model not found
romainGuiet opened this issue · 4 comments
Dear @cellSeg3d team ,
thank you for sharing your tool and for the documentation !
After creating my conda env and installing via:
pip install napari-cellseg3d
and
conda install -c conda-forge monai
I started napari, the plugin, in inference mode , define the folders but I got the error below in the log :
Starting...
********************
Worker started at 14:27:38
Saving results to : //path/
Worker is running...
MODEL DIMS : 128
SegResNet
--------------------
Parameters summary :
Model is : SegResNet
Window inference is disabled
Dataset loaded on cpu
--------------------
Loading weights...
Error : [Errno 2] No such file or directory: 'C:\\Users\\guiet\\.conda\\envs\\test\\lib\\site-packages\\napari_cellseg3d\\models\\pretrained\\pretrained_model_urls.json'
Worker finished at 14:27:38
********************
Indeed in the lib\site-packages\napari_cellseg3d\models\pretrained\ there is no pretrained_model_urls.json
I saw that in the model_workers.py , the show_progress is looking for this file but (so far) I couldn't localize this file... nor find a way to download the model
Thank you for your help
Romain
Please find below the information about the conda env
(test) C:\Users\guiet\.conda\envs\test>conda list
# packages in environment at C:\Users\guiet\.conda\envs\test:
#
# Name Version Build Channel
alabaster 0.7.12 pypi_0 pypi
app-model 0.1.1 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
asttokens 2.1.0 pypi_0 pypi
attrs 22.1.0 pypi_0 pypi
babel 2.11.0 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
blas 1.0 mkl
build 0.9.0 pypi_0 pypi
ca-certificates 2022.9.24 h5b45459_0 conda-forge
cachey 0.2.1 pypi_0 pypi
certifi 2022.9.24 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py39h0878f49_0 conda-forge
charset-normalizer 2.1.1 pypi_0 pypi
click 8.1.3 pypi_0 pypi
cloudpickle 2.2.0 pypi_0 pypi
colorama 0.4.6 pypi_0 pypi
commonmark 0.9.1 pypi_0 pypi
contourpy 1.0.6 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
dask 2022.11.1 pypi_0 pypi
dask-image 2022.9.0 pypi_0 pypi
debugpy 1.6.3 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
docstring-parser 0.15 pypi_0 pypi
docutils 0.17.1 pypi_0 pypi
einops 0.6.0 pypi_0 pypi
entrypoints 0.4 pypi_0 pypi
executing 1.2.0 pypi_0 pypi
fonttools 4.38.0 pypi_0 pypi
freetype-py 2.3.0 pypi_0 pypi
fsspec 2022.11.0 pypi_0 pypi
future 0.18.2 pyhd8ed1ab_6 conda-forge
heapdict 1.0.1 pypi_0 pypi
hsluv 5.0.3 pypi_0 pypi
idna 3.4 pypi_0 pypi
imageio 2.22.4 pypi_0 pypi
imageio-ffmpeg 0.4.7 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 5.0.0 pypi_0 pypi
in-n-out 0.1.6 pypi_0 pypi
intel-openmp 2022.1.0 h57928b3_3787 conda-forge
ipykernel 6.17.1 pypi_0 pypi
ipython 8.6.0 pypi_0 pypi
ipython-genutils 0.2.0 pypi_0 pypi
itk 5.2.1.post1 pypi_0 pypi
itk-core 5.2.1.post1 pypi_0 pypi
itk-filtering 5.2.1.post1 pypi_0 pypi
itk-io 5.2.1.post1 pypi_0 pypi
itk-numerics 5.2.1.post1 pypi_0 pypi
itk-registration 5.2.1.post1 pypi_0 pypi
itk-segmentation 5.2.1.post1 pypi_0 pypi
jedi 0.18.1 pypi_0 pypi
jinja2 3.1.2 pypi_0 pypi
jsonschema 4.17.0 pypi_0 pypi
jupyter-client 7.4.7 pypi_0 pypi
jupyter-core 5.0.0 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
libblas 3.9.0 12_win64_mkl conda-forge
libcblas 3.9.0 12_win64_mkl conda-forge
liblapack 3.9.0 12_win64_mkl conda-forge
libuv 1.44.2 h8ffe710_0 conda-forge
locket 1.0.0 pypi_0 pypi
magicgui 0.6.1 pypi_0 pypi
markupsafe 2.1.1 pypi_0 pypi
matplotlib 3.6.2 pypi_0 pypi
matplotlib-inline 0.1.6 pypi_0 pypi
mkl 2021.4.0 h0e2418a_729 conda-forge
mkl-service 2.4.0 py39h6b0492b_0 conda-forge
monai 1.0.1 pyhd8ed1ab_0 conda-forge
napari 0.4.17 pypi_0 pypi
napari-cellseg3d 0.0.1rc4 pypi_0 pypi
napari-console 0.0.6 pypi_0 pypi
napari-plugin-engine 0.2.0 pypi_0 pypi
napari-svg 0.1.6 pypi_0 pypi
nest-asyncio 1.5.6 pypi_0 pypi
networkx 2.8.8 pypi_0 pypi
nibabel 4.0.2 pypi_0 pypi
ninja 1.11.0 h2d74725_0 conda-forge
npe2 0.6.1 pypi_0 pypi
numpy 1.23.5 pypi_0 pypi
numpydoc 1.5.0 pypi_0 pypi
