674 lines
23 KiB
Python
674 lines
23 KiB
Python
|
from __future__ import division, print_function, absolute_import
|
||
|
|
||
|
from tempfile import mkdtemp, mktemp
|
||
|
import os
|
||
|
import shutil
|
||
|
|
||
|
import numpy as np
|
||
|
from numpy import array, transpose, pi
|
||
|
from numpy.testing import (assert_equal,
|
||
|
assert_array_equal, assert_array_almost_equal)
|
||
|
import pytest
|
||
|
from pytest import raises as assert_raises
|
||
|
|
||
|
import scipy.sparse
|
||
|
from scipy.io.mmio import mminfo, mmread, mmwrite
|
||
|
|
||
|
parametrize_args = [('integer', 'int'),
|
||
|
('unsigned-integer', 'uint')]
|
||
|
|
||
|
|
||
|
class TestMMIOArray(object):
|
||
|
def setup_method(self):
|
||
|
self.tmpdir = mkdtemp()
|
||
|
self.fn = os.path.join(self.tmpdir, 'testfile.mtx')
|
||
|
|
||
|
def teardown_method(self):
|
||
|
shutil.rmtree(self.tmpdir)
|
||
|
|
||
|
def check(self, a, info):
|
||
|
mmwrite(self.fn, a)
|
||
|
assert_equal(mminfo(self.fn), info)
|
||
|
b = mmread(self.fn)
|
||
|
assert_array_almost_equal(a, b)
|
||
|
|
||
|
def check_exact(self, a, info):
|
||
|
mmwrite(self.fn, a)
|
||
|
assert_equal(mminfo(self.fn), info)
|
||
|
b = mmread(self.fn)
|
||
|
assert_equal(a, b)
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_integer(self, typeval, dtype):
|
||
|
self.check_exact(array([[1, 2], [3, 4]], dtype=dtype),
|
||
|
(2, 2, 4, 'array', typeval, 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_32bit_integer(self, typeval, dtype):
|
||
|
a = array([[2**31-1, 2**31-2], [2**31-3, 2**31-4]], dtype=dtype)
|
||
|
self.check_exact(a, (2, 2, 4, 'array', typeval, 'general'))
|
||
|
|
||
|
def test_64bit_integer(self):
|
||
|
a = array([[2**31, 2**32], [2**63-2, 2**63-1]], dtype=np.int64)
|
||
|
if (np.intp(0).itemsize < 8):
|
||
|
assert_raises(OverflowError, mmwrite, self.fn, a)
|
||
|
else:
|
||
|
self.check_exact(a, (2, 2, 4, 'array', 'integer', 'general'))
|
||
|
|
||
|
def test_64bit_unsigned_integer(self):
|
||
|
a = array([[2**31, 2**32], [2**64-2, 2**64-1]], dtype=np.uint64)
|
||
|
self.check_exact(a, (2, 2, 4, 'array', 'unsigned-integer', 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_upper_triangle_integer(self, typeval, dtype):
|
||
|
self.check_exact(array([[0, 1], [0, 0]], dtype=dtype),
|
||
|
(2, 2, 4, 'array', typeval, 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_lower_triangle_integer(self, typeval, dtype):
|
||
|
self.check_exact(array([[0, 0], [1, 0]], dtype=dtype),
|
||
|
(2, 2, 4, 'array', typeval, 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_rectangular_integer(self, typeval, dtype):
|
||
|
self.check_exact(array([[1, 2, 3], [4, 5, 6]], dtype=dtype),
|
||
|
(2, 3, 6, 'array', typeval, 'general'))
|
||
|
|
||
|
def test_simple_rectangular_float(self):
|
||
|
self.check([[1, 2], [3.5, 4], [5, 6]],
|
||
|
(3, 2, 6, 'array', 'real', 'general'))
|
||
|
|
||
|
def test_simple_float(self):
