Quick fix of bug on treatment of alpha parameter on the mplot3d toolkit, reported in issue#25446, following@oscargus and@tacaswell directions on the issue thread.

For Patches, no changed seemed to be needed. Might need further testing since it's the same piece of code repeated:

matplotlib/lib/mpl_toolkits/mplot3d/art3d.py

Lines 588 to 596 in63b9b04

	def_maybe_depth_shade_and_sort_colors(self,color_array):
	color_array= (
	_zalpha(color_array,self._vzs)
	ifself._vzsisnotNoneandself._depthshade
	elsecolor_array
	)
	iflen(color_array)>1:
	color_array=color_array[self._z_markers_idx]
	returnmcolors.to_rgba_array(color_array,self._alpha)

A script to test the fix can be found in this gist:https://gist.github.com/ricmperes/a69d876d2cf7333ae9cf713ecb25b474

Result after fix:

PR Checklist

Documentation and Tests

Has pytest style unit tests (andpytest passes)
Documentation is sphinx and numpydoc compliant (the docs shouldbuild without error).
New plotting related features are documented with examples.

Release Notes

New features are marked with a.. versionadded:: directive in the docstring and documented indoc/users/next_whats_new/
API changes are marked with a.. versionchanged:: directive in the docstring and documented indoc/api/next_api_changes/
Release notes conform with instructions innext_whats_new/README.rst ornext_api_changes/README.rst

ricmperes added2 commits

March 16, 2023 14:01

Fix alpha bug on 3D PathCollection plots.

9b5a0ab

Fix flake8 linting errors

a941214

github-actionsbot reviewed

Mar 16, 2023

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oscargus added the topic: mplot3d label

Mar 16, 2023

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oscargus commentedMar 16, 2023

Thanks! Can you please add a test for this as well?

I think that plotting something like in the original issue and then checking that the alpha-value of the "correct" position(s) (row 10000 to 19999) ofscat3d.get_facecolor() is 0 would do. (No need for image tests.)

oscargus linked an issue

Mar 16, 2023

that may beclosed by this pull request

[Bug]: Nan values in scatter 3d plot show in black colour when alpha parameter is passed.#25446

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ksunden commentedMar 16, 2023

Test failure is related:

The test:

matplotlib/lib/mpl_toolkits/mplot3d/tests/test_axes3d.py

Lines 441 to 494 in63b9b04

	@pytest.mark.parametrize('depthshade', [True,False])
	@check_figures_equal(extensions=['png'])
	deftest_scatter3d_sorting(fig_ref,fig_test,depthshade):
	"""Test that marker properties are correctly sorted."""

	y,x=np.mgrid[:10, :10]
	z=np.arange(x.size).reshape(x.shape)

	sizes=np.full(z.shape,25)
	sizes[0::2,0::2]=100
	sizes[1::2,1::2]=100

	facecolors=np.full(z.shape,'C0')
	facecolors[:5, :5]='C1'
	facecolors[6:, :4]='C2'
	facecolors[6:,6:]='C3'

	edgecolors=np.full(z.shape,'C4')
	edgecolors[1:5,1:5]='C5'
	edgecolors[5:9,1:5]='C6'
	edgecolors[5:9,5:9]='C7'

	linewidths=np.full(z.shape,2)
	linewidths[0::2,0::2]=5
	linewidths[1::2,1::2]=5

	x,y,z,sizes,facecolors,edgecolors,linewidths= [
	a.flatten()
	forain [x,y,z,sizes,facecolors,edgecolors,linewidths]
	]

	ax_ref=fig_ref.add_subplot(projection='3d')
	sets= (np.unique(a)forain [sizes,facecolors,edgecolors,linewidths])
	fors,fc,ec,lwinitertools.product(*sets):
	subset= (
	(sizes!=s)\|
	(facecolors!=fc)\|
	(edgecolors!=ec)\|
	(linewidths!=lw)
	)
	subset=np.ma.masked_array(z,subset,dtype=float)

	# When depth shading is disabled, the colors are passed through as
	# single-item lists; this triggers single path optimization. The
	# following reshaping is a hack to disable that, since the optimization
	# would not occur for the full scatter which has multiple colors.
	fc=np.repeat(fc,sum(~subset.mask))

	ax_ref.scatter(x,y,subset,s=s,fc=fc,ec=ec,lw=lw,alpha=1,
	depthshade=depthshade)

	ax_test=fig_test.add_subplot(projection='3d')
	ax_test.scatter(x,y,z,s=sizes,fc=facecolors,ec=edgecolors,
	lw=linewidths,alpha=1,depthshade=depthshade)

Looks like an interaction withdepthshade = True. In this case it's a "compare equal" not a "compare to static reference" test, so pretty clear that the two methods of plotting should result in the same image (plotting in subsets of markers with the same properties vs plotting in one call).

tacaswell reviewed

Mar 16, 2023

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lib/mpl_toolkits/mplot3d/art3d.py Outdated

		return mcolors.to_rgba_array(color_array, self._alpha)

		if self._alpha is not None:
		converted_alphas = color_array[:, 3] * self._alpha

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tacaswellMar 16, 2023

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Are we sure this will never get an RGB (vs RGBA) array?

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ricmperesJun 30, 2023

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Hi@tacaswell. Good point, if depthshape is specified as False a RGBA type array might get passed. I put an escape clause for this case.

Suggested change

	converted_alphas=color_array[:,3]*self._alpha
	returnmcolors.to_rgba_array(color_array,self._alpha)

scottshambaugh added the PR: bugfixPull requests that fix identified bugs label

Mar 17, 2023

jklymak added the status: needs revision label

Jun 14, 2023

ricmperes added3 commits

June 30, 2023 18:53

Handle RGB instead of RGBA case.

09d2179

Clean main if clause.

69ad517

Merge branch 'matplotlib:main' into main

47de4ba

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ricmperes commentedJun 30, 2023

Debugging why thetest_scatter3d_sorting is failing I ran it with a clean version of matplotlib and the output seems to have no depth-related shading, likely becausealpha=1 is parsed. To be sure, whendepthshade=True this isnot the intended behaviour, right?
Output bellow:

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scottshambaugh commentedJul 16, 2024

Sincedepthshade=True is the default, I would expect that manually setting thealpha parameter would override the depth shading, but I don't actually know what the intent here is.@ricmperes I know this PR has been hanging for a bit - are you still interested in working on it?