EVOLUTION-MANAGER

Edit File: construct.py

"""Functions to construct sparse matrices """ from __future__ import division, print_function, absolute_import __docformat__ = "restructuredtext en" __all__ = ['spdiags', 'eye', 'identity', 'kron', 'kronsum', 'hstack', 'vstack', 'bmat', 'rand', 'random', 'diags', 'block_diag'] import numpy as np from scipy._lib._numpy_compat import get_randint from scipy._lib.six import xrange from .sputils import upcast, get_index_dtype, isscalarlike from .csr import csr_matrix from .csc import csc_matrix from .bsr import bsr_matrix from .coo import coo_matrix from .dia import dia_matrix from .base import issparse def spdiags(data, diags, m, n, format=None): """ Return a sparse matrix from diagonals. Parameters ---------- data : array_like matrix diagonals stored row-wise diags : diagonals to set - k = 0 the main diagonal - k > 0 the k-th upper diagonal - k < 0 the k-th lower diagonal m, n : int shape of the result format : str, optional Format of the result. By default (format=None) an appropriate sparse matrix format is returned. This choice is subject to change. See Also -------- diags : more convenient form of this function dia_matrix : the sparse DIAgonal format. Examples -------- >>> from scipy.sparse import spdiags >>> data = np.array([[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]]) >>> diags = np.array([0, -1, 2]) >>> spdiags(data, diags, 4, 4).toarray() array([[1, 0, 3, 0], [1, 2, 0, 4], [0, 2, 3, 0], [0, 0, 3, 4]]) """ return dia_matrix((data, diags), shape=(m,n)).asformat(format) def diags(diagonals, offsets=0, shape=None, format=None, dtype=None): """ Construct a sparse matrix from diagonals. Parameters ---------- diagonals : sequence of array_like Sequence of arrays containing the matrix diagonals, corresponding to `offsets`. offsets : sequence of int or an int, optional Diagonals to set: - k = 0 the main diagonal (default) - k > 0 the k-th upper diagonal - k < 0 the k-th lower diagonal shape : tuple of int, optional Shape of the result. If omitted, a square matrix large enough to contain the diagonals is returned. format : {"dia", "csr", "csc", "lil", ...}, optional Matrix format of the result. By default (format=None) an appropriate sparse matrix format is returned. This choice is subject to change. dtype : dtype, optional Data type of the matrix. See Also -------- spdiags : construct matrix from diagonals Notes ----- This function differs from `spdiags` in the way it handles off-diagonals. The result from `diags` is the sparse equivalent of:: np.diag(diagonals[0], offsets[0]) + ... + np.diag(diagonals[k], offsets[k]) Repeated diagonal offsets are disallowed. .. versionadded:: 0.11 Examples -------- >>> from scipy.sparse import diags >>> diagonals = [[1, 2, 3, 4], [1, 2, 3], [1, 2]] >>> diags(diagonals, [0, -1, 2]).toarray() array([[1, 0, 1, 0], [1, 2, 0, 2], [0, 2, 3, 0], [0, 0, 3, 4]]) Broadcasting of scalars is supported (but shape needs to be specified): >>> diags([1, -2, 1], [-1, 0, 1], shape=(4, 4)).toarray() array([[-2., 1., 0., 0.], [ 1., -2., 1., 0.], [ 0., 1., -2., 1.], [ 0., 0., 1., -2.]]) If only one diagonal is wanted (as in `numpy.diag`), the following works as well: >>> diags([1, 2, 3], 1).toarray() array([[ 0., 1., 0., 0.], [ 0., 0., 2., 0.], [ 0., 0., 0., 3.], [ 0., 0., 0., 0.]]) """ # if offsets is not a sequence, assume that there's only one diagonal if isscalarlike(offsets): # now check that there's actually only one diagonal if len(diagonals) == 0 or isscalarlike(diagonals[0]): diagonals = [np.atleast_1d(diagonals)] else: raise ValueError("Different number of diagonals and offsets.") else: diagonals = list(map(np.atleast_1d, diagonals)) offsets = np.atleast_1d(offsets) # Basic check if len(diagonals) != len(offsets): raise ValueError("Different number of diagonals and offsets.") # Determine shape, if omitted if shape is None: m = len(diagonals[0]) + abs(int(offsets[0])) shape = (m, m) # Determine data type, if omitted if dtype is None: dtype = np.common_type(*diagonals) # Construct data array m, n = shape M = max([min(m + offset, n - offset) + max(0, offset) for offset in offsets]) M = max(0, M) data_arr = np.zeros((len(offsets), M), dtype=dtype) K = min(m, n) for j, diagonal in enumerate(diagonals): offset = offsets[j] k = max(0, offset) length = min(m + offset, n - offset, K) if length < 0: raise ValueError("Offset %d (index %d) out of bounds" % (offset, j)) try: data_arr[j, k:k+length] = diagonal[...,:length] except ValueError: if len(diagonal) != length and len(diagonal) != 1: raise ValueError( "Diagonal length (index %d: %d at offset %d) does not " "agree with matrix size (%d, %d)." % ( j, len(diagonal), offset, m, n)) raise return dia_matrix((data_arr, offsets), shape=(m, n)).asformat(format) def identity(n, dtype='d', format=None): """Identity matrix in sparse format Returns an identity matrix with shape (n,n) using a given sparse format and dtype. Parameters ---------- n : int Shape of the identity matrix. dtype : dtype, optional Data type of the matrix format : str, optional Sparse format of the result, e.g. format="csr", etc. Examples -------- >>> from scipy.sparse import identity >>> identity(3).toarray() array([[ 1., 0., 0.], [ 0., 1., 0.], [ 0., 0., 1.]]) >>> identity(3, dtype='int8', format='dia') <3x3 sparse matrix of type '<class 'numpy.int8'>' with 3 stored elements (1 diagonals) in DIAgonal format> """ return eye(n, n, dtype=dtype, format=format) def eye(m, n=None, k=0, dtype=float, format=None): """Sparse matrix with ones on diagonal Returns a sparse (m x n) matrix where the k-th diagonal is all ones and everything else is zeros. Parameters ---------- m : int Number of rows in the matrix. n : int, optional Number of columns. Default: `m`. k : int, optional Diagonal to place ones on. Default: 0 (main diagonal). dtype : dtype, optional Data type of the matrix. format : str, optional Sparse format of the result, e.g. format="csr", etc. Examples -------- >>> from scipy import sparse >>> sparse.eye(3).toarray() array([[ 1., 0., 0.], [ 0., 1., 0.], [ 0., 0., 1.]]) >>> sparse.eye(3, dtype=np.int8) <3x3 sparse matrix of type '<class 'numpy.int8'>' with 3 stored elements (1 diagonals) in DIAgonal format> """ if n is None: n = m m,n = int(m),int(n) if m == n and k == 0: # fast branch for special formats if format in ['csr', 'csc']: idx_dtype = get_index_dtype(maxval=n) indptr = np.arange(n+1, dtype=idx_dtype) indices = np.arange(n, dtype=idx_dtype) data = np.ones(n, dtype=dtype) cls = {'csr': csr_matrix, 'csc': csc_matrix}[format] return cls((data,indices,indptr),(n,n)) elif format == 'coo': idx_dtype = get_index_dtype(maxval=n) row = np.arange(n, dtype=idx_dtype) col = np.arange(n, dtype=idx_dtype) data = np.ones(n, dtype=dtype) return coo_matrix((data,(row,col)),(n,n)) diags = np.ones((1, max(0, min(m + k, n))), dtype=dtype) return spdiags(diags, k, m, n).asformat(format) def kron(A, B, format=None): """kronecker product of sparse matrices A and B Parameters ---------- A : sparse or dense matrix first matrix of