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bioio-devs / bioio

Image reading, metadata management, and image writing for Microscopy images in Python
https://bioio-devs.github.io/bioio/OVERVIEW.html
BSD 3-Clause "New" or "Revised" License
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Features / Bugs / Eva Notes #18

Open evamaxfield opened 1 year ago

evamaxfield commented 1 year ago

Wanted to give the new libraries a whirl and figured I would make a couple of notes as I go along. I will try to resolve these issues / features this weekend or something as many of them are "optional" / maybe nice for dev and debugging experience.

  1. BIOIO_BASE_DIST_NAME needs to be updated from bioio-types to bioio-base

  2. It would be nice to have access to what plugin read the file somehow. Currently on image read, the __repr__ returns: <BioImage [Reader: Reader, Image-is-in-Memory: False]> but it might be better to return <BioImage [plugin: {plugin_name}, Image-is-in-Memory: False]>, esp. because most plugins will generally all use the same class name of Reader instead of say OmeTiffReader, better might be <BioImage [reader_path: {python_module_path_of_reader}, Image-is-in-Memory: False]>

  3. plugin_cache should be made into a set, dict, or deduped list:

In [2]: from bioio.plugins import get_plugins

In [3]: get_plugins()
Out[3]: 
[PluginEntry(entrypoint=EntryPoint(name='bioio-tifffile', value='bioio_tifffile', group='bioio.readers'), metadata=<class 'bioio_tifffile.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-tiff', value='bioio_ome_tiff', group='bioio.readers'), metadata=<class 'bioio_ome_tiff.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-zarr', value='bioio_ome_zarr', group='bioio.readers'), metadata=<class 'bioio_ome_zarr.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-lif', value='bioio_lif', group='bioio.readers'), metadata=<class 'bioio_lif.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347)]

In [4]: get_plugins()
Out[4]: 
[PluginEntry(entrypoint=EntryPoint(name='bioio-tifffile', value='bioio_tifffile', group='bioio.readers'), metadata=<class 'bioio_tifffile.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-tiff', value='bioio_ome_tiff', group='bioio.readers'), metadata=<class 'bioio_ome_tiff.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-zarr', value='bioio_ome_zarr', group='bioio.readers'), metadata=<class 'bioio_ome_zarr.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-lif', value='bioio_lif', group='bioio.readers'), metadata=<class 'bioio_lif.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-tifffile', value='bioio_tifffile', group='bioio.readers'), metadata=<class 'bioio_tifffile.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-tiff', value='bioio_ome_tiff', group='bioio.readers'), metadata=<class 'bioio_ome_tiff.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-zarr', value='bioio_ome_zarr', group='bioio.readers'), metadata=<class 'bioio_ome_zarr.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-lif', value='bioio_lif', group='bioio.readers'), metadata=<class 'bioio_lif.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347)]
  1. get_plugins should be called at the top of determine_reader? Currently cannot read files until manual get_plugins call (ignore debugging print statements):
In [1]: from bioio import BioImage, plugins

In [2]: img = BioImage("../aicsimageio/aicsimageio/tests/resources/3d-cell-viewer.ome.tiff")
---------------------------------------------------------------------------
UnsupportedFileFormatError                Traceback (most recent call last)
Cell In[2], line 1
----> 1 img = BioImage("../aicsimageio/aicsimageio/tests/resources/3d-cell-viewer.ome.tiff")

File ~/active/cell/bioio/bioio/bio_image.py:196, in BioImage.__init__(self, image, reader, reconstruct_mosaic, fs_kwargs, **kwargs)
    186 def __init__(
    187     self,
    188     image: biob.types.ImageLike,
   (...)
    192     **kwargs: Any,
    193 ):
    194     if reader is None:
    195         # Determine reader class and create dask delayed array
--> 196         ReaderClass = BioImage.determine_reader(
    197             image, fs_kwargs=fs_kwargs, **kwargs
    198         )
    199     else:
    200         # Init reader
    201         ReaderClass = reader

File ~/active/cell/bioio/bioio/bio_image.py:177, in BioImage.determine_reader(image, fs_kwargs, **kwargs)
    174 # If we haven't hit anything yet, we likely don't support this file / object
    175 # with the current plugins installed
    176 image_type = str(type(image))
--> 177 raise biob.exceptions.UnsupportedFileFormatError(
    178     "BioImage",
    179     image_type,
    180     msg_extra=(
    181         "You may need to install an extra format dependency. "
    182         "See bioio README for list of some known plugins."
    183     ),
    184 )

UnsupportedFileFormatError: BioImage does not support the image: '<class 'str'>'. You may need to install an extra format dependency. See bioio README for list of some known plugins.

