Fix marker overlap #10791
Fix marker overlap #10791
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Sort points by z coordinate values similar to Poly3DCollection
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This likely needs a test, right? |
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@jklymak Yes, I will be updating this PR with an image comparison test later. Still looking into how to make one. |
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| # Sort the points based on z coordinates | ||
| # Put vzs first to sort based on z value | ||
| z_markers = sorted(zip(vzs, np.column_stack([vxs, vys]), fcs, ecs), |
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I'm a bit worried that this could slow down the rendering when using many patches.
I know it's bad practice to base such an assumption on pure gut feeling. But before I'm going into any tests. Have you done benchmarking on the performance impact?
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Yes I had ran some benchmarking beforehand. I didn't notice any noticeable impact on performance.
I used the following script
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import random as rand
SIZE=10000
x = np.array([rand.uniform(-50, 50) for i in range(SIZE)])
y = np.array([rand.uniform(-50, 50) for i in range(SIZE)])
z = np.array([rand.uniform(-50, 50) for i in range(SIZE)])
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
patches = ax.scatter(x, y, z, s=100, c=x)
plt.savefig("tmp.png")Ran the script 5 times both before and after fix and didn't find any noticeable differences.
perf_fix.log
perf_vanilla.log
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These timings would have been swamped by all of the imports and figure creation and such. A real benchmark would involve seeing how long it would take to set up the plot, and then have it rotate around, like in one of the animation examples.
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I did a quick check on this part of the code, with numbers of points increased to 1000 000 (I think 100x100x100 is not unrealistic). With that the present sorting/zipping implementation is in the 100ms regime.
That's a size which gets relevant for performance in interactive use.
In a quick test, it's possible to get a roughly 10x speedup by using numpy.argsort on vzs and applying the index array to the other quantities.
lib/mpl_toolkits/mplot3d/art3d.py
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| # Put vzs first to sort based on z value | ||
| z_markers = sorted(zip(vzs, np.column_stack([vxs, vys]), fcs, ecs), | ||
| reverse=True) | ||
| vps = [ps for zs, ps, fc, ec in z_markers] |
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Can you just do:
[zzs, vps, fcs, ecs] = zip(*zmarkers)There was a problem hiding this comment.
I knew there should've been an easier way to do that. I did not know about the starred expression syntax though. I have also changed up Poly3DCollection's do_3d_projection method to use this.
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| # Sort the points based on z coordinates | ||
| # Put vzs first to sort based on z value | ||
| z_markers = sorted(zip(vzs, np.column_stack([vxs, vys]), fcs, ecs), |
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These timings would have been swamped by all of the imports and figure creation and such. A real benchmark would involve seeing how long it would take to set up the plot, and then have it rotate around, like in one of the animation examples.
| z_markers = sorted(zip(vzs, np.column_stack([vxs, vys]), fcs, ecs), | ||
| reverse=True) | ||
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| [zzs, vps, fcs, ecs] = zip(*z_markers) |
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you'll need a check for an empty z_markers before trying to doing this.
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| if vzs.size > 0 : | ||
| if vzs.size > 0: | ||
| return min(vzs) |
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we don't need to do min(vzs) anymore. we now have the sorted zzs. Just return the last element (since you did a reversed sort).
| @@ -634,17 +643,16 @@ def do_3d_projection(self, renderer): | |||
| else: | |||
| raise ValueError("whoops") | |||
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| segments_2d = [s for z, s, fc, ec, idx in z_segments_2d] | |||
| [zzs, segments_2d, self._facecolors2d, self._edgecolors2d, idxs] = \ | |||
| zip(*z_segments_2d) | |||
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another check for empty z_segments_2d before doing this.
| if len(self._edgecolors3d) == len(cface): | ||
| self._edgecolors2d = [ec for z, s, fc, ec, idx in z_segments_2d] | ||
| else: | ||
| if len(self._edgecolors3d) != len(cface): | ||
| self._edgecolors2d = self._edgecolors3d |
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edgecolors3d hasn't been sorted, if I understand this correctly.
| patches = ax.scatter(x, y, z, s=3500, c=['b', 'y']) | ||
| ax.view_init(elev=0, azim=130) | ||
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Can you add a bit more to these tests? Make sure the edge colors are getting sorted properly, too?
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@xenoryt Are you going to continue with this? As mentioned, I've found that using |
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Thanks a lot for the contribution. I'm going to close this as having had no action for quite a while. OTOH, if there is still a community that wants this, please feel free to re-open, with my apologies! |
PR Summary
Fixes issue addressed in addressed in #5830 with markers overlapping incorrectly.
Fixed by sorting markers by z coordinate values similar to Poly3DCollection so that closest ones are drawn last.
PR Checklist