def test_functions_callable(self):
arr = np.ones((5, 5))
mask = _sigma_clip(arr, cen_func=np.median)
mask = _sigma_clip(arr, dev_func=np.std)
# testing forced 1.0pm0.5
def _test_cen(*args, **kwargs):
return 1.0
def _test_dev(*args, **kwargs):
return 0.5
# 1.2 should not be masked with 1.0pm0.5, 2.0 and 1000 yes
arr[0, 0] = 1.2
arr[1, 1] = 2
arr[3, 2] = 1000
mask = _sigma_clip(arr, 1, cen_func=_test_cen, dev_func=_test_dev)
for i in range(5):
for j in range(5):
if (i, j) in [(1, 1), (3, 2)]:
assert_true(mask[i, j])
else:
assert_false(mask[i, j])
def test_reset_data(self, tmpdir):
d1 = np.array([[1, 2], [3, 4]]).astype('float32')
m = MemMapArray(d1,
os.path.join(tmpdir, 'reset.npy'),
dtype='float64',
memmap=True)
assert_true(np.issubdtype(m.dtype, np.float64))
assert_equal(m, d1)
assert_false(m.empty)
assert_true(m.memmap)
m.reset_data(d1)
assert_true(np.issubdtype(m.dtype, np.float32))
assert_equal(m, d1)
assert_false(m.empty)
assert_true(m.memmap)
m.reset_data(d1.astype('int16'))
assert_true(np.issubdtype(m.dtype, np.int16))
assert_equal(m, d1)
assert_false(m.empty)
assert_true(m.memmap)
m.reset_data(None)
assert_true(m.empty)
assert_true(m._contained is None)
assert_true(m.memmap)
m.disable_memmap()
m.reset_data(np.ones((10, 10)), dtype='float32')
assert_true(np.issubdtype(m.dtype, np.float32))
assert_equal(m, np.ones((10, 10)))
assert_false(m.empty)
assert_false(m.memmap)
def test_enable_disable_memmap(self, tmpdir):
f = os.path.join(tmpdir, 'npn_empty.npy')
arr = [[0, 1, 2, 3, 4, 5], [0, 1, 2, 3, 4, 5]]
a = MemMapArray(arr, filename=f, dtype=None, memmap=False)
assert_false(a.memmap)
assert_false(os.path.exists(f))
a.enable_memmap()
assert_true(a.memmap)
assert_true(os.path.exists(f))
assert_is_instance(a._contained, np.memmap)
# First keep the file
a.disable_memmap(remove=False)
assert_false(a.memmap)
assert_true(os.path.exists(f))
assert_is_not_instance(a._contained, np.memmap)
a.enable_memmap()
assert_true(a.memmap)
assert_true(os.path.exists(f))
assert_is_instance(a._contained, np.memmap)
# Remove the file
a.disable_memmap(remove=True)
assert_false(a.memmap)
assert_false(os.path.exists(f))
assert_is_not_instance(a._contained, np.memmap)
with pytest.raises(ValueError):
# raises error if name is locked
a.enable_memmap('not_the_same_name.npy')
def test_extract_header_nowcs(self):
header = fits.Header.fromstring(_base_header, sep='\n')
h, wcs = extract_header_wcs(header)
assert_is_none(wcs)
assert_is_instance(h, fits.Header)
assert_equal(h, header)
assert_false(h is header)
def test_simbad_catalog_check_filter_errors(self):
# default behavior is raise error
with pytest.raises(ValueError, match='This catalog does not support'):
self.cat.check_filter('inexisting')
with pytest.raises(ValueError, match='This catalog does not support'):
self.cat.check_filter('inexisting', raise_error=True)
assert_false(self.cat.check_filter('inexisting', raise_error=False))
def test_process_list(self):
def dummy_func(i):
i = 1
return i
a = np.zeros(20)
b = np.ones(20)
c = process_list(dummy_func, a)
assert_equal(b, c)
assert_false(np.array_equal(a, c))
def test_extract_invalid_wcs_header(self):
# It should no raise, just return empty wcs
# No header change too
header = fits.Header.fromstring(_base_header + _invalid_wcs, sep='\n')
del header['']
h, wcs = extract_header_wcs(header)
assert_is_none(wcs)
assert_is_instance(h, fits.Header)
assert_equal(h, header)
assert_false(h is header)
def test_extract_header_nosip(self):
header = fits.Header.fromstring(_base_header + _wcs_no_sip, sep='\n')
h, wcs = extract_header_wcs(header)
assert_is_instance(wcs, WCS)
assert_equal(wcs.wcs.ctype[0], 'RA---TAN')
assert_equal(wcs.wcs.ctype[1], 'DEC--TAN')
