TypeError

[jkh1]

Just cloned the repo and installation went fine. Now testing
membrain segment --tomogram-path some_tomo_gram.mrc --ckpt-path MemBrain_seg_v9b.ckpt

produces this error:
TypeError: The classmethod SemanticSegmentationUnet.load_from_checkpoint cannot be called on an instance. Please call it on the class type and make sure the return value is used.
coming from membrain_seg/segmentation/segment.py:82 in segment

│    80 │   # Initialize the model and load trained weights from checkpoint                        │
│    81 │   pl_model = SemanticSegmentationUnet()                                                  │
│ ❱  82 │   pl_model = pl_model.load_from_checkpoint(model_checkpoint, map_location=device)        │
│    83 │   pl_model.to(device)                                                                    │
│    84 │                                                                                          │
│    85 │   # Preprocess the new data       

Is this a bug or am I doing something wrong here?

[stav-ros]

Hi, I got the same issue and was about to report it. Fresh installation on a new workstation.

[DHouldershaw]

Hi Folks, Fresh install, getting the same error:
TypeError: The classmethod SemanticSegmentationUnet.load_from_checkpoint cannot be called on an instance. Please call it on the class type and make sure the return value is used.

│ /membrain-seg/lib/python3.9/site-packages/pytorch_lightning/utilities/model_helpers.py:93 in get
│ 90 │ │ # Workaround for pytorch/pytorch#67146 │
│ 91 │ │ is_scripting = any(os.path.join("torch", "jit") in frameinfo.filename for framei │
│ 92 │ │ if instance is not None and not is_scripting: │
│ ❱ 93 │ │ │ raise TypeError( │
│ 94 │ │ │ │ f"The classmethod {cls.__name__}.{self.method.__name__} cannot be call │
│ 95 │ │ │ │ " Please call it on the class type and make sure the return value is use │
│ 96 │ │ │ ) │

[alisterburt]

Hi all, just to say I know that @LorenzLamm is away at the moment on holiday.

Not sure this ever worked, the correct API is to call the method on the class

model = ModelClass.load_from_checkpoint()

Easy fix if someone wants to open a PR

[rdrighetto]

Thanks everyone who reported the issue. I managed to reproduce it in a fresh install. It looks like a recent update in pytorch-lightning (or some other dependency) broke our code.
My installation in an older environment works fine, so I post below the output of conda list for that environment if anyone feels like playing with version matching.

Please bear with us while we work on a fix, which might take a couple days.