|
||
|
self.check([[1, 2], [3, 4.0]],
|
||
|
(2, 2, 4, 'array', 'real', 'general'))
|
||
|
|
||
|
def test_simple_complex(self):
|
||
|
self.check([[1, 2], [3, 4j]],
|
||
|
(2, 2, 4, 'array', 'complex', 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_symmetric_integer(self, typeval, dtype):
|
||
|
self.check_exact(array([[1, 2], [2, 4]], dtype=dtype),
|
||
|
(2, 2, 4, 'array', typeval, 'symmetric'))
|
||
|
|
||
|
def test_simple_skew_symmetric_integer(self):
|
||
|
self.check_exact([[0, 2], [-2, 0]],
|
||
|
(2, 2, 4, 'array', 'integer', 'skew-symmetric'))
|
||
|
|
||
|
def test_simple_skew_symmetric_float(self):
|
||
|
self.check(array([[0, 2], [-2.0, 0.0]], 'f'),
|
||
|
(2, 2, 4, 'array', 'real', 'skew-symmetric'))
|
||
|
|
||
|
def test_simple_hermitian_complex(self):
|
||
|
self.check([[1, 2+3j], [2-3j, 4]],
|
||
|
(2, 2, 4, 'array', 'complex', 'hermitian'))
|
||
|
|
||
|
def test_random_symmetric_float(self):
|
||
|
sz = (20, 20)
|
||
|
a = np.random.random(sz)
|
||
|
a = a + transpose(a)
|
||
|
self.check(a, (20, 20, 400, 'array', 'real', 'symmetric'))
|
||
|
|
||
|
def test_random_rectangular_float(self):
|
||
|
sz = (20, 15)
|
||
|
a = np.random.random(sz)
|
||
|
self.check(a, (20, 15, 300, 'array', 'real', 'general'))
|
||
|
|
||
|
|
||
|
class TestMMIOSparseCSR(TestMMIOArray):
|
||
|
def setup_method(self):
|
||
|
self.tmpdir = mkdtemp()
|
||
|
self.fn = os.path.join(self.tmpdir, 'testfile.mtx')
|
||
|
|
||
|
def teardown_method(self):
|
||
|
shutil.rmtree(self.tmpdir)
|
||
|
|
||
|
def check(self, a, info):
|
||
|
mmwrite(self.fn, a)
|
||
|
assert_equal(mminfo(self.fn), info)
|
||
|
b = mmread(self.fn)
|
||
|
assert_array_almost_equal(a.todense(), b.todense())
|
||
|
|
||
|
def check_exact(self, a, info):
|
||
|
mmwrite(self.fn, a)
|
||
|
assert_equal(mminfo(self.fn), info)
|
||
|
b = mmread(self.fn)
|
||
|
assert_equal(a.todense(), b.todense())
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_integer(self, typeval, dtype):
|
||
|
self.check_exact(scipy.sparse.csr_matrix([[1, 2], [3, 4]], dtype=dtype),
|
||
|
(2, 2, 4, 'coordinate', typeval, 'general'))
|
||
|
|
||
|
def test_32bit_integer(self):
|
||
|
a = scipy.sparse.csr_matrix(array([[2**31-1, -2**31+2],
|
||
|
[2**31-3, 2**31-4]],
|
||
|
dtype=np.int32))
|
||
|
self.check_exact(a, (2, 2, 4, 'coordinate', 'integer', 'general'))
|
||
|
|
||
|
def test_64bit_integer(self):
|
||
|
a = scipy.sparse.csr_matrix(array([[2**32+1, 2**32+1],
|
||
|
[-2**63+2, 2**63-2]],
|
||
|
dtype=np.int64))
|
||
|
if (np.intp(0).itemsize < 8):
|
||
|
assert_raises(OverflowError, mmwrite, self.fn, a)
|
||
|
else:
|
||
|
self.check_exact(a, (2, 2, 4, 'coordinate', 'integer', 'general'))
|
||
|
|
||
|
def test_32bit_unsigned_integer(self):
|
||
|
a = scipy.sparse.csr_matrix(array([[2**31-1, 2**31-2],
|
||
|
[2**31-3, 2**31-4]],
|
||
|
dtype=np.uint32))
|
||
|
self.check_exact(a, (2, 2, 4, 'coordinate', 'unsigned-integer', 'general'))
