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- """ Utility functions for sparse matrix module
- """
- import sys
- import operator
- import numpy as np
- from scipy._lib._util import prod
- import scipy.sparse as sp
- __all__ = ['upcast', 'getdtype', 'getdata', 'isscalarlike', 'isintlike',
- 'isshape', 'issequence', 'isdense', 'ismatrix', 'get_sum_dtype']
- supported_dtypes = [np.bool_, np.byte, np.ubyte, np.short, np.ushort, np.intc,
- np.uintc, np.int_, np.uint, np.longlong, np.ulonglong,
- np.single, np.double,
- np.longdouble, np.csingle, np.cdouble, np.clongdouble]
- _upcast_memo = {}
- def upcast(*args):
- """Returns the nearest supported sparse dtype for the
- combination of one or more types.
- upcast(t0, t1, ..., tn) -> T where T is a supported dtype
- Examples
- --------
- >>> upcast('int32')
- <type 'numpy.int32'>
- >>> upcast('bool')
- <type 'numpy.bool_'>
- >>> upcast('int32','float32')
- <type 'numpy.float64'>
- >>> upcast('bool',complex,float)
- <type 'numpy.complex128'>
- """
- t = _upcast_memo.get(hash(args))
- if t is not None:
- return t
- upcast = np.result_type(*args)
- for t in supported_dtypes:
- if np.can_cast(upcast, t):
- _upcast_memo[hash(args)] = t
- return t
- raise TypeError('no supported conversion for types: %r' % (args,))
- def upcast_char(*args):
- """Same as `upcast` but taking dtype.char as input (faster)."""
- t = _upcast_memo.get(args)
- if t is not None:
- return t
- t = upcast(*map(np.dtype, args))
- _upcast_memo[args] = t
- return t
- def upcast_scalar(dtype, scalar):
- """Determine data type for binary operation between an array of
- type `dtype` and a scalar.
- """
- return (np.array([0], dtype=dtype) * scalar).dtype
- def downcast_intp_index(arr):
- """
- Down-cast index array to np.intp dtype if it is of a larger dtype.
- Raise an error if the array contains a value that is too large for
- intp.
- """
- if arr.dtype.itemsize > np.dtype(np.intp).itemsize:
- if arr.size == 0:
- return arr.astype(np.intp)
- maxval = arr.max()
- minval = arr.min()
- if maxval > np.iinfo(np.intp).max or minval < np.iinfo(np.intp).min:
- raise ValueError("Cannot deal with arrays with indices larger "
- "than the machine maximum address size "
- "(e.g. 64-bit indices on 32-bit machine).")
- return arr.astype(np.intp)
- return arr
- def to_native(A):
- """
- Ensure that the data type of the NumPy array `A` has native byte order.
- `A` must be a NumPy array. If the data type of `A` does not have native
- byte order, a copy of `A` with a native byte order is returned. Otherwise
- `A` is returned.
- """
- dt = A.dtype
- if dt.isnative:
- # Don't call `asarray()` if A is already native, to avoid unnecessarily
- # creating a view of the input array.
- return A
- return np.asarray(A, dtype=dt.newbyteorder('native'))
- def getdtype(dtype, a=None, default=None):
- """Function used to simplify argument processing. If 'dtype' is not
- specified (is None), returns a.dtype; otherwise returns a np.dtype
- object created from the specified dtype argument. If 'dtype' and 'a'
- are both None, construct a data type out of the 'default' parameter.
- Furthermore, 'dtype' must be in 'allowed' set.
- """
- # TODO is this really what we want?
- if dtype is None:
- try:
- newdtype = a.dtype
- except AttributeError as e:
- if default is not None:
- newdtype = np.dtype(default)
- else:
- raise TypeError("could not interpret data type") from e
- else:
- newdtype = np.dtype(dtype)
- if newdtype == np.object_:
- raise ValueError(
- "object dtype is not supported by sparse matrices"
- )
- return newdtype
- def getdata(obj, dtype=None, copy=False):
- """
- This is a wrapper of `np.array(obj, dtype=dtype, copy=copy)`
- that will generate a warning if the result is an object array.
- """
- data = np.array(obj, dtype=dtype, copy=copy)
- # Defer to getdtype for checking that the dtype is OK.
