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haesleinhuepf / napari-process-points-and-surfaces

Process and analyze surfaces using vedo in napari.
BSD 3-Clause "New" or "Revised" License
21 stars 4 forks source link

Error in Add reconstruct surface #70

Closed haesleinhuepf closed 1 year ago

haesleinhuepf commented 1 year ago

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:

image

And receive this error:

Traceback (most recent call last):
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari_tools_menu\__init__.py", line 125, in worker_func
    target_layer = next(x for x in viewer.layers if x.source.widget is gui)
StopIteration

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\psygnal\_signal.py", line 851, in _run_emit_loop
    if caller(args):
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\psygnal\_signal.py", line 1184, in __call__
    self._slot(*args)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\magicgui\widgets\_function_gui.py", line 212, in _disable_button_and_call
    self.__call__()
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\magicgui\widgets\_function_gui.py", line 324, in __call__
    value = self._function(*bound.args, **bound.kwargs)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari_tools_menu\__init__.py", line 144, in worker_func
    target_layer = viewer.add_surface(data, name=new_name)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\components\viewer_model.py", line 4, in add_surface
    import itertools
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\layers\surface\surface.py", line 217, in __init__
    self._contrast_limits_range = calc_data_range(self._vertex_values)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\layers\utils\layer_utils.py", line 235, in calc_data_range
    min_val = _nanmin(reduced_data)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\layers\utils\layer_utils.py", line 147, in _nanmin
    min = np.min(array)
  File "<__array_function__ internals>", line 180, in amin
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\numpy\core\fromnumeric.py", line 2918, in amin
    return _wrapreduction(a, np.minimum, 'min', axis, None, out,
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\numpy\core\fromnumeric.py", line 86, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation minimum which has no identity

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\magicgui\widgets\_bases\value_widget.py", line 57, in _on_value_change
    self.changed.emit(value)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\psygnal\_signal.py", line 805, in emit
    self._run_emit_loop(args)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\psygnal\_signal.py", line 856, in _run_emit_loop
    raise EmitLoopError(slot=caller.slot(), args=args, exc=e) from e
psygnal._signal.EmitLoopError: calling <function FunctionGui.__init__.<locals>._disable_button_and_call at 0x000002763F5B5280> with args=(False,) caused ValueError in emit loop.
[I 2023-03-07 11:46:51.812 ServerApp] Kernel restarted: 7c718746-427b-488c-992d-b34b95208d42
Traceback (most recent call last):
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari_tools_menu\__init__.py", line 125, in worker_func
    target_layer = next(x for x in viewer.layers if x.source.widget is gui)
StopIteration

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\psygnal\_signal.py", line 851, in _run_emit_loop
    if caller(args):
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\psygnal\_signal.py", line 1184, in __call__
    self._slot(*args)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\magicgui\widgets\_function_gui.py", line 212, in _disable_button_and_call
    self.__call__()
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\magicgui\widgets\_function_gui.py", line 324, in __call__
    value = self._function(*bound.args, **bound.kwargs)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari_tools_menu\__init__.py", line 144, in worker_func
    target_layer = viewer.add_surface(data, name=new_name)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\components\viewer_model.py", line 4, in add_surface
    import itertools
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\layers\surface\surface.py", line 230, in __init__
    self._update_dims()
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\layers\base\base.py", line 705, in _update_dims
    self.refresh()  # This call is need for invalidate cache of extent in LayerList. If you remove it pleas ad another workaround.
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\layers\base\base.py", line 1209, in refresh
    self.set_view_slice()
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\layers\base\base.py", line 959, in set_view_slice
    self._set_view_slice()
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\napari\layers\surface\surface.py", line 424, in _set_view_slice
    triangles = vertices[self.faces]
IndexError: arrays used as indices must be of integer (or boolean) type

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\magicgui\widgets\_bases\value_widget.py", line 57, in _on_value_change
    self.changed.emit(value)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\psygnal\_signal.py", line 805, in emit
    self._run_emit_loop(args)
  File "C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\psygnal\_signal.py", line 856, in _run_emit_loop
    raise EmitLoopError(slot=caller.slot(), args=args, exc=e) from e
psygnal._signal.EmitLoopError: calling <function FunctionGui.__init__.<locals>._disable_button_and_call at 0x000001B22F8ED700> with args=(False,) caused IndexError in emit loop.

