| @@ -16,18 +16,18 @@ import numpy as np | |||
| import networkx as nx | |||
| from control import dlyap | |||
| from gklearn.utils.parallel import parallel_gm, parallel_me | |||
| from gklearn.kernels import RandomWalk | |||
| from gklearn.kernels import RandomWalkMeta | |||
| class SylvesterEquation(RandomWalk): | |||
| class SylvesterEquation(RandomWalkMeta): | |||
| def __init__(self, **kwargs): | |||
| RandomWalk.__init__(self, **kwargs) | |||
| super().__init__(**kwargs) | |||
| def _compute_gm_series(self): | |||
| self._check_edge_weight(self._graphs) | |||
| self._check_edge_weight(self._graphs, self._verbose) | |||
| self._check_graphs(self._graphs) | |||
| if self._verbose >= 2: | |||
| import warnings | |||
| @@ -38,7 +38,7 @@ class SylvesterEquation(RandomWalk): | |||
| # compute Gram matrix. | |||
| gram_matrix = np.zeros((len(self._graphs), len(self._graphs))) | |||
| if self._q == None: | |||
| if self._q is None: | |||
| # don't normalize adjacency matrices if q is a uniform vector. Note | |||
| # A_wave_list actually contains the transposes of the adjacency matrices. | |||
| if self._verbose >= 2: | |||
| @@ -54,16 +54,16 @@ class SylvesterEquation(RandomWalk): | |||
| # norm[norm == 0] = 1 | |||
| # A_wave_list.append(A_tilde / norm) | |||
| if self._p == None: # p is uniform distribution as default. | |||
| if self._p is None: # p is uniform distribution as default. | |||
| from itertools import combinations_with_replacement | |||
| itr = combinations_with_replacement(range(0, len(self._graphs)), 2) | |||
| if self._verbose >= 2: | |||
| iterator = tqdm(itr, desc='calculating kernels', file=sys.stdout) | |||
| iterator = tqdm(itr, desc='Computing kernels', file=sys.stdout) | |||
| else: | |||
| iterator = itr | |||
| for i, j in iterator: | |||
| kernel = self.__kernel_do(A_wave_list[i], A_wave_list[j], lmda) | |||
| kernel = self._kernel_do(A_wave_list[i], A_wave_list[j], lmda) | |||
| gram_matrix[i][j] = kernel | |||
| gram_matrix[j][i] = kernel | |||
| @@ -76,7 +76,7 @@ class SylvesterEquation(RandomWalk): | |||
| def _compute_gm_imap_unordered(self): | |||
| self._check_edge_weight(self._graphs) | |||
| self._check_edge_weight(self._graphs, self._verbose) | |||
| self._check_graphs(self._graphs) | |||
| if self._verbose >= 2: | |||
| import warnings | |||
| @@ -85,7 +85,7 @@ class SylvesterEquation(RandomWalk): | |||
| # compute Gram matrix. | |||
| gram_matrix = np.zeros((len(self._graphs), len(self._graphs))) | |||
| if self._q == None: | |||
| if self._q is None: | |||
| # don't normalize adjacency matrices if q is a uniform vector. Note | |||
| # A_wave_list actually contains the transposes of the adjacency matrices. | |||
| if self._verbose >= 2: | |||
| @@ -94,7 +94,7 @@ class SylvesterEquation(RandomWalk): | |||
| iterator = self._graphs | |||
| A_wave_list = [nx.adjacency_matrix(G, self._edge_weight).todense().transpose() for G in iterator] # @todo: parallel? | |||
| if self._p == None: # p is uniform distribution as default. | |||
| if self._p is None: # p is uniform distribution as default. | |||
| def init_worker(A_wave_list_toshare): | |||
| global G_A_wave_list | |||
| G_A_wave_list = A_wave_list_toshare | |||
| @@ -113,7 +113,7 @@ class SylvesterEquation(RandomWalk): | |||
| def _compute_kernel_list_series(self, g1, g_list): | |||
| self._check_edge_weight(g_list + [g1]) | |||
| self._check_edge_weight(g_list + [g1], self._verbose) | |||
| self._check_graphs(g_list + [g1]) | |||
| if self._verbose >= 2: | |||
| import warnings | |||
| @@ -124,24 +124,24 @@ class SylvesterEquation(RandomWalk): | |||
| # compute kernel list. | |||
| kernel_list = [None] * len(g_list) | |||
| if self._q == None: | |||
| if self._q is None: | |||
| # don't normalize adjacency matrices if q is a uniform vector. Note | |||
| # A_wave_list actually contains the transposes of the adjacency matrices. | |||
| A_wave_1 = nx.adjacency_matrix(g1, self._edge_weight).todense().transpose() | |||
| if self._verbose >= 2: | |||
| iterator = tqdm(range(len(g_list)), desc='compute adjacency matrices', file=sys.stdout) | |||
| iterator = tqdm(g_list, desc='compute adjacency matrices', file=sys.stdout) | |||
| else: | |||
| iterator = range(len(g_list)) | |||
| iterator = g_list | |||
