%matplotlib inline

from sklearn.manifold import bhtsne
import sys
import numpy as np
import matplotlib.pyplot as plt
from time import time
from matplotlib import offsetbox
from sklearn import (manifold, datasets, decomposition, ensemble, lda, random_projection)
from sklearn.datasets import fetch_mldata

digits = datasets.load_digits(n_class=6)
X = digits.data
y = digits.target
n_samples, n_features = X.shape
n_neighbors = 30

def plot_embedding(X, title=None):
    x_min, x_max = np.min(X, 0), np.max(X, 0)
    X = (X - x_min) / (x_max - x_min)

    plt.figure(figsize=(15,15))
    ax = plt.subplot(111)
    for i in range(X.shape[0]):
        plt.text(X[i, 0], X[i, 1], str(digits.target[i]),
                 color=plt.cm.Set1(y[i] / 10.),
                 fontdict={'weight': 'bold', 'size': 9})

    if hasattr(offsetbox, 'AnnotationBbox'):
        # only print thumbnails with matplotlib > 1.0
        shown_images = np.array([[1., 1.]])  # just something big
        for i in range(digits.data.shape[0]):
            dist = np.sum((X[i] - shown_images) ** 2, 1)
            if np.min(dist) < 4e-3:
                # don't show points that are too close
                continue
            shown_images = np.r_[shown_images, [X[i]]]
            imagebox = offsetbox.AnnotationBbox(
                offsetbox.OffsetImage(digits.images[i], cmap=plt.cm.gray_r),
                X[i])
            ax.add_artist(imagebox)
    plt.xticks([]), plt.yticks([])
    if title is not None:
        plt.title(title)

tsne = manifold.TSNE(n_components=2, init='pca', random_state=1, method='barnes_hut', n_iter=1000, verbose=20)
t0 = time()
Xtbh = tsne.fit_transform(X)
t1 = time()
dtbh = t1 - t0

plot_embedding(Xtbh, title="Barnes-Hut t-SNE visualization of MNIST digits in %1.1f sec" % dtbh)

tsne = manifold.TSNE(n_components=2, init='pca', random_state=1, method='standard', n_iter=1000, verbose=20)
t0 = time()
Xts = tsne.fit_transform(X)
t1 = time()
dts = t1 - t0

plot_embedding(Xts, title="Standard t-SNE visualization of MNIST digits in %1.1f sec" % dts)