Would you mind taking a look what went wrong?

Thanks!

Best, Robert

jo-mueller commented 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 :)

jo-mueller commented 1 year ago

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?

haesleinhuepf commented 1 year ago

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: image

image

With the settings above, I see the error in the terminal:

image

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
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
condastats                0.2.1              pyhd8ed1ab_0    conda-forge
configargparse            1.5.3                    pypi_0    pypi
contourpy                 1.0.7            py39h1f6ef14_0    conda-forge
control                   0.9.3.post2        pyhd8ed1ab_0    conda-forge
cryptography              38.0.4           py39hb6bd5e6_0    conda-forge
csbdeep                   0.7.2                    pypi_0    pypi
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
dnspython                 2.2.1                    pypi_0    pypi
docstring_parser          0.15               pyhd8ed1ab_0    conda-forge
docutils                  0.17.1           py39hcbf5309_3    conda-forge
dominate                  2.7.0                    pypi_0    pypi
eigen                     3.4.0                h2d74725_0    conda-forge
elementpath               3.0.2                    pypi_0    pypi
email-validator           1.3.0                    pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et_xmlfile                1.1.0              pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.0              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h1537add_0    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
fastrlock                 0.8              py39h99910a6_3    conda-forge
ffmpeg                    5.1.2           gpl_h5b1d025_106    conda-forge
fftw                      3.3.10          nompi_h38027f0_106    conda-forge
finesse                   3.0a3            py39h1cfdcae_2    conda-forge
flask                     2.2.2                    pypi_0    pypi
flatbuffers               22.12.6                  pypi_0    pypi
flit-core                 3.8.0              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                 4.38.0           py39ha55989b_1    conda-forge
freetype                  2.12.1               h546665d_1    conda-forge
freetype-py               2.3.0              pyhd8ed1ab_0    conda-forge
frozenlist                1.3.3            py39ha55989b_0    conda-forge
fsspec                    2022.11.0          pyhd8ed1ab_0    conda-forge
funcsigs                  1.0.2                      py_3    conda-forge
gast                      0.4.0                    pypi_0    pypi
gettext                   0.21.1               h5728263_0    conda-forge
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
google-auth-oauthlib      0.4.6                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
greenlet                  2.0.1            py39h99910a6_0    conda-forge
grpcio                    1.51.1                   pypi_0    pypi
gst-plugins-base          1.21.2               h001b923_0    conda-forge
gstreamer                 1.21.2               h6b5321d_0    conda-forge
h11                       0.14.0                   pypi_0    pypi
h5py                      3.8.0           nompi_py39hbc6f334_100    conda-forge
hdbscan                   0.8.29           py39hc266a54_1    conda-forge
hdf5                      1.12.2          nompi_h57737ce_101    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
hsluv                     5.0.2              pyh44b312d_0    conda-forge
httpcore                  0.16.3                   pypi_0    pypi
httpx                     0.23.3                   pypi_0    pypi
icu                       70.1                 h0e60522_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagecodecs               2022.9.26        py39haf5b5c4_4    conda-forge
imagecodecs-lite          2019.12.3        py39hc266a54_6    conda-forge
imageio                   2.25.0             pyh24c5eb1_0    conda-forge
imageio-ffmpeg            0.4.8              pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib_resources       5.10.2             pyhd8ed1ab_0    conda-forge
in-n-out                  0.1.6              pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
intel-openmp              2022.2.1         h57928b3_19741    conda-forge
ipycanvas                 0.13.1             pyhd8ed1ab_0    conda-forge
ipyevents                 2.0.1              pyhd8ed1ab_0    conda-forge
ipykernel                 6.19.2             pyh025b116_0    conda-forge
ipython                   8.7.0              pyh08f2357_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipyvtklink                0.2.3                    pypi_0    pypi
ipywidgets                7.7.2                    pypi_0    pypi
itsdangerous              2.1.2                    pypi_0    pypi
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h8ffe710_2    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py39hcbf5309_8    conda-forge
