forked from numpy/numpy
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test_format.py
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test_format.py
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# doctest
r''' Test the .npy file format.
Set up:
>>> import sys
>>> from io import BytesIO
>>> from numpy.lib import format
>>>
>>> scalars = [
... np.uint8,
... np.int8,
... np.uint16,
... np.int16,
... np.uint32,
... np.int32,
... np.uint64,
... np.int64,
... np.float32,
... np.float64,
... np.complex64,
... np.complex128,
... object,
... ]
>>>
>>> basic_arrays = []
>>>
>>> for scalar in scalars:
... for endian in '<>':
... dtype = np.dtype(scalar).newbyteorder(endian)
... basic = np.arange(15).astype(dtype)
... basic_arrays.extend([
... np.array([], dtype=dtype),
... np.array(10, dtype=dtype),
... basic,
... basic.reshape((3,5)),
... basic.reshape((3,5)).T,
... basic.reshape((3,5))[::-1,::2],
... ])
...
>>>
>>> Pdescr = [
... ('x', 'i4', (2,)),
... ('y', 'f8', (2, 2)),
... ('z', 'u1')]
>>>
>>>
>>> PbufferT = [
... ([3,2], [[6.,4.],[6.,4.]], 8),
... ([4,3], [[7.,5.],[7.,5.]], 9),
... ]
>>>
>>>
>>> Ndescr = [
... ('x', 'i4', (2,)),
... ('Info', [
... ('value', 'c16'),
... ('y2', 'f8'),
... ('Info2', [
... ('name', 'S2'),
... ('value', 'c16', (2,)),
... ('y3', 'f8', (2,)),
... ('z3', 'u4', (2,))]),
... ('name', 'S2'),
... ('z2', 'b1')]),
... ('color', 'S2'),
... ('info', [
... ('Name', 'U8'),
... ('Value', 'c16')]),
... ('y', 'f8', (2, 2)),
... ('z', 'u1')]
>>>
>>>
>>> NbufferT = [
... ([3,2], (6j, 6., ('nn', [6j,4j], [6.,4.], [1,2]), 'NN', True), 'cc', ('NN', 6j), [[6.,4.],[6.,4.]], 8),
... ([4,3], (7j, 7., ('oo', [7j,5j], [7.,5.], [2,1]), 'OO', False), 'dd', ('OO', 7j), [[7.,5.],[7.,5.]], 9),
... ]
>>>
>>>
>>> record_arrays = [
... np.array(PbufferT, dtype=np.dtype(Pdescr).newbyteorder('<')),
... np.array(NbufferT, dtype=np.dtype(Ndescr).newbyteorder('<')),
... np.array(PbufferT, dtype=np.dtype(Pdescr).newbyteorder('>')),
... np.array(NbufferT, dtype=np.dtype(Ndescr).newbyteorder('>')),
... ]
Test the magic string writing.
>>> format.magic(1, 0)
'\x93NUMPY\x01\x00'
>>> format.magic(0, 0)
'\x93NUMPY\x00\x00'
>>> format.magic(255, 255)
'\x93NUMPY\xff\xff'
>>> format.magic(2, 5)
'\x93NUMPY\x02\x05'
Test the magic string reading.
>>> format.read_magic(BytesIO(format.magic(1, 0)))
(1, 0)
>>> format.read_magic(BytesIO(format.magic(0, 0)))
(0, 0)
>>> format.read_magic(BytesIO(format.magic(255, 255)))
(255, 255)
>>> format.read_magic(BytesIO(format.magic(2, 5)))
(2, 5)
Test the header writing.
>>> for arr in basic_arrays + record_arrays:
... f = BytesIO()
... format.write_array_header_1_0(f, arr) # XXX: arr is not a dict, items gets called on it
... print(repr(f.getvalue()))
...
