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computational-cell-analytics / micro-sam

Segment Anything for Microscopy
https://computational-cell-analytics.github.io/micro-sam/
MIT License
359 stars 43 forks source link

Error: Starting annotator throws error #237

Closed jo-mueller closed 1 year ago

jo-mueller commented 1 year ago

Hi all,

I was just trying to use the micro_sam annotator to play around with it. I installed the plugin according to the documentation into an environment with pytorch=2.0.1. Upon typing the micro_sam.annotator command in the terminal, I get this error:

(pytorch) E:\BiAPoL\Projects\napari-segment-anything>micro_sam.annotator
Traceback (most recent call last):
  File "C:\Users\johan\Anaconda3\envs\pytorch\Scripts\micro_sam.annotator-script.py", line 5, in <module>
    from micro_sam.sam_annotator.annotator import main
  File "C:\Users\johan\Anaconda3\envs\pytorch\lib\site-packages\micro_sam\sam_annotator\__init__.py", line 5, in <module>
    from .annotator import annotator
  File "C:\Users\johan\Anaconda3\envs\pytorch\lib\site-packages\micro_sam\sam_annotator\annotator.py", line 13, in <module>
    from .annotator_2d import annotator_2d
  File "C:\Users\johan\Anaconda3\envs\pytorch\lib\site-packages\micro_sam\sam_annotator\annotator_2d.py", line 11, in <module>
    from .. import instance_segmentation, util
  File "C:\Users\johan\Anaconda3\envs\pytorch\lib\site-packages\micro_sam\instance_segmentation.py", line 35, in <module>
    from ._vendored import batched_mask_to_box, mask_to_rle_pytorch
  File "C:\Users\johan\Anaconda3\envs\pytorch\lib\site-packages\micro_sam\_vendored.py", line 14, in <module>
    from numba import njit
  File "C:\Users\johan\Anaconda3\envs\pytorch\lib\site-packages\numba\__init__.py", line 43, in <module>
    from numba.np.ufunc import (vectorize, guvectorize, threading_layer,
  File "C:\Users\johan\Anaconda3\envs\pytorch\lib\site-packages\numba\np\ufunc\__init__.py", line 3, in <module>
    from numba.np.ufunc.decorators import Vectorize, GUVectorize, vectorize, guvectorize
  File "C:\Users\johan\Anaconda3\envs\pytorch\lib\site-packages\numba\np\ufunc\decorators.py", line 3, in <module>
    from numba.np.ufunc import _internal
SystemError: initialization of _internal failed without raising an exception

Napari version

napari: 0.4.18
Platform: Windows-10-10.0.19045-SP0
Python: 3.9.18 | packaged by conda-forge | (main, Aug 30 2023, 03:40:31) [MSC v.1929 64 bit (AMD64)]
Qt: 5.15.8
PyQt5: 5.15.9
NumPy: 1.26.0
SciPy: 1.11.3
Dask: 2023.10.0
VisPy: 0.12.2
magicgui: 0.7.3
superqt: 0.6.1
in-n-out: 0.1.9
app-model: 0.2.2
npe2: 0.7.2

OpenGL:
- GL version: 4.6.0 NVIDIA 537.58
- MAX_TEXTURE_SIZE: 32768

Screens:
- screen 1: resolution 2560x1440, scale 1.0
- screen 2: resolution 1920x1080, scale 1.0

Settings path:
- C:\Users\johan\AppData\Local\napari\pytorch_5a753838a770f30cc4cbc260f3688307fd5899f1\settings.yaml