|
||
|
|
||
|
def test_64bit_unsigned_integer(self):
|
||
|
a = scipy.sparse.csr_matrix(array([[2**32+1, 2**32+1],
|
||
|
[2**64-2, 2**64-1]],
|
||
|
dtype=np.uint64))
|
||
|
self.check_exact(a, (2, 2, 4, 'coordinate', 'unsigned-integer', 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_upper_triangle_integer(self, typeval, dtype):
|
||
|
self.check_exact(scipy.sparse.csr_matrix([[0, 1], [0, 0]], dtype=dtype),
|
||
|
(2, 2, 1, 'coordinate', typeval, 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_lower_triangle_integer(self, typeval, dtype):
|
||
|
self.check_exact(scipy.sparse.csr_matrix([[0, 0], [1, 0]], dtype=dtype),
|
||
|
(2, 2, 1, 'coordinate', typeval, 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_rectangular_integer(self, typeval, dtype):
|
||
|
self.check_exact(scipy.sparse.csr_matrix([[1, 2, 3], [4, 5, 6]], dtype=dtype),
|
||
|
(2, 3, 6, 'coordinate', typeval, 'general'))
|
||
|
|
||
|
def test_simple_rectangular_float(self):
|
||
|
self.check(scipy.sparse.csr_matrix([[1, 2], [3.5, 4], [5, 6]]),
|
||
|
(3, 2, 6, 'coordinate', 'real', 'general'))
|
||
|
|
||
|
def test_simple_float(self):
|
||
|
self.check(scipy.sparse.csr_matrix([[1, 2], [3, 4.0]]),
|
||
|
(2, 2, 4, 'coordinate', 'real', 'general'))
|
||
|
|
||
|
def test_simple_complex(self):
|
||
|
self.check(scipy.sparse.csr_matrix([[1, 2], [3, 4j]]),
|
||
|
(2, 2, 4, 'coordinate', 'complex', 'general'))
|
||
|
|
||
|
@pytest.mark.parametrize('typeval, dtype', parametrize_args)
|
||
|
def test_simple_symmetric_integer(self, typeval, dtype):
|
||
|
self.check_exact(scipy.sparse.csr_matrix([[1, 2], [2, 4]], dtype=dtype),
|
||
|
(2, 2, 3, 'coordinate', typeval, 'symmetric'))
|
||
|
|
||
|
def test_simple_skew_symmetric_integer(self):
|
||
|
self.check_exact(scipy.sparse.csr_matrix([[1, 2], [-2, 4]]),
|
||
|
(2, 2, 3, 'coordinate', 'integer', 'skew-symmetric'))
|
||
|
|
||
|
def test_simple_skew_symmetric_float(self):
|
||
|
self.check(scipy.sparse.csr_matrix(array([[1, 2], [-2.0, 4]], 'f')),
|
||
|
(2, 2, 3, 'coordinate', 'real', 'skew-symmetric'))
|
||
|
|
||
|
def test_simple_hermitian_complex(self):
|
||
|
self.check(scipy.sparse.csr_matrix([[1, 2+3j], [2-3j, 4]]),
|
||
|
(2, 2, 3, 'coordinate', 'complex', 'hermitian'))
|
||
|
|
||
|
def test_random_symmetric_float(self):
|
||
|
sz = (20, 20)
|
||
|
a = np.random.random(sz)
|
||
|
a = a + transpose(a)
|
||
|
a = scipy.sparse.csr_matrix(a)
|
||
|
self.check(a, (20, 20, 210, 'coordinate', 'real', 'symmetric'))
|
||
|
|
||
|
def test_random_rectangular_float(self):
|
||
|
sz = (20, 15)
|
||
|
a = np.random.random(sz)
|
||
|
a = scipy.sparse.csr_matrix(a)
|
||
|
self.check(a, (20, 15, 300, 'coordinate', 'real', 'general'))
|
||
|
|
||
|
def test_simple_pattern(self):
|
||
|
a = scipy.sparse.csr_matrix([[0, 1.5], [3.0, 2.5]])
|
||
|
p = np.zeros_like(a.todense())
|
||
|
p[a.todense() > 0] = 1
|
||
|
