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Title: Optimize 3D display by AlexandreAbraham · Pull Request #6085 · matplotlib/matplotlib · GitHub

Open Graph Title: Optimize 3D display by AlexandreAbraham · Pull Request #6085 · matplotlib/matplotlib

X Title: Optimize 3D display by AlexandreAbraham · Pull Request #6085 · matplotlib/matplotlib

Description: While printing 3D objects, I noticed that the display was pretty slow. The reason is that matplotlib relies a lot on list of objects instead of using big numpy arrays to fasten 3D projections. This PR aims at solving part of this problem. I replaced some airthmetic on list of vectors by artihmetic on big matrices. This impacts mainly 3D display. I work on neuroimaging data. I noticed an approximate 25% speedup optimization on 3D display (depending on the complexity of the figure). Refreshment in interactive plotting is also faster. Example script: from matplotlib import pyplot as plt from mpl_toolkits.mplot3d import Axes3D from nibabel import gifti surf_mesh = '/path/to/spm12b/canonical/cortex_20484.surf.gii' coords, faces = gifti.read(surf_mesh).getArraysFromIntent(1008)[0].data, \ gifti.read(surf_mesh).getArraysFromIntent(1009)[0].data limits = [coords.min(), coords.max()] cmap = 'coolwarm' fig = plt.figure() ax = fig.add_subplot(111, projection='3d', xlim=limits, ylim=limits) ax.view_init(elev=0, azim=0) ax.set_axis_off() p3dcollec = ax.plot_trisurf(coords[:, 0], coords[:, 1], coords[:, 2], triangles=faces, linewidth=0., antialiased=False, color='white') fig.savefig('brain.png') plt.close(fig) Possible other optimizations: For display, matplotlib relies on a list of Path objects. This could be made faster with numpy arrays. Poly3DCollection and others: a lot of unnecessary asarray and paddings of ones to obtain quaternions are done. This could be simplified by keeping a quaternion numpy array in the object and using appropriate numpy views but requires a deeper refactoring. not plotting unseen triangle: For the moment, all polygons are drawn. if there are a lot, isn't it worth to compute which one are hidden by others and remove them? @agramfort and @juhuntenburg, do you notice significant running time reduction with this PR?

Open Graph Description: While printing 3D objects, I noticed that the display was pretty slow. The reason is that matplotlib relies a lot on list of objects instead of using big numpy arrays to fasten 3D projections. This...

X Description: While printing 3D objects, I noticed that the display was pretty slow. The reason is that matplotlib relies a lot on list of objects instead of using big numpy arrays to fasten 3D projections. This...

Opengraph URL: https://github.com/matplotlib/matplotlib/pull/6085

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a4a8a86 Replace lists by numpy array in projection AlexandreAbraham Feb 29, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/a4a8a86ed3d134367d7fe8be1b9feb4da5f531fe
3d295af Remove profiling code AlexandreAbraham Feb 29, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/3d295afbf760f61e443b91001460fa5d61a7c5ef
5239e1a Vectorize output of proj_transform_vec AlexandreAbraham Feb 29, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/5239e1ae407f59b575fe10dcf61eea968ad00134
7285fed Reach vectorized projection functions directly AlexandreAbraham Feb 29, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/7285fed2c454ebec019d38b08b2edf38f29c4ebf
328c2f4 Address comments AlexandreAbraham Mar 2, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/328c2f4435fec294ef04c18ae1f0f169e6332c2e
a973da8 More fixes AlexandreAbraham Mar 3, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/a973da8086e5f1607646087535da49b081669d8b
14853d0 Fix rotation of axes AlexandreAbraham Mar 3, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/14853d0a5097633ef1847abdfd4a3f03d1999c50
c4de047 Fix some failures AlexandreAbraham Jun 8, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/c4de0478db70fc22110128357421b0182bc2c2fd
6315961 Use a contiguous representation in memory and views for the segments AlexandreAbraham Jun 8, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/63159615ca443d2e6be51fb5e9f28eeeeda42438
bb948bb Fix bug in PathPatch AlexandreAbraham Sep 20, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/bb948bb619b990003670b1afc22c80045e6a14ac
e6211bd Fix vstack bug AlexandreAbraham Sep 20, 2016 https://github.com/matplotlib/matplotlib/pull/6085/commits/e6211bd1768dbfe0eebd54ae82a03bc78ef6fae6
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