Using GDC tiled download as fallback when file is unreadable

Problem

Edge case found with file: https://portal.gdc.cancer.gov/files/7d711bf1-5a44-4bea-ae34-1dec9b3bee4f

For some reason, neither openslide nor TiffFile can read it. In TiffFile, we have an empty pages list, and in openslide we have a "no image data" error. Yet the file seems to appear fine on the GDC viewer.

Possible solution

Step 1: check by manually downloading -> maybe it was a download problem and the file was corrupted. There is a md5 hash in the manifest that we can use for that.

Step 2: add fallback mechanism to the sampler: if the file is corrupted, see if we can at least get the mag / MPP properties and determine the target dimensions, so that we can infer the target level from the tile server, then load it from there.

Edited Oct 10, 2023 by Adrien Foucart
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