Repository URL to install this package:
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Version:
5.0.3.post1 ▾
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import numpy as np
import scipy.sparse
import pytest
from qutip.core import data, qeye, CoreOptions
from qutip.core.data import dia, Dense, Dia
from . import conftest
# We only choose a small subset of dtypes to test so it isn't crazy.
_dtype_complex = ['complex128']
_dtype_float = ['float64']
_dtype_int = ['int32', 'int64']
_dtype_uint = ['uint32']
# Set up some fixtures for automatic parametrisation.
@pytest.fixture(params=[
pytest.param((1, 5), id='ket'),
pytest.param((5, 1), id='bra'),
pytest.param((5, 5), id='square'),
pytest.param((2, 4), id='wide'),
pytest.param((4, 2), id='tall'),
])
def shape(request): return request.param
@pytest.fixture(params=[
pytest.param(0, id='empty'),
pytest.param(1, id='full'),
pytest.param(0.2, id='sparse'),
])
def density(request): return request.param
@pytest.fixture(scope='function')
def scipy_dia(shape, density):
return conftest.random_scipy_dia(shape, density)
def _valid_scipy():
"""Arbitrary valid scipy Dia"""
return conftest.random_scipy_dia((10, 10), 0.5)
def _valid_arg():
"""
Arbitrary valid 3-tuple which is a valid `arg` parameter for __init__.
"""
sci = _valid_scipy()
return (sci.data, sci.offsets)
@pytest.fixture(scope='function')
def data_diag(shape, density):
return conftest.random_diag(shape, density)
class TestClassMethods:
def test_init_from_scipy(self, scipy_dia):
"""Test that __init__ can accept a scipy dia matrix."""
out = dia.Dia(scipy_dia)
assert out.shape == scipy_dia.shape
assert (out.as_scipy() - scipy_dia).nnz == 0
def test_init_from_tuple(self, scipy_dia):
"""
Test that __init__ does not throw when passed a 3-tuple. Also tests
the as_scipy() method succeeds.
"""
arg = (scipy_dia.data, scipy_dia.offsets)
out = dia.Dia(arg, shape=scipy_dia.shape)
assert out.shape == scipy_dia.shape
assert (out.as_scipy() - scipy_dia).nnz == 0
@pytest.mark.parametrize('d_type', (
_dtype_complex + _dtype_float + _dtype_int + _dtype_uint
))
@pytest.mark.parametrize('o_type', _dtype_int + _dtype_uint)
def test_init_from_tuple_allowed_dtypes(self, d_type, o_type):
"""
Test that initialisation can use a variety of dtypes and converts into
the correct type.
"""
sci = _valid_scipy()
data = sci.data.real.astype(d_type, casting='unsafe')
offsets = sci.offsets.astype(o_type, casting='unsafe')
scipy_dia = scipy.sparse.dia_matrix((data, offsets), shape=sci.shape)
out = dia.Dia((data, offsets), shape=sci.shape)
out_scipy = out.as_scipy()
assert out.shape == scipy_dia.shape
assert out_scipy.data.dtype == np.complex128
assert (out_scipy - scipy_dia).nnz == 0
@pytest.mark.parametrize(['arg', 'kwargs', 'error'], [
pytest.param((), {}, ValueError, id="arg 0 tuple"),
pytest.param((None,), {}, ValueError, id="arg 1 tuple"),
pytest.param((None,)*2, {}, TypeError, id="arg None tuple"),
pytest.param((None,)*3, {}, ValueError, id="arg 3 tuple"),
pytest.param(_valid_scipy(), {'shape': ()}, ValueError,
id="scipy-shape 0 tuple"),
pytest.param(_valid_scipy(), {'shape': (1,)}, ValueError,
id="scipy-shape 1 tuple"),
pytest.param(_valid_scipy(), {'shape': (None, None)}, ValueError,
id="scipy-shape None tuple"),
pytest.param(_valid_scipy(), {'shape': [2, 2]}, ValueError,
id="scipy-shape list"),
pytest.param(_valid_scipy(), {'shape': (1, 2, 3)}, ValueError,
id="scipy-shape 3 tuple"),
pytest.param(_valid_arg(), {'shape': ()}, ValueError,
id="arg-shape 0 tuple"),
pytest.param(_valid_arg(), {'shape': (1,)}, ValueError,
id="arg-shape 1 tuple"),
pytest.param(_valid_arg(), {'shape': (None, None)}, ValueError,
id="arg-shape None tuple"),
pytest.param(_valid_arg(), {'shape': [2, 2]}, TypeError,
id="arg-shape list"),
pytest.param(_valid_arg(), {'shape': (1, 2, 3)}, ValueError,
id="arg-shape 3 tuple"),
pytest.param(_valid_arg(), {'shape': (-1, -1)}, ValueError,
id="arg-negative shape"),
])
def test_init_from_wrong_input(self, arg, kwargs, error):
"""
Test that the __init__ method raises a suitable error when passed
incorrectly formatted inputs.
