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- #
- # Authors: Travis Oliphant, Ed Schofield, Robert Cimrman, Nathan Bell, and others
- """ Test functions for sparse matrices. Each class in the "Matrix class
- based tests" section become subclasses of the classes in the "Generic
- tests" section. This is done by the functions in the "Tailored base
- class for generic tests" section.
- """
- import contextlib
- import functools
- import operator
- import platform
- import itertools
- import sys
- from scipy._lib import _pep440
- import numpy as np
- from numpy import (arange, zeros, array, dot, asarray,
- vstack, ndarray, transpose, diag, kron, inf, conjugate,
- int8, ComplexWarning)
- import random
- from numpy.testing import (assert_equal, assert_array_equal,
- assert_array_almost_equal, assert_almost_equal, assert_,
- assert_allclose,suppress_warnings)
- from pytest import raises as assert_raises
- import scipy.linalg
- import scipy.sparse as sparse
- from scipy.sparse import (csc_matrix, csr_matrix, dok_matrix,
- coo_matrix, lil_matrix, dia_matrix, bsr_matrix,
- eye, isspmatrix, SparseEfficiencyWarning)
- from scipy.sparse._sputils import (supported_dtypes, isscalarlike,
- get_index_dtype, asmatrix, matrix)
- from scipy.sparse.linalg import splu, expm, inv
- from scipy._lib.decorator import decorator
- import pytest
- IS_COLAB = ('google.colab' in sys.modules)
- def assert_in(member, collection, msg=None):
- assert_(member in collection, msg=msg if msg is not None else "%r not found in %r" % (member, collection))
- def assert_array_equal_dtype(x, y, **kwargs):
- assert_(x.dtype == y.dtype)
- assert_array_equal(x, y, **kwargs)
- NON_ARRAY_BACKED_FORMATS = frozenset(['dok'])
- def sparse_may_share_memory(A, B):
- # Checks if A and B have any numpy array sharing memory.
- def _underlying_arrays(x):
- # Given any object (e.g. a sparse array), returns all numpy arrays
- # stored in any attribute.
- arrays = []
- for a in x.__dict__.values():
- if isinstance(a, (np.ndarray, np.generic)):
- arrays.append(a)
- return arrays
- for a in _underlying_arrays(A):
- for b in _underlying_arrays(B):
- if np.may_share_memory(a, b):
- return True
- return False
- sup_complex = suppress_warnings()
- sup_complex.filter(ComplexWarning)
- def with_64bit_maxval_limit(maxval_limit=None, random=False, fixed_dtype=None,
- downcast_maxval=None, assert_32bit=False):
- """
- Monkeypatch the maxval threshold at which scipy.sparse switches to
- 64-bit index arrays, or make it (pseudo-)random.
- """
- if maxval_limit is None:
- maxval_limit = np.int64(10)
- else:
- # Ensure we use numpy scalars rather than Python scalars (matters for
- # NEP 50 casting rule changes)
- maxval_limit = np.int64(maxval_limit)
- if assert_32bit:
- def new_get_index_dtype(arrays=(), maxval=None, check_contents=False):
- tp = get_index_dtype(arrays, maxval, check_contents)
- assert_equal(np.iinfo(tp).max, np.iinfo(np.int32).max)
- assert_(tp == np.int32 or tp == np.intc)
- return tp
- elif fixed_dtype is not None:
- def new_get_index_dtype(arrays=(), maxval=None, check_contents=False):
- return fixed_dtype
- elif random:
- counter = np.random.RandomState(seed=1234)
- def new_get_index_dtype(arrays=(), maxval=None, check_contents=False):
- return (np.int32, np.int64)[counter.randint(2)]
- else:
- def new_get_index_dtype(arrays=(), maxval=None, check_contents=False):
- dtype = np.int32
- if maxval is not None:
- if maxval > maxval_limit:
- dtype = np.int64
- for arr in arrays:
- arr = np.asarray(arr)
- if 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 >= -maxval_limit and maxval <= maxval_limit:
- # a bigger type not needed
- continue
- dtype = np.int64
- return dtype
- if downcast_maxval is not None:
- def new_downcast_intp_index(arr):
- if arr.max() > downcast_maxval:
- raise AssertionError("downcast limited")
- return arr.astype(np.intp)
- @decorator
- def deco(func, *a, **kw):
- backup = []
- modules = [scipy.sparse._bsr, scipy.sparse._coo, scipy.sparse._csc,
- scipy.sparse._csr, scipy.sparse._dia, scipy.sparse._dok,
- scipy.sparse._lil, scipy.sparse._sputils,
- scipy.sparse._compressed, scipy.sparse._construct]
- try:
- for mod in modules:
- backup.append((mod, 'get_index_dtype',
- getattr(mod, 'get_index_dtype', None)))
- setattr(mod, 'get_index_dtype', new_get_index_dtype)
- if downcast_maxval is not None:
- backup.append((mod, 'downcast_intp_index',
- getattr(mod, 'downcast_intp_index', None)))
- setattr(mod, 'downcast_intp_index', new_downcast_intp_index)
- return func(*a, **kw)
- finally:
- for mod, name, oldfunc in backup:
- if oldfunc is not None:
- setattr(mod, name, oldfunc)
- return deco
- def toarray(a):
- if isinstance(a, np.ndarray) or isscalarlike(a):
- return a
- return a.toarray()
- class BinopTester:
- # Custom type to test binary operations on sparse matrices.
- def __add__(self, mat):
- return "matrix on the right"
- def __mul__(self, mat):
- return "matrix on the right"
- def __sub__(self, mat):
- return "matrix on the right"
- def __radd__(self, mat):
- return "matrix on the left"
- def __rmul__(self, mat):
- return "matrix on the left"
- def __rsub__(self, mat):
- return "matrix on the left"
- def __matmul__(self, mat):
- return "matrix on the right"
- def __rmatmul__(self, mat):
- return "matrix on the left"
- class BinopTester_with_shape:
- # Custom type to test binary operations on sparse matrices
- # with object which has shape attribute.
- def __init__(self,shape):
- self._shape = shape
- def shape(self):
- return self._shape
- def ndim(self):
- return len(self._shape)
- def __add__(self, mat):
- return "matrix on the right"
- def __mul__(self, mat):
- return "matrix on the right"
- def __sub__(self, mat):
- return "matrix on the right"
- def __radd__(self, mat):
- return "matrix on the left"
- def __rmul__(self, mat):
- return "matrix on the left"
- def __rsub__(self, mat):
- return "matrix on the left"
- def __matmul__(self, mat):
- return "matrix on the right"
- def __rmatmul__(self, mat):
- return "matrix on the left"
- #------------------------------------------------------------------------------
- # Generic tests
- #------------------------------------------------------------------------------
- # TODO test prune
- # TODO test has_sorted_indices
- class _TestCommon:
- """test common functionality shared by all sparse formats"""
- math_dtypes = supported_dtypes
- @classmethod
- def init_class(cls):
- # Canonical data.
- cls.dat = array([[1, 0, 0, 2], [3, 0, 1, 0], [0, 2, 0, 0]], 'd')
- cls.datsp = cls.spmatrix(cls.dat)
- # Some sparse and dense matrices with data for every supported
- # dtype.
- # This set union is a workaround for numpy#6295, which means that
- # two np.int64 dtypes don't hash to the same value.
- cls.checked_dtypes = set(supported_dtypes).union(cls.math_dtypes)
- cls.dat_dtypes = {}
- cls.datsp_dtypes = {}
- for dtype in cls.checked_dtypes:
- cls.dat_dtypes[dtype] = cls.dat.astype(dtype)
- cls.datsp_dtypes[dtype] = cls.spmatrix(cls.dat.astype(dtype))
- # Check that the original data is equivalent to the
- # corresponding dat_dtypes & datsp_dtypes.
- assert_equal(cls.dat, cls.dat_dtypes[np.float64])
- assert_equal(cls.datsp.toarray(),
- cls.datsp_dtypes[np.float64].toarray())
- def test_bool(self):
- def check(dtype):
- datsp = self.datsp_dtypes[dtype]
- assert_raises(ValueError, bool, datsp)
- assert_(self.spmatrix([1]))
- assert_(not self.spmatrix([0]))
- if isinstance(self, TestDOK):
- pytest.skip("Cannot create a rank <= 2 DOK matrix.")
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_bool_rollover(self):
- # bool's underlying dtype is 1 byte, check that it does not
- # rollover True -> False at 256.
- dat = array([[True, False]])
- datsp = self.spmatrix(dat)
- for _ in range(10):
- datsp = datsp + datsp
- dat = dat + dat
- assert_array_equal(dat, datsp.toarray())
- def test_eq(self):
- sup = suppress_warnings()
- sup.filter(SparseEfficiencyWarning)
- @sup
- @sup_complex
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- datbsr = bsr_matrix(dat)
- datcsr = csr_matrix(dat)
- datcsc = csc_matrix(dat)
- datlil = lil_matrix(dat)
- # sparse/sparse
- assert_array_equal_dtype(dat == dat2, (datsp == datsp2).toarray())
- # mix sparse types
- assert_array_equal_dtype(dat == dat2, (datbsr == datsp2).toarray())
- assert_array_equal_dtype(dat == dat2, (datcsr == datsp2).toarray())
- assert_array_equal_dtype(dat == dat2, (datcsc == datsp2).toarray())
- assert_array_equal_dtype(dat == dat2, (datlil == datsp2).toarray())
- # sparse/dense
- assert_array_equal_dtype(dat == datsp2, datsp2 == dat)
- # sparse/scalar
- assert_array_equal_dtype(dat == 0, (datsp == 0).toarray())
- assert_array_equal_dtype(dat == 1, (datsp == 1).toarray())
- assert_array_equal_dtype(dat == np.nan,
- (datsp == np.nan).toarray())
- if not isinstance(self, (TestBSR, TestCSC, TestCSR)):
- pytest.skip("Bool comparisons only implemented for BSR, CSC, and CSR.")
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_ne(self):
- sup = suppress_warnings()
- sup.filter(SparseEfficiencyWarning)
- @sup
- @sup_complex
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- datbsr = bsr_matrix(dat)
- datcsc = csc_matrix(dat)
- datcsr = csr_matrix(dat)
- datlil = lil_matrix(dat)
- # sparse/sparse
- assert_array_equal_dtype(dat != dat2, (datsp != datsp2).toarray())
- # mix sparse types
- assert_array_equal_dtype(dat != dat2, (datbsr != datsp2).toarray())
- assert_array_equal_dtype(dat != dat2, (datcsc != datsp2).toarray())
- assert_array_equal_dtype(dat != dat2, (datcsr != datsp2).toarray())
- assert_array_equal_dtype(dat != dat2, (datlil != datsp2).toarray())
- # sparse/dense
- assert_array_equal_dtype(dat != datsp2, datsp2 != dat)
- # sparse/scalar
- assert_array_equal_dtype(dat != 0, (datsp != 0).toarray())
- assert_array_equal_dtype(dat != 1, (datsp != 1).toarray())
- assert_array_equal_dtype(0 != dat, (0 != datsp).toarray())
- assert_array_equal_dtype(1 != dat, (1 != datsp).toarray())
- assert_array_equal_dtype(dat != np.nan,
- (datsp != np.nan).toarray())
- if not isinstance(self, (TestBSR, TestCSC, TestCSR)):
- pytest.skip("Bool comparisons only implemented for BSR, CSC, and CSR.")
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_lt(self):
- sup = suppress_warnings()
- sup.filter(SparseEfficiencyWarning)
- @sup
- @sup_complex
- def check(dtype):
- # data
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- datcomplex = dat.astype(complex)
- datcomplex[:,0] = 1 + 1j
- datspcomplex = self.spmatrix(datcomplex)
- datbsr = bsr_matrix(dat)
- datcsc = csc_matrix(dat)
- datcsr = csr_matrix(dat)
- datlil = lil_matrix(dat)
- # sparse/sparse
- assert_array_equal_dtype(dat < dat2, (datsp < datsp2).toarray())
- assert_array_equal_dtype(datcomplex < dat2,
- (datspcomplex < datsp2).toarray())
- # mix sparse types
- assert_array_equal_dtype(dat < dat2, (datbsr < datsp2).toarray())
- assert_array_equal_dtype(dat < dat2, (datcsc < datsp2).toarray())
- assert_array_equal_dtype(dat < dat2, (datcsr < datsp2).toarray())
- assert_array_equal_dtype(dat < dat2, (datlil < datsp2).toarray())
- assert_array_equal_dtype(dat2 < dat, (datsp2 < datbsr).toarray())
- assert_array_equal_dtype(dat2 < dat, (datsp2 < datcsc).toarray())
- assert_array_equal_dtype(dat2 < dat, (datsp2 < datcsr).toarray())
- assert_array_equal_dtype(dat2 < dat, (datsp2 < datlil).toarray())
- # sparse/dense
- assert_array_equal_dtype(dat < dat2, datsp < dat2)
- assert_array_equal_dtype(datcomplex < dat2, datspcomplex < dat2)
- # sparse/scalar
- for val in [2, 1, 0, -1, -2]:
- val = np.int64(val) # avoid Python scalar (due to NEP 50 changes)
- assert_array_equal_dtype((datsp < val).toarray(), dat < val)
- assert_array_equal_dtype((val < datsp).toarray(), val < dat)
- with np.errstate(invalid='ignore'):
- assert_array_equal_dtype((datsp < np.nan).toarray(),
- dat < np.nan)
- # data
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- # dense rhs
- assert_array_equal_dtype(dat < datsp2, datsp < dat2)
- if not isinstance(self, (TestBSR, TestCSC, TestCSR)):
- pytest.skip("Bool comparisons only implemented for BSR, CSC, and CSR.")
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_gt(self):
- sup = suppress_warnings()
- sup.filter(SparseEfficiencyWarning)
- @sup
- @sup_complex
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- datcomplex = dat.astype(complex)
- datcomplex[:,0] = 1 + 1j
- datspcomplex = self.spmatrix(datcomplex)
- datbsr = bsr_matrix(dat)
- datcsc = csc_matrix(dat)
- datcsr = csr_matrix(dat)
- datlil = lil_matrix(dat)
- # sparse/sparse
- assert_array_equal_dtype(dat > dat2, (datsp > datsp2).toarray())
- assert_array_equal_dtype(datcomplex > dat2,
- (datspcomplex > datsp2).toarray())
- # mix sparse types
- assert_array_equal_dtype(dat > dat2, (datbsr > datsp2).toarray())
- assert_array_equal_dtype(dat > dat2, (datcsc > datsp2).toarray())
- assert_array_equal_dtype(dat > dat2, (datcsr > datsp2).toarray())
- assert_array_equal_dtype(dat > dat2, (datlil > datsp2).toarray())
- assert_array_equal_dtype(dat2 > dat, (datsp2 > datbsr).toarray())
- assert_array_equal_dtype(dat2 > dat, (datsp2 > datcsc).toarray())
- assert_array_equal_dtype(dat2 > dat, (datsp2 > datcsr).toarray())
- assert_array_equal_dtype(dat2 > dat, (datsp2 > datlil).toarray())
- # sparse/dense
- assert_array_equal_dtype(dat > dat2, datsp > dat2)
- assert_array_equal_dtype(datcomplex > dat2, datspcomplex > dat2)
- # sparse/scalar
- for val in [2, 1, 0, -1, -2]:
- val = np.int64(val) # avoid Python scalar (due to NEP 50 changes)
- assert_array_equal_dtype((datsp > val).toarray(), dat > val)
- assert_array_equal_dtype((val > datsp).toarray(), val > dat)
- with np.errstate(invalid='ignore'):
- assert_array_equal_dtype((datsp > np.nan).toarray(),
- dat > np.nan)
- # data
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- # dense rhs
- assert_array_equal_dtype(dat > datsp2, datsp > dat2)
- if not isinstance(self, (TestBSR, TestCSC, TestCSR)):
- pytest.skip("Bool comparisons only implemented for BSR, CSC, and CSR.")
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_le(self):
- sup = suppress_warnings()
- sup.filter(SparseEfficiencyWarning)
- @sup
- @sup_complex
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- datcomplex = dat.astype(complex)
- datcomplex[:,0] = 1 + 1j
- datspcomplex = self.spmatrix(datcomplex)
- datbsr = bsr_matrix(dat)
- datcsc = csc_matrix(dat)
- datcsr = csr_matrix(dat)
- datlil = lil_matrix(dat)
- # sparse/sparse
- assert_array_equal_dtype(dat <= dat2, (datsp <= datsp2).toarray())
- assert_array_equal_dtype(datcomplex <= dat2,
- (datspcomplex <= datsp2).toarray())
- # mix sparse types
- assert_array_equal_dtype((datbsr <= datsp2).toarray(), dat <= dat2)
- assert_array_equal_dtype((datcsc <= datsp2).toarray(), dat <= dat2)
- assert_array_equal_dtype((datcsr <= datsp2).toarray(), dat <= dat2)
- assert_array_equal_dtype((datlil <= datsp2).toarray(), dat <= dat2)
- assert_array_equal_dtype((datsp2 <= datbsr).toarray(), dat2 <= dat)
- assert_array_equal_dtype((datsp2 <= datcsc).toarray(), dat2 <= dat)
- assert_array_equal_dtype((datsp2 <= datcsr).toarray(), dat2 <= dat)
- assert_array_equal_dtype((datsp2 <= datlil).toarray(), dat2 <= dat)
- # sparse/dense
- assert_array_equal_dtype(datsp <= dat2, dat <= dat2)
- assert_array_equal_dtype(datspcomplex <= dat2, datcomplex <= dat2)
- # sparse/scalar
- for val in [2, 1, -1, -2]:
- val = np.int64(val) # avoid Python scalar (due to NEP 50 changes)
- assert_array_equal_dtype((datsp <= val).toarray(), dat <= val)
- assert_array_equal_dtype((val <= datsp).toarray(), val <= dat)
- # data
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- # dense rhs
- assert_array_equal_dtype(dat <= datsp2, datsp <= dat2)
- if not isinstance(self, (TestBSR, TestCSC, TestCSR)):
- pytest.skip("Bool comparisons only implemented for BSR, CSC, and CSR.")
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_ge(self):
- sup = suppress_warnings()
- sup.filter(SparseEfficiencyWarning)
- @sup
- @sup_complex
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- datcomplex = dat.astype(complex)
- datcomplex[:,0] = 1 + 1j
- datspcomplex = self.spmatrix(datcomplex)
- datbsr = bsr_matrix(dat)
- datcsc = csc_matrix(dat)
- datcsr = csr_matrix(dat)
- datlil = lil_matrix(dat)
- # sparse/sparse
- assert_array_equal_dtype(dat >= dat2, (datsp >= datsp2).toarray())
- assert_array_equal_dtype(datcomplex >= dat2,
- (datspcomplex >= datsp2).toarray())
- # mix sparse types
- assert_array_equal_dtype((datbsr >= datsp2).toarray(), dat >= dat2)
- assert_array_equal_dtype((datcsc >= datsp2).toarray(), dat >= dat2)
- assert_array_equal_dtype((datcsr >= datsp2).toarray(), dat >= dat2)
- assert_array_equal_dtype((datlil >= datsp2).toarray(), dat >= dat2)
- assert_array_equal_dtype((datsp2 >= datbsr).toarray(), dat2 >= dat)
- assert_array_equal_dtype((datsp2 >= datcsc).toarray(), dat2 >= dat)
- assert_array_equal_dtype((datsp2 >= datcsr).toarray(), dat2 >= dat)
- assert_array_equal_dtype((datsp2 >= datlil).toarray(), dat2 >= dat)
- # sparse/dense
- assert_array_equal_dtype(datsp >= dat2, dat >= dat2)
- assert_array_equal_dtype(datspcomplex >= dat2, datcomplex >= dat2)
- # sparse/scalar
- for val in [2, 1, -1, -2]:
- val = np.int64(val) # avoid Python scalar (due to NEP 50 changes)
- assert_array_equal_dtype((datsp >= val).toarray(), dat >= val)
- assert_array_equal_dtype((val >= datsp).toarray(), val >= dat)
- # dense data
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- dat2 = dat.copy()
- dat2[:,0] = 0
- datsp2 = self.spmatrix(dat2)
- # dense rhs
- assert_array_equal_dtype(dat >= datsp2, datsp >= dat2)
- if not isinstance(self, (TestBSR, TestCSC, TestCSR)):
- pytest.skip("Bool comparisons only implemented for BSR, CSC, and CSR.")
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_empty(self):
- # create empty matrices
- assert_equal(self.spmatrix((3, 3)).toarray(), zeros((3, 3)))
- assert_equal(self.spmatrix((3, 3)).nnz, 0)
- assert_equal(self.spmatrix((3, 3)).count_nonzero(), 0)
- def test_count_nonzero(self):
- expected = np.count_nonzero(self.datsp.toarray())
- assert_equal(self.datsp.count_nonzero(), expected)
- assert_equal(self.datsp.T.count_nonzero(), expected)
- def test_invalid_shapes(self):
- assert_raises(ValueError, self.spmatrix, (-1,3))
- assert_raises(ValueError, self.spmatrix, (3,-1))
- assert_raises(ValueError, self.spmatrix, (-1,-1))
- def test_repr(self):
- repr(self.datsp)
- def test_str(self):
- str(self.datsp)
- def test_empty_arithmetic(self):
- # Test manipulating empty matrices. Fails in SciPy SVN <= r1768
- shape = (5, 5)
- for mytype in [np.dtype('int32'), np.dtype('float32'),
- np.dtype('float64'), np.dtype('complex64'),
- np.dtype('complex128')]:
- a = self.spmatrix(shape, dtype=mytype)
- b = a + a
- c = 2 * a
- d = a * a.tocsc()
- e = a * a.tocsr()
- f = a * a.tocoo()
- for m in [a,b,c,d,e,f]:
- assert_equal(m.A, a.A*a.A)
- # These fail in all revisions <= r1768:
- assert_equal(m.dtype,mytype)
- assert_equal(m.A.dtype,mytype)
- def test_abs(self):
- A = array([[-1, 0, 17], [0, -5, 0], [1, -4, 0], [0, 0, 0]], 'd')
- assert_equal(abs(A), abs(self.spmatrix(A)).toarray())
- def test_round(self):
- decimal = 1
- A = array([[-1.35, 0.56], [17.25, -5.98]], 'd')
- assert_equal(np.around(A, decimals=decimal),
- round(self.spmatrix(A), ndigits=decimal).toarray())
- def test_elementwise_power(self):
- A = array([[-4, -3, -2], [-1, 0, 1], [2, 3, 4]], 'd')
- assert_equal(np.power(A, 2), self.spmatrix(A).power(2).toarray())
- #it's element-wise power function, input has to be a scalar
- assert_raises(NotImplementedError, self.spmatrix(A).power, A)
- def test_neg(self):
- A = array([[-1, 0, 17], [0, -5, 0], [1, -4, 0], [0, 0, 0]], 'd')
- assert_equal(-A, (-self.spmatrix(A)).toarray())
- # see gh-5843
- A = array([[True, False, False], [False, False, True]])
- assert_raises(NotImplementedError, self.spmatrix(A).__neg__)
- def test_real(self):
- D = array([[1 + 3j, 2 - 4j]])
- A = self.spmatrix(D)
- assert_equal(A.real.toarray(), D.real)
- def test_imag(self):
- D = array([[1 + 3j, 2 - 4j]])
- A = self.spmatrix(D)
- assert_equal(A.imag.toarray(), D.imag)
- def test_diagonal(self):
- # Does the matrix's .diagonal() method work?
