Python/Jython code that doesn't work in ImageJ

[J. Daniel Fenn]

The following code works fine on my desktop version of python (2.7) but
it does not work using the ImageJ/Fiji code editor (which I believe is
using python 2.5.2)


dirRawIn = os.path.join(dirBase, dirRaw)
dirAnlOut = os.path.join(dirBase, dirAnl)
dirMntOut = os.path.join(dirBase, dirMnt)

def mkdir_p(path):
    print path
    try:
        os.makedirs(path)
    except OSError, exc:
        if exc.errno == errno.EEXIST and os.path.isdir(path):
            pass
        else:
            raise

mkdir_p(dirAnlOut)
mkdir_p(dirMntOut)


I'm pretty sure everything I've read suggests that code should work even
on python 2.5.  Does anyone have any ideas why this code doesn't work
within Fiji?

I just get a huge block of Traceback error text that doesn't give me any
real information.  I can post if it is needed.

Thanks

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[Leon Espinosa-3]

Dear Daniel, I had problems with Jython in Fiji that were solved with the advice of Brian Northan (see below, the discussions was started in this list around May 6 2014 with "new error in  python script" subject). You need also import each python and ImageJ class. Hope it helps...


>
Hi Leon

I got the same thing.  I believe it is because of a conflict between
components packaged with both jython and jruby.

jruby was updated recently.   When I deleted ruby-complete-1.7.11.jar from
the jars directory the jython scripts started working again.  This is a
hack though because then jruby doesn't work.

Brian
>


All the best, Leon








Le 7 juil. 2014 à 23:01, J. Daniel Fenn a écrit :

> The following code works fine on my desktop version of python (2.7) but
> it does not work using the ImageJ/Fiji code editor (which I believe is
> using python 2.5.2)
>
>
> dirRawIn = os.path.join(dirBase, dirRaw)
> dirAnlOut = os.path.join(dirBase, dirAnl)
> dirMntOut = os.path.join(dirBase, dirMnt)
>
> def mkdir_p(path):
>    print path
>    try:
>        os.makedirs(path)
>    except OSError, exc:
>        if exc.errno == errno.EEXIST and os.path.isdir(path):
>            pass
>        else:
>            raise
>
> mkdir_p(dirAnlOut)
> mkdir_p(dirMntOut)
>
>
> I'm pretty sure everything I've read suggests that code should work even
> on python 2.5.  Does anyone have any ideas why this code doesn't work
> within Fiji?
>
> I just get a huge block of Traceback error text that doesn't give me any
> real information.  I can post if it is needed.
>
> Thanks
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Emanuele Martini]

Hi,
I don't try directly your code, but I use os in my jython script.
I think that could be a problem of ImageJ 2/Fiji; because i can run my script with last imagej 1 version using FIJI script editor, but they don't work if I update to ImageJ2.

So maybe you can try to run your script a ImageJ1 version.
Have a nice day,
Emanuele Martini
Image Analys @ifom-ieo ressearch campus

[ctrueden]

Hi everyone,

> The following code works fine on my desktop version of python (2.7)
> but it does not work using the ImageJ/Fiji code editor (which I
> believe is using python 2.5.2)

This bug is being tracked at:
https://github.com/fiji/fiji/issues/83

As a workaround, you can delete jffi-1.2.7jar and Jython will work again.

I figured this out as follows:

* Plugins > Utilities > Find Jar for Class
* Paste name of problematic class from the exception:
com.kenai.jffi.InvocationBuffer
* Click OK
* Note the warning that appears about how the class is present in two
different locations.

Regards,
Curtis


On Tue, Jul 8, 2014 at 4:38 AM, Emanuele Martini <[hidden email]>
wrote:

> Hi,
> I don't try directly your code, but I use os in my jython script.
> I think that could be a problem of ImageJ 2/Fiji; because i can run my
> script with last imagej 1 version using FIJI script editor, but they don't
> work if I update to ImageJ2.
>
> So maybe you can try to run your script a ImageJ1 version.
> Have a nice day,
> Emanuele Martini
> Image Analys @ifom-ieo ressearch campus
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Python-Jython-code-that-doesn-t-work-in-ImageJ-tp5008609p5008619.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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