import os no longer working in .py files?

[Snider, Kaitlin]

I updated today (first time in about a week) and immediately thereafter realized my "batch" macros are broken.  I use .py macros to extract file names to run a function on all of the image files in a folder, and this requrires "import os."  "import os" no longer finds an os module.  Is this deleted and needs replaced?  If so, where can I find it and where does it go?  Or is this a change in IJ2 that no longer allows os-module python macros?  If that's the case, any great sample batch macros in the IJ Macro language that you could refer me to?

Thanks very much :)

Kaitlin Snider

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[Aryeh Weiss]

On 8/14/14, 9:08 PM, Snider, Kaitlin wrote:
> I updated today (first time in about a week) and immediately thereafter realized my "batch" macros are broken.  I use .py macros to extract file names to run a function on all of the image files in a folder, and this requrires "import os."  "import os" no longer finds an os module.  Is this deleted and needs replaced?  If so, where can I find it and where does it go?  Or is this a change in IJ2 that no longer allows os-module python macros?  If that's the case, any great sample batch macros in the IJ Macro language that you could refer me to?
>
> Thanks very much :)
>
> Kaitlin Snider
>
>

See bug 890:
http://fiji.sc/bugzilla/show_bug.cgi?id=890

Here is my workaround:

You can work around this by downloading the Jython 2.5.2 distribution,
unzipping
the downloaded distribution, and copying the Lib/ directory to the Fiji
jars/ directory. Then your python will find os and will work.

I found that I could not do this with Jython 2.5.3. If you use 2.5.3, it
will find os, but it will report an error having to do with a feature
that is not compatible with your Jython. I do not remember exactly what
it was, because I no longer have the 2.5.3 Jython on my computer.

--aryeh

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Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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[Mark Hiner-2]

Hi Kaitlin,

>"import os" no longer finds an os module.

We just diagnosed this problem but haven't settled on or fully tested a
resolution yet. Basically, we upgraded from a custom 2.5.2
jython-standalone jar to 2.5.3 "just jython". The standalone jar included
necessary dependencies, like the os module, but also conflicted with other
dependencies of Fiji (jruby).

You can read more and follow any discussion of fixes or workarounds here:
http://fiji.sc/bugzilla/show_bug.cgi?id=890

Thank you for taking the time to report this issue. Let us know if you have
any other questions.

Thanks,
Mark



On Thu, Aug 14, 2014 at 1:08 PM, Snider, Kaitlin <
[hidden email]> wrote:

> I updated today (first time in about a week) and immediately thereafter
> realized my "batch" macros are broken.  I use .py macros to extract file
> names to run a function on all of the image files in a folder, and this
> requrires "import os."  "import os" no longer finds an os module.  Is this
> deleted and needs replaced?  If so, where can I find it and where does it
> go?  Or is this a change in IJ2 that no longer allows os-module python
> macros?  If that's the case, any great sample batch macros in the IJ Macro
> language that you could refer me to?
>
> Thanks very much :)
>
> Kaitlin Snider
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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