Python sparse.dia_matrix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 dia_matrix [as 别名]
def _scale_normalize(X):
    """Normalize ``X`` by scaling rows and columns independently.

    Returns the normalized matrix and the row and column scaling
    factors.

    """
    X = make_nonnegative(X)
    row_diag = np.asarray(1.0 / np.sqrt(X.sum(axis=1))).squeeze()
    col_diag = np.asarray(1.0 / np.sqrt(X.sum(axis=0))).squeeze()
    row_diag = np.where(np.isnan(row_diag), 0, row_diag)
    col_diag = np.where(np.isnan(col_diag), 0, col_diag)
    if issparse(X):
        n_rows, n_cols = X.shape
        r = dia_matrix((row_diag, [0]), shape=(n_rows, n_rows))
        c = dia_matrix((col_diag, [0]), shape=(n_cols, n_cols))
        an = r * X * c
    else:
        an = row_diag[:, np.newaxis] * X * col_diag
    return an, row_diag, col_diag 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def _zeropi_operator_in_product_basis(self, zeropi_operator, zeropi_evecs=None):
        """Helper method that converts a zeropi operator into one in the product basis.

        Returns
        -------
        scipy.sparse.csc_matrix
            operator written in the product basis
        """
        zeropi_dim = self.zeropi_cutoff
        zeta_dim = self.zeta_cutoff

        if zeropi_evecs is None:
            _, zeropi_evecs = self._zeropi.eigensys(evals_count=zeropi_dim)

        op_eigen_basis = sparse.dia_matrix((zeropi_dim, zeropi_dim),
                                           dtype=np.complex_)  # is this guaranteed to be zero?

        op_zeropi = spec_utils.get_matrixelement_table(zeropi_operator, zeropi_evecs)
        for n in range(zeropi_dim):
            for m in range(zeropi_dim):
                op_eigen_basis += op_zeropi[n, m] * op.hubbard_sparse(n, m, zeropi_dim)

        return sparse.kron(op_eigen_basis, sparse.identity(zeta_dim, format='csc', dtype=np.complex_), format='csc') 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def sparse_kinetic_mat(self):
        """
        Kinetic energy portion of the Hamiltonian.
        TODO: update this method to use single-variable operator methods

        Returns
        -------
        scipy.sparse.csc_matrix
            matrix representing the kinetic energy operator
        """
        pt_count = self.grid.pt_count
        dim_theta = 2 * self.ncut + 1
        identity_phi = sparse.identity(pt_count, format='csc', dtype=np.complex_)
        identity_theta = sparse.identity(dim_theta, format='csc', dtype=np.complex_)

        kinetic_matrix_phi = self.grid.second_derivative_matrix(prefactor=-2.0 * self.ECJ)

        diag_elements = 2.0 * self.ECS * np.square(np.arange(-self.ncut + self.ng, self.ncut + 1 + self.ng))
        kinetic_matrix_theta = sparse.dia_matrix((diag_elements, [0]), shape=(dim_theta, dim_theta)).tocsc()

        kinetic_matrix = (sparse.kron(kinetic_matrix_phi, identity_theta, format='csc')
                          + sparse.kron(identity_phi, kinetic_matrix_theta, format='csc'))

        kinetic_matrix -= 2.0 * self.ECS * self.dCJ * self.i_d_dphi_operator() * self.n_theta_operator()
        return kinetic_matrix 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def new_realization(self):
        """
        Generate a new channel realization and save the time-variant convolution matrix in "self.imp_convolution_matrix" 
        
        """       
        if self.imp_pdp_string=='AWGN':
            impulse_response_squeezed = np.ones((self.nr_samples,1))
        elif self.imp_pdp_string=='Flat':
            h = np.random.randn(1) +  1j * np.random.randn(1)
            impulse_response_squeezed = h * np.ones((self.nr_samples,1))
        else:
            impulse_response_squeezed = np.zeros((self.nr_samples,self.imp_pdp_index.size), dtype=np.complex)
            t = np.arange(self.nr_samples).reshape(self.nr_samples,1)*self.phy_dt
    
