test with pyarrow installed

[joshua-gould]

No description provided.

[joshua-gould]

I'm unable to read czi files on Windows when I have pyarrow installed using pip

[BrianWhitneyAI]

Hey @joshua-gould can you provide the traceback for this issue?

[joshua-gould]

I don't get a traceback-python just crashes

[joshua-gould]

This is what I get:

Windows fatal exception: access violation

Current thread 0x00001208 (most recent call first):
  File "mamba\envs\test\Lib\site-packages\aicspylibczi\CziFile.py", line 63 in __init__
  File "mamba\envs\test\Lib\site-packages\aicsimageio\readers\czi_reader.py", line 98 in _is_supported_image

[BrianWhitneyAI]

This is what I get:

Windows fatal exception: access violation

Current thread 0x00001208 (most recent call first):
  File "mamba\envs\test\Lib\site-packages\aicspylibczi\CziFile.py", line 63 in __init__
  File "mamba\envs\test\Lib\site-packages\aicsimageio\readers\czi_reader.py", line 98 in _is_supported_image

This seems like an environment issue to me. I would try creating a new environment and installing with pip. Maybe try pyenv for better env/python-version control.

[m-albert]

Just wanted to add here I'm also getting this issue in a fresh conda environment (pip installing bioio-czi). Example file tested with: https://github.com/multiview-stitcher/multiview-stitcher/blob/main/src/multiview_stitcher/test-datasets/mosaic_test.czi

[toloudis]

Thanks for posting this issue. We will try to get a good repro over here and debug this.

It may be something in the way that AllenCellModeling/aicspylibczi is being built. If you are interested in the meantime you may try building it from source to see if that helps. That's probably one of the things I will try.

[toloudis]

@joshua-gould @m-albert any particular Python version of interest?

[toloudis]

This is what I get:

Windows fatal exception: access violation

Current thread 0x00001208 (most recent call first):
  File "mamba\envs\test\Lib\site-packages\aicspylibczi\CziFile.py", line 63 in __init__
  File "mamba\envs\test\Lib\site-packages\aicsimageio\readers\czi_reader.py", line 98 in _is_supported_image

I just noticed that this trace shows aicsimageio. Do you get the same thing using bioio? (They do both use aicspylibczi)

[m-albert]

Hi @toloudis, thanks a lot! Unfortunately I currently don't have access to a windows machine and will try to post a reproducer in the next days.

I did get this problem for both aicsimageio and bioio. Python version was 3.10 in both cases.

[joshua-gould]

The following code works fine on Windows, however if you uncomment the pandas import it will crash (if pyarrow is installed)

# import pandas as pd
from aicspylibczi import CziFile

p = './mosaic_test.czi'
CziFile(p)
print('open')

[evamaxfield]

This might be something we want to ask the dask / xarray folks since we aren't doing anything with pyarrow. I think dask recently switched to using parquet dtypes in their dataframe methods (specifically string methods) but I don't see how that would affect us here.