8000 Optimize 3D display by AlexandreAbraham · Pull Request #6085 · matplotlib/matplotlib · GitHub
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Optimize 3D display #6085

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Optimize 3D display #6085

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a4a8a86
Replace lists by numpy array in projection
AlexandreAbraham Feb 29, 2016
3d295af
Remove profiling code
AlexandreAbraham Feb 29, 2016
5239e1a
Vectorize output of proj_transform_vec
AlexandreAbraham Feb 29, 2016
7285fed
Reach vectorized projection functions directly
AlexandreAbraham Feb 29, 2016
328c2f4
Address comments
AlexandreAbraham Mar 2, 2016
a973da8
More fixes
AlexandreAbraham Mar 3, 2016
14853d0
Fix rotation of axes
AlexandreAbraham Mar 3, 2016
c4de047
Fix some failures
AlexandreAbraham Jun 8, 2016
6315961
Use a contiguous representation in memory and views for the segments
AlexandreAbraham Jun 8, 2016
bb948bb
Fix bug in PathPatch
AlexandreAbraham Sep 20, 2016
e6211bd
Fix vstack bug
AlexandreAbraham Sep 20, 2016
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Use a contiguous representation in memory and views for the segments
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@AlexandreAbraham
AlexandreAbraham committed Jun 8, 2016
commit 63159615ca443d2e6be51fb5e9f28eeeeda42438
77 changes: 50 additions & 27 deletions lib/mpl_toolkits/mplot3d/art3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -217,23 +217,39 @@ def set_segments(self, segments):
'''
Set 3D segments
'''
self._segments3d = np.asanyarray(segments)
self._seg_sizes = [len(c) for c in segments]
self._segments3d = []
if len(segments) > 0:
# Store the points in a single array for easier projection
n_segments = np.sum(self._seg_sizes)
# Put all segments in a big array
self._segments3d_data = np.vstack(segments)
# Add a fourth dimension for quaternions
self._segments3d_data = np.hstack([self._segments3d_data,
np.ones((n_segments, 1))])
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This would be marginally better as

self._segments3d_data  = np.empty((n_segments, 4))
self._segments3d_data[:,:3] = segments
self._segments3d_data[:,3] = 1

Also, are you sure you mean "quaternion" and not "homogenous coordinate"?


# For coveniency, store a view of the array in the original shape
cum_s = 0
for s in self._seg_sizes:
self._segments3d.append(
self._segments3d_data[cum_s:cum_s + s, :3])
cum_s += s
LineCollection.set_segments(self, [])

def do_3d_projection(self, renderer):
'''
Project the points according to renderer matrix.
'''
shape = self._segments3d.shape
segments3d = np.transpose(self._segments3d, axes=[2, 0, 1])
segments3d = segments3d.reshape((3, -1))
# Pad ones
segments3d = np.vstack([segments3d, np.ones((1, segments3d.shape[1]))])
xys = proj3d.proj_transform_vec(segments3d, renderer.M)
xys = np.reshape(xys.T, shape)
segments_2d = xys[:, :, 0:2]
if len(self._segments3d) == 0:
return 1e9
xys = proj3d.proj_transform_vec(self._segments3d_data.T, renderer.M).T
segments_2d = []
cum_s = 0
for s in self._seg_sizes:
segments_2d.append(xys[cum_s:cum_s + s, :2])
cum_s += s
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I think this loop is np.split in some form

LineCollection.set_segments(self, segments_2d)
minz = np.min(xys[:, :, 2]) if xys.size > 0 else 1e9
minz = np.min(xys[:, 2])
return minz

def draw(self, renderer, project=False):
Expand Down Expand Up @@ -301,7 +317,7 @@ def set_3d_properties(self, path, zs=0, zdir='z'):

def do_3d_projection(self, renderer):
# pad ones
s = np.vstack(self._segmenta3d, np.ones(self._segment3d.shape[1]))
s = np.vstack(self._segments3d, np.ones(self._segments3d.shape[1]))
vxyzis = proj3d.proj_transform_vec_clip(s, renderer.M)
self._path2d = mpath.Path(vxyzis[0:2].T, self._code3d)
# FIXME: coloring
Expand Down Expand Up @@ -433,8 +449,10 @@ def set_3d_properties(self, zs, zdir):
# Force the collection to initialize the face and edgecolors
# just in case it is a scalarmappable with a colormap.
self.update_scalarmappable()
offsets = np.vstack(self.get_offsets(), np.ones(len(verts)) * zs)
self._offsets3d = juggle_axes_vec(offsets, zdir)
offsets = self.get_offsets()
offsets = np.hstack([offsets,
(np.ones(len(offsets)) * zs)[:, np.newaxis]])
self._offsets3d = juggle_axes_vec(offsets, zdir).T
self._facecolor3d = self.get_facecolor()
self._edgecolor3d = self.get_edgecolor()
self.stale = True
Expand Down Expand Up @@ -539,14 +557,16 @@ def set_zsort(self, zsort):

def get_vector(self, segments3d):
"""Optimize points for projection"""
segments3d = np.asarray(segments3d)
# Segments 3d are given in shape (n_segments, segsize, 3)
self._segsize = segments3d.shape[1]
# Flatten
xyz = segments3d.T.reshape((3, -1))
# Add a fourth dimension with only ones
ones = np.ones(xyz.shape[1])
self._vec = np.vstack([xyz, ones])

self._seg_sizes = [len(c) for c in segments3d]
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np.full(len(segments3d), len(c))

self._vec = []
if len(segments3d) > 0:
# Store the points in a single array for easier projection
n_segments = np.sum(self._seg_sizes)
# Put all segments in a big array
self._vec = np.vstack(segments3d)
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Do not use self._vec as a temporary value.

# Add a fourth dimension for quaternions
self._vec = np.hstack([self._vec, np.ones((n_segments, 1))]).T

def set_verts(self, verts, closed=True):
'''Set 3D vertices.'''
Expand Down Expand Up @@ -574,7 +594,7 @@ 8000 def set_3d_properties(self):
self._alpha3d = PolyCollection.get_alpha(self)
self.stale = True

def set_sort_zpos(self,val):
def set_sort_zpos(self, val):
'''Set the position to use for z-sorting.'''
self._sort_zpos = val
self.stale = True
Expand All @@ -588,9 +608,12 @@ def do_3d_projection(self, renderer):
self.update_scalarmappable()
self._facecolors3d = self._facecolors

xys = proj3d.proj_transform_vec(self._vec, renderer.M)
xys = np.reshape(xys, (3, self._segsize, -1))
xyzlist = xys.T
xys = proj3d.proj_transform_vec(self._vec, renderer.M).T
xyzlist = []
cum_s = 0
for s in self._seg_sizes:
xyzlist.append(xys[cum_s:cum_s + s, :3])
cum_s += s

# This extra fuss is to re-order face / edge colors
cface = self._facecolors3d
Expand All @@ -605,11 +628,11 @@ def do_3d_projection(self, renderer):
# if required sort by depth (furthest drawn first)
if self._zsort:
z_argsort = np.argsort(
self._zsortfunc(xyzlist[:, :, 2], axis=1))[::-1]
[self._zsortfunc(xyz[:, 2]) for xyz in xyzlist])[::-1]
else:
raise ValueError("whoops")

segments_2d = xyzlist[z_argsort, :, 0:2]
segments_2d = [xyzlist[i][:, 0:2] for i in z_argsort]
if self._codes3d is not None:
codes = self._codes3d[z_argsort]
PolyCollection.set_verts_and_codes(self, segments_2d, codes)
Expand Down
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