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UserWarning thrown when all values are "bad", but not when only some are #18294
Description
Bug report
Bug summary
If all values passed as colors are "bad" (np.nan), a warning is thrown from numpy about converting masked values to null. If some of the values are "bad", this does not happen.
Code for reproduction
import numpy as np, matplotlib.pyplot as pltThis does not warn:
c = np.full(10, np.nan)
c[0] = 1.
plt.scatter(np.ones(10), np.ones(10), c=c)
plt.show()This does:
plt.scatter(np.ones(10), np.ones(10), c=np.full(10, np.nan))
plt.show()<__array_function__ internals>:5: UserWarning: Warning: converting a masked element to nan.
/usr/local/lib/python3.8/site-packages/numpy/core/_asarray.py:85: UserWarning: Warning: converting a masked element to nan.
return array(a, dtype, copy=False, order=order)This is difficult to hide since since the warning is not thrown when the figure is being constructed, but when it is shown. Here's a full traceback to show this:
Full traceback File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.8/site-packages/matplotlib/pyplot.py", line 337, in show
return _backend_mod.show(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 3544, in show
cls.mainloop()
File "/usr/local/lib/python3.8/site-packages/matplotlib/backends/backend_macosx.py", line 171, in mainloop
_macosx.show()
File "/usr/local/lib/python3.8/site-packages/matplotlib/backends/backend_macosx.py", line 61, in _draw
self.figure.draw(renderer)
File "/usr/local/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/figure.py", line 1863, in draw
mimage._draw_list_compositing_images(
File "/usr/local/lib/python3.8/site-packages/matplotlib/image.py", line 131, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/cbook/deprecation.py", line 411, in wrapper
return func(*inner_args, **inner_kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/axes/_base.py", line 2748, in draw
mimage._draw_list_compositing_images(renderer, self, artists)
File "/usr/local/lib/python3.8/site-packages/matplotlib/image.py", line 131, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/collections.py", line 931, in draw
Collection.draw(self, renderer)
File "/usr/local/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/collections.py", line 346, in draw
self.update_scalarmappable()
File "/usr/local/lib/python3.8/site-packages/matplotlib/collections.py", line 855, in update_scalarmappable
self._facecolors = self.to_rgba(self._A, self._alpha)
File "/usr/local/lib/python3.8/site-packages/matplotlib/cm.py", line 332, in to_rgba
x = self.norm(x)
File "/usr/local/lib/python3.8/site-packages/matplotlib/colors.py", line 1048, in __call__
(vmin,), _ = self.process_value(self.vmin)
File "/usr/local/lib/python3.8/site-packages/matplotlib/colors.py", line 1012, in process_value
dtype = np.min_scalar_type(value)
File "<__array_function__ internals>", line 5, in min_scalar_type
File "/usr/local/lib/python3.8/site-packages/numpy/ma/core.py", line 4331, in __float__
warnings.warn("Warning: converting a masked element to nan.", stacklevel=2)
File "/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/warnings.py", line 109, in _showwarnmsg
sw(msg.message, msg.category, msg.filename, msg.lineno,
File "<stdin>", line 3, in warn_with_traceback
<__array_function__ internals>:5: UserWarning: Warning: converting a masked element to nan.
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.8/site-packages/matplotlib/pyplot.py", line 337, in show
return _backend_mod.show(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 3544, in show
cls.mainloop()
File "/usr/local/lib/python3.8/site-packages/matplotlib/backends/backend_macosx.py", line 171, in mainloop
_macosx.show()
File "/usr/local/lib/python3.8/site-packages/matplotlib/backends/backend_macosx.py", line 61, in _draw
self.figure.draw(renderer)
File "/usr/local/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/figure.py", line 1863, in draw
mimage._draw_list_compositing_images(
File "/usr/local/lib/python3.8/site-packages/matplotlib/image.py", line 131, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/cbook/deprecation.py", line 411, in wrapper
return func(*inner_args, **inner_kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/axes/_base.py", line 2748, in draw
mimage._draw_list_compositing_images(renderer, self, artists)
File "/usr/local/lib/python3.8/site-packages/matplotlib/image.py", line 131, in _draw_list_compositing_images
a.draw(renderer)
File "/usr/local/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/collections.py", line 931, in draw
Collection.draw(self, renderer)
File "/usr/local/lib/python3.8/site-packages/matplotlib/artist.py", line 41, in draw_wrapper
return draw(artist, renderer, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/matplotlib/collections.py", line 346, in draw
self.update_scalarmappable()
File "/usr/local/lib/python3.8/site-packages/matplotlib/collections.py", line 855, in update_scalarmappable
self._facecolors = self.to_rgba(self._A, self._alpha)
File "/usr/local/lib/python3.8/site-packages/matplotlib/cm.py", line 332, in to_rgba
x = self.norm(x)
File "/usr/local/lib/python3.8/site-packages/matplotlib/colors.py", line 1048, in __call__
(vmin,), _ = self.process_value(self.vmin)
File "/usr/local/lib/python3.8/site-packages/matplotlib/colors.py", line 1019, in process_value
data = np.asarray(value)
File "/usr/local/lib/python3.8/site-packages/numpy/core/_asarray.py", line 85, in asarray
return array(a, dtype, copy=False, order=order)
File "/usr/local/lib/python3.8/site-packages/numpy/ma/core.py", line 4331, in __float__
warnings.warn("Warning: converting a masked element to nan.", stacklevel=2)
File "/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/warnings.py", line 109, in _showwarnmsg
sw(msg.message, msg.category, msg.filename, msg.lineno,
File "<stdin>", line 3, in warn_with_traceback
/usr/local/lib/python3.8/site-packages/numpy/core/_asarray.py:85: UserWarning: Warning: converting a masked element to nan.