- # This is called for the validation only; we don't need the return value.
- getdtype(data.dtype)
- return data
- def get_index_dtype(arrays=(), maxval=None, check_contents=False):
- """
- Based on input (integer) arrays `a`, determine a suitable index data
- type that can hold the data in the arrays.
- Parameters
- ----------
- arrays : tuple of array_like
- Input arrays whose types/contents to check
- maxval : float, optional
- Maximum value needed
- check_contents : bool, optional
- Whether to check the values in the arrays and not just their types.
- Default: False (check only the types)
- Returns
- -------
- dtype : dtype
- Suitable index data type (int32 or int64)
- """
- int32min = np.int32(np.iinfo(np.int32).min)
- int32max = np.int32(np.iinfo(np.int32).max)
- # not using intc directly due to misinteractions with pythran
- dtype = np.int32 if np.intc().itemsize == 4 else np.int64
- if maxval is not None:
- maxval = np.int64(maxval)
- if maxval > int32max:
- dtype = np.int64
- if isinstance(arrays, np.ndarray):
- arrays = (arrays,)
- for arr in arrays:
- arr = np.asarray(arr)
- if not np.can_cast(arr.dtype, np.int32):
- if check_contents:
- if arr.size == 0:
- # a bigger type not needed
- continue
- elif np.issubdtype(arr.dtype, np.integer):
- maxval = arr.max()
- minval = arr.min()
- if minval >= int32min and maxval <= int32max:
- # a bigger type not needed
- continue
- dtype = np.int64
- break
- return dtype
- def get_sum_dtype(dtype):
- """Mimic numpy's casting for np.sum"""
- if dtype.kind == 'u' and np.can_cast(dtype, np.uint):
- return np.uint
- if np.can_cast(dtype, np.int_):
- return np.int_
- return dtype
- def isscalarlike(x):
- """Is x either a scalar, an array scalar, or a 0-dim array?"""
- return np.isscalar(x) or (isdense(x) and x.ndim == 0)
- def isintlike(x):
- """Is x appropriate as an index into a sparse matrix? Returns True
- if it can be cast safely to a machine int.
- """
- # Fast-path check to eliminate non-scalar values. operator.index would
- # catch this case too, but the exception catching is slow.
- if np.ndim(x) != 0:
- return False
- try:
- operator.index(x)
- except (TypeError, ValueError):
- try:
- loose_int = bool(int(x) == x)
- except (TypeError, ValueError):
- return False
- if loose_int:
- msg = "Inexact indices into sparse matrices are not allowed"
- raise ValueError(msg)
- return loose_int
- return True
- def isshape(x, nonneg=False):
- """Is x a valid 2-tuple of dimensions?
- If nonneg, also checks that the dimensions are non-negative.
- """
- try:
- # Assume it's a tuple of matrix dimensions (M, N)
- (M, N) = x
- except Exception:
- return False
- else:
- if isintlike(M) and isintlike(N):
- if np.ndim(M) == 0 and np.ndim(N) == 0:
- if not nonneg or (M >= 0 and N >= 0):
- return True
- return False
- def issequence(t):
- return ((isinstance(t, (list, tuple)) and
- (len(t) == 0 or np.isscalar(t[0]))) or
- (isinstance(t, np.ndarray) and (t.ndim == 1)))
- def ismatrix(t):
- return ((isinstance(t, (list, tuple)) and
- len(t) > 0 and issequence(t[0])) or
- (isinstance(t, np.ndarray) and t.ndim == 2))
- def isdense(x):
- return isinstance(x, np.ndarray)
- def validateaxis(axis):
- if axis is not None:
- axis_type = type(axis)
- # In NumPy, you can pass in tuples for 'axis', but they are
- # not very useful for sparse matrices given their limited
- # dimensions, so let's make it explicit that they are not
- # allowed to be passed in
- if axis_type == tuple:
- raise TypeError(("Tuples are not accepted for the 'axis' "
- "parameter. Please pass in one of the "
- "following: {-2, -1, 0, 1, None}."))