This test also serves as a *partial* check that Dia safely handles
deallocation in the presence of exceptions in its __init__ method. If
the tests segfault, it's quite likely that the memory management isn't
being done correctly in the hand-off us setting our data buffers up and
marking the numpy actually owns the data.
"""
with pytest.raises(error):
dia.Dia(arg, **kwargs)
def test_copy_returns_a_correct_copy(self, data_diag):
"""
Test that the copy() method produces an actual copy, and that the
result represents the same matrix.
"""
original = data_diag
copy = data_diag.copy()
assert original is not copy
assert np.all(original.to_array() == copy.to_array())
def test_as_scipy_returns_a_view(self, data_diag):
"""
Test that modifying the views in the result of as_scipy() also modifies
the underlying data structures. This is important for allowing minor
data modifications from within Python-space.
"""
unmodified_copy = data_diag.copy()
data_diag.as_scipy().data += 1
modified_copy = data_diag.copy()
assert np.any(data_diag.to_array() != unmodified_copy.to_array())
assert np.all(data_diag.to_array() == modified_copy.to_array())
def test_as_scipy_caches_result(self, data_diag):
"""
Test that the as_scipy() method always returns the same view, even if
called multiple times.
"""
assert data_diag.as_scipy() is data_diag.as_scipy()
def test_as_scipy_of_dia_from_scipy_is_different(self, scipy_dia):
"""
Test that we produce a new scipy matrix, regardless of how we have
initialised the type.
"""
assert dia.Dia(scipy_dia).as_scipy() is not scipy_dia
def test_as_scipy_of_copy_is_different(self, data_diag):
"""
Test that as_scipy() does not return the same array, or the same views
if it's not the same input matrix. We don't want two Dia matrices to
be linked.
"""
original = data_diag.as_scipy()
copy = data_diag.copy().as_scipy()
assert original is not copy
assert not np.may_share_memory(original.data, copy.data)
assert not np.may_share_memory(original.offsets, copy.offsets)
def test_as_scipy_is_correct_result(self, scipy_dia):
"""
Test that as_scipy is actually giving the matrix we expect for a given
input.
"""
data_diag = dia.Dia(scipy_dia)
assert isinstance(data_diag.as_scipy(), scipy.sparse.dia_matrix)
assert (data_diag.as_scipy() - scipy_dia).nnz == 0
def test_as_scipy_of_uninitialised_is_empty(self, shape):
ndiag = 0
base = dia.empty(shape[0], shape[1], ndiag)
sci = base.as_scipy()
assert len(sci.data) == 0
assert len(sci.offsets) == 0
def test_to_array_is_correct_result(self, data_diag):
test_array = data_diag.to_array()
assert isinstance(test_array, np.ndarray)
# It's not enough to be accurate within a tolerance here - there's no
# mathematics, so they should be _identical_.
assert np.all(test_array == data_diag.as_scipy().toarray())
class TestFactoryMethods:
def test_empty(self, shape, density):
ndiag = int(shape[0] * shape[1] * density) or 1
base = dia.empty(shape[0], shape[1], ndiag)
sci = base.as_scipy(full=True)
assert isinstance(base, dia.Dia)
assert isinstance(sci, scipy.sparse.dia_matrix)
assert base.shape == shape
assert sci.data.shape == (ndiag, shape[1])
assert sci.offsets.shape == (ndiag,)
def test_zeros(self, shape):
base = dia.zeros(shape[0], shape[1])
sci = base.as_scipy()
assert isinstance(base, dia.Dia)
assert base.shape == shape
assert sci.nnz == 0
assert np.all(base.to_array() == 0)
@pytest.mark.parametrize('dimension', [1, 5, 100])
@pytest.mark.parametrize(
'scale',
[None, 2, -0.1, 1.5, 1.5+1j],
ids=['none', 'int', 'negative', 'float', 'complex']
)
def test_identity(self, dimension, scale):