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '|u1', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '|u1', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '|u1', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '|i1', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '|i1', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '|i1', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<u2', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<u2', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<u2', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<u2', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<u2', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<u2', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>u2', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>u2', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>u2', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>u2', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>u2', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>u2', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<i2', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<i2', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<i2', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<i2', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<i2', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<i2', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>i2', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>i2', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>i2', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>i2', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>i2', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>i2', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<u4', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<u4', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<u4', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<u4', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<u4', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<u4', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>u4', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>u4', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>u4', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>u4', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>u4', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>u4', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<i4', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<i4', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<i4', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<i4', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<i4', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<i4', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>i4', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>i4', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>i4', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>i4', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>i4', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>i4', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<u8', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<u8', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<u8', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<u8', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<u8', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<u8', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>u8', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>u8', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>u8', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>u8', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>u8', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>u8', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<i8', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<i8', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<i8', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<i8', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<i8', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<i8', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>i8', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>i8', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>i8', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>i8', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>i8', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>i8', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<f4', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<f4', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<f4', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<f4', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<f4', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<f4', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>f4', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>f4', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>f4', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>f4', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>f4', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>f4', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<f8', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<f8', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<f8', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<f8', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<f8', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<f8', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>f8', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>f8', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>f8', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>f8', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>f8', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>f8', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<c8', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<c8', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<c8', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<c8', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<c8', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<c8', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>c8', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>c8', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>c8', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>c8', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>c8', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>c8', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '<c16', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '<c16', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '<c16', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '<c16', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '<c16', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '<c16', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': '>c16', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': '>c16', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': '>c16', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': '>c16', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': '>c16', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': '>c16', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': 'O', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': (3, 3)} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': (0,)} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': ()} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': (15,)} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': (3, 5)} \n"
"F\x00{'descr': 'O', 'fortran_order': True, 'shape': (5, 3)} \n"
"F\x00{'descr': 'O', 'fortran_order': False, 'shape': (3, 3)} \n"
"v\x00{'descr': [('x', '<i4', (2,)), ('y', '<f8', (2, 2)), ('z', '|u1')],\n 'fortran_order': False,\n 'shape': (2,)} \n"
"\x16\x02{'descr': [('x', '<i4', (2,)),\n ('Info',\n [('value', '<c16'),\n ('y2', '<f8'),\n ('Info2',\n [('name', '|S2'),\n ('value', '<c16', (2,)),\n ('y3', '<f8', (2,)),\n ('z3', '<u4', (2,))]),\n ('name', '|S2'),\n ('z2', '|b1')]),\n ('color', '|S2'),\n ('info', [('Name', '<U8'), ('Value', '<c16')]),\n ('y', '<f8', (2, 2)),\n ('z', '|u1')],\n 'fortran_order': False,\n 'shape': (2,)} \n"
"v\x00{'descr': [('x', '>i4', (2,)), ('y', '>f8', (2, 2)), ('z', '|u1')],\n 'fortran_order': False,\n 'shape': (2,)} \n"
"\x16\x02{'descr': [('x', '>i4', (2,)),\n ('Info',\n [('value', '>c16'),\n ('y2', '>f8'),\n ('Info2',\n [('name', '|S2'),\n ('value', '>c16', (2,)),\n ('y3', '>f8', (2,)),\n ('z3', '>u4', (2,))]),\n ('name', '|S2'),\n ('z2', '|b1')]),\n ('color', '|S2'),\n ('info', [('Name', '>U8'), ('Value', '>c16')]),\n ('y', '>f8', (2, 2)),\n ('z', '|u1')],\n 'fortran_order': False,\n 'shape': (2,)} \n"
'''
import sys
import os
import warnings
import pytest
from io import BytesIO
import numpy as np
from numpy.testing import (
assert_, assert_array_equal, assert_raises, assert_raises_regex,
assert_warns, IS_PYPY,
)
from numpy.testing._private.utils import requires_memory
from numpy.lib import format
# Generate some basic arrays to test with.
scalars = [
np.uint8,
np.int8,
np.uint16,
np.int16,
np.uint32,
np.int32,
np.uint64,
np.int64,
np.float32,
np.float64,
np.complex64,
np.complex128,
object,
]
basic_arrays = []
for scalar in scalars:
for endian in '<>':
dtype = np.dtype(scalar).newbyteorder(endian)
basic = np.arange(1500).astype(dtype)
basic_arrays.extend([
# Empty
np.array([], dtype=dtype),
# Rank-0
np.array(10, dtype=dtype),
# 1-D
basic,
# 2-D C-contiguous
basic.reshape((30, 50)),
# 2-D F-contiguous
basic.reshape((30, 50)).T,
# 2-D non-contiguous
basic.reshape((30, 50))[::-1, ::2],
])
