673 lines
22 KiB
Python
673 lines
22 KiB
Python
"""Dictionary Of Keys based matrix"""
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__docformat__ = "restructuredtext en"
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__all__ = ['dok_array', 'dok_matrix', 'isspmatrix_dok']
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import itertools
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import numpy as np
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from ._matrix import spmatrix
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from ._base import _spbase, sparray, issparse
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from ._index import IndexMixin
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from ._sputils import (isdense, getdtype, isshape, isintlike, isscalarlike,
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upcast, upcast_scalar, check_shape)
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class _dok_base(_spbase, IndexMixin, dict):
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_format = 'dok'
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def __init__(self, arg1, shape=None, dtype=None, copy=False):
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_spbase.__init__(self)
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is_array = isinstance(self, sparray)
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if isinstance(arg1, tuple) and isshape(arg1, allow_1d=is_array):
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self._shape = check_shape(arg1, allow_1d=is_array)
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self._dict = {}
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self.dtype = getdtype(dtype, default=float)
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elif issparse(arg1): # Sparse ctor
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if arg1.format == self.format:
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arg1 = arg1.copy() if copy else arg1
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else:
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arg1 = arg1.todok()
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if dtype is not None:
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arg1 = arg1.astype(dtype, copy=False)
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self._dict = arg1._dict
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self._shape = check_shape(arg1.shape, allow_1d=is_array)
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self.dtype = arg1.dtype
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else: # Dense ctor
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try:
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arg1 = np.asarray(arg1)
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except Exception as e:
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raise TypeError('Invalid input format.') from e
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if arg1.ndim > 2:
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raise TypeError('Expected rank <=2 dense array or matrix.')
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if arg1.ndim == 1:
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if dtype is not None:
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arg1 = arg1.astype(dtype)
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self._dict = {i: v for i, v in enumerate(arg1) if v != 0}
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self.dtype = arg1.dtype
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else:
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d = self._coo_container(arg1, dtype=dtype).todok()
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self._dict = d._dict
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self.dtype = d.dtype
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self._shape = check_shape(arg1.shape, allow_1d=is_array)
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def update(self, val):
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# Prevent direct usage of update
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raise NotImplementedError("Direct update to DOK sparse format is not allowed.")
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def _getnnz(self, axis=None):
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if axis is not None:
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raise NotImplementedError(
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"_getnnz over an axis is not implemented for DOK format."
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)
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return len(self._dict)
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def count_nonzero(self):
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return sum(x != 0 for x in self.values())
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_getnnz.__doc__ = _spbase._getnnz.__doc__
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count_nonzero.__doc__ = _spbase.count_nonzero.__doc__
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def __len__(self):
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return len(self._dict)
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def __contains__(self, key):
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return key in self._dict
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def setdefault(self, key, default=None, /):
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return self._dict.setdefault(key, default)
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def __delitem__(self, key, /):
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del self._dict[key]
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def clear(self):
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return self._dict.clear()
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def pop(self, /, *args):
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return self._dict.pop(*args)
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def __reversed__(self):
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raise TypeError("reversed is not defined for dok_array type")
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def __or__(self, other):
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type_names = f"{type(self).__name__} and {type(other).__name__}"
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raise TypeError(f"unsupported operand type for |: {type_names}")
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def __ror__(self, other):
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type_names = f"{type(self).__name__} and {type(other).__name__}"
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raise TypeError(f"unsupported operand type for |: {type_names}")
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def __ior__(self, other):
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type_names = f"{type(self).__name__} and {type(other).__name__}"
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raise TypeError(f"unsupported operand type for |: {type_names}")
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def popitem(self):
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return self._dict.popitem()
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def items(self):
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return self._dict.items()
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def keys(self):
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return self._dict.keys()
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def values(self):
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return self._dict.values()
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def get(self, key, default=0.0):
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"""This provides dict.get method functionality with type checking"""
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if key in self._dict:
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return self._dict[key]
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if isintlike(key) and self.ndim == 1:
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key = (key,)
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if self.ndim != len(key):
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raise IndexError(f'Index {key} length needs to match self.shape')
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try:
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for i in key:
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assert isintlike(i)
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except (AssertionError, TypeError, ValueError) as e:
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raise IndexError('Index must be or consist of integers.') from e
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key = tuple(i + M if i < 0 else i for i, M in zip(key, self.shape))
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if any(i < 0 or i >= M for i, M in zip(key, self.shape)):
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raise IndexError('Index out of bounds.')