jupyter_client            7.4.8              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.4              pyhd8ed1ab_0    conda-forge
jupyter_core              5.1.0            py39hcbf5309_0    conda-forge
jupyter_server            1.23.3             pyhd8ed1ab_0    conda-forge
jupyterlab                3.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab-widgets        1.1.1                    pypi_0    pypi
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.19.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.5              pyhd8ed1ab_0    conda-forge
jupytext                  1.14.4             pyhcff175f_0    conda-forge
jxrlib                    1.1                  h8ffe710_2    conda-forge
keras                     2.11.0                   pypi_0    pypi
khronos-opencl-icd-loader 2022.09.30           h64bf75a_2    conda-forge
kiwisolver                1.4.4            py39h1f6ef14_1    conda-forge
krb5                      1.19.3               hc8ab02b_0    conda-forge
lazy-loader               0.1                      pypi_0    pypi
lcms2                     2.14                 h90d422f_0    conda-forge
lerc                      4.0.0                h63175ca_0    conda-forge
libabseil                 20220623.0      cxx17_h1a56200_6    conda-forge
libaec                    1.0.6                h63175ca_1    conda-forge
libarrow                  10.0.1           h226723c_3_cpu    conda-forge
libavif                   0.11.1               h8f5c5bc_0    conda-forge
libblas                   3.9.0              16_win64_mkl    conda-forge
libbrotlicommon           1.0.9                hcfcfb64_8    conda-forge
libbrotlidec              1.0.9                hcfcfb64_8    conda-forge
libbrotlienc              1.0.9                hcfcfb64_8    conda-forge
libcblas                  3.9.0              16_win64_mkl    conda-forge
libclang                  14.0.6                   pypi_0    pypi
libclang13                15.0.6          default_h77d9078_0    conda-forge
libcrc32c                 1.1.2                h0e60522_0    conda-forge
libcurl                   7.86.0               heaf79c2_1    conda-forge
libdeflate                1.14                 hcfcfb64_0    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libflang                  11.0.1          h0e60522_20210131    conda-forge
libglib                   2.74.1               he8f3873_1    conda-forge
libgoogle-cloud           2.5.0                h5fc25aa_1    conda-forge
libgrpc                   1.51.1               h6a6baca_0    conda-forge
libhwloc                  2.8.0                h039e092_1    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
libitk                    5.3.0                h6e1890f_0    conda-forge
liblapack                 3.9.0              16_win64_mkl    conda-forge
liblapacke                3.9.0              16_win64_mkl    conda-forge
libogg                    1.3.4                h8ffe710_1    conda-forge
libopus                   1.3.1                h8ffe710_1    conda-forge
libpng                    1.6.39               h19919ed_0    conda-forge
libprotobuf               3.21.12              h12be248_0    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.40.0               hcfcfb64_0    conda-forge
libssh2                   1.10.0               h9a1e1f7_3    conda-forge
libthrift                 0.16.0               h9ce19ad_2    conda-forge
libtiff                   4.4.0                h8e97e67_4    conda-forge
libutf8proc               2.8.0                h82a8f57_0    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libwebp-base              1.2.4                h8ffe710_0    conda-forge
libxcb                    1.13              hcd874cb_1004    conda-forge
libxml2                   2.10.3               hc3477c8_0    conda-forge
libzlib                   1.2.13               hcfcfb64_4    conda-forge
libzopfli                 1.0.3                h0e60522_0    conda-forge
llvm-openmp               11.0.1               h2d74725_0    conda-forge
llvmlite                  0.39.1           py39hd28a505_1    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
loguru                    0.6.0            py39hcbf5309_2    conda-forge
lxml                      4.9.2                    pypi_0    pypi
lz4                       4.0.2            py39hf617134_0    conda-forge
lz4-c                     1.9.3                h8ffe710_1    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                  0.6.1              pyhd8ed1ab_0    conda-forge
mako                      1.2.4              pyhd8ed1ab_0    conda-forge
markdown                  3.4.1                    pypi_0    pypi
markdown-it-py            2.1.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1            py39ha55989b_2    conda-forge
matplotlib-base           3.6.3            py39haf65ace_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mbstrdecoder              1.1.1                    pypi_0    pypi
mdit-py-plugins           0.3.3              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    conda-forge
