def test_pca_init_with_only_affinities_passed(self):
aff = affinity.PerplexityBasedNN(self.x, 5, method="exact")
desired_init = initialization.spectral(aff.P)
embedding = TSNE(early_exaggeration_iter=0,
n_iter=0,
initialization="pca").fit(affinities=aff)
np.testing.assert_array_equal(embedding, desired_init)
def test_precomputed_dist_matrix_via_affinities_uses_spectral_init(self):
x = np.random.normal(0, 1, (200, 5))
d = squareform(pdist(x))
aff = affinity.PerplexityBasedNN(d, metric="precomputed")
desired_init = initialization.spectral(aff.P)
embedding = TSNE(early_exaggeration_iter=0,
n_iter=0).fit(affinities=aff)
np.testing.assert_array_equal(embedding, desired_init)