http://imagej.273.s1.nabble.com/Fiji-ImageJ-Headless-if-not-in-path-tp5012586p5012600.html
Thanks, that is correct Juan. I'll try out the alias
> 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:
>
>
>
>
> alias fiji=/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx
>
> On Fri, Apr 24, 2015 at 8:27 AM, Curtis Rueden <
[hidden email]> wrote:
>
> > 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> >>
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> --
> ImageJ mailing list:
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