CellSeg3d
CellSeg3d copied to clipboard
Published
20 hours ago •
AdaptiveMotorControlLab
AdaptiveMotorControlLab
TypeError: reshape() got an unexpected keyword argument 'newshape' when running inference
Hello,
I am getting the error TypeError: reshape() got an unexpected keyword argument 'newshape' when I use CellSeg3D to perform inference on my data using a pretrained model.
My sequence of actions:
- Open Napari on a folder that consists of an image stack
- Go to Plugins -> CellSeg3D -> Inference
- In the widget that pops up, without changing any of the default parameters, click "Start"
Then after about 30 seconds, napari might crash with a segmentation fault. Even in the case that napari doesn't crash, nothing seems to change (no inferred images are created). This is the log in the terminal:
(cellseg) ┌─[yul4024@wulab-precision1] - [~/Documents/downsample_stack] - [229]
└─[$] napari cellseg_test_stack [8:24:32]
/home/yul4024/miniforge3/envs/cellseg/lib/python3.9/site-packages/pytools/persistent_dict.py:63: RecommendedHashNotFoundWarning: Unable to import recommended hash 'siphash24.siphash13', falling back to 'hashlib.sha256'. Run 'python3 -m pip install siphash24' to install the recommended hash.!
08:24:48 INFO pydensecrf not installed, CRF post-processing will not be available. Please install by running : pip install pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=masterThis is not a hard requirement, you do not need it to install it unless you want to use the CRF post-processing step.
08:24:48 INFO wandb not installed, wandb config will not be taken into account
08:24:50 INFO Starting...
08:24:50 INFO ********************
08:24:50 INFO Worker started at 08:24:50
08:24:50 INFO Saving results to : /home/yul4024/cellseg3d/inference
08:24:50 INFO Worker is running...
08:24:50 INFO MODEL DIMS : 64
08:24:50 INFO Model name : SegResNet
08:24:50 INFO Instantiating model...
08:24:50 INFO ********************
08:24:50 INFO Weight file SegResNet_latest.pth already exists, skipping download
08:24:50 INFO Loading weights...
08:24:51 ERROR reshape() got an unexpected keyword argument 'newshape'
Traceback (most recent call last):
File "/home/yul4024/miniforge3/envs/cellseg/lib/python3.9/site-packages/napari_cellseg3d/code_models/worker_inference.py", line 969, in inference
input_image = self.load_layer()
File "/home/yul4024/miniforge3/envs/cellseg/lib/python3.9/site-packages/napari_cellseg3d/code_models/worker_inference.py", line 283, in load_layer
volume = np.reshape(volume, newshape=(1, *volume.shape))
File "/home/yul4024/miniforge3/envs/cellseg/lib/python3.9/site-packages/dask/array/core.py", line 1753, in __array_function__
return da_func(*args, **kwargs)
TypeError: reshape() got an unexpected keyword argument 'newshape'
08:24:51 INFO Weights status : <All keys matched successfully>
08:24:51 INFO Done
08:24:51 INFO --------------------
08:24:51 INFO Parameters summary :
08:24:51 INFO Model is : SegResNet
08:24:51 INFO Window inference is disabled
08:24:51 INFO Dataset loaded on cuda:0 device
08:24:51 INFO --------------------
08:24:51 INFO Loading layer
08:24:51 INFO
Worker finished at 08:24:51
08:24:51 INFO ********************
08:24:51 INFO Emptying cache...
