Python sparse.diags方法代码示例

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def normalize_features(feat):

    degree = np.asarray(feat.sum(1)).flatten()

    # set zeros to inf to avoid dividing by zero
    degree[degree == 0.] = np.inf

    degree_inv = 1. / degree
    degree_inv_mat = sp.diags([degree_inv], [0])
    feat_norm = degree_inv_mat.dot(feat)

    if feat_norm.nnz == 0:
        print('ERROR: normalized adjacency matrix has only zero entries!!!!!')
        exit

    return feat_norm 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def normalize_adj(A, is_sym=True, exponent=0.5):
  """
    Normalize adjacency matrix

    is_sym=True: D^{-1/2} A D^{-1/2}
    is_sym=False: D^{-1} A
  """
  rowsum = np.array(A.sum(1))

  if is_sym:
    r_inv = np.power(rowsum, -exponent).flatten()
  else:
    r_inv = np.power(rowsum, -1.0).flatten()

  r_inv[np.isinf(r_inv)] = 0.

  if sp.isspmatrix(A):
    r_mat_inv = sp.diags(r_inv.squeeze())
  else:
    r_mat_inv = np.diag(r_inv)

  if is_sym:
    return r_mat_inv.dot(A).dot(r_mat_inv)
  else:
    return r_mat_inv.dot(A) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def pre_factorization(G, n_components, exponent):
        """
        Network Embedding as Sparse Matrix Factorization
        """
        C1 = preprocessing.normalize(G, "l1")
        # Prepare negative samples
        neg = np.array(C1.sum(axis=0))[0] ** exponent
        neg = neg / neg.sum()
        neg = sparse.diags(neg, format="csr")
        neg = G.dot(neg)
        # Set negative elements to 1 -> 0 when log
        C1.data[C1.data <= 0] = 1
        neg.data[neg.data <= 0] = 1
        C1.data = np.log(C1.data)
        neg.data = np.log(neg.data)
        C1 -= neg
        features_matrix = ProNE.tsvd_rand(C1, n_components=n_components)
        return features_matrix 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def degree_power(A, k):
    r"""
    Computes \(\D^{k}\) from the given adjacency matrix. Useful for computing
    normalised Laplacian.
    :param A: rank 2 array or sparse matrix.
    :param k: exponent to which elevate the degree matrix.
    :return: if A is a dense array, a dense array; if A is sparse, a sparse
    matrix in DIA format.
    """
    degrees = np.power(np.array(A.sum(1)), k).flatten()
    degrees[np.isinf(degrees)] = 0.
    if sp.issparse(A):
        D = sp.diags(degrees)
    else:
        D = np.diag(degrees)
    return D 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def compute_lambda(pairs, Z, lmdb, lmdb_data):
    numsamples = len(Z)

    R = csr_matrix((lmdb * pairs[:,2], (pairs[:,0].astype(int), pairs[:,1].astype(int))), shape=(numsamples, numsamples))
    R = R + R.transpose()

    D = diags(np.squeeze(np.array(np.sum(R,1))), 0)
    I = diags(lmdb_data, 0)

    spndata = np.linalg.norm(I * Z, ord=2)
    eiglmdbdata,_ = sparse.linalg.eigsh(I, k=1)
    eigM,_ = sparse.linalg.eigsh(D - R, k=1)

    _lambda = float(spndata / (eiglmdbdata + eigM))

    return _lambda 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def _create_A_L(self, graph, node2idx):
        node_size = graph.number_of_nodes()
        A_data = []
        A_row_index = []
        A_col_index = []

        for edge in graph.edges():
            v1, v2 = edge
            edge_weight = graph[v1][v2].get('weight', 1)

            A_data.append(edge_weight)
            A_row_index.append(node2idx[v1])
            A_col_index.append(node2idx[v2])