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if self.ndim == 1:
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key = key[0]
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return self._dict.get(key, default)
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# override IndexMixin.__getitem__ for 1d case until fully implemented
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def __getitem__(self, key):
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if self.ndim == 2:
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return super().__getitem__(key)
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if isinstance(key, tuple) and len(key) == 1:
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key = key[0]
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INT_TYPES = (int, np.integer)
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if isinstance(key, INT_TYPES):
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if key < 0:
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key += self.shape[-1]
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if key < 0 or key >= self.shape[-1]:
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raise IndexError('index value out of bounds')
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return self._get_int(key)
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else:
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raise IndexError('array/slice index for 1d dok_array not yet supported')
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# 1D get methods
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def _get_int(self, idx):
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return self._dict.get(idx, self.dtype.type(0))
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# 2D get methods
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def _get_intXint(self, row, col):
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return self._dict.get((row, col), self.dtype.type(0))
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def _get_intXslice(self, row, col):
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return self._get_sliceXslice(slice(row, row + 1), col)
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def _get_sliceXint(self, row, col):
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return self._get_sliceXslice(row, slice(col, col + 1))
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def _get_sliceXslice(self, row, col):
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row_start, row_stop, row_step = row.indices(self.shape[0])
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col_start, col_stop, col_step = col.indices(self.shape[1])
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row_range = range(row_start, row_stop, row_step)
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col_range = range(col_start, col_stop, col_step)
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shape = (len(row_range), len(col_range))
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# Switch paths only when advantageous
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# (count the iterations in the loops, adjust for complexity)
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if len(self) >= 2 * shape[0] * shape[1]:
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# O(nr*nc) path: loop over <row x col>
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return self._get_columnXarray(row_range, col_range)
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# O(nnz) path: loop over entries of self
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newdok = self._dok_container(shape, dtype=self.dtype)
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for key in self.keys():
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i, ri = divmod(int(key[0]) - row_start, row_step)
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if ri != 0 or i < 0 or i >= shape[0]:
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continue
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j, rj = divmod(int(key[1]) - col_start, col_step)
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if rj != 0 or j < 0 or j >= shape[1]:
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continue
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newdok._dict[i, j] = self._dict[key]
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return newdok
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def _get_intXarray(self, row, col):
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col = col.squeeze()
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return self._get_columnXarray([row], col)
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def _get_arrayXint(self, row, col):
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row = row.squeeze()
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return self._get_columnXarray(row, [col])
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def _get_sliceXarray(self, row, col):
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row = list(range(*row.indices(self.shape[0])))
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return self._get_columnXarray(row, col)
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def _get_arrayXslice(self, row, col):
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col = list(range(*col.indices(self.shape[1])))
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return self._get_columnXarray(row, col)
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def _get_columnXarray(self, row, col):
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# outer indexing
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newdok = self._dok_container((len(row), len(col)), dtype=self.dtype)
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for i, r in enumerate(row):
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for j, c in enumerate(col):
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v = self._dict.get((r, c), 0)
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if v:
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newdok._dict[i, j] = v
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return newdok
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def _get_arrayXarray(self, row, col):
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# inner indexing
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i, j = map(np.atleast_2d, np.broadcast_arrays(row, col))
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newdok = self._dok_container(i.shape, dtype=self.dtype)
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for key in itertools.product(range(i.shape[0]), range(i.shape[1])):
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v = self._dict.get((i[key], j[key]), 0)
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if v:
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newdok._dict[key] = v
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return newdok
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# override IndexMixin.__setitem__ for 1d case until fully implemented
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def __setitem__(self, key, value):
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if self.ndim == 2:
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return super().__setitem__(key, value)
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if isinstance(key, tuple) and len(key) == 1:
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key = key[0]
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INT_TYPES = (int, np.integer)
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if isinstance(key, INT_TYPES):
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if key < 0:
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key += self.shape[-1]
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if key < 0 or key >= self.shape[-1]:
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raise IndexError('index value out of bounds')
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return self._set_int(key, value)
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else:
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raise IndexError('array index for 1d dok_array not yet provided')
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# 1D set methods
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def _set_int(self, idx, x):
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if x:
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self._dict[idx] = x
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elif idx in self._dict:
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del self._dict[idx]
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# 2D set methods
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def _set_intXint(self, row, col, x):
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key = (row, col)
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if x:
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self._dict[key] = x
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elif key in self._dict:
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del self._dict[key]
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def _set_arrayXarray(self, row, col, x):
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row = list(map(int, row.ravel()))
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col = list(map(int, col.ravel()))
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x = x.ravel()
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self._dict.update(zip(zip(row, col), x))
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for i in np.nonzero(x == 0)[0]:
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key = (row[i], col[i])
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if self._dict[key] == 0:
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# may have been superseded by later update
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del self._dict[key]
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def __add__(self, other):
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if isscalarlike(other):
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res_dtype = upcast_scalar(self.dtype, other)
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new = self._dok_container(self.shape, dtype=res_dtype)
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# Add this scalar to each element.
