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from __future__ import absolute_import, division, unicode_literals
import datetime
import warnings
import pytest
try:
import numpy as np
import numpy.testing as npt
from numpy.compat import asbytes
from numpy.testing import assert_equal
except ImportError:
pytest.skip('numpy is not available', allow_module_level=True)
import jsonpickle
import jsonpickle.ext.numpy
from jsonpickle import handlers
@pytest.fixture(scope='module', autouse=True)
def numpy_extension():
"""Initialize the numpy extension for this test module"""
jsonpickle.ext.numpy.register_handlers()
yield # control to the test function.
jsonpickle.ext.numpy.unregister_handlers()
def roundtrip(obj):
return jsonpickle.decode(jsonpickle.encode(obj))
def test_dtype_roundtrip():
dtypes = [
np.int_,
np.int32,
np.float_,
np.float64,
np.complex_,
np.complex128,
np.str_,
np.object_,
np.compat.unicode,
np.dtype(np.void),
np.dtype(np.int32),
np.dtype(np.float32),
np.dtype('f4,i4,f2,i1'),
np.dtype(('f4', 'i4'), ('f2', 'i1')),
np.dtype('i4', align=True),
np.dtype('M8[7D]'),
np.dtype(
{
'names': ['f0', 'f1', 'f2'],
'formats': ['<u4', '<u2', '<u2'],
'offsets': [0, 0, 2],
},
align=True,
),
np.dtype([('f0', 'i4'), ('f2', 'i1')]),
np.dtype(
[
(
'top',
[
('tiles', ('>f4', (64, 64)), (1,)),
('rtile', '>f4', (64, 36)),
],
(3,),
),
(
'bottom',
[
('bleft', ('>f4', (8, 64)), (1,)),
('bright', '>f4', (8, 36)),
],
),
]
),
]
for dtype in dtypes:
encoded = jsonpickle.encode(dtype)
decoded = jsonpickle.decode(encoded)
assert dtype == decoded
def test_generic_roundtrip():
values = [
np.int_(1),
np.int32(-2),
np.float_(2.5),
np.nan,
-np.inf,
np.inf,
np.datetime64('2014-01-01'),
np.str_('foo'),
np.unicode_('bar'),
np.object_({'a': 'b'}),
np.complex_(1 - 2j),
]
for value in values:
decoded = roundtrip(value)
assert_equal(decoded, value)
assert isinstance(decoded, type(value))
def test_ndarray_roundtrip():
arrays = [
np.random.random((10, 20)),
np.array([[True, False, True]]),
np.array(['foo', 'bar']),
np.array(['baz'.encode('utf-8')]),
np.array(['2010', 'NaT', '2030']).astype('M'),
np.rec.array(asbytes('abcdefg') * 100, formats='i2,a3,i4', shape=3),
np.rec.array(
[
(1, 11, 'a'),
(2, 22, 'b'),
(3, 33, 'c'),
(4, 44, 'd'),
(5, 55, 'ex'),
(6, 66, 'f'),
(7, 77, 'g'),
],
formats='u1,f4,a1',
),
np.array(['1960-03-12', datetime.date(1960, 3, 12)], dtype='M8[D]'),
np.array([0, 1, -1, np.inf, -np.inf, np.nan], dtype='f2'),
]
arrays.extend(
[
np.rec.array(
[('NGC1001', 11), ('NGC1002', 1.0), ('NGC1003', 1.0)],
dtype=[('target', 'S20'), ('V_mag', 'f4')],
)
]
)
for array in arrays:
decoded = roundtrip(array)
assert_equal(decoded, array)
assert decoded.dtype == array.dtype
def test_shapes_containing_zeroes():
"""Test shapes which cannot be represented as nested lists"""
expect = np.eye(3)[3:]
actual = roundtrip(expect)
npt.assert_array_equal(expect, actual)
def test_accuracy():
"""Test the accuracy of the string representation"""
expect = np.random.randn(3, 3)
actual = roundtrip(expect)
npt.assert_array_equal(expect, actual)
def test_b64():
"""Test the binary encoding"""
# Array of substantial size is stored as b64.
expect = np.random.rand(10, 10)
actual = roundtrip(expect)
npt.assert_array_equal(expect, actual)
def test_views():
"""Test views under serialization"""
rng = np.arange(20) # a range of an array
view = rng[10:] # a view referencing a portion of an array
data = [rng, view]
actual = roundtrip(data)
actual[0][15] = -1
assert actual[1][5] == -1
def test_strides():
"""Test non-standard strides and offsets"""
arr = np.eye(3)
view = arr[1:, 1:]
assert view.base is arr
data = [arr, view]
actual = roundtrip(data)
# test that the deserialized arrays indeed view the same memory
new_arr, new_view = actual
new_arr[1, 2] = -1
assert new_view[0, 1] == -1
assert new_view.base is new_arr
def test_weird_arrays():
"""Test references to arrays that do not effectively own their memory"""
a = np.arange(9)
b = a[5:]
a.strides = 1
# this is kinda fishy; a has overlapping memory, _a does not
warn_count = 1
with warnings.catch_warnings(record=True) as w:
_a = roundtrip(a)
assert len(w) == warn_count
npt.assert_array_equal(a, _a)
# this also requires a deepcopy to work
with warnings.catch_warnings(record=True) as w:
_a, _b = roundtrip([a, b])
assert len(w) == warn_count
npt.assert_array_equal(a, _a)
npt.assert_array_equal(b, _b)
def test_transpose():
"""test handling of non-c-contiguous memory layout"""
# simple case; view a c-contiguous array
a = np.arange(9).reshape(3, 3)
b = a[1:, 1:]
assert b.base is a.base
_a, _b = roundtrip([a, b])
assert _b.base is _a.base
npt.assert_array_equal(a, _a)
npt.assert_array_equal(b, _b)
# a and b both view the same contiguous array
a = np.arange(9).reshape(3, 3).T
b = a[1:, 1:]
assert b.base is a.base
_a, _b = roundtrip([a, b])
assert _b.base is _a.base
npt.assert_array_equal(a, _a)
npt.assert_array_equal(b, _b)
# view an f-contiguous array
a = a.copy()
a.strides = a.strides[::-1]
b = a[1:, 1:]
assert b.base is a
_a, _b = roundtrip([a, b])
assert _b.base is _a
npt.assert_array_equal(a, _a)
npt.assert_array_equal(b, _b)