Versions:

absl-py                   2.0.0              pyhd8ed1ab_0    conda-forge
affogato                  0.3.3            py39h32e6231_3    conda-forge
aiohttp                   3.8.6            py39ha55989b_1    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
alabaster                 0.7.13                   pypi_0    pypi
albumentations            1.3.1              pyhd8ed1ab_0    conda-forge
ansicon                   1.89.0           py39hcbf5309_7    conda-forge
anyio                     4.0.0              pyhd8ed1ab_0    conda-forge
aom                       3.6.1                h63175ca_0    conda-forge
app-model                 0.2.2                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asciitree                 0.3.3                      py_2    conda-forge
asttokens                 2.4.0              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
babel                     2.13.0                   pypi_0    pypi
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backoff                   2.2.1              pyhd8ed1ab_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bioimageio.core           0.5.9              pyhd8ed1ab_0    conda-forge
bioimageio.spec           0.4.9.post4        pyhd8ed1ab_0    conda-forge
blas                      2.118                       mkl    conda-forge
blas-devel                3.9.0              18_win64_mkl    conda-forge
blessed                   1.19.1             pyh95a074a_2    conda-forge
blinker                   1.6.3              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               hdccc3a2_0    conda-forge
brotli                    1.1.0                hcfcfb64_1    conda-forge
brotli-bin                1.1.0                hcfcfb64_1    conda-forge
brotli-python             1.1.0            py39h99910a6_1    conda-forge
bzip2                     1.0.8                h8ffe710_4    conda-forge
c-ares                    1.20.1               hcfcfb64_0    conda-forge
c-blosc2                  2.10.5               h183a6f4_0    conda-forge
ca-certificates           2023.08.22           haa95532_0
cachecontrol              0.13.1             pyhd8ed1ab_0    conda-forge
cachecontrol-with-filecache 0.13.1             pyhd8ed1ab_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.1              pyhd8ed1ab_0    conda-forge
cachey                    0.2.1                    pypi_0    pypi
cairo                     1.18.0               h1fef639_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.16.0           py39ha55989b_0    conda-forge
charls                    2.4.2                h1537add_0    conda-forge
charset-normalizer        3.3.0              pyhd8ed1ab_0    conda-forge
cleo                      2.0.1              pyhd8ed1ab_0    conda-forge
click                     8.1.7           win_pyh7428d3b_0    conda-forge
cloudpickle               3.0.0                    pypi_0    pypi
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
coloredlogs               15.0.1           py39hcbf5309_2    conda-forge
comm                      0.1.4              pyhd8ed1ab_0    conda-forge
contourpy                 1.1.1            py39h1f6ef14_1    conda-forge
crashtest                 0.4.1              pyhd8ed1ab_0    conda-forge
croniter                  1.4.1              pyhd8ed1ab_0    conda-forge
cryptography              41.0.4           py39hb6bd5e6_0    conda-forge
cuda-cccl                 12.2.140                      0    nvidia
cuda-cudart               12.1.105                      0    nvidia
cuda-cudart-dev           12.1.105                      0    nvidia
cuda-cupti                12.1.105                      0    nvidia
cuda-libraries            12.1.0                        0    nvidia
cuda-libraries-dev        12.1.0                        0    nvidia
cuda-nvrtc                12.1.105                      0    nvidia
cuda-nvrtc-dev            12.1.105                      0    nvidia
cuda-nvtx                 12.1.105                      0    nvidia
cuda-opencl               12.2.140                      0    nvidia
cuda-opencl-dev           12.2.140                      0    nvidia
cuda-profiler-api         12.2.140                      0    nvidia
cuda-runtime              12.1.0                        0    nvidia
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cython                    3.0.4            py39h99910a6_0    conda-forge
dask                      2023.10.0                pypi_0    pypi
dateutils                 0.6.12                     py_0    conda-forge
dav1d                     1.2.1                hcfcfb64_0    conda-forge
debugpy                   1.8.0            py39h99910a6_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
deepdiff                  6.6.0              pyhd8ed1ab_0    conda-forge
distlib                   0.3.7              pyhd8ed1ab_0    conda-forge
