python类SpectralEmbedding()的实例源码

def apply_lens(df, lens='pca', dist='euclidean', n_dim=2, **kwargs):
    """
    input: N x F dataframe of observations
    output: N x n_dim image of input data under lens function
    """
    if n_dim != 2:
        raise 'error: image of data set must be two-dimensional'
    if dist not in ['euclidean', 'correlation']:
        raise 'error: only euclidean and correlation distance metrics are supported'
    if lens == 'pca' and dist != 'euclidean':
        raise 'error: PCA requires the use of euclidean distance metric'

    if lens == 'pca':
        df_lens = pd.DataFrame(decomposition.PCA(n_components=n_dim, **kwargs).fit_transform(df), df.index)
    elif lens == 'mds':
        D = metrics.pairwise.pairwise_distances(df, metric=dist)
        df_lens = pd.DataFrame(manifold.MDS(n_components=n_dim, **kwargs).fit_transform(D), df.index)
    elif lens == 'neighbor':
        D = metrics.pairwise.pairwise_distances(df, metric=dist)
        df_lens = pd.DataFrame(manifold.SpectralEmbedding(n_components=n_dim, **kwargs).fit_transform(D), df.index)
    else:
        raise 'error: only PCA, MDS, neighborhood lenses are supported'

    return df_lens

def do_embedding(self, event=None):
        converted = self.parent.converted
        if converted is None:
            #self.conversion.convert_frames()
            self.parent.converted = np.load(self.parent.output_folder+'/converted.npy') #FIXME For debugging
            converted = self.parent.converted

        method_ind = self.method.currentIndex()
        print('Doing %s' % self.method.currentText())
        if method_ind == 0:
            self.embedder = manifold.SpectralEmbedding(n_components=4, n_jobs=-1)
        elif method_ind == 1:
            self.embedder = manifold.Isomap(n_components=4, n_jobs=-1)
        elif method_ind == 2:
            self.embedder = manifold.LocallyLinearEmbedding(n_components=4, n_jobs=-1, n_neighbors=20, method='modified')
        elif method_ind == 3:
            self.embedder = manifold.LocallyLinearEmbedding(n_components=4, n_jobs=-1, n_neighbors=20, method='hessian', eigen_solver='dense')
        elif method_ind == 4:
            self.embedder = manifold.MDS(n_components=4, n_jobs=-1)
        elif method_ind == 5:
            self.embedder = manifold.TSNE(n_components=3, init='pca')
        self.embedder.fit(converted)
        self.embed = self.embedder.embedding_
        self.embed_plot = self.embed

        self.gen_hist()
        self.plot_embedding()
        if not self.embedded:
            self.add_classes_frame()
        self.embedded = True

def cluster_scatter_plot(similarity_file):
  def get_cmap(N):
    '''Returns a function that maps each index in 0, 1, ... N-1 to a distinct 
    RGB color.'''
    color_norm  = colors.Normalize(vmin=0, vmax=N-1)
    scalar_map = cmx.ScalarMappable(norm=color_norm, cmap='hsv') 
    def map_index_to_rgb_color(index):
        return scalar_map.to_rgba(index)
    return map_index_to_rgb_color

  with open(similarity_file, 'r', 'utf-8') as f:
    similarity_data = json.load(f)
  labels = []
  point_colors = []
  num_clusters = len(similarity_data['cluster2doc'].keys())
  cmap = get_cmap(num_clusters)
  for model_name in similarity_data['model_names']:
    model_name = os.path.splitext(os.path.basename(model_name))[0]
    cluster_label = similarity_data['doc2cluster'][model_name]
    point_colors.append(cmap(cluster_label))
    labels.append(re.compile(r"\s\([0-9]*\)-iter.*", re.IGNORECASE).split(model_name, 1)[0])
  embeddings = SpectralEmbedding(affinity='precomputed').fit_transform(np.array(similarity_data['similarity_matrix']))
  fig, ax = plt.subplots()
  x = embeddings[:, 0]
  y = embeddings[:, 1]
  annotes = ['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j'] * 10
  N = 100
  scatter = ax.scatter(x, y, c=point_colors[:],s=100*np.ones(shape=N))
  tooltip = mpld3.plugins.PointLabelTooltip(scatter, labels=labels)
  mpld3.plugins.connect(fig, tooltip)
  mpld3.show()
  # plt.scatter(tsne_embeddings[20:40, 0], tsne_embeddings[20:40, 1], c='b')
  # for label, x, y in zip(labels, tsne_embeddings[:, 0], tsne_embeddings[:, 1]):
  #   plt.annotate(
  #       label, 
  #       xy = (x, y),
  #       # textcoords = 'offset points',
  #       bbox = dict(boxstyle = 'round,pad=0.5', fc = 'yellow', alpha = 0.5))
  # plt.show()