08:24:51 INFO Attempt complete : Cache emptied
Here is how I installed these packages. I uninstalled and reinstalled this environment in this exact manner to make sure it was not a one-time corrupt install of Numpy:
(base) ┌─[yul4024@wulab-precision1] - [~/Documents/downsample_stack] - [206]
└─[$] mamba create -n cellseg python=3.9 napari=0.4 pyqt [8:01:37]
Looking for: ['python=3.9', 'napari=0.4', 'pyqt']
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
Transaction
Prefix: /home/yul4024/miniforge3/envs/cellseg
Updating specs:
- python=3.9
- napari=0.4
- pyqt
Package Version Build Channel Size
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Install:
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+ pydantic 2.9.2 pyhd8ed1ab_0 conda-forge Cached
+ tifffile 2024.6.18 pyhd8ed1ab_0 conda-forge Cached
+ zarr 2.18.2 pyhd8ed1ab_0 conda-forge Cached
+ urllib3 2.2.3 pyhd8ed1ab_0 conda-forge Cached
+ ipykernel 6.29.5 pyh3099207_0 conda-forge Cached
+ jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge Cached
+ napari-svg 0.2.0 pyhd8ed1ab_0 conda-forge Cached
+ pydantic-compat 0.1.2 pyhd8ed1ab_0 conda-forge Cached
+ npe2 0.7.7 pyhd8ed1ab_0 conda-forge Cached
+ requests 2.32.3 pyhd8ed1ab_0 conda-forge Cached
+ qtconsole-base 5.6.0 pyha770c72_0 conda-forge Cached
+ jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge Cached
+ app-model 0.2.8 pyhd8ed1ab_0 conda-forge Cached
+ sphinx 7.4.7 pyhd8ed1ab_0 conda-forge Cached
+ sphinxcontrib-applehelp 2.0.0 pyhd8ed1ab_0 conda-forge Cached
+ pyconify 0.1.6 pyhd8ed1ab_0 conda-forge Cached
+ pooch 1.8.2 pyhd8ed1ab_0 conda-forge Cached
+ napari-console 0.0.9 pyh9208f05_0 conda-forge Cached
+ sphinxcontrib-qthelp 2.0.0 pyhd8ed1ab_0 conda-forge Cached
+ superqt 0.6.7 pyh9208f05_0 conda-forge Cached
+ sphinxcontrib-devhelp 2.0.0 pyhd8ed1ab_0 conda-forge Cached
+ magicgui 0.8.3 pyhd8ed1ab_0 conda-forge Cached
+ sphinxcontrib-htmlhelp 2.1.0 pyhd8ed1ab_0 conda-forge Cached
+ sphinxcontrib-serializinghtml 1.1.10 pyhd8ed1ab_0 conda-forge Cached
+ numpydoc 1.8.0 pyhd8ed1ab_0 conda-forge Cached
+ scikit-image 0.24.0 py39h5114956_2 conda-forge Cached
+ napari 0.4.19.post1 pyh9208f05_0 conda-forge Cached
Summary:
Install: 304 packages
Total download: 24MB
──────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n]
python 23.7MB @ 46.2MB/s 0.5s
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
To activate this environment, use
$ mamba activate cellseg
To deactivate an active environment, use
$ mamba deactivate
(base) ┌─[yul4024@wulab-precision1] - [~/Documents/downsample_stack] - [207]
└─[$] conda activate cellseg [8:02:24]
(cellseg) ┌─[yul4024@wulab-precision1] - [~/Documents/downsample_stack] - [209]
└─[$] mamba install pytorch torchvision torchaudio pytorch-cuda=12.4 -c pytorch -c nvidia [8:02:33]
Looking for: ['pytorch', 'torchvision', 'torchaudio', 'pytorch-cuda=12.4']
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pytorch/noarch No change
nvidia/linux-64 No change
nvidia/noarch No change
pytorch/linux-64 No change
Pinned packages:
- python 3.9.*
Transaction
Prefix: /home/yul4024/miniforge3/envs/cellseg
Updating specs:
- pytorch
- torchvision
- torchaudio
- pytorch-cuda=12.4
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────────────────────────────
+ pytorch-mutex 1.0 cuda pytorch Cached
+ llvm-openmp 15.0.7 h0cdce71_0 conda-forge Cached
+ libvpx 1.14.1 hac33072_0 conda-forge Cached
+ openh264 2.4.1 h59595ed_0 conda-forge Cached
+ gmp 6.3.0 hac33072_2 conda-forge Cached
+ x264 1!164.3095 h166bdaf_2 conda-forge Cached
+ x265 3.5 h924138e_3 conda-forge Cached
+ pugixml 1.14 h59595ed_0 conda-forge Cached
+ wayland 1.23.1 h3e06ad9_0 conda-forge Cached
+ libhwloc 2.11.1 default_hecaa2ac_1000 conda-forge Cached
+ xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge Cached