info = (2, 2, 3, 'coordinate', 'pattern', 'general')
|
||
|
mmwrite(self.fn, a, field='pattern')
|
||
|
assert_equal(mminfo(self.fn), info)
|
||
|
b = mmread(self.fn)
|
||
|
assert_array_almost_equal(p, b.todense())
|
||
|
|
||
|
|
||
|
_32bit_integer_dense_example = '''\
|
||
|
%%MatrixMarket matrix array integer general
|
||
|
2 2
|
||
|
2147483647
|
||
|
2147483646
|
||
|
2147483647
|
||
|
2147483646
|
||
|
'''
|
||
|
|
||
|
_32bit_integer_sparse_example = '''\
|
||
|
%%MatrixMarket matrix coordinate integer symmetric
|
||
|
2 2 2
|
||
|
1 1 2147483647
|
||
|
2 2 2147483646
|
||
|
'''
|
||
|
|
||
|
_64bit_integer_dense_example = '''\
|
||
|
%%MatrixMarket matrix array integer general
|
||
|
2 2
|
||
|
2147483648
|
||
|
-9223372036854775806
|
||
|
-2147483648
|
||
|
9223372036854775807
|
||
|
'''
|
||
|
|
||
|
_64bit_integer_sparse_general_example = '''\
|
||
|
%%MatrixMarket matrix coordinate integer general
|
||
|
2 2 3
|
||
|
1 1 2147483648
|
||
|
1 2 9223372036854775807
|
||
|
2 2 9223372036854775807
|
||
|
'''
|
||
|
|
||
|
_64bit_integer_sparse_symmetric_example = '''\
|
||
|
%%MatrixMarket matrix coordinate integer symmetric
|
||
|
2 2 3
|
||
|
1 1 2147483648
|
||
|
1 2 -9223372036854775807
|
||
|
2 2 9223372036854775807
|
||
|
'''
|
||
|
|
||
|
_64bit_integer_sparse_skew_example = '''\
|
||
|
%%MatrixMarket matrix coordinate integer skew-symmetric
|
||
|
2 2 3
|
||
|
1 1 2147483648
|
||
|
1 2 -9223372036854775807
|
||
|
2 2 9223372036854775807
|
||
|
'''
|
||
|
|
||
|
_over64bit_integer_dense_example = '''\
|
||
|
%%MatrixMarket matrix array integer general
|
||
|
2 2
|
||
|
2147483648
|
||
|
9223372036854775807
|
||
|
2147483648
|
||
|
9223372036854775808
|
||
|
'''
|
||
|
|
||
|
_over64bit_integer_sparse_example = '''\
|
||
|
%%MatrixMarket matrix coordinate integer symmetric
|
||
|
2 2 2
|
||
|
1 1 2147483648
|
||
|
2 2 19223372036854775808
|
||
|
'''
|
||
|
|
||
|
class TestMMIOReadLargeIntegers(object):
|
||
|
def setup_method(self):
|
||
|
self.tmpdir = mkdtemp()
|
||
|
self.fn = os.path.join(self.tmpdir, 'testfile.mtx')
|
||
|
|
||
|
def teardown_method(self):
|
||
|
shutil.rmtree(self.tmpdir)
|
||
|
|
||
|
def check_read(self, example, a, info, dense, over32, over64):
|
||
|
with open(self.fn, 'w') as f:
|
||
|
f.write(example)
|
||
|
assert_equal(mminfo(self.fn), info)
|
||
|
if (over32 and (np.intp(0).itemsize < 8)) or over64:
|
||
|
assert_raises(OverflowError, mmread, self.fn)
|
||
|
else:
|
||
|
b = mmread(self.fn)
|
||
|
if not dense:
|
||
|
b = b.todense()
|
||
|
assert_equal(a, b)
|
||
|
|
||
|
def test_read_32bit_integer_dense(self):
|
||
|
a = array([[2**31-1, 2**31-1],
|
||
|
[2**31-2, 2**31-2]], dtype=np.int64)
|
||
|
self.check_read(_32bit_integer_dense_example,
|
||
|
a,
|
||
|
(2, 2, 4, 'array', 'integer', 'general'),
|
||
|
dense=True,
|
||
|
over32=False,
|
||
|
over64=False)
|
||
|
|
||
|
def test_read_32bit_integer_sparse(self):
|
||
|
