Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
431 lines
14 KiB
431 lines
14 KiB
"""Sparse DIAgonal format"""
|
|
|
|
__docformat__ = "restructuredtext en"
|
|
|
|
__all__ = ['dia_matrix', 'isspmatrix_dia']
|
|
|
|
import numpy as np
|
|
|
|
from .base import isspmatrix, _formats, spmatrix
|
|
from .data import _data_matrix
|
|
from .sputils import (isshape, upcast_char, getdtype, get_index_dtype,
|
|
get_sum_dtype, validateaxis, check_shape, matrix)
|
|
from ._sparsetools import dia_matvec
|
|
|
|
|
|
class dia_matrix(_data_matrix):
|
|
"""Sparse matrix with DIAgonal storage
|
|
|
|
This can be instantiated in several ways:
|
|
dia_matrix(D)
|
|
with a dense matrix
|
|
|
|
dia_matrix(S)
|
|
with another sparse matrix S (equivalent to S.todia())
|
|
|
|
dia_matrix((M, N), [dtype])
|
|
to construct an empty matrix with shape (M, N),
|
|
dtype is optional, defaulting to dtype='d'.
|
|
|
|
dia_matrix((data, offsets), shape=(M, N))
|
|
where the ``data[k,:]`` stores the diagonal entries for
|
|
diagonal ``offsets[k]`` (See example below)
|
|
|
|
Attributes
|
|
----------
|
|
dtype : dtype
|
|
Data type of the matrix
|
|
shape : 2-tuple
|
|
Shape of the matrix
|
|
ndim : int
|
|
Number of dimensions (this is always 2)
|
|
nnz
|
|
Number of stored values, including explicit zeros
|
|
data
|
|
DIA format data array of the matrix
|
|
offsets
|
|
DIA format offset array of the matrix
|
|
|
|
Notes
|
|
-----
|
|
|
|
Sparse matrices can be used in arithmetic operations: they support
|
|
addition, subtraction, multiplication, division, and matrix power.
|
|
|
|
Examples
|
|
--------
|
|
|
|
>>> import numpy as np
|
|
>>> from scipy.sparse import dia_matrix
|
|
>>> dia_matrix((3, 4), dtype=np.int8).toarray()
|
|
array([[0, 0, 0, 0],
|
|
[0, 0, 0, 0],
|
|
[0, 0, 0, 0]], dtype=int8)
|
|
|
|
>>> data = np.array([[1, 2, 3, 4]]).repeat(3, axis=0)
|
|
>>> offsets = np.array([0, -1, 2])
|
|
>>> dia_matrix((data, offsets), shape=(4, 4)).toarray()
|
|
array([[1, 0, 3, 0],
|
|
[1, 2, 0, 4],
|
|
[0, 2, 3, 0],
|
|
[0, 0, 3, 4]])
|
|
|
|
>>> from scipy.sparse import dia_matrix
|
|
>>> n = 10
|
|
>>> ex = np.ones(n)
|
|
>>> data = np.array([ex, 2 * ex, ex])
|
|
>>> offsets = np.array([-1, 0, 1])
|
|
>>> dia_matrix((data, offsets), shape=(n, n)).toarray()
|
|
array([[2., 1., 0., ..., 0., 0., 0.],
|
|
[1., 2., 1., ..., 0., 0., 0.],
|
|
[0., 1., 2., ..., 0., 0., 0.],
|
|
...,
|
|
[0., 0., 0., ..., 2., 1., 0.],
|
|
[0., 0., 0., ..., 1., 2., 1.],
|
|
[0., 0., 0., ..., 0., 1., 2.]])
