SyntaxError in FatSegNet running on CPU Docker

[AlbCol]

Dear FatSegNet developers,

When trying to run FatSegNet using CPU docker image with below command.

docker run -it --rm --name fatsegnet -u $(id -u) -v //c/Users/PWS1/Desktop/dataset/:/tool/Data -v //c/Users/PWS1/Desktop/output/:/tool/Output adipose_tool:cpu_v1

I am facing this issue:

/usr/local/lib/python3.5/dist-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File "./run_FatSegNet.py", line 8, in
from Code.adipose_pipeline import run_adipose_pipeline
File "/tool/Code/adipose_pipeline.py", line 27, in
from Code.utilities.metrics import calculate_statistics_v2
File "/tool/Code/utilities/metrics.py", line 17, in
from skimage.measure import perimeter
File "/usr/local/lib/python3.5/dist-packages/skimage/init.py", line 135, in
from .data import data_dir
File "/usr/local/lib/python3.5/dist-packages/skimage/data/init.py", line 13, in
from ..io import imread, use_plugin
File "/usr/local/lib/python3.5/dist-packages/skimage/io/init.py", line 15, in
reset_plugins()
File "/usr/local/lib/python3.5/dist-packages/skimage/io/manage_plugins.py", line 91, in reset_plugins
_load_preferred_plugins()
File "/usr/local/lib/python3.5/dist-packages/skimage/io/manage_plugins.py", line 71, in _load_preferred_plugins
_set_plugin(p_type, preferred_plugins['all'])
File "/usr/local/lib/python3.5/dist-packages/skimage/io/manage_plugins.py", line 83, in _set_plugin
use_plugin(plugin, kind=plugin_type)
File "/usr/local/lib/python3.5/dist-packages/skimage/io/manage_plugins.py", line 254, in use_plugin
_load(name)
File "/usr/local/lib/python3.5/dist-packages/skimage/io/manage_plugins.py", line 298, in _load
fromlist=[modname])
File "/usr/local/lib/python3.5/dist-packages/skimage/io/_plugins/imageio_plugin.py", line 3, in
from imageio import imread, imsave
File "/usr/local/lib/python3.5/dist-packages/imageio/init.py", line 21, in
from . import config
File "/usr/local/lib/python3.5/dist-packages/imageio/config/init.py", line 1, in
from .extensions import known_extensions
File "/usr/local/lib/python3.5/dist-packages/imageio/config/extensions.py", line 828
_extension_dict: Dict[str, List[FileExtension]] = dict()
^
SyntaxError: invalid syntax

Any leads would be truly appreciated!
Thanks!

[santiestrada32]

Which operating system are you running the docker?

[AlbCol]

I'm using WSL2 on a Windows10 PC.
I tried Ubuntu 16.04, 18.04 and 20.04 and the message is always the same.

[AlbCol]

Dear @santiestrada32,
Do you have any suggestions as to why this error occurred?

Many thanks

[santiestrada32]

There is an error in the skiimage library you can try to set up a newer version of the library in docker image creation. We are moving our all code to pytorch you can try our pytorch version https://github.com/reuter-lab/FatSegNet_pytorch.

[AlbCol]

I used the pytorch version and it works.

Thanks!