        A = sp.csr_matrix((A_data, (A_row_index, A_col_index)), shape=(node_size, node_size))
        A_ = sp.csr_matrix((A_data + A_data, (A_row_index + A_col_index, A_col_index + A_row_index)),
                           shape=(node_size, node_size))

        D = sp.diags(A_.sum(axis=1).flatten().tolist()[0])
        L = D - A_
        return A, L 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def normalize_feature(mx):
    """Row-normalize sparse matrix

    Parameters
    ----------
    mx : scipy.sparse.csr_matrix
        matrix to be normalized

    Returns
    -------
    scipy.sprase.lil_matrix
        normalized matrix
    """
    if type(mx) is not sp.lil.lil_matrix:
        mx = mx.tolil()
    rowsum = np.array(mx.sum(1))
    r_inv = np.power(rowsum, -1).flatten()
    r_inv[np.isinf(r_inv)] = 0.
    r_mat_inv = sp.diags(r_inv)
    mx = r_mat_inv.dot(mx)
    return mx 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def test_dual_infeasible_qp(self):

        # Dual infeasible example
        self.P = sparse.diags([4., 0.], format='csc')
        self.q = np.array([0, 2])
        self.A = sparse.csc_matrix([[1., 1.], [-1., 1.]])
        self.l = np.array([-np.inf, -np.inf])
        self.u = np.array([2., 3.])

        self.model = osqp.OSQP()
        self.model.setup(P=self.P, q=self.q, A=self.A, l=self.l, u=self.u,
                         **self.opts)

        # Solve problem with OSQP
        res = self.model.solve()

        # Assert close
        self.assertEqual(res.info.status_val,
                         constant('OSQP_DUAL_INFEASIBLE')) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def setUp(self):
        # Simple QP problem
        self.P = sparse.diags([11., 0.1], format='csc')
        self.P_new = sparse.eye(2, format='csc')
        self.q = np.array([3, 4])
        self.A = sparse.csc_matrix([[-1, 0], [0, -1], [-1, -3],
                                    [2, 5], [3, 4]])
        self.A_new = sparse.csc_matrix([[-1, 0], [0, -1], [-2, -2],
                                        [2, 5], [3, 4]])
        self.u = np.array([0, 0, -15, 100, 80])
        self.l = -np.inf * np.ones(len(self.u))
        self.n = self.P.shape[0]
        self.m = self.A.shape[0]
        self.opts = {'verbose': False,
                     'eps_abs': 1e-08,
                     'eps_rel': 1e-08,
                     'alpha': 1.6,
                     'max_iter': 3000,
                     'warm_start': True}
        self.model = osqp.OSQP()
        self.model.setup(P=self.P, q=self.q, A=self.A, l=self.l, u=self.u,
                         **self.opts) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def setUp(self):
        """
        Setup unconstrained quadratic problem
        """
        # Unconstrained QP problem
        sp.random.seed(4)

        self.n = 30
        self.m = 0
        P = sparse.diags(np.random.rand(self.n)) + 0.2*sparse.eye(self.n)
        self.P = P.tocsc()
        self.q = np.random.randn(self.n)
        self.A = sparse.csc_matrix((self.m, self.n))
        self.l = np.array([])
        self.u = np.array([])
        self.opts = {'verbose': False,
                     'eps_abs': 1e-08,
                     'eps_rel': 1e-08,
                     'polish': False}
        self.model = osqp.OSQP()
        self.model.setup(P=self.P, q=self.q, A=self.A, l=self.l, u=self.u,
                         **self.opts) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def test_polish_simple(self):

        # Simple QP problem
        self.P = sparse.diags([11., 0.], format='csc')
        self.q = np.array([3, 4])
        self.A = sparse.csc_matrix([[-1, 0], [0, -1], [-1, -3], [2, 5], [3, 4]])
        self.u = np.array([0, 0, -15, 100, 80])
        self.l = -np.inf * np.ones(len(self.u))
        self.n = self.P.shape[0]
        self.m = self.A.shape[0]
        self.model = osqp.OSQP()
        self.model.setup(P=self.P, q=self.q, A=self.A, l=self.l, u=self.u,
                         **self.opts)