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for key in itertools.product(*[range(d) for d in self.shape]):
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aij = self._dict.get(key, 0) + other
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if aij:
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new[key] = aij
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elif issparse(other):
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if other.shape != self.shape:
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raise ValueError("Matrix dimensions are not equal.")
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res_dtype = upcast(self.dtype, other.dtype)
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new = self._dok_container(self.shape, dtype=res_dtype)
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new._dict = self._dict.copy()
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if other.format == "dok":
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o_items = other.items()
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else:
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other = other.tocoo()
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if self.ndim == 1:
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o_items = zip(other.coords[0], other.data)
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else:
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o_items = zip(zip(*other.coords), other.data)
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with np.errstate(over='ignore'):
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new._dict.update((k, new[k] + v) for k, v in o_items)
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elif isdense(other):
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new = self.todense() + other
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else:
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return NotImplemented
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return new
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def __radd__(self, other):
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return self + other # addition is comutative
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def __neg__(self):
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if self.dtype.kind == 'b':
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raise NotImplementedError(
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'Negating a sparse boolean matrix is not supported.'
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)
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new = self._dok_container(self.shape, dtype=self.dtype)
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new._dict.update((k, -v) for k, v in self.items())
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return new
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def _mul_scalar(self, other):
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res_dtype = upcast_scalar(self.dtype, other)
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# Multiply this scalar by every element.
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new = self._dok_container(self.shape, dtype=res_dtype)
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new._dict.update(((k, v * other) for k, v in self.items()))
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return new
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def _matmul_vector(self, other):
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res_dtype = upcast(self.dtype, other.dtype)
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# vector @ vector
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if self.ndim == 1:
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if issparse(other):
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if other.format == "dok":
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keys = self.keys() & other.keys()
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else:
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keys = self.keys() & other.tocoo().coords[0]
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return res_dtype(sum(self._dict[k] * other._dict[k] for k in keys))
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elif isdense(other):
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return res_dtype(sum(other[k] * v for k, v in self.items()))
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else:
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return NotImplemented
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# matrix @ vector
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result = np.zeros(self.shape[0], dtype=res_dtype)
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for (i, j), v in self.items():
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result[i] += v * other[j]
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return result
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def _matmul_multivector(self, other):
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result_dtype = upcast(self.dtype, other.dtype)
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# vector @ multivector
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if self.ndim == 1:
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# works for other 1d or 2d
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return sum(v * other[j] for j, v in self._dict.items())
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# matrix @ multivector
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M = self.shape[0]
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new_shape = (M,) if other.ndim == 1 else (M, other.shape[1])
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result = np.zeros(new_shape, dtype=result_dtype)
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for (i, j), v in self.items():
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result[i] += v * other[j]
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return result
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def __imul__(self, other):
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if isscalarlike(other):
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self._dict.update((k, v * other) for k, v in self.items())
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return self
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return NotImplemented
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def __truediv__(self, other):
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if isscalarlike(other):
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res_dtype = upcast_scalar(self.dtype, other)
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new = self._dok_container(self.shape, dtype=res_dtype)
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new._dict.update(((k, v / other) for k, v in self.items()))
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return new
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return self.tocsr() / other
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def __itruediv__(self, other):
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if isscalarlike(other):
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self._dict.update((k, v / other) for k, v in self.items())
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return self
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return NotImplemented
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def __reduce__(self):
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# this approach is necessary because __setstate__ is called after
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# __setitem__ upon unpickling and since __init__ is not called there
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# is no shape attribute hence it is not possible to unpickle it.
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return dict.__reduce__(self)
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def diagonal(self, k=0):
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if self.ndim == 2:
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return super().diagonal(k)
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raise ValueError("diagonal requires two dimensions")
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def transpose(self, axes=None, copy=False):
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if self.ndim == 1:
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return self.copy()
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if axes is not None and axes != (1, 0):
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raise ValueError(
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"Sparse arrays/matrices do not support "
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"an 'axes' parameter because swapping "
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"dimensions is the only logical permutation."
