aicsimageio
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Published
20 hours ago •
AllenCellModeling
AllenCellModeling
Update fsspec dependency to have a hard requirement on >= 2022.8.1
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System and Software
- aicsimageio Version: 4.9.1
- Python Version: 3.9
- Operating System: macOS 12.4 (arm64)
Description
In [1]: from pathlib import Path
In [2]: import aicsimageio
In [3]: path = Path(Path.home() / "Dev/napari-aicsimageio/napari_aicsimageio/tests/resources/s_1_t_1_c_1_z_1.czi")
In [4]: img = aicsimageio.AICSImage(path)
In 4.9.0 this works fine (and napari-aicsimageio works) After updating to 4.9.1 this results in an error:
---------------------------------------------------------------------------
In [4]: path = Path("/Users/piotrsobolewski/Dev/napari-aicsimageio/napari_aicsim
...: ageio/tests/resources/s_1_t_1_c_1_z_1.czi")
In [5]: img = aicsimageio.AICSImage(path)
21-Aug-22 13:50:21 - aicsimageio.aics_image - WARNING - Attempted file (/Users/piotrsobolewski/Dev/napari-aicsimageio/napari_aicsimageio/tests/resources/s_1_t_1_c_1_z_1.czi) load with reader: aicsimageio.readers.czi_reader.CziReader failed with error: '_io.BufferedReader' object has no attribute 'f'
---------------------------------------------------------------------------
UnsupportedFileFormatError Traceback (most recent call last)
Input In [5], in <cell line: 1>()
----> 1 img = aicsimageio.AICSImage(path)
File ~/Dev/miniforge3/envs/apple-TF29/lib/python3.9/site-packages/aicsimageio/aics_image.py:264, in AICSImage.__init__(self, image, reader, reconstruct_mosaic, fs_kwargs, **kwargs)
254 def __init__(
255 self,
256 image: types.ImageLike,
(...)
260 **kwargs: Any,
261 ):
262 if reader is None:
263 # Determine reader class and create dask delayed array
--> 264 ReaderClass = self.determine_reader(image, fs_kwargs=fs_kwargs, **kwargs)
265 else:
266 # Init reader
267 ReaderClass = reader
File ~/Dev/miniforge3/envs/apple-TF29/lib/python3.9/site-packages/aicsimageio/aics_image.py:218, in AICSImage.determine_reader(image, fs_kwargs, **kwargs)
216 if readers[0] in READER_TO_INSTALL:
217 installer = READER_TO_INSTALL[readers[0]]
--> 218 raise exceptions.UnsupportedFileFormatError(
219 "AICSImage",
220 path,
221 msg_extra=(
222 f"File extension suggests format: '{format_ext}'. "
223 f"Install extra format dependency with: "
224 f"`pip install {installer}`. "
225 f"See all known format extensions and their "
226 f"extra install name with "
227 f"`aicsimageio.formats.FORMAT_IMPLEMENTATIONS`. "
228 f"If the extra dependency is already installed this "
229 f"error may have raised because the file is "
230 f"corrupt or similar issue. For potentially more "
231 f"information and to help debug, try loading the file "
232 f"directly with the desired file format reader "
233 f"instead of with the AICSImage object."
234 ),
235 )
236 else:
237 raise exceptions.UnsupportedFileFormatError(
238 "AICSImage",
239 path,
240 )
UnsupportedFileFormatError: AICSImage does not support the image: '/Users/piotrsobolewski/Dev/napari-aicsimageio/napari_aicsimageio/tests/resources/s_1_t_1_c_1_z_1.czi'. File extension suggests format: 'czi'. Install extra format dependency with: `pip install aicspylibczi>=3.0.5`. See all known format extensions and their extra install name with `aicsimageio.formats.FORMAT_IMPLEMENTATIONS`. If the extra dependency is already installed this error may have raised because the file is corrupt or similar issue. For potentially more information and to help debug, try loading the file directly with the desired file format reader instead of with the AICSImage object.
and likewise napari-aicsimageio fails to import.
Expected Behavior
Import the file, just as with 4.9.0
Reproduction
See above
Environment
No changes other than updating to 4.9.1, same aicspylibczi
We have been having issues with this since an fsspec update. Can you let us know which version of fsspec you are using / was installed?