+ libabseil 20240722.0 cxx17_h5888daf_1 conda-forge Cached
+ ocl-icd 2.3.2 hd590300_1 conda-forge Cached
+ fribidi 1.0.10 h36c2ea0_0 conda-forge Cached
+ mpfr 4.2.1 h90cbb55_3 conda-forge Cached
+ tbb 2021.13.0 h84d6215_0 conda-forge Cached
+ libprotobuf 5.27.5 h5b01275_2 conda-forge Cached
+ libass 0.17.3 h1dc1e6a_0 conda-forge Cached
+ mpc 1.3.1 h24ddda3_1 conda-forge Cached
+ libopenvino 2024.4.0 hac27bb2_1 conda-forge Cached
+ mkl 2022.2.1 h84fe81f_16997 conda-forge Cached
+ gmpy2 2.1.5 py39h7196dd7_2 conda-forge Cached
+ libopenvino-auto-batch-plugin 2024.4.0 h4d9b6c2_1 conda-forge Cached
+ libopenvino-auto-plugin 2024.4.0 h4d9b6c2_1 conda-forge Cached
+ libopenvino-hetero-plugin 2024.4.0 h3f63f65_1 conda-forge Cached
+ libopenvino-intel-cpu-plugin 2024.4.0 hac27bb2_1 conda-forge Cached
+ libopenvino-intel-gpu-plugin 2024.4.0 hac27bb2_1 conda-forge Cached
+ libopenvino-intel-npu-plugin 2024.4.0 hac27bb2_1 conda-forge Cached
+ libopenvino-ir-frontend 2024.4.0 h3f63f65_1 conda-forge Cached
+ libopenvino-onnx-frontend 2024.4.0 he882d9a_1 conda-forge Cached
+ libopenvino-paddle-frontend 2024.4.0 he882d9a_1 conda-forge Cached
+ libopenvino-pytorch-frontend 2024.4.0 h5888daf_1 conda-forge Cached
+ libopenvino-tensorflow-frontend 2024.4.0 h9718a47_1 conda-forge Cached
+ libopenvino-tensorflow-lite-frontend 2024.4.0 h5888daf_1 conda-forge Cached
+ blas 1.0 mkl conda-forge Cached
+ filelock 3.16.1 pyhd8ed1ab_0 conda-forge Cached
+ mpmath 1.3.0 pyhd8ed1ab_0 conda-forge Cached
+ wayland-protocols 1.37 hd8ed1ab_0 conda-forge Cached
+ sympy 1.13.3 pypyh2585a3b_103 conda-forge Cached
+ cuda-cudart 12.4.127 0 nvidia Cached
+ cuda-cupti 12.4.127 0 nvidia Cached
+ cuda-nvrtc 12.4.127 0 nvidia Cached
+ cuda-nvtx 12.4.127 0 nvidia Cached
+ libcublas 12.4.2.65 0 nvidia Cached
+ libcufft 11.2.0.44 0 nvidia Cached
+ libcusolver 11.6.0.99 0 nvidia Cached
+ libcusparse 12.3.0.142 0 nvidia Cached
+ libnpp 12.2.5.2 0 nvidia Cached
+ libnvjitlink 12.4.99 0 nvidia Cached
+ libnvjpeg 12.3.1.89 0 nvidia Cached
+ cuda-version 12.6 3 nvidia Cached
+ libva 2.22.0 h8a09558_1 conda-forge Cached
+ ffmpeg 7.0.2 gpl_h8657690_705 conda-forge Cached
+ libnvfatbin 12.6.68 0 nvidia Cached
+ libcurand 10.3.7.68 0 nvidia Cached
+ libcufile 1.11.1.6 0 nvidia Cached
+ cuda-opencl 12.6.68 0 nvidia Cached
+ cuda-libraries 12.4.0 0 nvidia Cached
+ cuda-runtime 12.4.0 0 nvidia Cached
+ pytorch-cuda 12.4 hc786d27_6 pytorch Cached
+ pytorch 2.4.0 py3.9_cuda12.4_cudnn9.1.0_0 pytorch 1GB
+ torchtriton 3.0.0 py39 pytorch 245MB
+ torchaudio 2.4.0 py39_cu124 pytorch 7MB
+ torchvision 0.19.0 py39_cu124 pytorch 8MB
Change:
───────────────────────────────────────────────────────────────────────────────────────────────────────────
- _openmp_mutex 4.5 2_gnu conda-forge Cached
+ _openmp_mutex 4.5 2_kmp_llvm conda-forge Cached
- libblas 3.9.0 24_linux64_openblas conda-forge Cached
+ libblas 3.9.0 16_linux64_mkl conda-forge Cached
- libcblas 3.9.0 24_linux64_openblas conda-forge Cached
+ libcblas 3.9.0 16_linux64_mkl conda-forge Cached
- liblapack 3.9.0 24_linux64_openblas conda-forge Cached
+ liblapack 3.9.0 16_linux64_mkl conda-forge Cached
Summary:
Install: 64 packages
Change: 4 packages
Total download: 2GB
───────────────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n]
torchvision 8.3MB @ 50.2MB/s 0.2s
torchaudio 6.6MB @ 29.7MB/s 0.2s
torchtriton 244.9MB @ 42.3MB/s 5.8s
pytorch 1.4GB @ 91.8MB/s 15.7s
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(cellseg) ┌─[yul4024@wulab-precision1] - [~/Documents/downsample_stack] - [213]
└─[$] pip install napari-cellseg3d [8:07:20]
Collecting napari-cellseg3d
Using cached napari_cellseg3d-0.2.0-py3-none-any.whl.metadata (10 kB)
(omitted due to github comment length limit)
Installing collected packages: napari-cellseg3d
Successfully installed napari-cellseg3d-0.2.0
Thanks in advance.
