Examples for plotting a simplicial complex with plotly / matplotlib

2 files changed, 68 insertions, 0 deletions

diff --git a/src/python/example/plot_alpha_complex.py b/src/python/example/plot_alpha_complex.py
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+++ b/src/python/example/plot_alpha_complex.py
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+#!/usr/bin/env python
+
+import numpy as np
+import gudhi
+ac = gudhi.AlphaComplex(off_file='../../data/points/tore3D_1307.off')
+st = ac.create_simplex_tree()
+points = np.array([ac.get_point(i) for i in range(st.num_vertices())])
+# We want to plot the alpha-complex with alpha=0.1.
+# We are only going to plot the triangles
+triangles = np.array([s[0] for s in st.get_skeleton(2) if len(s[0])==3 and s[1] <= .1])
+
+# First possibility: plotly
+import plotly.graph_objects as go
+fig = go.Figure(data=[
+    go.Mesh3d(
+        x=points[:,0],
+        y=points[:,1],
+        z=points[:,2],
+        i = triangles[:,0],
+        j = triangles[:,1],
+        k = triangles[:,2],
+    )
+])
+fig.show()
+
+# Second possibility: matplotlib
+from mpl_toolkits.mplot3d import Axes3D
+import matplotlib.pyplot as plt
+fig = plt.figure()
+ax = fig.gca(projection='3d')
+ax.plot_trisurf(points[:,0], points[:,1], points[:,2], triangles=triangles)
+plt.show()
+
+# Third possibility: mayavi.mlab.triangular_mesh
diff --git a/src/python/example/plot_rips_complex.py b/src/python/example/plot_rips_complex.py
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+++ b/src/python/example/plot_rips_complex.py
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+#!/usr/bin/env python
+
+import numpy as np
+import gudhi
+points = np.array(gudhi.read_off('../../data/points/Kl.off'))
+rc = gudhi.RipsComplex(points=points, max_edge_length=.2)
+st = rc.create_simplex_tree(max_dimension=2)
+# We are only going to plot the triangles
+triangles = np.array([s[0] for s in st.get_skeleton(2) if len(s[0])==3])
+
+# First possibility: plotly
+import plotly.graph_objects as go
+fig = go.Figure(data=[
+    go.Mesh3d(
+        # Use the first 3 coordinates, but we could as easily pick others
+        x=points[:,0],
+        y=points[:,1],
+        z=points[:,2],
+        i = triangles[:,0],
+        j = triangles[:,1],
+        k = triangles[:,2],
+    )
+])
+fig.show()
+
+# Second possibility: matplotlib
+from mpl_toolkits.mplot3d import Axes3D
+import matplotlib.pyplot as plt
+fig = plt.figure()
+ax = fig.gca(projection='3d')
+ax.plot_trisurf(points[:,0], points[:,1], points[:,2], triangles=triangles)
+plt.show()
+
+# Third possibility: mayavi.mlab.triangular_mesh