the product B : sparse or dense matrix second matrix of the product format : str, optional format of the result (e.g. "csr") Returns ------- kronecker product in a sparse matrix format Examples -------- >>> from scipy import sparse >>> A = sparse.csr_matrix(np.array([[0, 2], [5, 0]])) >>> B = sparse.csr_matrix(np.array([[1, 2], [3, 4]])) >>> sparse.kron(A, B).toarray() array([[ 0, 0, 2, 4], [ 0, 0, 6, 8], [ 5, 10, 0, 0], [15, 20, 0, 0]]) >>> sparse.kron(A, [[1, 2], [3, 4]]).toarray() array([[ 0, 0, 2, 4], [ 0, 0, 6, 8], [ 5, 10, 0, 0], [15, 20, 0, 0]]) """ B = coo_matrix(B) if (format is None or format == "bsr") and 2*B.nnz >= B.shape[0] * B.shape[1]: # B is fairly dense, use BSR A = csr_matrix(A,copy=True) output_shape = (A.shape[0]*B.shape[0], A.shape[1]*B.shape[1]) if A.nnz == 0 or B.nnz == 0: # kronecker product is the zero matrix return coo_matrix(output_shape) B = B.toarray() data = A.data.repeat(B.size).reshape(-1,B.shape[0],B.shape[1]) data = data * B return bsr_matrix((data,A.indices,A.indptr), shape=output_shape) else: # use COO A = coo_matrix(A) output_shape = (A.shape[0]*B.shape[0], A.shape[1]*B.shape[1]) if A.nnz == 0 or B.nnz == 0: # kronecker product is the zero matrix return coo_matrix(output_shape) # expand entries of a into blocks row = A.row.repeat(B.nnz) col = A.col.repeat(B.nnz) data = A.data.repeat(B.nnz) row *= B.shape[0] col *= B.shape[1] # increment block indices row,col = row.reshape(-1,B.nnz),col.reshape(-1,B.nnz) row += B.row col += B.col row,col = row.reshape(-1),col.reshape(-1) # compute block entries data = data.reshape(-1,B.nnz) * B.data data = data.reshape(-1) return coo_matrix((data,(row,col)), shape=output_shape).asformat(format) def kronsum(A, B, format=None): """kronecker sum of sparse matrices A and B Kronecker sum of two sparse matrices is a sum of two Kronecker products kron(I_n,A) + kron(B,I_m) where A has shape (m,m) and B has shape (n,n) and I_m and I_n are identity matrices of shape (m,m) and (n,n) respectively. Parameters ---------- A square matrix B square matrix format : str format of the result (e.g. "csr") Returns ------- kronecker sum in a sparse matrix format Examples -------- """ A = coo_matrix(A) B = coo_matrix(B) if A.shape[0] != A.shape[1]: raise ValueError('A is not square') if B.shape[0] != B.shape[1]: raise ValueError('B is not square') dtype = upcast(A.dtype, B.dtype) L = kron(eye(B.shape[0],dtype=dtype), A, format=format) R = kron(B, eye(A.shape[0],dtype=dtype), format=format) return (L+R).asformat(format) # since L + R is not always same format def _compressed_sparse_stack(blocks, axis): """ Stacking fast path for CSR/CSC matrices (i) vstack for CSR, (ii) hstack for CSC. """ other_axis = 1 if axis == 0 else 0 data = np.concatenate([b.data for b in blocks]) constant_dim = blocks[0].shape[other_axis] idx_dtype = get_index_dtype(arrays=[b.indptr for b in blocks], maxval=max(data.size, constant_dim)) indices = np.empty(data.size, dtype=idx_dtype) indptr = np.empty(sum(b.shape[axis] for b in blocks) + 1, dtype=idx_dtype) last_indptr = idx_dtype(0) sum_dim = 0 sum_indices = 0 for b in blocks: if b.shape[other_axis] != constant_dim: raise ValueError('incompatible dimensions for axis %d' % other_axis) indices[sum_indices:sum_indices+b.indices.size] = b.indices sum_indices += b.indices.size idxs = slice(sum_dim, sum_dim + b.shape[axis]) indptr[idxs] = b.indptr[:-1] indptr[idxs] += last_indptr sum_dim += b.shape[axis] last_indptr += b.indptr[-1] indptr[-1] = last_indptr if axis == 0: return