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Jupyter notebook plotting issue with numpy 2.1.1
When running the example notebook on a fresh installation, I get a trait error TraitError: The 'width' trait of a Line instance expected a float or a dict, not the float32 np.float32(0.054083023)."
Downgrading numpy to version 1.26.4 solved the issue for me.
{
"name": "TraitError",
"message": "The 'width' trait of a Line instance expected a float or a dict, not the float32 np.float32(0.054083023).",
"stack": "---------------------------------------------------------------------------
TraitError Traceback (most recent call last)
Cell In[2], line 30
1 nurbs = spp.NURBS(
2 degrees=[1, 2],
3 knot_vectors=[[0, 0, 1, 1], [0, 0, 0, 1, 1, 2, 2, 2]],
(...)
27 ],
28 )
---> 30 gus.show(nurbs)
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/gustaf/show.py:48, in _CallableShowDotPy.__call__(self, *args, **kwargs)
46 def __call__(self, *args, **kwargs):
47 \"\"\"call show()\"\"\"
---> 48 return show(*args, **kwargs)
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/gustaf/show.py:203, in show(*args, **kwargs)
201 # set interactive to true at last element
202 if int(i + 1) == len(args):
--> 203 plt.show(
204 list_of_showables,
205 at=i,
206 interactive=interact,
207 camera=cam_tuple_to_list(cam),
208 axes=axes,
209 )
211 else:
212 plt.show(
213 list_of_showables,
214 at=i,
(...)
217 axes=axes,
218 )
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/gustaf/helpers/notebook.py:127, in K3DPlotterN.show(self, list_of_showables, at, interactive, camera, axes, *args, **kwargs)
123 self._logd(f\"*args ({args}) and **kwargs ({kwargs}) ignored\")
125 # this converts vedo plotter to k3d plot.
126 # after this, vedo plotter has no relevance to what you see
--> 127 self[self._at_get_location(at)] = self.vedo_plotters[at].show(
128 list_of_showables,
129 interactive=interactive,
130 camera=camera,
131 axes=axes,
132 )
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/vedo/plotter.py:3317, in Plotter.show(self, at, axes, resetcam, zoom, interactive, viewup, azimuth, elevation, roll, camera, mode, rate, bg, bg2, size, title, screenshot, *objects)
3315 # Backend ###############################################################
3316 if vedo.settings.default_backend in [\"k3d\"]:
-> 3317 return backends.get_notebook_backend(self.objects)
3318 #########################################################################
3320 for ia in utils.flatten(objects):
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/vedo/backends.py:31, in get_notebook_backend(actors2show)
29 #########################################
30 if settings.default_backend == \"k3d\":
---> 31 return start_k3d(actors2show)
33 #########################################
34 if settings.default_backend.startswith(\"trame\"):
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/vedo/backends.py:245, in start_k3d(actors2show)
241 pts = ia.vertices[ln_idx]
243 aves = ia.diagonal_size() * iap.GetLineWidth() / 100
--> 245 kobj = k3d.line(
246 pts.astype(np.float32),
247 color=_rgb2int(iap.GetColor()),
248 opacity=iap.GetOpacity(),
249 shader=settings.k3d_line_shader,
250 width=aves,
251 name=name,
252 )
253 vedo.notebook_plotter += kobj
255 ################################################################## Mesh
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/k3d/factory.py:244, in line(vertices, color, colors, attribute, color_map, color_range, width, opacity, shader, radial_segments, name, group, custom_data, compression_level, **kwargs)
237 attribute = (
238 np.array(attribute, np.float32) if type(
239 attribute) is not dict else attribute
240 )
241 color_range = check_attribute_color_range(attribute, color_range)
243 return process_transform_arguments(
--> 244 Line(
245 vertices=vertices,
246 color=color,
247 width=width,
248 shader=shader,
249 radial_segments=radial_segments,
250 colors=colors,
251 attribute=attribute,
252 color_map=color_map,
253 color_range=color_range,
254 opacity=opacity,
255 name=name,
256 group=group,
257 custom_data=custom_data,
258 compression_level=compression_level,
259 ),
260 **kwargs
261 )
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/k3d/objects.py:310, in Line.__init__(self, **kwargs)
309 def __init__(self, **kwargs):
--> 310 super(Line, self).__init__(**kwargs)
312 self.set_trait(\"type\", \"Line\")
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/k3d/objects.py:108, in Drawable.__init__(self, **kwargs)
105 def __init__(self, **kwargs):
106 self.id = id(self)
--> 108 super(Drawable, self).__init__(**kwargs)
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/ipywidgets/widgets/widget.py:503, in Widget.__init__(self, **kwargs)
501 \"\"\"Public constructor\"\"\"
502 self._model_id = kwargs.pop('model_id', None)
--> 503 super().__init__(**kwargs)
505 Widget._call_widget_constructed(self)
506 self.open()
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/traitlets/traitlets.py:1355, in HasTraits.__init__(self, *args, **kwargs)
1353 for key, value in kwargs.items():
1354 if self.has_trait(key):
-> 1355 setattr(self, key, value)
1356 changes[key] = Bunch(
1357 name=key,
1358 old=None,
(...)
