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kevinjohncutler / omnipose

Omnipose: a high-precision solution for morphology-independent cell segmentation
https://omnipose.readthedocs.io
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ImportError: cannot import name 'ifft' from 'scipy' #78

Open romainGuiet opened 4 months ago

romainGuiet commented 4 months ago

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

romainGuiet commented 4 months ago

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

romainGuiet commented 4 months ago

and pip install torch_optimizer to use -RAdam

tinevez commented 3 months ago

Can reproduce the bug.

tinevez commented 3 months ago

Current workaround suggested by @lacan :

The fix also works for me.

romainGuiet commented 3 months ago

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

JulianoGianlupi commented 2 months ago

pip install torch_optimizer

I can confirm the bug and the solution. The solution also works with python 3.10.13

Nicolas-G-Biologeek commented 2 months ago

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
QuentinRapilly commented 1 month ago

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 ?

MoZhou519 commented 1 week ago

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

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!!