to one (or all) of these result images in
>> my
>> > calling script.  Is there a way (in Jython) to 'drill down' into the
>> plugin
>> > in order to get the ImagePlus objects for these results?
>> >
>> > Thanks!
>> > -Marcello
>> >
>> > --
>> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> >
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>

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