stav-ros
commented
8 months ago Hi, I got the same issue and was about to report it. Fresh installation on a new workstation.
Closed jkh1 closed 7 months ago
stav-ros
commented
8 months ago Hi, I got the same issue and was about to report it. Fresh installation on a new workstation.
DHouldershaw
commented
8 months ago Hi Folks, Fresh install, getting the same error:
TypeError: The classmethodSemanticSegmentationUnet.load_from_checkpointcannot 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 https://github.com/pytorch/pytorch/issues/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
commented
8 months ago 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
commented
8 months ago 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
commented
8 months ago 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 (https://github.com/teamtomo/membrain-seg/pull/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
commented
8 months ago Just to confirm that it's all good on my side. Thanks.
LorenzLamm
commented
7 months ago Great, thanks for the feedback. Closing this issue now.
Just cloned the repo and installation went fine. Now testing
membrain segment --tomogram-path some_tomo_gram.mrc --ckpt-path MemBrain_seg_v9b.ckptproduces this error:
TypeError: The classmethodSemanticSegmentationUnet.load_from_checkpointcannot 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 segmentIs this a bug or am I doing something wrong here?