Extending ImageSequence reader when only imageio (but not skimage/matplotlib) is installed

[GenevieveBuckley]

Closes #363

Adds a fallback path to imageio imread for pims/image_sequence.py

This is a "nice to have" extension of the current capabilities, aimed at allowing a lightweight minimal-ish set of pims dependencies that can cover most of the basic use cases (eg tifffile and imageio) without requiring more heavyweight dependencies like scikit-image/matplotlib are also installed.

[nkeim]

The problem is in image_reader.py, which defines a PIMS class to read a single frame (I forget why we have this). Once both image_sequence.py and image_reader.py are updated we should be good to go!

[GenevieveBuckley]

Once both image_sequence.py and image_reader.py are updated we should be good to go!

This is the build log after adding an imageio fallback path to image_reader.py: https://travis-ci.org/github/soft-matter/pims/jobs/703756047

I haven't dug deeply into the errors yet, but I think it's something to do with the plugin= kwarg being passed into imread.

[GenevieveBuckley]

Also, should we consider making the order of preference for imread go: scikit-image > imageio > matplotlib, given the warning about "imread() works differently between scikit-image and matplotlib? "We don't require users to have scikit-image, but if we fall back to matplotlib, make sure the user is aware of the consequences." Any opinion here @nkeim ?

[GenevieveBuckley]

FYI: TestImageSequenceNaturalSorting is failing locally if imageio imread is used (because of the plugin= kwarg).

I've pushed an update to skip this test class for now while we sort the other stuff out, but this either needs to be fixed, or for a new test to be added covering the same functionality with imageio.

[nkeim]

Great catch, @GenevieveBuckley ! Yes, assuming that imageio's imread is more similar to scikit-image's, we definitely want to prefer it over matplotlib's.

[tacaswell]

I think this is obsoleted by #392 which removes Matplotlib as a reader all together and adds a hard dependency on imageio.

Thank you for this @GenevieveBuckley and sorry we did not get it merged 2 years ago.