io plugin issue (8bits 16bits)

[Thouis (Ray) Jones]

On Tue, Dec 6, 2011 at 07:52, Neil Yager <yager.neil at gmail.com> wrote:
> Coincidentally, I also noticed the 16-bit tiff issue the other day,
> and started working on a fix. I was using an approach based on this:
>
> http://stackoverflow.com/questions/7684695/numpy-array-of-an-i16-image-file
>
> Changing the last line of imread in pil_plugin to:
>
> return np.array(im.getdata()).reshape(im.size[::-1])
>
> fixes that specific problems, but causes others (e.g. can't load
> colour images). At that point I got side-tracked by something else, so
> I'm not sure if it's a good fix.

The CellProfiler project used to use PIL, though we've moved to
bioformats.  The (potentially) stale code for dealing with TIF and
other images is here:
https://raw.github.com/thouis/CellProfiler/master/cellprofiler/modules/loadimages.py
(search  for load_using_PIL).

For color images, we end up using matplotlib.image.pil_to_array(),
located in this file:
https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/image.py

As I said, our code is potentially stale, and some parts may not be
needed or even functional.  But it has had the benefit of having been
tested on a fairly wide variety of formats.  If you're looking for
potentially problematic images, you might snoop around our the
CellProfiler examples:
https://svn.broadinstitute.org/CellProfiler/trunk/ExampleImages/

Ray Jones