99 lines
3.6 KiB
Python
99 lines
3.6 KiB
Python
"""
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===================================
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Demo of OPTICS clustering algorithm
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===================================
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Finds core samples of high density and expands clusters from them.
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This example uses data that is generated so that the clusters have
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different densities.
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The :class:`sklearn.cluster.OPTICS` is first used with its Xi cluster detection
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method, and then setting specific thresholds on the reachability, which
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corresponds to :class:`sklearn.cluster.DBSCAN`. We can see that the different
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clusters of OPTICS's Xi method can be recovered with different choices of
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thresholds in DBSCAN.
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"""
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# Authors: Shane Grigsby <refuge@rocktalus.com>
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# Adrin Jalali <adrin.jalali@gmail.com>
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# License: BSD 3 clause
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from sklearn.cluster import OPTICS, cluster_optics_dbscan
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import matplotlib.gridspec as gridspec
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import matplotlib.pyplot as plt
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import numpy as np
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# Generate sample data
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np.random.seed(0)
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n_points_per_cluster = 250
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C1 = [-5, -2] + .8 * np.random.randn(n_points_per_cluster, 2)
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C2 = [4, -1] + .1 * np.random.randn(n_points_per_cluster, 2)
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C3 = [1, -2] + .2 * np.random.randn(n_points_per_cluster, 2)
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C4 = [-2, 3] + .3 * np.random.randn(n_points_per_cluster, 2)
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C5 = [3, -2] + 1.6 * np.random.randn(n_points_per_cluster, 2)
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C6 = [5, 6] + 2 * np.random.randn(n_points_per_cluster, 2)
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X = np.vstack((C1, C2, C3, C4, C5, C6))
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clust = OPTICS(min_samples=50, xi=.05, min_cluster_size=.05)
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# Run the fit
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clust.fit(X)
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labels_050 = cluster_optics_dbscan(reachability=clust.reachability_,
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core_distances=clust.core_distances_,
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ordering=clust.ordering_, eps=0.5)
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labels_200 = cluster_optics_dbscan(reachability=clust.reachability_,
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core_distances=clust.core_distances_,
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ordering=clust.ordering_, eps=2)
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space = np.arange(len(X))
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reachability = clust.reachability_[clust.ordering_]
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labels = clust.labels_[clust.ordering_]
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plt.figure(figsize=(10, 7))
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G = gridspec.GridSpec(2, 3)
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ax1 = plt.subplot(G[0, :])
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ax2 = plt.subplot(G[1, 0])
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ax3 = plt.subplot(G[1, 1])
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ax4 = plt.subplot(G[1, 2])
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# Reachability plot
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colors = ['g.', 'r.', 'b.', 'y.', 'c.']
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for klass, color in zip(range(0, 5), colors):
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Xk = space[labels == klass]
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Rk = reachability[labels == klass]
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ax1.plot(Xk, Rk, color, alpha=0.3)
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ax1.plot(space[labels == -1], reachability[labels == -1], 'k.', alpha=0.3)
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ax1.plot(space, np.full_like(space, 2., dtype=float), 'k-', alpha=0.5)
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ax1.plot(space, np.full_like(space, 0.5, dtype=float), 'k-.', alpha=0.5)
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ax1.set_ylabel('Reachability (epsilon distance)')
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ax1.set_title('Reachability Plot')
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# OPTICS
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colors = ['g.', 'r.', 'b.', 'y.', 'c.']
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for klass, color in zip(range(0, 5), colors):
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Xk = X[clust.labels_ == klass]
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ax2.plot(Xk[:, 0], Xk[:, 1], color, alpha=0.3)
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ax2.plot(X[clust.labels_ == -1, 0], X[clust.labels_ == -1, 1], 'k+', alpha=0.1)
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ax2.set_title('Automatic Clustering\nOPTICS')
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# DBSCAN at 0.5
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colors = ['g', 'greenyellow', 'olive', 'r', 'b', 'c']
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for klass, color in zip(range(0, 6), colors):
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Xk = X[labels_050 == klass]
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ax3.plot(Xk[:, 0], Xk[:, 1], color, alpha=0.3, marker='.')
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ax3.plot(X[labels_050 == -1, 0], X[labels_050 == -1, 1], 'k+', alpha=0.1)
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ax3.set_title('Clustering at 0.5 epsilon cut\nDBSCAN')
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# DBSCAN at 2.
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colors = ['g.', 'm.', 'y.', 'c.']
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for klass, color in zip(range(0, 4), colors):
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Xk = X[labels_200 == klass]
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ax4.plot(Xk[:, 0], Xk[:, 1], color, alpha=0.3)
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ax4.plot(X[labels_200 == -1, 0], X[labels_200 == -1, 1], 'k+', alpha=0.1)
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ax4.set_title('Clustering at 2.0 epsilon cut\nDBSCAN')
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plt.tight_layout()
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plt.show()
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