Closed
Description
Bug summary
In axis 3D projection NaN values are not handled correctly, apparently the values are masked out (as it should be) but the mask is not applied to a color array that may not have NaN in the same position.
Code for reproduction
import numpy as np
from matplotlib import pylab as plt
fig = plt.figure()
ax = fig.add_subplot(projection='3d')
ax.scatter([1,np.nan,3], [2,np.nan,4], [3, np.nan,5], color=[[.5,.5,.5,.5]]*3, s=11.5)Actual outcome
ValueError Traceback (most recent call last)
Cell In[24], line 1
----> 1 ax.scatter([1,np.nan,3], [2,np.nan,4], [3, np.nan,5], color=[[.5,.5,.5,.5]]*3, s=11.5)
File ~/Python/lib/python3.11/site-packages/matplotlib/__init__.py:1442, in _preprocess_data.<locals>.inner(ax, data, *args, **kwargs)
1439 @functools.wraps(func)
1440 def inner(ax, *args, data=None, **kwargs):
1441 if data is None:
-> 1442 return func(ax, *map(sanitize_sequence, args), **kwargs)
1444 bound = new_sig.bind(ax, *args, **kwargs)
1445 auto_label = (bound.arguments.get(label_namer)
1446 or bound.kwargs.get(label_namer))
File ~/Python/lib/python3.11/site-packages/mpl_toolkits/mplot3d/axes3d.py:2275, in Axes3D.scatter(self, xs, ys, zs, zdir, s, c, depthshade, *args, **kwargs)
2272 if np.may_share_memory(zs_orig, zs): # Avoid unnecessary copies.
2273 zs = zs.copy()
-> 2275 patches = super().scatter(xs, ys, s=s, c=c, *args, **kwargs)
2276 art3d.patch_collection_2d_to_3d(patches, zs=zs, zdir=zdir,
2277 depthshade=depthshade)
2279 if self._zmargin < 0.05 and xs.size > 0:
File ~/Python/lib/python3.11/site-packages/matplotlib/__init__.py:1442, in _preprocess_data.<locals>.inner(ax, data, *args, **kwargs)
1439 @functools.wraps(func)
1440 def inner(ax, *args, data=None, **kwargs):
1441 if data is None:
-> 1442 return func(ax, *map(sanitize_sequence, args), **kwargs)
1444 bound = new_sig.bind(ax, *args, **kwargs)
1445 auto_label = (bound.arguments.get(label_namer)
1446 or bound.kwargs.get(label_namer))
File ~/Python/lib/python3.11/site-packages/matplotlib/axes/_axes.py:4602, in Axes.scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, edgecolors, plotnonfinite, **kwargs)
4599 if edgecolors is None:
4600 orig_edgecolor = kwargs.get('edgecolor', None)
4601 c, colors, edgecolors = \
-> 4602 self._parse_scatter_color_args(
4603 c, edgecolors, kwargs, x.size,
4604 get_next_color_func=self._get_patches_for_fill.get_next_color)
4606 if plotnonfinite and colors is None:
4607 c = np.ma.masked_invalid(c)
File ~/Python/lib/python3.11/site-packages/matplotlib/axes/_axes.py:4455, in Axes._parse_scatter_color_args(c, edgecolors, kwargs, xsize, get_next_color_func)
4451 else:
4452 if len(colors) not in (0, 1, xsize):
4453 # NB: remember that a single color is also acceptable.
4454 # Besides *colors* will be an empty array if c == 'none'.
-> 4455 raise invalid_shape_exception(len(colors), xsize)
4456 else:
4457 colors = None # use cmap, norm after collection is created
ValueError: 'c' argument has 3 elements, which is inconsistent with 'x' and 'y' with size 2.Expected outcome
A plot with the first and 3rd data point.
Additional information
Unconditionally reproducible.
I have not seen this before, but I may never have called it this way before.
Operating system
Fedora 38
Matplotlib Version
3.7.1
Matplotlib Backend
TkAgg
Python version
3.11.4
Jupyter version
IPython 8.14.0
Installation
pip