opencv-python 4.6.0.66 pypi_0 pypi
openssl 1.1.1s h2bbff1b_0
packaging 21.3 pypi_0 pypi
pandas 1.5.1 pypi_0 pypi
parso 0.8.3 pypi_0 pypi
partd 1.3.0 pypi_0 pypi
pep517 0.13.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 9.3.0 pypi_0 pypi
pims 0.6.1 pypi_0 pypi
pint 0.20.1 pypi_0 pypi
pip 22.2.2 py39haa95532_0
platformdirs 2.5.4 pypi_0 pypi
pooch 1.6.0 pypi_0 pypi
prompt-toolkit 3.0.32 pypi_0 pypi
psutil 5.9.4 pypi_0 pypi
psygnal 0.6.1 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.10.2 pypi_0 pypi
pygments 2.13.0 pypi_0 pypi
pyopengl 3.1.6 pypi_0 pypi
pyparsing 3.0.9 pypi_0 pypi
pyqt5 5.15.7 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.11.0 pypi_0 pypi
pyrsistent 0.19.2 pypi_0 pypi
python 3.9.15 h6244533_0
python-dateutil 2.8.2 pypi_0 pypi
python_abi 3.9 2_cp39 conda-forge
pytomlpp 1.0.11 pypi_0 pypi
pytorch 1.10.2 cpu_py39h907fbb5_0
pytz 2022.6 pypi_0 pypi
pywavelets 1.4.1 pypi_0 pypi
pywin32 305 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
pyzmq 24.0.1 pypi_0 pypi
qtconsole 5.4.0 pypi_0 pypi
qtpy 2.3.0 pypi_0 pypi
requests 2.28.1 pypi_0 pypi
rich 12.6.0 pypi_0 pypi
scikit-image 0.19.3 pypi_0 pypi
scipy 1.9.3 pypi_0 pypi
setuptools 65.5.0 py39haa95532_0
six 1.16.0 pyh6c4a22f_0 conda-forge
slicerator 1.1.0 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
sphinx 4.5.0 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi
sqlite 3.39.3 h2bbff1b_0
stack-data 0.6.1 pypi_0 pypi
superqt 0.4.0 pypi_0 pypi
tbb 2021.6.0 h59b6b97_0
tifffile 2022.10.10 pypi_0 pypi
tomli 2.0.1 pypi_0 pypi
toolz 0.12.0 pypi_0 pypi
torch 1.13.0 pypi_0 pypi
tornado 6.2 pypi_0 pypi
tqdm 4.64.1 pypi_0 pypi
traitlets 5.5.0 pypi_0 pypi
typer 0.7.0 pypi_0 pypi
typing-extensions 4.4.0 hd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_0 conda-forge
tzdata 2022f h04d1e81_0
urllib3 1.26.12 pypi_0 pypi
vc 14.2 h21ff451_1
vispy 0.11.0 pypi_0 pypi
vs2015_runtime 14.27.29016 h5e58377_2
wcwidth 0.2.5 pypi_0 pypi
wheel 0.37.1 pyhd3eb1b0_0
wincertstore 0.2 py39haa95532_2
wrapt 1.14.1 pypi_0 pypi
zipp 3.10.0 pypi_0 pypi
I found on your github repo the pretrained_model_urls.json so I created a file at the proper location and now the error is different :
Starting...
********************
Worker started at 16:47:44
Saving results to : //sv-01-159/e$/anthony/AR008/AR008_LH_tiff_sp/BIOP_test
Worker is running...
MODEL DIMS : 128
SegResNet
--------------------
Parameters summary :
Model is : SegResNet
Window inference is disabled
Dataset loaded on cpu
--------------------
Loading weights...
Error : <urlopen error [WinError 10060] A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond>
Worker finished at 16:48:16
same error for all the models
and try to download the file through wget also failed :
wget http://deeplabcut.rowland.harvard.edu/cellseg3dmodels/SegResNet.tar.gz
--2022-11-21 16:06:28-- http://deeplabcut.rowland.harvard.edu/cellseg3dmodels/SegResNet.tar.gz
Resolving deeplabcut.rowland.harvard.edu (deeplabcut.rowland.harvard.edu)... 192.131.102.16
Connecting to deeplabcut.rowland.harvard.edu (deeplabcut.rowland.harvard.edu)|192.131.102.16|:80... failed: No route to host.
Thank you for your help
Best
Hello @romainGuiet,
Thanks for trying out the plugin !
It seems that indeed the .json with the model URLs is missing on PyPi, we will fix this in the next release, thank you for pointing it out.
As for the second error, it seems the website on which we host the weights is down, as I cannot reach it either.
This should be temporary, but if you'd like, I can send you an email with a drive containing the weights.
You could then either put them in the mentioned folder C:\\Users\\guiet\\.conda\\envs\\test\\lib\\site-packages\\napari_cellseg3d\\models\\pretrained, or store them anywhere on your computer and provide the path to the weights file when you load the model.
Sorry again for the inconvenience and best regards
We have moved the weights to HuggingFace, weights download should be functional again !