Image class

[Matthew Brett]

Hi,

On Mon, Sep 1, 2014 at 2:45 AM, Guillaume Gay
<guillaume at mitotic-machine.org> wrote:
> Hi all
>
> +1 on metadata handling, it is surely of prime importance.
>
> Maybe this is far too domain specific, but I would suggest relying on
> OME.XML tags as keys for the metadata dic (or the subset of it that concerns
> images). The whole schema can be found here:
> http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd
>
>  Those tags are used in the ome.tiff format, and are recognized by lots of
> tools, of which by C. Gohlke's tifffile.py is used as io in skimage...
>
> Of course that doesn't have the out of the box advantage of being able to
> call func(image, **metadata).
>
> One last advantage is providing an easy route to persistence via the
> ome.tiff image format.
>
> Best,
>
> Guillaume
>
>
> Le 01/09/2014 08:03, Juan Nunez-Iglesias a écrit :
>
> Hi everyone,
>
> I generally love scikit-image’s approach of a numpy array is identically an
> image, with no added cruft. Having a subclass can be problematic, as we saw
> with the various bugs caused by things like:
>
> ```python
>>>> im[0, 0]
> Image([255], dtype=np.uint8)
> ```
>
> However, watching the below talk from Image.jl’s Tim Holy, I was reminded of
> the importance of metadata in a lot of image processing:
>
> https://www.youtube.com/watch?v=FA-1B_amwt8
>
> (Incidentally, the talk is worth watching, especially towards the end when
> he talks about performance tricks.)
>
> Someone (I forget who, sorry!) told me that they’d solved the
> slicing/scalars problem in a different numpy wrapper, so that might be
> feasible if we went back to having a light numpy array subclass, which could
> have a simple metadata attribute in the form of a dict with arbitrary keys
> (with some prescriptions, such as “spacing” for the resolution, same as we
> have prescribed ranges for specific image data types).
>
> Alternatively, we might want to have a unified “metadata” dictionary format
> that would unwrap nicely into our preferred kwarg format, e.g. if we did
> `slic(image, **metadata)` it would just work.
>
> Just a couple of ideas. There may be other solutions, but my main point is
> that we might want to unify our metadata handling, rather than letting the
> user always worry about it.
>
> Thanks for listening! =)
>
> Juan.

We run into this a lot in brain imaging too.  It made me think of some
work that Fernando Perez and Mike Trumpis were doing on attaching data
to axes:

https://github.com/fperez/datarray

Cheers,

Matthew