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ENH: spatial: faster 2D Voronoi and Convex Hull plotting #5061

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Oct 10, 2015
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ENH: spatial: faster 2D Voronoi and Convex Hull plotting #5061

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1815994
use matplotlib LineCollection to speed up diagram plotting
grlee77 Jul 16, 2015
844f4d9
add show_vertices option so vertex plotting can be disabled
grlee77 Jul 16, 2015
262e78a
fix PEP8 errors
grlee77 Jul 16, 2015
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32 changes: 25 additions & 7 deletions scipy/spatial/_plotutils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,20 +94,25 @@ def convex_hull_plot_2d(hull, ax=None):
Requires Matplotlib.

"""
from matplotlib.collections import LineCollection

if hull.points.shape[1] != 2:
raise ValueError("Convex hull is not 2-D")

ax.plot(hull.points[:,0], hull.points[:,1], 'o')
line_segments = []
for simplex in hull.simplices:
ax.plot(hull.points[simplex,0], hull.points[simplex,1], 'k-')

line_segments.append([(x, y) for x, y in hull.points[simplex]])
ax.add_collection(LineCollection(line_segments,
colors='k',
linestyle='solid'))
_adjust_bounds(ax, hull.points)

return ax.figure


@_held_figure
def voronoi_plot_2d(vor, ax=None):
def voronoi_plot_2d(vor, ax=None, **kw):
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Why not just add show_vertices=True here?

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I tried it as you suggest initially, but the _held_figure decorator was raising the following error:

TypeError: _held_figure() takes from 2 to 3 positional arguments but 4 were given

"""
Plot the given Voronoi diagram in 2-D

Expand All @@ -117,6 +122,8 @@ def voronoi_plot_2d(vor, ax=None):
Diagram to plot
ax : matplotlib.axes.Axes instance, optional
Axes to plot on
show_vertices : bool, optional
Add the Voronoi vertices to the plot.

Returns
-------
Expand All @@ -132,19 +139,27 @@ def voronoi_plot_2d(vor, ax=None):
Requires Matplotlib.

"""
from matplotlib.collections import LineCollection

if vor.points.shape[1] != 2:
raise ValueError("Voronoi diagram is not 2-D")

ax.plot(vor.points[:,0], vor.points[:,1], '.')
ax.plot(vor.vertices[:,0], vor.vertices[:,1], 'o')
if kw.get('show_vertices', True):
ax.plot(vor.vertices[:,0], vor.vertices[:,1], 'o')

line_segments = []
for simplex in vor.ridge_vertices:
simplex = np.asarray(simplex)
if np.all(simplex >= 0):
ax.plot(vor.vertices[simplex,0], vor.vertices[simplex,1], 'k-')
line_segments.append([(x, y) for x, y in vor.vertices[simplex]])

ax.add_collection(LineCollection(line_segments,
colors='k',
linestyle='solid'))
ptp_bound = vor.points.ptp(axis=0)

line_segments = []
center = vor.points.mean(axis=0)
for pointidx, simplex in zip(vor.ridge_points, vor.ridge_vertices):
simplex = np.asarray(simplex)
Expand All @@ -159,9 +174,12 @@ def voronoi_plot_2d(vor, ax=None):
direction = np.sign(np.dot(midpoint - center, n)) * n
far_point = vor.vertices[i] + direction * ptp_bound.max()

ax.plot([vor.vertices[i,0], far_point[0]],
[vor.vertices[i,1], far_point[1]], 'k--')
line_segments.append([(vor.vertices[i, 0], vor.vertices[i, 1]),
(far_point[0], far_point[1])])

ax.add_collection(LineCollection(line_segments,
colors='k',
linestyle='dashed'))
_adjust_bounds(ax, vor.points)

return ax.figure
2 changes: 2 additions & 0 deletions scipy/spatial/tests/test__plotutils.py
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Expand Up @@ -6,6 +6,7 @@
import matplotlib
matplotlib.rcParams['backend'] = 'Agg'
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
has_matplotlib = True
except:
has_matplotlib = False
Expand Down Expand Up @@ -37,6 +38,7 @@ def test_voronoi(self):
r = voronoi_plot_2d(obj, ax=fig.gca())
assert_(r is fig)
voronoi_plot_2d(obj)
voronoi_plot_2d(obj, show_vertices=False)

@dec.skipif(not has_matplotlib, "Matplotlib not available")
def test_convex_hull(self):
Expand Down