Why does `bioio-imageio` read tiff files?

[TimMonko]

From my understanding of the documentation, supported extensions for a plugin are defined by the plugin itself, such as:

bioio-imageio/bioio_imageio/reader_metadata.py

Lines 20 to 26 in 6829370

	def get_supported_extensions() -> List[str]:
	"""
	Return a list of file extensions this plugin supports reading.
	"""
	# See ever growing list from imageio
	# https://imageio.readthedocs.io/en/stable/formats/index.html
	return [

However, in an environment with bioio_imageio and tifffile, a file such as RGB_metadata.tiff will be read by bioio_imageio. This leads to different behavior (not that I mind) compared to bioio_tifffile so it took me a bit to debug and understand that bioio was reader with bioio_imageio isntead. (img.reader.__module__ was a solution I figured out)

note, bioio-tifffile doesn't even need to be in the environment as bioio-ome-tiff brings in tifffile

{'bioio-ome-tiff': PluginSupport(supported=False, error="bioio-ome-tiff does not support the image: 'C:/Users/timmo/ndev-kit/ndevio/tests/resources/RGB_bad_metadata.tiff'. Failed to parse XML for the provided file. Error: no element found: line 1, column 0"),
 'bioio-imageio': PluginSupport(supported=True, error=None),
 'bioio-tifffile': PluginSupport(supported=True, error=None),
 'bioio-ome-zarr': PluginSupport(supported=False, error=None),
 'bioio-czi': PluginSupport(supported=False, error="bioio-czi  does not support the image: 'C:/Users/timmo/ndev-kit/ndevio/tests/resources/RGB_bad_metadata.tiff'. bioio-czi[pylibczirw mode] does not support the image: 'C:/Users/timmo/ndev-kit/ndevio/tests/resources/RGB_bad_metadata.tiff'. Illegal data detected at offset 0 -> Invalid FileHdr-magic, bioio-czi[aicspylibczi mode] does not support the image: 'C:/Users/timmo/ndev-kit/ndevio/tests/resources/RGB_bad_metadata.tiff'. Illegal data detected at offset 0 -> Invalid FileHdr-magic"),
 'ArrayLike': PluginSupport(supported=False, error="ArrayLikeReader does not support the image: 'Unsupported image type: <class 'fsspec.implementations.local.LocalFileSystem'>. ArrayLikeReader supported types are numpy ndarray, dask Array,or xarray DataArray.'.")}

[BrianWhitneyAI]

Hm thats a good question, it definitely should not if its not in the ext list. Looking into this thanks for submitting.

[BrianWhitneyAI]

This is a repeat of what I said on bioio-devs/bioio#159

Plugin Feasibility

There was some hidden nuance around the plugin_feasibility_report The list of extensions is actually a approved list by bioio, the reader itself can support more file types (and often will). At runtime BioImage will only read files with the specific instruction. plugin_feasibility_report is not bound by extension and will try all readers regardless. This shows things like bioio-imageio supporting tiff images. This is intended but not explained.

The use case for this is if you have a file with a strange or new ext. you want to see if any of the readers can parse it. you use the plugin_feasibility_report to assess the file and see that bioio-bioformats can read it! you can then override the extension restriction by passing the the bioio-bioformats reader directly.

I have opened bioio-devs/bioio#162 and added a warning around this to clarify this behavior