a = array([[2**31-1, 0],
|
||
|
[0, 2**31-2]], dtype=np.int64)
|
||
|
self.check_read(_32bit_integer_sparse_example,
|
||
|
a,
|
||
|
(2, 2, 2, 'coordinate', 'integer', 'symmetric'),
|
||
|
dense=False,
|
||
|
over32=False,
|
||
|
over64=False)
|
||
|
|
||
|
def test_read_64bit_integer_dense(self):
|
||
|
a = array([[2**31, -2**31],
|
||
|
[-2**63+2, 2**63-1]], dtype=np.int64)
|
||
|
self.check_read(_64bit_integer_dense_example,
|
||
|
a,
|
||
|
(2, 2, 4, 'array', 'integer', 'general'),
|
||
|
dense=True,
|
||
|
over32=True,
|
||
|
over64=False)
|
||
|
|
||
|
def test_read_64bit_integer_sparse_general(self):
|
||
|
a = array([[2**31, 2**63-1],
|
||
|
[0, 2**63-1]], dtype=np.int64)
|
||
|
self.check_read(_64bit_integer_sparse_general_example,
|
||
|
a,
|
||
|
(2, 2, 3, 'coordinate', 'integer', 'general'),
|
||
|
dense=False,
|
||
|
over32=True,
|
||
|
over64=False)
|
||
|
|
||
|
def test_read_64bit_integer_sparse_symmetric(self):
|
||
|
a = array([[2**31, -2**63+1],
|
||
|
[-2**63+1, 2**63-1]], dtype=np.int64)
|
||
|
self.check_read(_64bit_integer_sparse_symmetric_example,
|
||
|
a,
|
||
|
(2, 2, 3, 'coordinate', 'integer', 'symmetric'),
|
||
|
dense=False,
|
||
|
over32=True,
|
||
|
over64=False)
|
||
|
|
||
|
def test_read_64bit_integer_sparse_skew(self):
|
||
|
a = array([[2**31, -2**63+1],
|
||
|
[2**63-1, 2**63-1]], dtype=np.int64)
|
||
|
self.check_read(_64bit_integer_sparse_skew_example,
|
||
|
a,
|
||
|
(2, 2, 3, 'coordinate', 'integer', 'skew-symmetric'),
|
||
|
dense=False,
|
||
|
over32=True,
|
||
|
over64=False)
|
||
|
|
||
|
def test_read_over64bit_integer_dense(self):
|
||
|
self.check_read(_over64bit_integer_dense_example,
|
||
|
None,
|
||
|
(2, 2, 4, 'array', 'integer', 'general'),
|
||
|
dense=True,
|
||
|
over32=True,
|
||
|
over64=True)
|
||
|
|
||
|
def test_read_over64bit_integer_sparse(self):
|
||
|
self.check_read(_over64bit_integer_sparse_example,
|
||
|
None,
|
||
|
(2, 2, 2, 'coordinate', 'integer', 'symmetric'),
|
||
|
dense=False,
|
||
|
over32=True,
|
||
|
over64=True)
|
||
|
|
||
|
|
||
|
_general_example = '''\
|
||
|
%%MatrixMarket matrix coordinate real general
|
||
|
%=================================================================================
|
||
|
%
|
||
|
% This ASCII file represents a sparse MxN matrix with L
|
||
|
% nonzeros in the following Matrix Market format:
|
||
|
%
|
||
|
% +----------------------------------------------+
|
||
|
% |%%MatrixMarket matrix coordinate real general | <--- header line
|
||
|
% |% | <--+
|
||
|
% |% comments | |-- 0 or more comment lines
|
||
|
% |% | <--+
|
||
|
% | M N L | <--- rows, columns, entries
|
||
|
% | I1 J1 A(I1, J1) | <--+
|
||
|
% | I2 J2 A(I2, J2) | |
|
||
|
% | I3 J3 A(I3, J3) | |-- L lines
|
||
|
% | . . . | |
|
||
|
% | IL JL A(IL, JL) | <--+
|
||
|
% +----------------------------------------------+
|
||
|
%
|
||
|
% Indices are 1-based, i.e. A(1,1) is the first element.
