On 2/25/2012 11:10 AM, Tony Yu wrote:

2012/2/24 St�fan van der Walt <stefan@sun.ac.za <mailto:stefan@sun.ac.za>>

On Fri, Feb 24, 2012 at 12:02 AM, Guillaume Gay <guillaume@mitotic-machine.org <mailto:guillaume@mitotic-machine.org>> wrote: > I forked sckimage on github and pushed the plugin there: > > https://github.com/glyg/scikits-image/blob/master/skimage/io/_plugins/matplo...

Cute! I like it.

St�fan

Hi Guillaume,

Hmm, this is much more interesting than what I expected when you mentioned a line scan tool. :)

I made a PR to your repo, which I guess you already noticed (and merged) and I have some more specific comments I want to add to your PR, but I had some more general thoughts (i.e. probably not stuff that should be implemented in this PR) that I want to post here:

Plugin system ------ It might be nice to have some sort of plugin system for the image viewer. That way, tools like this could be implemented a bit more easily and, also, easily added to the viewer or ignored by the user. I think someone mentioned on the list that scikits-image should be careful not to stray too far into GUI tools (I could be completely mis-representing the idea here), and I agree to an extent. Nevertheless, I think providing a viewer that supplies *an infrastructure* for creating GUI tools might be really valuable. I haven't really thought through what this plugin system would look like, so it may just be a pipe dream.

TIFFFile Viewer ------ There was talk of integrating the viewer from TIFFFile---was the idea to write a wrapper around the viewer (like Zach did for `imread`/`imsave`) or to copy it into skimage and modify it. If it's the latter, we should make sure that Christophe Gohlke is OK with that (Christophe mentioned that it wouldn't make sense to fork TIFFFile into skimage, but presumably, this would be different for `tifffile.imshow` since we would likely want to modify it).

Best, -Tony

Hi Tony, sure it's OK to take imview or parts of it out of tifffile.py. I'm not sure how much of its functionality applies to skimage, which seems to limit itself to well defined image formats. Tifffile has to deal with n-dimensional, planar, any bit depth per channel, two channel "RGB", and 16 bit paletted images. The tifffile.imshow function is a hack to provide a preview of such (often ambiguous) data. Christoph