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Patch3DCollection not displaying correctly using add_collection3d #14298

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ghost opened this issue May 22, 2019 · 4 comments
Open

Patch3DCollection not displaying correctly using add_collection3d #14298

ghost opened this issue May 22, 2019 · 4 comments
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topic: mplot3d
Milestone
future releases

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@ghost
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ghost commented May 22, 2019

Code for reproduction

import matplotlib as mpl
import matplotlib.pyplot
import mpl_toolkits as mplt
import mpl_toolkits.mplot3d.axes3d
fig = mpl.pyplot.figure() # make Figure
ax = mpl.pyplot.gca(projection="3d")
circle1 = mpl.patches.Circle((5,1))
circle2 = mpl.patches.Circle((2,2))

# test 1 (throws ValueError):
#pc1 = matplotlib.collections.PatchCollection([circle1, circle2])
#ax.add_collection3d(pc1, zs=[1,2])

# test 2:
pc2 = mplt.mplot3d.art3d.Patch3DCollection([circle1, circle2], match_original=True)
ax.add_collection3d(pc2)

test 1 results into a ValueError:

Traceback (most recent call last):
  File "/usr/lib/python3.6/site-packages/matplotlib/backends/backend_qt5.py", line 519, in _draw_idle
    self.draw()
  File "/usr/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py", line 402, in draw
    self.figure.draw(self.renderer)
  File "/usr/lib/python3.6/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python3.6/site-packages/matplotlib/figure.py", line 1649, in draw
    renderer, self, artists, self.suppressComposite)
  File "/usr/lib/python3.6/site-packages/matplotlib/image.py", line 138, in _draw_list_compositing_images
    a.draw(renderer)
  File "/usr/lib/python3.6/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 287, in draw
    reverse=True)):
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 286, in <lambda>
    key=lambda col: col.do_3d_projection(renderer),
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 400, in do_3d_projection
    fcs = (zalpha(self._facecolor3d, vzs) if self._depthshade else
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 776, in zalpha
    colors = get_colors(colors, len(zs))
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 767, in get_colors
    (num, 4))
  File "/usr/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 176, in broadcast_to
    return _broadcast_to(array, shape, subok=subok, readonly=True)
  File "/usr/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 128, in _broadcast_to
    op_flags=[op_flag], itershape=shape, order='C')
ValueError: operands could not be broadcast together with remapped shapes [original->remapped]: (2,4) and requested shape (1,4)
Traceback (most recent call last):
  File "/usr/lib/python3.6/site-packages/matplotlib/backends/backend_qt5.py", line 519, in _draw_idle
    self.draw()
  File "/usr/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py", line 402, in draw
    self.figure.draw(self.renderer)
  File "/usr/lib/python3.6/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python3.6/site-packages/matplotlib/figure.py", line 1649, in draw
    renderer, self, artists, self.suppressComposite)
  File "/usr/lib/python3.6/site-packages/matplotlib/image.py", line 138, in _draw_list_compositing_images
    a.draw(renderer)
  File "/usr/lib/python3.6/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 287, in draw
    reverse=True)):
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 286, in <lambda>
    key=lambda col: col.do_3d_projection(renderer),
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 400, in do_3d_projection
    fcs = (zalpha(self._facecolor3d, vzs) if self._depthshade else
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 776, in zalpha
    colors = get_colors(colors, len(zs))
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 767, in get_colors
    (num, 4))
  File "/usr/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 176, in broadcast_to
    return _broadcast_to(array, shape, subok=subok, readonly=True)
  File "/usr/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 128, in _broadcast_to
    op_flags=[op_flag], itershape=shape, order='C')
ValueError: operands could not be broadcast together with remapped shapes [original->remapped]: (2,4) and requested shape (1,4)
Traceback (most recent call last):
  File "/usr/lib/python3.6/site-packages/matplotlib/backends/backend_qt5.py", line 519, in _draw_idle
    self.draw()
  File "/usr/lib/python3.6/site-packages/matplotlib/backends/backend_agg.py", line 402, in draw
    self.figure.draw(self.renderer)
  File "/usr/lib/python3.6/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python3.6/site-packages/matplotlib/figure.py", line 1649, in draw
    renderer, self, artists, self.suppressComposite)
  File "/usr/lib/python3.6/site-packages/matplotlib/image.py", line 138, in _draw_list_compositing_images
    a.draw(renderer)
  File "/usr/lib/python3.6/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 287, in draw
    reverse=True)):
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py", line 286, in <lambda>
    key=lambda col: col.do_3d_projection(renderer),
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 400, in do_3d_projection
    fcs = (zalpha(self._facecolor3d, vzs) if self._depthshade else
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 776, in zalpha
    colors = get_colors(colors, len(zs))
  File "/usr/lib/python3.6/site-packages/mpl_toolkits/mplot3d/art3d.py", line 767, in get_colors
    (num, 4))
  File "/usr/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 176, in broadcast_to
    return _broadcast_to(array, shape, subok=subok, readonly=True)
  File "/usr/lib/python3.6/site-packages/numpy/lib/stride_tricks.py", line 128, in _broadcast_to
    op_flags=[op_flag], itershape=shape, order='C')
ValueError: operands could not be broadcast together with remapped shapes [original->remapped]: (2,4) and requested shape (1,4)