# More complicated record arrays.
# This is the structure of the table used for plain objects:
#
# +-+-+-+
# |x|y|z|
# +-+-+-+
# Structure of a plain array description:
Pdescr = [
('x', 'i4', (2,)),
('y', 'f8', (2, 2)),
('z', 'u1')]
# A plain list of tuples with values for testing:
PbufferT = [
# x y z
([3, 2], [[6., 4.], [6., 4.]], 8),
([4, 3], [[7., 5.], [7., 5.]], 9),
]
# This is the structure of the table used for nested objects (DON'T PANIC!):
#
# +-+---------------------------------+-----+----------+-+-+
# |x|Info |color|info |y|z|
# | +-----+--+----------------+----+--+ +----+-----+ | |
# | |value|y2|Info2 |name|z2| |Name|Value| | |
# | | | +----+-----+--+--+ | | | | | | |
# | | | |name|value|y3|z3| | | | | | | |
# +-+-----+--+----+-----+--+--+----+--+-----+----+-----+-+-+
#
# The corresponding nested array description:
Ndescr = [
('x', 'i4', (2,)),
('Info', [
('value', 'c16'),
('y2', 'f8'),
('Info2', [
('name', 'S2'),
('value', 'c16', (2,)),
('y3', 'f8', (2,)),
('z3', 'u4', (2,))]),
('name', 'S2'),
('z2', 'b1')]),
('color', 'S2'),
('info', [
('Name', 'U8'),
('Value', 'c16')]),
('y', 'f8', (2, 2)),
('z', 'u1')]
NbufferT = [
# x Info color info y z
# value y2 Info2 name z2 Name Value
# name value y3 z3
([3, 2], (6j, 6., ('nn', [6j, 4j], [6., 4.], [1, 2]), 'NN', True),
'cc', ('NN', 6j), [[6., 4.], [6., 4.]], 8),
([4, 3], (7j, 7., ('oo', [7j, 5j], [7., 5.], [2, 1]), 'OO', False),
'dd', ('OO', 7j), [[7., 5.], [7., 5.]], 9),
]
record_arrays = [
np.array(PbufferT, dtype=np.dtype(Pdescr).newbyteorder('<')),
np.array(NbufferT, dtype=np.dtype(Ndescr).newbyteorder('<')),
np.array(PbufferT, dtype=np.dtype(Pdescr).newbyteorder('>')),
np.array(NbufferT, dtype=np.dtype(Ndescr).newbyteorder('>')),
np.zeros(1, dtype=[('c', ('<f8', (5,)), (2,))])
]
#BytesIO that reads a random number of bytes at a time
class BytesIOSRandomSize(BytesIO):
def read(self, size=None):
import random
size = random.randint(1, size)
return super().read(size)
def roundtrip(arr):
f = BytesIO()
format.write_array(f, arr)
f2 = BytesIO(f.getvalue())
arr2 = format.read_array(f2, allow_pickle=True)
return arr2
def roundtrip_randsize(arr):
f = BytesIO()
format.write_array(f, arr)
f2 = BytesIOSRandomSize(f.getvalue())
arr2 = format.read_array(f2)
return arr2
def roundtrip_truncated(arr):
f = BytesIO()
format.write_array(f, arr)
#BytesIO is one byte short
f2 = BytesIO(f.getvalue()[0:-1])
arr2 = format.read_array(f2)
return arr2
def assert_equal_(o1, o2):
assert_(o1 == o2)
def test_roundtrip():
for arr in basic_arrays + record_arrays:
arr2 = roundtrip(arr)
assert_array_equal(arr, arr2)
def test_roundtrip_randsize():
for arr in basic_arrays + record_arrays:
if arr.dtype != object:
arr2 = roundtrip_randsize(arr)
assert_array_equal(arr, arr2)
def test_roundtrip_truncated():
for arr in basic_arrays:
if arr.dtype != object:
assert_raises(ValueError, roundtrip_truncated, arr)
def test_long_str():
# check items larger than internal buffer size, gh-4027
long_str_arr = np.ones(1, dtype=np.dtype((str, format.BUFFER_SIZE + 1)))
long_str_arr2 = roundtrip(long_str_arr)
assert_array_equal(long_str_arr, long_str_arr2)
@pytest.mark.slow
def test_memmap_roundtrip(tmpdir):
for i, arr in enumerate(basic_arrays + record_arrays):
if arr.dtype.hasobject:
# Skip these since they can't be mmap'ed.
continue
# Write it out normally and through mmap.
nfn = os.path.join(tmpdir, f'normal{i}.npy')
mfn = os.path.join(tmpdir, f'memmap{i}.npy')
with open(nfn, 'wb') as fp:
format.write_array(fp, arr)
fortran_order = (
arr.flags.f_contiguous and not arr.flags.c_contiguous)
ma = format.open_memmap(mfn, mode='w+', dtype=arr.dtype,
shape=arr.shape, fortran_order=fortran_order)
ma[...] = arr
ma.flush()
# Check that both of these files' contents are the same.
with open(nfn, 'rb') as fp:
normal_bytes = fp.read()
with open(mfn, 'rb') as fp:
memmap_bytes = fp.read()
assert_equal_(normal_bytes, memmap_bytes)
# Check that reading the file using memmap works.
ma = format.open_memmap(nfn, mode='r')
ma.flush()
def test_compressed_roundtrip(tmpdir):
arr = np.random.rand(200, 200)
npz_file = os.path.join(tmpdir, 'compressed.npz')
np.savez_compressed(npz_file, arr=arr)
with np.load(npz_file) as npz:
arr1 = npz['arr']
assert_array_equal(arr, arr1)
# aligned
dt1 = np.dtype('i1, i4, i1', align=True)
# non-aligned, explicit offsets
dt2 = np.dtype({'names': ['a', 'b'], 'formats': ['i4', 'i4'],
'offsets': [1, 6]})
# nested struct-in-struct
dt3 = np.dtype({'names': ['c', 'd'], 'formats': ['i4', dt2]})
# field with '' name
dt4 = np.dtype({'names': ['a', '', 'b'], 'formats': ['i4']*3})
# titles
dt5 = np.dtype({'names': ['a', 'b'], 'formats': ['i4', 'i4'],
'offsets': [1, 6], 'titles': ['aa', 'bb']})
# empty
dt6 = np.dtype({'names': [], 'formats': [], 'itemsize': 8})
@pytest.mark.parametrize("dt", [dt1, dt2, dt3, dt4, dt5, dt6])
def test_load_padded_dtype(tmpdir, dt):
arr = np.zeros(3, dt)
for i in range(3):
arr[i] = i + 5
npz_file = os.path.join(tmpdir, 'aligned.npz')
np.savez(npz_file, arr=arr)
with np.load(npz_file) as npz:
arr1 = npz['arr']
assert_array_equal(arr, arr1)
def test_python2_python3_interoperability():
fname = 'win64python2.npy'
path = os.path.join(os.path.dirname(__file__), 'data', fname)
data = np.load(path)
assert_array_equal(data, np.ones(2))
def test_pickle_python2_python3():
# Test that loading object arrays saved on Python 2 works both on
# Python 2 and Python 3 and vice versa
data_dir = os.path.join(os.path.dirname(__file__), 'data')
expected = np.array([None, range, u'\u512a\u826f',
b'\xe4\xb8\x8d\xe8\x89\xaf'],
dtype=object)
for fname in ['py2-objarr.npy', 'py2-objarr.npz',
'py3-objarr.npy', 'py3-objarr.npz']:
path = os.path.join(data_dir, fname)
for encoding in ['bytes', 'latin1']:
data_f = np.load(path, allow_pickle=True, encoding=encoding)
if fname.endswith('.npz'):
data = data_f['x']
data_f.close()
else:
data = data_f
if encoding == 'latin1' and fname.startswith('py2'):
assert_(isinstance(data[3], str))
assert_array_equal(data[:-1], expected[:-1])
# mojibake occurs
assert_array_equal(data[-1].encode(encoding), expected[-1])
else:
assert_(isinstance(data[3], bytes))
assert_array_equal(data, expected)
if fname.startswith('py2'):
if fname.endswith('.npz'):
data = np.load(path, allow_pickle=True)
assert_raises(UnicodeError, data.__getitem__, 'x')