- mats = []
- mats.append([[1,0,2]])
- mats.append([[1],[0],[2]])
- mats.append([[0,1],[0,2],[0,3]])
- mats.append([[0,0,1],[0,0,2],[0,3,0]])
- mats.append([[1,0],[0,0]])
- mats.append(kron(mats[0],[[1,2]]))
- mats.append(kron(mats[0],[[1],[2]]))
- mats.append(kron(mats[1],[[1,2],[3,4]]))
- mats.append(kron(mats[2],[[1,2],[3,4]]))
- mats.append(kron(mats[3],[[1,2],[3,4]]))
- mats.append(kron(mats[3],[[1,2,3,4]]))
- for m in mats:
- rows, cols = array(m).shape
- sparse_mat = self.spmatrix(m)
- for k in range(-rows-1, cols+2):
- assert_equal(sparse_mat.diagonal(k=k), diag(m, k=k))
- # Test for k beyond boundaries(issue #11949)
- assert_equal(sparse_mat.diagonal(k=10), diag(m, k=10))
- assert_equal(sparse_mat.diagonal(k=-99), diag(m, k=-99))
- # Test all-zero matrix.
- assert_equal(self.spmatrix((40, 16130)).diagonal(), np.zeros(40))
- # Test empty matrix
- # https://github.com/scipy/scipy/issues/11949
- assert_equal(self.spmatrix((0, 0)).diagonal(), np.empty(0))
- assert_equal(self.spmatrix((15, 0)).diagonal(), np.empty(0))
- assert_equal(self.spmatrix((0, 5)).diagonal(10), np.empty(0))
- def test_trace(self):
- # For square matrix
- A = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
- B = self.spmatrix(A)
- for k in range(-2, 3):
- assert_equal(A.trace(offset=k), B.trace(offset=k))
- # For rectangular matrix
- A = np.array([[1, 2, 3], [4, 5, 6]])
- B = self.spmatrix(A)
- for k in range(-1, 3):
- assert_equal(A.trace(offset=k), B.trace(offset=k))
- def test_reshape(self):
- # This first example is taken from the lil_matrix reshaping test.
- x = self.spmatrix([[1, 0, 7], [0, 0, 0], [0, 3, 0], [0, 0, 5]])
- for order in ['C', 'F']:
- for s in [(12, 1), (1, 12)]:
- assert_array_equal(x.reshape(s, order=order).toarray(),
- x.toarray().reshape(s, order=order))
- # This example is taken from the stackoverflow answer at
- # https://stackoverflow.com/q/16511879
- x = self.spmatrix([[0, 10, 0, 0], [0, 0, 0, 0], [0, 20, 30, 40]])
- y = x.reshape((2, 6)) # Default order is 'C'
- desired = [[0, 10, 0, 0, 0, 0], [0, 0, 0, 20, 30, 40]]
- assert_array_equal(y.A, desired)
- # Reshape with negative indexes
- y = x.reshape((2, -1))
- assert_array_equal(y.A, desired)
- y = x.reshape((-1, 6))
- assert_array_equal(y.A, desired)
- assert_raises(ValueError, x.reshape, (-1, -1))
- # Reshape with star args
- y = x.reshape(2, 6)
- assert_array_equal(y.A, desired)
- assert_raises(TypeError, x.reshape, 2, 6, not_an_arg=1)
- # Reshape with same size is noop unless copy=True
- y = x.reshape((3, 4))
- assert_(y is x)
- y = x.reshape((3, 4), copy=True)
- assert_(y is not x)
- # Ensure reshape did not alter original size
- assert_array_equal(x.shape, (3, 4))
- # Reshape in place
- x.shape = (2, 6)
- assert_array_equal(x.A, desired)
- # Reshape to bad ndim
- assert_raises(ValueError, x.reshape, (x.size,))
- assert_raises(ValueError, x.reshape, (1, x.size, 1))
- @pytest.mark.slow
- def test_setdiag_comprehensive(self):
- def dense_setdiag(a, v, k):
- v = np.asarray(v)
- if k >= 0:
- n = min(a.shape[0], a.shape[1] - k)
- if v.ndim != 0:
- n = min(n, len(v))
- v = v[:n]
- i = np.arange(0, n)
- j = np.arange(k, k + n)
- a[i,j] = v
- elif k < 0:
- dense_setdiag(a.T, v, -k)
- def check_setdiag(a, b, k):
- # Check setting diagonal using a scalar, a vector of
- # correct length, and too short or too long vectors
- for r in [-1, len(np.diag(a, k)), 2, 30]:
- if r < 0:
- v = np.random.choice(range(1, 20))
- else:
- v = np.random.randint(1, 20, size=r)
- dense_setdiag(a, v, k)
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning, "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- b.setdiag(v, k)
- # check that dense_setdiag worked
- d = np.diag(a, k)
- if np.asarray(v).ndim == 0:
- assert_array_equal(d, v, err_msg="%s %d" % (msg, r))
- else:
- n = min(len(d), len(v))
- assert_array_equal(d[:n], v[:n], err_msg="%s %d" % (msg, r))
- # check that sparse setdiag worked
- assert_array_equal(b.A, a, err_msg="%s %d" % (msg, r))
- # comprehensive test
- np.random.seed(1234)
- shapes = [(0,5), (5,0), (1,5), (5,1), (5,5)]
- for dtype in [np.int8, np.float64]:
- for m,n in shapes:
- ks = np.arange(-m+1, n-1)
- for k in ks:
- msg = repr((dtype, m, n, k))
- a = np.zeros((m, n), dtype=dtype)
- b = self.spmatrix((m, n), dtype=dtype)
- check_setdiag(a, b, k)
- # check overwriting etc
- for k2 in np.random.choice(ks, size=min(len(ks), 5)):
- check_setdiag(a, b, k2)
- def test_setdiag(self):
- # simple test cases
- m = self.spmatrix(np.eye(3))
- m2 = self.spmatrix((4, 4))
- values = [3, 2, 1]
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- assert_raises(ValueError, m.setdiag, values, k=4)
- m.setdiag(values)
- assert_array_equal(m.diagonal(), values)
- m.setdiag(values, k=1)
- assert_array_equal(m.A, np.array([[3, 3, 0],
- [0, 2, 2],
- [0, 0, 1]]))
- m.setdiag(values, k=-2)
- assert_array_equal(m.A, np.array([[3, 3, 0],
- [0, 2, 2],
- [3, 0, 1]]))
- m.setdiag((9,), k=2)
- assert_array_equal(m.A[0,2], 9)
- m.setdiag((9,), k=-2)
- assert_array_equal(m.A[2,0], 9)
- # test short values on an empty matrix
- m2.setdiag([1], k=2)
- assert_array_equal(m2.A[0], [0, 0, 1, 0])
- # test overwriting that same diagonal
- m2.setdiag([1, 1], k=2)
- assert_array_equal(m2.A[:2], [[0, 0, 1, 0],
- [0, 0, 0, 1]])
- def test_nonzero(self):
- A = array([[1, 0, 1],[0, 1, 1],[0, 0, 1]])
- Asp = self.spmatrix(A)
- A_nz = set([tuple(ij) for ij in transpose(A.nonzero())])
- Asp_nz = set([tuple(ij) for ij in transpose(Asp.nonzero())])
- assert_equal(A_nz, Asp_nz)
- def test_numpy_nonzero(self):
- # See gh-5987
- A = array([[1, 0, 1], [0, 1, 1], [0, 0, 1]])
- Asp = self.spmatrix(A)
- A_nz = set([tuple(ij) for ij in transpose(np.nonzero(A))])
- Asp_nz = set([tuple(ij) for ij in transpose(np.nonzero(Asp))])
- assert_equal(A_nz, Asp_nz)
- def test_getrow(self):
- assert_array_equal(self.datsp.getrow(1).toarray(), self.dat[[1], :])
- assert_array_equal(self.datsp.getrow(-1).toarray(), self.dat[[-1], :])
- def test_getcol(self):
- assert_array_equal(self.datsp.getcol(1).toarray(), self.dat[:, [1]])
- assert_array_equal(self.datsp.getcol(-1).toarray(), self.dat[:, [-1]])
- def test_sum(self):
- np.random.seed(1234)
- dat_1 = matrix([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- dat_2 = np.random.rand(5, 5)
- dat_3 = np.array([[]])
- dat_4 = np.zeros((40, 40))
- dat_5 = sparse.rand(5, 5, density=1e-2).A
- matrices = [dat_1, dat_2, dat_3, dat_4, dat_5]
- def check(dtype, j):
- dat = matrix(matrices[j], dtype=dtype)
- datsp = self.spmatrix(dat, dtype=dtype)
- with np.errstate(over='ignore'):
- assert_array_almost_equal(dat.sum(), datsp.sum())
- assert_equal(dat.sum().dtype, datsp.sum().dtype)
- assert_(np.isscalar(datsp.sum(axis=None)))
- assert_array_almost_equal(dat.sum(axis=None),
- datsp.sum(axis=None))
- assert_equal(dat.sum(axis=None).dtype,
- datsp.sum(axis=None).dtype)
- assert_array_almost_equal(dat.sum(axis=0), datsp.sum(axis=0))
- assert_equal(dat.sum(axis=0).dtype, datsp.sum(axis=0).dtype)
- assert_array_almost_equal(dat.sum(axis=1), datsp.sum(axis=1))
- assert_equal(dat.sum(axis=1).dtype, datsp.sum(axis=1).dtype)
- assert_array_almost_equal(dat.sum(axis=-2), datsp.sum(axis=-2))
- assert_equal(dat.sum(axis=-2).dtype, datsp.sum(axis=-2).dtype)
- assert_array_almost_equal(dat.sum(axis=-1), datsp.sum(axis=-1))
- assert_equal(dat.sum(axis=-1).dtype, datsp.sum(axis=-1).dtype)
- for dtype in self.checked_dtypes:
- for j in range(len(matrices)):
- check(dtype, j)
- def test_sum_invalid_params(self):
- out = np.zeros((1, 3))
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- assert_raises(ValueError, datsp.sum, axis=3)
- assert_raises(TypeError, datsp.sum, axis=(0, 1))
- assert_raises(TypeError, datsp.sum, axis=1.5)
- assert_raises(ValueError, datsp.sum, axis=1, out=out)
- def test_sum_dtype(self):
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- def check(dtype):
- dat_mean = dat.mean(dtype=dtype)
- datsp_mean = datsp.mean(dtype=dtype)
- assert_array_almost_equal(dat_mean, datsp_mean)
- assert_equal(dat_mean.dtype, datsp_mean.dtype)
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_sum_out(self):
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- dat_out = array([[0]])
- datsp_out = matrix([[0]])
- dat.sum(out=dat_out, keepdims=True)
- datsp.sum(out=datsp_out)
- assert_array_almost_equal(dat_out, datsp_out)
- dat_out = np.zeros((3, 1))
- datsp_out = asmatrix(np.zeros((3, 1)))
- dat.sum(axis=1, out=dat_out, keepdims=True)
- datsp.sum(axis=1, out=datsp_out)
- assert_array_almost_equal(dat_out, datsp_out)
- def test_numpy_sum(self):
- # See gh-5987
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- dat_mean = np.sum(dat)
- datsp_mean = np.sum(datsp)
- assert_array_almost_equal(dat_mean, datsp_mean)
- assert_equal(dat_mean.dtype, datsp_mean.dtype)
- def test_mean(self):
- def check(dtype):
- dat = array([[0, 1, 2],
- [3, 4, 5],
- [6, 7, 9]], dtype=dtype)
- datsp = self.spmatrix(dat, dtype=dtype)
- assert_array_almost_equal(dat.mean(), datsp.mean())
- assert_equal(dat.mean().dtype, datsp.mean().dtype)
- assert_(np.isscalar(datsp.mean(axis=None)))
- assert_array_almost_equal(
- dat.mean(axis=None, keepdims=True), datsp.mean(axis=None)
- )
- assert_equal(dat.mean(axis=None).dtype, datsp.mean(axis=None).dtype)
- assert_array_almost_equal(
- dat.mean(axis=0, keepdims=True), datsp.mean(axis=0)
- )
- assert_equal(dat.mean(axis=0).dtype, datsp.mean(axis=0).dtype)
- assert_array_almost_equal(
- dat.mean(axis=1, keepdims=True), datsp.mean(axis=1)
- )
- assert_equal(dat.mean(axis=1).dtype, datsp.mean(axis=1).dtype)
- assert_array_almost_equal(
- dat.mean(axis=-2, keepdims=True), datsp.mean(axis=-2)
- )
- assert_equal(dat.mean(axis=-2).dtype, datsp.mean(axis=-2).dtype)
- assert_array_almost_equal(
- dat.mean(axis=-1, keepdims=True), datsp.mean(axis=-1)
- )
- assert_equal(dat.mean(axis=-1).dtype, datsp.mean(axis=-1).dtype)
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_mean_invalid_params(self):
- out = asmatrix(np.zeros((1, 3)))
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- assert_raises(ValueError, datsp.mean, axis=3)
- assert_raises(TypeError, datsp.mean, axis=(0, 1))
- assert_raises(TypeError, datsp.mean, axis=1.5)
- assert_raises(ValueError, datsp.mean, axis=1, out=out)
- def test_mean_dtype(self):
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- def check(dtype):
- dat_mean = dat.mean(dtype=dtype)
- datsp_mean = datsp.mean(dtype=dtype)
- assert_array_almost_equal(dat_mean, datsp_mean)
- assert_equal(dat_mean.dtype, datsp_mean.dtype)
- for dtype in self.checked_dtypes:
- check(dtype)
- def test_mean_out(self):
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- dat_out = array([[0]])
- datsp_out = matrix([[0]])
- dat.mean(out=dat_out, keepdims=True)
- datsp.mean(out=datsp_out)
- assert_array_almost_equal(dat_out, datsp_out)
- dat_out = np.zeros((3, 1))
- datsp_out = matrix(np.zeros((3, 1)))
- dat.mean(axis=1, out=dat_out, keepdims=True)
- datsp.mean(axis=1, out=datsp_out)
- assert_array_almost_equal(dat_out, datsp_out)
- def test_numpy_mean(self):
- # See gh-5987
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- dat_mean = np.mean(dat)
- datsp_mean = np.mean(datsp)
- assert_array_almost_equal(dat_mean, datsp_mean)
- assert_equal(dat_mean.dtype, datsp_mean.dtype)
- def test_expm(self):
- M = array([[1, 0, 2], [0, 0, 3], [-4, 5, 6]], float)
- sM = self.spmatrix(M, shape=(3,3), dtype=float)
- Mexp = scipy.linalg.expm(M)
- N = array([[3., 0., 1.], [0., 2., 0.], [0., 0., 0.]])
- sN = self.spmatrix(N, shape=(3,3), dtype=float)
- Nexp = scipy.linalg.expm(N)
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "splu converted its input to CSC format")
- sup.filter(SparseEfficiencyWarning,
- "spsolve is more efficient when sparse b is in the CSC matrix format")
- sup.filter(SparseEfficiencyWarning,
- "spsolve requires A be CSC or CSR matrix format")
- sMexp = expm(sM).toarray()
- sNexp = expm(sN).toarray()
- assert_array_almost_equal((sMexp - Mexp), zeros((3, 3)))
- assert_array_almost_equal((sNexp - Nexp), zeros((3, 3)))
- def test_inv(self):
- def check(dtype):
- M = array([[1, 0, 2], [0, 0, 3], [-4, 5, 6]], dtype)
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "spsolve requires A be CSC or CSR matrix format")
- sup.filter(SparseEfficiencyWarning,
- "spsolve is more efficient when sparse b is in the CSC matrix format")
- sup.filter(SparseEfficiencyWarning,
- "splu converted its input to CSC format")
- sM = self.spmatrix(M, shape=(3,3), dtype=dtype)
- sMinv = inv(sM)
- assert_array_almost_equal(sMinv.dot(sM).toarray(), np.eye(3))
- assert_raises(TypeError, inv, M)
- for dtype in [float]:
- check(dtype)
- @sup_complex
- def test_from_array(self):
- A = array([[1,0,0],[2,3,4],[0,5,0],[0,0,0]])
- assert_array_equal(self.spmatrix(A).toarray(), A)
- A = array([[1.0 + 3j, 0, 0],
- [0, 2.0 + 5, 0],
- [0, 0, 0]])
- assert_array_equal(self.spmatrix(A).toarray(), A)
- assert_array_equal(self.spmatrix(A, dtype='int16').toarray(), A.astype('int16'))
- @sup_complex
- def test_from_matrix(self):
- A = matrix([[1, 0, 0], [2, 3, 4], [0, 5, 0], [0, 0, 0]])
- assert_array_equal(self.spmatrix(A).todense(), A)
- A = matrix([[1.0 + 3j, 0, 0],
- [0, 2.0 + 5, 0],
- [0, 0, 0]])
- assert_array_equal(self.spmatrix(A).todense(), A)
- assert_array_equal(
- self.spmatrix(A, dtype='int16').todense(), A.astype('int16')
- )
- @sup_complex
- def test_from_list(self):
- A = [[1,0,0],[2,3,4],[0,5,0],[0,0,0]]
- assert_array_equal(self.spmatrix(A).toarray(), A)
- A = [[1.0 + 3j, 0, 0],
- [0, 2.0 + 5, 0],
- [0, 0, 0]]
- assert_array_equal(self.spmatrix(A).toarray(), array(A))
- assert_array_equal(
- self.spmatrix(A, dtype='int16').toarray(), array(A).astype('int16')
- )
- @sup_complex
- def test_from_sparse(self):
- D = array([[1,0,0],[2,3,4],[0,5,0],[0,0,0]])
- S = csr_matrix(D)
- assert_array_equal(self.spmatrix(S).toarray(), D)
- S = self.spmatrix(D)
- assert_array_equal(self.spmatrix(S).toarray(), D)
- D = array([[1.0 + 3j, 0, 0],
- [0, 2.0 + 5, 0],
- [0, 0, 0]])
- S = csr_matrix(D)
- assert_array_equal(self.spmatrix(S).toarray(), D)
- assert_array_equal(self.spmatrix(S, dtype='int16').toarray(), D.astype('int16'))
- S = self.spmatrix(D)
- assert_array_equal(self.spmatrix(S).toarray(), D)
- assert_array_equal(self.spmatrix(S, dtype='int16').toarray(), D.astype('int16'))
- # def test_array(self):
- # """test array(A) where A is in sparse format"""
- # assert_equal( array(self.datsp), self.dat )
- def test_todense(self):
- # Check C- or F-contiguous (default).
- chk = self.datsp.todense()
- assert isinstance(chk, np.matrix)
- assert_array_equal(chk, self.dat)
- assert_(chk.flags.c_contiguous != chk.flags.f_contiguous)
- # Check C-contiguous (with arg).
- chk = self.datsp.todense(order='C')
- assert_array_equal(chk, self.dat)
- assert_(chk.flags.c_contiguous)
- assert_(not chk.flags.f_contiguous)
- # Check F-contiguous (with arg).
- chk = self.datsp.todense(order='F')
- assert_array_equal(chk, self.dat)
- assert_(not chk.flags.c_contiguous)
- assert_(chk.flags.f_contiguous)
- # Check with out argument (array).
- out = np.zeros(self.datsp.shape, dtype=self.datsp.dtype)
- chk = self.datsp.todense(out=out)
- assert_array_equal(self.dat, out)
- assert_array_equal(self.dat, chk)
- assert_(chk.base is out)
- # Check with out array (matrix).
- out = asmatrix(np.zeros(self.datsp.shape, dtype=self.datsp.dtype))
- chk = self.datsp.todense(out=out)
- assert_array_equal(self.dat, out)
- assert_array_equal(self.dat, chk)
- assert_(chk is out)
- a = array([[1.,2.,3.]])
- dense_dot_dense = a @ self.dat
- check = a * self.datsp.todense()
- assert_array_equal(dense_dot_dense, check)
- b = array([[1.,2.,3.,4.]]).T
- dense_dot_dense = self.dat @ b
- check2 = self.datsp.todense() @ b
- assert_array_equal(dense_dot_dense, check2)
- # Check bool data works.
- spbool = self.spmatrix(self.dat, dtype=bool)
- matbool = self.dat.astype(bool)
- assert_array_equal(spbool.todense(), matbool)
- def test_toarray(self):
- # Check C- or F-contiguous (default).
- dat = asarray(self.dat)
- chk = self.datsp.toarray()
- assert_array_equal(chk, dat)
- assert_(chk.flags.c_contiguous != chk.flags.f_contiguous)
- # Check C-contiguous (with arg).
- chk = self.datsp.toarray(order='C')
- assert_array_equal(chk, dat)
- assert_(chk.flags.c_contiguous)
- assert_(not chk.flags.f_contiguous)
- # Check F-contiguous (with arg).
- chk = self.datsp.toarray(order='F')
- assert_array_equal(chk, dat)
- assert_(not chk.flags.c_contiguous)
- assert_(chk.flags.f_contiguous)
- # Check with output arg.
- out = np.zeros(self.datsp.shape, dtype=self.datsp.dtype)
- self.datsp.toarray(out=out)
- assert_array_equal(chk, dat)
- # Check that things are fine when we don't initialize with zeros.
- out[...] = 1.
- self.datsp.toarray(out=out)
- assert_array_equal(chk, dat)
- a = array([1.,2.,3.])
- dense_dot_dense = dot(a, dat)
- check = dot(a, self.datsp.toarray())
- assert_array_equal(dense_dot_dense, check)
- b = array([1.,2.,3.,4.])
- dense_dot_dense = dot(dat, b)
- check2 = dot(self.datsp.toarray(), b)
- assert_array_equal(dense_dot_dense, check2)
- # Check bool data works.