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)
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M, N = self.shape
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new = self._dok_container((N, M), dtype=self.dtype, copy=copy)
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new._dict.update((((right, left), val) for (left, right), val in self.items()))
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return new
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transpose.__doc__ = _spbase.transpose.__doc__
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def conjtransp(self):
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"""Return the conjugate transpose."""
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if self.ndim == 1:
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new = self.tocoo()
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new.data = new.data.conjugate()
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return new
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M, N = self.shape
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new = self._dok_container((N, M), dtype=self.dtype)
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new._dict = {(right, left): np.conj(val) for (left, right), val in self.items()}
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return new
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def copy(self):
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new = self._dok_container(self.shape, dtype=self.dtype)
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new._dict.update(self._dict)
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return new
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copy.__doc__ = _spbase.copy.__doc__
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@classmethod
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def fromkeys(cls, iterable, value=1, /):
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tmp = dict.fromkeys(iterable, value)
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if isinstance(next(iter(tmp)), tuple):
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shape = tuple(max(idx) + 1 for idx in zip(*tmp))
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else:
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shape = (max(tmp) + 1,)
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result = cls(shape, dtype=type(value))
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result._dict = tmp
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return result
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def tocoo(self, copy=False):
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nnz = self.nnz
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if nnz == 0:
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return self._coo_container(self.shape, dtype=self.dtype)
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idx_dtype = self._get_index_dtype(maxval=max(self.shape))
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data = np.fromiter(self.values(), dtype=self.dtype, count=nnz)
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# handle 1d keys specially b/c not a tuple
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inds = zip(*self.keys()) if self.ndim > 1 else (self.keys(),)
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coords = tuple(np.fromiter(ix, dtype=idx_dtype, count=nnz) for ix in inds)
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A = self._coo_container((data, coords), shape=self.shape, dtype=self.dtype)
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A.has_canonical_format = True
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return A
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tocoo.__doc__ = _spbase.tocoo.__doc__
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def todok(self, copy=False):
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if copy:
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return self.copy()
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return self
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todok.__doc__ = _spbase.todok.__doc__
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def tocsc(self, copy=False):
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if self.ndim == 1:
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raise NotImplementedError("tocsr() not valid for 1d sparse array")
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return self.tocoo(copy=False).tocsc(copy=copy)
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tocsc.__doc__ = _spbase.tocsc.__doc__
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def resize(self, *shape):
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is_array = isinstance(self, sparray)
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shape = check_shape(shape, allow_1d=is_array)
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if len(shape) != len(self.shape):
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# TODO implement resize across dimensions
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raise NotImplementedError
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if self.ndim == 1:
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newN = shape[-1]
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for i in list(self._dict):
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if i >= newN:
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del self._dict[i]
|
|
self._shape = shape
|
|
return
|
|
|
|
newM, newN = shape
|
|
M, N = self.shape
|
|
if newM < M or newN < N:
|
|
# Remove all elements outside new dimensions
|
|
for i, j in list(self.keys()):
|
|
if i >= newM or j >= newN:
|
|
del self._dict[i, j]
|
|
self._shape = shape
|
|
|
|
resize.__doc__ = _spbase.resize.__doc__
|
|
|
|
# Added for 1d to avoid `tocsr` from _base.py
|
|
def astype(self, dtype, casting='unsafe', copy=True):
|
|
dtype = np.dtype(dtype)
|
|
if self.dtype != dtype:
|
|
result = self._dok_container(self.shape, dtype=dtype)
|
|
data = np.array(list(self._dict.values()), dtype=dtype)
|
|
result._dict = dict(zip(self._dict, data))
|
|
return result
|
|
elif copy:
|
|
return self.copy()
|
|
return self
|
|
|
|
|
|
def isspmatrix_dok(x):
|
|
"""Is `x` of dok_array type?
|
|
|
|
Parameters
|
|
----------
|
|
x
|
|
object to check for being a dok matrix
|
|
|
|
Returns
|
|
-------
|
|
bool
|
|
True if `x` is a dok matrix, False otherwise
|
|
|
|
Examples
|
|
--------
|
|
>>> from scipy.sparse import dok_array, dok_matrix, coo_matrix, isspmatrix_dok
|
|
>>> isspmatrix_dok(dok_matrix([[5]]))
|
|
True
|
|
>>> isspmatrix_dok(dok_array([[5]]))
|
|
False
|
|
>>> isspmatrix_dok(coo_matrix([[5]]))
|
|
False
|
|
"""
|
|
return isinstance(x, dok_matrix)
|
|
|
|
|
|
# This namespace class separates array from matrix with isinstance
|
|
class dok_array(_dok_base, sparray):
|
|
"""
|
|
Dictionary Of Keys based sparse array.