data.close()
data = np.load(path, allow_pickle=True, fix_imports=False,
encoding='latin1')
assert_raises(ImportError, data.__getitem__, 'x')
data.close()
else:
assert_raises(UnicodeError, np.load, path,
allow_pickle=True)
assert_raises(ImportError, np.load, path,
allow_pickle=True, fix_imports=False,
encoding='latin1')
def test_pickle_disallow(tmpdir):
data_dir = os.path.join(os.path.dirname(__file__), 'data')
path = os.path.join(data_dir, 'py2-objarr.npy')
assert_raises(ValueError, np.load, path,
allow_pickle=False, encoding='latin1')
path = os.path.join(data_dir, 'py2-objarr.npz')
with np.load(path, allow_pickle=False, encoding='latin1') as f:
assert_raises(ValueError, f.__getitem__, 'x')
path = os.path.join(tmpdir, 'pickle-disabled.npy')
assert_raises(ValueError, np.save, path, np.array([None], dtype=object),
allow_pickle=False)
@pytest.mark.parametrize('dt', [
np.dtype(np.dtype([('a', np.int8),
('b', np.int16),
('c', np.int32),
], align=True),
(3,)),
np.dtype([('x', np.dtype({'names':['a','b'],
'formats':['i1','i1'],
'offsets':[0,4],
'itemsize':8,
},
(3,)),
(4,),
)]),
np.dtype([('x',
('<f8', (5,)),
(2,),
)]),
np.dtype([('x', np.dtype((
np.dtype((
np.dtype({'names':['a','b'],
'formats':['i1','i1'],
'offsets':[0,4],
'itemsize':8}),
(3,)
)),
(4,)
)))
]),
np.dtype([
('a', np.dtype((
np.dtype((
np.dtype((
np.dtype([
('a', int),
('b', np.dtype({'names':['a','b'],
'formats':['i1','i1'],
'offsets':[0,4],
'itemsize':8})),
]),
(3,),
)),
(4,),
)),
(5,),
)))
]),
])
def test_descr_to_dtype(dt):
dt1 = format.descr_to_dtype(dt.descr)
assert_equal_(dt1, dt)
arr1 = np.zeros(3, dt)
arr2 = roundtrip(arr1)
assert_array_equal(arr1, arr2)
def test_version_2_0():
f = BytesIO()
# requires more than 2 byte for header
dt = [(("%d" % i) * 100, float) for i in range(500)]
d = np.ones(1000, dtype=dt)
format.write_array(f, d, version=(2, 0))
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', '', UserWarning)
format.write_array(f, d)
assert_(w[0].category is UserWarning)
# check alignment of data portion
f.seek(0)
header = f.readline()
assert_(len(header) % format.ARRAY_ALIGN == 0)
f.seek(0)
n = format.read_array(f, max_header_size=200000)
assert_array_equal(d, n)
# 1.0 requested but data cannot be saved this way
assert_raises(ValueError, format.write_array, f, d, (1, 0))
def test_version_2_0_memmap(tmpdir):
# requires more than 2 byte for header
dt = [(("%d" % i) * 100, float) for i in range(500)]
d = np.ones(1000, dtype=dt)
tf1 = os.path.join(tmpdir, f'version2_01.npy')
tf2 = os.path.join(tmpdir, f'version2_02.npy')
# 1.0 requested but data cannot be saved this way
assert_raises(ValueError, format.open_memmap, tf1, mode='w+', dtype=d.dtype,
shape=d.shape, version=(1, 0))
ma = format.open_memmap(tf1, mode='w+', dtype=d.dtype,
shape=d.shape, version=(2, 0))
ma[...] = d
ma.flush()
ma = format.open_memmap(tf1, mode='r', max_header_size=200000)
assert_array_equal(ma, d)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', '', UserWarning)
ma = format.open_memmap(tf2, mode='w+', dtype=d.dtype,
