Threshold TypingError in example notebook

[lezra1]

Hi - I'm running through the FlyWing notebook example and have been running into a TypingError when reaching the threshold calculation step. I'm running numpy v1.2.6, and I've pasted part of the error below. Any ideas on how to fix this?

TypingError: Failed in nopython mode pipeline (step: nopython frontend)
No implementation of function Function(<built-in function zeros>) found for signature:
 
 >>> zeros(UniTuple(int64 x 2), dtype=Function(<class 'int'>))
 
There are 2 candidate implementations:
  - Of which 2 did not match due to:
  Overload in function 'ol_np_zeros': File: numba\np\arrayobj.py: Line 4452.
    With argument(s): '(UniTuple(int64 x 2), dtype=Function(<class 'int'>))':
   Rejected as the implementation raised a specific error:
     TypingError: Failed in nopython mode pipeline (step: nopython frontend)
   No implementation of function Function(<built-in function empty>) found for signature:
    
    >>> empty(UniTuple(int64 x 2), dtype=Function(<class 'int'>))
    
   There are 2 candidate implementations:
         - Of which 2 did not match due to:
         Overload in function 'ol_np_empty': File: numba\np\arrayobj.py: Line 4374.
           With argument(s): '(UniTuple(int64 x 2), dtype=Function(<class 'int'>))':
          Rejected as the implementation raised a specific error:
            TypingError: Cannot parse input types to function np.empty(UniTuple(int64 x 2), Function(<class 'int'>))
     raised from c:\Users\ezra0001\Anaconda3\envs\DenoiSeg3\lib\site-packages\numba\np\arrayobj.py:4393
   
   During: resolving callee type: Function(<built-in function empty>)
   During: typing of call at c:\Users\ezra0001\Anaconda3\envs\DenoiSeg3\lib\site-packages\numba\np\arrayobj.py (4457)
   
   
   File "..\..\..\..\Anaconda3\envs\DenoiSeg3\lib\site-packages\numba\np\arrayobj.py", line 4457:
       def impl(shape, dtype=float):
           arr = np.empty(shape, dtype=dtype)
           ^

  raised from c:\Users\ezra0001\Anaconda3\envs\DenoiSeg3\lib\site-packages\numba\core\typeinfer.py:1091

During: resolving callee type: Function(<built-in function zeros>)
During: typing of call at c:\Users\ezra0001\Anaconda3\envs\DenoiSeg3\lib\site-packages\denoiseg\utils\compute_precision_threshold.py (10)


File "..\..\..\..\Anaconda3\envs\DenoiSeg3\lib\site-packages\denoiseg\utils\compute_precision_threshold.py", line 10:
def pixel_sharing_bipartite(lab1, lab2):
    <source elided>
    assert lab1.shape == lab2.shape
    psg = np.zeros((lab1.max() + 1, lab2.max() + 1), dtype=int)
    ^

[tibuch]

Could you provide the output of conda list?

[lezra1]