        # Solve problem
        res = self.model.solve()

        # Assert close
        nptest.assert_array_almost_equal(res.x, np.array([0., 5.]))
        nptest.assert_array_almost_equal(res.y, np.array([1.66666667, 0.,
                                                          1.33333333, 0., 0.]))
        nptest.assert_array_almost_equal(res.info.obj_val, 20.) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def setUp(self):
        # Simple QP problem
        self.P = sparse.diags([11., 0.], format='csc')
        self.q = np.array([3, 4])
        self.A = sparse.csc_matrix([[-1, 0], [0, -1], [-1, -3], [2, 5], [3, 4]])
        self.u = np.array([0, 0, -15, 100, 80])
        self.l = -np.inf * np.ones(len(self.u))
        self.n = self.P.shape[0]
        self.m = self.A.shape[0]
        self.opts = {'verbose': False,
                     'eps_abs': 1e-08,
                     'eps_rel': 1e-08,
                     'rho': 0.01,
                     'alpha': 1.6,
                     'max_iter': 10000,
                     'warm_start': True}
        self.model = osqp.OSQP()
        self.model.setup(P=self.P, q=self.q, A=self.A, l=self.l, u=self.u,
                         **self.opts) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def matrix(self, shape, *args, **kwargs):
        """ Matrix representation of given operator product on an equidistant grid of given shape.

        :param shape: tuple with the shape of the grid
        :return: scipy sparse matrix representing the operator product
        """

        if isinstance(self.left, np.ndarray):
            left = sparse.diags(self.left.reshape(-1), 0)
        elif isinstance(self.left, LinearMap) or isinstance(self.left, BinaryOperator):
            left = self.left.matrix(shape, *args, **kwargs)
        else:
            left = self.left * sparse.diags(np.ones(shape).reshape(-1), 0)

        if isinstance(self.right, np.ndarray):
            right = sparse.diags(self.right.reshape(-1), 0)
        elif isinstance(self.right, LinearMap) or isinstance(self.right, BinaryOperator):
            right = self.right.matrix(shape, *args, **kwargs)
        else:
            right = self.right * sparse.diags(np.ones(shape).reshape(-1), 0)

        return left.dot(right) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def jacobian(self, x, into=None):
        x = flattest(x)
        z = sps.diags(-sine(x))
        return safe_into(into, z) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import diags [as 别名]
def globally_normalize_bipartite_adjacency(adjacencies, verbose=False, symmetric=True):
    """ Globally Normalizes set of bipartite adjacency matrices """

    if verbose:
        print('Symmetrically normalizing bipartite adj')
    # degree_u and degree_v are row and column sums of adj+I

    adj_tot = np.sum(adj for adj in adjacencies)
    degree_u = np.asarray(adj_tot.sum(1)).flatten()
    degree_v = np.asarray(adj_tot.sum(0)).flatten()

    # set zeros to inf to avoid dividing by zero
    degree_u[degree_u == 0.] = np.inf
    degree_v[degree_v == 0.] = np.inf

    degree_u_inv_sqrt = 1. / np.sqrt(degree_u)
    degree_v_inv_sqrt = 1. / np.sqrt(degree_v)
    degree_u_inv_sqrt_mat = sp.diags([degree_u_inv_sqrt], [0])
    degree_v_inv_sqrt_mat = sp.diags([degree_v_inv_sqrt], [0])

    degree_u_inv = degree_u_inv_sqrt_mat.dot(degree_u_inv_sqrt_mat)

    if symmetric:
        adj_norm = [degree_u_inv_sqrt_mat.dot(adj).dot(degree_v_inv_sqrt_mat) for adj in adjacencies]

    else:
        adj_norm = [degree_u_inv.dot(adj) for adj in adjacencies]

    return adj_norm