            # Use a for loop because it is more memory efficient (but takes longer)
            for i in range(self.imp_nr_paths_wssus):
                doppler_shifts = np.cos(np.random.random((1,self.imp_pdp_index.size))*2*np.pi) * self.phy_max_doppler_shift 
                random_phase = np.random.random((1,self.imp_pdp_index.size))  
                argument = 2 * np.pi * (random_phase + doppler_shifts*t)  
                impulse_response_squeezed += np.cos(argument) + 1j*np.sin(argument)  
            impulse_response_squeezed *= np.sqrt(self.imp_pdp[self.imp_pdp_index]/self.imp_nr_paths_wssus)
        
        self.imp_convolution_matrix = sparse.dia_matrix((np.transpose(impulse_response_squeezed), -self.imp_pdp_index), shape=(self.nr_samples, self.nr_samples)).tocsr() 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def _diagonalize_interslice_kernels(interslice_kernels, method='dia'):
    n = interslice_kernels[0].shape[0]
    m = len(interslice_kernels)
    if method == 'dia':
        diags = np.zeros((2*n-1, n*m))
        for vertex, A in enumerate(interslice_kernels):
            diags[(np.tile(np.arange(n, 2*n), n) - np.repeat(np.arange(1, n+1), n), 
                   np.tile(np.arange(0, n*m, m), n) + vertex)] = A.flatten()
        offsets = np.arange(-n*m + m, n*m, m)
        # set main diagonal to 0
        diags[offsets == 0] = 0
        K = sparse.dia_matrix((diags, offsets), shape=(n*m, n*m))
    else:
        assert method == 'csr'
        # this is inefficient
        K = sparse.csr_matrix((n*m, n*m))
        for vertex, A in enumerate(interslice_kernels):
            K = graphtools.matrix.set_submatrix(
                K, np.arange(n) * m + vertex, np.arange(n) * m + vertex, A)
        # set main diagonal to 0
        K = graphtools.matrix.set_diagonal(K, 0)
    return K 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def get_laplacian(self, sims, ids, alpha=0.99):
        """Get Laplacian_alpha matrix
        """
        logger.info('get_affinity')
        affinity = self.get_affinity(sims, ids)
        logger.info('get_affinity ... done')
        num = affinity.shape[0]
        degrees = affinity @ np.ones(num) + 1e-12
        # mat: degree matrix ^ (-1/2)
        mat = sparse.dia_matrix(
            (degrees ** (-0.5), [0]), shape=(num, num), dtype=np.float32)
        logger.info('calc stochastic = mat @ affinity @ mat')
        stochastic = mat @ affinity @ mat
        sparse_eye = sparse.dia_matrix(
            (np.ones(num), [0]), shape=(num, num), dtype=np.float32)
        lap_alpha = sparse_eye - alpha * stochastic
        return lap_alpha

    # @cache('affinity.jbl') 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def get_laplacian(self, sims, ids, alpha=0.99):
        """Get Laplacian_alpha matrix
        """
        affinity = self.get_affinity(sims, ids)
        num = affinity.shape[0]
        degrees = affinity @ np.ones(num) + 1e-12
        # mat: degree matrix ^ (-1/2)
        mat = sparse.dia_matrix(
            (degrees ** (-0.5), [0]), shape=(num, num), dtype=np.float32)
        stochastic = mat @ affinity @ mat
        sparse_eye = sparse.dia_matrix(
            (np.ones(num), [0]), shape=(num, num), dtype=np.float32)
        lap_alpha = sparse_eye - alpha * stochastic
        return lap_alpha