- spbool = self.spmatrix(self.dat, dtype=bool)
- arrbool = dat.astype(bool)
- assert_array_equal(spbool.toarray(), arrbool)
- @sup_complex
- def test_astype(self):
- D = array([[2.0 + 3j, 0, 0],
- [0, 4.0 + 5j, 0],
- [0, 0, 0]])
- S = self.spmatrix(D)
- for x in supported_dtypes:
- # Check correctly casted
- D_casted = D.astype(x)
- for copy in (True, False):
- S_casted = S.astype(x, copy=copy)
- assert_equal(S_casted.dtype, D_casted.dtype) # correct type
- assert_equal(S_casted.toarray(), D_casted) # correct values
- assert_equal(S_casted.format, S.format) # format preserved
- # Check correctly copied
- assert_(S_casted.astype(x, copy=False) is S_casted)
- S_copied = S_casted.astype(x, copy=True)
- assert_(S_copied is not S_casted)
- def check_equal_but_not_same_array_attribute(attribute):
- a = getattr(S_casted, attribute)
- b = getattr(S_copied, attribute)
- assert_array_equal(a, b)
- assert_(a is not b)
- i = (0,) * b.ndim
- b_i = b[i]
- b[i] = not b[i]
- assert_(a[i] != b[i])
- b[i] = b_i
- if S_casted.format in ('csr', 'csc', 'bsr'):
- for attribute in ('indices', 'indptr', 'data'):
- check_equal_but_not_same_array_attribute(attribute)
- elif S_casted.format == 'coo':
- for attribute in ('row', 'col', 'data'):
- check_equal_but_not_same_array_attribute(attribute)
- elif S_casted.format == 'dia':
- for attribute in ('offsets', 'data'):
- check_equal_but_not_same_array_attribute(attribute)
- def test_asfptype(self):
- A = self.spmatrix(arange(6,dtype='int32').reshape(2,3))
- assert_equal(A.dtype, np.dtype('int32'))
- assert_equal(A.asfptype().dtype, np.dtype('float64'))
- assert_equal(A.asfptype().format, A.format)
- assert_equal(A.astype('int16').asfptype().dtype, np.dtype('float32'))
- assert_equal(A.astype('complex128').asfptype().dtype, np.dtype('complex128'))
- B = A.asfptype()
- C = B.asfptype()
- assert_(B is C)
- def test_mul_scalar(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- assert_array_equal(dat*2, (datsp*2).toarray())
- assert_array_equal(dat*17.3, (datsp*17.3).toarray())
- for dtype in self.math_dtypes:
- check(dtype)
- def test_rmul_scalar(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- assert_array_equal(2*dat, (2*datsp).toarray())
- assert_array_equal(17.3*dat, (17.3*datsp).toarray())
- for dtype in self.math_dtypes:
- check(dtype)
- # github issue #15210
- def test_rmul_scalar_type_error(self):
- datsp = self.datsp_dtypes[np.float64]
- with assert_raises(TypeError):
- None * datsp
- def test_add(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- a = dat.copy()
- a[0,2] = 2.0
- b = datsp
- c = b + a
- assert_array_equal(c, b.toarray() + a)
- c = b + b.tocsr()
- assert_array_equal(c.toarray(),
- b.toarray() + b.toarray())
- # test broadcasting
- c = b + a[0]
- assert_array_equal(c, b.toarray() + a[0])
- for dtype in self.math_dtypes:
- check(dtype)
- def test_radd(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- a = dat.copy()
- a[0,2] = 2.0
- b = datsp
- c = a + b
- assert_array_equal(c, a + b.toarray())
- for dtype in self.math_dtypes:
- check(dtype)
- def test_sub(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- assert_array_equal((datsp - datsp).toarray(), np.zeros((3, 4)))
- assert_array_equal((datsp - 0).toarray(), dat)
- A = self.spmatrix(
- np.array([[1, 0, 0, 4], [-1, 0, 0, 0], [0, 8, 0, -5]], 'd')
- )
- assert_array_equal((datsp - A).toarray(), dat - A.toarray())
- assert_array_equal((A - datsp).toarray(), A.toarray() - dat)
- # test broadcasting
- assert_array_equal(datsp - dat[0], dat - dat[0])
- for dtype in self.math_dtypes:
- if dtype == np.dtype('bool'):
- # boolean array subtraction deprecated in 1.9.0
- continue
- check(dtype)
- def test_rsub(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- assert_array_equal((dat - datsp),[[0,0,0,0],[0,0,0,0],[0,0,0,0]])
- assert_array_equal((datsp - dat),[[0,0,0,0],[0,0,0,0],[0,0,0,0]])
- assert_array_equal((0 - datsp).toarray(), -dat)
- A = self.spmatrix(matrix([[1,0,0,4],[-1,0,0,0],[0,8,0,-5]],'d'))
- assert_array_equal((dat - A), dat - A.toarray())
- assert_array_equal((A - dat), A.toarray() - dat)
- assert_array_equal(A.toarray() - datsp, A.toarray() - dat)
- assert_array_equal(datsp - A.toarray(), dat - A.toarray())
- # test broadcasting
- assert_array_equal(dat[0] - datsp, dat[0] - dat)
- for dtype in self.math_dtypes:
- if dtype == np.dtype('bool'):
- # boolean array subtraction deprecated in 1.9.0
- continue
- check(dtype)
- def test_add0(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- # Adding 0 to a sparse matrix
- assert_array_equal((datsp + 0).toarray(), dat)
- # use sum (which takes 0 as a starting value)
- sumS = sum([k * datsp for k in range(1, 3)])
- sumD = sum([k * dat for k in range(1, 3)])
- assert_almost_equal(sumS.toarray(), sumD)
- for dtype in self.math_dtypes:
- check(dtype)
- def test_elementwise_multiply(self):
- # real/real
- A = array([[4,0,9],[2,-3,5]])
- B = array([[0,7,0],[0,-4,0]])
- Asp = self.spmatrix(A)
- Bsp = self.spmatrix(B)
- assert_almost_equal(Asp.multiply(Bsp).toarray(), A*B) # sparse/sparse
- assert_almost_equal(Asp.multiply(B).toarray(), A*B) # sparse/dense
- # complex/complex
- C = array([[1-2j,0+5j,-1+0j],[4-3j,-3+6j,5]])
- D = array([[5+2j,7-3j,-2+1j],[0-1j,-4+2j,9]])
- Csp = self.spmatrix(C)
- Dsp = self.spmatrix(D)
- assert_almost_equal(Csp.multiply(Dsp).toarray(), C*D) # sparse/sparse
- assert_almost_equal(Csp.multiply(D).toarray(), C*D) # sparse/dense
- # real/complex
- assert_almost_equal(Asp.multiply(Dsp).toarray(), A*D) # sparse/sparse
- assert_almost_equal(Asp.multiply(D).toarray(), A*D) # sparse/dense
- def test_elementwise_multiply_broadcast(self):
- A = array([4])
- B = array([[-9]])
- C = array([1,-1,0])
- D = array([[7,9,-9]])
- E = array([[3],[2],[1]])
- F = array([[8,6,3],[-4,3,2],[6,6,6]])
- G = [1, 2, 3]
- H = np.ones((3, 4))
- J = H.T
- K = array([[0]])
- L = array([[[1,2],[0,1]]])
- # Some arrays can't be cast as spmatrices (A,C,L) so leave
- # them out.
- Bsp = self.spmatrix(B)
- Dsp = self.spmatrix(D)
- Esp = self.spmatrix(E)
- Fsp = self.spmatrix(F)
- Hsp = self.spmatrix(H)
- Hspp = self.spmatrix(H[0,None])
- Jsp = self.spmatrix(J)
- Jspp = self.spmatrix(J[:,0,None])
- Ksp = self.spmatrix(K)
- matrices = [A, B, C, D, E, F, G, H, J, K, L]
- spmatrices = [Bsp, Dsp, Esp, Fsp, Hsp, Hspp, Jsp, Jspp, Ksp]
- # sparse/sparse
- for i in spmatrices:
- for j in spmatrices:
- try:
- dense_mult = i.toarray() * j.toarray()
- except ValueError:
- assert_raises(ValueError, i.multiply, j)
- continue
- sp_mult = i.multiply(j)
- assert_almost_equal(sp_mult.toarray(), dense_mult)
- # sparse/dense
- for i in spmatrices:
- for j in matrices:
- try:
- dense_mult = i.toarray() * j
- except TypeError:
- continue
- except ValueError:
- assert_raises(ValueError, i.multiply, j)
- continue
- sp_mult = i.multiply(j)
- if isspmatrix(sp_mult):
- assert_almost_equal(sp_mult.toarray(), dense_mult)
- else:
- assert_almost_equal(sp_mult, dense_mult)
- def test_elementwise_divide(self):
- expected = [[1,np.nan,np.nan,1],
- [1,np.nan,1,np.nan],
- [np.nan,1,np.nan,np.nan]]
- assert_array_equal(toarray(self.datsp / self.datsp), expected)
- denom = self.spmatrix(matrix([[1,0,0,4],[-1,0,0,0],[0,8,0,-5]],'d'))
- expected = [[1,np.nan,np.nan,0.5],
- [-3,np.nan,inf,np.nan],
- [np.nan,0.25,np.nan,0]]
- assert_array_equal(toarray(self.datsp / denom), expected)
- # complex
- A = array([[1-2j,0+5j,-1+0j],[4-3j,-3+6j,5]])
- B = array([[5+2j,7-3j,-2+1j],[0-1j,-4+2j,9]])
- Asp = self.spmatrix(A)
- Bsp = self.spmatrix(B)
- assert_almost_equal(toarray(Asp / Bsp), A/B)
- # integer
- A = array([[1,2,3],[-3,2,1]])
- B = array([[0,1,2],[0,-2,3]])
- Asp = self.spmatrix(A)
- Bsp = self.spmatrix(B)
- with np.errstate(divide='ignore'):
- assert_array_equal(toarray(Asp / Bsp), A / B)
- # mismatching sparsity patterns
- A = array([[0,1],[1,0]])
- B = array([[1,0],[1,0]])
- Asp = self.spmatrix(A)
- Bsp = self.spmatrix(B)
- with np.errstate(divide='ignore', invalid='ignore'):
- assert_array_equal(np.array(toarray(Asp / Bsp)), A / B)
- def test_pow(self):
- A = array([[1, 0, 2, 0], [0, 3, 4, 0], [0, 5, 0, 0], [0, 6, 7, 8]])
- B = self.spmatrix(A)
- for exponent in [0,1,2,3]:
- ret_sp = B**exponent
- ret_np = np.linalg.matrix_power(A, exponent)
- assert_array_equal(ret_sp.toarray(), ret_np)
- assert_equal(ret_sp.dtype, ret_np.dtype)
- # invalid exponents
- for exponent in [-1, 2.2, 1 + 3j]:
- assert_raises(Exception, B.__pow__, exponent)
- # nonsquare matrix
- B = self.spmatrix(A[:3,:])
- assert_raises(Exception, B.__pow__, 1)
- def test_rmatvec(self):
- M = self.spmatrix(matrix([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]]))
- assert_array_almost_equal([1,2,3,4]*M, dot([1,2,3,4], M.toarray()))
- row = array([[1,2,3,4]])
- assert_array_almost_equal(row * M, row @ M.toarray())
- def test_small_multiplication(self):
- # test that A*x works for x with shape () (1,) (1,1) and (1,0)
- A = self.spmatrix([[1],[2],[3]])
- assert_(isspmatrix(A * array(1)))
- assert_equal((A * array(1)).toarray(), [[1], [2], [3]])
- assert_equal(A * array([1]), array([1, 2, 3]))
- assert_equal(A * array([[1]]), array([[1], [2], [3]]))
- assert_equal(A * np.ones((1, 0)), np.ones((3, 0)))
- def test_binop_custom_type(self):
- # Non-regression test: previously, binary operations would raise
- # NotImplementedError instead of returning NotImplemented
- # (https://docs.python.org/library/constants.html#NotImplemented)
- # so overloading Custom + matrix etc. didn't work.
- A = self.spmatrix([[1], [2], [3]])
- B = BinopTester()
- assert_equal(A + B, "matrix on the left")
- assert_equal(A - B, "matrix on the left")
- assert_equal(A * B, "matrix on the left")
- assert_equal(B + A, "matrix on the right")
- assert_equal(B - A, "matrix on the right")
- assert_equal(B * A, "matrix on the right")
- assert_equal(eval('A @ B'), "matrix on the left")
- assert_equal(eval('B @ A'), "matrix on the right")
- def test_binop_custom_type_with_shape(self):
- A = self.spmatrix([[1], [2], [3]])
- B = BinopTester_with_shape((3,1))
- assert_equal(A + B, "matrix on the left")
- assert_equal(A - B, "matrix on the left")
- assert_equal(A * B, "matrix on the left")
- assert_equal(B + A, "matrix on the right")
- assert_equal(B - A, "matrix on the right")
- assert_equal(B * A, "matrix on the right")
- assert_equal(eval('A @ B'), "matrix on the left")
- assert_equal(eval('B @ A'), "matrix on the right")
- def test_dot_scalar(self):
- M = self.spmatrix(array([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]]))
- scalar = 10
- actual = M.dot(scalar)
- expected = M * scalar
- assert_allclose(actual.toarray(), expected.toarray())
- def test_matmul(self):
- M = self.spmatrix(array([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]]))
- B = self.spmatrix(array([[0,1],[1,0],[0,2]],'d'))
- col = array([[1,2,3]]).T
- # check matrix-vector
- assert_array_almost_equal(operator.matmul(M, col),
- M.toarray() @ col)
- # check matrix-matrix
- assert_array_almost_equal(operator.matmul(M, B).toarray(),
- (M * B).toarray())
- assert_array_almost_equal(operator.matmul(M.toarray(), B),
- (M * B).toarray())
- assert_array_almost_equal(operator.matmul(M, B.toarray()),
- (M * B).toarray())
- # check error on matrix-scalar
- assert_raises(ValueError, operator.matmul, M, 1)
- assert_raises(ValueError, operator.matmul, 1, M)
- def test_matvec(self):
- M = self.spmatrix(matrix([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]]))
- col = array([[1,2,3]]).T
- assert_array_almost_equal(M * col, M.toarray() @ col)
- # check result dimensions (ticket #514)
- assert_equal((M * array([1,2,3])).shape,(4,))
- assert_equal((M * array([[1],[2],[3]])).shape,(4,1))
- assert_equal((M * matrix([[1],[2],[3]])).shape,(4,1))
- # check result type
- assert_(isinstance(M * array([1,2,3]), ndarray))
- assert_(isinstance(M * matrix([1,2,3]).T, np.matrix))
- # ensure exception is raised for improper dimensions
- bad_vecs = [array([1,2]), array([1,2,3,4]), array([[1],[2]]),
- matrix([1,2,3]), matrix([[1],[2]])]
- for x in bad_vecs:
- assert_raises(ValueError, M.__mul__, x)
- # The current relationship between sparse matrix products and array
- # products is as follows:
- assert_array_almost_equal(M*array([1,2,3]), dot(M.A,[1,2,3]))
- assert_array_almost_equal(M*[[1],[2],[3]], asmatrix(dot(M.A,[1,2,3])).T)
- # Note that the result of M * x is dense if x has a singleton dimension.
- # Currently M.matvec(asarray(col)) is rank-1, whereas M.matvec(col)
- # is rank-2. Is this desirable?
- def test_matmat_sparse(self):
- a = matrix([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]])
- a2 = array([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]])
- b = matrix([[0,1],[1,0],[0,2]],'d')
- asp = self.spmatrix(a)
- bsp = self.spmatrix(b)
- assert_array_almost_equal((asp*bsp).toarray(), a@b)
- assert_array_almost_equal(asp*b, a@b)
- assert_array_almost_equal(a*bsp, a@b)
- assert_array_almost_equal(a2*bsp, a@b)
- # Now try performing cross-type multplication:
- csp = bsp.tocsc()
- c = b
- want = a@c
- assert_array_almost_equal((asp*csp).toarray(), want)
- assert_array_almost_equal(asp*c, want)
- assert_array_almost_equal(a*csp, want)
- assert_array_almost_equal(a2*csp, want)
- csp = bsp.tocsr()
- assert_array_almost_equal((asp*csp).toarray(), want)
- assert_array_almost_equal(asp*c, want)
- assert_array_almost_equal(a*csp, want)
- assert_array_almost_equal(a2*csp, want)
- csp = bsp.tocoo()
- assert_array_almost_equal((asp*csp).toarray(), want)
- assert_array_almost_equal(asp*c, want)
- assert_array_almost_equal(a*csp, want)
- assert_array_almost_equal(a2*csp, want)
- # Test provided by Andy Fraser, 2006-03-26
- L = 30
- frac = .3
- random.seed(0) # make runs repeatable
- A = zeros((L,2))
- for i in range(L):
- for j in range(2):
- r = random.random()
- if r < frac:
- A[i,j] = r/frac
- A = self.spmatrix(A)
- B = A*A.T
- assert_array_almost_equal(B.toarray(), A.toarray() @ A.T.toarray())
- assert_array_almost_equal(B.toarray(), A.toarray() @ A.toarray().T)
- # check dimension mismatch 2x2 times 3x2
- A = self.spmatrix([[1,2],[3,4]])
- B = self.spmatrix([[1,2],[3,4],[5,6]])
- assert_raises(ValueError, A.__mul__, B)
- def test_matmat_dense(self):
- a = matrix([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]])
- asp = self.spmatrix(a)
- # check both array and matrix types
- bs = [array([[1,2],[3,4],[5,6]]), matrix([[1,2],[3,4],[5,6]])]
- for b in bs:
- result = asp*b
- assert_(isinstance(result, type(b)))
- assert_equal(result.shape, (4,2))
- assert_equal(result, dot(a,b))
- def test_sparse_format_conversions(self):
- A = sparse.kron([[1,0,2],[0,3,4],[5,0,0]], [[1,2],[0,3]])
- D = A.toarray()
- A = self.spmatrix(A)
- for format in ['bsr','coo','csc','csr','dia','dok','lil']:
- a = A.asformat(format)
- assert_equal(a.format,format)
- assert_array_equal(a.toarray(), D)
- b = self.spmatrix(D+3j).asformat(format)
- assert_equal(b.format,format)
- assert_array_equal(b.toarray(), D+3j)
- c = eval(format + '_matrix')(A)
- assert_equal(c.format,format)
- assert_array_equal(c.toarray(), D)
- for format in ['array', 'dense']:
- a = A.asformat(format)
- assert_array_equal(a, D)
- b = self.spmatrix(D+3j).asformat(format)
- assert_array_equal(b, D+3j)
- def test_tobsr(self):
- x = array([[1,0,2,0],[0,0,0,0],[0,0,4,5]])
- y = array([[0,1,2],[3,0,5]])
- A = kron(x,y)
- Asp = self.spmatrix(A)
- for format in ['bsr']:
- fn = getattr(Asp, 'to' + format)
- for X in [1, 2, 3, 6]:
- for Y in [1, 2, 3, 4, 6, 12]:
- assert_equal(fn(blocksize=(X, Y)).toarray(), A)
- def test_transpose(self):
- dat_1 = self.dat
- dat_2 = np.array([[]])
- matrices = [dat_1, dat_2]
- def check(dtype, j):
- dat = array(matrices[j], dtype=dtype)
- datsp = self.spmatrix(dat)
- a = datsp.transpose()
- b = dat.transpose()
- assert_array_equal(a.toarray(), b)
- assert_array_equal(a.transpose().toarray(), dat)
- assert_equal(a.dtype, b.dtype)
- # See gh-5987
- empty = self.spmatrix((3, 4))
- assert_array_equal(np.transpose(empty).toarray(),
- np.transpose(zeros((3, 4))))
- assert_array_equal(empty.T.toarray(), zeros((4, 3)))
- assert_raises(ValueError, empty.transpose, axes=0)
- for dtype in self.checked_dtypes:
- for j in range(len(matrices)):
- check(dtype, j)
- def test_add_dense(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- # adding a dense matrix to a sparse matrix
- sum1 = dat + datsp
- assert_array_equal(sum1, dat + dat)
- sum2 = datsp + dat
- assert_array_equal(sum2, dat + dat)
- for dtype in self.math_dtypes:
- check(dtype)
- def test_sub_dense(self):
- # subtracting a dense matrix to/from a sparse matrix
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- # Behavior is different for bool.
- if dat.dtype == bool:
- sum1 = dat - datsp
- assert_array_equal(sum1, dat - dat)
- sum2 = datsp - dat
- assert_array_equal(sum2, dat - dat)
- else:
- # Manually add to avoid upcasting from scalar
- # multiplication.
- sum1 = (dat + dat + dat) - datsp
- assert_array_equal(sum1, dat + dat)
- sum2 = (datsp + datsp + datsp) - dat
- assert_array_equal(sum2, dat + dat)
- for dtype in self.math_dtypes:
- if dtype == np.dtype('bool'):
- # boolean array subtraction deprecated in 1.9.0
- continue
- check(dtype)
- def test_maximum_minimum(self):
- A_dense = np.array([[1, 0, 3], [0, 4, 5], [0, 0, 0]])
- B_dense = np.array([[1, 1, 2], [0, 3, 6], [1, -1, 0]])
- A_dense_cpx = np.array([[1, 0, 3], [0, 4+2j, 5], [0, 1j, -1j]])
- def check(dtype, dtype2, btype):
- if np.issubdtype(dtype, np.complexfloating):
- A = self.spmatrix(A_dense_cpx.astype(dtype))
- else:
- A = self.spmatrix(A_dense.astype(dtype))
- if btype == 'scalar':
- B = dtype2.type(1)
- elif btype == 'scalar2':
- B = dtype2.type(-1)
- elif btype == 'dense':
- B = B_dense.astype(dtype2)
- elif btype == 'sparse':
- B = self.spmatrix(B_dense.astype(dtype2))
- else:
- raise ValueError()
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Taking maximum .minimum. with > 0 .< 0. number results to a dense matrix")
- max_s = A.maximum(B)
- min_s = A.minimum(B)
- max_d = np.maximum(toarray(A), toarray(B))
- assert_array_equal(toarray(max_s), max_d)
- assert_equal(max_s.dtype, max_d.dtype)
- min_d = np.minimum(toarray(A), toarray(B))
- assert_array_equal(toarray(min_s), min_d)
- assert_equal(min_s.dtype, min_d.dtype)
- for dtype in self.math_dtypes:
- for dtype2 in [np.int8, np.float_, np.complex_]:
- for btype in ['scalar', 'scalar2', 'dense', 'sparse']:
- check(np.dtype(dtype), np.dtype(dtype2), btype)
- def test_copy(self):
- # Check whether the copy=True and copy=False keywords work
- A = self.datsp
- # check that copy preserves format
- assert_equal(A.copy().format, A.format)
- assert_equal(A.__class__(A,copy=True).format, A.format)
- assert_equal(A.__class__(A,copy=False).format, A.format)
- assert_equal(A.copy().toarray(), A.toarray())
- assert_equal(A.__class__(A, copy=True).toarray(), A.toarray())
- assert_equal(A.__class__(A, copy=False).toarray(), A.toarray())
- # check that XXX_matrix.toXXX() works
- toself = getattr(A,'to' + A.format)
- assert_(toself() is A)
- assert_(toself(copy=False) is A)
- assert_equal(toself(copy=True).format, A.format)
- assert_equal(toself(copy=True).toarray(), A.toarray())
- # check whether the data is copied?
- assert_(not sparse_may_share_memory(A.copy(), A))
- # test that __iter__ is compatible with NumPy matrix
- def test_iterator(self):
- B = matrix(np.arange(50).reshape(5, 10))
- A = self.spmatrix(B)
- for x, y in zip(A, B):
- assert_equal(x.toarray(), y)
- def test_size_zero_matrix_arithmetic(self):
- # Test basic matrix arithmetic with shapes like (0,0), (10,0),
- # (0, 3), etc.