|
||
|
%
|
||
|
%=================================================================================
|
||
|
5 5 8
|
||
|
1 1 1.000e+00
|
||
|
2 2 1.050e+01
|
||
|
3 3 1.500e-02
|
||
|
1 4 6.000e+00
|
||
|
4 2 2.505e+02
|
||
|
4 4 -2.800e+02
|
||
|
4 5 3.332e+01
|
||
|
5 5 1.200e+01
|
||
|
'''
|
||
|
|
||
|
_hermitian_example = '''\
|
||
|
%%MatrixMarket matrix coordinate complex hermitian
|
||
|
5 5 7
|
||
|
1 1 1.0 0
|
||
|
2 2 10.5 0
|
||
|
4 2 250.5 22.22
|
||
|
3 3 1.5e-2 0
|
||
|
4 4 -2.8e2 0
|
||
|
5 5 12. 0
|
||
|
5 4 0 33.32
|
||
|
'''
|
||
|
|
||
|
_skew_example = '''\
|
||
|
%%MatrixMarket matrix coordinate real skew-symmetric
|
||
|
5 5 7
|
||
|
1 1 1.0
|
||
|
2 2 10.5
|
||
|
4 2 250.5
|
||
|
3 3 1.5e-2
|
||
|
4 4 -2.8e2
|
||
|
5 5 12.
|
||
|
5 4 0
|
||
|
'''
|
||
|
|
||
|
_symmetric_example = '''\
|
||
|
%%MatrixMarket matrix coordinate real symmetric
|
||
|
5 5 7
|
||
|
1 1 1.0
|
||
|
2 2 10.5
|
||
|
4 2 250.5
|
||
|
3 3 1.5e-2
|
||
|
4 4 -2.8e2
|
||
|
5 5 12.
|
||
|
5 4 8
|
||
|
'''
|
||
|
|
||
|
_symmetric_pattern_example = '''\
|
||
|
%%MatrixMarket matrix coordinate pattern symmetric
|
||
|
5 5 7
|
||
|
1 1
|
||
|
2 2
|
||
|
4 2
|
||
|
3 3
|
||
|
4 4
|
||
|
5 5
|
||
|
5 4
|
||
|
'''
|
||
|
|
||
|
|
||
|
class TestMMIOCoordinate(object):
|
||
|
def setup_method(self):
|
||
|
self.tmpdir = mkdtemp()
|
||
|
self.fn = os.path.join(self.tmpdir, 'testfile.mtx')
|
||
|
|
||
|
def teardown_method(self):
|
||
|
shutil.rmtree(self.tmpdir)
|
||
|
|
||
|
def check_read(self, example, a, info):
|
||
|
f = open(self.fn, 'w')
|
||
|
f.write(example)
|
||
|
f.close()
|
||
|
assert_equal(mminfo(self.fn), info)
|
||
|
b = mmread(self.fn).todense()
|
||
|
assert_array_almost_equal(a, b)
|
||
|
|
||
|
def test_read_general(self):
|
||
|
a = [[1, 0, 0, 6, 0],
|
||
|
[0, 10.5, 0, 0, 0],
|
||
|