mkl                       2022.1.0           h6a75c08_874    conda-forge
more-itertools            9.0.0              pyhd8ed1ab_0    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.4            py39h1f6ef14_1    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
multidict                 6.0.4            py39ha55989b_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           0.4.3            py39hcbf5309_6    conda-forge
napari                    0.4.17          pyh275ddea_0_pyqt    conda-forge
napari-3d-ortho-viewer    0.0.1              pyhd8ed1ab_0    conda-forge
napari-accelerated-pixel-and-object-classification 0.12.3                    dev_0    <develop>
napari-animation          0.0.5              pyhd8ed1ab_0    conda-forge
napari-assistant          0.4.4                     dev_0    <develop>
napari-blob-detection     0.0.2              pyhd8ed1ab_0    conda-forge
napari-brightness-contrast 0.1.8              pyhd8ed1ab_0    conda-forge
napari-clusters-plotter   0.6.1                     dev_0    <develop>
napari-console            0.0.7              pyhd8ed1ab_0    conda-forge
napari-crop               0.1.6              pyhd8ed1ab_0    conda-forge
napari-curtain            0.1.1              pyhd8ed1ab_0    conda-forge
napari-czifile2           0.2.7              pyhd8ed1ab_0    conda-forge
napari-folder-browser     0.1.3              pyhd8ed1ab_0    conda-forge
napari-layer-details-display 0.1.4              pyhd8ed1ab_0    conda-forge
napari-matplotlib         0.2.1                    pypi_0    pypi
napari-mouse-controls     0.1.3              pyhd8ed1ab_0    conda-forge
napari-plot-profile       0.2.2              pyhd8ed1ab_0    conda-forge
napari-plugin-engine      0.2.0              pyhd8ed1ab_2    conda-forge
napari-plugin-search      0.1.4                     dev_0    <develop>
napari-process-points-and-surfaces 0.4.1                     dev_0    <develop>
napari-pyclesperanto-assistant 0.22.1                    dev_0    <develop>
napari-pystackreg         0.1.4              pyhd8ed1ab_0    conda-forge
napari-roi                0.1.7              pyhd8ed1ab_0    conda-forge
napari-segment-blobs-and-things-with-membranes 0.3.4                     dev_0    <develop>
napari-simpleitk-image-processing 0.4.5                     dev_0    <develop>
napari-skimage-regionprops 0.8.2                     dev_0    <develop>
napari-svg                0.1.6              pyhd8ed1ab_1    conda-forge
napari-tabu               0.1.5              pyhd8ed1ab_0    conda-forge
napari-time-slicer        0.4.9              pyhd8ed1ab_1    conda-forge
napari-tools-menu         0.1.19                   pypi_0    pypi
napari-workflow-inspector 0.2.2              pyhd8ed1ab_0    conda-forge
napari-workflow-optimizer 0.1.4              pyhd8ed1ab_0    conda-forge
napari-workflows          0.2.8              pyhd8ed1ab_0    conda-forge
nbclassic                 0.4.8              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.6              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.6              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.6              pyhd8ed1ab_0    conda-forge
nbformat                  5.5.0                    pypi_0    pypi
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
npe2                      0.6.1              pyhd8ed1ab_1    conda-forge
numba                     0.56.4           py39h99ae161_0    conda-forge
numcodecs                 0.11.0           py39h99910a6_1    conda-forge
numpy                     1.23.5           py39hbccbffa_0    conda-forge
numpydoc                  1.5.0              pyhd8ed1ab_0    conda-forge
oauthlib                  3.2.2                    pypi_0    pypi
oclgrind                  21.10                h6fda50d_0    conda-forge
ome-types                 0.3.2                    pypi_0    pypi
open3d                    0.16.0                   pypi_0    pypi
openh264                  2.3.1                h63175ca_1    conda-forge
openjpeg                  2.5.0                hc9384bd_1    conda-forge
openpyxl                  3.1.1            py39ha55989b_0    conda-forge
openssl                   3.0.8                hcfcfb64_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 22.0               pyhd8ed1ab_0    conda-forge
pandas                    1.5.2            py39h2ba5b7c_0    conda-forge
pandasql                  0.7.3              pyhd8ed1ab_0    conda-forge
pandoc                    2.19.2               h57928b3_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parquet-cpp               1.5.1                         2    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
partd                     1.3.0              pyhd8ed1ab_0    conda-forge
pathvalidate              2.5.2                    pypi_0    pypi
pcre2                     10.40                h17e33f8_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.2.0            py39h595c93f_3    conda-forge
pint                      0.20.1             pyhd8ed1ab_0    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              2.6.0              pyhd8ed1ab_0    conda-forge
