Posted by
Adam Hughes on
Apr 23, 2015; 8:32pm
URL: http://imagej.273.s1.nabble.com/Fiji-ImageJ-Headless-if-not-in-path-tp5012586.html
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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