AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead.

[kavandeloo97]

Getting this error when trying to use visualqc_freesurfer -h:

(base) admin@Katies-iMac scripts % visualqc_freesurfer -h
Traceback (most recent call last):
File "/Users/admin/miniconda3/bin/visualqc_freesurfer", line 5, in
from visualqc.freesurfer import main
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/init.py", line 24, in
from visualqc.readers import (gather_freesurfer_data, read_aparc_stats_in_hemi,
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/readers.py", line 10, in
from visualqc import config as cfg
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/config.py", line 180, in
line_break = [np.NaN, np.NaN]
^^^^^^
File "/Users/admin/miniconda3/lib/python3.11/site-packages/numpy/init.py", line 400, in getattr
raise AttributeError(
AttributeError: np.NaN was removed in the NumPy 2.0 release. Use np.nan instead.
(base) admin@Katies-iMac scripts % vqcfs -h
Traceback (most recent call last):
File "/Users/admin/miniconda3/bin/vqcfs", line 5, in
from visualqc.freesurfer import main
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/init.py", line 24, in
from visualqc.readers import (gather_freesurfer_data, read_aparc_stats_in_hemi,
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/readers.py", line 10, in
from visualqc import config as cfg
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/config.py", line 180, in
line_break = [np.NaN, np.NaN]
^^^^^^
File "/Users/admin/miniconda3/lib/python3.11/site-packages/numpy/init.py", line 400, in getattr
raise AttributeError(
AttributeError: np.NaN was removed in the NumPy 2.0 release. Use np.nan instead.

[raamana]

Thanks @kavandeloo97 for reporting the issue - I will take a look and try to fix it asap. if you need it in the meanwhile, just downgrade your numpy version for now e.g., use one version earlier with pip install numpy==1.26.4 and try rerun visualqc?

[raamana]

Hi @kavandeloo97 , sorry for the delay. I just released a new version 0.6.7 that fixes this issue. Run these commands to use the latest version:

pip uninstall visualqc
pip install -U visualqc --no-cache-dir

if you still have issues, please feel free to reopen this issue.

[raamana]

Hi @kavandeloo97 , did this help? was this working for you?

[kavandeloo97]

Hey, I just tried it this morning - I had to step back from this for a bit but would be great to get back into it. Just installed the new version but have this error when trying vqcfs -h. I could still try running with an earlier version of numpy but am a bit unsure about messing with it.

(base) admin@Katies-iMac ~ % vqcfs -h
Traceback (most recent call last):
File "/Users/admin/miniconda3/bin/vqcfs", line 5, in
from visualqc.freesurfer import main
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/freesurfer.py", line 4, in
from visualqc import freesurfer
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/freesurfer.py", line 24, in
from mrivis.color_maps import get_freesurfer_cmap
File "/Users/admin/miniconda3/lib/python3.11/site-packages/mrivis/init.py", line 15, in
from mrivis.workflow import (checkerboard, color_mix, voxelwise_diff, collage,
File "/Users/admin/miniconda3/lib/python3.11/site-packages/mrivis/workflow.py", line 10, in
from mrivis.base import Collage
File "/Users/admin/miniconda3/lib/python3.11/site-packages/mrivis/base.py", line 12, in
from mrivis.utils import check_num_slices, check_views, load_image_from_disk,
File "/Users/admin/miniconda3/lib/python3.11/site-packages/mrivis/utils.py", line 108, in
max_value=np.Inf):
^^^^^^
File "/Users/admin/miniconda3/lib/python3.11/site-packages/numpy/init.py", line 400, in getattr
raise AttributeError(
AttributeError: np.Inf was removed in the NumPy 2.0 release. Use np.inf instead.

[raamana]

did you run these commands before trying it?

pip uninstall visualqc
pip install -U visualqc --no-cache-dir

[joshleelab]

I am still getting the same error as kavandeloo97 following your last post's instructions. Since I was using this in its own env, going to numpy==1.26.4 was not a problem for me, personally. Just letting you know.

[raamana]

Thanks @nimzodisaster for reporting back. I will double check to ensure the latest release doesnt have the bug it is supposed to fix. perhaps something else is coming in the way?