[0, 0, .015, 0, 0],
|
||
|
[0, 250.5, 0, -280, 33.32],
|
||
|
[0, 0, 0, 0, 12]]
|
||
|
self.check_read(_general_example, a,
|
||
|
(5, 5, 8, 'coordinate', 'real', 'general'))
|
||
|
|
||
|
def test_read_hermitian(self):
|
||
|
a = [[1, 0, 0, 0, 0],
|
||
|
[0, 10.5, 0, 250.5 - 22.22j, 0],
|
||
|
[0, 0, .015, 0, 0],
|
||
|
[0, 250.5 + 22.22j, 0, -280, -33.32j],
|
||
|
[0, 0, 0, 33.32j, 12]]
|
||
|
self.check_read(_hermitian_example, a,
|
||
|
(5, 5, 7, 'coordinate', 'complex', 'hermitian'))
|
||
|
|
||
|
def test_read_skew(self):
|
||
|
a = [[1, 0, 0, 0, 0],
|
||
|
[0, 10.5, 0, -250.5, 0],
|
||
|
[0, 0, .015, 0, 0],
|
||
|
[0, 250.5, 0, -280, 0],
|
||
|
[0, 0, 0, 0, 12]]
|
||
|
self.check_read(_skew_example, a,
|
||
|
(5, 5, 7, 'coordinate', 'real', 'skew-symmetric'))
|
||
|
|
||
|
def test_read_symmetric(self):
|
||
|
a = [[1, 0, 0, 0, 0],
|
||
|
[0, 10.5, 0, 250.5, 0],
|
||
|
[0, 0, .015, 0, 0],
|
||
|
[0, 250.5, 0, -280, 8],
|
||
|
[0, 0, 0, 8, 12]]
|
||
|
self.check_read(_symmetric_example, a,
|
||
|
(5, 5, 7, 'coordinate', 'real', 'symmetric'))
|
||
|
|
||
|
def test_read_symmetric_pattern(self):
|
||
|
a = [[1, 0, 0, 0, 0],
|
||
|
[0, 1, 0, 1, 0],
|
||
|
[0, 0, 1, 0, 0],
|
||
|
[0, 1, 0, 1, 1],
|
||
|
[0, 0, 0, 1, 1]]
|
||
|
self.check_read(_symmetric_pattern_example, a,
|
||
|
(5, 5, 7, 'coordinate', 'pattern', 'symmetric'))
|
||
|
|
||
|
def test_empty_write_read(self):
|
||
|
# http://projects.scipy.org/scipy/ticket/883
|
||
|
|
||
|
b = scipy.sparse.coo_matrix((10, 10))
|
||
|
mmwrite(self.fn, b)
|
||
|
|
||
|
assert_equal(mminfo(self.fn),
|
||
|
(10, 10, 0, 'coordinate', 'real', 'symmetric'))
|
||
|
a = b.todense()
|
||
|
b = mmread(self.fn).todense()
|
||
|
assert_array_almost_equal(a, b)
|
||
|
|
||
|
def test_bzip2_py3(self):
|
||
|
# test if fix for #2152 works
|
||
|
try:
|
||
|
# bz2 module isn't always built when building Python.
|
||
|
import bz2
|
||
|
except:
|
||
|
return
|
||
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
V = array([1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0])
|
||
|
|
||
|
b = scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5))
|
||
|
|
||
|
mmwrite(self.fn, b)
|
||
|
|
||
|
fn_bzip2 = "%s.bz2" % self.fn
|
||
|
with open(self.fn, 'rb') as f_in:
|
||
|
f_out = bz2.BZ2File(fn_bzip2, 'wb')
|
||
|
f_out.write(f_in.read())
|
||
|
f_out.close()
|
||
|
|
||
|
a = mmread(fn_bzip2).todense()
|
||
|
assert_array_almost_equal(a, b.todense())
|
||
|
|
||
|
def test_gzip_py3(self):
|
||
|
# test if fix for #2152 works
|
||
|
try:
|
||
|
# gzip module can be missing from Python installation
|
||
|
import gzip
|
||
|
except:
|
||
|
return
|
||
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
V = array([1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0])
|
||
|
|
||
|
b = scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5))
|
||
|
|
||
|
mmwrite(self.fn, b)
|
||
|
|
||
|
fn_gzip = "%s.gz" % self.fn
|
||
|
with open(self.fn, 'rb') as f_in:
|
||
|
f_out = gzip.open(fn_gzip, 'wb')
|
||
|
f_out.write(f_in.read())
|
||
|
f_out.close()
|
||
|
|
||
|
a = mmread(fn_gzip).todense()
|
||
|
assert_array_almost_equal(a, b.todense())
|
||
|
|
||
|
def test_real_write_read(self):
|
||
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
V = array([1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0])
|
||
|
|
||
|
b = scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5))
|
||
|
|
||
|
mmwrite(self.fn, b)
|
||
|
|
||
|
assert_equal(mminfo(self.fn),
|
||
|
(5, 5, 8, 'coordinate', 'real', 'general'))
|
||
|
a = b.todense()
|
||
|
b = mmread(self.fn).todense()
|
||
|
assert_array_almost_equal(a, b)
|
||
|
|
||
|
def test_complex_write_read(self):
|
||
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
V = array([1.0 + 3j, 6.0 + 2j, 10.50 + 0.9j, 0.015 + -4.4j,
|
||
|
250.5 + 0j, -280.0 + 5j, 33.32 + 6.4j, 12.00 + 0.8j])
|
||
|
|
||
|
b = scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5))
|
||
|
|
||
|
mmwrite(self.fn, b)
|
||
|
|
||
|
assert_equal(mminfo(self.fn),
|
||
|
(5, 5, 8, 'coordinate', 'complex', 'general'))
|
||
|
a = b.todense()
|
||
|
b = mmread(self.fn).todense()
|
||
|
assert_array_almost_equal(a, b)
|
||
|
|
||
|
def test_sparse_formats(self):
|
||
|
mats = []
|
||
|
|
||
|
I = array([0, 0, 1, 2, 3, 3, 3, 4])
|
||
|
J = array([0, 3, 1, 2, 1, 3, 4, 4])
|
||
|
|
||
|
V = array([1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0])
|
||
|
mats.append(scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5)))
|
||
|
|
||
|
V = array([1.0 + 3j, 6.0 + 2j, 10.50 + 0.9j, 0.015 + -4.4j,
|
||
|
250.5 + 0j, -280.0 + 5j, 33.32 + 6.4j, 12.00 + 0.8j])
|
||
|
mats.append(scipy.sparse.coo_matrix((V, (I, J)), shape=(5, 5)))
|
||
|
|
||
|
for mat in mats:
|
||
|
expected = mat.todense()
|
||
|
for fmt in ['csr', 'csc', 'coo']:
|
||
|
fn = mktemp(dir=self.tmpdir) # safe, we own tmpdir
|
||
|
mmwrite(fn, mat.asformat(fmt))
|
||
|
|
||
|
result = mmread(fn).todense()
|
||
|
assert_array_almost_equal(result, expected)
|
||
|
|
||
|
def test_precision(self):
|
||
|
test_values = [pi] + [10**(i) for i in range(0, -10, -1)]
|
||
|
test_precisions = range(1, 10)
|
||
|
for value in test_values:
|
||
|
for precision in test_precisions:
|
||
|
# construct sparse matrix with test value at last main diagonal
|
||
|
n = 10**precision + 1
|
||
|
A = scipy.sparse.dok_matrix((n, n))
|
||
|
A[n-1, n-1] = value
|
||
|
# write matrix with test precision and read again
|
||
|
mmwrite(self.fn, A, precision=precision)
|
||
|
A = scipy.io.mmread(self.fn)
|
||
|
# check for right entries in matrix
|
||
|
assert_array_equal(A.row, [n-1])
|
||
|
assert_array_equal(A.col, [n-1])
|
||
|
assert_array_almost_equal(A.data,
|
||
|
[float('%%.%dg' % precision % value)])
|