shape=d.shape, version=None)
assert_(w[0].category is UserWarning)
ma[...] = d
ma.flush()
ma = format.open_memmap(tf2, mode='r', max_header_size=200000)
assert_array_equal(ma, d)
@pytest.mark.parametrize("mmap_mode", ["r", None])
def test_huge_header(tmpdir, mmap_mode):
f = os.path.join(tmpdir, f'large_header.npy')
arr = np.array(1, dtype="i,"*10000+"i")
with pytest.warns(UserWarning, match=".*format 2.0"):
np.save(f, arr)
with pytest.raises(ValueError, match="Header.*large"):
np.load(f, mmap_mode=mmap_mode)
with pytest.raises(ValueError, match="Header.*large"):
np.load(f, mmap_mode=mmap_mode, max_header_size=20000)
res = np.load(f, mmap_mode=mmap_mode, allow_pickle=True)
assert_array_equal(res, arr)
res = np.load(f, mmap_mode=mmap_mode, max_header_size=180000)
assert_array_equal(res, arr)
def test_huge_header_npz(tmpdir):
f = os.path.join(tmpdir, f'large_header.npz')
arr = np.array(1, dtype="i,"*10000+"i")
with pytest.warns(UserWarning, match=".*format 2.0"):
np.savez(f, arr=arr)
# Only getting the array from the file actually reads it
with pytest.raises(ValueError, match="Header.*large"):
np.load(f)["arr"]
with pytest.raises(ValueError, match="Header.*large"):
np.load(f, max_header_size=20000)["arr"]
res = np.load(f, allow_pickle=True)["arr"]
assert_array_equal(res, arr)
res = np.load(f, max_header_size=180000)["arr"]
assert_array_equal(res, arr)
def test_write_version():
f = BytesIO()
arr = np.arange(1)
# These should pass.
format.write_array(f, arr, version=(1, 0))
format.write_array(f, arr)
format.write_array(f, arr, version=None)
format.write_array(f, arr)
format.write_array(f, arr, version=(2, 0))
format.write_array(f, arr)
# These should all fail.
bad_versions = [
(1, 1),
(0, 0),
(0, 1),
(2, 2),
(255, 255),
]
for version in bad_versions:
with assert_raises_regex(ValueError,
'we only support format version.*'):
format.write_array(f, arr, version=version)
bad_version_magic = [
b'\x93NUMPY\x01\x01',
b'\x93NUMPY\x00\x00',
b'\x93NUMPY\x00\x01',
b'\x93NUMPY\x02\x00',
b'\x93NUMPY\x02\x02',
b'\x93NUMPY\xff\xff',
]
malformed_magic = [
b'\x92NUMPY\x01\x00',
b'\x00NUMPY\x01\x00',
b'\x93numpy\x01\x00',
b'\x93MATLB\x01\x00',
b'\x93NUMPY\x01',
b'\x93NUMPY',
b'',
]
def test_read_magic():
s1 = BytesIO()
s2 = BytesIO()
arr = np.ones((3, 6), dtype=float)
format.write_array(s1, arr, version=(1, 0))
format.write_array(s2, arr, version=(2, 0))
s1.seek(0)
s2.seek(0)
version1 = format.read_magic(s1)
version2 = format.read_magic(s2)
assert_(version1 == (1, 0))
assert_(version2 == (2, 0))
assert_(s1.tell() == format.MAGIC_LEN)
assert_(s2.tell() == format.MAGIC_LEN)
def test_read_magic_bad_magic():
for magic in malformed_magic:
f = BytesIO(magic)
assert_raises(ValueError, format.read_array, f)
def test_read_version_1_0_bad_magic():
for magic in bad_version_magic + malformed_magic:
f = BytesIO(magic)
assert_raises(ValueError, format.read_array, f)
def test_bad_magic_args():
assert_raises(ValueError, format.magic, -1, 1)
assert_raises(ValueError, format.magic, 256, 1)