- mat = array([])
- a = mat.reshape((0, 0))
- b = mat.reshape((0, 1))
- c = mat.reshape((0, 5))
- d = mat.reshape((1, 0))
- e = mat.reshape((5, 0))
- f = np.ones([5, 5])
- asp = self.spmatrix(a)
- bsp = self.spmatrix(b)
- csp = self.spmatrix(c)
- dsp = self.spmatrix(d)
- esp = self.spmatrix(e)
- fsp = self.spmatrix(f)
- # matrix product.
- assert_array_equal(asp.dot(asp).A, np.dot(a, a))
- assert_array_equal(bsp.dot(dsp).A, np.dot(b, d))
- assert_array_equal(dsp.dot(bsp).A, np.dot(d, b))
- assert_array_equal(csp.dot(esp).A, np.dot(c, e))
- assert_array_equal(csp.dot(fsp).A, np.dot(c, f))
- assert_array_equal(esp.dot(csp).A, np.dot(e, c))
- assert_array_equal(dsp.dot(csp).A, np.dot(d, c))
- assert_array_equal(fsp.dot(esp).A, np.dot(f, e))
- # bad matrix products
- assert_raises(ValueError, dsp.dot, e)
- assert_raises(ValueError, asp.dot, d)
- # elemente-wise multiplication
- assert_array_equal(asp.multiply(asp).A, np.multiply(a, a))
- assert_array_equal(bsp.multiply(bsp).A, np.multiply(b, b))
- assert_array_equal(dsp.multiply(dsp).A, np.multiply(d, d))
- assert_array_equal(asp.multiply(a).A, np.multiply(a, a))
- assert_array_equal(bsp.multiply(b).A, np.multiply(b, b))
- assert_array_equal(dsp.multiply(d).A, np.multiply(d, d))
- assert_array_equal(asp.multiply(6).A, np.multiply(a, 6))
- assert_array_equal(bsp.multiply(6).A, np.multiply(b, 6))
- assert_array_equal(dsp.multiply(6).A, np.multiply(d, 6))
- # bad element-wise multiplication
- assert_raises(ValueError, asp.multiply, c)
- assert_raises(ValueError, esp.multiply, c)
- # Addition
- assert_array_equal(asp.__add__(asp).A, a.__add__(a))
- assert_array_equal(bsp.__add__(bsp).A, b.__add__(b))
- assert_array_equal(dsp.__add__(dsp).A, d.__add__(d))
- # bad addition
- assert_raises(ValueError, asp.__add__, dsp)
- assert_raises(ValueError, bsp.__add__, asp)
- def test_size_zero_conversions(self):
- mat = array([])
- a = mat.reshape((0, 0))
- b = mat.reshape((0, 5))
- c = mat.reshape((5, 0))
- for m in [a, b, c]:
- spm = self.spmatrix(m)
- assert_array_equal(spm.tocoo().A, m)
- assert_array_equal(spm.tocsr().A, m)
- assert_array_equal(spm.tocsc().A, m)
- assert_array_equal(spm.tolil().A, m)
- assert_array_equal(spm.todok().A, m)
- assert_array_equal(spm.tobsr().A, m)
- def test_pickle(self):
- import pickle
- sup = suppress_warnings()
- sup.filter(SparseEfficiencyWarning)
- @sup
- def check():
- datsp = self.datsp.copy()
- for protocol in range(pickle.HIGHEST_PROTOCOL):
- sploaded = pickle.loads(pickle.dumps(datsp, protocol=protocol))
- assert_equal(datsp.shape, sploaded.shape)
- assert_array_equal(datsp.toarray(), sploaded.toarray())
- assert_equal(datsp.format, sploaded.format)
- for key, val in datsp.__dict__.items():
- if isinstance(val, np.ndarray):
- assert_array_equal(val, sploaded.__dict__[key])
- else:
- assert_(val == sploaded.__dict__[key])
- check()
- def test_unary_ufunc_overrides(self):
- def check(name):
- if name == "sign":
- pytest.skip("sign conflicts with comparison op "
- "support on Numpy")
- if self.spmatrix in (dok_matrix, lil_matrix):
- pytest.skip("Unary ops not implemented for dok/lil")
- ufunc = getattr(np, name)
- X = self.spmatrix(np.arange(20).reshape(4, 5) / 20.)
- X0 = ufunc(X.toarray())
- X2 = ufunc(X)
- assert_array_equal(X2.toarray(), X0)
- for name in ["sin", "tan", "arcsin", "arctan", "sinh", "tanh",
- "arcsinh", "arctanh", "rint", "sign", "expm1", "log1p",
- "deg2rad", "rad2deg", "floor", "ceil", "trunc", "sqrt",
- "abs"]:
- check(name)
- def test_resize(self):
- # resize(shape) resizes the matrix in-place
- D = np.array([[1, 0, 3, 4],
- [2, 0, 0, 0],
- [3, 0, 0, 0]])
- S = self.spmatrix(D)
- assert_(S.resize((3, 2)) is None)
- assert_array_equal(S.A, [[1, 0],
- [2, 0],
- [3, 0]])
- S.resize((2, 2))
- assert_array_equal(S.A, [[1, 0],
- [2, 0]])
- S.resize((3, 2))
- assert_array_equal(S.A, [[1, 0],
- [2, 0],
- [0, 0]])
- S.resize((3, 3))
- assert_array_equal(S.A, [[1, 0, 0],
- [2, 0, 0],
- [0, 0, 0]])
- # test no-op
- S.resize((3, 3))
- assert_array_equal(S.A, [[1, 0, 0],
- [2, 0, 0],
- [0, 0, 0]])
- # test *args
- S.resize(3, 2)
- assert_array_equal(S.A, [[1, 0],
- [2, 0],
- [0, 0]])
- for bad_shape in [1, (-1, 2), (2, -1), (1, 2, 3)]:
- assert_raises(ValueError, S.resize, bad_shape)
- def test_constructor1_base(self):
- A = self.datsp
- self_format = A.format
- C = A.__class__(A, copy=False)
- assert_array_equal_dtype(A.toarray(), C.toarray())
- if self_format not in NON_ARRAY_BACKED_FORMATS:
- assert_(sparse_may_share_memory(A, C))
- C = A.__class__(A, dtype=A.dtype, copy=False)
- assert_array_equal_dtype(A.toarray(), C.toarray())
- if self_format not in NON_ARRAY_BACKED_FORMATS:
- assert_(sparse_may_share_memory(A, C))
- C = A.__class__(A, dtype=np.float32, copy=False)
- assert_array_equal(A.toarray(), C.toarray())
- C = A.__class__(A, copy=True)
- assert_array_equal_dtype(A.toarray(), C.toarray())
- assert_(not sparse_may_share_memory(A, C))
- for other_format in ['csr', 'csc', 'coo', 'dia', 'dok', 'lil']:
- if other_format == self_format:
- continue
- B = A.asformat(other_format)
- C = A.__class__(B, copy=False)
- assert_array_equal_dtype(A.toarray(), C.toarray())
- C = A.__class__(B, copy=True)
- assert_array_equal_dtype(A.toarray(), C.toarray())
- assert_(not sparse_may_share_memory(B, C))
- class _TestInplaceArithmetic:
- def test_inplace_dense(self):
- a = np.ones((3, 4))
- b = self.spmatrix(a)
- x = a.copy()
- y = a.copy()
- x += a
- y += b
- assert_array_equal(x, y)
- x = a.copy()
- y = a.copy()
- x -= a
- y -= b
- assert_array_equal(x, y)
- # This is matrix product, from __rmul__
- assert_raises(ValueError, operator.imul, x, b)
- x = a.copy()
- y = a.copy()
- x = x.dot(a.T)
- y *= b.T
- assert_array_equal(x, y)
- # Matrix (non-elementwise) floor division is not defined
- assert_raises(TypeError, operator.ifloordiv, x, b)
- def test_imul_scalar(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- # Avoid implicit casting.
- if np.can_cast(type(2), dtype, casting='same_kind'):
- a = datsp.copy()
- a *= 2
- b = dat.copy()
- b *= 2
- assert_array_equal(b, a.toarray())
- if np.can_cast(type(17.3), dtype, casting='same_kind'):
- a = datsp.copy()
- a *= 17.3
- b = dat.copy()
- b *= 17.3
- assert_array_equal(b, a.toarray())
- for dtype in self.math_dtypes:
- check(dtype)
- def test_idiv_scalar(self):
- def check(dtype):
- dat = self.dat_dtypes[dtype]
- datsp = self.datsp_dtypes[dtype]
- if np.can_cast(type(2), dtype, casting='same_kind'):
- a = datsp.copy()
- a /= 2
- b = dat.copy()
- b /= 2
- assert_array_equal(b, a.toarray())
- if np.can_cast(type(17.3), dtype, casting='same_kind'):
- a = datsp.copy()
- a /= 17.3
- b = dat.copy()
- b /= 17.3
- assert_array_equal(b, a.toarray())
- for dtype in self.math_dtypes:
- # /= should only be used with float dtypes to avoid implicit
- # casting.
- if not np.can_cast(dtype, np.int_):
- check(dtype)
- def test_inplace_success(self):
- # Inplace ops should work even if a specialized version is not
- # implemented, falling back to x = x <op> y
- a = self.spmatrix(np.eye(5))
- b = self.spmatrix(np.eye(5))
- bp = self.spmatrix(np.eye(5))
- b += a
- bp = bp + a
- assert_allclose(b.A, bp.A)
- b *= a
- bp = bp * a
- assert_allclose(b.A, bp.A)
- b -= a
- bp = bp - a
- assert_allclose(b.A, bp.A)
- assert_raises(TypeError, operator.ifloordiv, a, b)
- class _TestGetSet:
- def test_getelement(self):
- def check(dtype):
- D = array([[1,0,0],
- [4,3,0],
- [0,2,0],
- [0,0,0]], dtype=dtype)
- A = self.spmatrix(D)
- M,N = D.shape
- for i in range(-M, M):
- for j in range(-N, N):
- assert_equal(A[i,j], D[i,j])
- assert_equal(type(A[1,1]), dtype)
- for ij in [(0,3),(-1,3),(4,0),(4,3),(4,-1), (1, 2, 3)]:
- assert_raises((IndexError, TypeError), A.__getitem__, ij)
- for dtype in supported_dtypes:
- check(np.dtype(dtype))
- def test_setelement(self):
- def check(dtype):
- A = self.spmatrix((3,4), dtype=dtype)
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- A[0, 0] = dtype.type(0) # bug 870
- A[1, 2] = dtype.type(4.0)
- A[0, 1] = dtype.type(3)
- A[2, 0] = dtype.type(2.0)
- A[0,-1] = dtype.type(8)
- A[-1,-2] = dtype.type(7)
- A[0, 1] = dtype.type(5)
- if dtype != np.bool_:
- assert_array_equal(
- A.toarray(),
- [
- [0, 5, 0, 8],
- [0, 0, 4, 0],
- [2, 0, 7, 0]
- ]
- )
- for ij in [(0,4),(-1,4),(3,0),(3,4),(3,-1)]:
- assert_raises(IndexError, A.__setitem__, ij, 123.0)
- for v in [[1,2,3], array([1,2,3])]:
- assert_raises(ValueError, A.__setitem__, (0,0), v)
- if (not np.issubdtype(dtype, np.complexfloating) and
- dtype != np.bool_):
- for v in [3j]:
- assert_raises(TypeError, A.__setitem__, (0,0), v)
- for dtype in supported_dtypes:
- check(np.dtype(dtype))
- def test_negative_index_assignment(self):
- # Regression test for github issue 4428.
- def check(dtype):
- A = self.spmatrix((3, 10), dtype=dtype)
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- A[0, -4] = 1
- assert_equal(A[0, -4], 1)
- for dtype in self.math_dtypes:
- check(np.dtype(dtype))
- def test_scalar_assign_2(self):
- n, m = (5, 10)
- def _test_set(i, j, nitems):
- msg = "%r ; %r ; %r" % (i, j, nitems)
- A = self.spmatrix((n, m))
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- A[i, j] = 1
- assert_almost_equal(A.sum(), nitems, err_msg=msg)
- assert_almost_equal(A[i, j], 1, err_msg=msg)
- # [i,j]
- for i, j in [(2, 3), (-1, 8), (-1, -2), (array(-1), -2), (-1, array(-2)),
- (array(-1), array(-2))]:
- _test_set(i, j, 1)
- def test_index_scalar_assign(self):
- A = self.spmatrix((5, 5))
- B = np.zeros((5, 5))
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- for C in [A, B]:
- C[0,1] = 1
- C[3,0] = 4
- C[3,0] = 9
- assert_array_equal(A.toarray(), B)
- class _TestSolve:
- def test_solve(self):
- # Test whether the lu_solve command segfaults, as reported by Nils
- # Wagner for a 64-bit machine, 02 March 2005 (EJS)
- n = 20
- np.random.seed(0) # make tests repeatable
- A = zeros((n,n), dtype=complex)
- x = np.random.rand(n)
- y = np.random.rand(n-1)+1j*np.random.rand(n-1)
- r = np.random.rand(n)
- for i in range(len(x)):
- A[i,i] = x[i]
- for i in range(len(y)):
- A[i,i+1] = y[i]
- A[i+1,i] = conjugate(y[i])
- A = self.spmatrix(A)
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "splu converted its input to CSC format")
- x = splu(A).solve(r)
- assert_almost_equal(A*x,r)
- class _TestSlicing:
- def test_dtype_preservation(self):
- assert_equal(self.spmatrix((1,10), dtype=np.int16)[0,1:5].dtype, np.int16)
- assert_equal(self.spmatrix((1,10), dtype=np.int32)[0,1:5].dtype, np.int32)
- assert_equal(self.spmatrix((1,10), dtype=np.float32)[0,1:5].dtype, np.float32)
- assert_equal(self.spmatrix((1,10), dtype=np.float64)[0,1:5].dtype, np.float64)
- def test_dtype_preservation_empty_slice(self):
- # This should be parametrized with pytest, but something in the parent
- # class creation used in this file breaks pytest.mark.parametrize.
- for dt in [np.int16, np.int32, np.float32, np.float64]:
- A = self.spmatrix((3, 2), dtype=dt)
- assert_equal(A[:, 0:0:2].dtype, dt)
- assert_equal(A[0:0:2, :].dtype, dt)
- assert_equal(A[0, 0:0:2].dtype, dt)
- assert_equal(A[0:0:2, 0].dtype, dt)
- def test_get_horiz_slice(self):
- B = asmatrix(arange(50.).reshape(5,10))
- A = self.spmatrix(B)
- assert_array_equal(B[1, :], A[1, :].toarray())
- assert_array_equal(B[1, 2:5], A[1, 2:5].toarray())
- C = matrix([[1, 2, 1], [4, 0, 6], [0, 0, 0], [0, 0, 1]])
- D = self.spmatrix(C)
- assert_array_equal(C[1, 1:3], D[1, 1:3].toarray())
- # Now test slicing when a row contains only zeros
- E = matrix([[1, 2, 1], [4, 0, 0], [0, 0, 0], [0, 0, 1]])
- F = self.spmatrix(E)
- assert_array_equal(E[1, 1:3], F[1, 1:3].toarray())
- assert_array_equal(E[2, -2:], F[2, -2:].A)
- # The following should raise exceptions:
- assert_raises(IndexError, A.__getitem__, (slice(None), 11))
- assert_raises(IndexError, A.__getitem__, (6, slice(3, 7)))
- def test_get_vert_slice(self):
- B = arange(50.).reshape(5, 10)
- A = self.spmatrix(B)
- assert_array_equal(B[2:5, [0]], A[2:5, 0].toarray())
- assert_array_equal(B[:, [1]], A[:, 1].toarray())
- C = array([[1, 2, 1], [4, 0, 6], [0, 0, 0], [0, 0, 1]])
- D = self.spmatrix(C)
- assert_array_equal(C[1:3, [1]], D[1:3, 1].toarray())
- assert_array_equal(C[:, [2]], D[:, 2].toarray())
- # Now test slicing when a column contains only zeros
- E = array([[1, 0, 1], [4, 0, 0], [0, 0, 0], [0, 0, 1]])
- F = self.spmatrix(E)
- assert_array_equal(E[:, [1]], F[:, 1].toarray())
- assert_array_equal(E[-2:, [2]], F[-2:, 2].toarray())
- # The following should raise exceptions:
- assert_raises(IndexError, A.__getitem__, (slice(None), 11))
- assert_raises(IndexError, A.__getitem__, (6, slice(3, 7)))
- def test_get_slices(self):
- B = arange(50.).reshape(5, 10)
- A = self.spmatrix(B)
- assert_array_equal(A[2:5, 0:3].toarray(), B[2:5, 0:3])
- assert_array_equal(A[1:, :-1].toarray(), B[1:, :-1])
- assert_array_equal(A[:-1, 1:].toarray(), B[:-1, 1:])
- # Now test slicing when a column contains only zeros
- E = array([[1, 0, 1], [4, 0, 0], [0, 0, 0], [0, 0, 1]])
- F = self.spmatrix(E)
- assert_array_equal(E[1:2, 1:2], F[1:2, 1:2].toarray())
- assert_array_equal(E[:, 1:], F[:, 1:].toarray())
- def test_non_unit_stride_2d_indexing(self):
- # Regression test -- used to silently ignore the stride.
- v0 = np.random.rand(50, 50)
- try:
- v = self.spmatrix(v0)[0:25:2, 2:30:3]
- except ValueError:
- # if unsupported
- raise pytest.skip("feature not implemented")
- assert_array_equal(v.toarray(), v0[0:25:2, 2:30:3])
- def test_slicing_2(self):
- B = asmatrix(arange(50).reshape(5,10))
- A = self.spmatrix(B)
- # [i,j]
- assert_equal(A[2,3], B[2,3])
- assert_equal(A[-1,8], B[-1,8])
- assert_equal(A[-1,-2],B[-1,-2])
- assert_equal(A[array(-1),-2],B[-1,-2])
- assert_equal(A[-1,array(-2)],B[-1,-2])
- assert_equal(A[array(-1),array(-2)],B[-1,-2])
- # [i,1:2]
- assert_equal(A[2, :].toarray(), B[2, :])
- assert_equal(A[2, 5:-2].toarray(), B[2, 5:-2])
- assert_equal(A[array(2), 5:-2].toarray(), B[2, 5:-2])
- # [1:2,j]
- assert_equal(A[:, 2].toarray(), B[:, 2])
- assert_equal(A[3:4, 9].toarray(), B[3:4, 9])
- assert_equal(A[1:4, -5].toarray(), B[1:4, -5])
- assert_equal(A[2:-1, 3].toarray(), B[2:-1, 3])
- assert_equal(A[2:-1, array(3)].toarray(), B[2:-1, 3])
- # [1:2,1:2]
- assert_equal(A[1:2, 1:2].toarray(), B[1:2, 1:2])
- assert_equal(A[4:, 3:].toarray(), B[4:, 3:])
- assert_equal(A[:4, :5].toarray(), B[:4, :5])
- assert_equal(A[2:-1, :5].toarray(), B[2:-1, :5])
- # [i]
- assert_equal(A[1, :].toarray(), B[1, :])
- assert_equal(A[-2, :].toarray(), B[-2, :])
- assert_equal(A[array(-2), :].toarray(), B[-2, :])
- # [1:2]
- assert_equal(A[1:4].toarray(), B[1:4])
- assert_equal(A[1:-2].toarray(), B[1:-2])
- # Check bug reported by Robert Cimrman:
- # http://thread.gmane.org/gmane.comp.python.scientific.devel/7986 (dead link)
- s = slice(int8(2),int8(4),None)
- assert_equal(A[s, :].toarray(), B[2:4, :])
- assert_equal(A[:, s].toarray(), B[:, 2:4])
- def test_slicing_3(self):
- B = asmatrix(arange(50).reshape(5,10))
- A = self.spmatrix(B)
- s_ = np.s_
- slices = [s_[:2], s_[1:2], s_[3:], s_[3::2],
- s_[15:20], s_[3:2],
- s_[8:3:-1], s_[4::-2], s_[:5:-1],
- 0, 1, s_[:], s_[1:5], -1, -2, -5,
- array(-1), np.int8(-3)]
- def check_1(a):
- x = A[a]
- y = B[a]
- if y.shape == ():
- assert_equal(x, y, repr(a))
- else:
- if x.size == 0 and y.size == 0:
- pass
- else:
- assert_array_equal(x.toarray(), y, repr(a))
- for j, a in enumerate(slices):
- check_1(a)
- def check_2(a, b):
- # Indexing np.matrix with 0-d arrays seems to be broken,
- # as they seem not to be treated as scalars.
- # https://github.com/numpy/numpy/issues/3110
- if isinstance(a, np.ndarray):
- ai = int(a)
- else:
- ai = a
- if isinstance(b, np.ndarray):
- bi = int(b)
- else:
- bi = b
- x = A[a, b]
- y = B[ai, bi]
- if y.shape == ():
- assert_equal(x, y, repr((a, b)))
- else:
- if x.size == 0 and y.size == 0:
- pass
- else:
- assert_array_equal(x.toarray(), y, repr((a, b)))
- for i, a in enumerate(slices):
- for j, b in enumerate(slices):
- check_2(a, b)
- # Check out of bounds etc. systematically
- extra_slices = []
- for a, b, c in itertools.product(*([(None, 0, 1, 2, 5, 15,
- -1, -2, 5, -15)]*3)):
- if c == 0:
- continue
- extra_slices.append(slice(a, b, c))
- for a in extra_slices:
- check_2(a, a)
- check_2(a, -2)
- check_2(-2, a)
- def test_ellipsis_slicing(self):
- b = asmatrix(arange(50).reshape(5,10))
- a = self.spmatrix(b)
- assert_array_equal(a[...].A, b[...].A)
- assert_array_equal(a[...,].A, b[...,].A)
- assert_array_equal(a[1, ...].A, b[1, ...].A)
- assert_array_equal(a[..., 1].A, b[..., 1].A)
- assert_array_equal(a[1:, ...].A, b[1:, ...].A)
- assert_array_equal(a[..., 1:].A, b[..., 1:].A)
- assert_array_equal(a[1:, 1, ...].A, b[1:, 1, ...].A)
- assert_array_equal(a[1, ..., 1:].A, b[1, ..., 1:].A)
- # These return ints
- assert_equal(a[1, 1, ...], b[1, 1, ...])