platymatch                0.0.3              pyhd8ed1ab_0    conda-forge
plotly                    5.12.0                   pypi_0    pypi
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
ply                       3.11                       py_1    conda-forge
pooch                     1.6.0              pyhd8ed1ab_0    conda-forge
prettytable               3.6.0                    pypi_0    pypi
prometheus_client         0.15.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.36             pyha770c72_0    conda-forge
prompt_toolkit            3.0.36               hd8ed1ab_0    conda-forge
protobuf                  3.19.6                   pypi_0    pypi
psutil                    5.9.4            py39ha55989b_0    conda-forge
psygnal                   0.7.0              pyhd8ed1ab_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pyarrow                   10.0.1          py39hafeb24e_3_cpu    conda-forge
pyasn1                    0.4.8                    pypi_0    pypi
pyasn1-modules            0.2.8                    pypi_0    pypi
pyclesperanto-prototype   0.23.2                    dev_0    <develop>
pycodestyle               2.10.0             pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.4           py39ha55989b_1    conda-forge
pyerfa                    2.0.0.1                  pypi_0    pypi
pygeodesic                0.1.7                    pypi_0    pypi
pygments                  2.14.0                   pypi_0    pypi
pynndescent               0.5.8              pyh1a96a4e_0    conda-forge
pyopencl                  2022.3.1         py39he9b43b8_0    conda-forge
pyopengl                  3.1.6              pyhd8ed1ab_1    conda-forge
pyopenssl                 22.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pypdf2                    3.0.1                    pypi_0    pypi
pyperclip                 1.8.2              pyhd8ed1ab_2    conda-forge
pypistats                 1.2.1                    pypi_0    pypi
pyproject_hooks           1.0.0              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.7           py39hb77abff_2    conda-forge
pyqt5-sip                 12.11.0          py39h99910a6_2    conda-forge
pyqtgraph                 0.13.1             pyhd8ed1ab_1    conda-forge
pyrsistent                0.19.3           py39ha55989b_0    conda-forge
pyshtools                 4.10                     pypi_0    pypi
pysocks                   1.7.1              pyh0701188_6    conda-forge
pyspellchecker            0.7.0              pyhd8ed1ab_0    conda-forge
pystackreg                0.2.7            py39h2ba5b7c_1    conda-forge
pytablewriter             0.64.2                   pypi_0    pypi
pytest                    7.2.1              pyhd8ed1ab_0    conda-forge
pytest-qt                 4.2.0                    pypi_0    pypi
python                    3.9.15          h4de0772_0_cpython    conda-forge
python-build              0.10.0             pyhd8ed1ab_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-slugify            7.0.0                    pypi_0    pypi
python-snappy             0.6.1            py39h643d002_0    conda-forge
python_abi                3.9                      3_cp39    conda-forge
pytomlpp                  1.0.11           py39h1f6ef14_1    conda-forge
pytools                   2022.1.14          pyhd8ed1ab_0    conda-forge
pytz                      2022.6             pyhd8ed1ab_0    conda-forge
pywavelets                1.4.1            py39hc266a54_0    conda-forge
pywin32                   304              py39h99910a6_2    conda-forge
pywinpty                  2.0.9            py39h99910a6_0    conda-forge
pyyaml                    6.0              py39ha55989b_5    conda-forge
pyzmq                     24.0.1           py39hea35a22_1    conda-forge
qt-main                   5.15.6               hb9439ea_4    conda-forge
qtconsole                 5.4.0              pyhd8ed1ab_0    conda-forge
qtconsole-base            5.4.0              pyha770c72_0    conda-forge
qtpy                      2.3.0              pyhd8ed1ab_0    conda-forge
re2                       2022.06.01           h0e60522_1    conda-forge
readlif                   0.6.5                    pypi_0    pypi
redlionfish               0.8              py39hcbf5309_2    conda-forge
reikna                    0.8.0              pyhd8ed1ab_0    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1                    pypi_0    pypi
resource-backed-dask-array 0.1.0                    pypi_0    pypi
rfc3986                   1.5.0                    pypi_0    pypi
rich                      13.3.1             pyhd8ed1ab_0    conda-forge
rsa                       4.9                      pypi_0    pypi
s3fs                      2022.11.0          pyhd8ed1ab_0    conda-forge
scikit-image              0.20.0                   pypi_0    pypi
scikit-learn              1.2.1            py39h6fe01c0_0    conda-forge
scipy                     1.9.1                    pypi_0    pypi
seaborn                   0.12.1                   pypi_0    pypi
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                65.5.1             pyhd8ed1ab_0    conda-forge
