Closed haesleinhuepf closed 1 year ago
Hm...from the error it seems like the error comes from the function not being able to reconstruct the surface and returning a tuple with a zero-sized faces
array.
I'll see whether I can reproduce the error and whether it goes away by changing the parameters.
In any case, the error message should reflect what's wrong which it currently doesn't. I'll see to it :)
Hi @haesleinhuepf ,
I checked and couldn't reproduce that error, neither in VSCode nor in Jupyterlab. For me, running this widget with "bad" settings simply returns an invisible surface, i.e., a surface with no faces. If you change the settings to something like number_of_sampling_voxels=40
, point_influence_radius=2
, padding=1.10
- does that work?
If you change the settings to something like
number_of_sampling_voxels=40
,point_influence_radius=2
,padding=1.10
- does that work?
With these settings, it works:
With the settings above, I see the error in the terminal:
Here comes my conda list
... Is there any python library/version that I should try in different versions?
# packages in environment at C:\Users\haase\mambaforge\envs\bio39:
#
# Name Version Build Channel
_ipython_minor_entry_point 8.7.0 h8cf3c4a_0 conda-forge
absl-py 1.3.0 pypi_0 pypi
aicsimageio 4.9.4 pypi_0 pypi
aicspylibczi 3.0.5 pypi_0 pypi
aiobotocore 2.4.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.8.3 py39ha55989b_1 conda-forge
aioitertools 0.11.0 pyhd8ed1ab_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
alabaster 0.7.13 pyhd8ed1ab_0 conda-forge
anyio 3.6.2 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h63175ca_0 conda-forge
apoc 0.12.0 dev_0 <develop>
apoc-backend 0.12.0 pyhd8ed1ab_0 conda-forge
app-model 0.1.1 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39ha55989b_3 conda-forge
arrow-cpp 10.0.1 h9c18f36_3_cpu conda-forge
asciitree 0.3.3 py_2 conda-forge
astropy 5.2.1 pypi_0 pypi
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pypi_0 pypi
async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge
attrs 22.1.0 pyh71513ae_1 conda-forge
autopep8 2.0.1 pyhd8ed1ab_0 conda-forge
aws-c-auth 0.6.21 h1ba0662_1 conda-forge
aws-c-cal 0.5.20 h4b5e85a_3 conda-forge
aws-c-common 0.8.5 hcfcfb64_0 conda-forge
aws-c-compression 0.2.16 h3dc32ea_0 conda-forge
aws-c-event-stream 0.2.16 hb67f86a_0 conda-forge
aws-c-http 0.6.29 h844ee93_0 conda-forge
aws-c-io 0.13.11 hea55e33_2 conda-forge
aws-c-mqtt 0.7.13 h461ce70_10 conda-forge
aws-c-s3 0.2.1 h0f2ed3e_2 conda-forge
aws-c-sdkutils 0.1.7 h3dc32ea_0 conda-forge
aws-checksums 0.1.14 h3dc32ea_0 conda-forge
aws-crt-cpp 0.18.16 h09df7fd_5 conda-forge
aws-sdk-cpp 1.9.379 h4d30238_6 conda-forge
babel 2.11.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.3 hdccc3a2_0 conda-forge
bokeh 2.4.3 pyhd8ed1ab_3 conda-forge
botocore 1.27.59 pyhd8ed1ab_0 conda-forge
brotli 1.0.9 hcfcfb64_8 conda-forge
brotli-bin 1.0.9 hcfcfb64_8 conda-forge
brotlipy 0.7.0 py39ha55989b_1005 conda-forge
bzip2 1.0.8 h8ffe710_4 conda-forge
c-ares 1.18.1 h8ffe710_0 conda-forge
c-blosc2 2.6.1 h183a6f4_0 conda-forge
ca-certificates 2022.12.7 h5b45459_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.2.0 pypi_0 pypi
cachey 0.2.1 pyh9f0ad1d_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py39h68f70e3_3 conda-forge
cfitsio 4.2.0 h9ebe7e4_0 conda-forge
chardet 5.1.0 pypi_0 pypi
charls 2.3.4 h39d44d4_0 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
click 8.1.3 win_pyhd8ed1ab_2 conda-forge
click-default-group 1.2.2 pyhd8ed1ab_1 conda-forge
cloudpickle 2.2.0 pyhd8ed1ab_0 conda-forge
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comm 0.1.2 pyhd8ed1ab_0 conda-forge
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configargparse 1.5.3 pypi_0 pypi
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control 0.9.3.post2 pyhd8ed1ab_0 conda-forge
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cudatoolkit 11.2.2 h7d7167e_11 conda-forge
cupy 11.4.0 py39hc474d4a_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.33 pypi_0 pypi
cytoolz 0.12.0 py39ha55989b_1 conda-forge
czifile 2019.7.2 pyh9f0ad1d_0 conda-forge
dash 2.7.1 pypi_0 pypi
dash-core-components 2.0.0 pypi_0 pypi
dash-html-components 2.0.0 pypi_0 pypi
dash-table 5.0.0 pypi_0 pypi
dask 2022.12.1 pyhd8ed1ab_0 conda-forge
dask-core 2022.12.1 pyhd8ed1ab_0 conda-forge
dataproperty 0.55.0 pypi_0 pypi
dav1d 1.0.0 h8ffe710_1 conda-forge
debugpy 1.6.4 py39h99910a6_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.13 pyh6c4a22f_0 conda-forge
devbio-napari 0.8.1 win_h08f2357_0 conda-forge
distributed 2022.12.1 pyhd8ed1ab_0 conda-forge
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font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 hbde0cde_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
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gflags 2.2.2 ha925a31_1004 conda-forge
giflib 5.2.1 h8d14728_2 conda-forge
glib 2.74.1 h12be248_1 conda-forge
glib-tools 2.74.1 h12be248_1 conda-forge
glog 0.6.0 h4797de2_0 conda-forge
google-auth 2.15.0 pypi_0 pypi
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grpcio 1.51.1 pypi_0 pypi
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h11 0.14.0 pypi_0 pypi
h5py 3.8.0 nompi_py39hbc6f334_100 conda-forge
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keras 2.11.0 pypi_0 pypi
khronos-opencl-icd-loader 2022.09.30 h64bf75a_2 conda-forge
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lerc 4.0.0 h63175ca_0 conda-forge
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m2w64-gmp 6.1.0 2 conda-forge
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napari-svg 0.1.6 pyhd8ed1ab_1 conda-forge
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pyasn1 0.4.8 pypi_0 pypi
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pyclesperanto-prototype 0.23.2 dev_0 <develop>
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Hi @haesleinhuepf ,
thanks for checking. Strangely, I really only see the error in the terminal when I start napari from the terminal.
Here comes my conda list... Is there any python library/version that I should try in different versions?
Nah, it's really just that the set of parameters doesn't produce a surface which napari could visualize. I'll send a PR that throws an error to point this out. Or would you think a warning would be better?
Hi Johannes @jo-mueller ,
I was just testing the new
Add reconstruct surface
function. After executing demo.ipynb I attempted to run the function like this from the GUI:And receive this error:
Would you mind taking a look what went wrong?
Thanks!
Best, Robert