csr_matrix((data, indices, indptr), shape=(sum_dim, constant_dim)) else: return csc_matrix((data, indices, indptr), shape=(constant_dim, sum_dim)) def hstack(blocks, format=None, dtype=None): """ Stack sparse matrices horizontally (column wise) Parameters ---------- blocks sequence of sparse matrices with compatible shapes format : str sparse format of the result (e.g. "csr") by default an appropriate sparse matrix format is returned. This choice is subject to change. dtype : dtype, optional The data-type of the output matrix. If not given, the dtype is determined from that of `blocks`. See Also -------- vstack : stack sparse matrices vertically (row wise) Examples -------- >>> from scipy.sparse import coo_matrix, hstack >>> A = coo_matrix([[1, 2], [3, 4]]) >>> B = coo_matrix([[5], [6]]) >>> hstack([A,B]).toarray() array([[1, 2, 5], [3, 4, 6]]) """ return bmat([blocks], format=format, dtype=dtype) def vstack(blocks, format=None, dtype=None): """ Stack sparse matrices vertically (row wise) Parameters ---------- blocks sequence of sparse matrices with compatible shapes format : str, optional sparse format of the result (e.g. "csr") by default an appropriate sparse matrix format is returned. This choice is subject to change. dtype : dtype, optional The data-type of the output matrix. If not given, the dtype is determined from that of `blocks`. See Also -------- hstack : stack sparse matrices horizontally (column wise) Examples -------- >>> from scipy.sparse import coo_matrix, vstack >>> A = coo_matrix([[1, 2], [3, 4]]) >>> B = coo_matrix([[5, 6]]) >>> vstack([A, B]).toarray() array([[1, 2], [3, 4], [5, 6]]) """ return bmat([[b] for b in blocks], format=format, dtype=dtype) def bmat(blocks, format=None, dtype=None): """ Build a sparse matrix from sparse sub-blocks Parameters ---------- blocks : array_like Grid of sparse matrices with compatible shapes. An entry of None implies an all-zero matrix. format : {'bsr', 'coo', 'csc', 'csr', 'dia', 'dok', 'lil'}, optional The sparse format of the result (e.g. "csr"). By default an appropriate sparse matrix format is returned. This choice is subject to change. dtype : dtype, optional The data-type of the output matrix. If not given, the dtype is determined from that of `blocks`. Returns ------- bmat : sparse matrix See Also -------- block_diag, diags Examples -------- >>> from scipy.sparse import coo_matrix, bmat >>> A = coo_matrix([[1, 2], [3, 4]]) >>> B = coo_matrix([[5], [6]]) >>> C = coo_matrix([[7]]) >>> bmat([[A, B], [None, C]]).toarray() array([[1, 2, 5], [3, 4, 6], [0, 0, 7]]) >>> bmat([[A, None], [None, C]]).toarray() array([[1, 2, 0], [3, 4, 0], [0, 0, 7]]) """ blocks = np.asarray(blocks, dtype='object') if blocks.ndim != 2: raise ValueError('blocks must be 2-D') M,N = blocks.shape # check for fast path cases if (N == 1 and format in (None, 'csr') and all(isinstance(b, csr_matrix) for b in blocks.flat)): A = _compressed_sparse_stack(blocks[:,0], 0) if dtype is not None: A = A.astype(dtype) return A elif (M == 1 and format in (None, 'csc') and all(isinstance(b, csc_matrix) for b in blocks.flat)): A = _compressed_sparse_stack(blocks[0,:], 1) if dtype is not None: A = A.astype(dtype) return A block_mask = np.zeros(blocks.shape, dtype=bool) brow_lengths = np.zeros(M, dtype=np.int64) bcol_lengths = np.zeros(N, dtype=np.int64) # convert everything to COO format for i in range(M): for j in range(N): if blocks[i,j] is not None: A = coo_matrix(blocks[i,j]) blocks[i,j] = A block_mask[i,j] = True if brow_lengths[i] == 0: brow_lengths[i] = A.shape[0] elif brow_lengths[i] != A.shape[0]: msg = ('blocks[{i},:] has incompatible row dimensions. ' 'Got blocks[{i},{j}].shape[0] == {got}, ' 'expected {exp}.'