omnipose
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kevinjohncutler
ImportError: cannot import name 'ifft' from 'scipy'
Dear omnipose team,
Thank you for making your tool available for the community!
Following your installation instructions I created a new environment :
mamba create -n omnipose-106 'python==3.10.12' pytorch torchvision pytorch-cuda=11.8 -c pytorch -c nvidia -y
mamba activate omnipose-106
pip install omnipose
and to check the installation I ran: omnipose --help which returns :
Traceback (most recent call last):
File "D:\conda\conda-envs\omnipose-106\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "D:\conda\conda-envs\omnipose-106\lib\runpy.py", line 86, in _run_code
exec(code, run_globals)
File "D:\conda\conda-envs\omnipose-106\Scripts\omnipose.exe\__main__.py", line 4, in <module>
File "D:\conda\conda-envs\omnipose-106\lib\site-packages\omnipose\__init__.py", line 1, in <module>
from . import core, utils, loss, plot, misc, cli, data, gpu
File "D:\conda\conda-envs\omnipose-106\lib\site-packages\omnipose\misc.py", line 648, in <module>
import peakdetect
File "D:\conda\conda-envs\omnipose-106\lib\site-packages\peakdetect\__init__.py", line 3, in <module>
from .peakdetect import *
File "D:\conda\conda-envs\omnipose-106\lib\site-packages\peakdetect\peakdetect.py", line 5, in <module>
from scipy import fft, ifft
ImportError: cannot import name 'ifft' from 'scipy' (D:\conda\conda-envs\omnipose-106\lib\site-packages\scipy\__init__.py)
I tried to pip install scipy but it returns :
Requirement already satisfied: scipy in d:\conda\conda-envs\omnipose-106\lib\site-packages (1.12.0)
Requirement already satisfied: numpy<1.29.0,>=1.22.4 in d:\conda\conda-envs\omnipose-106\lib\site-packages (from scipy) (1.26.3)
Please find below the packages content :
# packages in environment at D:\conda\conda-envs\omnipose-106:
#
# Name Version Build Channel
blas 1.0 mkl
brotli-python 1.0.9 py310hd77b12b_7
bzip2 1.0.8 he774522_0
ca-certificates 2023.12.12 haa95532_0
certifi 2024.2.2 py310haa95532_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
colorama 0.4.6 pypi_0 pypi
contourpy 1.2.0 pypi_0 pypi
cuda-cccl 12.3.101 0 nvidia
cuda-cudart 11.8.89 0 nvidia
cuda-cudart-dev 11.8.89 0 nvidia
cuda-cupti 11.8.87 0 nvidia
cuda-libraries 11.8.0 0 nvidia
cuda-libraries-dev 11.8.0 0 nvidia
cuda-nvrtc 11.8.89 0 nvidia
cuda-nvrtc-dev 11.8.89 0 nvidia
cuda-nvtx 11.8.86 0 nvidia
cuda-profiler-api 12.3.101 0 nvidia
cuda-runtime 11.8.0 0 nvidia
cycler 0.12.1 pypi_0 pypi
edt 2.4.0 pypi_0 pypi
fastremap 1.14.1 pypi_0 pypi
filelock 3.13.1 py310haa95532_0
fonttools 4.49.0 pypi_0 pypi
freetype 2.12.1 ha860e81_0
fsspec 2024.2.0 pypi_0 pypi
gmpy2 2.1.2 py310h7f96b67_0
idna 3.4 py310haa95532_0
