Posted by
Curtis Rueden-2 on
Nov 13, 2019; 7:20pm
URL: http://imagej.273.s1.nabble.com/macro-convert-calibrated-value-to-raw-pixel-value-tp5022651p5022679.html
Hi Kenneth,
> Is there a current, comprehensive discussion on the "limitations and
> bugs"? The statement above is likely to dissuade me from trying this
> - but I'm willing to look more closely if there is clear documentation
> of the "limitations and bugs".
The issue tracker covers it:
https://github.com/imagej/pyimagej/issuesAlso, since I forgot to mention it in my previous email:
* Jython is Python 2.7 only.
* pyimagej is Python 3 only.
You said you wanted Python 3, so that's another point for pyimagej.
In general: if what you want is to mix-and-match PyData stack
(NumPy/SciPy/scikit/pandas/et al.) with ImageJ, I know of no other feasible
way than pyimagej. In that case your best bet would be to suffer the
"limitations and bugs" and participate in the development to push the
project forward. On the other hand, if you are just looking for the best
script language to use _on the JVM_ then it's really in the eye of the
beholder: see
https://imagej.net/Scripting#Supported_languages for a list
of possibilities.
Regards,
Curtis
--
Curtis Rueden
Software architect, LOCI/Eliceiri lab -
https://loci.wisc.edu/softwareImageJ2 lead, Fiji maintainer -
https://imagej.net/User:RuedenHave you tried the Image.sc Forum?
https://forum.image.sc/On Tue, Nov 12, 2019 at 3:01 PM Kenneth Sloan <
[hidden email]>
wrote:
> Curtis-
>
> Thank you for your reply.
>
> I suspect I'm primarily interested in embedding ImageJ into a Python3
> program - perhaps from inside a Jupyter notebook.
>
> I followed your link and got as far as:
>
> Disadvantage: Wrapping ImageJ in Python has some limitations and bugs,
> particularly surrounding use of ImageJ1 <
https://imagej.net/ImageJ1>
> features, compared to using ImageJ from Java-based kernels such as BeakerX <
>
https://beakerx.com/>
>
> Is there a current, comprehensive discussion on the "limitations and
> bugs"? The statement above is likely to dissuade me from trying this - but
> I'm willing to look more closely if there is clear documentation of the
> "limitations and bugs".
>
> I will check out the pyimagej tutorial.
>
> --
> Kenneth Sloan
>
[hidden email]
> Vision is the art of seeing what is invisible to others.
>
>
>
>
>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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