assert_is_instance(h, fits.Header)
for i in _comon_wcs_keys:
assert_not_in(f'{i}1', h.keys())
assert_not_in(f'{i}2', h.keys())
assert_in('DATE-OBS', h.keys())
assert_false(h is header)
assert_not_equal(h, header)
def test_create_memmap(self, tmpdir, memmap):
f = os.path.join(tmpdir, 'npn_empty.npy')
arr = [[0, 1, 2, 3, 4, 5], [0, 1, 2, 3, 4, 5]]
a = MemMapArray(arr, filename=f, dtype=None, memmap=memmap)
assert_equal(a.filename, f)
assert_equal(a, arr)
assert_false(a.empty)
assert_equal(a.memmap, memmap)
assert_equal(os.path.exists(f), memmap)
assert_true(a.dtype == np.int64)
a[0][0] = 10
assert_equal(a[0][0], 10)
a[0][:] = 20
assert_equal(a[0], [20, 20, 20, 20, 20, 20])
def test_create_empty_memmap(self, tmpdir, memmap):
f = os.path.join(tmpdir, 'empty.npy')
a = MemMapArray(None, filename=f, dtype=None, memmap=memmap)
assert_equal(a.filename, f)
assert_true(a._contained is None)
assert_equal(a.memmap, memmap)
assert_true(a.empty)
assert_false(os.path.exists(f))
with pytest.raises(EmptyDataError):
# dtype whould rise
a.dtype
with pytest.raises(EmptyDataError):
# shape whould rise
a.shape
with pytest.raises(EmptyDataError):
# item whould rise
a[0]
with pytest.raises(EmptyDataError):
# set item whould rise
a[0] = 1
def test_create_and_delete_memmap(tmpdir):
# Creation
f = os.path.join(tmpdir, 'testarray.npy')
g = os.path.join(tmpdir, 'test2array.npy')
a = np.ones((30, 30), dtype='f8')
b = create_array_memmap(f, a)
c = create_array_memmap(g, a, dtype=bool)
assert_is_instance(b, np.memmap)
assert_is_instance(c, np.memmap)
assert_equal(a, b)
assert_almost_equal(a, c)
assert_true(os.path.exists(f))
assert_true(os.path.exists(g))
# Deletion
# Since for the uses the object is overwritten, we do it here too
d = delete_array_memmap(b, read=True, remove=False)
e = delete_array_memmap(c, read=True, remove=False)
assert_is_not_instance(d, np.memmap)
assert_is_not_instance(e, np.memmap)
assert_is_instance(d, np.ndarray)
assert_is_instance(e, np.ndarray)
assert_equal(a, d)
assert_almost_equal(a, e)
assert_true(os.path.exists(f))
assert_true(os.path.exists(g))
d = delete_array_memmap(b, read=False, remove=True)
e = delete_array_memmap(c, read=False, remove=True)
assert_true(d is None)
assert_true(e is None)
assert_false(os.path.exists(f))
assert_false(os.path.exists(g))
# None should not raise errors
create_array_memmap('dummy', None)
delete_array_memmap(None)
def test_all_equal_1d_false(self):
a = np.ones(10)
a[2] = 2
assert_false(all_equal(a))
a = np.zeros(10)
a[2] = 2
assert_false(all_equal(a))
a = np.array(['aAa']*10)
a[2] = 'bBb'
assert_false(all_equal(a))
def test_all_equal_2d_false(self):
a = np.ones((5, 5))
a[2][2] = 2
assert_false(all_equal(a))
a = np.zeros((5, 5))
a[2][2] = 2
assert_false(all_equal(a))
a = ['aAa']*5
a = np.array([a]*5)
a[2][2] = 'bBb'
assert_false(all_equal(a))
def test_math_bool_all_any(tmpdir, memmap, value, other):
f = os.path.join(tmpdir, 'bool.npy')
arr = np.array([[0, 1, 0, 1], [1, 0, 1, 0]])
a = MemMapArray(arr, filename=f, memmap=memmap)
with pytest.raises(ValueError):
bool(a)
assert_false(a.all())
assert_true(a.any())
arr = np.array([0, 0, 0])
a = MemMapArray(arr, filename=f + '1', memmap=memmap)
assert_false(a.all())
assert_false(a.any())
arr = np.array([1, 1, 1])
a = MemMapArray(arr, filename=f + '2', memmap=memmap)
assert_true(a.all())
assert_true(a.any())
def test_check_number(v, exp):
if exp:
assert_true(check_number(v))
else:
assert_false(check_number(v))
def test_check_iterabel_number(self):
a = 10
assert_false(check_iterable(a))
def test_check_iterabel_string(self):
a = '12345'
assert_false(check_iterable(a))
def test_assert_false(self):
assert_false(False)
with pytest.raises(AssertionError):
assert_false(True)