igraph 0.11.4 pypi_0 pypi
imageio 2.34.0 pypi_0 pypi
intel-openmp 2023.1.0 h59b6b97_46320
jinja2 3.1.3 py310haa95532_0
joblib 1.3.2 pypi_0 pypi
jpeg 9e h2bbff1b_1
kiwisolver 1.4.5 pypi_0 pypi
lazy-loader 0.3 pypi_0 pypi
lerc 3.0 hd77b12b_0
libcublas 11.11.3.6 0 nvidia
libcublas-dev 11.11.3.6 0 nvidia
libcufft 10.9.0.58 0 nvidia
libcufft-dev 10.9.0.58 0 nvidia
libcurand 10.3.4.107 0 nvidia
libcurand-dev 10.3.4.107 0 nvidia
libcusolver 11.4.1.48 0 nvidia
libcusolver-dev 11.4.1.48 0 nvidia
libcusparse 11.7.5.86 0 nvidia
libcusparse-dev 11.7.5.86 0 nvidia
libdeflate 1.17 h2bbff1b_1
libffi 3.4.4 hd77b12b_0
libjpeg-turbo 2.0.0 h196d8e1_0
libnpp 11.8.0.86 0 nvidia
libnpp-dev 11.8.0.86 0 nvidia
libnvjpeg 11.9.0.86 0 nvidia
libnvjpeg-dev 11.9.0.86 0 nvidia
libpng 1.6.39 h8cc25b3_0
libtiff 4.5.1 hd77b12b_0
libuv 1.44.2 h2bbff1b_0
libwebp-base 1.3.2 h2bbff1b_0
llvmlite 0.42.0 pypi_0 pypi
lz4-c 1.9.4 h2bbff1b_0
mahotas 1.4.13 pypi_0 pypi
markupsafe 2.1.3 py310h2bbff1b_0
matplotlib 3.8.3 pypi_0 pypi
mgen 1.2.1 pypi_0 pypi
mkl 2023.1.0 h6b88ed4_46358
mkl-service 2.4.0 py310h2bbff1b_1
mkl_fft 1.3.8 py310h2bbff1b_0
mkl_random 1.2.4 py310h59b6b97_0
mpc 1.1.0 h7edee0f_1
mpfr 4.0.2 h62dcd97_1
mpir 3.0.0 hec2e145_1
mpmath 1.3.0 py310haa95532_0
ncolor 1.2.1 pypi_0 pypi
networkx 3.1 py310haa95532_0
numba 0.59.0 pypi_0 pypi
numpy 1.26.3 py310h055cbcc_0
numpy-base 1.26.3 py310h65a83cf_0
omnipose 1.0.6 pypi_0 pypi
opencv-python-headless 4.9.0.80 pypi_0 pypi
openjpeg 2.4.0 h4fc8c34_0
openssl 3.0.13 h2bbff1b_0
packaging 23.2 pypi_0 pypi
pandas 2.2.0 pypi_0 pypi
pbr 6.0.0 pypi_0 pypi
peakdetect 1.2 pypi_0 pypi
pillow 10.2.0 py310h2bbff1b_0
pip 23.3.1 py310haa95532_0
pyparsing 3.1.1 pypi_0 pypi
pysocks 1.7.1 py310haa95532_0
python 3.10.12 he1021f5_0
python-dateutil 2.8.2 pypi_0 pypi
pytorch 2.2.0 py3.10_cuda11.8_cudnn8_0 pytorch
pytorch-cuda 11.8 h24eeafa_5 pytorch
pytorch-mutex 1.0 cuda pytorch
pytz 2024.1 pypi_0 pypi
pyyaml 6.0.1 py310h2bbff1b_0
requests 2.31.0 py310haa95532_1
scikit-image 0.22.0 pypi_0 pypi
scikit-learn 1.4.1.post1 pypi_0 pypi
scipy 1.12.0 pypi_0 pypi
setuptools 68.2.2 py310haa95532_0
six 1.16.0 pypi_0 pypi
sqlite 3.41.2 h2bbff1b_0
sympy 1.12 py310haa95532_0
tbb 2021.8.0 h59b6b97_0
texttable 1.7.0 pypi_0 pypi
threadpoolctl 3.3.0 pypi_0 pypi
tifffile 2024.2.12 pypi_0 pypi
tk 8.6.12 h2bbff1b_0
torchvf 0.1.4 pypi_0 pypi
torchvision 0.17.0 pypi_0 pypi
tqdm 4.66.2 pypi_0 pypi
typing_extensions 4.9.0 py310haa95532_1
tzdata 2024.1 pypi_0 pypi
urllib3 2.1.0 py310haa95532_1
vc 14.2 h21ff451_1
vs2015_runtime 14.27.29016 h5e58377_2
wheel 0.41.2 py310haa95532_0
win_inet_pton 1.1.0 py310haa95532_0
xz 5.4.5 h8cc25b3_0
yaml 0.2.5 he774522_0
zlib 1.2.13 h8cc25b3_0
zstd 1.5.5 hd43e919_0
Do you have any recommendations ?
