Example #1
0
    def get_S(self, dimensions=2, pub=None):
        similarity = self.get_similarity(self.statistic)
        if pub is not None:
            pub.array_as_image('similarity', similarity,
                               caption='Similarity statistic')
            plot_spectrum(pub, 'similarity', similarity)

        if self.scale_score:
            R = scale_score(similarity).astype('float32')
            R = R / R.max()
            if pub is not None:
                pub.array_as_image('scale_score', R)

        else:
            R = similarity

        D = 1 - R
        D = D * np.pi / D.max()
        np.fill_diagonal(D, 0)

        if pub is not None:
            #            pub.array_as_image('D', D)
            P = D * D
            B = double_center(P)
            #            plot_spectrum(pub, 'D', D)
            #            plot_spectrum(pub, 'P', P)
            plot_spectrum(pub, 'B', B)

        S = mds(D, ndim=dimensions)
#        S = inner_product_embedding(similarity, 3)
#        S = S[1:3, :]
        return S
Example #2
0
def rank_test():
    ''' Check that the double-centered matrix has small rank. '''
    for n in range(5, 50, 5):
        for k in range(1, 5):
            P = np.random.rand(k, n)
            D = euclidean_distances(P)
            B = double_center(D * D)
            w, v = eigh(B)  #@UnusedVariable
            w = w[::-1]  # descending
            # normalize
            wn = w / w[0]
            small = np.abs(wn[k])
            assert_allclose(0, small, atol=1e-7)
Example #3
0
def rank_test():
    ''' Check that the double-centered matrix has small rank. '''
    for n in range(5, 50, 5):
        for k in range(1, 5):
            P = np.random.rand(k, n)
            D = euclidean_distances(P)
            B = double_center(D * D)
            w, v = eigh(B)  #@UnusedVariable
            w = w[::-1]  # descending
            # normalize
            wn = w / w[0]
            small = np.abs(wn[k])
            assert_allclose(0, small, atol=1e-7)