- assert_equal(a[1, ..., 1], b[1, ..., 1])
- def test_multiple_ellipsis_slicing(self):
- b = asmatrix(arange(50).reshape(5,10))
- a = self.spmatrix(b)
- assert_array_equal(a[..., ...].A, b[:, :].A)
- assert_array_equal(a[..., ..., ...].A, b[:, :].A)
- assert_array_equal(a[1, ..., ...].A, b[1, :].A)
- assert_array_equal(a[1:, ..., ...].A, b[1:, :].A)
- assert_array_equal(a[..., ..., 1:].A, b[:, 1:].A)
- assert_array_equal(a[..., ..., 1].A, b[:, 1].A)
- class _TestSlicingAssign:
- def test_slice_scalar_assign(self):
- A = self.spmatrix((5, 5))
- B = np.zeros((5, 5))
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- for C in [A, B]:
- C[0:1,1] = 1
- C[3:0,0] = 4
- C[3:4,0] = 9
- C[0,4:] = 1
- C[3::-1,4:] = 9
- assert_array_equal(A.toarray(), B)
- def test_slice_assign_2(self):
- n, m = (5, 10)
- def _test_set(i, j):
- msg = "i=%r; j=%r" % (i, j)
- A = self.spmatrix((n, m))
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- A[i, j] = 1
- B = np.zeros((n, m))
- B[i, j] = 1
- assert_array_almost_equal(A.toarray(), B, err_msg=msg)
- # [i,1:2]
- for i, j in [(2, slice(3)), (2, slice(None, 10, 4)), (2, slice(5, -2)),
- (array(2), slice(5, -2))]:
- _test_set(i, j)
- def test_self_self_assignment(self):
- # Tests whether a row of one lil_matrix can be assigned to
- # another.
- B = self.spmatrix((4,3))
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- B[0,0] = 2
- B[1,2] = 7
- B[2,1] = 3
- B[3,0] = 10
- A = B / 10
- B[0,:] = A[0,:]
- assert_array_equal(A[0,:].A, B[0,:].A)
- A = B / 10
- B[:,:] = A[:1,:1]
- assert_array_equal(np.zeros((4,3)) + A[0,0], B.A)
- A = B / 10
- B[:-1,0] = A[0,:].T
- assert_array_equal(A[0,:].A.T, B[:-1,0].A)
- def test_slice_assignment(self):
- B = self.spmatrix((4,3))
- expected = array([[10,0,0],
- [0,0,6],
- [0,14,0],
- [0,0,0]])
- block = [[1,0],[0,4]]
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- B[0,0] = 5
- B[1,2] = 3
- B[2,1] = 7
- B[:,:] = B+B
- assert_array_equal(B.toarray(), expected)
- B[:2,:2] = csc_matrix(array(block))
- assert_array_equal(B.toarray()[:2, :2], block)
- def test_sparsity_modifying_assignment(self):
- B = self.spmatrix((4,3))
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- B[0,0] = 5
- B[1,2] = 3
- B[2,1] = 7
- B[3,0] = 10
- B[:3] = csr_matrix(np.eye(3))
- expected = array([[1,0,0],[0,1,0],[0,0,1],[10,0,0]])
- assert_array_equal(B.toarray(), expected)
- def test_set_slice(self):
- A = self.spmatrix((5,10))
- B = array(zeros((5, 10), float))
- s_ = np.s_
- slices = [s_[:2], s_[1:2], s_[3:], s_[3::2],
- s_[8:3:-1], s_[4::-2], s_[:5:-1],
- 0, 1, s_[:], s_[1:5], -1, -2, -5,
- array(-1), np.int8(-3)]
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- for j, a in enumerate(slices):
- A[a] = j
- B[a] = j
- assert_array_equal(A.toarray(), B, repr(a))
- for i, a in enumerate(slices):
- for j, b in enumerate(slices):
- A[a,b] = 10*i + 1000*(j+1)
- B[a,b] = 10*i + 1000*(j+1)
- assert_array_equal(A.toarray(), B, repr((a, b)))
- A[0, 1:10:2] = range(1, 10, 2)
- B[0, 1:10:2] = range(1, 10, 2)
- assert_array_equal(A.toarray(), B)
- A[1:5:2, 0] = np.arange(1, 5, 2)[:, None]
- B[1:5:2, 0] = np.arange(1, 5, 2)[:]
- assert_array_equal(A.toarray(), B)
- # The next commands should raise exceptions
- assert_raises(ValueError, A.__setitem__, (0, 0), list(range(100)))
- assert_raises(ValueError, A.__setitem__, (0, 0), arange(100))
- assert_raises(ValueError, A.__setitem__, (0, slice(None)),
- list(range(100)))
- assert_raises(ValueError, A.__setitem__, (slice(None), 1),
- list(range(100)))
- assert_raises(ValueError, A.__setitem__, (slice(None), 1), A.copy())
- assert_raises(ValueError, A.__setitem__,
- ([[1, 2, 3], [0, 3, 4]], [1, 2, 3]), [1, 2, 3, 4])
- assert_raises(ValueError, A.__setitem__,
- ([[1, 2, 3], [0, 3, 4], [4, 1, 3]],
- [[1, 2, 4], [0, 1, 3]]), [2, 3, 4])
- assert_raises(ValueError, A.__setitem__, (slice(4), 0),
- [[1, 2], [3, 4]])
- def test_assign_empty_spmatrix(self):
- A = self.spmatrix(np.ones((2, 3)))
- B = self.spmatrix((1, 2))
- A[1, :2] = B
- assert_array_equal(A.toarray(), [[1, 1, 1], [0, 0, 1]])
- def test_assign_1d_slice(self):
- A = self.spmatrix(np.ones((3, 3)))
- x = np.zeros(3)
- A[:, 0] = x
- A[1, :] = x
- assert_array_equal(A.toarray(), [[0, 1, 1], [0, 0, 0], [0, 1, 1]])
- class _TestFancyIndexing:
- """Tests fancy indexing features. The tests for any matrix formats
- that implement these features should derive from this class.
- """
- def test_dtype_preservation_empty_index(self):
- # This should be parametrized with pytest, but something in the parent
- # class creation used in this file breaks pytest.mark.parametrize.
- for dt in [np.int16, np.int32, np.float32, np.float64]:
- A = self.spmatrix((3, 2), dtype=dt)
- assert_equal(A[:, [False, False]].dtype, dt)
- assert_equal(A[[False, False, False], :].dtype, dt)
- assert_equal(A[:, []].dtype, dt)
- assert_equal(A[[], :].dtype, dt)
- def test_bad_index(self):
- A = self.spmatrix(np.zeros([5, 5]))
- assert_raises((IndexError, ValueError, TypeError), A.__getitem__, "foo")
- assert_raises((IndexError, ValueError, TypeError), A.__getitem__, (2, "foo"))
- assert_raises((IndexError, ValueError), A.__getitem__,
- ([1, 2, 3], [1, 2, 3, 4]))
- def test_fancy_indexing(self):
- B = asmatrix(arange(50).reshape(5,10))
- A = self.spmatrix(B)
- # [i]
- assert_equal(A[[1, 3]].toarray(), B[[1, 3]])
- # [i,[1,2]]
- assert_equal(A[3, [1, 3]].toarray(), B[3, [1, 3]])
- assert_equal(A[-1, [2, -5]].toarray(), B[-1, [2, -5]])
- assert_equal(A[array(-1), [2, -5]].toarray(), B[-1, [2, -5]])
- assert_equal(A[-1, array([2, -5])].toarray(), B[-1, [2, -5]])
- assert_equal(A[array(-1), array([2, -5])].toarray(), B[-1, [2, -5]])
- # [1:2,[1,2]]
- assert_equal(A[:, [2, 8, 3, -1]].toarray(), B[:, [2, 8, 3, -1]])
- assert_equal(A[3:4, [9]].toarray(), B[3:4, [9]])
- assert_equal(A[1:4, [-1, -5]].toarray(), B[1:4, [-1, -5]])
- assert_equal(A[1:4, array([-1, -5])].toarray(), B[1:4, [-1, -5]])
- # [[1,2],j]
- assert_equal(A[[1, 3], 3].toarray(), B[[1, 3], 3])
- assert_equal(A[[2, -5], -4].toarray(), B[[2, -5], -4])
- assert_equal(A[array([2, -5]), -4].toarray(), B[[2, -5], -4])
- assert_equal(A[[2, -5], array(-4)].toarray(), B[[2, -5], -4])
- assert_equal(A[array([2, -5]), array(-4)].toarray(), B[[2, -5], -4])
- # [[1,2],1:2]
- assert_equal(A[[1, 3], :].toarray(), B[[1, 3], :])
- assert_equal(A[[2, -5], 8:-1].toarray(), B[[2, -5], 8:-1])
- assert_equal(A[array([2, -5]), 8:-1].toarray(), B[[2, -5], 8:-1])
- # [[1,2],[1,2]]
- assert_equal(toarray(A[[1, 3], [2, 4]]), B[[1, 3], [2, 4]])
- assert_equal(toarray(A[[-1, -3], [2, -4]]), B[[-1, -3], [2, -4]])
- assert_equal(
- toarray(A[array([-1, -3]), [2, -4]]), B[[-1, -3], [2, -4]]
- )
- assert_equal(
- toarray(A[[-1, -3], array([2, -4])]), B[[-1, -3], [2, -4]]
- )
- assert_equal(
- toarray(A[array([-1, -3]), array([2, -4])]), B[[-1, -3], [2, -4]]
- )
- # [[[1],[2]],[1,2]]
- assert_equal(A[[[1], [3]], [2, 4]].toarray(), B[[[1], [3]], [2, 4]])
- assert_equal(
- A[[[-1], [-3], [-2]], [2, -4]].toarray(),
- B[[[-1], [-3], [-2]], [2, -4]]
- )
- assert_equal(
- A[array([[-1], [-3], [-2]]), [2, -4]].toarray(),
- B[[[-1], [-3], [-2]], [2, -4]]
- )
- assert_equal(
- A[[[-1], [-3], [-2]], array([2, -4])].toarray(),
- B[[[-1], [-3], [-2]], [2, -4]]
- )
- assert_equal(
- A[array([[-1], [-3], [-2]]), array([2, -4])].toarray(),
- B[[[-1], [-3], [-2]], [2, -4]]
- )
- # [[1,2]]
- assert_equal(A[[1, 3]].toarray(), B[[1, 3]])
- assert_equal(A[[-1, -3]].toarray(), B[[-1, -3]])
- assert_equal(A[array([-1, -3])].toarray(), B[[-1, -3]])
- # [[1,2],:][:,[1,2]]
- assert_equal(
- A[[1, 3], :][:, [2, 4]].toarray(), B[[1, 3], :][:, [2, 4]]
- )
- assert_equal(
- A[[-1, -3], :][:, [2, -4]].toarray(), B[[-1, -3], :][:, [2, -4]]
- )
- assert_equal(
- A[array([-1, -3]), :][:, array([2, -4])].toarray(),
- B[[-1, -3], :][:, [2, -4]]
- )
- # [:,[1,2]][[1,2],:]
- assert_equal(
- A[:, [1, 3]][[2, 4], :].toarray(), B[:, [1, 3]][[2, 4], :]
- )
- assert_equal(
- A[:, [-1, -3]][[2, -4], :].toarray(), B[:, [-1, -3]][[2, -4], :]
- )
- assert_equal(
- A[:, array([-1, -3])][array([2, -4]), :].toarray(),
- B[:, [-1, -3]][[2, -4], :]
- )
- # Check bug reported by Robert Cimrman:
- # http://thread.gmane.org/gmane.comp.python.scientific.devel/7986 (dead link)
- s = slice(int8(2),int8(4),None)
- assert_equal(A[s, :].toarray(), B[2:4, :])
- assert_equal(A[:, s].toarray(), B[:, 2:4])
- # Regression for gh-4917: index with tuple of 2D arrays
- i = np.array([[1]], dtype=int)
- assert_equal(A[i, i].toarray(), B[i, i])
- # Regression for gh-4917: index with tuple of empty nested lists
- assert_equal(A[[[]], [[]]].toarray(), B[[[]], [[]]])
- def test_fancy_indexing_randomized(self):
- np.random.seed(1234) # make runs repeatable
- NUM_SAMPLES = 50
- M = 6
- N = 4
- D = asmatrix(np.random.rand(M,N))
- D = np.multiply(D, D > 0.5)
- I = np.random.randint(-M + 1, M, size=NUM_SAMPLES)
- J = np.random.randint(-N + 1, N, size=NUM_SAMPLES)
- S = self.spmatrix(D)
- SIJ = S[I,J]
- if isspmatrix(SIJ):
- SIJ = SIJ.toarray()
- assert_equal(SIJ, D[I,J])
- I_bad = I + M
- J_bad = J - N
- assert_raises(IndexError, S.__getitem__, (I_bad,J))
- assert_raises(IndexError, S.__getitem__, (I,J_bad))
- def test_fancy_indexing_boolean(self):
- np.random.seed(1234) # make runs repeatable
- B = asmatrix(arange(50).reshape(5,10))
- A = self.spmatrix(B)
- I = np.array(np.random.randint(0, 2, size=5), dtype=bool)
- J = np.array(np.random.randint(0, 2, size=10), dtype=bool)
- X = np.array(np.random.randint(0, 2, size=(5, 10)), dtype=bool)
- assert_equal(toarray(A[I]), B[I])
- assert_equal(toarray(A[:, J]), B[:, J])
- assert_equal(toarray(A[X]), B[X])
- assert_equal(toarray(A[B > 9]), B[B > 9])
- I = np.array([True, False, True, True, False])
- J = np.array([False, True, True, False, True,
- False, False, False, False, False])
- assert_equal(toarray(A[I, J]), B[I, J])
- Z1 = np.zeros((6, 11), dtype=bool)
- Z2 = np.zeros((6, 11), dtype=bool)
- Z2[0,-1] = True
- Z3 = np.zeros((6, 11), dtype=bool)
- Z3[-1,0] = True
- assert_equal(A[Z1], np.array([]))
- assert_raises(IndexError, A.__getitem__, Z2)
- assert_raises(IndexError, A.__getitem__, Z3)
- assert_raises((IndexError, ValueError), A.__getitem__, (X, 1))
- def test_fancy_indexing_sparse_boolean(self):
- np.random.seed(1234) # make runs repeatable
- B = asmatrix(arange(50).reshape(5,10))
- A = self.spmatrix(B)
- X = np.array(np.random.randint(0, 2, size=(5, 10)), dtype=bool)
- Xsp = csr_matrix(X)
- assert_equal(toarray(A[Xsp]), B[X])
- assert_equal(toarray(A[A > 9]), B[B > 9])
- Z = np.array(np.random.randint(0, 2, size=(5, 11)), dtype=bool)
- Y = np.array(np.random.randint(0, 2, size=(6, 10)), dtype=bool)
- Zsp = csr_matrix(Z)
- Ysp = csr_matrix(Y)
- assert_raises(IndexError, A.__getitem__, Zsp)
- assert_raises(IndexError, A.__getitem__, Ysp)
- assert_raises((IndexError, ValueError), A.__getitem__, (Xsp, 1))
- def test_fancy_indexing_regression_3087(self):
- mat = self.spmatrix(array([[1, 0, 0], [0,1,0], [1,0,0]]))
- desired_cols = np.ravel(mat.sum(0)) > 0
- assert_equal(mat[:, desired_cols].A, [[1, 0], [0, 1], [1, 0]])
- def test_fancy_indexing_seq_assign(self):
- mat = self.spmatrix(array([[1, 0], [0, 1]]))
- assert_raises(ValueError, mat.__setitem__, (0, 0), np.array([1,2]))
- def test_fancy_indexing_2d_assign(self):
- # regression test for gh-10695
- mat = self.spmatrix(array([[1, 0], [2, 3]]))
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure")
- mat[[0, 1], [1, 1]] = mat[[1, 0], [0, 0]]
- assert_equal(toarray(mat), array([[1, 2], [2, 1]]))
- def test_fancy_indexing_empty(self):
- B = asmatrix(arange(50).reshape(5,10))
- B[1,:] = 0
- B[:,2] = 0
- B[3,6] = 0
- A = self.spmatrix(B)
- K = np.array([False, False, False, False, False])
- assert_equal(toarray(A[K]), B[K])
- K = np.array([], dtype=int)
- assert_equal(toarray(A[K]), B[K])
- assert_equal(toarray(A[K, K]), B[K, K])
- J = np.array([0, 1, 2, 3, 4], dtype=int)[:,None]
- assert_equal(toarray(A[K, J]), B[K, J])
- assert_equal(toarray(A[J, K]), B[J, K])
- @contextlib.contextmanager
- def check_remains_sorted(X):
- """Checks that sorted indices property is retained through an operation
- """
- if not hasattr(X, 'has_sorted_indices') or not X.has_sorted_indices:
- yield
- return
- yield
- indices = X.indices.copy()
- X.has_sorted_indices = False
- X.sort_indices()
- assert_array_equal(indices, X.indices,
- 'Expected sorted indices, found unsorted')
- class _TestFancyIndexingAssign:
- def test_bad_index_assign(self):
- A = self.spmatrix(np.zeros([5, 5]))
- assert_raises((IndexError, ValueError, TypeError), A.__setitem__, "foo", 2)
- assert_raises((IndexError, ValueError, TypeError), A.__setitem__, (2, "foo"), 5)
- def test_fancy_indexing_set(self):
- n, m = (5, 10)
- def _test_set_slice(i, j):
- A = self.spmatrix((n, m))
- B = asmatrix(np.zeros((n, m)))
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- B[i, j] = 1
- with check_remains_sorted(A):
- A[i, j] = 1
- assert_array_almost_equal(A.toarray(), B)
- # [1:2,1:2]
- for i, j in [((2, 3, 4), slice(None, 10, 4)),
- (np.arange(3), slice(5, -2)),
- (slice(2, 5), slice(5, -2))]:
- _test_set_slice(i, j)
- for i, j in [(np.arange(3), np.arange(3)), ((0, 3, 4), (1, 2, 4))]:
- _test_set_slice(i, j)
- def test_fancy_assignment_dtypes(self):
- def check(dtype):
- A = self.spmatrix((5, 5), dtype=dtype)
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- A[[0,1],[0,1]] = dtype.type(1)
- assert_equal(A.sum(), dtype.type(1)*2)
- A[0:2,0:2] = dtype.type(1.0)
- assert_equal(A.sum(), dtype.type(1)*4)
- A[2,2] = dtype.type(1.0)
- assert_equal(A.sum(), dtype.type(1)*4 + dtype.type(1))
- for dtype in supported_dtypes:
- check(np.dtype(dtype))
- def test_sequence_assignment(self):
- A = self.spmatrix((4,3))
- B = self.spmatrix(eye(3,4))
- i0 = [0,1,2]
- i1 = (0,1,2)
- i2 = array(i0)
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- with check_remains_sorted(A):
- A[0,i0] = B[i0,0].T
- A[1,i1] = B[i1,1].T
- A[2,i2] = B[i2,2].T
- assert_array_equal(A.toarray(), B.T.toarray())
- # column slice
- A = self.spmatrix((2,3))
- with check_remains_sorted(A):
- A[1,1:3] = [10,20]
- assert_array_equal(A.toarray(), [[0, 0, 0], [0, 10, 20]])
- # row slice
- A = self.spmatrix((3,2))
- with check_remains_sorted(A):
- A[1:3,1] = [[10],[20]]
- assert_array_equal(A.toarray(), [[0, 0], [0, 10], [0, 20]])
- # both slices
- A = self.spmatrix((3,3))
- B = asmatrix(np.zeros((3,3)))
- with check_remains_sorted(A):
- for C in [A, B]:
- C[[0,1,2], [0,1,2]] = [4,5,6]
- assert_array_equal(A.toarray(), B)
- # both slices (2)
- A = self.spmatrix((4, 3))
- with check_remains_sorted(A):
- A[(1, 2, 3), (0, 1, 2)] = [1, 2, 3]
- assert_almost_equal(A.sum(), 6)
- B = asmatrix(np.zeros((4, 3)))
- B[(1, 2, 3), (0, 1, 2)] = [1, 2, 3]
- assert_array_equal(A.toarray(), B)
- def test_fancy_assign_empty(self):
- B = asmatrix(arange(50).reshape(5,10))
- B[1,:] = 0
- B[:,2] = 0
- B[3,6] = 0
- A = self.spmatrix(B)
- K = np.array([False, False, False, False, False])
- A[K] = 42
- assert_equal(toarray(A), B)
- K = np.array([], dtype=int)
- A[K] = 42
- assert_equal(toarray(A), B)
- A[K,K] = 42
- assert_equal(toarray(A), B)
- J = np.array([0, 1, 2, 3, 4], dtype=int)[:,None]
- A[K,J] = 42
- assert_equal(toarray(A), B)
- A[J,K] = 42
- assert_equal(toarray(A), B)
- class _TestFancyMultidim:
- def test_fancy_indexing_ndarray(self):
- sets = [
- (np.array([[1], [2], [3]]), np.array([3, 4, 2])),
- (np.array([[1], [2], [3]]), np.array([[3, 4, 2]])),
- (np.array([[1, 2, 3]]), np.array([[3], [4], [2]])),
- (np.array([1, 2, 3]), np.array([[3], [4], [2]])),
- (np.array([[1, 2, 3], [3, 4, 2]]),
- np.array([[5, 6, 3], [2, 3, 1]]))
- ]
- # These inputs generate 3-D outputs
- # (np.array([[[1], [2], [3]], [[3], [4], [2]]]),
- # np.array([[[5], [6], [3]], [[2], [3], [1]]])),
- for I, J in sets:
- np.random.seed(1234)
- D = asmatrix(np.random.rand(5, 7))
- S = self.spmatrix(D)
- SIJ = S[I,J]
- if isspmatrix(SIJ):
- SIJ = SIJ.toarray()
- assert_equal(SIJ, D[I,J])
- I_bad = I + 5
- J_bad = J + 7
- assert_raises(IndexError, S.__getitem__, (I_bad,J))
- assert_raises(IndexError, S.__getitem__, (I,J_bad))
- # This would generate 3-D arrays -- not supported
- assert_raises(IndexError, S.__getitem__, ([I, I], slice(None)))
- assert_raises(IndexError, S.__getitem__, (slice(None), [J, J]))
- class _TestFancyMultidimAssign:
- def test_fancy_assign_ndarray(self):
- np.random.seed(1234)
- D = asmatrix(np.random.rand(5, 7))
- S = self.spmatrix(D)
- X = np.random.rand(2, 3)
- I = np.array([[1, 2, 3], [3, 4, 2]])