    # @cache('affinity.jbl') 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def vnl_coo(self): 
    """  Non-local part of the Hamiltonian due to Kleinman-Bylander projectors  """
    from pyscf.nao.m_overlap_am import overlap_am
    from scipy.sparse import dia_matrix
    sop = self.overlap_coo(ao_log=self.ao_log, ao_log2=self.kb_log, funct=overlap_am).tocsr()
    nkb = sop.shape[1]
    vkb_dia = dia_matrix( ( self.get_vkb(), [0] ), shape = (nkb,nkb) )
    return ((sop*vkb_dia)*sop.T).tocoo() 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def _rescale_data(X, weights):
    if issparse(X):
        size = weights.shape[0]
        weight_dia = sparse.dia_matrix((1 - weights, 0), (size, size))
        X_rescaled = X * weight_dia
    else:
        X_rescaled = X * (1 - weights)

    return X_rescaled 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def _rescale_data(X, y, sample_weight):
    """Rescale data so as to support sample_weight"""
    n_samples = X.shape[0]
    sample_weight = np.full(n_samples, sample_weight,
                            dtype=np.array(sample_weight).dtype)
    sample_weight = np.sqrt(sample_weight)
    sw_matrix = sparse.dia_matrix((sample_weight, 0),
                                  shape=(n_samples, n_samples))
    X = safe_sparse_dot(sw_matrix, X)
    y = safe_sparse_dot(sw_matrix, y)
    return X, y 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def get_subset_cpd(self, sub_idx):
        """ Get the cpd over a subset of the variables.
        :param np.ndarray[int]|np.ndarray[bool] sub_idx: indices of variables to keep
        :return: a new Gaussian CPD
        :rtype: GaussianCPD
        """
        if len(sub_idx) == 0 or (sub_idx.dtype == bool and not np.sum(sub_idx)):
            raise ValueError("sub_idx must not be empty")
        sub_mean = self.mean[sub_idx]
        sub_dim = len(sub_mean)
        if isinstance(self.precision, sp.dia_matrix):
            sub_precision = sp.dia_matrix((self.precision.diagonal()[sub_idx], np.zeros(1)),
                                          shape=(sub_dim, sub_dim))
        elif np.isscalar(self.precision):
            sub_precision = self.precision
        elif isinstance(self.precision, np.ndarray):
            if np.prod(self.precision.shape) == self.dim:
                sub_precision = self.precision[sub_idx]
            else:
                # We do the indexing this way for performance reasons.
                sub_precision = self.precision[sub_idx, :][:, sub_idx]
        else:
            # We do the indexing this way for performance reasons.
            sub_precision = self.precision.tocsr()[sub_idx, :][:, sub_idx]
        return GaussianCPD(dim=sub_dim, mean=sub_mean, precision=sub_precision,
                           mean_lin_op=get_subset_lin_op(self.mean_lin_op, sub_idx)) 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def hamiltonian(self, return_parts=False):
        """Returns Hamiltonian in basis obtained by discretizing phi, employing charge basis for theta, and Fock
        basis for zeta.

        Parameters
        ----------
        return_parts: bool, optional
            If set to true, `hamiltonian` returns [hamiltonian, evals, evecs, g_coupling_matrix]

        Returns
        -------
        scipy.sparse.csc_matrix or list
        """
        zeropi_dim = self.zeropi_cutoff
        zeropi_evals, zeropi_evecs = self._zeropi.eigensys(evals_count=zeropi_dim)
        zeropi_diag_hamiltonian = sparse.dia_matrix((zeropi_dim, zeropi_dim), dtype=np.complex_)
        zeropi_diag_hamiltonian.setdiag(zeropi_evals)

        zeta_dim = self.zeta_cutoff
        prefactor = self.E_zeta
        zeta_diag_hamiltonian = op.number_sparse(zeta_dim, prefactor)

        hamiltonian_mat = sparse.kron(zeropi_diag_hamiltonian,
                                      sparse.identity(zeta_dim, format='dia', dtype=np.complex_))
        hamiltonian_mat += sparse.kron(sparse.identity(zeropi_dim, format='dia', dtype=np.complex_),
                                       zeta_diag_hamiltonian)

