Re: Fiji/ImageJ Headless if not in path?

Posted by ctrueden on Apr 23, 2015; 8:44pm
URL: http://imagej.273.s1.nabble.com/Fiji-ImageJ-Headless-if-not-in-path-tp5012586p5012588.html

Hi Adam,

> Does anyone know how to configure a Mac and/or Ubuntu system path so
> that we could just run fiji from any terminal?

The issue is complicated by the fact that the launcher executable is named
differently for every platform.

Personally, I work around it via the following shell script:
*
https://github.com/imagej/imagej-omero/blob/imagej-omero-0.2.1/bin/run-class

Alternately, the ImageJ.sh script (
https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-29/bin/ImageJ.sh)
tries very hard to launch ImageJ without using any launcher executable. In
that way, you can run ImageJ on platforms for which no launcher has been
compiled, such as the Raspberry Pi.

HTH,
Curtis

On Thu, Apr 23, 2015 at 3:32 PM, Adam Hughes <[hidden email]> wrote:

> Hi,
>
> I'm trying to run a fiji macro in headless mode through python.  I'm on
> ubuntu, but also need to do this on a Mac.  I've downloaded fiji from
> source, and can doubleclick the icon to launch the application fine.  The
> icon refers to the file:
>
> ~/Fiji.app/ImageJ2.desktop
>
> However, to use Fiji in headless mode, the guides imply that I want to do
> this:
>
>  ImageJ --headless -macro path-to-Macro.ijm
>
> Or
>
>  fiji --headless -macro path-to-Macro.ijm
>
> However, fiji and ImageJ are not in python.  So this command doesn't work.
> Does anyone know how to configure a Mac and/or Ubuntu system path so that
> we could just run fiji from any terminal?  At the end of the day, my python
> function looks like this (currently not working):
>
> def IJwatershed(bw_image):
>     imsave('fooing', bw_image)
>     macro_file = 'Watershed.imj'
>    * path_to_fiji* = '/home/glue/Desktop/Fiji.app/ImageJ2.desktop'
>     command = "%s --headless %s" % (path_to_fiji, macro_file)
>     with open('foo', 'w') as dnull:
>         p = subprocess.call(command, shell=False)# stderr=subprocess.PIPE)
>
> And it seems to not work because of my *path_to_fiji *not being understood.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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