1361 type=\"change\",
1362 )
1363 else:
1364 # passthrough args that don't set traits to super
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/traitlets/traitlets.py:716, in TraitType.__set__(self, obj, value)
714 if self.read_only:
715 raise TraitError('The \"%s\" trait is read-only.' % self.name)
--> 716 self.set(obj, value)
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/traitlets/traitlets.py:690, in TraitType.set(self, obj, value)
689 def set(self, obj: HasTraits, value: S) -> None:
--> 690 new_value = self._validate(obj, value)
691 assert self.name is not None
692 try:
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/traitlets/traitlets.py:722, in TraitType._validate(self, obj, value)
720 return value
721 if hasattr(self, \"validate\"):
--> 722 value = self.validate(obj, value)
723 if obj._cross_validation_lock is False:
724 value = self._cross_validate(obj, value)
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/traitlets/traitlets.py:2460, in Union.validate(self, obj, value)
2458 except TraitError:
2459 continue
-> 2460 self.error(obj, value)
File ~/anaconda3/envs/fresh_env/lib/python3.12/site-packages/traitlets/traitlets.py:831, in TraitType.error(self, obj, value, error, info)
825 else:
826 e = \"The '{}' trait expected {}, not {}.\".format(
827 self.name,
828 info or self.info(),
829 describe(\"the\", value),
830 )
--> 831 raise TraitError(e)
TraitError: The 'width' trait of a Line instance expected a float or a dict, not the float32 np.float32(0.054083023)."
}
Relevant conda environment specs:
gustaf 0.0.26
ipykernel 6.29.5
ipython 8.27.0
ipywidgets 8.1.5
jupyter_client 8.6.0
jupyter_core 5.7.2
jupyterlab-widgets 3.0.13
numpy 2.1.1
numpy-base 2.0.1
k3d 2.16.1
python 3.12.5
splinepy 0.1.3
Did anything else downgrade as well? Or just numpy? Could you provide the package list with versions for the downgraded environment?
I have looked into it a bit. This seems to be a problem with how vedo converts points and lines to k3d. If I change in vedo.backends the corresponding lines to not include conversion to numpy floats or explicitly convert them back it seems to work again.
Specifically the lines 316 onward to:
aves = float(ia.average_size() * iap.GetPointSize() / 200)
kobj = k3d.points(
ia.vertices.astype(float),
color=_rgb2int(iap.GetColor()),
colors=kcols,
opacity=iap.GetOpacity(),
shader=settings.k3d_point_shader,
point_size=aves,
name=name,
)
and lines from 243 onward
aves = float(ia.diagonal_size() * iap.GetLineWidth() / 100)
kobj = k3d.line(
pts.astype(float),
color=_rgb2int(iap.GetColor()),
opacity=iap.GetOpacity(),
shader=settings.k3d_line_shader,
width=aves,
name=name,
)
it works again for me. I am not sure why this is just changing its functionality now and not before. Why traitlets was ok with this before and now it is not I am not sure.
I opened an issue for this on vedo for this https://github.com/marcomusy/vedo/issues/1197#issue-2635555643.
Vedo has pushed the fix I have suggested. I will not make a determination on what vedo version has to be used yet since they have not had a new release. But if you have this issue it should be fixed if you install vedo from source.
I am closing this issue since the fix has been applied in vedo for more than 6 month now.