.format(i=i, j=j, exp=brow_lengths[i], got=A.shape[0])) raise ValueError(msg) if bcol_lengths[j] == 0: bcol_lengths[j] = A.shape[1] elif bcol_lengths[j] != A.shape[1]: msg = ('blocks[:,{j}] has incompatible row dimensions. ' 'Got blocks[{i},{j}].shape[1] == {got}, ' 'expected {exp}.'.format(i=i, j=j, exp=bcol_lengths[j], got=A.shape[1])) raise ValueError(msg) nnz = sum(block.nnz for block in blocks[block_mask]) if dtype is None: all_dtypes = [blk.dtype for blk in blocks[block_mask]] dtype = upcast(*all_dtypes) if all_dtypes else None row_offsets = np.append(0, np.cumsum(brow_lengths)) col_offsets = np.append(0, np.cumsum(bcol_lengths)) shape = (row_offsets[-1], col_offsets[-1]) data = np.empty(nnz, dtype=dtype) idx_dtype = get_index_dtype(maxval=max(shape)) row = np.empty(nnz, dtype=idx_dtype) col = np.empty(nnz, dtype=idx_dtype) nnz = 0 ii, jj = np.nonzero(block_mask) for i, j in zip(ii, jj): B = blocks[i, j] idx = slice(nnz, nnz + B.nnz) data[idx] = B.data row[idx] = B.row + row_offsets[i] col[idx] = B.col + col_offsets[j] nnz += B.nnz return coo_matrix((data, (row, col)), shape=shape).asformat(format) def block_diag(mats, format=None, dtype=None): """ Build a block diagonal sparse matrix from provided matrices. Parameters ---------- mats : sequence of matrices Input matrices. format : str, optional The sparse format of the result (e.g. "csr"). If not given, the matrix is returned in "coo" format. dtype : dtype specifier, optional The data-type of the output matrix. If not given, the dtype is determined from that of `blocks`. Returns ------- res : sparse matrix Notes ----- .. versionadded:: 0.11.0 See Also -------- bmat, diags Examples -------- >>> from scipy.sparse import coo_matrix, block_diag >>> A = coo_matrix([[1, 2], [3, 4]]) >>> B = coo_matrix([[5], [6]]) >>> C = coo_matrix([[7]]) >>> block_diag((A, B, C)).toarray() array([[1, 2, 0, 0], [3, 4, 0, 0], [0, 0, 5, 0], [0, 0, 6, 0], [0, 0, 0, 7]]) """ nmat = len(mats) rows = [] for ia, a in enumerate(mats): row = [None]*nmat if issparse(a): row[ia] = a else: row[ia] = coo_matrix(a) rows.append(row) return bmat(rows, format=format, dtype=dtype) def random(m, n, density=0.01, format='coo', dtype=None, random_state=None, data_rvs=None): """Generate a sparse matrix of the given shape and density with randomly distributed values. Parameters ---------- m, n : int shape of the matrix density : real, optional density of the generated matrix: density equal to one means a full matrix, density of 0 means a matrix with no non-zero items. format : str, optional sparse matrix format. dtype : dtype, optional type of the returned matrix values. random_state : {numpy.random.RandomState, int}, optional Random number generator or random seed. If not given, the singleton numpy.random will be used. This random state will be used for sampling the sparsity structure, but not necessarily for sampling the values of the structurally nonzero entries of the matrix. data_rvs : callable, optional Samples a requested number of random values. This function should take a single argument specifying the length of the ndarray that it will return. The structurally nonzero entries of the sparse random matrix will be taken from the array sampled by this function. By default, uniform [0, 1) random values will be sampled using the same random state as is used