# packages in environment at /scicore/home/engel0006/GROUP/pool-engel/soft/membrain-seg/membrain-seg_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
aiohttp                   3.8.4                    pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
anyio                     3.7.1                    pypi_0    pypi
argon2-cffi               21.3.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
arrow                     1.2.3                    pypi_0    pypi
asttokens                 2.2.1                    pypi_0    pypi
async-lru                 2.0.4                    pypi_0    pypi
async-timeout             4.0.2                    pypi_0    pypi
attrs                     23.1.0                   pypi_0    pypi
babel                     2.12.1                   pypi_0    pypi
backcall                  0.2.0                    pypi_0    pypi
beautifulsoup4            4.12.2                   pypi_0    pypi
bleach                    6.0.0                    pypi_0    pypi
ca-certificates           2023.05.30           h06a4308_0  
certifi                   2023.5.7                 pypi_0    pypi
cffi                      1.15.1                   pypi_0    pypi
charset-normalizer        3.1.0                    pypi_0    pypi
click                     8.1.3                    pypi_0    pypi
cmake                     3.26.4                   pypi_0    pypi
colorama                  0.4.6                    pypi_0    pypi
comm                      0.1.4                    pypi_0    pypi
debugpy                   1.6.7.post1              pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
exceptiongroup            1.1.2                    pypi_0    pypi
executing                 1.2.0                    pypi_0    pypi
fastjsonschema            2.18.0                   pypi_0    pypi
filelock                  3.12.2                   pypi_0    pypi
fqdn                      1.5.1                    pypi_0    pypi
frozenlist                1.3.3                    pypi_0    pypi
fsspec                    2023.6.0                 pypi_0    pypi
idna                      3.4                      pypi_0    pypi
imageio                   2.31.1                   pypi_0    pypi
importlib-metadata        6.8.0                    pypi_0    pypi
ipykernel                 6.25.1                   pypi_0    pypi
ipython                   8.14.0                   pypi_0    pypi
isoduration               20.11.0                  pypi_0    pypi
jedi                      0.19.0                   pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
json5                     0.9.14                   pypi_0    pypi
jsonpointer               2.4                      pypi_0    pypi
jsonschema                4.19.0                   pypi_0    pypi
jsonschema-specifications 2023.7.1                 pypi_0    pypi
jupyter-client            8.3.0                    pypi_0    pypi
jupyter-core              5.3.1                    pypi_0    pypi
jupyter-events            0.7.0                    pypi_0    pypi
jupyter-lsp               2.2.0                    pypi_0    pypi
jupyter-server            2.7.0                    pypi_0    pypi
jupyter-server-terminals  0.4.4                    pypi_0    pypi
jupyterlab                4.0.4                    pypi_0    pypi
jupyterlab-pygments       0.2.2                    pypi_0    pypi
jupyterlab-server         2.24.0                   pypi_0    pypi
lazy-loader               0.2                      pypi_0    pypi
ld_impl_linux-64          2.38                 h1181459_1  
libffi                    3.4.4                h6a678d5_0  
libgcc-ng                 11.2.0               h1234567_1  
libgomp                   11.2.0               h1234567_1  
libstdcxx-ng              11.2.0               h1234567_1  
lightning-utilities       0.8.0                    pypi_0    pypi
lit                       16.0.6                   pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.3                    pypi_0    pypi
matplotlib-inline         0.1.6                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
membrain-seg              0.1.dev44+gc132a79          pypi_0    pypi
mistune                   3.0.1                    pypi_0    pypi
monai                     1.2.0                    pypi_0    pypi
mpmath                    1.3.0                    pypi_0    pypi
mrcfile                   1.4.3                    pypi_0    pypi
multidict                 6.0.4                    pypi_0    pypi
nbclient                  0.8.0                    pypi_0    pypi
nbconvert                 7.7.3                    pypi_0    pypi
nbformat                  5.9.2                    pypi_0    pypi
ncurses                   6.4                  h6a678d5_0  
nest-asyncio              1.5.7                    pypi_0    pypi
networkx                  3.1                      pypi_0    pypi
notebook                  7.0.2                    pypi_0    pypi
notebook-shim             0.2.3                    pypi_0    pypi
numexpr                   2.8.5                    pypi_0    pypi
numpy                     1.25.0                   pypi_0    pypi
nvidia-cublas-cu11        11.10.3.66               pypi_0    pypi
nvidia-cuda-cupti-cu11    11.7.101                 pypi_0    pypi
nvidia-cuda-nvrtc-cu11    11.7.99                  pypi_0    pypi
nvidia-cuda-runtime-cu11  11.7.99                  pypi_0    pypi