|
|
"""
|
|
format = 'dia'
|
|
|
|
def __init__(self, arg1, shape=None, dtype=None, copy=False):
|
|
_data_matrix.__init__(self)
|
|
|
|
if isspmatrix_dia(arg1):
|
|
if copy:
|
|
arg1 = arg1.copy()
|
|
self.data = arg1.data
|
|
self.offsets = arg1.offsets
|
|
self._shape = check_shape(arg1.shape)
|
|
elif isspmatrix(arg1):
|
|
if isspmatrix_dia(arg1) and copy:
|
|
A = arg1.copy()
|
|
else:
|
|
A = arg1.todia()
|
|
self.data = A.data
|
|
self.offsets = A.offsets
|
|
self._shape = check_shape(A.shape)
|
|
elif isinstance(arg1, tuple):
|
|
if isshape(arg1):
|
|
# It's a tuple of matrix dimensions (M, N)
|
|
# create empty matrix
|
|
self._shape = check_shape(arg1)
|
|
self.data = np.zeros((0,0), getdtype(dtype, default=float))
|
|
idx_dtype = get_index_dtype(maxval=max(self.shape))
|
|
self.offsets = np.zeros((0), dtype=idx_dtype)
|
|
else:
|
|
try:
|
|
# Try interpreting it as (data, offsets)
|
|
data, offsets = arg1
|
|
except Exception:
|
|
raise ValueError('unrecognized form for dia_matrix constructor')
|
|
else:
|
|
if shape is None:
|
|
raise ValueError('expected a shape argument')
|
|
self.data = np.atleast_2d(np.array(arg1[0], dtype=dtype, copy=copy))
|
|
self.offsets = np.atleast_1d(np.array(arg1[1],
|
|
dtype=get_index_dtype(maxval=max(shape)),
|
|
copy=copy))
|
|
self._shape = check_shape(shape)
|
|
else:
|
|
#must be dense, convert to COO first, then to DIA
|
|
try:
|
|
arg1 = np.asarray(arg1)
|
|
except Exception:
|
|
raise ValueError("unrecognized form for"
|
|
" %s_matrix constructor" % self.format)
|
|
from .coo import coo_matrix
|
|
A = coo_matrix(arg1, dtype=dtype, shape=shape).todia()
|
|
self.data = A.data
|
|
self.offsets = A.offsets
|
|
self._shape = check_shape(A.shape)
|
|
|
|
if dtype is not None:
|
|
self.data = self.data.astype(dtype)
|
|
|
|
#check format
|
|
if self.offsets.ndim != 1:
|
|
raise ValueError('offsets array must have rank 1')
|
|
|
|
if self.data.ndim != 2:
|
|
raise ValueError('data array must have rank 2')
|
|
|
|
if self.data.shape[0] != len(self.offsets):
|
|
raise ValueError('number of diagonals (%d) '
|
|
'does not match the number of offsets (%d)'
|
|
% (self.data.shape[0], len(self.offsets)))
|
|
|
|
if len(np.unique(self.offsets)) != len(self.offsets):
|
|
raise ValueError('offset array contains duplicate values')
|
|
|
|
def __repr__(self):
|
|
format = _formats[self.getformat()][1]
|
|
return "<%dx%d sparse matrix of type '%s'\n" \
|
|
"\twith %d stored elements (%d diagonals) in %s format>" % \
|
|
(self.shape + (self.dtype.type, self.nnz, self.data.shape[0],
|
|
format))
|
|
|
|
def _data_mask(self):
|
|
"""Returns a mask of the same shape as self.data, where
|
|
mask[i,j] is True when data[i,j] corresponds to a stored element."""
|
|
num_rows, num_cols = self.shape
|
|
offset_inds = np.arange(self.data.shape[1])
|
|
row = offset_inds - self.offsets[:,None]
|
|
mask = (row >= 0)
|
|
mask &= (row < num_rows)
|
|
mask &= (offset_inds < num_cols)
|
|
return mask
|
|
|
|
def count_nonzero(self):
|
|
mask = self._data_mask()
|
|
return np.count_nonzero(self.data[mask])
|
|
|
|
def getnnz(self, axis=None):
|
|