test 2 results into a weird plot drenched into a blueish color, there is a visible object also (perhaps change the viewing angle) but it's not a circle.
Figure_1

Matplotlib 3.1.0

  • Operating system: Void Linux
  • Matplotlib version: 3.1.0
  • Matplotlib backend Qt5Agg:
  • Python version: 3.6.8
@fidelram
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I am also getting the same error when saving a 3D image.

@fidelram fidelram mentioned this issue May 27, 2019
Merged
@tacaswell tacaswell added this to the v3.1.2 milestone Jul 1, 2019
This was referenced Sep 16, 2019
Closed
Closed
@tacaswell tacaswell modified the milestones: v3.1.2, v3.3.0 Oct 22, 2019
@QuLogic QuLogic modified the milestones: v3.3.0, v3.4.0 May 7, 2020
@ivirshup
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@QuLogic, was this fixed by #18929? The plots at scanpy seem to be working with matplotlib 3.3.3.

@qrzhang
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qrzhang commented Nov 17, 2020

@ivirshup Yes, I think you're right. It works after I upgrade the matplotlib to version 3.3.3

pip install matplotlib --upgrade

@QuLogic QuLogic modified the milestones: v3.4.0, v3.5.0 Jan 27, 2021
@QuLogic QuLogic modified the milestones: v3.5.0, v3.6.0 Sep 25, 2021
@Qrox Qrox mentioned this issue Jun 21, 2022
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@oscargus
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Parts of this seems to be related to scaling of the patches. Consider the following code:

import matplotlib as mpl
import matplotlib.pyplot
fig = mpl.pyplot.figure() # make Figure
ax = fig.add_subplot(projection="3d")
rect = mpl.patches.Rectangle((-0.05,-0.05), 0.1, 0.1)
circle1 = mpl.patches.Circle((0,0), radius=0.01)
circle2 = mpl.patches.Circle((0.01,0.01), radius=0.01)
ax.set_xlim(-10, 10)
ax.set_ylim(-10, 10)
ax.set_zlim(-10, 10)
pc1 = matplotlib.collections.PatchCollection([rect, circle1, circle2])
ax.add_collection3d(pc1, zs=[1,2,3])
#pc2 = mplt.mplot3d.art3d.Patch3DCollection([rect, circle1, circle2], zs=[1, 2, 3], match_original=True)
#ax.add_collection3d(pc2)

Either version works, and gives the following plot:
image

@QuLogic QuLogic modified the milestones: v3.6.0, v3.7.0 Aug 24, 2022
@ksunden ksunden modified the milestones: v3.7.0, v3.7.1 Feb 14, 2023
@QuLogic QuLogic modified the milestones: v3.7.1, future releases Mar 4, 2023
@scottshambaugh scottshambaugh mentioned this issue May 5, 2023
Closed
7 tasks
@Chrillebon Chrillebon mentioned this issue Aug 8, 2024
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19 tasks
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@tacaswell @QuLogic @ksunden @fidelram @dstansby @oscargus @ivirshup @qrzhang