nvidia-cudnn-cu11         8.5.0.96                 pypi_0    pypi
nvidia-cufft-cu11         10.9.0.58                pypi_0    pypi
nvidia-curand-cu11        10.2.10.91               pypi_0    pypi
nvidia-cusolver-cu11      11.4.0.1                 pypi_0    pypi
nvidia-cusparse-cu11      11.7.4.91                pypi_0    pypi
nvidia-nccl-cu11          2.14.3                   pypi_0    pypi
nvidia-nvtx-cu11          11.7.91                  pypi_0    pypi
openssl                   3.0.8                h7f8727e_0  
overrides                 7.4.0                    pypi_0    pypi
packaging                 23.1                     pypi_0    pypi
pandas                    2.0.3                    pypi_0    pypi
pandocfilters             1.5.0                    pypi_0    pypi
parso                     0.8.3                    pypi_0    pypi
pexpect                   4.8.0                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pillow                    9.5.0                    pypi_0    pypi
pip                       23.1.2           py39h06a4308_0  
platformdirs              3.10.0                   pypi_0    pypi
prometheus-client         0.17.1                   pypi_0    pypi
prompt-toolkit            3.0.39                   pypi_0    pypi
psutil                    5.9.5                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
pycparser                 2.21                     pypi_0    pypi
pygments                  2.15.1                   pypi_0    pypi
python                    3.9.16               h955ad1f_3  
python-dateutil           2.8.2                    pypi_0    pypi
python-json-logger        2.0.7                    pypi_0    pypi
pytorch-lightning         2.0.3                    pypi_0    pypi
pytz                      2023.3                   pypi_0    pypi
pywavelets                1.4.1                    pypi_0    pypi
pyyaml                    6.0                      pypi_0    pypi
pyzmq                     25.1.1                   pypi_0    pypi
readline                  8.2                  h5eee18b_0  
referencing               0.30.2                   pypi_0    pypi
requests                  2.31.0                   pypi_0    pypi
rfc3339-validator         0.1.4                    pypi_0    pypi
rfc3986-validator         0.1.1                    pypi_0    pypi
rich                      13.4.2                   pypi_0    pypi
rpds-py                   0.9.2                    pypi_0    pypi
scikit-image              0.21.0                   pypi_0    pypi
scipy                     1.10.1                   pypi_0    pypi
send2trash                1.8.2                    pypi_0    pypi
setuptools                67.8.0           py39h06a4308_0  
shellingham               1.5.0.post1              pypi_0    pypi
simpleitk                 2.2.1                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
sniffio                   1.3.0                    pypi_0    pypi
soupsieve                 2.4.1                    pypi_0    pypi
sqlite                    3.41.2               h5eee18b_0  
stack-data                0.6.2                    pypi_0    pypi
sympy                     1.12                     pypi_0    pypi
terminado                 0.17.1                   pypi_0    pypi
tifffile                  2023.4.12                pypi_0    pypi
tinycss2                  1.2.1                    pypi_0    pypi
tk                        8.6.12               h1ccaba5_0  
tomli                     2.0.1                    pypi_0    pypi
torch                     2.0.1                    pypi_0    pypi
torchmetrics              0.11.4                   pypi_0    pypi
tornado                   6.3.2                    pypi_0    pypi
tqdm                      4.65.0                   pypi_0    pypi
traitlets                 5.9.0                    pypi_0    pypi
triton                    2.0.0                    pypi_0    pypi
typer                     0.9.0                    pypi_0    pypi
typing-extensions         4.6.3                    pypi_0    pypi
tzdata                    2023.3                   pypi_0    pypi
uri-template              1.3.0                    pypi_0    pypi
urllib3                   2.0.3                    pypi_0    pypi
wcwidth                   0.2.6                    pypi_0    pypi
webcolors                 1.13                     pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
websocket-client          1.6.1                    pypi_0    pypi
wheel                     0.38.4           py39h06a4308_0  
xz                        5.4.2                h5eee18b_0  
yarl                      1.9.2                    pypi_0    pypi
zipp                      3.16.2                   pypi_0    pypi
zlib                      1.2.13               h5eee18b_0 

[LorenzLamm]

Hi everyone,
Thanks a lot for reporting this issue and really sorry for the delay on fixing this.
The issue was a mix of new versions of Pytorch-lightning and MONAI. In our new PR (#41), we have fixed this issue.

So if you now git pull the latest version of the repository and re-install MemBrain-seg, it should work normally again.

I'll leave this issue open for a couple of days in case a problem comes up.

[jkh1]

Just to confirm that it's all good on my side. Thanks.

[LorenzLamm]

Great, thanks for the feedback. Closing this issue now.