for sampling the sparsity structure. Returns ------- res : sparse matrix Notes ----- Only float types are supported for now. Examples -------- >>> from scipy.sparse import random >>> from scipy import stats >>> class CustomRandomState(np.random.RandomState): ... def randint(self, k): ... i = np.random.randint(k) ... return i - i % 2 >>> np.random.seed(12345) >>> rs = CustomRandomState() >>> rvs = stats.poisson(25, loc=10).rvs >>> S = random(3, 4, density=0.25, random_state=rs, data_rvs=rvs) >>> S.A array([[ 36., 0., 33., 0.], # random [ 0., 0., 0., 0.], [ 0., 0., 36., 0.]]) >>> from scipy.sparse import random >>> from scipy.stats import rv_continuous >>> class CustomDistribution(rv_continuous): ... def _rvs(self, *args, **kwargs): ... return self._random_state.randn(*self._size) >>> X = CustomDistribution(seed=2906) >>> Y = X() # get a frozen version of the distribution >>> S = random(3, 4, density=0.25, random_state=2906, data_rvs=Y.rvs) >>> S.A array([[ 0. , 0. , 0. , 0. ], [ 0.13569738, 1.9467163 , -0.81205367, 0. ], [ 0. , 0. , 0. , 0. ]]) """ if density < 0 or density > 1: raise ValueError("density expected to be 0 <= density <= 1") dtype = np.dtype(dtype) mn = m * n tp = np.intc if mn > np.iinfo(tp).max: tp = np.int64 if mn > np.iinfo(tp).max: msg = """\ Trying to generate a random sparse matrix such as the product of dimensions is greater than %d - this is not supported on this machine """ raise ValueError(msg % np.iinfo(tp).max) # Number of non zero values k = int(density * m * n) if random_state is None: random_state = np.random elif isinstance(random_state, (int, np.integer)): random_state = np.random.RandomState(random_state) if data_rvs is None: if np.issubdtype(dtype, np.integer): randint = get_randint(random_state) def data_rvs(n): return randint(np.iinfo(dtype).min, np.iinfo(dtype).max, n, dtype=dtype) elif np.issubdtype(dtype, np.complexfloating): def data_rvs(n): return random_state.rand(n) + random_state.rand(n) * 1j else: data_rvs = random_state.rand ind = random_state.choice(mn, size=k, replace=False) j = np.floor(ind * 1. / m).astype(tp, copy=False) i = (ind - j * m).astype(tp, copy=False) vals = data_rvs(k).astype(dtype, copy=False) return coo_matrix((vals, (i, j)), shape=(m, n)).asformat(format, copy=False) def rand(m, n, density=0.01, format="coo", dtype=None, random_state=None): """Generate a sparse matrix of the given shape and density with uniformly distributed values. Parameters ---------- m, n : int shape of the matrix density : real, optional density of the generated matrix: density equal to one means a full matrix, density of 0 means a matrix with no non-zero items. format : str, optional sparse matrix format. dtype : dtype, optional type of the returned matrix values. random_state : {numpy.random.RandomState, int}, optional Random number generator or random seed. If not given, the singleton numpy.random will be used. Returns ------- res : sparse matrix Notes ----- Only float types are supported for now. See Also -------- scipy.sparse.random : Similar function that allows a user-specified random data source. Examples -------- >>> from scipy.sparse import rand >>> matrix = rand(3, 4, density=0.25, format="csr", random_state=42) >>> matrix <3x4 sparse matrix of type '<class 'numpy.float64'>' with 3 stored elements in Compressed Sparse Row format> >>> matrix.todense() matrix([[0.05641158, 0. , 0. , 0.65088847], [0. , 0. , 0. , 0.14286682], [0. , 0. , 0. , 0. ]]) """ return random(m, n, density, format, dtype, random_state)