shellingham               1.5.0.post1        pyhd8ed1ab_0    conda-forge
simpleitk                 2.2.1            py39h138a4a7_1    conda-forge
sip                       6.7.5            py39h99910a6_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sly                       0.4                pyhd8ed1ab_0    conda-forge
slycot                    0.5.2            py39h73a3b6d_0    conda-forge
snappy                    1.1.9                hfb803bf_2    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sphinx                    4.5.0              pyh6c4a22f_0    conda-forge
sphinxcontrib-applehelp   1.0.4              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
sqlalchemy                1.4.45           py39ha55989b_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
stackview                 0.5.2                     dev_0    <develop>
stardist                  0.8.3                    pypi_0    pypi
stardist-napari           2022.12.6                pypi_0    pypi
suitesparse               5.4.0                h5d0cbe0_1    conda-forge
superqt                   0.4.1              pyhd8ed1ab_0    conda-forge
svt-av1                   1.4.1                h63175ca_0    conda-forge
sympy                     1.11.1           py39hcbf5309_2    conda-forge
tabledata                 1.3.0                    pypi_0    pypi
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tbb                       2021.7.0             h91493d7_1    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
tcolorpy                  0.1.2                    pypi_0    pypi
tenacity                  8.1.0                    pypi_0    pypi
tensorboard               2.11.0                   pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-wit    1.8.1                    pypi_0    pypi
tensorflow                2.11.0                   pypi_0    pypi
tensorflow-estimator      2.11.0                   pypi_0    pypi
tensorflow-intel          2.11.0                   pypi_0    pypi
tensorflow-io-gcs-filesystem 0.29.0                   pypi_0    pypi
termcolor                 2.1.1                    pypi_0    pypi
terminado                 0.17.0             pyh08f2357_0    conda-forge
text-unidecode            1.3                      pypi_0    pypi
the-segmentation-game     0.2.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tifffile                  2022.10.10         pyhd8ed1ab_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h8ffe710_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2              py39ha55989b_1    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.7.1              pyhd8ed1ab_0    conda-forge
transforms3d              0.4.1              pyhd8ed1ab_0    conda-forge
typepy                    1.3.0                    pypi_0    pypi
typer                     0.4.2              pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
umap-learn                0.5.3            py39hcbf5309_0    conda-forge
unicodedata2              15.0.0           py39ha55989b_0    conda-forge
urllib3                   1.26.13            pyhd8ed1ab_0    conda-forge
vc                        14.3                 h3d8a991_9    conda-forge
vedo                      2023.4.3                 pypi_0    pypi
vispy                     0.11.0           py39hc266a54_1    conda-forge
vs2015_runtime            14.32.31332          h1d6e394_9    conda-forge
vtk                       9.2.5                    pypi_0    pypi
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.4.2              pyhd8ed1ab_0    conda-forge
werkzeug                  2.2.2                    pypi_0    pypi
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.1                    pypi_0    pypi
win32_setctime            1.1.0              pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0              pyhd8ed1ab_6    conda-forge
winpty                    0.4.3                         4    conda-forge
wrapt                     1.14.1           py39ha55989b_1    conda-forge
x264                      1!164.3095           h8ffe710_2    conda-forge
x265                      3.5                  h2d74725_3    conda-forge
xarray                    2022.12.0                pypi_0    pypi
xmlschema                 2.1.1                    pypi_0    pypi
xorg-libxau               1.0.9                hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
yarl                      1.8.2            py39ha55989b_0    conda-forge
zarr                      2.13.3             pyhd8ed1ab_0    conda-forge
zeromq                    4.3.4                h0e60522_1    conda-forge
zfp                       1.0.0                h63175ca_3    conda-forge
zict                      2.2.0              pyhd8ed1ab_0    conda-forge
zipp                      3.12.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hcfcfb64_4    conda-forge
zlib-ng                   2.0.6                h8ffe710_0    conda-forge
zstd                      1.5.2                h7755175_4    conda-forge
jo-mueller commented 1 year ago

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?