Error on membrain launch after following installation guide

[GenevieveBuckley]

• membrain-seg version: current git main branch
• Python version: tested with python 3.9 and python 3.11
• Operating System: Zorin OS 16.3

Description

I followed the instructions in the installation guide, and all the packages appeared to install correctly with pip.
But, when I tried to launch membrain from the command line, I got an error.

What I Did

git clone https://github.com/teamtomo/membrain-seg.git
cd membrain_seg
conda create -n membrainseg python=3.9 pip
conda activate membrainseg
pip install .
membrain

$ membrain

Traceback (most recent call last):
  File "/home/supervisor/miniforge3/envs/membrainseg/bin/membrain", line 5, in <module>
    from membrain_seg.segmentation.cli import cli
  File "/home/supervisor/miniforge3/envs/membrainseg/lib/python3.9/site-packages/membrain_seg/segmentation/cli/__init__.py", line 5, in <module>
    from .segment_cli import segment  # noqa: F401
  File "/home/supervisor/miniforge3/envs/membrainseg/lib/python3.9/site-packages/membrain_seg/segmentation/cli/segment_cli.py", line 12, in <module>
    from ..segment import segment as _segment
  File "/home/supervisor/miniforge3/envs/membrainseg/lib/python3.9/site-packages/membrain_seg/segmentation/segment.py", line 17, in <module>
    from .dataloading.memseg_augmentation import get_mirrored_img, get_prediction_transforms
  File "/home/supervisor/miniforge3/envs/membrainseg/lib/python3.9/site-packages/membrain_seg/segmentation/dataloading/memseg_augmentation.py", line 18, in <module>
    from membrain_seg.segmentation.dataloading.transforms import (
  File "/home/supervisor/miniforge3/envs/membrainseg/lib/python3.9/site-packages/membrain_seg/segmentation/dataloading/transforms.py", line 608, in <module>
    AxesShuffle = Compose(
  File "/home/supervisor/miniforge3/envs/membrainseg/lib/python3.9/site-packages/monai/transforms/compose.py", line 251, in __init__
    self.set_random_state(seed=get_seed())
  File "/home/supervisor/miniforge3/envs/membrainseg/lib/python3.9/site-packages/monai/transforms/compose.py", line 263, in set_random_state
    _transform.set_random_state(seed=self.R.randint(MAX_SEED, dtype="uint32"))
  File "/home/supervisor/miniforge3/envs/membrainseg/lib/python3.9/site-packages/monai/transforms/transform.py", line 207, in set_random_state
    _seed = _seed % MAX_SEED
OverflowError: Python integer 4294967296 out of bounds for uint32

Additional info

• I tested this again, this time with a python 3.11 environment, but found the same error.
• I double checked my installed version of the monai dependency is the latest available version (it is, version 1.3.1)
• I searched the monai issues list, but didn't see an issue where the title obviously referred this particular error. Perhaps membrain_seg is passing in a seed value with an unexpected type? It's weird that 4294967296 is only just higher than the dtype range allowed.
• ... I could try again with a different operating system, but have not done this yet

conda list (click to expand)

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiohttp                   3.9.5                    pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
async-timeout             4.0.3                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2024.6.2             hbcca054_0    conda-forge
click                     8.1.7                    pypi_0    pypi
filelock                  3.15.3                   pypi_0    pypi
frozenlist                1.4.1                    pypi_0    pypi
fsspec                    2024.6.0                 pypi_0    pypi
idna                      3.7                      pypi_0    pypi
imageio                   2.34.1                   pypi_0    pypi
jinja2                    3.1.4                    pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0              h77fa898_11    conda-forge
libgomp                   13.2.0              h77fa898_11    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
lightning-utilities       0.11.2                   pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.5                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
membrain-seg              0.0.2                    pypi_0    pypi
monai                     1.3.1                    pypi_0    pypi
mpmath                    1.3.0                    pypi_0    pypi
mrcfile                   1.5.0                    pypi_0    pypi
multidict                 6.0.5                    pypi_0    pypi
ncurses                   6.5                  h59595ed_0    conda-forge
networkx                  3.2.1                    pypi_0    pypi
numpy                     2.0.0                    pypi_0    pypi
nvidia-cublas-cu12        12.1.3.1                 pypi_0    pypi
nvidia-cuda-cupti-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-nvrtc-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-runtime-cu12  12.1.105                 pypi_0    pypi
nvidia-cudnn-cu12         8.9.2.26                 pypi_0    pypi
nvidia-cufft-cu12         11.0.2.54                pypi_0    pypi
nvidia-curand-cu12        10.3.2.106               pypi_0    pypi
nvidia-cusolver-cu12      11.4.5.107               pypi_0    pypi
nvidia-cusparse-cu12      12.1.0.106               pypi_0    pypi
nvidia-nccl-cu12          2.20.5                   pypi_0    pypi
nvidia-nvjitlink-cu12     12.5.40                  pypi_0    pypi
nvidia-nvtx-cu12          12.1.105                 pypi_0    pypi
openssl                   3.3.1                h4ab18f5_0    conda-forge
packaging                 24.1                     pypi_0    pypi
pandas                    2.2.2                    pypi_0    pypi
pillow                    10.3.0                   pypi_0    pypi
pip                       24.0               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0                   pypi_0    pypi
python                    3.9.19          h0755675_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
pytorch-lightning         2.3.0                    pypi_0    pypi
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
rich                      13.7.1                   pypi_0    pypi
scikit-image              0.24.0                   pypi_0    pypi
scipy                     1.13.1                   pypi_0    pypi
setuptools                70.1.0             pyhd8ed1ab_0    conda-forge
shellingham               1.5.4                    pypi_0    pypi
simpleitk                 2.3.1                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
sympy                     1.12.1                   pypi_0    pypi
tifffile                  2024.6.18                pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
torch                     2.3.1                    pypi_0    pypi
torchmetrics              1.4.0.post0              pypi_0    pypi
tqdm                      4.66.4                   pypi_0    pypi
triton                    2.3.1                    pypi_0    pypi
typer                     0.12.3                   pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
tzdata                    2024.1                   pypi_0    pypi
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yarl                      1.9.4                    pypi_0    pypi

[xingxingjiukunkun]

"Have you resolved this issue? I am encountering the same problem."

[GenevieveBuckley]

"Have you resolved this issue? I am encountering the same problem."

I found changing line 207 in monai.transforms.transform.py to

_seed = int(_seed) % MAX_SEED

fixed the problem for me. You may like to install an editable version of the MONAI dependency and do the same until a proper fix is available.

See Project-MONAI/MONAI#7871

[GenevieveBuckley]

According to one of the MONAI devs downgrading numpy to v1 (instead of v2) will also fix things.

[LorenzLamm]

Thanks a lot @GenevieveBuckley for reporting this issue and even fixing it!
I also encountered other issues -- it seems like numpy v2 has not arrived everywhere yet. I just set the dependency of numpy to <2.0.0 (#72) and this will hopefully resolve this.

[kevinyamauchi]

Thanks for all of the sleuthing, @GenevieveBuckley ! It's nice to see you here 😄

[LorenzLamm]

As commented by @GenevieveBuckley in #72 (comment), this problem seems to be solved for now, so I'm closing this issue.

Thanks a lot again for the fix and quick feedback @GenevieveBuckley :)