docstring-parser          0.15                     pypi_0    pypi
docutils                  0.17.1                   pypi_0    pypi
dulwich                   0.21.6           py39ha55989b_2    conda-forge
efficientnet-pytorch      0.7.1              pyhd8ed1ab_1    conda-forge
et_xmlfile                1.1.0              pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h63175ca_1    conda-forge
fastapi                   0.99.1             pyhd8ed1ab_0    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
ffmpeg                    6.0.0           gpl_h1627b0f_105    conda-forge
fftw                      3.3.10          nompi_h38027f0_108    conda-forge
filelock                  3.12.4             pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               hbde0cde_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.43.1           py39ha55989b_0    conda-forge
freeglut                  3.2.2                h63175ca_2    conda-forge
freetype                  2.12.1               hdaf720e_2    conda-forge
freetype-py               2.4.0                    pypi_0    pypi
fribidi                   1.0.10               h8d14728_0    conda-forge
frozenlist                1.4.0            py39ha55989b_1    conda-forge
fsspec                    2023.9.2           pyh1a96a4e_0    conda-forge
getopt-win32              0.1                  hcfcfb64_1    conda-forge
gettext                   0.21.1               h5728263_0    conda-forge
giflib                    5.2.1                h64bf75a_3    conda-forge
glib                      2.78.0               h12be248_0    conda-forge
glib-tools                2.78.0               h12be248_0    conda-forge
glpk                      5.0                  h8ffe710_0    conda-forge
google-auth               2.23.3             pyhca7485f_0    conda-forge
google-auth-oauthlib      1.0.0              pyhd8ed1ab_1    conda-forge
graphite2                 1.3.14               hd77b12b_1
graphviz                  8.1.0                h51cb2cd_0    conda-forge
grpcio                    1.58.1           py39hd28a505_0    conda-forge
gst-plugins-base          1.22.6               h001b923_2    conda-forge
gstreamer                 1.22.6               hb4038d2_2    conda-forge
gts                       0.7.6                h6b5321d_4    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h5py                      3.10.0          nompi_py39h7371b1f_100    conda-forge
harfbuzz                  8.2.1                h7ab893a_0    conda-forge
hdf5                      1.14.2          nompi_h73e8ff5_100    conda-forge
heapdict                  1.0.1                    pypi_0    pypi
hsluv                     5.0.4                    pypi_0    pypi
huggingface_hub           0.18.0             pyhd8ed1ab_0    conda-forge
humanfriendly             10.0             py39hcbf5309_5    conda-forge
icu                       73.2                 h63175ca_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagecodecs               2023.9.18        py39h445c58b_2    conda-forge
imageio                   2.31.5             pyh8c1a49c_0    conda-forge
imagesize                 1.4.1                    pypi_0    pypi
imath                     3.1.9                h12be248_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib-resources       6.1.0              pyhd8ed1ab_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       6.1.0              pyhd8ed1ab_0    conda-forge
in-n-out                  0.1.9                    pypi_0    pypi
inquirer                  3.1.3              pyhd8ed1ab_0    conda-forge
intel-openmp              2023.2.0         h57928b3_50496    conda-forge
ipykernel                 6.25.2             pyh60829e3_0    conda-forge
ipython                   8.16.1             pyh5737063_0    conda-forge
ipython-genutils          0.2.0                    pypi_0    pypi
itsdangerous              2.1.2              pyhd8ed1ab_0    conda-forge
jaraco.classes            3.3.0              pyhd8ed1ab_0    conda-forge
jasper                    4.0.0                h28f2b1a_2    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jinxed                    1.2.0              pyh95a074a_0    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            8.4.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.4.0            py39hcbf5309_0    conda-forge
jxrlib                    1.1                  h8ffe710_2    conda-forge
keyring                   24.2.0           py39hcbf5309_1    conda-forge
khronos-opencl-icd-loader 2023.04.17           h64bf75a_0    conda-forge
kiwisolver                1.4.5            py39h1f6ef14_1    conda-forge
kornia                    0.7.0              pyhd8ed1ab_0    conda-forge
krb5                      1.21.2               heb0366b_0    conda-forge
lazy_loader               0.3                pyhd8ed1ab_0    conda-forge