|
|
|
|
This is an efficient structure for constructing sparse
|
|
arrays incrementally.
|
|
|
|
This can be instantiated in several ways:
|
|
dok_array(D)
|
|
where D is a 2-D ndarray
|
|
|
|
dok_array(S)
|
|
with another sparse array or matrix S (equivalent to S.todok())
|
|
|
|
dok_array((M,N), [dtype])
|
|
create the array with initial shape (M,N)
|
|
dtype is optional, defaulting to dtype='d'
|
|
|
|
Attributes
|
|
----------
|
|
dtype : dtype
|
|
Data type of the array
|
|
shape : 2-tuple
|
|
Shape of the array
|
|
ndim : int
|
|
Number of dimensions (this is always 2)
|
|
nnz
|
|
Number of nonzero elements
|
|
size
|
|
T
|
|
|
|
Notes
|
|
-----
|
|
|
|
Sparse arrays can be used in arithmetic operations: they support
|
|
addition, subtraction, multiplication, division, and matrix power.
|
|
|
|
- Allows for efficient O(1) access of individual elements.
|
|
- Duplicates are not allowed.
|
|
- Can be efficiently converted to a coo_array once constructed.
|
|
|
|
Examples
|
|
--------
|
|
>>> import numpy as np
|
|
>>> from scipy.sparse import dok_array
|
|
>>> S = dok_array((5, 5), dtype=np.float32)
|
|
>>> for i in range(5):
|
|
... for j in range(5):
|
|
... S[i, j] = i + j # Update element
|
|
|
|
"""
|
|
|
|
|
|
class dok_matrix(spmatrix, _dok_base):
|
|
"""
|
|
Dictionary Of Keys based sparse matrix.
|
|
|
|
This is an efficient structure for constructing sparse
|
|
matrices incrementally.
|
|
|
|
This can be instantiated in several ways:
|
|
dok_matrix(D)
|
|
where D is a 2-D ndarray
|
|
|
|
dok_matrix(S)
|
|
with another sparse array or matrix S (equivalent to S.todok())
|
|
|
|
dok_matrix((M,N), [dtype])
|
|
create the matrix with initial shape (M,N)
|
|
dtype is optional, defaulting to dtype='d'
|
|
|
|
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 nonzero elements
|
|
size
|
|
T
|
|
|
|
Notes
|
|
-----
|
|
|
|
Sparse matrices can be used in arithmetic operations: they support
|
|
addition, subtraction, multiplication, division, and matrix power.
|
|
|
|
- Allows for efficient O(1) access of individual elements.
|
|
- Duplicates are not allowed.
|
|
- Can be efficiently converted to a coo_matrix once constructed.
|
|
|
|
Examples
|
|
--------
|
|
>>> import numpy as np
|
|
>>> from scipy.sparse import dok_matrix
|
|
>>> S = dok_matrix((5, 5), dtype=np.float32)
|
|
>>> for i in range(5):
|
|
... for j in range(5):
|
|
... S[i, j] = i + j # Update element
|
|
|
|
"""
|
|
|
|
def set_shape(self, shape):
|
|
new_matrix = self.reshape(shape, copy=False).asformat(self.format)
|
|
self.__dict__ = new_matrix.__dict__
|
|
|
|
def get_shape(self):
|
|
"""Get shape of a sparse matrix."""
|
|
return self._shape
|
|
|
|
shape = property(fget=get_shape, fset=set_shape)
|
|
|
|
def __reversed__(self):
|
|
return self._dict.__reversed__()
|
|
|
|
def __or__(self, other):
|
|
if isinstance(other, _dok_base):
|
|
return self._dict | other._dict
|
|
return self._dict | other
|
|
|
|
def __ror__(self, other):
|
|
if isinstance(other, _dok_base):
|
|
return self._dict | other._dict
|
|
return self._dict | other
|
|
|
|
def __ior__(self, other):
|
|
if isinstance(other, _dok_base):
|
|
self._dict |= other._dict
|
|
else:
|
|
self._dict |= other
|
|
return self
|