DenoiSeg
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Threshold TypingError in example notebook
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)
^
(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?