bioio-tiff-glob takes precedence over bioio-tifffile, but does not support the image

[TimMonko]

Describe the Bug

I have an RGB image that I have been using for tests. It has been working with AICSImage, and now bioio (with bioio-tifffile). If I have bioio-tiff-glob installed, then this results in attempting to read in with bioio-tiff-glob, but the image can't be read. The RGB image in question

Expected Behavior

Either 1. bioio-tiff-glob recognizes that it does not support the image or 2. bioio-tifffile takes precedence since it is less niche in use, perhaps expecting an informed user to input bioio-tiff-glob.Reader if needed.

Reproduction

from bioio import BioImage
import bioio
import bioio_tifffile
from pathlib import Path
bioio.plugin_feasibility_report(r'./resources/RGB.tiff')

outputs this plugin matrix

{'bioio-ome-tiff': PluginSupport(supported=False, error=None),
 'bioio-imageio': PluginSupport(supported=True, error=None),
 'bioio-tiff-glob': PluginSupport(supported=True, error=None),
 'bioio-tifffile': PluginSupport(supported=True, error=None),
 'bioio-ome-zarr': PluginSupport(supported=False, error=None),
 'bioio-sldy': PluginSupport(supported=False, error=None),
 'bioio-czi': PluginSupport(supported=False, error=None),
 'bioio-dv': PluginSupport(supported=False, error=None),
 'bioio-lif': PluginSupport(supported=False, error=None),
 'bioio-nd2': PluginSupport(supported=False, error=None),
 'ArrayLike': PluginSupport(supported=False, error=None)}

this does not work (since it tries to use tiff-glob

file = Path(r'./resources/RGB.tiff')
img = BioImage(file)

error output

{
	"name": "TypeError",
	"message": "Invalid type glob_in - got type <class 'pathlib.WindowsPath'>",
	"stack": "---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[15], line 4
      1 import bioio_tifffile
      3 file = Path(r'./resources/RGB.tiff')
----> 4 img = BioImage(file)
      5 img.dims

File c:\\Users\\timmo\\mambaforge\\envs\
dev-bioio\\Lib\\site-packages\\bioio\\bio_image.py:297, in BioImage.__init__(self, image, reader, reconstruct_mosaic, use_plugin_cache, fs_kwargs, **kwargs)
    287 def __init__(
    288     self,
    289     image: biob.types.ImageLike,
   (...)
    294     **kwargs: Any,
    295 ):
    296     try:
--> 297         self._reader, self._plugin = self._get_reader(
    298             image,
    299             reader,
    300             use_plugin_cache,
    301             fs_kwargs,
    302             **kwargs,
    303         )
    304     except biob.exceptions.UnsupportedFileFormatError:
    305         # When reading from S3 if we failed trying to read
    306         # try reading as an anonymous user otherwise re-raise
    307         # the error
    308         if not str(image).startswith(\"s3://\"):

File c:\\Users\\timmo\\mambaforge\\envs\
dev-bioio\\Lib\\site-packages\\bioio\\bio_image.py:285, in BioImage._get_reader(image, reader, use_plugin_cache, fs_kwargs, **kwargs)
    281 plugin = BioImage.determine_plugin(
    282     image, fs_kwargs=fs_kwargs, use_plugin_cache=use_plugin_cache, **kwargs
    283 )
    284 ReaderClass = plugin.metadata.get_reader()
--> 285 return ReaderClass(image, fs_kwargs=fs_kwargs, **kwargs), plugin

File c:\\Users\\timmo\\mambaforge\\envs\
dev-bioio\\Lib\\site-packages\\bioio_tiff_glob\\reader.py:158, in Reader.__init__(self, glob_in, indexer, scene_glob_character, chunk_dims, dim_order, channel_names, single_file_shape, single_file_dims, fs_kwargs, **kwargs)
    156     file_series = pd.Series(glob_in)
    157 else:
--> 158     raise TypeError(f\"Invalid type glob_in - got type {type(glob_in)}\")
    160 if len(file_series) == 0:
    161     raise ValueError(\"No files found matching glob pattern\")

TypeError: Invalid type glob_in - got type <class 'pathlib.WindowsPath'>"
}

explicitly specifying bioio_tifffile.Reader works

file = Path(r'./resources/RGB.tiff')
img = BioImage(file, reader=bioio_tifffile.Reader)
img.dims

successfuly loads an RGB image

<Dimensions [T: 1, C: 1, Z: 1, Y: 1440, X: 1920, S: 3]>

Environment

• OS Version: Windows 11
• bioio-tiff-glob Version: [e.g. 0.5.0]

[toloudis]

Thanks for reporting this.

I believe we should convert this TypeError to be the equivalent of UnsupportedFileFormatError in order to make this behave as expected.

[toloudis]

Also Reader._is_supported_image should check for a properly glob-able path.