# scale=None is testing that the default value returns the identity.
base = (dia.identity(dimension) if scale is None
else dia.identity(dimension, scale))
sci = base.as_scipy()
scipy_test = scipy.sparse.eye(dimension,
dtype=np.complex128, format='dia')
if scale is not None:
scipy_test *= scale
assert isinstance(base, dia.Dia)
assert base.shape == (dimension, dimension)
assert sci.nnz == dimension
assert (sci - scipy_test).nnz == 0
@pytest.mark.parametrize(['diagonals', 'offsets', 'shape'], [
pytest.param([2j, 3, 5, 9], None, None, id='main diagonal'),
pytest.param([1], None, None, id='1x1'),
pytest.param([[0.2j, 0.3]], None, None, id='main diagonal list'),
pytest.param([0.2j, 0.3], 2, None, id='superdiagonal'),
pytest.param([0.2j, 0.3], -2, None, id='subdiagonal'),
pytest.param([[0.2, 0.3, 0.4], [0.1, 0.9]], [-2, 3], None,
id='two diagonals'),
pytest.param([1, 2, 3], 0, (3, 5), id='main wide'),
pytest.param([1, 2, 3], 0, (5, 3), id='main tall'),
pytest.param([[1, 2, 3], [4, 5]], [-1, -2], (4, 8), id='two wide sub'),
pytest.param([[1, 2, 3, 4], [4, 5, 4j, 1j]], [1, 2], (4, 8),
id='two wide super'),
pytest.param([[1, 2, 3], [4, 5]], [1, 2], (8, 4), id='two tall super'),
pytest.param([[1, 2, 3, 4], [4, 5, 4j, 1j]], [-1, -2], (8, 4),
id='two tall sub'),
pytest.param([[1, 2, 3], [4, 5, 6], [1, 2]], [1, -1, -2], (4, 4),
id='out of order'),
pytest.param([[1, 2, 3], [4, 5, 6], [1, 2]], [1, 1, -2], (4, 4),
id='sum duplicates'),
])
def test_diags(self, diagonals, offsets, shape):
base = dia.diags(diagonals, offsets, shape)
# Build numpy version test.
if not isinstance(diagonals[0], list):
diagonals = [diagonals]
offsets = np.atleast_1d(offsets if offsets is not None else [0])
if shape is None:
size = len(diagonals[0]) + abs(offsets[0])
shape = (size, size)
test = np.zeros(shape, dtype=np.complex128)
for diagonal, offset in zip(diagonals, offsets):
test[np.where(np.eye(*shape, k=offset) == 1)] += diagonal
assert isinstance(base, dia.Dia)
assert base.shape == shape
np.testing.assert_allclose(base.to_array(), test, rtol=1e-10)
@pytest.mark.parametrize(['shape', 'position', 'value'], [
pytest.param((1, 1), (0, 0), None, id='minimal'),
pytest.param((10, 10), (5, 5), 1.j, id='on diagonal'),
pytest.param((10, 10), (1, 5), 1., id='upper'),
pytest.param((10, 10), (5, 1), 2., id='lower'),
pytest.param((10, 1), (5, 0), None, id='column'),
pytest.param((1, 10), (0, 5), -5.j, id='row'),
pytest.param((10, 2), (5, 1), 1+2j, id='tall'),
pytest.param((2, 10), (1, 5), 10, id='wide'),
])
def test_one_element(self, shape, position, value):
test = np.zeros(shape, dtype=np.complex128)
if value is None:
base = data.one_element_dia(shape, position)
test[position] = 1.0+0.0j
else:
base = data.one_element_dia(shape, position, value)
test[position] = value
assert isinstance(base, data.Dia)
assert base.shape == shape
assert np.allclose(base.to_array(), test, atol=1e-10)
@pytest.mark.parametrize(['shape', 'position', 'value'], [
pytest.param((0, 0), (0, 0), None, id='zero shape'),
pytest.param((10, -2), (5, 0), 1.j, id='neg shape'),
pytest.param((10, 10), (10, 5), 1., id='outside'),
pytest.param((10, 10), (5, -1), 2., id='outside neg'),
])
def test_one_element_error(self, shape, position, value):
with pytest.raises(ValueError) as exc:
base = data.one_element_dia(shape, position, value)
assert str(exc.value).startswith("Position of the elements"
" out of bound: ")
def test_tidyup(data_diag):
before = data_diag.to_array()
sp_before = data_diag.as_scipy().toarray()
largest = max(np.abs(before.real).max(), np.abs(before.imag).max())
min_r = np.abs(before.real[np.abs(before.real) > 0]).min()
min_i = np.abs(before.imag[np.abs(before.imag) > 0]).min()
smallest = min(min_r, min_i)
print(largest, smallest)
if largest == smallest:
return
tol = (largest + smallest) / 2
tidy = data.tidyup_dia(data_diag, tol, False)
# Inplace=False, does not modify the original
np.testing.assert_array_equal(data_diag.to_array(), before)
np.testing.assert_array_equal(data_diag.as_scipy().toarray(), sp_before)
# Is tidyup
assert not np.allclose(tidy.to_array(), before)
assert not np.allclose(tidy.as_scipy().toarray(), sp_before)
data.tidyup_dia(data_diag, tol, True)
assert not np.allclose(data_diag.to_array(), before)
assert not np.allclose(data_diag.as_scipy().toarray(), sp_before)
def test_autotidyup():
small = qeye(1) * 1e-5
with CoreOptions(auto_tidyup_atol=1e-3):
assert (small + small).tr() == 0
with CoreOptions(auto_tidyup_atol=1e-3, auto_tidyup=False):
assert (small + small).tr() == 2e-5