viewer.add_labels crashes napari 0.5.3 on Mac M1

[mathieuboudreau]

Hi there,

Working on our plugin,

https://github.com/axondeepseg/axondeepseg/tree/ac/nnunet_migration/plugins

in one of our PRs,

axondeepseg/axondeepseg#800 (comment)

I encounter an issue where when we load our mask/label, specifically this call:

https://github.com/axondeepseg/axondeepseg/blob/b2533989851d204ca575dc502f7b920b6ec58beb/plugins/napari_ADS/_widget.py#L385-L391

(where note, I've updated according to #112),

Napari crashes and throws me these warnings (but no error):

/Users/mathieuboudreau/neuropoly/github/axondeepseg/ads_conda/envs/venv_ads/lib/python3.11/site-packages/numba/np/ufunc/parallel.py:371: NumbaWarning: The TBB threading layer requires TBB version 2021 update 6 or later i.e., TBB_INTERFACE_VERSION >= 12060. Found TBB_INTERFACE_VERSION = 12050. The TBB threading layer is disabled.!
OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.

Though I can remove the first warning by updating the tbb version manually, I can't seem to fix the second warning (and I'm not sure if this is the cause). In our PR, we're updated our python versionv from 3.8 to >=3.11.

I'm running a Macboookpro M1 (Sonoma 14.6.1). A colleague tried on his Windows machine, encountered a different issue with napari 0.5.3, but downgrading to napari 0.4.19 and then re-upgrading it to 0.5.3 resolved it for him (but not me),

axondeepseg/axondeepseg#800 (comment)
axondeepseg/axondeepseg#800 (comment)

We've also switched from a conda-install to pip-install in this PR, through:

axondeepseg/axondeepseg#821

Here's our current requirements file,

https://github.com/axondeepseg/axondeepseg/blob/ac/nnunet_migration/requirements.txt

And here's the pip freeze output on my machine inside my conda environment:

acvl_utils==0.2
alabaster==1.0.0
annotated-types==0.7.0
app-model==0.2.8
appdirs==1.4.4
appnope==0.1.4
asciitree==0.3.3
asttokens==2.4.1
attrs==24.2.0
-e git+https://www.github.com/axondeepseg/axondeepseg.git@3db40cf0e41ab19b54e5a646187cbc490f90ca4e#egg=AxonDeepSeg
babel==2.16.0
batchgenerators==0.25
build==1.2.1
cachey==0.2.1
certifi==2024.8.30
charset-normalizer==3.3.2
click==8.1.7
cloudpickle==3.0.0
comm==0.2.2
connected-components-3d==3.18.0
contourpy==1.3.0
coverage==7.6.1
cycler==0.12.1
dask==2024.8.1
debugpy==1.8.5
decorator==5.1.1
dicom2nifti==2.4.11
docstring_parser==0.16
docutils==0.21.2
dynamic_network_architectures==0.3.1
et-xmlfile==1.1.0
executing==2.0.1
fasteners==0.19
filelock==3.15.4
flexcache==0.3
flexparser==0.3.1
fonttools==4.53.1
freetype-py==2.5.1
fsspec==2024.6.1
future==1.0.0
graphviz==0.20.3
HeapDict==1.0.1
hsluv==5.0.4
idna==3.8
imagecodecs==2024.6.1
imageio==2.35.1
imagesize==1.4.1
importlib_metadata==8.4.0
in-n-out==0.2.1
iniconfig==2.0.0
ipykernel==6.29.5
ipython==8.27.0
ipython-genutils==0.2.0
jedi==0.19.1
Jinja2==3.1.4
joblib==1.4.2
jsonschema==4.23.0
jsonschema-specifications==2023.12.1
jupyter_client==8.6.2
jupyter_core==5.7.2
kiwisolver==1.4.5
lazy_loader==0.4
linecache2==1.0.0
llvmlite==0.43.0
locket==1.0.0
loguru==0.7.2
magicgui==0.9.1
markdown-it-py==3.0.0
MarkupSafe==2.1.5
matplotlib==3.9.2
matplotlib-inline==0.1.7
mdurl==0.1.2
mpld3==0.5.10
mpmath==1.3.0
napari==0.5.3
napari-ADS @ file:///Users/mathieuboudreau/neuropoly/github/axondeepseg/plugins
napari-console==0.0.9
napari-plugin-engine==0.2.0
napari-plugin-manager==0.1.0
napari-svg==0.2.0
nest-asyncio==1.6.0
networkx==3.3
nibabel==5.2.1
nnunetv2==2.2.1
npe2==0.7.7
numba==0.60.0
numcodecs==0.13.0
numpy==1.26.4
numpydoc==1.8.0
openpyxl==3.1.5
packaging==24.1
pandas==2.2.2
parso==0.8.4
partd==1.4.2
pexpect==4.9.0
pillow==10.4.0
Pint==0.24.3
platformdirs==4.2.2
pluggy==1.5.0
pooch==1.8.2
prettytable==3.11.0
prompt_toolkit==3.0.47
psutil==6.0.0
psygnal==0.11.1
ptyprocess==0.7.0
pure_eval==0.2.3
pyconify==0.1.6
pydantic==2.8.2
pydantic-compat==0.1.2
pydantic_core==2.20.1
pydicom==2.4.4
Pygments==2.18.0
PyOpenGL==3.1.7
pyparsing==3.1.4
pyproject_hooks==1.1.0
PyQt5==5.15.11
PyQt5-Qt5==5.15.14
PyQt5_sip==12.15.0
pytest==8.3.2
pytest-cov==5.0.0
python-dateutil==2.9.0.post0
python-gdcm==3.0.24.1
pytz==2024.1
PyYAML==6.0.2
pyzmq==26.2.0
qtconsole==5.4.1
QtPy==2.4.1
referencing==0.35.1
requests==2.32.3
rich==13.8.0
rpds-py==0.20.0
scikit-image==0.24.0
scikit-learn==1.5.1
scipy==1.14.1
seaborn==0.13.2
shellingham==1.5.4
SimpleITK==2.4.0
six==1.16.0
snowballstemmer==2.2.0
Sphinx==8.0.2
sphinxcontrib-applehelp==2.0.0
sphinxcontrib-devhelp==2.0.0
sphinxcontrib-htmlhelp==2.1.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==2.0.0
sphinxcontrib-serializinghtml==2.0.0
stack-data==0.6.3
superqt==0.6.7
sympy==1.13.2
tabulate==0.9.0
threadpoolctl==3.5.0
tifffile==2024.8.28
tomli_w==1.0.0
toolz==0.12.1
torch==2.2.2
tornado==6.4.1
tqdm==4.66.5
traceback2==1.4.0
traitlets==5.14.3
triangle==20230923
typer==0.12.5
typing_extensions==4.12.2
tzdata==2024.1
unittest2==1.1.0
urllib3==2.2.2
vispy==0.14.3
wcwidth==0.2.13
wrapt==1.16.0
yacs==0.1.8
zarr==2.18.2
zipp==3.20.1

Any help would be greatly appreciated.

[mathieuboudreau]

Woops my google-fu seems to have failed me, that was a repo for a plugin not napari itself haha.

Let me find a better place to post this haha