        gmat = self.g_coupling_matrix(zeropi_evecs)
        zeropi_coupling = sparse.dia_matrix((zeropi_dim, zeropi_dim), dtype=np.complex_)
        for l1 in range(zeropi_dim):
            for l2 in range(zeropi_dim):
                zeropi_coupling += gmat[l1, l2] * op.hubbard_sparse(l1, l2, zeropi_dim)
        hamiltonian_mat += sparse.kron(zeropi_coupling,
                                       op.annihilation_sparse(zeta_dim)) + sparse.kron(zeropi_coupling.conjugate().T,
                                                                                       op.creation_sparse(zeta_dim))

        if return_parts:
            return [hamiltonian_mat.tocsc(), zeropi_evals, zeropi_evecs, gmat]

        return hamiltonian_mat.tocsc() 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def sparse_potential_mat(self):
        """
        Potential energy portion of the Hamiltonian.
        TODO: update this method to use single-variable operator methods

        Returns
        -------
        scipy.sparse.csc_matrix
            matrix representing the potential energy operator
        """
        pt_count = self.grid.pt_count
        grid_linspace = self.grid.make_linspace()
        dim_theta = 2 * self.ncut + 1

        phi_inductive_vals = self.EL * np.square(grid_linspace)
        phi_inductive_potential = sparse.dia_matrix((phi_inductive_vals, [0]), shape=(pt_count, pt_count)).tocsc()
        phi_cos_vals = np.cos(grid_linspace - 2.0 * np.pi * self.flux / 2.0)
        phi_cos_potential = sparse.dia_matrix((phi_cos_vals, [0]), shape=(pt_count, pt_count)).tocsc()
        phi_sin_vals = np.sin(grid_linspace - 2.0 * np.pi * self.flux / 2.0)
        phi_sin_potential = sparse.dia_matrix((phi_sin_vals, [0]), shape=(pt_count, pt_count)).tocsc()

        theta_cos_potential = (-self.EJ
                               * (sparse.dia_matrix(([1.0] * dim_theta, [-1]), shape=(dim_theta, dim_theta)) +
                                  sparse.dia_matrix(([1.0] * dim_theta, [1]), shape=(dim_theta, dim_theta)))).tocsc()
        potential_mat = (sparse.kron(phi_cos_potential, theta_cos_potential, format='csc')
                         + sparse.kron(phi_inductive_potential, self._identity_theta(), format='csc')
                         + 2 * self.EJ * sparse.kron(self._identity_phi(), self._identity_theta(), format='csc'))
        potential_mat += (self.EJ * self.dEJ * sparse.kron(phi_sin_potential, self._identity_theta(), format='csc')
                          * self.sin_theta_operator())
        return potential_mat 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def _phi_operator(self):
        r"""
        Operator :math:`\varphi`, acting only on the `\varphi` Hilbert subspace.


        Returns
        -------
            scipy.sparse.csc_matrix
        """
        pt_count = self.grid.pt_count

        phi_matrix = sparse.dia_matrix((pt_count, pt_count), dtype=np.complex_)
        diag_elements = self.grid.make_linspace()
        phi_matrix.setdiag(diag_elements)
        return phi_matrix 

# 需要导入模块: from scipy import sparse [as 别名]
# 或者: from scipy.sparse import dia_matrix [as 别名]
def _sin_phi_operator(self, x=0):
        r"""
        Operator :math:`\sin(\phi + x)`, acting only on the `\phi` Hilbert subspace.

        Returns
        -------
            scipy.sparse.csc_matrix
        """
        pt_count = self.grid.pt_count

        vals = np.sin(self.grid.make_linspace() + x)
        sin_phi_matrix = sparse.dia_matrix((vals, [0]), shape=(pt_count, pt_count)).tocsc()
        return sin_phi_matrix