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ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

Open gionanide opened this issue 1 year ago • 0 comments

Commands to reproduce

  1. conda create --name myenv python=3.10
  2. conda activate myenv
  3. pip install --upgrade pip setuptools wheel (tried with and without)
  4. pip install fastMONAI

Python -> Python 3.10.0

####################################################################################### pip list Package Version

aiofiles 23.2.1 annotated-types 0.7.0 anyio 4.6.2.post1 asttokens 2.4.1 beautifulsoup4 4.12.3 blis 1.0.1 catalogue 2.0.10 certifi 2024.8.30 charset-normalizer 3.4.0 click 8.1.7 click-option-group 0.5.6 cloudpathlib 0.20.0 cmake 3.31.0.1 comm 0.2.2 confection 0.1.5 contourpy 1.3.1 cycler 0.12.1 cymem 2.0.8 debugpy 1.8.9 decorator 5.1.1 Deprecated 1.2.15 distro 1.9.0 exceptiongroup 1.2.2 executing 2.1.0 fastai 2.7.12 fastapi 0.115.5 fastcore 1.5.55 fastdownload 0.0.7 fastMONAI 0.4.0.2 fastprogress 1.0.3 ffmpy 0.4.0 filelock 3.16.1 fonttools 4.55.0 fsspec 2024.10.0 gdown 5.2.0 gradio 5.6.0 gradio_client 1.4.3 h11 0.14.0 httpcore 1.0.7 httpx 0.27.2 huggingface-hub 0.26.2 humanize 4.11.0 idna 3.10 imagedata 2.1.3 imageio 2.36.0 importlib-metadata 6.11.0 importlib_resources 6.4.5 ipykernel 6.29.5 ipython 8.29.0 isodate 0.7.2 itk-core 5.4.0 itk-io 5.4.0 jedi 0.19.2 Jinja2 3.1.4 joblib 1.4.2 jupyter_client 8.6.3 jupyter_core 5.7.2 kiwisolver 1.4.7 langcodes 3.5.0 language_data 1.3.0 lit 18.1.8 marisa-trie 1.2.1 markdown-it-py 3.0.0 MarkupSafe 2.1.5 matplotlib 3.9.2 matplotlib-inline 0.1.7 mdurl 0.1.2 monai 1.2.0 mpmath 1.3.0 murmurhash 1.0.10 nest_asyncio 1.6.0 networkx 3.4.2 nibabel 5.3.2 numpy 2.0.2 nvidia-cublas-cu11 11.10.3.66 nvidia-cuda-cupti-cu11 11.7.101 nvidia-cuda-nvrtc-cu11 11.7.99 nvidia-cuda-runtime-cu11 11.7.99 nvidia-cudnn-cu11 8.5.0.96 nvidia-cufft-cu11 10.9.0.58 nvidia-curand-cu11 10.2.10.91 nvidia-cusolver-cu11 11.4.0.1 nvidia-cusparse-cu11 11.7.4.91 nvidia-nccl-cu11 2.14.3 nvidia-nvtx-cu11 11.7.91 opencv-python 4.10.0.84 orjson 3.10.11 packaging 24.2 pandas 2.2.3 parso 0.8.4 pexpect 4.9.0 pickleshare 0.7.5 pillow 11.0.0 pip 24.3.1 platformdirs 4.3.6 preshed 3.0.9 progressbar2 4.5.0 prompt_toolkit 3.0.48 psutil 6.1.0 ptyprocess 0.7.0 pure_eval 0.2.3 pydantic 2.10.1 pydantic_core 2.27.1 pydicom 2.4.4 pydub 0.25.1 Pygments 2.18.0 pynetdicom 1.5.7 pyparsing 3.2.0 PySocks 1.7.1 python-dateutil 2.8.2 python-magic 0.4.27 python-multipart 0.0.12 python-utils 3.9.0 pytz 2024.2 PyWavelets 1.7.0 PyYAML 6.0.2 pyzmq 26.2.0 requests 2.32.3 rich 13.9.4 ruff 0.8.0 safehttpx 0.1.1 scikit-build 0.18.1 scikit-image 0.19.3 scikit-learn 1.5.2 scipy 1.14.1 semantic-version 2.10.0 setuptools 75.6.0 shellingham 1.5.4 SimpleITK 2.4.0 six 1.16.0 smart-open 7.0.5 sniffio 1.3.1 sortedcontainers 2.4.0 soupsieve 2.6 spacy 3.8.2 spacy-legacy 3.0.12 spacy-loggers 1.0.5 srsly 2.4.8 stack-data 0.6.2 starlette 0.41.3 sympy 1.13.3 thinc 8.3.2 threadpoolctl 3.5.0 tifffile 2024.9.20 tomli 2.1.0 tomlkit 0.12.0 torch 2.0.1 torchio 0.18.91 torchvision 0.15.2 tornado 6.4.1 tqdm 4.67.0 traitlets 5.14.3 triton 2.0.0 typer 0.13.1 typing_extensions 4.12.2 tzdata 2024.2 urllib3 2.2.3 uvicorn 0.32.1 wasabi 1.1.3 wcwidth 0.2.13 weasel 0.4.1 websockets 12.0 wheel 0.45.0 wrapt 1.17.0 xlrd 2.0.1 xnat 0.6.2 zipp 3.21.0