return array(a, dtype, copy=False, order=order)Expected outcome
I wouldn't expect the second to warn if the first doesn't.
Matplotlib version
- Operating system: macOS
- Matplotlib version: 3.3.1
- Matplotlib backend (print(matplotlib.get_backend())): MacOSX and module://ipykernel.pylab.backend_inline
- Python version: 3.8.5
- Jupyter version (if applicable): Replicates in python repl, but also was happening in ipython and jupyter lab
- Other libraries:
Installed with pip
Activity
oscargus commented on Dec 15, 2022
The warning comes from NumPy, so not sure there is much Matplotlib can do? I'll close this, but feel free to reopen if you have another opinion (and sorry for letting this go unnoticed for so long).
ivirshup commented on Dec 15, 2022
@oscargus, could matplotlib just catch the warning at plot time?
I figure if the behavior is intentional from matplotlib, it would be nice if it didn't warn.
oscargus commented on Dec 15, 2022
Ahh, I should have checked what happens in latest Matplotlib. Now it actually breaks:
--------------------------------------------------------------------------- StopIteration Traceback (most recent call last) <ipython-input-2-18fe43def80a> in <cell line: 1>() ----> 1 plt.scatter(np.ones(10), np.ones(10), c=np.full(10, np.nan)) ~\matplotlib\lib\matplotlib\pyplot.py in scatter(x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, edgecolors, plotnonfinite, data, **kwargs) 2820 vmin=None, vmax=None, alpha=None, linewidths=None, *, 2821 edgecolors=None, plotnonfinite=False, data=None, **kwargs): -> 2822 __ret = gca().scatter( 2823 x, y, s=s, c=c, marker=marker, cmap=cmap, norm=norm, 2824 vmin=vmin, vmax=vmax, alpha=alpha, linewidths=linewidths, ~\matplotlib\lib\matplotlib\__init__.py in inner(ax, data, *args, **kwargs) 1446 def inner(ax, *args, data=None, **kwargs): 1447 if data is None: -> 1448 return func(ax, *map(sanitize_sequence, args), **kwargs) 1449 1450 bound = new_sig.bind(ax, *args, **kwargs) ~\matplotlib\lib\matplotlib\axes\_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, edgecolors, plotnonfinite, **kwargs) 4590 orig_edgecolor = kwargs.get('edgecolor', None) 4591 c, colors, edgecolors = \ -> 4592 self._parse_scatter_color_args( 4593 c, edgecolors, kwargs, x.size, 4594 get_next_color_func=self._get_patches_for_fill.get_next_color) ~\matplotlib\lib\matplotlib\axes\_axes.py in _parse_scatter_color_args(c, edgecolors, kwargs, xsize, get_next_color_func) 4388 isinstance(c, str) 4389 or (np.iterable(c) and len(c) > 0 -> 4390 and isinstance(cbook._safe_first_finite(c), str))) 4391 4392 def invalid_shape_exception(csize, xsize): ~\matplotlib\lib\matplotlib\cbook\__init__.py in _safe_first_finite(obj, skip_nonfinite) 1713 "support generators as input") 1714 else: -> 1715 return next(val for val in obj if safe_isfinite(val)) 1716 1717 StopIteration:Pinging @tacaswell who seems to have worked on _safe_first_finite most recently (although not sure when the issue arise).
Regarding if it is intentional or not can be discussed. We don't raise the warning and if we catch it, it may lead to confusion. At least in the general case.