(DenoiSeg3) C:\Users\ezra0001>conda list
# packages in environment at C:\Users\ezra0001\Anaconda3\envs\DenoiSeg3:
#
# Name                    Version                   Build  Channel
absl-py                   2.1.0                    pypi_0    pypi
annotated-types           0.7.0                    pypi_0    pypi
asttokens                 2.0.5              pyhd3eb1b0_0
astunparse                1.6.3                    pypi_0    pypi
backcall                  0.2.0              pyhd3eb1b0_0
bioimageio-core           0.6.7                    pypi_0    pypi
bioimageio-spec           0.5.3.post4              pypi_0    pypi
ca-certificates           2024.7.2             haa95532_0
cachetools                5.4.0                    pypi_0    pypi
certifi                   2024.7.4                 pypi_0    pypi
charset-normalizer        3.3.2                    pypi_0    pypi
colorama                  0.4.6            py39haa95532_0
comm                      0.2.1            py39haa95532_0
contourpy                 1.2.1                    pypi_0    pypi
csbdeep                   0.7.4                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
debugpy                   1.6.7            py39hd77b12b_0
decorator                 5.1.1              pyhd3eb1b0_0
denoiseg                  0.3.1                    pypi_0    pypi
distro                    1.9.0                    pypi_0    pypi
dnspython                 2.6.1                    pypi_0    pypi
email-validator           2.2.0                    pypi_0    pypi
exceptiongroup            1.2.0            py39haa95532_0
executing                 0.8.3              pyhd3eb1b0_0
fire                      0.6.0                    pypi_0    pypi
flatbuffers               24.3.25                  pypi_0    pypi
fonttools                 4.53.1                   pypi_0    pypi
gast                      0.4.0                    pypi_0    pypi
google-auth               2.32.0                   pypi_0    pypi
google-auth-oauthlib      0.4.6                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
grpcio                    1.64.1                   pypi_0    pypi
h5py                      3.11.0                   pypi_0    pypi
idna                      3.7                      pypi_0    pypi
imagecodecs               2024.6.1                 pypi_0    pypi
imageio                   2.34.2                   pypi_0    pypi
importlib-metadata        8.0.0                    pypi_0    pypi
importlib-resources       6.4.0                    pypi_0    pypi
importlib_metadata        7.0.1                hd3eb1b0_0
ipykernel                 6.28.0           py39haa95532_0
ipython                   8.15.0           py39haa95532_0
ipywidgets                8.1.3                    pypi_0    pypi
jedi                      0.19.1           py39haa95532_0
joblib                    1.4.2                    pypi_0    pypi
jupyter_client            8.6.0            py39haa95532_0
jupyter_core              5.7.2            py39haa95532_0
jupyterlab-widgets        3.0.11                   pypi_0    pypi
keras                     2.10.0                   pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
libclang                  18.1.1                   pypi_0    pypi
libsodium                 1.0.18               h62dcd97_0
llvmlite                  0.43.0                   pypi_0    pypi
loguru                    0.7.2                    pypi_0    pypi
markdown                  3.6                      pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.5                    pypi_0    pypi
matplotlib                3.9.1                    pypi_0    pypi
matplotlib-inline         0.1.6            py39haa95532_0
mdurl                     0.1.2                    pypi_0    pypi
n2v                       0.3.3                    pypi_0    pypi
nest-asyncio              1.6.0            py39haa95532_0
networkx                  3.2.1                    pypi_0    pypi
numba                     0.60.0                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
oauthlib                  3.2.2                    pypi_0    pypi
openssl                   3.0.14               h827c3e9_0
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 24.1             py39haa95532_0
pandas                    2.2.2                    pypi_0    pypi
parso                     0.8.3              pyhd3eb1b0_0
pickleshare               0.7.5           pyhd3eb1b0_1003
pillow                    10.4.0                   pypi_0    pypi
pip                       24.0             py39haa95532_0
platformdirs              4.2.2                    pypi_0    pypi
pooch                     1.8.2                    pypi_0    pypi
prompt-toolkit            3.0.43           py39haa95532_0
protobuf                  3.19.6                   pypi_0    pypi
psutil                    5.9.0            py39h2bbff1b_0
pure_eval                 0.2.2              pyhd3eb1b0_0
pyasn1                    0.6.0                    pypi_0    pypi
pyasn1-modules            0.4.0                    pypi_0    pypi
pydantic                  2.8.2                    pypi_0    pypi
pydantic-core             2.20.1                   pypi_0    pypi
pydantic-settings         2.3.4                    pypi_0    pypi
pygments                  2.18.0                   pypi_0    pypi
pyparsing                 3.1.2                    pypi_0    pypi
python                    3.9.19               h1aa4202_1
python-dateutil           2.9.0post0       py39haa95532_2
python-dotenv             1.0.1                    pypi_0    pypi
pytz                      2024.1                   pypi_0    pypi
pywin32                   305              py39h2bbff1b_0
pyzmq                     25.1.2           py39hd77b12b_0
requests                  2.32.3                   pypi_0    pypi
requests-oauthlib         2.0.0                    pypi_0    pypi
rich                      13.7.1                   pypi_0    pypi
rsa                       4.9                      pypi_0    pypi
ruamel-yaml               0.18.6                   pypi_0    pypi
ruamel-yaml-clib          0.2.8                    pypi_0    pypi
ruyaml                    0.91.0                   pypi_0    pypi
scikit-image              0.24.0                   pypi_0    pypi
scikit-learn              1.5.1                    pypi_0    pypi
scipy                     1.13.1                   pypi_0    pypi
setuptools                69.5.1           py39haa95532_0
six                       1.16.0             pyhd3eb1b0_1
sqlite                    3.45.3               h2bbff1b_0
stack_data                0.2.0              pyhd3eb1b0_0
tensorboard               2.10.1                   pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-wit    1.8.1                    pypi_0    pypi
tensorflow                2.10.1                   pypi_0    pypi
tensorflow-estimator      2.10.0                   pypi_0    pypi
tensorflow-io-gcs-filesystem 0.31.0                   pypi_0    pypi
termcolor                 2.4.0                    pypi_0    pypi
threadpoolctl             3.5.0                    pypi_0    pypi
tifffile                  2024.7.2                 pypi_0    pypi
tornado                   6.4.1            py39h827c3e9_0
tqdm                      4.66.4                   pypi_0    pypi
traitlets                 5.14.3           py39haa95532_0
typing-extensions         4.12.2                   pypi_0    pypi
typing_extensions         4.11.0           py39haa95532_0
tzdata                    2024.1                   pypi_0    pypi
urllib3                   2.2.2                    pypi_0    pypi
vc                        14.2                 h2eaa2aa_4
vs2015_runtime            14.29.30133          h43f2093_4
wcwidth                   0.2.5              pyhd3eb1b0_0
werkzeug                  3.0.3                    pypi_0    pypi
wheel                     0.43.0           py39haa95532_0
widgetsnbextension        4.0.11                   pypi_0    pypi
win32-setctime            1.1.0                    pypi_0    pypi
wrapt                     1.12.1                   pypi_0    pypi
xarray                    2024.6.0                 pypi_0    pypi
zeromq                    4.3.5                hd77b12b_0
zipp                      3.19.2                   pypi_0    pypi

Am I missing a dependency?