Simplify SciCat thumbnail logic

[davramov]

As part of the HPSS PR #62, Kate found a few improvements for SciCat thumbnail ingestion. I'm tracking these as a new issue rather than incorporating into that PR.

This is kind of a big block for the thumbnail creation, suggest splitting it into a one or a few separate functions so it can be tested independently.

Also fwiw I found that just saving the imshow of an array with [2,98] percentile and no axes to .png makes a good thumbnail without having to do 8 bit conversion and deal with PIL and all and and all the normalization... maybe worth exploring for you because it would get rid of a lot of code. But I guess it would add numpy and matplotlib as dependencies.

from pyscicat.client import (
    encode_thumbnail
)
thumbnail = data[slice] # this is a numpy array of whatever type
vmin, vmax = np.percentile(thumbnail, [2, 98])
np.clip(thumbnail, vmin, vmax)
 with tempfile.TemporaryDirectory() as tmpdir:
        fig = plt.figure(figsize=(10,10))
        # Add an axes that fills the entire figure
        ax = fig.add_axes([0, 0, 1, 1])
        # Turn off the axes
        ax.set_axis_off()
        ax.imshow(thumbnail, cmap='gray')
        fig.show()
        fig.savefig(os.path.join(tmpdir, 'thumbnail.png'))

        thumbnail_encoded = encode_thumbnail(os.path.join(tmpdir, 'thumbnail.png'))

Originally posted by @kkamdin in #62 (comment)

With regards to encode_image_2_thumbnail(), SciCat now has a built in encode_thumbnail() function

I thought scicat has a method for this already, but maybe we're on an older version of the API.

Originally posted by @kkamdin in #62 (comment)

same comment here about piggybacking on matplot lib if you're not happy with the thumbnail resolution. Here are some of my results from trying different methods:

Originally posted by @kkamdin in #62 (comment)

[davramov]

A couple more SciCat suggestions:

1. When calculating the access_groups, there is a string cleaning step that could be made more robust

# make an access group list that includes the name of the proposal and the name of the beamline
access_groups = []
# sometimes the beamline name is super dirty  " '8.3.2', "" '8.3.2', "

can we use an Enum somewhere to make the beamline name less dirty by the time it gets here?

Originally posted by @kkamdin in #62 (comment)

2. We can check SciCat client permissions for archivemanager to see if it has dataset location removal privileges before attempting.

is there a way to check this permission before we try to do all the work?

Originally posted by @kkamdin in #62 (comment)