- # If not a tuple, check that the provided axis is actually
- # an integer and raise a TypeError similar to NumPy's
- if not np.issubdtype(np.dtype(axis_type), np.integer):
- raise TypeError("axis must be an integer, not {name}"
- .format(name=axis_type.__name__))
- if not (-2 <= axis <= 1):
- raise ValueError("axis out of range")
- def check_shape(args, current_shape=None):
- """Imitate numpy.matrix handling of shape arguments"""
- if len(args) == 0:
- raise TypeError("function missing 1 required positional argument: "
- "'shape'")
- elif len(args) == 1:
- try:
- shape_iter = iter(args[0])
- except TypeError:
- new_shape = (operator.index(args[0]), )
- else:
- new_shape = tuple(operator.index(arg) for arg in shape_iter)
- else:
- new_shape = tuple(operator.index(arg) for arg in args)
- if current_shape is None:
- if len(new_shape) != 2:
- raise ValueError('shape must be a 2-tuple of positive integers')
- elif any(d < 0 for d in new_shape):
- raise ValueError("'shape' elements cannot be negative")
- else:
- # Check the current size only if needed
- current_size = prod(current_shape)
- # Check for negatives
- negative_indexes = [i for i, x in enumerate(new_shape) if x < 0]
- if len(negative_indexes) == 0:
- new_size = prod(new_shape)
- if new_size != current_size:
- raise ValueError('cannot reshape array of size {} into shape {}'
- .format(current_size, new_shape))
- elif len(negative_indexes) == 1:
- skip = negative_indexes[0]
- specified = prod(new_shape[0:skip] + new_shape[skip+1:])
- unspecified, remainder = divmod(current_size, specified)
- if remainder != 0:
- err_shape = tuple('newshape' if x < 0 else x for x in new_shape)
- raise ValueError('cannot reshape array of size {} into shape {}'
- ''.format(current_size, err_shape))
- new_shape = new_shape[0:skip] + (unspecified,) + new_shape[skip+1:]
- else:
- raise ValueError('can only specify one unknown dimension')
- if len(new_shape) != 2:
- raise ValueError('matrix shape must be two-dimensional')
- return new_shape
- def check_reshape_kwargs(kwargs):
- """Unpack keyword arguments for reshape function.
- This is useful because keyword arguments after star arguments are not
- allowed in Python 2, but star keyword arguments are. This function unpacks
- 'order' and 'copy' from the star keyword arguments (with defaults) and
- throws an error for any remaining.
- """
- order = kwargs.pop('order', 'C')
- copy = kwargs.pop('copy', False)
- if kwargs: # Some unused kwargs remain
- raise TypeError('reshape() got unexpected keywords arguments: {}'
- .format(', '.join(kwargs.keys())))
- return order, copy
- def is_pydata_spmatrix(m):
- """
- Check whether object is pydata/sparse matrix, avoiding importing the module.
- """
- base_cls = getattr(sys.modules.get('sparse'), 'SparseArray', None)
- return base_cls is not None and isinstance(m, base_cls)
- ###############################################################################
- # Wrappers for NumPy types that are deprecated
- # Numpy versions of these functions raise deprecation warnings, the
- # ones below do not.
- def matrix(*args, **kwargs):
- return np.array(*args, **kwargs).view(np.matrix)
- def asmatrix(data, dtype=None):
- if isinstance(data, np.matrix) and (dtype is None or data.dtype == dtype):
- return data
- return np.asarray(data, dtype=dtype).view(np.matrix)
- ###############################################################################
- def _todata(s: 'sp.spmatrix') -> np.ndarray:
- """Access nonzero values, possibly after summing duplicates.
- Parameters
- ----------
- s : sparse matrix
- Input sparse matrix.
- Returns
- -------
- data: ndarray
- Nonzero values of the array, with shape (s.nnz,)
- """
- if isinstance(s, sp._data._data_matrix):
- return s._deduped_data()
- if isinstance(s, sp.dok_matrix):
- return np.fromiter(s.values(), dtype=s.dtype, count=s.nnz)
- if isinstance(s, sp.lil_matrix):
- data = np.empty(s.nnz, dtype=s.dtype)
- sp._csparsetools.lil_flatten_to_array(s.data, data)
- return data
- return s.tocoo()._deduped_data()
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