- J = np.array([[5, 6, 3], [2, 3, 1]])
- with check_remains_sorted(S):
- S[I,J] = X
- D[I,J] = X
- assert_equal(S.toarray(), D)
- I_bad = I + 5
- J_bad = J + 7
- C = [1, 2, 3]
- with check_remains_sorted(S):
- S[I,J] = C
- D[I,J] = C
- assert_equal(S.toarray(), D)
- with check_remains_sorted(S):
- S[I,J] = 3
- D[I,J] = 3
- assert_equal(S.toarray(), D)
- assert_raises(IndexError, S.__setitem__, (I_bad,J), C)
- assert_raises(IndexError, S.__setitem__, (I,J_bad), C)
- def test_fancy_indexing_multidim_set(self):
- n, m = (5, 10)
- def _test_set_slice(i, j):
- A = self.spmatrix((n, m))
- with check_remains_sorted(A), suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- A[i, j] = 1
- B = asmatrix(np.zeros((n, m)))
- B[i, j] = 1
- assert_array_almost_equal(A.toarray(), B)
- # [[[1, 2], [1, 2]], [1, 2]]
- for i, j in [(np.array([[1, 2], [1, 3]]), [1, 3]),
- (np.array([0, 4]), [[0, 3], [1, 2]]),
- ([[1, 2, 3], [0, 2, 4]], [[0, 4, 3], [4, 1, 2]])]:
- _test_set_slice(i, j)
- def test_fancy_assign_list(self):
- np.random.seed(1234)
- D = asmatrix(np.random.rand(5, 7))
- S = self.spmatrix(D)
- X = np.random.rand(2, 3)
- I = [[1, 2, 3], [3, 4, 2]]
- J = [[5, 6, 3], [2, 3, 1]]
- S[I,J] = X
- D[I,J] = X
- assert_equal(S.toarray(), D)
- I_bad = [[ii + 5 for ii in i] for i in I]
- J_bad = [[jj + 7 for jj in j] for j in J]
- C = [1, 2, 3]
- S[I,J] = C
- D[I,J] = C
- assert_equal(S.toarray(), D)
- S[I,J] = 3
- D[I,J] = 3
- assert_equal(S.toarray(), D)
- assert_raises(IndexError, S.__setitem__, (I_bad,J), C)
- assert_raises(IndexError, S.__setitem__, (I,J_bad), C)
- def test_fancy_assign_slice(self):
- np.random.seed(1234)
- D = asmatrix(np.random.rand(5, 7))
- S = self.spmatrix(D)
- I = [1, 2, 3, 3, 4, 2]
- J = [5, 6, 3, 2, 3, 1]
- I_bad = [ii + 5 for ii in I]
- J_bad = [jj + 7 for jj in J]
- C1 = [1, 2, 3, 4, 5, 6, 7]
- C2 = np.arange(5)[:, None]
- assert_raises(IndexError, S.__setitem__, (I_bad, slice(None)), C1)
- assert_raises(IndexError, S.__setitem__, (slice(None), J_bad), C2)
- class _TestArithmetic:
- """
- Test real/complex arithmetic
- """
- def __arith_init(self):
- # these can be represented exactly in FP (so arithmetic should be exact)
- self.__A = array([[-1.5, 6.5, 0, 2.25, 0, 0],
- [3.125, -7.875, 0.625, 0, 0, 0],
- [0, 0, -0.125, 1.0, 0, 0],
- [0, 0, 8.375, 0, 0, 0]], 'float64')
- self.__B = array([[0.375, 0, 0, 0, -5, 2.5],
- [14.25, -3.75, 0, 0, -0.125, 0],
- [0, 7.25, 0, 0, 0, 0],
- [18.5, -0.0625, 0, 0, 0, 0]], 'complex128')
- self.__B.imag = array([[1.25, 0, 0, 0, 6, -3.875],
- [2.25, 4.125, 0, 0, 0, 2.75],
- [0, 4.125, 0, 0, 0, 0],
- [-0.0625, 0, 0, 0, 0, 0]], 'float64')
- # fractions are all x/16ths
- assert_array_equal((self.__A*16).astype('int32'),16*self.__A)
- assert_array_equal((self.__B.real*16).astype('int32'),16*self.__B.real)
- assert_array_equal((self.__B.imag*16).astype('int32'),16*self.__B.imag)
- self.__Asp = self.spmatrix(self.__A)
- self.__Bsp = self.spmatrix(self.__B)
- def test_add_sub(self):
- self.__arith_init()
- # basic tests
- assert_array_equal(
- (self.__Asp + self.__Bsp).toarray(), self.__A + self.__B
- )
- # check conversions
- for x in supported_dtypes:
- with np.errstate(invalid="ignore"):
- A = self.__A.astype(x)
- Asp = self.spmatrix(A)
- for y in supported_dtypes:
- if not np.issubdtype(y, np.complexfloating):
- with np.errstate(invalid="ignore"):
- B = self.__B.real.astype(y)
- else:
- B = self.__B.astype(y)
- Bsp = self.spmatrix(B)
- # addition
- D1 = A + B
- S1 = Asp + Bsp
- assert_equal(S1.dtype,D1.dtype)
- assert_array_equal(S1.toarray(), D1)
- assert_array_equal(Asp + B,D1) # check sparse + dense
- assert_array_equal(A + Bsp,D1) # check dense + sparse
- # subtraction
- if np.dtype('bool') in [x, y]:
- # boolean array subtraction deprecated in 1.9.0
- continue
- D1 = A - B
- S1 = Asp - Bsp
- assert_equal(S1.dtype,D1.dtype)
- assert_array_equal(S1.toarray(), D1)
- assert_array_equal(Asp - B,D1) # check sparse - dense
- assert_array_equal(A - Bsp,D1) # check dense - sparse
- def test_mu(self):
- self.__arith_init()
- # basic tests
- assert_array_equal((self.__Asp * self.__Bsp.T).toarray(),
- self.__A @ self.__B.T)
- for x in supported_dtypes:
- with np.errstate(invalid="ignore"):
- A = self.__A.astype(x)
- Asp = self.spmatrix(A)
- for y in supported_dtypes:
- if np.issubdtype(y, np.complexfloating):
- B = self.__B.astype(y)
- else:
- with np.errstate(invalid="ignore"):
- B = self.__B.real.astype(y)
- Bsp = self.spmatrix(B)
- D1 = A @ B.T
- S1 = Asp * Bsp.T
- assert_allclose(S1.toarray(), D1,
- atol=1e-14*abs(D1).max())
- assert_equal(S1.dtype,D1.dtype)
- class _TestMinMax:
- def test_minmax(self):
- for dtype in [np.float32, np.float64, np.int32, np.int64, np.complex128]:
- D = np.arange(20, dtype=dtype).reshape(5,4)
- X = self.spmatrix(D)
- assert_equal(X.min(), 0)
- assert_equal(X.max(), 19)
- assert_equal(X.min().dtype, dtype)
- assert_equal(X.max().dtype, dtype)
- D *= -1
- X = self.spmatrix(D)
- assert_equal(X.min(), -19)
- assert_equal(X.max(), 0)
- D += 5
- X = self.spmatrix(D)
- assert_equal(X.min(), -14)
- assert_equal(X.max(), 5)
- # try a fully dense matrix
- X = self.spmatrix(np.arange(1, 10).reshape(3, 3))
- assert_equal(X.min(), 1)
- assert_equal(X.min().dtype, X.dtype)
- X = -X
- assert_equal(X.max(), -1)
- # and a fully sparse matrix
- Z = self.spmatrix(np.zeros(1))
- assert_equal(Z.min(), 0)
- assert_equal(Z.max(), 0)
- assert_equal(Z.max().dtype, Z.dtype)
- # another test
- D = np.arange(20, dtype=float).reshape(5,4)
- D[0:2, :] = 0
- X = self.spmatrix(D)
- assert_equal(X.min(), 0)
- assert_equal(X.max(), 19)
- # zero-size matrices
- for D in [np.zeros((0, 0)), np.zeros((0, 10)), np.zeros((10, 0))]:
- X = self.spmatrix(D)
- assert_raises(ValueError, X.min)
- assert_raises(ValueError, X.max)
- def test_minmax_axis(self):
- D = np.arange(50).reshape(5, 10)
- # completely empty rows, leaving some completely full:
- D[1, :] = 0
- # empty at end for reduceat:
- D[:, 9] = 0
- # partial rows/cols:
- D[3, 3] = 0
- # entries on either side of 0:
- D[2, 2] = -1
- X = self.spmatrix(D)
- axes = [-2, -1, 0, 1]
- for axis in axes:
- assert_array_equal(
- X.max(axis=axis).A, D.max(axis=axis, keepdims=True)
- )
- assert_array_equal(
- X.min(axis=axis).A, D.min(axis=axis, keepdims=True)
- )
- # full matrix
- D = np.arange(1, 51).reshape(10, 5)
- X = self.spmatrix(D)
- for axis in axes:
- assert_array_equal(
- X.max(axis=axis).A, D.max(axis=axis, keepdims=True)
- )
- assert_array_equal(
- X.min(axis=axis).A, D.min(axis=axis, keepdims=True)
- )
- # empty matrix
- D = np.zeros((10, 5))
- X = self.spmatrix(D)
- for axis in axes:
- assert_array_equal(
- X.max(axis=axis).A, D.max(axis=axis, keepdims=True)
- )
- assert_array_equal(
- X.min(axis=axis).A, D.min(axis=axis, keepdims=True)
- )
- axes_even = [0, -2]
- axes_odd = [1, -1]
- # zero-size matrices
- D = np.zeros((0, 10))
- X = self.spmatrix(D)
- for axis in axes_even:
- assert_raises(ValueError, X.min, axis=axis)
- assert_raises(ValueError, X.max, axis=axis)
- for axis in axes_odd:
- assert_array_equal(np.zeros((0, 1)), X.min(axis=axis).A)
- assert_array_equal(np.zeros((0, 1)), X.max(axis=axis).A)
- D = np.zeros((10, 0))
- X = self.spmatrix(D)
- for axis in axes_odd:
- assert_raises(ValueError, X.min, axis=axis)
- assert_raises(ValueError, X.max, axis=axis)
- for axis in axes_even:
- assert_array_equal(np.zeros((1, 0)), X.min(axis=axis).A)
- assert_array_equal(np.zeros((1, 0)), X.max(axis=axis).A)
- def test_minmax_invalid_params(self):
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- for fname in ('min', 'max'):
- func = getattr(datsp, fname)
- assert_raises(ValueError, func, axis=3)
- assert_raises(TypeError, func, axis=(0, 1))
- assert_raises(TypeError, func, axis=1.5)
- assert_raises(ValueError, func, axis=1, out=1)
- def test_numpy_minmax(self):
- # See gh-5987
- # xref gh-7460 in 'numpy'
- from scipy.sparse import _data
- dat = array([[0, 1, 2],
- [3, -4, 5],
- [-6, 7, 9]])
- datsp = self.spmatrix(dat)
- # We are only testing sparse matrices who have
- # implemented 'min' and 'max' because they are
- # the ones with the compatibility issues with
- # the 'numpy' implementation.
- if isinstance(datsp, _data._minmax_mixin):
- assert_array_equal(np.min(datsp), np.min(dat))
- assert_array_equal(np.max(datsp), np.max(dat))
- def test_argmax(self):
- D1 = np.array([
- [-1, 5, 2, 3],
- [0, 0, -1, -2],
- [-1, -2, -3, -4],
- [1, 2, 3, 4],
- [1, 2, 0, 0],
- ])
- D2 = D1.transpose()
- for D in [D1, D2]:
- mat = csr_matrix(D)
- assert_equal(mat.argmax(), np.argmax(D))
- assert_equal(mat.argmin(), np.argmin(D))
- assert_equal(mat.argmax(axis=0),
- asmatrix(np.argmax(D, axis=0)))
- assert_equal(mat.argmin(axis=0),
- asmatrix(np.argmin(D, axis=0)))
- assert_equal(mat.argmax(axis=1),
- asmatrix(np.argmax(D, axis=1).reshape(-1, 1)))
- assert_equal(mat.argmin(axis=1),
- asmatrix(np.argmin(D, axis=1).reshape(-1, 1)))
- D1 = np.empty((0, 5))
- D2 = np.empty((5, 0))
- for axis in [None, 0]:
- mat = self.spmatrix(D1)
- assert_raises(ValueError, mat.argmax, axis=axis)
- assert_raises(ValueError, mat.argmin, axis=axis)
- for axis in [None, 1]:
- mat = self.spmatrix(D2)
- assert_raises(ValueError, mat.argmax, axis=axis)
- assert_raises(ValueError, mat.argmin, axis=axis)
- class _TestGetNnzAxis:
- def test_getnnz_axis(self):
- dat = array([[0, 2],
- [3, 5],
- [-6, 9]])
- bool_dat = dat.astype(bool)
- datsp = self.spmatrix(dat)
- accepted_return_dtypes = (np.int32, np.int64)
- assert_array_equal(bool_dat.sum(axis=None), datsp.getnnz(axis=None))
- assert_array_equal(bool_dat.sum(), datsp.getnnz())
- assert_array_equal(bool_dat.sum(axis=0), datsp.getnnz(axis=0))
- assert_in(datsp.getnnz(axis=0).dtype, accepted_return_dtypes)
- assert_array_equal(bool_dat.sum(axis=1), datsp.getnnz(axis=1))
- assert_in(datsp.getnnz(axis=1).dtype, accepted_return_dtypes)
- assert_array_equal(bool_dat.sum(axis=-2), datsp.getnnz(axis=-2))
- assert_in(datsp.getnnz(axis=-2).dtype, accepted_return_dtypes)
- assert_array_equal(bool_dat.sum(axis=-1), datsp.getnnz(axis=-1))
- assert_in(datsp.getnnz(axis=-1).dtype, accepted_return_dtypes)
- assert_raises(ValueError, datsp.getnnz, axis=2)
- #------------------------------------------------------------------------------
- # Tailored base class for generic tests
- #------------------------------------------------------------------------------
- def _possibly_unimplemented(cls, require=True):
- """
- Construct a class that either runs tests as usual (require=True),
- or each method skips if it encounters a common error.
- """
- if require:
- return cls
- else:
- def wrap(fc):
- @functools.wraps(fc)
- def wrapper(*a, **kw):
- try:
- return fc(*a, **kw)
- except (NotImplementedError, TypeError, ValueError,
- IndexError, AttributeError):
- raise pytest.skip("feature not implemented")
- return wrapper
- new_dict = dict(cls.__dict__)
- for name, func in cls.__dict__.items():
- if name.startswith('test_'):
- new_dict[name] = wrap(func)
- return type(cls.__name__ + "NotImplemented",
- cls.__bases__,
- new_dict)
- def sparse_test_class(getset=True, slicing=True, slicing_assign=True,
- fancy_indexing=True, fancy_assign=True,
- fancy_multidim_indexing=True, fancy_multidim_assign=True,
- minmax=True, nnz_axis=True):
- """
- Construct a base class, optionally converting some of the tests in
- the suite to check that the feature is not implemented.
- """
- bases = (_TestCommon,
- _possibly_unimplemented(_TestGetSet, getset),
- _TestSolve,
- _TestInplaceArithmetic,
- _TestArithmetic,
- _possibly_unimplemented(_TestSlicing, slicing),
- _possibly_unimplemented(_TestSlicingAssign, slicing_assign),
- _possibly_unimplemented(_TestFancyIndexing, fancy_indexing),
- _possibly_unimplemented(_TestFancyIndexingAssign,
- fancy_assign),
- _possibly_unimplemented(_TestFancyMultidim,
- fancy_indexing and fancy_multidim_indexing),
- _possibly_unimplemented(_TestFancyMultidimAssign,
- fancy_multidim_assign and fancy_assign),
- _possibly_unimplemented(_TestMinMax, minmax),
- _possibly_unimplemented(_TestGetNnzAxis, nnz_axis))
- # check that test names do not clash
- names = {}
- for cls in bases:
- for name in cls.__dict__:
- if not name.startswith('test_'):
- continue
- old_cls = names.get(name)
- if old_cls is not None:
- raise ValueError("Test class %s overloads test %s defined in %s" % (
- cls.__name__, name, old_cls.__name__))
- names[name] = cls
- return type("TestBase", bases, {})
- #------------------------------------------------------------------------------
- # Matrix class based tests
- #------------------------------------------------------------------------------
- class TestCSR(sparse_test_class()):
- @classmethod
- def spmatrix(cls, *args, **kwargs):
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a csr_matrix is expensive")
- return csr_matrix(*args, **kwargs)
- math_dtypes = [np.bool_, np.int_, np.float_, np.complex_]
- def test_constructor1(self):
- b = array([[0, 4, 0],
- [3, 0, 0],
- [0, 2, 0]], 'd')
- bsp = csr_matrix(b)
- assert_array_almost_equal(bsp.data,[4,3,2])
- assert_array_equal(bsp.indices,[1,0,1])
- assert_array_equal(bsp.indptr,[0,1,2,3])
- assert_equal(bsp.getnnz(),3)
- assert_equal(bsp.getformat(),'csr')
- assert_array_equal(bsp.toarray(), b)
- def test_constructor2(self):
- b = zeros((6,6),'d')
- b[3,4] = 5
- bsp = csr_matrix(b)
- assert_array_almost_equal(bsp.data,[5])
- assert_array_equal(bsp.indices,[4])
- assert_array_equal(bsp.indptr,[0,0,0,0,1,1,1])
- assert_array_almost_equal(bsp.toarray(), b)
- def test_constructor3(self):
- b = array([[1, 0],
- [0, 2],
- [3, 0]], 'd')
- bsp = csr_matrix(b)
- assert_array_almost_equal(bsp.data,[1,2,3])
- assert_array_equal(bsp.indices,[0,1,0])
- assert_array_equal(bsp.indptr,[0,1,2,3])
- assert_array_almost_equal(bsp.toarray(), b)
- def test_constructor4(self):
- # using (data, ij) format
- row = array([2, 3, 1, 3, 0, 1, 3, 0, 2, 1, 2])
- col = array([0, 1, 0, 0, 1, 1, 2, 2, 2, 2, 1])
- data = array([6., 10., 3., 9., 1., 4.,
- 11., 2., 8., 5., 7.])
- ij = vstack((row,col))
- csr = csr_matrix((data,ij),(4,3))
- assert_array_equal(arange(12).reshape(4, 3), csr.toarray())
- # using Python lists and a specified dtype
- csr = csr_matrix(([2**63 + 1, 1], ([0, 1], [0, 1])), dtype=np.uint64)
- dense = array([[2**63 + 1, 0], [0, 1]], dtype=np.uint64)
- assert_array_equal(dense, csr.toarray())
- def test_constructor5(self):
- # infer dimensions from arrays
- indptr = array([0,1,3,3])
- indices = array([0,5,1,2])
- data = array([1,2,3,4])
- csr = csr_matrix((data, indices, indptr))
- assert_array_equal(csr.shape,(3,6))
- def test_constructor6(self):
- # infer dimensions and dtype from lists
- indptr = [0, 1, 3, 3]
- indices = [0, 5, 1, 2]
- data = [1, 2, 3, 4]
- csr = csr_matrix((data, indices, indptr))
- assert_array_equal(csr.shape, (3,6))
- assert_(np.issubdtype(csr.dtype, np.signedinteger))
- def test_constructor_smallcol(self):
- # int64 indices not required
- data = arange(6) + 1
- col = array([1, 2, 1, 0, 0, 2], dtype=np.int64)
- ptr = array([0, 2, 4, 6], dtype=np.int64)
- a = csr_matrix((data, col, ptr), shape=(3, 3))
- b = array([[0, 1, 2],
- [4, 3, 0],
- [5, 0, 6]], 'd')
- assert_equal(a.indptr.dtype, np.dtype(np.int32))
- assert_equal(a.indices.dtype, np.dtype(np.int32))
- assert_array_equal(a.toarray(), b)
- def test_constructor_largecol(self):
- # int64 indices required
- data = arange(6) + 1
- large = np.iinfo(np.int32).max + 100
- col = array([0, 1, 2, large, large+1, large+2], dtype=np.int64)
- ptr = array([0, 2, 4, 6], dtype=np.int64)
- a = csr_matrix((data, col, ptr))
- assert_equal(a.indptr.dtype, np.dtype(np.int64))
- assert_equal(a.indices.dtype, np.dtype(np.int64))
- assert_array_equal(a.shape, (3, max(col)+1))
- def test_sort_indices(self):
- data = arange(5)
- indices = array([7, 2, 1, 5, 4])
- indptr = array([0, 3, 5])
- asp = csr_matrix((data, indices, indptr), shape=(2,10))
- bsp = asp.copy()
- asp.sort_indices()
- assert_array_equal(asp.indices,[1, 2, 7, 4, 5])
- assert_array_equal(asp.toarray(), bsp.toarray())
- def test_eliminate_zeros(self):
- data = array([1, 0, 0, 0, 2, 0, 3, 0])
- indices = array([1, 2, 3, 4, 5, 6, 7, 8])
- indptr = array([0, 3, 8])
- asp = csr_matrix((data, indices, indptr), shape=(2,10))
- bsp = asp.copy()
- asp.eliminate_zeros()
- assert_array_equal(asp.nnz, 3)
- assert_array_equal(asp.data,[1, 2, 3])
- assert_array_equal(asp.toarray(), bsp.toarray())
- def test_ufuncs(self):
- X = csr_matrix(np.arange(20).reshape(4, 5) / 20.)