# now a.data.contiguous is False; we have to make a deepcopy to make
# this work note that this is a pretty contrived example though!
a = np.arange(8).reshape(2, 2, 2).copy()
a.strides = a.strides[0], a.strides[2], a.strides[1]
b = a[1:, 1:]
assert b.base is a
warn_count = 1
with warnings.catch_warnings(record=True) as w:
_a, _b = roundtrip([a, b])
assert len(w) == warn_count
npt.assert_array_equal(a, _a)
npt.assert_array_equal(b, _b)
def test_fortran_base():
"""Test a base array in fortran order"""
a = np.asfortranarray(np.arange(100).reshape((10, 10)))
_a = roundtrip(a)
npt.assert_array_equal(a, _a)
def test_buffer():
"""test behavior with memoryviews which are not ndarrays"""
bstring = 'abcdefgh'.encode('utf-8')
a = np.frombuffer(bstring, dtype=np.byte)
warn_count = 1
with warnings.catch_warnings(record=True) as w:
_a = roundtrip(a)
npt.assert_array_equal(a, _a)
assert len(w) == warn_count
def test_as_strided():
"""Test the result of as_strided()
as_strided() returns an object that implements the array interface but
is not an ndarray.
"""
warn_count = 1
a = np.arange(10)
b = np.lib.stride_tricks.as_strided(a, shape=(5,), strides=(a.dtype.itemsize * 2,))
data = [a, b]
with warnings.catch_warnings(record=True) as w:
# as_strided returns a DummyArray object, which we can not
# currently serialize correctly FIXME: would be neat to add
# support for all objects implementing the __array_interface__
_data = roundtrip(data)
assert len(w) == warn_count
# as we were warned, deserialized result is no longer a view
_data[0][0] = -1
assert _data[1][0] == 0
def test_immutable():
"""test that immutability flag is copied correctly"""
a = np.arange(10)
a.flags.writeable = False
_a = roundtrip(a)
with pytest.raises(ValueError):
_a[0] = 0
def test_byteorder():
"""Test the byteorder for text and binary encodings"""
# small arr is stored as text
a = np.arange(10).newbyteorder()
b = a[:].newbyteorder()
_a, _b = roundtrip([a, b])
npt.assert_array_equal(a, _a)
npt.assert_array_equal(b, _b)
# bigger arr is stored as binary
a = np.arange(100).newbyteorder()
b = a[:].newbyteorder()
_a, _b = roundtrip([a, b])
npt.assert_array_equal(a, _a)
npt.assert_array_equal(b, _b)
def test_zero_dimensional_array():
expect = np.array(float(0.0), dtype="float64")
actual = jsonpickle.decode(jsonpickle.encode(expect))
npt.assert_array_equal(expect, actual)
def test_nested_data_list_of_dict_with_list_keys():
"""Ensure we can handle numpy arrays within a nested structure"""
expect = [{'key': [np.array(0)]}]
actual = roundtrip(expect)
npt.assert_array_equal(expect[0]['key'][0], actual[0]['key'][0])
expect = [{'key': [np.array([1.0])]}]
actual = roundtrip(expect)
npt.assert_array_equal(expect[0]['key'][0], actual[0]['key'][0])
def test_size_threshold_None():
handler = jsonpickle.ext.numpy.NumpyNDArrayHandlerView(size_threshold=None)
handlers.registry.unregister(np.ndarray)
handlers.registry.register(np.ndarray, handler, base=True)
expect = np.array([0, 1])
actual = roundtrip(expect)
npt.assert_array_equal(expect, actual)
def test_ndarray_dtype_object():
a = np.array(['F' + str(i) for i in range(30)], dtype=object)
buf = jsonpickle.encode(a)
# This is critical for reproducing the numpy segfault issue when
# restoring ndarray of dtype object.
del a
expect = np.array(['F' + str(i) for i in range(30)], dtype=object)
actual = jsonpickle.decode(buf)
npt.assert_array_equal(expect, actual)
def test_np_random():
"""Ensure random.random() arrays can be serialized"""
obj = np.random.random(100)
encoded = jsonpickle.encode(obj)
clone = jsonpickle.decode(encoded)
assert 100 == len(clone)
for idx, (expect, actual) in enumerate(zip(obj, clone)):
assert expect == actual
def test_np_poly1d():
# issue 391, test poly1d roundtrip
obj = np.poly1d([1, 2, 3])
assert obj == jsonpickle.decode(jsonpickle.encode(obj))
if __name__ == '__main__':
pytest.main([__file__])
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