lcms2                     2.15                 h67d730c_3    conda-forge
lemon                     1.3.1                h5be432b_7    conda-forge
lerc                      4.0.0                h63175ca_0    conda-forge
libabseil                 20230802.1      cxx17_h63175ca_0    conda-forge
libaec                    1.1.2                h63175ca_1    conda-forge
libavif                   1.0.1                hea6d26e_2    conda-forge
libblas                   3.9.0              18_win64_mkl    conda-forge
libboost                  1.82.0               h65993cd_6    conda-forge
libboost-python           1.82.0           py39h5c3ab46_6    conda-forge
libbrotlicommon           1.1.0                hcfcfb64_1    conda-forge
libbrotlidec              1.1.0                hcfcfb64_1    conda-forge
libbrotlienc              1.1.0                hcfcfb64_1    conda-forge
libcblas                  3.9.0              18_win64_mkl    conda-forge
libclang                  15.0.7          default_h77d9078_3    conda-forge
libclang13                15.0.7          default_h77d9078_3    conda-forge
libcublas                 12.1.0.26                     0    nvidia
libcublas-dev             12.1.0.26                     0    nvidia
libcufft                  11.0.2.4                      0    nvidia
libcufft-dev              11.0.2.4                      0    nvidia
libcurand                 10.3.3.141                    0    nvidia
libcurand-dev             10.3.3.141                    0    nvidia
libcurl                   8.4.0                hd5e4a3a_0    conda-forge
libcusolver               11.4.4.55                     0    nvidia
libcusolver-dev           11.4.4.55                     0    nvidia
libcusparse               12.0.2.55                     0    nvidia
libcusparse-dev           12.0.2.55                     0    nvidia
libdeflate                1.19                 hcfcfb64_0    conda-forge
libexpat                  2.5.0                h63175ca_1    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libgd                     2.3.3                h312136b_9    conda-forge
libglib                   2.78.0               he8f3873_0    conda-forge
libgrpc                   1.58.1               h43eea02_0    conda-forge
libhwloc                  2.9.3           default_haede6df_1009    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
libjpeg-turbo             3.0.0                hcfcfb64_1    conda-forge
liblapack                 3.9.0              18_win64_mkl    conda-forge
liblapacke                3.9.0              18_win64_mkl    conda-forge
libnpp                    12.0.2.50                     0    nvidia
libnpp-dev                12.0.2.50                     0    nvidia
libnvjitlink              12.1.105                      0    nvidia
libnvjitlink-dev          12.1.105                      0    nvidia
libnvjpeg                 12.1.1.14                     0    nvidia
libnvjpeg-dev             12.1.1.14                     0    nvidia
libogg                    1.3.4                h8ffe710_1    conda-forge
libopencv                 4.8.1            py39he2c65a9_2    conda-forge
libopenvino               2023.1.0             h63175ca_0    conda-forge
libopenvino-auto-batch-plugin 2023.1.0             h63175ca_0    conda-forge
libopenvino-auto-plugin   2023.1.0             h63175ca_0    conda-forge
libopenvino-hetero-plugin 2023.1.0             h63175ca_0    conda-forge
libopenvino-intel-cpu-plugin 2023.1.0             h63175ca_0    conda-forge
libopenvino-intel-gpu-plugin 2023.1.0             h63175ca_0    conda-forge
libopenvino-ir-frontend   2023.1.0             h63175ca_0    conda-forge
libopenvino-onnx-frontend 2023.1.0             h63175ca_0    conda-forge
libopenvino-paddle-frontend 2023.1.0             h63175ca_0    conda-forge
libopenvino-pytorch-frontend 2023.1.0             h63175ca_0    conda-forge
libopenvino-tensorflow-frontend 2023.1.0             h63175ca_0    conda-forge
libopenvino-tensorflow-lite-frontend 2023.1.0             h63175ca_0    conda-forge
libopus                   1.3.1                h8ffe710_1    conda-forge
libpng                    1.6.39               h19919ed_0    conda-forge
libprotobuf               4.24.3               hb8276f3_0    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.43.2               hcfcfb64_0    conda-forge
libssh2                   1.11.0               h7dfc565_0    conda-forge
libtiff                   4.6.0                h6e2ebb7_2    conda-forge
libuv                     1.44.2               hcfcfb64_1    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libwebp                   1.3.2                hcfcfb64_1    conda-forge
libwebp-base              1.3.2                hcfcfb64_0    conda-forge
libxcb                    1.15                 hcd874cb_0    conda-forge
libxml2                   2.11.5               hc3477c8_1    conda-forge
