checking examples (brats task 001 ipynb) again

[bhralzz]

Hello,
After installing latest version of Monai[all], I think the example brats task001 dont work correctly.

Is it possible to check it and bug fixing?

thanks

[KumoLiu]

Hi @bhralzz, thanks for the report.
Could you please share more information? Such as the command you install the MONAI, and the whole error log you get from which notebook.
Thanks.

[bhralzz]

@KumoLiu
thanks for your response:

goal is to rerun brats_segmentation_3d

os : win10

command tested for monai installation: pip install monai[all]

test on python versions: 3.8, 3.9, 3.10

AttributeError: module 'numpy' has no attribute 'bool'.

by changing torch.bool: np.bool_ in misc.py or by donwgrading numpy version it changed to the below errors:

cannot import name 'Invertd' from 'monai.transforms'

[KumoLiu]

I didn't find where we use np.bool in the source code.
Could you please refer to the install guide to install and see whether the monai can be imported successfully.
https://docs.monai.io/en/latest/installation.html

[bhralzz]

the source of error is:

File C:\ProgramData\anaconda3\envs\b8\lib\site-packages\monai\utils\misc.py:266
torch.bool: np.bool

another test based on installation.html verification of install:
the result of execution of
import monai
monai.config.print_config()

C:\Users\BHR.conda\envs\b9\lib\site-packages\monai\utils\misc.py:266: FutureWarning: In the future np.bool will be defined as the corresponding NumPy scalar.
torch.bool: np.bool,
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\BHR.conda\envs\b9\lib\site-packages\monai_init_.py", line 36, in
from .utils.module import load_submodules # noqa: E402
File "C:\Users\BHR.conda\envs\b9\lib\site-packages\monai\utils_init_.py", line 16, in
from .misc import *
File "C:\Users\BHR.conda\envs\b9\lib\site-packages\monai\utils\misc.py", line 266, in
torch.bool: np.bool,
File "C:\Users\BHR.conda\envs\b9\lib\site-packages\numpy_init_.py", line 353, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'bool'.
np.bool was a deprecated alias for the builtin bool. To avoid this error in existing code, use bool by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.bool_ here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

[KumoLiu]

Perhaps upgrade your MONAI version.
https://github.com/Project-MONAI/MONAI/blob/dev/monai/utils/misc.py

MONAI/requirements.txt

Line 2 in 95f69de

numpy>=1.20

Thanks.

[bhralzz]

by saving torch and monai[all] updated the below error emerged. there is a conflict of version

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
pytorch-ignite 0.4.2 requires torch<2,>=1.3, but you have torch 2.2.1 which is incompatible.
torchvision 0.14.1 requires torch==1.13.1, but you have torch 2.2.1 which is incompatible.

is it possible to serve step by step installation command for monai[all] in windows 10?

[KumoLiu]

Hi @bhralzz,
I think we set pytorch-ignite==0.4.11 in requirement and didn't fixed the version of torchvision

MONAI/requirements-dev.txt

Line 3 in 95f69de

pytorch-ignite==0.4.11

MONAI/requirements-dev.txt

Line 27 in 95f69de

torchvision

[bhralzz]

whats your idea to rerun the example?
Should I follow a step by step guide? in installation or need to modify code? any requirements list?...

[KumoLiu]

Hi @bhralzz, here is the installation guide https://docs.monai.io/en/latest/installation.html.
What I suggest is that create a new virtual env or using docker.
Hope it helps, thanks.

[bhralzz]

thanks