http://imagej.273.s1.nabble.com/Fiji-ImageJ-Headless-if-not-in-path-tp5012586p5012602.html
This is becoming a can of worms due to my inexperience. When I make the
alias and the bash_profile, it overwrites my enthought canopy links. In
python. Before I go down this road of putting canopy back into the
bash_profile path, I just wanted to ask something. I had this working on
> Thanks, that is correct Juan. I'll try out the alias
>
> On Thu, Apr 23, 2015 at 10:42 PM, Juan Nunez-Iglesias <
[hidden email]>
> wrote:
>
>> 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:
http://imagej.nih.gov/ij/list.html>>
>
>