- for f in ["sin", "tan", "arcsin", "arctan", "sinh", "tanh",
- "arcsinh", "arctanh", "rint", "sign", "expm1", "log1p",
- "deg2rad", "rad2deg", "floor", "ceil", "trunc", "sqrt"]:
- assert_equal(hasattr(csr_matrix, f), True)
- X2 = getattr(X, f)()
- assert_equal(X.shape, X2.shape)
- assert_array_equal(X.indices, X2.indices)
- assert_array_equal(X.indptr, X2.indptr)
- assert_array_equal(X2.toarray(), getattr(np, f)(X.toarray()))
- def test_unsorted_arithmetic(self):
- data = arange(5)
- indices = array([7, 2, 1, 5, 4])
- indptr = array([0, 3, 5])
- asp = csr_matrix((data, indices, indptr), shape=(2,10))
- data = arange(6)
- indices = array([8, 1, 5, 7, 2, 4])
- indptr = array([0, 2, 6])
- bsp = csr_matrix((data, indices, indptr), shape=(2,10))
- assert_equal((asp + bsp).toarray(), asp.toarray() + bsp.toarray())
- def test_fancy_indexing_broadcast(self):
- # broadcasting indexing mode is supported
- I = np.array([[1], [2], [3]])
- J = np.array([3, 4, 2])
- np.random.seed(1234)
- D = asmatrix(np.random.rand(5, 7))
- S = self.spmatrix(D)
- SIJ = S[I,J]
- if isspmatrix(SIJ):
- SIJ = SIJ.toarray()
- assert_equal(SIJ, D[I,J])
- def test_has_sorted_indices(self):
- "Ensure has_sorted_indices memoizes sorted state for sort_indices"
- sorted_inds = np.array([0, 1])
- unsorted_inds = np.array([1, 0])
- data = np.array([1, 1])
- indptr = np.array([0, 2])
- M = csr_matrix((data, sorted_inds, indptr)).copy()
- assert_equal(True, M.has_sorted_indices)
- assert type(M.has_sorted_indices) == bool
- M = csr_matrix((data, unsorted_inds, indptr)).copy()
- assert_equal(False, M.has_sorted_indices)
- # set by sorting
- M.sort_indices()
- assert_equal(True, M.has_sorted_indices)
- assert_array_equal(M.indices, sorted_inds)
- M = csr_matrix((data, unsorted_inds, indptr)).copy()
- # set manually (although underlyingly unsorted)
- M.has_sorted_indices = True
- assert_equal(True, M.has_sorted_indices)
- assert_array_equal(M.indices, unsorted_inds)
- # ensure sort bypassed when has_sorted_indices == True
- M.sort_indices()
- assert_array_equal(M.indices, unsorted_inds)
- def test_has_canonical_format(self):
- "Ensure has_canonical_format memoizes state for sum_duplicates"
- M = csr_matrix((np.array([2]), np.array([0]), np.array([0, 1])))
- assert_equal(True, M.has_canonical_format)
- indices = np.array([0, 0]) # contains duplicate
- data = np.array([1, 1])
- indptr = np.array([0, 2])
- M = csr_matrix((data, indices, indptr)).copy()
- assert_equal(False, M.has_canonical_format)
- assert type(M.has_canonical_format) == bool
- # set by deduplicating
- M.sum_duplicates()
- assert_equal(True, M.has_canonical_format)
- assert_equal(1, len(M.indices))
- M = csr_matrix((data, indices, indptr)).copy()
- # set manually (although underlyingly duplicated)
- M.has_canonical_format = True
- assert_equal(True, M.has_canonical_format)
- assert_equal(2, len(M.indices)) # unaffected content
- # ensure deduplication bypassed when has_canonical_format == True
- M.sum_duplicates()
- assert_equal(2, len(M.indices)) # unaffected content
- def test_scalar_idx_dtype(self):
- # Check that index dtype takes into account all parameters
- # passed to sparsetools, including the scalar ones
- indptr = np.zeros(2, dtype=np.int32)
- indices = np.zeros(0, dtype=np.int32)
- vals = np.zeros(0)
- a = csr_matrix((vals, indices, indptr), shape=(1, 2**31-1))
- b = csr_matrix((vals, indices, indptr), shape=(1, 2**31))
- ij = np.zeros((2, 0), dtype=np.int32)
- c = csr_matrix((vals, ij), shape=(1, 2**31-1))
- d = csr_matrix((vals, ij), shape=(1, 2**31))
- e = csr_matrix((1, 2**31-1))
- f = csr_matrix((1, 2**31))
- assert_equal(a.indptr.dtype, np.int32)
- assert_equal(b.indptr.dtype, np.int64)
- assert_equal(c.indptr.dtype, np.int32)
- assert_equal(d.indptr.dtype, np.int64)
- assert_equal(e.indptr.dtype, np.int32)
- assert_equal(f.indptr.dtype, np.int64)
- # These shouldn't fail
- for x in [a, b, c, d, e, f]:
- x + x
- def test_binop_explicit_zeros(self):
- # Check that binary ops don't introduce spurious explicit zeros.
- # See gh-9619 for context.
- a = csr_matrix([0, 1, 0])
- b = csr_matrix([1, 1, 0])
- assert (a + b).nnz == 2
- assert a.multiply(b).nnz == 1
- TestCSR.init_class()
- class TestCSC(sparse_test_class()):
- @classmethod
- def spmatrix(cls, *args, **kwargs):
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a csc_matrix is expensive")
- return csc_matrix(*args, **kwargs)
- math_dtypes = [np.bool_, np.int_, np.float_, np.complex_]
- def test_constructor1(self):
- b = array([[1, 0, 0, 0], [0, 0, 1, 0], [0, 2, 0, 3]], 'd')
- bsp = csc_matrix(b)
- assert_array_almost_equal(bsp.data,[1,2,1,3])
- assert_array_equal(bsp.indices,[0,2,1,2])
- assert_array_equal(bsp.indptr,[0,1,2,3,4])
- assert_equal(bsp.getnnz(),4)
- assert_equal(bsp.shape,b.shape)
- assert_equal(bsp.getformat(),'csc')
- def test_constructor2(self):
- b = zeros((6,6),'d')
- b[2,4] = 5
- bsp = csc_matrix(b)
- assert_array_almost_equal(bsp.data,[5])
- assert_array_equal(bsp.indices,[2])
- assert_array_equal(bsp.indptr,[0,0,0,0,0,1,1])
- def test_constructor3(self):
- b = array([[1, 0], [0, 0], [0, 2]], 'd')
- bsp = csc_matrix(b)
- assert_array_almost_equal(bsp.data,[1,2])
- assert_array_equal(bsp.indices,[0,2])
- assert_array_equal(bsp.indptr,[0,1,2])
- def test_constructor4(self):
- # using (data, ij) format
- row = array([2, 3, 1, 3, 0, 1, 3, 0, 2, 1, 2])
- col = array([0, 1, 0, 0, 1, 1, 2, 2, 2, 2, 1])
- data = array([6., 10., 3., 9., 1., 4.,
- 11., 2., 8., 5., 7.])
- ij = vstack((row,col))
- csc = csc_matrix((data,ij),(4,3))
- assert_array_equal(arange(12).reshape(4, 3), csc.toarray())
- def test_constructor5(self):
- # infer dimensions from arrays
- indptr = array([0,1,3,3])
- indices = array([0,5,1,2])
- data = array([1,2,3,4])
- csc = csc_matrix((data, indices, indptr))
- assert_array_equal(csc.shape,(6,3))
- def test_constructor6(self):
- # infer dimensions and dtype from lists
- indptr = [0, 1, 3, 3]
- indices = [0, 5, 1, 2]
- data = [1, 2, 3, 4]
- csc = csc_matrix((data, indices, indptr))
- assert_array_equal(csc.shape,(6,3))
- assert_(np.issubdtype(csc.dtype, np.signedinteger))
- def test_eliminate_zeros(self):
- data = array([1, 0, 0, 0, 2, 0, 3, 0])
- indices = array([1, 2, 3, 4, 5, 6, 7, 8])
- indptr = array([0, 3, 8])
- asp = csc_matrix((data, indices, indptr), shape=(10,2))
- bsp = asp.copy()
- asp.eliminate_zeros()
- assert_array_equal(asp.nnz, 3)
- assert_array_equal(asp.data,[1, 2, 3])
- assert_array_equal(asp.toarray(), bsp.toarray())
- def test_sort_indices(self):
- data = arange(5)
- row = array([7, 2, 1, 5, 4])
- ptr = [0, 3, 5]
- asp = csc_matrix((data, row, ptr), shape=(10,2))
- bsp = asp.copy()
- asp.sort_indices()
- assert_array_equal(asp.indices,[1, 2, 7, 4, 5])
- assert_array_equal(asp.toarray(), bsp.toarray())
- def test_ufuncs(self):
- X = csc_matrix(np.arange(21).reshape(7, 3) / 21.)
- for f in ["sin", "tan", "arcsin", "arctan", "sinh", "tanh",
- "arcsinh", "arctanh", "rint", "sign", "expm1", "log1p",
- "deg2rad", "rad2deg", "floor", "ceil", "trunc", "sqrt"]:
- assert_equal(hasattr(csr_matrix, f), True)
- X2 = getattr(X, f)()
- assert_equal(X.shape, X2.shape)
- assert_array_equal(X.indices, X2.indices)
- assert_array_equal(X.indptr, X2.indptr)
- assert_array_equal(X2.toarray(), getattr(np, f)(X.toarray()))
- def test_unsorted_arithmetic(self):
- data = arange(5)
- indices = array([7, 2, 1, 5, 4])
- indptr = array([0, 3, 5])
- asp = csc_matrix((data, indices, indptr), shape=(10,2))
- data = arange(6)
- indices = array([8, 1, 5, 7, 2, 4])
- indptr = array([0, 2, 6])
- bsp = csc_matrix((data, indices, indptr), shape=(10,2))
- assert_equal((asp + bsp).toarray(), asp.toarray() + bsp.toarray())
- def test_fancy_indexing_broadcast(self):
- # broadcasting indexing mode is supported
- I = np.array([[1], [2], [3]])
- J = np.array([3, 4, 2])
- np.random.seed(1234)
- D = asmatrix(np.random.rand(5, 7))
- S = self.spmatrix(D)
- SIJ = S[I,J]
- if isspmatrix(SIJ):
- SIJ = SIJ.toarray()
- assert_equal(SIJ, D[I,J])
- def test_scalar_idx_dtype(self):
- # Check that index dtype takes into account all parameters
- # passed to sparsetools, including the scalar ones
- indptr = np.zeros(2, dtype=np.int32)
- indices = np.zeros(0, dtype=np.int32)
- vals = np.zeros(0)
- a = csc_matrix((vals, indices, indptr), shape=(2**31-1, 1))
- b = csc_matrix((vals, indices, indptr), shape=(2**31, 1))
- ij = np.zeros((2, 0), dtype=np.int32)
- c = csc_matrix((vals, ij), shape=(2**31-1, 1))
- d = csc_matrix((vals, ij), shape=(2**31, 1))
- e = csr_matrix((1, 2**31-1))
- f = csr_matrix((1, 2**31))
- assert_equal(a.indptr.dtype, np.int32)
- assert_equal(b.indptr.dtype, np.int64)
- assert_equal(c.indptr.dtype, np.int32)
- assert_equal(d.indptr.dtype, np.int64)
- assert_equal(e.indptr.dtype, np.int32)
- assert_equal(f.indptr.dtype, np.int64)
- # These shouldn't fail
- for x in [a, b, c, d, e, f]:
- x + x
- TestCSC.init_class()
- class TestDOK(sparse_test_class(minmax=False, nnz_axis=False)):
- spmatrix = dok_matrix
- math_dtypes = [np.int_, np.float_, np.complex_]
- def test_mult(self):
- A = dok_matrix((10,10))
- A[0,3] = 10
- A[5,6] = 20
- D = A*A.T
- E = A*A.H
- assert_array_equal(D.A, E.A)
- def test_add_nonzero(self):
- A = self.spmatrix((3,2))
- A[0,1] = -10
- A[2,0] = 20
- A = A + 10
- B = array([[10, 0], [10, 10], [30, 10]])
- assert_array_equal(A.toarray(), B)
- A = A + 1j
- B = B + 1j
- assert_array_equal(A.toarray(), B)
- def test_dok_divide_scalar(self):
- A = self.spmatrix((3,2))
- A[0,1] = -10
- A[2,0] = 20
- assert_array_equal((A/1j).toarray(), A.toarray()/1j)
- assert_array_equal((A/9).toarray(), A.toarray()/9)
- def test_convert(self):
- # Test provided by Andrew Straw. Fails in SciPy <= r1477.
- (m, n) = (6, 7)
- a = dok_matrix((m, n))
- # set a few elements, but none in the last column
- a[2,1] = 1
- a[0,2] = 2
- a[3,1] = 3
- a[1,5] = 4
- a[4,3] = 5
- a[4,2] = 6
- # assert that the last column is all zeros
- assert_array_equal(a.toarray()[:,n-1], zeros(m,))
- # make sure it still works for CSC format
- csc = a.tocsc()
- assert_array_equal(csc.toarray()[:,n-1], zeros(m,))
- # now test CSR
- (m, n) = (n, m)
- b = a.transpose()
- assert_equal(b.shape, (m, n))
- # assert that the last row is all zeros
- assert_array_equal(b.toarray()[m-1,:], zeros(n,))
- # make sure it still works for CSR format
- csr = b.tocsr()
- assert_array_equal(csr.toarray()[m-1,:], zeros(n,))
- def test_ctor(self):
- # Empty ctor
- assert_raises(TypeError, dok_matrix)
- # Dense ctor
- b = array([[1, 0, 0, 0], [0, 0, 1, 0], [0, 2, 0, 3]], 'd')
- A = dok_matrix(b)
- assert_equal(b.dtype, A.dtype)
- assert_equal(A.toarray(), b)
- # Sparse ctor
- c = csr_matrix(b)
- assert_equal(A.toarray(), c.toarray())
- data = [[0, 1, 2], [3, 0, 0]]
- d = dok_matrix(data, dtype=np.float32)
- assert_equal(d.dtype, np.float32)
- da = d.toarray()
- assert_equal(da.dtype, np.float32)
- assert_array_equal(da, data)
- def test_ticket1160(self):
- # Regression test for ticket #1160.
- a = dok_matrix((3,3))
- a[0,0] = 0
- # This assert would fail, because the above assignment would
- # incorrectly call __set_item__ even though the value was 0.
- assert_((0,0) not in a.keys(), "Unexpected entry (0,0) in keys")
- # Slice assignments were also affected.
- b = dok_matrix((3,3))
- b[:,0] = 0
- assert_(len(b.keys()) == 0, "Unexpected entries in keys")
- TestDOK.init_class()
- class TestLIL(sparse_test_class(minmax=False)):
- spmatrix = lil_matrix
- math_dtypes = [np.int_, np.float_, np.complex_]
- def test_dot(self):
- A = zeros((10, 10), np.complex128)
- A[0, 3] = 10
- A[5, 6] = 20j
- B = lil_matrix((10, 10), dtype=np.complex128)
- B[0, 3] = 10
- B[5, 6] = 20j
- # TODO: properly handle this assertion on ppc64le
- if platform.machine() != 'ppc64le':
- assert_array_equal(A @ A.T, (B * B.T).toarray())
- assert_array_equal(A @ A.conjugate().T, (B * B.H).toarray())
- def test_scalar_mul(self):
- x = lil_matrix((3, 3))
- x[0, 0] = 2
- x = x*2
- assert_equal(x[0, 0], 4)
- x = x*0
- assert_equal(x[0, 0], 0)
- def test_inplace_ops(self):
- A = lil_matrix([[0, 2, 3], [4, 0, 6]])
- B = lil_matrix([[0, 1, 0], [0, 2, 3]])
- data = {'add': (B, A + B),
- 'sub': (B, A - B),
- 'mul': (3, A * 3)}
- for op, (other, expected) in data.items():
- result = A.copy()
- getattr(result, '__i%s__' % op)(other)
- assert_array_equal(result.toarray(), expected.toarray())
- # Ticket 1604.
- A = lil_matrix((1, 3), dtype=np.dtype('float64'))
- B = array([0.1, 0.1, 0.1])
- A[0, :] += B
- assert_array_equal(A[0, :].toarray().squeeze(), B)
- def test_lil_iteration(self):
- row_data = [[1, 2, 3], [4, 5, 6]]
- B = lil_matrix(array(row_data))
- for r, row in enumerate(B):
- assert_array_equal(row.toarray(), array(row_data[r], ndmin=2))
- def test_lil_from_csr(self):
- # Tests whether a lil_matrix can be constructed from a
- # csr_matrix.
- B = lil_matrix((10, 10))
- B[0, 3] = 10
- B[5, 6] = 20
- B[8, 3] = 30
- B[3, 8] = 40
- B[8, 9] = 50
- C = B.tocsr()
- D = lil_matrix(C)
- assert_array_equal(C.A, D.A)
- def test_fancy_indexing_lil(self):
- M = asmatrix(arange(25).reshape(5, 5))
- A = lil_matrix(M)
- assert_equal(A[array([1, 2, 3]), 2:3].toarray(),
- M[array([1, 2, 3]), 2:3])
- def test_point_wise_multiply(self):
- l = lil_matrix((4, 3))
- l[0, 0] = 1
- l[1, 1] = 2
- l[2, 2] = 3
- l[3, 1] = 4
- m = lil_matrix((4, 3))
- m[0, 0] = 1
- m[0, 1] = 2
- m[2, 2] = 3
- m[3, 1] = 4
- m[3, 2] = 4
- assert_array_equal(l.multiply(m).toarray(),
- m.multiply(l).toarray())
- assert_array_equal(l.multiply(m).toarray(),
- [[1, 0, 0],
- [0, 0, 0],
- [0, 0, 9],
- [0, 16, 0]])
- def test_lil_multiply_removal(self):
- # Ticket #1427.
- a = lil_matrix(np.ones((3, 3)))
- a *= 2.
- a[0, :] = 0
- TestLIL.init_class()
- class TestCOO(sparse_test_class(getset=False,
- slicing=False, slicing_assign=False,
- fancy_indexing=False, fancy_assign=False)):
- spmatrix = coo_matrix
- math_dtypes = [np.int_, np.float_, np.complex_]
- def test_constructor1(self):
- # unsorted triplet format
- row = array([2, 3, 1, 3, 0, 1, 3, 0, 2, 1, 2])
- col = array([0, 1, 0, 0, 1, 1, 2, 2, 2, 2, 1])
- data = array([6., 10., 3., 9., 1., 4., 11., 2., 8., 5., 7.])
- coo = coo_matrix((data,(row,col)),(4,3))
- assert_array_equal(arange(12).reshape(4, 3), coo.toarray())
- # using Python lists and a specified dtype
- coo = coo_matrix(([2**63 + 1, 1], ([0, 1], [0, 1])), dtype=np.uint64)
- dense = array([[2**63 + 1, 0], [0, 1]], dtype=np.uint64)
- assert_array_equal(dense, coo.toarray())
- def test_constructor2(self):
- # unsorted triplet format with duplicates (which are summed)
- row = array([0,1,2,2,2,2,0,0,2,2])
- col = array([0,2,0,2,1,1,1,0,0,2])
- data = array([2,9,-4,5,7,0,-1,2,1,-5])
- coo = coo_matrix((data,(row,col)),(3,3))
- mat = array([[4, -1, 0], [0, 0, 9], [-3, 7, 0]])
- assert_array_equal(mat, coo.toarray())
- def test_constructor3(self):
- # empty matrix
- coo = coo_matrix((4,3))
- assert_array_equal(coo.shape,(4,3))
- assert_array_equal(coo.row,[])
- assert_array_equal(coo.col,[])
- assert_array_equal(coo.data,[])
- assert_array_equal(coo.toarray(), zeros((4, 3)))
- def test_constructor4(self):
- # from dense matrix
- mat = array([[0,1,0,0],
- [7,0,3,0],
- [0,4,0,0]])
- coo = coo_matrix(mat)
- assert_array_equal(coo.toarray(), mat)
- # upgrade rank 1 arrays to row matrix
- mat = array([0,1,0,0])
- coo = coo_matrix(mat)
- assert_array_equal(coo.toarray(), mat.reshape(1, -1))
- # error if second arg interpreted as shape (gh-9919)
- with pytest.raises(TypeError, match=r'object cannot be interpreted'):
- coo_matrix([0, 11, 22, 33], ([0, 1, 2, 3], [0, 0, 0, 0]))
- # error if explicit shape arg doesn't match the dense matrix
- with pytest.raises(ValueError, match=r'inconsistent shapes'):
- coo_matrix([0, 11, 22, 33], shape=(4, 4))
- def test_constructor_data_ij_dtypeNone(self):
- data = [1]
- coo = coo_matrix((data, ([0], [0])), dtype=None)
- assert coo.dtype == np.array(data).dtype
- @pytest.mark.xfail(run=False, reason='COO does not have a __getitem__')
- def test_iterator(self):
- pass
- def test_todia_all_zeros(self):
- zeros = [[0, 0]]
- dia = coo_matrix(zeros).todia()
- assert_array_equal(dia.A, zeros)
- def test_sum_duplicates(self):
- coo = coo_matrix((4,3))
- coo.sum_duplicates()
- coo = coo_matrix(([1,2], ([1,0], [1,0])))
- coo.sum_duplicates()
- assert_array_equal(coo.A, [[2,0],[0,1]])
- coo = coo_matrix(([1,2], ([1,1], [1,1])))
- coo.sum_duplicates()
- assert_array_equal(coo.A, [[0,0],[0,3]])
- assert_array_equal(coo.row, [1])
- assert_array_equal(coo.col, [1])
- assert_array_equal(coo.data, [3])
- def test_todok_duplicates(self):
- coo = coo_matrix(([1,1,1,1], ([0,2,2,0], [0,1,1,0])))
- dok = coo.todok()
- assert_array_equal(dok.A, coo.A)
- def test_eliminate_zeros(self):
- data = array([1, 0, 0, 0, 2, 0, 3, 0])
- row = array([0, 0, 0, 1, 1, 1, 1, 1])
- col = array([1, 2, 3, 4, 5, 6, 7, 8])
- asp = coo_matrix((data, (row, col)), shape=(2,10))
- bsp = asp.copy()
- asp.eliminate_zeros()
- assert_((asp.data != 0).all())
- assert_array_equal(asp.A, bsp.A)
- def test_reshape_copy(self):
- arr = [[0, 10, 0, 0], [0, 0, 0, 0], [0, 20, 30, 40]]
- new_shape = (2, 6)
- x = coo_matrix(arr)
- y = x.reshape(new_shape)
- assert_(y.data is x.data)
- y = x.reshape(new_shape, copy=False)
- assert_(y.data is x.data)
- y = x.reshape(new_shape, copy=True)
- assert_(not np.may_share_memory(y.data, x.data))
- def test_large_dimensions_reshape(self):
- # Test that reshape is immune to integer overflow when number of elements
- # exceeds 2^31-1
- mat1 = coo_matrix(([1], ([3000000], [1000])), (3000001, 1001))
- mat2 = coo_matrix(([1], ([1000], [3000000])), (1001, 3000001))
- # assert_array_equal is slow for big matrices because it expects dense
- # Using __ne__ and nnz instead
- assert_((mat1.reshape((1001, 3000001), order='C') != mat2).nnz == 0)
- assert_((mat2.reshape((3000001, 1001), order='F') != mat1).nnz == 0)
- TestCOO.init_class()
- class TestDIA(sparse_test_class(getset=False, slicing=False, slicing_assign=False,
- fancy_indexing=False, fancy_assign=False,
- minmax=False, nnz_axis=False)):
- spmatrix = dia_matrix
- math_dtypes = [np.int_, np.float_, np.complex_]
- def test_constructor1(self):
- D = array([[1, 0, 3, 0],
- [1, 2, 0, 4],
- [0, 2, 3, 0],
- [0, 0, 3, 4]])
- data = np.array([[1,2,3,4]]).repeat(3,axis=0)
- offsets = np.array([0,-1,2])
- assert_equal(dia_matrix((data, offsets), shape=(4, 4)).toarray(), D)
- @pytest.mark.xfail(run=False, reason='DIA does not have a __getitem__')
- def test_iterator(self):
- pass
- @with_64bit_maxval_limit(3)
- def test_setdiag_dtype(self):
- m = dia_matrix(np.eye(3))
- assert_equal(m.offsets.dtype, np.int32)
- m.setdiag((3,), k=2)
- assert_equal(m.offsets.dtype, np.int32)
- m = dia_matrix(np.eye(4))
- assert_equal(m.offsets.dtype, np.int64)
- m.setdiag((3,), k=3)
- assert_equal(m.offsets.dtype, np.int64)
- @pytest.mark.skip(reason='DIA stores extra zeros')
- def test_getnnz_axis(self):
- pass
- def test_convert_gh14555(self):
- # regression test for gh-14555
- m = dia_matrix(([[1, 1, 0]], [-1]), shape=(4, 2))
- expected = m.toarray()
- assert_array_equal(m.tocsc().toarray(), expected)
- assert_array_equal(m.tocsr().toarray(), expected)
- TestDIA.init_class()
- class TestBSR(sparse_test_class(getset=False,
- slicing=False, slicing_assign=False,
- fancy_indexing=False, fancy_assign=False,
- nnz_axis=False)):
- spmatrix = bsr_matrix
- math_dtypes = [np.int_, np.float_, np.complex_]
- def test_constructor1(self):
- # check native BSR format constructor
- indptr = array([0,2,2,4])
- indices = array([0,2,2,3])
- data = zeros((4,2,3))
- data[0] = array([[0, 1, 2],
- [3, 0, 5]])
- data[1] = array([[0, 2, 4],
- [6, 0, 10]])
- data[2] = array([[0, 4, 8],
- [12, 0, 20]])
- data[3] = array([[0, 5, 10],
- [15, 0, 25]])
- A = kron([[1,0,2,0],[0,0,0,0],[0,0,4,5]], [[0,1,2],[3,0,5]])
- Asp = bsr_matrix((data,indices,indptr),shape=(6,12))
- assert_equal(Asp.toarray(), A)
- # infer shape from arrays
- Asp = bsr_matrix((data,indices,indptr))
- assert_equal(Asp.toarray(), A)
- def test_constructor2(self):
- # construct from dense
- # test zero mats
- for shape in [(1,1), (5,1), (1,10), (10,4), (3,7), (2,1)]:
- A = zeros(shape)
- assert_equal(bsr_matrix(A).toarray(), A)
- A = zeros((4,6))
- assert_equal(bsr_matrix(A, blocksize=(2, 2)).toarray(), A)
- assert_equal(bsr_matrix(A, blocksize=(2, 3)).toarray(), A)
- A = kron([[1,0,2,0],[0,0,0,0],[0,0,4,5]], [[0,1,2],[3,0,5]])
- assert_equal(bsr_matrix(A).toarray(), A)
- assert_equal(bsr_matrix(A, shape=(6, 12)).toarray(), A)
- assert_equal(bsr_matrix(A, blocksize=(1, 1)).toarray(), A)
- assert_equal(bsr_matrix(A, blocksize=(2, 3)).toarray(), A)
- assert_equal(bsr_matrix(A, blocksize=(2, 6)).toarray(), A)
- assert_equal(bsr_matrix(A, blocksize=(2, 12)).toarray(), A)
- assert_equal(bsr_matrix(A, blocksize=(3, 12)).toarray(), A)
- assert_equal(bsr_matrix(A, blocksize=(6, 12)).toarray(), A)
- A = kron([[1,0,2,0],[0,1,0,0],[0,0,0,0]], [[0,1,2],[3,0,5]])
- assert_equal(bsr_matrix(A, blocksize=(2, 3)).toarray(), A)
- def test_constructor3(self):
- # construct from coo-like (data,(row,col)) format
- arg = ([1,2,3], ([0,1,1], [0,0,1]))
- A = array([[1,0],[2,3]])
- assert_equal(bsr_matrix(arg, blocksize=(2, 2)).toarray(), A)
- def test_constructor4(self):
- # regression test for gh-6292: bsr_matrix((data, indices, indptr)) was
- # trying to compare an int to a None
- n = 8
- data = np.ones((n, n, 1), dtype=np.int8)
- indptr = np.array([0, n], dtype=np.int32)
- indices = np.arange(n, dtype=np.int32)
- bsr_matrix((data, indices, indptr), blocksize=(n, 1), copy=False)
- def test_constructor5(self):
- # check for validations introduced in gh-13400
- n = 8
- data_1dim = np.ones(n)
- data = np.ones((n, n, n))
- indptr = np.array([0, n])
- indices = np.arange(n)
- with assert_raises(ValueError):
- # data ndim check
- bsr_matrix((data_1dim, indices, indptr))
- with assert_raises(ValueError):
- # invalid blocksize
- bsr_matrix((data, indices, indptr), blocksize=(1, 1, 1))
- with assert_raises(ValueError):
- # mismatching blocksize
- bsr_matrix((data, indices, indptr), blocksize=(1, 1))
- def test_default_dtype(self):
- # As a numpy array, `values` has shape (2, 2, 1).