| A_wave_list = [nx.adjacency_matrix(G, self._edge_weight).todense().transpose() for G in iterator] | |||
| if self._p == None: # p is uniform distribution as default. | |||
| if self._p is None: # p is uniform distribution as default. | |||
| if self._verbose >= 2: | |||
| iterator = tqdm(range(len(g_list)), desc='calculating kernels', file=sys.stdout) | |||
| iterator = tqdm(range(len(g_list)), desc='Computing kernels', file=sys.stdout) | |||
| else: | |||
| iterator = range(len(g_list)) | |||
| for i in iterator: | |||
| kernel = self.__kernel_do(A_wave_1, A_wave_list[i], lmda) | |||
| kernel = self._kernel_do(A_wave_1, A_wave_list[i], lmda) | |||
| kernel_list[i] = kernel | |||
| else: # @todo | |||
| @@ -153,7 +153,7 @@ class SylvesterEquation(RandomWalk): | |||
| def _compute_kernel_list_imap_unordered(self, g1, g_list): | |||
| self._check_edge_weight(g_list + [g1]) | |||
| self._check_edge_weight(g_list + [g1], self._verbose) | |||
| self._check_graphs(g_list + [g1]) | |||
| if self._verbose >= 2: | |||
| import warnings | |||
| @@ -162,17 +162,17 @@ class SylvesterEquation(RandomWalk): | |||
| # compute kernel list. | |||
| kernel_list = [None] * len(g_list) | |||
| if self._q == None: | |||
| if self._q is None: | |||
| # don't normalize adjacency matrices if q is a uniform vector. Note | |||
| # A_wave_list actually contains the transposes of the adjacency matrices. | |||
| A_wave_1 = nx.adjacency_matrix(g1, self._edge_weight).todense().transpose() | |||
| if self._verbose >= 2: | |||
| iterator = tqdm(range(len(g_list)), desc='compute adjacency matrices', file=sys.stdout) | |||
| iterator = tqdm(g_list, desc='compute adjacency matrices', file=sys.stdout) | |||
| else: | |||
| iterator = range(len(g_list)) | |||
| iterator = g_list | |||
| A_wave_list = [nx.adjacency_matrix(G, self._edge_weight).todense().transpose() for G in iterator] # @todo: parallel? | |||
| if self._p == None: # p is uniform distribution as default. | |||
| if self._p is None: # p is uniform distribution as default. | |||
| def init_worker(A_wave_1_toshare, A_wave_list_toshare): | |||
| global G_A_wave_1, G_A_wave_list | |||
| G_A_wave_1 = A_wave_1_toshare | |||
| @@ -186,7 +186,7 @@ class SylvesterEquation(RandomWalk): | |||
| len_itr = len(g_list) | |||
| parallel_me(do_fun, func_assign, kernel_list, itr, len_itr=len_itr, | |||
| init_worker=init_worker, glbv=(A_wave_1, A_wave_list), method='imap_unordered', | |||
| n_jobs=self._n_jobs, itr_desc='calculating kernels', verbose=self._verbose) | |||
| n_jobs=self._n_jobs, itr_desc='Computing kernels', verbose=self._verbose) | |||
| else: # @todo | |||
| pass | |||
| @@ -201,7 +201,7 @@ class SylvesterEquation(RandomWalk): | |||
| def _compute_single_kernel_series(self, g1, g2): | |||
| self._check_edge_weight([g1] + [g2]) | |||
| self._check_edge_weight([g1] + [g2], self._verbose) | |||
| self._check_graphs([g1] + [g2]) | |||
| if self._verbose >= 2: | |||
| import warnings | |||
| @@ -209,13 +209,13 @@ class SylvesterEquation(RandomWalk): | |||
| lmda = self._weight | |||
| if self._q == None: | |||
| if self._q is None: | |||
| # don't normalize adjacency matrices if q is a uniform vector. Note | |||
| # A_wave_list actually contains the transposes of the adjacency matrices. | |||
| A_wave_1 = nx.adjacency_matrix(g1, self._edge_weight).todense().transpose() | |||
| A_wave_2 = nx.adjacency_matrix(g2, self._edge_weight).todense().transpose() | |||
| if self._p == None: # p is uniform distribution as default. | |||
| kernel = self.__kernel_do(A_wave_1, A_wave_2, lmda) | |||
| if self._p is None: # p is uniform distribution as default. | |||
| kernel = self._kernel_do(A_wave_1, A_wave_2, lmda) | |||
| else: # @todo | |||
| pass | |||
| else: # @todo | |||
| @@ -224,7 +224,7 @@ class SylvesterEquation(RandomWalk): | |||
| return kernel | |||
| def __kernel_do(self, A_wave1, A_wave2, lmda): | |||
| def _kernel_do(self, A_wave1, A_wave2, lmda): | |||
| S = lmda * A_wave2 | |||
| T_t = A_wave1 | |||
| @@ -242,4 +242,4 @@ class SylvesterEquation(RandomWalk): | |||
| def _wrapper_kernel_do(self, itr): | |||
| i = itr[0] | |||
| j = itr[1] | |||
| return i, j, self.__kernel_do(G_A_wave_list[i], G_A_wave_list[j], self._weight) | |||
| return i, j, self._kernel_do(G_A_wave_list[i], G_A_wave_list[j], self._weight) | |||