Best regards,
Romain
Current workaround suggested by @lacan :
mamba create -n omnipose-106_2 'python==3.9.18' pytorch torchvision pytorch-cuda=11.8 -c pytorch -c nvidia -y
mamba activate omnipose-106_2
git clone https://github.com/kevinjohncutler/omnipose.git
cd omnipose
pip install -e .
But I had to also add : pip install aicsimageio
This install works with GPU support !
Cheers
R
We recently observed an issue when calling omnipose from QuPath on Windows (but it works fine on Linux / WSL) if installation is made with conda/mamba:
mamba create -n omnipose 'python==3.9.18' pytorch torchvision pytorch-cuda=11.8 -c pytorch -c nvidia -y
mamba activate omnipose
pip install git+https://github.com/kevinjohncutler/omnipose.git@bf456e475be4490821f782cb785bbc943bb12abb
pip install aicsimageio torch_optimizer
BUT if installation is done with pip it works fine (but installation is a bit messier)
mamba create -n omnipose python=3.9 -y
mamba activate omnipose
pip install git+https://github.com/kevinjohncutler/omnipose.git@bf456e475be4490821f782cb785bbc943bb12abb
pip uninstall torch torchvision
pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118
pip install aicsimageio torch_optimizer scikit-image
We documented the issue on our wiki
pip install torch_optimizer
I can confirm the bug and the solution. The solution also works with python 3.10.13
Thanks Romain it's fixed and work for me too with these little correction for anaconda distribution on windows
conda create -n omnipose 'python==3.9.18' pytorch torchvision pytorch-cuda=11.8 -c pytorch -c nvidia
conda activate omnipose
conda install -c anaconda git
pip install git+https://github.com/kevinjohncutler/omnipose.git@bf456e475be4490821f782cb785bbc943bb12abb
pip uninstall torch torchvision
pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118
pip install aicsimageio torch_optimizer scikit-image
Hi everyone, I encountered the same issue.
After some investigations, I realized that there are a fft and ifft in scipy but they are in scipy.fft.
https://docs.scipy.org/doc/scipy/reference/generated/scipy.fft.fft.html
Shouldn't the code be:
from scipy.ftt import fft, ifft
instead of:
from scipy import fft, ifft ?
Current workaround suggested by @lacan :
mamba create -n omnipose-106_2 'python==3.9.18' pytorch torchvision pytorch-cuda=11.8 -c pytorch -c nvidia -y mamba activate omnipose-106_2 git clone https://github.com/kevinjohncutler/omnipose.git cd omnipose pip install -e .But I had to also add :
pip install aicsimageioThis install works with GPU support !
Cheers
R
Hi everyone,
I tried this method on my iMac with M3 chip and ran Omnipose from my terminal, but got error message as:
pkg_resources.DistributionNotFound: The 'omnipose' distribution was not found and is required by the application
Does anyone know what's going wrong? Thanks a lot!!
Hi, I think @QuentinRapilly has the right idea. Bit it looks like the import code is in the peakdetect package, rather than omnipose. Unfortunately that package doesn't seem to be updated anymore, as far as I can tell.