- values = [[[1], [1]], [[1], [1]]]
- indptr = np.array([0, 2], dtype=np.int32)
- indices = np.array([0, 1], dtype=np.int32)
- b = bsr_matrix((values, indices, indptr), blocksize=(2, 1))
- assert b.dtype == np.array(values).dtype
- def test_bsr_tocsr(self):
- # check native conversion from BSR to CSR
- indptr = array([0, 2, 2, 4])
- indices = array([0, 2, 2, 3])
- data = zeros((4, 2, 3))
- data[0] = array([[0, 1, 2],
- [3, 0, 5]])
- data[1] = array([[0, 2, 4],
- [6, 0, 10]])
- data[2] = array([[0, 4, 8],
- [12, 0, 20]])
- data[3] = array([[0, 5, 10],
- [15, 0, 25]])
- A = kron([[1, 0, 2, 0], [0, 0, 0, 0], [0, 0, 4, 5]],
- [[0, 1, 2], [3, 0, 5]])
- Absr = bsr_matrix((data, indices, indptr), shape=(6, 12))
- Acsr = Absr.tocsr()
- Acsr_via_coo = Absr.tocoo().tocsr()
- assert_equal(Acsr.toarray(), A)
- assert_equal(Acsr.toarray(), Acsr_via_coo.toarray())
- def test_eliminate_zeros(self):
- data = kron([1, 0, 0, 0, 2, 0, 3, 0], [[1,1],[1,1]]).T
- data = data.reshape(-1,2,2)
- indices = array([1, 2, 3, 4, 5, 6, 7, 8])
- indptr = array([0, 3, 8])
- asp = bsr_matrix((data, indices, indptr), shape=(4,20))
- bsp = asp.copy()
- asp.eliminate_zeros()
- assert_array_equal(asp.nnz, 3*4)
- assert_array_equal(asp.toarray(), bsp.toarray())
- # github issue #9687
- def test_eliminate_zeros_all_zero(self):
- np.random.seed(0)
- m = bsr_matrix(np.random.random((12, 12)), blocksize=(2, 3))
- # eliminate some blocks, but not all
- m.data[m.data <= 0.9] = 0
- m.eliminate_zeros()
- assert_equal(m.nnz, 66)
- assert_array_equal(m.data.shape, (11, 2, 3))
- # eliminate all remaining blocks
- m.data[m.data <= 1.0] = 0
- m.eliminate_zeros()
- assert_equal(m.nnz, 0)
- assert_array_equal(m.data.shape, (0, 2, 3))
- assert_array_equal(m.toarray(), np.zeros((12, 12)))
- # test fast path
- m.eliminate_zeros()
- assert_equal(m.nnz, 0)
- assert_array_equal(m.data.shape, (0, 2, 3))
- assert_array_equal(m.toarray(), np.zeros((12, 12)))
- def test_bsr_matvec(self):
- A = bsr_matrix(arange(2*3*4*5).reshape(2*4,3*5), blocksize=(4,5))
- x = arange(A.shape[1]).reshape(-1,1)
- assert_equal(A*x, A.toarray() @ x)
- def test_bsr_matvecs(self):
- A = bsr_matrix(arange(2*3*4*5).reshape(2*4,3*5), blocksize=(4,5))
- x = arange(A.shape[1]*6).reshape(-1,6)
- assert_equal(A*x, A.toarray() @ x)
- @pytest.mark.xfail(run=False, reason='BSR does not have a __getitem__')
- def test_iterator(self):
- pass
- @pytest.mark.xfail(run=False, reason='BSR does not have a __setitem__')
- def test_setdiag(self):
- pass
- def test_resize_blocked(self):
- # test resize() with non-(1,1) blocksize
- D = np.array([[1, 0, 3, 4],
- [2, 0, 0, 0],
- [3, 0, 0, 0]])
- S = self.spmatrix(D, blocksize=(1, 2))
- assert_(S.resize((3, 2)) is None)
- assert_array_equal(S.A, [[1, 0],
- [2, 0],
- [3, 0]])
- S.resize((2, 2))
- assert_array_equal(S.A, [[1, 0],
- [2, 0]])
- S.resize((3, 2))
- assert_array_equal(S.A, [[1, 0],
- [2, 0],
- [0, 0]])
- S.resize((3, 4))
- assert_array_equal(S.A, [[1, 0, 0, 0],
- [2, 0, 0, 0],
- [0, 0, 0, 0]])
- assert_raises(ValueError, S.resize, (2, 3))
- @pytest.mark.xfail(run=False, reason='BSR does not have a __setitem__')
- def test_setdiag_comprehensive(self):
- pass
- @pytest.mark.skipif(IS_COLAB, reason="exceeds memory limit")
- def test_scalar_idx_dtype(self):
- # Check that index dtype takes into account all parameters
- # passed to sparsetools, including the scalar ones
- indptr = np.zeros(2, dtype=np.int32)
- indices = np.zeros(0, dtype=np.int32)
- vals = np.zeros((0, 1, 1))
- a = bsr_matrix((vals, indices, indptr), shape=(1, 2**31-1))
- b = bsr_matrix((vals, indices, indptr), shape=(1, 2**31))
- c = bsr_matrix((1, 2**31-1))
- d = bsr_matrix((1, 2**31))
- assert_equal(a.indptr.dtype, np.int32)
- assert_equal(b.indptr.dtype, np.int64)
- assert_equal(c.indptr.dtype, np.int32)
- assert_equal(d.indptr.dtype, np.int64)
- try:
- vals2 = np.zeros((0, 1, 2**31-1))
- vals3 = np.zeros((0, 1, 2**31))
- e = bsr_matrix((vals2, indices, indptr), shape=(1, 2**31-1))
- f = bsr_matrix((vals3, indices, indptr), shape=(1, 2**31))
- assert_equal(e.indptr.dtype, np.int32)
- assert_equal(f.indptr.dtype, np.int64)
- except (MemoryError, ValueError):
- # May fail on 32-bit Python
- e = 0
- f = 0
- # These shouldn't fail
- for x in [a, b, c, d, e, f]:
- x + x
- TestBSR.init_class()
- #------------------------------------------------------------------------------
- # Tests for non-canonical representations (with duplicates, unsorted indices)
- #------------------------------------------------------------------------------
- def _same_sum_duplicate(data, *inds, **kwargs):
- """Duplicates entries to produce the same matrix"""
- indptr = kwargs.pop('indptr', None)
- if np.issubdtype(data.dtype, np.bool_) or \
- np.issubdtype(data.dtype, np.unsignedinteger):
- if indptr is None:
- return (data,) + inds
- else:
- return (data,) + inds + (indptr,)
- zeros_pos = (data == 0).nonzero()
- # duplicate data
- data = data.repeat(2, axis=0)
- data[::2] -= 1
- data[1::2] = 1
- # don't spoil all explicit zeros
- if zeros_pos[0].size > 0:
- pos = tuple(p[0] for p in zeros_pos)
- pos1 = (2*pos[0],) + pos[1:]
- pos2 = (2*pos[0]+1,) + pos[1:]
- data[pos1] = 0
- data[pos2] = 0
- inds = tuple(indices.repeat(2) for indices in inds)
- if indptr is None:
- return (data,) + inds
- else:
- return (data,) + inds + (indptr * 2,)
- class _NonCanonicalMixin:
- def spmatrix(self, D, sorted_indices=False, **kwargs):
- """Replace D with a non-canonical equivalent: containing
- duplicate elements and explicit zeros"""
- construct = super().spmatrix
- M = construct(D, **kwargs)
- zero_pos = (M.A == 0).nonzero()
- has_zeros = (zero_pos[0].size > 0)
- if has_zeros:
- k = zero_pos[0].size//2
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- M = self._insert_explicit_zero(M, zero_pos[0][k], zero_pos[1][k])
- arg1 = self._arg1_for_noncanonical(M, sorted_indices)
- if 'shape' not in kwargs:
- kwargs['shape'] = M.shape
- NC = construct(arg1, **kwargs)
- # check that result is valid
- if NC.dtype in [np.float32, np.complex64]:
- # For single-precision floats, the differences between M and NC
- # that are introduced by the extra operations involved in the
- # construction of NC necessitate a more lenient tolerance level
- # than the default.
- rtol = 1e-05
- else:
- rtol = 1e-07
- assert_allclose(NC.A, M.A, rtol=rtol)
- # check that at least one explicit zero
- if has_zeros:
- assert_((NC.data == 0).any())
- # TODO check that NC has duplicates (which are not explicit zeros)
- return NC
- @pytest.mark.skip(reason='bool(matrix) counts explicit zeros')
- def test_bool(self):
- pass
- @pytest.mark.skip(reason='getnnz-axis counts explicit zeros')
- def test_getnnz_axis(self):
- pass
- @pytest.mark.skip(reason='nnz counts explicit zeros')
- def test_empty(self):
- pass
- class _NonCanonicalCompressedMixin(_NonCanonicalMixin):
- def _arg1_for_noncanonical(self, M, sorted_indices=False):
- """Return non-canonical constructor arg1 equivalent to M"""
- data, indices, indptr = _same_sum_duplicate(M.data, M.indices,
- indptr=M.indptr)
- if not sorted_indices:
- for start, stop in zip(indptr, indptr[1:]):
- indices[start:stop] = indices[start:stop][::-1].copy()
- data[start:stop] = data[start:stop][::-1].copy()
- return data, indices, indptr
- def _insert_explicit_zero(self, M, i, j):
- M[i,j] = 0
- return M
- class _NonCanonicalCSMixin(_NonCanonicalCompressedMixin):
- def test_getelement(self):
- def check(dtype, sorted_indices):
- D = array([[1,0,0],
- [4,3,0],
- [0,2,0],
- [0,0,0]], dtype=dtype)
- A = self.spmatrix(D, sorted_indices=sorted_indices)
- M,N = D.shape
- for i in range(-M, M):
- for j in range(-N, N):
- assert_equal(A[i,j], D[i,j])
- for ij in [(0,3),(-1,3),(4,0),(4,3),(4,-1), (1, 2, 3)]:
- assert_raises((IndexError, TypeError), A.__getitem__, ij)
- for dtype in supported_dtypes:
- for sorted_indices in [False, True]:
- check(np.dtype(dtype), sorted_indices)
- def test_setitem_sparse(self):
- D = np.eye(3)
- A = self.spmatrix(D)
- B = self.spmatrix([[1,2,3]])
- D[1,:] = B.toarray()
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- A[1,:] = B
- assert_array_equal(A.toarray(), D)
- D[:,2] = B.toarray().ravel()
- with suppress_warnings() as sup:
- sup.filter(SparseEfficiencyWarning,
- "Changing the sparsity structure of a cs[cr]_matrix is expensive")
- A[:,2] = B.T
- assert_array_equal(A.toarray(), D)
- @pytest.mark.xfail(run=False, reason='inverse broken with non-canonical matrix')
- def test_inv(self):
- pass
- @pytest.mark.xfail(run=False, reason='solve broken with non-canonical matrix')
- def test_solve(self):
- pass
- class TestCSRNonCanonical(_NonCanonicalCSMixin, TestCSR):
- pass
- class TestCSCNonCanonical(_NonCanonicalCSMixin, TestCSC):
- pass
- class TestBSRNonCanonical(_NonCanonicalCompressedMixin, TestBSR):
- def _insert_explicit_zero(self, M, i, j):
- x = M.tocsr()
- x[i,j] = 0
- return x.tobsr(blocksize=M.blocksize)
- @pytest.mark.xfail(run=False, reason='diagonal broken with non-canonical BSR')
- def test_diagonal(self):
- pass
- @pytest.mark.xfail(run=False, reason='expm broken with non-canonical BSR')
- def test_expm(self):
- pass
- class TestCOONonCanonical(_NonCanonicalMixin, TestCOO):
- def _arg1_for_noncanonical(self, M, sorted_indices=None):
- """Return non-canonical constructor arg1 equivalent to M"""
- data, row, col = _same_sum_duplicate(M.data, M.row, M.col)
- return data, (row, col)
- def _insert_explicit_zero(self, M, i, j):
- M.data = np.r_[M.data.dtype.type(0), M.data]
- M.row = np.r_[M.row.dtype.type(i), M.row]
- M.col = np.r_[M.col.dtype.type(j), M.col]
- return M
- def test_setdiag_noncanonical(self):
- m = self.spmatrix(np.eye(3))
- m.sum_duplicates()
- m.setdiag([3, 2], k=1)
- m.sum_duplicates()
- assert_(np.all(np.diff(m.col) >= 0))
- def cases_64bit():
- TEST_CLASSES = [TestBSR, TestCOO, TestCSC, TestCSR, TestDIA,
- # lil/dok->other conversion operations have get_index_dtype
- TestDOK, TestLIL
- ]
- # The following features are missing, so skip the tests:
- SKIP_TESTS = {
- 'test_expm': 'expm for 64-bit indices not available',
- 'test_inv': 'linsolve for 64-bit indices not available',
- 'test_solve': 'linsolve for 64-bit indices not available',
- 'test_scalar_idx_dtype': 'test implemented in base class',
- 'test_large_dimensions_reshape': 'test actually requires 64-bit to work',
- 'test_constructor_smallcol': 'test verifies int32 indexes',
- 'test_constructor_largecol': 'test verifies int64 indexes',
- }
- for cls in TEST_CLASSES:
- for method_name in sorted(dir(cls)):
- method = getattr(cls, method_name)
- if (method_name.startswith('test_') and
- not getattr(method, 'slow', False)):
- marks = []
- msg = SKIP_TESTS.get(method_name)
- if bool(msg):
- marks += [pytest.mark.skip(reason=msg)]
- if _pep440.parse(pytest.__version__) >= _pep440.Version("3.6.0"):
- markers = getattr(method, 'pytestmark', [])
- for mark in markers:
- if mark.name in ('skipif', 'skip', 'xfail', 'xslow'):
- marks.append(mark)
- else:
- for mname in ['skipif', 'skip', 'xfail', 'xslow']:
- if hasattr(method, mname):
- marks += [getattr(method, mname)]
- yield pytest.param(cls, method_name, marks=marks)
- class Test64Bit:
- MAT_CLASSES = [bsr_matrix, coo_matrix, csc_matrix, csr_matrix, dia_matrix]
- def _create_some_matrix(self, mat_cls, m, n):
- return mat_cls(np.random.rand(m, n))
- def _compare_index_dtype(self, m, dtype):
- dtype = np.dtype(dtype)
- if isinstance(m, (csc_matrix, csr_matrix, bsr_matrix)):
- return (m.indices.dtype == dtype) and (m.indptr.dtype == dtype)
- elif isinstance(m, coo_matrix):
- return (m.row.dtype == dtype) and (m.col.dtype == dtype)
- elif isinstance(m, dia_matrix):
- return (m.offsets.dtype == dtype)
- else:
- raise ValueError("matrix %r has no integer indices" % (m,))
- def test_decorator_maxval_limit(self):
- # Test that the with_64bit_maxval_limit decorator works
- @with_64bit_maxval_limit(maxval_limit=10)
- def check(mat_cls):
- m = mat_cls(np.random.rand(10, 1))
- assert_(self._compare_index_dtype(m, np.int32))
- m = mat_cls(np.random.rand(11, 1))
- assert_(self._compare_index_dtype(m, np.int64))
- for mat_cls in self.MAT_CLASSES:
- check(mat_cls)
- def test_decorator_maxval_random(self):
- # Test that the with_64bit_maxval_limit decorator works (2)
- @with_64bit_maxval_limit(random=True)
- def check(mat_cls):
- seen_32 = False
- seen_64 = False
- for k in range(100):
- m = self._create_some_matrix(mat_cls, 9, 9)
- seen_32 = seen_32 or self._compare_index_dtype(m, np.int32)
- seen_64 = seen_64 or self._compare_index_dtype(m, np.int64)
- if seen_32 and seen_64:
- break
- else:
- raise AssertionError("both 32 and 64 bit indices not seen")
- for mat_cls in self.MAT_CLASSES:
- check(mat_cls)
- def _check_resiliency(self, cls, method_name, **kw):
- # Resiliency test, to check that sparse matrices deal reasonably
- # with varying index data types.
- @with_64bit_maxval_limit(**kw)
- def check(cls, method_name):
- instance = cls()
- if hasattr(instance, 'setup_method'):
- instance.setup_method()
- try:
- getattr(instance, method_name)()
- finally:
- if hasattr(instance, 'teardown_method'):
- instance.teardown_method()
- check(cls, method_name)
- @pytest.mark.parametrize('cls,method_name', cases_64bit())
- def test_resiliency_limit_10(self, cls, method_name):
- self._check_resiliency(cls, method_name, maxval_limit=10)
- @pytest.mark.parametrize('cls,method_name', cases_64bit())
- def test_resiliency_random(self, cls, method_name):
- # bsr_matrix.eliminate_zeros relies on csr_matrix constructor
- # not making copies of index arrays --- this is not
- # necessarily true when we pick the index data type randomly
- self._check_resiliency(cls, method_name, random=True)
- @pytest.mark.parametrize('cls,method_name', cases_64bit())
- def test_resiliency_all_32(self, cls, method_name):
- self._check_resiliency(cls, method_name, fixed_dtype=np.int32)
- @pytest.mark.parametrize('cls,method_name', cases_64bit())
- def test_resiliency_all_64(self, cls, method_name):
- self._check_resiliency(cls, method_name, fixed_dtype=np.int64)
- @pytest.mark.parametrize('cls,method_name', cases_64bit())
- def test_no_64(self, cls, method_name):
- self._check_resiliency(cls, method_name, assert_32bit=True)
- def test_downcast_intp(self):
- # Check that bincount and ufunc.reduceat intp downcasts are
- # dealt with. The point here is to trigger points in the code
- # that can fail on 32-bit systems when using 64-bit indices,
- # due to use of functions that only work with intp-size
- # indices.
- @with_64bit_maxval_limit(fixed_dtype=np.int64,
- downcast_maxval=1)
- def check_limited():
- # These involve indices larger than `downcast_maxval`
- a = csc_matrix([[1, 2], [3, 4], [5, 6]])
- assert_raises(AssertionError, a.getnnz, axis=1)
- assert_raises(AssertionError, a.sum, axis=0)
- a = csr_matrix([[1, 2, 3], [3, 4, 6]])
- assert_raises(AssertionError, a.getnnz, axis=0)
- a = coo_matrix([[1, 2, 3], [3, 4, 5]])
- assert_raises(AssertionError, a.getnnz, axis=0)
- @with_64bit_maxval_limit(fixed_dtype=np.int64)
- def check_unlimited():
- # These involve indices larger than `downcast_maxval`
- a = csc_matrix([[1, 2], [3, 4], [5, 6]])
- a.getnnz(axis=1)
- a.sum(axis=0)
- a = csr_matrix([[1, 2, 3], [3, 4, 6]])
- a.getnnz(axis=0)
- a = coo_matrix([[1, 2, 3], [3, 4, 5]])
- a.getnnz(axis=0)
- check_limited()
- check_unlimited()
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