if axis is not None:
|
|
raise NotImplementedError("getnnz over an axis is not implemented "
|
|
"for DIA format")
|
|
M,N = self.shape
|
|
nnz = 0
|
|
for k in self.offsets:
|
|
if k > 0:
|
|
nnz += min(M,N-k)
|
|
else:
|
|
nnz += min(M+k,N)
|
|
return int(nnz)
|
|
|
|
getnnz.__doc__ = spmatrix.getnnz.__doc__
|
|
count_nonzero.__doc__ = spmatrix.count_nonzero.__doc__
|
|
|
|
def sum(self, axis=None, dtype=None, out=None):
|
|
validateaxis(axis)
|
|
|
|
if axis is not None and axis < 0:
|
|
axis += 2
|
|
|
|
res_dtype = get_sum_dtype(self.dtype)
|
|
num_rows, num_cols = self.shape
|
|
ret = None
|
|
|
|
if axis == 0:
|
|
mask = self._data_mask()
|
|
x = (self.data * mask).sum(axis=0)
|
|
if x.shape[0] == num_cols:
|
|
res = x
|
|
else:
|
|
res = np.zeros(num_cols, dtype=x.dtype)
|
|
res[:x.shape[0]] = x
|
|
ret = matrix(res, dtype=res_dtype)
|
|
|
|
else:
|
|
row_sums = np.zeros(num_rows, dtype=res_dtype)
|
|
one = np.ones(num_cols, dtype=res_dtype)
|
|
dia_matvec(num_rows, num_cols, len(self.offsets),
|
|
self.data.shape[1], self.offsets, self.data, one, row_sums)
|
|
|
|
row_sums = matrix(row_sums)
|
|
|
|
if axis is None:
|
|
return row_sums.sum(dtype=dtype, out=out)
|
|
|
|
if axis is not None:
|
|
row_sums = row_sums.T
|
|
|
|
ret = matrix(row_sums.sum(axis=axis))
|
|
|
|
if out is not None and out.shape != ret.shape:
|
|
raise ValueError("dimensions do not match")
|
|
|
|
return ret.sum(axis=(), dtype=dtype, out=out)
|
|
|
|
sum.__doc__ = spmatrix.sum.__doc__
|
|
|
|
def _mul_vector(self, other):
|
|
x = other
|
|
|
|
y = np.zeros(self.shape[0], dtype=upcast_char(self.dtype.char,
|
|
x.dtype.char))
|
|
|
|
L = self.data.shape[1]
|
|
|
|
M,N = self.shape
|
|
|
|
dia_matvec(M,N, len(self.offsets), L, self.offsets, self.data, x.ravel(), y.ravel())
|
|
|
|
return y
|
|
|
|
def _mul_multimatrix(self, other):
|
|
return np.hstack([self._mul_vector(col).reshape(-1,1) for col in other.T])
|
|
|
|
def _setdiag(self, values, k=0):
|
|
M, N = self.shape
|
|
|
|
if values.ndim == 0:
|
|
# broadcast
|
|
values_n = np.inf
|
|
else:
|
|
values_n = len(values)
|
|
|
|
if k < 0:
|
|
n = min(M + k, N, values_n)
|
|
min_index = 0
|
|
max_index = n
|
|
else:
|
|
n = min(M, N - k, values_n)
|
|
min_index = k
|
|
max_index = k + n
|
|
|
|
if values.ndim != 0:
|
|
# allow also longer sequences
|
|
values = values[:n]
|
|
|
|
if k in self.offsets:
|
|
self.data[self.offsets == k, min_index:max_index] = values
|
|
else:
|
|
self.offsets = np.append(self.offsets, self.offsets.dtype.type(k))
|
|
m = max(max_index, self.data.shape[1])
|
|
data = np.zeros((self.data.shape[0]+1, m), dtype=self.data.dtype)
|
|
data[:-1,:self.data.shape[1]] = self.data
|
|
data[-1, min_index:max_index] = values
|
|
self.data = data
|
|
|
|
def todia(self, copy=False):
|
|
if copy:
|
|
return self.copy()
|
|
else:
|
|
return self
|
|
|
|
todia.__doc__ = spmatrix.todia.__doc__
|
|
|
|
def transpose(self, axes=None, copy=False):
|
|
if axes is not None:
|
|
raise ValueError(("Sparse matrices do not support "
|
|
"an 'axes' parameter because swapping "
|
|
"dimensions is the only logical permutation."))