libzlib                   1.2.13               hcfcfb64_5    conda-forge
libzopfli                 1.0.3                h0e60522_0    conda-forge
lightning                 2.0.9.post0        pyhd8ed1ab_0    conda-forge
lightning-cloud           0.5.39             pyhd8ed1ab_0    conda-forge
lightning-utilities       0.9.0              pyhd8ed1ab_0    conda-forge
llvmlite                  0.36.0           py39ha0cd8c8_0    conda-forge
locket                    1.0.0                    pypi_0    pypi
lz4-c                     1.9.4                hcfcfb64_0    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
magicgui                  0.7.3                    pypi_0    pypi
markdown                  3.5                pyhd8ed1ab_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.3            py39ha55989b_1    conda-forge
marshmallow               3.20.1             pyhd8ed1ab_0    conda-forge
marshmallow-jsonschema    0.13.0             pyhd8ed1ab_0    conda-forge
marshmallow-union         0.1.15.post1       pyhd8ed1ab_0    conda-forge
matplotlib                3.8.0            py39hcbf5309_2    conda-forge
matplotlib-base           3.8.0            py39hf19769e_2    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
micro_sam                 0.3.0post1         pyhd8ed1ab_0    conda-forge
mkl                       2022.1.0           h6a75c08_874    conda-forge
mkl-devel                 2022.1.0           h57928b3_875    conda-forge
mkl-include               2022.1.0           h6a75c08_874    conda-forge
more-itertools            10.1.0             pyhd8ed1ab_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
mrcfile                   1.4.3              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.6            py39h1f6ef14_0    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
multidict                 6.0.4            py39ha55989b_1    conda-forge
munch                     4.0.0              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy-extensions           1.0.0                    pypi_0    pypi
napari                    0.4.18                   pypi_0    pypi
napari-console            0.0.8                    pypi_0    pypi
napari-plugin-engine      0.2.0                    pypi_0    pypi
napari-segment-anything   0.1.4                    pypi_0    pypi
napari-svg                0.1.10                   pypi_0    pypi
nest-asyncio              1.5.8              pyhd8ed1ab_0    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
nifty                     1.2.1            py39h9fe8808_4    conda-forge
npe2                      0.7.2                    pypi_0    pypi
numba                     0.53.0           py39hf11a4ad_0
numcodecs                 0.12.1           py39h99910a6_0    conda-forge
numpy                     1.26.0           py39hddb5d58_0    conda-forge
numpydoc                  1.5.0                    pypi_0    pypi
oauthlib                  3.2.2              pyhd8ed1ab_0    conda-forge
onnx                      1.14.1           py39h21324fe_3    conda-forge
onnxruntime               1.16.1          py39h40b49ea_0_cpu    conda-forge
opencv                    4.8.1            py39hcbf5309_2    conda-forge
openexr                   3.2.1                h5fba010_0    conda-forge
openh264                  2.3.1                h63175ca_2    conda-forge
openjpeg                  2.5.0                h3d672ee_3    conda-forge
openpyxl                  3.1.2            py39ha55989b_1    conda-forge
openssl                   3.1.3                hcfcfb64_0    conda-forge
ordered-set               4.1.0              pyhd8ed1ab_0    conda-forge
orjson                    3.9.8            py39h6c6a30e_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    2.1.1            py39h32e6231_1    conda-forge
pango                     1.50.14              h07c897b_2    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
partd                     1.4.1                    pypi_0    pypi
pcre2                     10.40                h17e33f8_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.0.1           py39h368b509_2    conda-forge
pint                      0.22                     pypi_0    pypi
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pixman                    0.42.2               h63175ca_0    conda-forge
pkginfo                   1.9.6              pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              3.11.0             pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
poetry                    1.6.1           win_pyh7428d3b_0    conda-forge
poetry-core               1.7.0              pyhd8ed1ab_0    conda-forge
poetry-plugin-export      1.5.0              pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyhd8ed1ab_4    conda-forge
pretrainedmodels          0.7.4              pyhd8ed1ab_2    conda-forge
prompt-toolkit            3.0.39             pyha770c72_0    conda-forge
prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge
protobuf                  4.24.3           py39hb5342b9_1    conda-forge
psutil                    5.9.5            py39ha55989b_1    conda-forge
psygnal                   0.9.4                    pypi_0    pypi
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pugixml                   1.13                 h63175ca_1    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py-opencv                 4.8.1            py39h5b92f00_2    conda-forge
pyasn1                    0.5.0              pyhd8ed1ab_0    conda-forge
pyasn1-modules            0.3.0              pyhd8ed1ab_0    conda-forge
pycocotools               2.0.6            py39hc266a54_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.13          py39ha55989b_0    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pyjwt                     2.8.0              pyhd8ed1ab_0    conda-forge
pyopengl                  3.1.7                    pypi_0    pypi
pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyproject_hooks           1.0.0              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.9           py39hb77abff_5    conda-forge
pyqt5-sip                 12.12.2          py39h99910a6_5    conda-forge
pyreadline3               3.4.1            py39hcbf5309_3    conda-forge
pyrsistent                0.19.3           py39ha55989b_1    conda-forge
pysocks                   1.7.1              pyh0701188_6    conda-forge
python                    3.9.18          h4de0772_0_cpython    conda-forge
python-build              0.10.0             pyhd8ed1ab_1    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-editor             1.0.4                      py_0    conda-forge
python-elf                0.4.8              pyhd8ed1ab_0    conda-forge
python-flatbuffers        23.5.26            pyhd8ed1ab_0    conda-forge
python-installer          0.7.0              pyhd8ed1ab_0    conda-forge
python-multipart          0.0.6              pyhd8ed1ab_0    conda-forge
python-stdnum             1.19               pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      4_cp39    conda-forge
pytorch                   2.1.0           py3.9_cuda12.1_cudnn8_0    pytorch
pytorch-cuda              12.1                 hde6ce7c_5    pytorch
pytorch-lightning         2.0.9              pyhd8ed1ab_0    conda-forge
pytorch-mutex             1.0                        cuda    pytorch
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pywavelets                1.4.1            py39hd88c2e4_1    conda-forge
pywin32                   306              py39h99910a6_2    conda-forge
pywin32-ctypes            0.2.2            py39hcbf5309_1    conda-forge
pyyaml                    6.0.1            py39ha55989b_1    conda-forge
pyzmq                     25.1.1           py39hea35a22_1    conda-forge
qt-main                   5.15.8              h9e85ed6_17    conda-forge
qtconsole                 5.4.4                    pypi_0    pypi
qtpy                      2.4.0                    pypi_0    pypi
qudida                    0.0.4              pyhd8ed1ab_0    conda-forge
rapidfuzz                 2.15.2           py39h99910a6_0    conda-forge
rav1e                     0.6.6                h975169c_2    conda-forge
re2                       2023.03.02           hd4eee63_0    conda-forge
readchar                  4.0.5              pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    conda-forge
requests-toolbelt         1.0.0              pyhd8ed1ab_0    conda-forge
rich                      13.6.0             pyhd8ed1ab_0    conda-forge
rsa                       4.9                pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.39          py39ha55989b_0    conda-forge
ruamel.yaml.clib          0.2.7            py39ha55989b_2    conda-forge
safetensors               0.3.3            py39hf21820d_1    conda-forge
scikit-image              0.22.0           py39h32e6231_2    conda-forge
scikit-learn              1.3.1            py39h7c199eb_1    conda-forge
scipy                     1.11.3           py39hddb5d58_1    conda-forge
segment-anything          1.0                      pypi_0    pypi
segmentation-models-pytorch 0.3.3              pyhd8ed1ab_0    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
shellingham               1.5.3              pyhd8ed1ab_0    conda-forge
sip                       6.7.11           py39h99910a6_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
skan                      0.11.1             pyhd8ed1ab_0    conda-forge
snappy                    1.1.10               hfb803bf_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0                    pypi_0    pypi
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    4.5.0                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.4                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.0.1                    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                    3.43.2               hcfcfb64_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
