[SciPy-User] FreeImage <-> numpy IO wrappers

[jake bolewski]

As someone who has struggled with getting some proprietary microscope images
into python I would love to see this get into scikits.image.  The more
coverage of formats I say the better given the flexibility of the plugin
system.

I would be willing to write some code or help test to help make the
integration happen.

Best,
Jake B.

2010/5/13 Stéfan van der Walt <stefan at sun.ac.za>

> Hi Ray
>
> On 13 May 2010 18:00, Thouis (Ray) Jones <thouis at broadinstitute.org>
> wrote:
> > 2010/5/13 Stéfan van der Walt <stefan at sun.ac.za>:
> >> [...]
> >> I converted your wrappers to plugins for scikits.image.  At the
> >> moment, it still segfaults---could you help me to iron out the
> >> problems?
> >
> > (I mentioned this to Zach, but it may be of general interest to the
> > imaging scikit developers as well, as another source of useful format
> > information, if nothing else...)
> >
> > On a related note, we've been collaborating with the Bio-Formats
> > project (http://www.loci.wisc.edu/software/bio-formats), and we have a
> > wrapper for their library in CellProfiler (but it's not too difficult
> > to use separately).  This is probably *not* something for the majority
> > of people, since it requires using a Java JNI wrapper (written in
> > Cython).  And using it to save images on the Mac is risky in GUI
> > applications.
> >
> > Examining the bio-formats code can be useful when writing new format
> > parsers, as well.
>
> We've added a plugin framework for I/O so that we can easily add this
> sort of optional functionality.  The more formats we can support the
> better!  Would you like to integrate said code?
>
> The procedure is fairly straightforward:
>
> 1) Add a .ini file for the plugin.  Format something like:
>
> [bio]
> description = Load x, y and z formats using the foo library.
> provides = imread, imsave
>
> 2) Add a bio_plugin.py file, and provide the functions imread and imsave.
>
> Regards
> Stéfan
>
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