scikit-learn/benchmarks/bench_plot_neighbors.py

"""
Plot the scaling of the nearest neighbors algorithms with k, D, and N
"""
from time import time

import numpy as np
import matplotlib.pyplot as plt
from matplotlib import ticker

from sklearn import neighbors, datasets


def get_data(N, D, dataset='dense'):
    if dataset == 'dense':
        np.random.seed(0)
        return np.random.random((N, D))
    elif dataset == 'digits':
        X = datasets.load_digits().data
        i = np.argsort(X[0])[::-1]
        X = X[:, i]
        return X[:N, :D]
    else:
        raise ValueError("invalid dataset: %s" % dataset)


def barplot_neighbors(Nrange=2 ** np.arange(1, 11),
                      Drange=2 ** np.arange(7),
                      krange=2 ** np.arange(10),
                      N=1000,
                      D=64,
                      k=5,
                      leaf_size=30,
                      dataset='digits'):
    algorithms = ('kd_tree', 'brute', 'ball_tree')
    fiducial_values = {'N': N,
                       'D': D,
                       'k': k}

    #------------------------------------------------------------
    # varying N
    N_results_build = dict([(alg, np.zeros(len(Nrange)))
                            for alg in algorithms])
    N_results_query = dict([(alg, np.zeros(len(Nrange)))
                            for alg in algorithms])

    for i, NN in enumerate(Nrange):
        print("N = %i (%i out of %i)" % (NN, i + 1, len(Nrange)))
        X = get_data(NN, D, dataset)
        for algorithm in algorithms:
            nbrs = neighbors.NearestNeighbors(n_neighbors=min(NN, k),
                                              algorithm=algorithm,
                                              leaf_size=leaf_size)
            t0 = time()
            nbrs.fit(X)
            t1 = time()
            nbrs.kneighbors(X)
            t2 = time()

            N_results_build[algorithm][i] = (t1 - t0)
            N_results_query[algorithm][i] = (t2 - t1)

    #------------------------------------------------------------
    # varying D
    D_results_build = dict([(alg, np.zeros(len(Drange)))
                            for alg in algorithms])
    D_results_query = dict([(alg, np.zeros(len(Drange)))
                            for alg in algorithms])

    for i, DD in enumerate(Drange):
        print("D = %i (%i out of %i)" % (DD, i + 1, len(Drange)))
        X = get_data(N, DD, dataset)
        for algorithm in algorithms:
            nbrs = neighbors.NearestNeighbors(n_neighbors=k,
                                              algorithm=algorithm,
                                              leaf_size=leaf_size)
            t0 = time()
            nbrs.fit(X)
            t1 = time()
            nbrs.kneighbors(X)
            t2 = time()

            D_results_build[algorithm][i] = (t1 - t0)
            D_results_query[algorithm][i] = (t2 - t1)

    #------------------------------------------------------------
    # varying k
    k_results_build = dict([(alg, np.zeros(len(krange)))
                            for alg in algorithms])
    k_results_query = dict([(alg, np.zeros(len(krange)))
                            for alg in algorithms])

    X = get_data(N, DD, dataset)

    for i, kk in enumerate(krange):
        print("k = %i (%i out of %i)" % (kk, i + 1, len(krange)))
        for algorithm in algorithms:
            nbrs = neighbors.NearestNeighbors(n_neighbors=kk,
                                              algorithm=algorithm,
                                              leaf_size=leaf_size)
            t0 = time()
            nbrs.fit(X)
            t1 = time()
            nbrs.kneighbors(X)
            t2 = time()

            k_results_build[algorithm][i] = (t1 - t0)
            k_results_query[algorithm][i] = (t2 - t1)

    plt.figure(figsize=(8, 11))

    for (sbplt, vals, quantity,
         build_time, query_time) in [(311, Nrange, 'N',
                                      N_results_build,
                                      N_results_query),
                                     (312, Drange, 'D',
                                      D_results_build,
                                      D_results_query),
                                     (313, krange, 'k',
                                      k_results_build,
                                      k_results_query)]:
        ax = plt.subplot(sbplt, yscale='log')
        plt.grid(True)

        tick_vals = []
        tick_labels = []

        bottom = 10 ** np.min([min(np.floor(np.log10(build_time[alg])))
                               for alg in algorithms])

        for i, alg in enumerate(algorithms):
            xvals = 0.1 + i * (1 + len(vals)) + np.arange(len(vals))
            width = 0.8

            c_bar = plt.bar(xvals, build_time[alg] - bottom,
                            width, bottom, color='r')
            q_bar = plt.bar(xvals, query_time[alg],
                            width, build_time[alg], color='b')

            tick_vals += list(xvals + 0.5 * width)
            tick_labels += ['%i' % val for val in vals]

            plt.text((i + 0.02) / len(algorithms), 0.98, alg,
                     transform=ax.transAxes,
                     ha='left',
                     va='top',
                     bbox=dict(facecolor='w', edgecolor='w', alpha=0.5))

            plt.ylabel('Time (s)')

        ax.xaxis.set_major_locator(ticker.FixedLocator(tick_vals))
        ax.xaxis.set_major_formatter(ticker.FixedFormatter(tick_labels))

        for label in ax.get_xticklabels():
            label.set_rotation(-90)
            label.set_fontsize(10)

        title_string = 'Varying %s' % quantity

        descr_string = ''

        for s in 'NDk':
            if s == quantity:
                pass
            else:
                descr_string += '%s = %i, ' % (s, fiducial_values[s])

        descr_string = descr_string[:-2]

        plt.text(1.01, 0.5, title_string,
                 transform=ax.transAxes, rotation=-90,
                 ha='left', va='center', fontsize=20)

        plt.text(0.99, 0.5, descr_string,
                 transform=ax.transAxes, rotation=-90,
                 ha='right', va='center')

        plt.gcf().suptitle("%s data set" % dataset.capitalize(), fontsize=16)

    plt.figlegend((c_bar, q_bar), ('construction', 'N-point query'),
                  'upper right')

if __name__ == '__main__':
    barplot_neighbors(dataset='digits')
    barplot_neighbors(dataset='dense')
    plt.show()