|
|
|
|
num_rows, num_cols = self.shape
|
|
max_dim = max(self.shape)
|
|
|
|
# flip diagonal offsets
|
|
offsets = -self.offsets
|
|
|
|
# re-align the data matrix
|
|
r = np.arange(len(offsets), dtype=np.intc)[:, None]
|
|
c = np.arange(num_rows, dtype=np.intc) - (offsets % max_dim)[:, None]
|
|
pad_amount = max(0, max_dim-self.data.shape[1])
|
|
data = np.hstack((self.data, np.zeros((self.data.shape[0], pad_amount),
|
|
dtype=self.data.dtype)))
|
|
data = data[r, c]
|
|
return dia_matrix((data, offsets), shape=(
|
|
num_cols, num_rows), copy=copy)
|
|
|
|
transpose.__doc__ = spmatrix.transpose.__doc__
|
|
|
|
def diagonal(self, k=0):
|
|
rows, cols = self.shape
|
|
if k <= -rows or k >= cols:
|
|
return np.empty(0, dtype=self.data.dtype)
|
|
idx, = np.nonzero(self.offsets == k)
|
|
first_col, last_col = max(0, k), min(rows + k, cols)
|
|
if idx.size == 0:
|
|
return np.zeros(last_col - first_col, dtype=self.data.dtype)
|
|
return self.data[idx[0], first_col:last_col]
|
|
|
|
diagonal.__doc__ = spmatrix.diagonal.__doc__
|
|
|
|
def tocsc(self, copy=False):
|
|
from .csc import csc_matrix
|
|
if self.nnz == 0:
|
|
return csc_matrix(self.shape, dtype=self.dtype)
|
|
|
|
num_rows, num_cols = self.shape
|
|
num_offsets, offset_len = self.data.shape
|
|
offset_inds = np.arange(offset_len)
|
|
|
|
row = offset_inds - self.offsets[:,None]
|
|
mask = (row >= 0)
|
|
mask &= (row < num_rows)
|
|
mask &= (offset_inds < num_cols)
|
|
mask &= (self.data != 0)
|
|
|
|
idx_dtype = get_index_dtype(maxval=max(self.shape))
|
|
indptr = np.zeros(num_cols + 1, dtype=idx_dtype)
|
|
indptr[1:offset_len+1] = np.cumsum(mask.sum(axis=0))
|
|
indptr[offset_len+1:] = indptr[offset_len]
|
|
indices = row.T[mask.T].astype(idx_dtype, copy=False)
|
|
data = self.data.T[mask.T]
|
|
return csc_matrix((data, indices, indptr), shape=self.shape,
|
|
dtype=self.dtype)
|
|
|
|
tocsc.__doc__ = spmatrix.tocsc.__doc__
|
|
|
|
def tocoo(self, copy=False):
|
|
num_rows, num_cols = self.shape
|
|
num_offsets, offset_len = self.data.shape
|
|
offset_inds = np.arange(offset_len)
|
|
|
|
row = offset_inds - self.offsets[:,None]
|
|
mask = (row >= 0)
|
|
mask &= (row < num_rows)
|
|
mask &= (offset_inds < num_cols)
|
|
mask &= (self.data != 0)
|
|
row = row[mask]
|
|
col = np.tile(offset_inds, num_offsets)[mask.ravel()]
|
|
data = self.data[mask]
|
|
|
|
from .coo import coo_matrix
|
|
A = coo_matrix((data,(row,col)), shape=self.shape, dtype=self.dtype)
|
|
A.has_canonical_format = True
|
|
return A
|
|
|
|
tocoo.__doc__ = spmatrix.tocoo.__doc__
|
|
|
|
# needed by _data_matrix
|
|
def _with_data(self, data, copy=True):
|
|
"""Returns a matrix with the same sparsity structure as self,
|
|
but with different data. By default the structure arrays are copied.
|
|
"""
|
|
if copy:
|
|
return dia_matrix((data, self.offsets.copy()), shape=self.shape)
|
|
else:
|
|
return dia_matrix((data,self.offsets), shape=self.shape)
|
|
|
|
def resize(self, *shape):
|
|
shape = check_shape(shape)
|
|
M, N = shape
|
|
# we do not need to handle the case of expanding N
|
|
self.data = self.data[:, :N]
|
|
|
|
if (M > self.shape[0] and
|
|
np.any(self.offsets + self.shape[0] < self.data.shape[1])):
|
|
# explicitly clear values that were previously hidden
|
|
mask = (self.offsets[:, None] + self.shape[0] <=
|
|
np.arange(self.data.shape[1]))
|
|
self.data[mask] = 0
|
|
|
|
self._shape = shape
|
|
|
|
resize.__doc__ = spmatrix.resize.__doc__
|
|
|
|
|
|
def isspmatrix_dia(x):
|
|
"""Is x of dia_matrix type?
|
|
|
|
Parameters
|
|
----------
|
|
x
|
|
object to check for being a dia matrix
|
|
|
|
Returns
|
|
-------
|
|
bool
|
|
True if x is a dia matrix, False otherwise
|
|
|
|
Examples
|
|
--------
|
|
>>> from scipy.sparse import dia_matrix, isspmatrix_dia
|
|
>>> isspmatrix_dia(dia_matrix([[5]]))
|
|
True
|
|
|
|
>>> from scipy.sparse import dia_matrix, csr_matrix, isspmatrix_dia
|
|
>>> isspmatrix_dia(csr_matrix([[5]]))
|
|
False
|
|
"""
|
|
return isinstance(x, dia_matrix)
|
|
|