In [3]: plugins.get_plugins()
Out[3]: 
[PluginEntry(entrypoint=EntryPoint(name='bioio-tifffile', value='bioio_tifffile', group='bioio.readers'), metadata=<class 'bioio_tifffile.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-tiff', value='bioio_ome_tiff', group='bioio.readers'), metadata=<class 'bioio_ome_tiff.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-zarr', value='bioio_ome_zarr', group='bioio.readers'), metadata=<class 'bioio_ome_zarr.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347),
 PluginEntry(entrypoint=EntryPoint(name='bioio-lif', value='bioio_lif', group='bioio.readers'), metadata=<class 'bioio_lif.reader_metadata.ReaderMetadata'>, timestamp=1698949015.0319347)]

In [4]: img = BioImage("../aicsimageio/aicsimageio/tests/resources/3d-cell-viewer.ome.tiff")

In [5]: img
Out[5]: <BioImage [Reader: Reader, Image-is-in-Memory: False]>

  1. I think the error that is throw in determine_reader should include the image path (and parameter type) rather than just the parameter type. For example: UnsupportedFileFormatError: BioImage does not support the image: '<class 'str'>'. You may need to install an extra format dependency. See bioio README for list of some known plugins. is a confusing error because uhhh "what do you mean you don't take a str path? Do you want a pathlib.Path path?"

  2. Related to 2 and 4, I think all of the readers calling their image reading class Reader is causing namespace / object override issues? I have bioio-lif installed locally and can read LIF files directly using it's reader but reading fails from bioio directly. I think this is especially true because I installed bioio-tifffile later than bioio-ome-tiff and even though I am trying to read an OME-TIFF, it is using the tifffile reader. I also wonder if this is because each of the plugins has this line in their base level __init__.py: from .reader import Reader and that is causing the namespace override, whichever plugin is installed most recently is the only plugin that has a "valid" Reader object. All the others are just pointers to the newly installed Reader?

In [1]: import bioio_lif

In [2]: bioio_lif.Reader("../aicsimageio/aicsimageio/tests/resources/tiled.lif")
Out[2]: <Reader [Image-is-in-Memory: False]>

In [3]: from bioio import BioImage, plugins

In [4]: plugins.get_plugins()
Out[4]: 
[PluginEntry(entrypoint=EntryPoint(name='bioio-tifffile', value='bioio_tifffile', group='bioio.readers'), metadata=<class 'bioio_tifffile.reader_metadata.ReaderMetadata'>, timestamp=1698950076.8994923),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-tiff', value='bioio_ome_tiff', group='bioio.readers'), metadata=<class 'bioio_ome_tiff.reader_metadata.ReaderMetadata'>, timestamp=1698950076.8994923),
 PluginEntry(entrypoint=EntryPoint(name='bioio-ome-zarr', value='bioio_ome_zarr', group='bioio.readers'), metadata=<class 'bioio_ome_zarr.reader_metadata.ReaderMetadata'>, timestamp=1698950076.8994923),
 PluginEntry(entrypoint=EntryPoint(name='bioio-lif', value='bioio_lif', group='bioio.readers'), metadata=<class 'bioio_lif.reader_metadata.ReaderMetadata'>, timestamp=1698950076.8994923)]

In [5]: BioImage("../aicsimageio/aicsimageio/tests/resources/tiled.lif")
---------------------------------------------------------------------------
UnsupportedFileFormatError                Traceback (most recent call last)
Cell In[5], line 1
----> 1 BioImage("../aicsimageio/aicsimageio/tests/resources/tiled.lif")

File ~/active/cell/bioio/bioio/bio_image.py:191, in BioImage.__init__(self, image, reader, reconstruct_mosaic, fs_kwargs, **kwargs)
    181 def __init__(
    182     self,
    183     image: biob.types.ImageLike,
   (...)
    187     **kwargs: Any,
    188 ):
    189     if reader is None:
    190         # Determine reader class and create dask delayed array
--> 191         ReaderClass = BioImage.determine_reader(
    192             image, fs_kwargs=fs_kwargs, **kwargs
    193         )
    194     else:
    195         # Init reader
    196         ReaderClass = reader

File ~/active/cell/bioio/bioio/bio_image.py:172, in BioImage.determine_reader(image, fs_kwargs, **kwargs)
    170 image_value = str(image)
    171 image_type = str(type(image))
--> 172 raise biob.exceptions.UnsupportedFileFormatError(
    173     "BioImage",
    174     f"{image_value} ({image_type})",
    175     msg_extra=(
    176         "You may need to install an extra format dependency. "
    177         "See bioio README for list of some known plugins."
    178     ),
    179 )

UnsupportedFileFormatError: BioImage does not support the image: '../aicsimageio/aicsimageio/tests/resources/tiled.lif (<class 'str'>)'. You may need to install an extra format dependency. See bioio README for list of some known plugins.

In [6]: img = BioImage("../aicsimageio/aicsimageio/tests/resources/3d-cell-viewer.ome.tiff")

In [7]: type(img.metadata)
Out[7]: str
toloudis commented 1 year ago

I put a quick PR to address item 1. https://github.com/bioio-devs/bioio/pull/19

toloudis commented 1 year ago

Item number 5 is addressed here : https://github.com/bioio-devs/bioio/pull/20

SeanLeRoy commented 1 year ago

Item number 2 is address here: #21

SeanLeRoy commented 1 year ago

Item numbers 3 & 4 are addressed here: #22

SeanLeRoy commented 1 year ago

I think this will address item number 6 #23. I did not try all the readers, but I tried ome-tiff sldy ome-zarr and tifffile which seemed problematic in your and Dan's tests

BrianWhitneyAI commented 5 months ago

@evamaxfield @SeanLeRoy @toloudis looks like all 6 of these have been addressed! Anything else here?