Updating fsspec (to 2022.7.1) resolved the issue. Edit: downgrading to 2022.3.0 or 2022.2.0 is also bad.
Edit2: if I downgrade aicsimageio to 4.9.0 with fsspec 2022.7.1 I also get an error (below). So it seems that 4.9.0 and below is fine with earlier fsspec and 4.9.1 requires the newest 2022.7.1.
In [4]: img = aicsimageio.AICSImage(path)
21-Aug-22 18:08:48 - aicsimageio.aics_image - WARNING - Attempted file (/Users/piotrsobolewski/Dev/napari-aicsimageio/napari_aicsimageio/tests/resources/s_1_t_1_c_1_z_1.czi) load with reader: aicsimageio.readers.czi_reader.CziReader failed with error: __init__(): incompatible constructor arguments. The following argument types are supported:
1. _aicspylibczi.Reader(arg0: IOBufferedReader)
Invoked with: <fsspec.implementations.local.LocalFileOpener object at 0x1072376d0>
---------------------------------------------------------------------------
UnsupportedFileFormatError Traceback (most recent call last)
Input In [4], in <cell line: 1>()
----> 1 img = aicsimageio.AICSImage(path)
File ~/Dev/miniforge3/envs/apple-TF29/lib/python3.9/site-packages/aicsimageio/aics_image.py:264, in AICSImage.__init__(self, image, reader, reconstruct_mosaic, fs_kwargs, **kwargs)
254 def __init__(
255 self,
256 image: types.ImageLike,
(...)
260 **kwargs: Any,
261 ):
262 if reader is None:
263 # Determine reader class and create dask delayed array
--> 264 ReaderClass = self.determine_reader(image, fs_kwargs=fs_kwargs, **kwargs)
265 else:
266 # Init reader
267 ReaderClass = reader
File ~/Dev/miniforge3/envs/apple-TF29/lib/python3.9/site-packages/aicsimageio/aics_image.py:218, in AICSImage.determine_reader(image, fs_kwargs, **kwargs)
216 if readers[0] in READER_TO_INSTALL:
217 installer = READER_TO_INSTALL[readers[0]]
--> 218 raise exceptions.UnsupportedFileFormatError(
219 "AICSImage",
220 path,
221 msg_extra=(
222 f"File extension suggests format: '{format_ext}'. "
223 f"Install extra format dependency with: "
224 f"`pip install {installer}`. "
225 f"See all known format extensions and their "
226 f"extra install name with "
227 f"`aicsimageio.formats.FORMAT_IMPLEMENTATIONS`. "
228 f"If the extra dependency is already installed this "
229 f"error may have raised because the file is "
230 f"corrupt or similar issue. For potentially more "
231 f"information and to help debug, try loading the file "
232 f"directly with the desired file format reader "
233 f"instead of with the AICSImage object."
234 ),
235 )
236 else:
237 raise exceptions.UnsupportedFileFormatError(
238 "AICSImage",
239 path,
240 )
UnsupportedFileFormatError: AICSImage does not support the image: '/Users/piotrsobolewski/Dev/napari-aicsimageio/napari_aicsimageio/tests/resources/s_1_t_1_c_1_z_1.czi'. File extension suggests format: 'czi'. Install extra format dependency with: `pip install aicspylibczi>=3.0.5`. See all known format extensions and their extra install name with `aicsimageio.formats.FORMAT_IMPLEMENTATIONS`. If the extra dependency is already installed this error may have raised because the file is corrupt or similar issue. For potentially more information and to help debug, try loading the file directly with the desired file format reader instead of with the AICSImage object.
Apologies for hijacking this thread as it seems to be a fsspec issue.
SPECS:
- Windows 10 machine, with Miniconda
- aicsimageio 4.9.4
- python 3.9.13
- fsspec 2022.5.0
I'm getting another error when opening czi files..
WARNING Attempted file (C:/RBC_tiny.czi) load with reader: aicsimageio.readers.czi_reader.CziReader failed with error: '_io.BufferedReader' object has no attribute 'f'
Upgrading fsspec to 2022.8.2 fixed it.
I think we have encountered enough of these bug reports to warrant a change of the dependency minimal version to be bumped to 2022.8.0.