####################################################################################### conda list

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge aiofiles 23.2.1 pypi_0 pypi annotated-types 0.7.0 pypi_0 pypi anyio 4.6.2.post1 pypi_0 pypi asttokens 2.4.1 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pypi_0 pypi blis 1.0.1 pypi_0 pypi bzip2 1.0.8 h4bc722e_7 conda-forge ca-certificates 2024.8.30 hbcca054_0 conda-forge catalogue 2.0.10 pypi_0 pypi certifi 2024.8.30 pypi_0 pypi charset-normalizer 3.4.0 pypi_0 pypi click 8.1.7 pypi_0 pypi click-option-group 0.5.6 pypi_0 pypi cloudpathlib 0.20.0 pypi_0 pypi cmake 3.31.0.1 pypi_0 pypi comm 0.2.2 pyhd8ed1ab_0 conda-forge confection 0.1.5 pypi_0 pypi contourpy 1.3.1 pypi_0 pypi cycler 0.12.1 pypi_0 pypi cymem 2.0.8 pypi_0 pypi debugpy 1.8.9 py310hf71b8c6_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge deprecated 1.2.15 pypi_0 pypi distro 1.9.0 pypi_0 pypi exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.1.0 pyhd8ed1ab_0 conda-forge fastai 2.7.12 pypi_0 pypi fastapi 0.115.5 pypi_0 pypi fastcore 1.5.55 pypi_0 pypi fastdownload 0.0.7 pypi_0 pypi fastmonai 0.4.0.2 pypi_0 pypi fastprogress 1.0.3 pypi_0 pypi ffmpy 0.4.0 pypi_0 pypi filelock 3.16.1 pypi_0 pypi fonttools 4.55.0 pypi_0 pypi fsspec 2024.10.0 pypi_0 pypi gdown 5.2.0 pypi_0 pypi gradio 5.6.0 pypi_0 pypi gradio-client 1.4.3 pypi_0 pypi h11 0.14.0 pypi_0 pypi httpcore 1.0.7 pypi_0 pypi httpx 0.27.2 pypi_0 pypi huggingface-hub 0.26.2 pypi_0 pypi humanize 4.11.0 pypi_0 pypi idna 3.10 pypi_0 pypi imagedata 2.1.3 pypi_0 pypi imageio 2.36.0 pypi_0 pypi importlib-metadata 6.11.0 pypi_0 pypi importlib-resources 6.4.5 pypi_0 pypi ipykernel 6.29.5 pyh3099207_0 conda-forge ipython 8.29.0 pyh707e725_0 conda-forge isodate 0.7.2 pypi_0 pypi itk-core 5.4.0 pypi_0 pypi itk-io 5.4.0 pypi_0 pypi jedi 0.19.2 pyhff2d567_0 conda-forge jinja2 3.1.4 pypi_0 pypi joblib 1.4.2 pypi_0 pypi jupyter_client 8.6.3 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 pyh31011fe_1 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.7 pypi_0 pypi krb5 1.21.3 h659f571_0 conda-forge langcodes 3.5.0 pypi_0 pypi language-data 1.3.0 pypi_0 pypi ld_impl_linux-64 2.43 h712a8e2_2 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc 14.2.0 h77fa898_1 conda-forge libgcc-ng 14.2.0 h69a702a_1 conda-forge libgomp 14.2.0 h77fa898_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libsodium 1.0.20 h4ab18f5_0 conda-forge libsqlite 3.47.0 hadc24fc_1 conda-forge libstdcxx 14.2.0 hc0a3c3a_1 conda-forge libstdcxx-ng 14.2.0 h4852527_1 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libzlib 1.3.1 hb9d3cd8_2 conda-forge lit 18.1.8 pypi_0 pypi marisa-trie 1.2.1 pypi_0 pypi markdown-it-py 3.0.0 pypi_0 pypi markupsafe 2.1.5 pypi_0 pypi matplotlib 3.9.2 pypi_0 pypi matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mdurl 0.1.2 pypi_0 pypi monai 1.2.0 pypi_0 pypi mpmath 1.3.0 pypi_0 pypi murmurhash 1.0.10 pypi_0 pypi ncurses 6.5 he02047a_1 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge networkx 3.4.2 pypi_0 pypi nibabel 5.3.2 pypi_0 pypi numpy 2.0.2 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 opencv-python 4.10.0.84 pypi_0 pypi openssl 3.4.0 hb9d3cd8_0 conda-forge orjson 3.10.11 pypi_0 pypi packaging 24.2 pyhff2d567_1 conda-forge pandas 2.2.3 pypi_0 pypi parso 0.8.4 pyhd8ed1ab_0 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 11.0.0 pypi_0 pypi pip 24.3.1 pyh8b19718_0 conda-forge platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge preshed 3.0.9 pypi_0 pypi progressbar2 4.5.0 pypi_0 pypi prompt-toolkit 3.0.48 pyha770c72_0 conda-forge psutil 6.1.0 py310ha75aee5_0 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge pydantic 2.10.1 pypi_0 pypi pydantic-core 2.27.1 pypi_0 pypi pydicom 2.4.4 pypi_0 pypi pydub 0.25.1 pypi_0 pypi pygments 2.18.0 pyhd8ed1ab_0 conda-forge pynetdicom 1.5.7 pypi_0 pypi pyparsing 3.2.0 pypi_0 pypi pysocks 1.7.1 pypi_0 pypi python 3.10.0 h543edf9_3_cpython conda-forge python-dateutil 2.8.2 pypi_0 pypi python-magic 0.4.27 pypi_0 pypi python-multipart 0.0.12 pypi_0 pypi python-utils 3.9.0 pypi_0 pypi python_abi 3.10 5_cp310 conda-forge pytz 2024.2 pypi_0 pypi pywavelets 1.7.0 pypi_0 pypi pyyaml 6.0.2 pypi_0 pypi pyzmq 26.2.0 py310h71f11fc_3 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.32.3 pypi_0 pypi rich 13.9.4 pypi_0 pypi ruff 0.8.0 pypi_0 pypi safehttpx 0.1.1 pypi_0 pypi scikit-build 0.18.1 pypi_0 pypi scikit-image 0.19.3 pypi_0 pypi scikit-learn 1.5.2 pypi_0 pypi scipy 1.14.1 pypi_0 pypi semantic-version 2.10.0 pypi_0 pypi setuptools 75.6.0 pyhff2d567_0 conda-forge shellingham 1.5.4 pypi_0 pypi simpleitk 2.4.0 pypi_0 pypi six 1.16.0 pyh6c4a22f_0 conda-forge smart-open 7.0.5 pypi_0 pypi sniffio 1.3.1 pypi_0 pypi sortedcontainers 2.4.0 pypi_0 pypi soupsieve 2.6 pypi_0 pypi spacy 3.8.2 pypi_0 pypi spacy-legacy 3.0.12 pypi_0 pypi spacy-loggers 1.0.5 pypi_0 pypi sqlite 3.47.0 h9eae976_1 conda-forge srsly 2.4.8 pypi_0 pypi stack_data 0.6.2 pyhd8ed1ab_0 conda-forge starlette 0.41.3 pypi_0 pypi sympy 1.13.3 pypi_0 pypi thinc 8.3.2 pypi_0 pypi threadpoolctl 3.5.0 pypi_0 pypi tifffile 2024.9.20 pypi_0 pypi tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.1.0 pypi_0 pypi tomlkit 0.12.0 pypi_0 pypi torch 2.0.1 pypi_0 pypi torchio 0.18.91 pypi_0 pypi torchvision 0.15.2 pypi_0 pypi tornado 6.4.1 py310ha75aee5_1 conda-forge tqdm 4.67.0 pypi_0 pypi traitlets 5.14.3 pyhd8ed1ab_0 conda-forge triton 2.0.0 pypi_0 pypi typer 0.13.1 pypi_0 pypi typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024.2 pypi_0 pypi urllib3 2.2.3 pypi_0 pypi uvicorn 0.32.1 pypi_0 pypi wasabi 1.1.3 pypi_0 pypi wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge weasel 0.4.1 pypi_0 pypi websockets 12.0 pypi_0 pypi wheel 0.45.0 pyhd8ed1ab_0 conda-forge wrapt 1.17.0 pypi_0 pypi xlrd 2.0.1 pypi_0 pypi xnat 0.6.2 pypi_0 pypi xz 5.2.6 h166bdaf_0 conda-forge zeromq 4.3.5 h3b0a872_7 conda-forge zipp 3.21.0 pyhd8ed1ab_0 conda-forge

