http://imagej.273.s1.nabble.com/Fiji-ImageJ-Headless-if-not-in-path-tp5012586p5012592.html
Curtis, I'm guessing Adam was asking whether there is a Fiji installer that would place the ImageJ-macosx binary (perhaps renamed) in a system path such as /usr/local/bin.
For what it's worth, on Mac OS X, I usually alias the binary executable inside the Fiji.app:
> Hi Adam,
>> Is there a version of fiji on MAC that would install itself to the
>> system path?
> Sorry, I don't understand the question. Even if you include the ImageJ
> launcher's directory on the system path, it still wouldn't be enough, since
> the executable file name differs across OSes.
> Given a path to a Fiji.app directory, your Python code could synthesize the
> correct launcher to use, similar to the shell script I linked -- but in
> Python, of course.
> Another option would be to make it an installation requirement for users to
> symlink "fiji" somewhere on their path, so that your Python code doesn't
> need to worry about it.
>> is everyone using this workaround or am I using the wrong version of
>> fiji or something?
> I don't think many people call ImageJ from Python. Usually it is the other
> way around: call Python (or Jython) from ImageJ:
> *
http://imagej.net/Python> *
https://github.com/scijava/scripting-cpython> *
https://github.com/scijava/scripting-jython> Someone else did just ask about this on StackOverflow, though:
> *
http://stackoverflow.com/q/29749687/1207769> Regards,
> Curtis
> On Thu, Apr 23, 2015 at 4:11 PM, Adam Hughes <
[hidden email]> wrote:
>> Thanks. Is there a version of fiji on MAC that would install itself to the
>> system path? I mean, is everyone using this workaround or am I using the
>> wrong version of fiji or something?
>>
>> On Thu, Apr 23, 2015 at 4:44 PM, Curtis Rueden <
[hidden email]> wrote:
>>
>> > 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.
>> > >
>> > > --
>> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>> > >
>> >
>> > --
>> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>> >
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
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> ImageJ mailing list:
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