starlette                 0.27.0             pyhd8ed1ab_0    conda-forge
starsessions              1.3.0              pyhd8ed1ab_0    conda-forge
superqt                   0.6.1                    pypi_0    pypi
svt-av1                   1.7.0                h63175ca_0    conda-forge
sympy                     1.12               pyh04b8f61_3    conda-forge
tbb                       2021.10.0            h91493d7_1    conda-forge
tensorboard               2.14.1             pyhd8ed1ab_0    conda-forge
tensorboard-data-server   0.7.0            py39hcbf5309_1    conda-forge
threadpoolctl             3.2.0              pyha21a80b_0    conda-forge
tifffile                  2023.9.26          pyhd8ed1ab_0    conda-forge
timm                      0.9.2              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               hcfcfb64_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tomli-w                   1.0.0                    pypi_0    pypi
tomlkit                   0.12.1             pyha770c72_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
torch_em                  0.5.2              pyhd8ed1ab_0    conda-forge
torchmetrics              1.2.0              pyhd8ed1ab_0    conda-forge
torchvision               0.16.0                   pypi_0    pypi
tornado                   6.3.3            py39ha55989b_1    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.11.2             pyhd8ed1ab_0    conda-forge
trove-classifiers         2023.9.19          pyhd8ed1ab_0    conda-forge
typer                     0.9.0              pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.8.19.14          pyhd8ed1ab_0    conda-forge
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
unicodedata2              15.1.0           py39ha55989b_0    conda-forge
urllib3                   2.0.6              pyhd8ed1ab_0    conda-forge
uvicorn                   0.23.2           py39hcbf5309_1    conda-forge
vc                        14.3                h64f974e_17    conda-forge
vc14_runtime              14.36.32532         hdcecf7f_17    conda-forge
vigra                     1.11.2           py39h2f10253_3    conda-forge
virtualenv                20.24.4            pyhd8ed1ab_0    conda-forge
vispy                     0.12.2                   pypi_0    pypi
vs2015_runtime            14.36.32532         h05e6639_17    conda-forge
wcwidth                   0.2.8              pyhd8ed1ab_0    conda-forge
websocket-client          1.6.4              pyhd8ed1ab_0    conda-forge
websockets                11.0.3           py39ha55989b_1    conda-forge
werkzeug                  3.0.0              pyhd8ed1ab_0    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0              pyhd8ed1ab_6    conda-forge
wrapt                     1.15.0                   pypi_0    pypi
x264                      1!164.3095           h8ffe710_2    conda-forge
x265                      3.5                  h2d74725_3    conda-forge
xarray                    2023.7.0           pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             hcd874cb_1002    conda-forge
xorg-libice               1.1.1                hcd874cb_0    conda-forge
xorg-libsm                1.2.4                hcd874cb_0    conda-forge
xorg-libx11               1.8.7                hefa74cf_0    conda-forge
xorg-libxau               1.0.11               hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xorg-libxext              1.3.4                hcd874cb_2    conda-forge
xorg-libxpm               3.5.17               hcd874cb_0    conda-forge
xorg-libxt                1.3.0                hcd874cb_1    conda-forge
xorg-xextproto            7.3.0             hcd874cb_1003    conda-forge
xorg-xproto               7.0.31            hcd874cb_1007    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
yarl                      1.9.2            py39ha55989b_1    conda-forge
z5py                      2.0.16           py39h1f31114_1    conda-forge
zarr                      2.16.1             pyhd8ed1ab_0    conda-forge
zeromq                    4.3.4                h0e60522_1    conda-forge
zfp                       1.0.0                h63175ca_4    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hcfcfb64_5    conda-forge
zlib-ng                   2.0.7                hcfcfb64_0    conda-forge
zstd                      1.5.5                h12be248_0    conda-forge
constantinpape commented 1 year ago

Hi @jo-mueller, the error you report seems to come from an issue with numba. There are two ways to address it:

constantinpape commented 1 year ago

Hi @jo-mueller, this should be fixed if you pull the current master branch.

jo-mueller commented 1 year ago

Thanks big time for looking at it!