####################################################################################### ERROR ####################################################################################### from fastMONAI.vision_all import * #######################################################################################

ValueError Traceback (most recent call last) Cell In[2], line 1 ----> 1 from fastMONAI.vision_all import *

File ~/anaconda3/envs/fastmonai/lib/python3.10/site-packages/fastMONAI/vision_all.py:7 5 from .vision_loss import * 6 from .vision_metrics import * ----> 7 from .vision_inference import * 8 from .utils import * 9 from .external_data import *

File ~/anaconda3/envs/fastmonai/lib/python3.10/site-packages/fastMONAI/vision_inference.py:13 11 import numpy as np 12 from scipy.ndimage import label ---> 13 from skimage.morphology import remove_small_objects 14 from SimpleITK import DICOMOrient, GetArrayFromImage 15 from torchio import Resize, Image

File ~/anaconda3/envs/fastmonai/lib/python3.10/site-packages/skimage/init.py:151 147 # We are not importing the rest of the scikit during the build 148 # process, as it may not be compiled yet 149 else: 150 try: --> 151 from ._shared import geometry 152 del geometry 153 except ImportError as e:

File ~/anaconda3/envs/fastmonai/lib/python3.10/site-packages/skimage/_shared/geometry.pyx:1, in init skimage._shared.geometry()

ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

gionanide avatar Nov 22 '24 13:11 gionanide