assert_raises(ValueError, format.magic, 1, -1)
assert_raises(ValueError, format.magic, 1, 256)
def test_large_header():
s = BytesIO()
d = {'a': 1, 'b': 2}
format.write_array_header_1_0(s, d)
s = BytesIO()
d = {'a': 1, 'b': 2, 'c': 'x'*256*256}
assert_raises(ValueError, format.write_array_header_1_0, s, d)
def test_read_array_header_1_0():
s = BytesIO()
arr = np.ones((3, 6), dtype=float)
format.write_array(s, arr, version=(1, 0))
s.seek(format.MAGIC_LEN)
shape, fortran, dtype = format.read_array_header_1_0(s)
assert_(s.tell() % format.ARRAY_ALIGN == 0)
assert_((shape, fortran, dtype) == ((3, 6), False, float))
def test_read_array_header_2_0():
s = BytesIO()
arr = np.ones((3, 6), dtype=float)
format.write_array(s, arr, version=(2, 0))
s.seek(format.MAGIC_LEN)
shape, fortran, dtype = format.read_array_header_2_0(s)
assert_(s.tell() % format.ARRAY_ALIGN == 0)
assert_((shape, fortran, dtype) == ((3, 6), False, float))
def test_bad_header():
# header of length less than 2 should fail
s = BytesIO()
assert_raises(ValueError, format.read_array_header_1_0, s)
s = BytesIO(b'1')
assert_raises(ValueError, format.read_array_header_1_0, s)
# header shorter than indicated size should fail
s = BytesIO(b'\x01\x00')
assert_raises(ValueError, format.read_array_header_1_0, s)
# headers without the exact keys required should fail
d = {"shape": (1, 2),
"descr": "x"}
s = BytesIO()
format.write_array_header_1_0(s, d)
assert_raises(ValueError, format.read_array_header_1_0, s)
d = {"shape": (1, 2),
"fortran_order": False,
"descr": "x",
"extrakey": -1}
s = BytesIO()
format.write_array_header_1_0(s, d)
assert_raises(ValueError, format.read_array_header_1_0, s)
def test_large_file_support(tmpdir):
if (sys.platform == 'win32' or sys.platform == 'cygwin'):
pytest.skip("Unknown if Windows has sparse filesystems")
# try creating a large sparse file
tf_name = os.path.join(tmpdir, 'sparse_file')
try:
# seek past end would work too, but linux truncate somewhat
# increases the chances that we have a sparse filesystem and can
# avoid actually writing 5GB
import subprocess as sp
sp.check_call(["truncate", "-s", "5368709120", tf_name])
except Exception:
pytest.skip("Could not create 5GB large file")
# write a small array to the end
with open(tf_name, "wb") as f:
f.seek(5368709120)
d = np.arange(5)
np.save(f, d)
# read it back
with open(tf_name, "rb") as f:
f.seek(5368709120)
r = np.load(f)
assert_array_equal(r, d)
@pytest.mark.skipif(np.dtype(np.intp).itemsize < 8,
reason="test requires 64-bit system")
@pytest.mark.slow
@requires_memory(free_bytes=2 * 2**30)
def test_large_archive(tmpdir):
# Regression test for product of saving arrays with dimensions of array
# having a product that doesn't fit in int32. See gh-7598 for details.
shape = (2**30, 2)
try:
a = np.empty(shape, dtype=np.uint8)
except MemoryError:
pytest.skip("Could not create large file")
fname = os.path.join(tmpdir, "large_archive")
with open(fname, "wb") as f:
np.savez(f, arr=a)
del a
with open(fname, "rb") as f:
new_a = np.load(f)["arr"]
assert new_a.shape == shape
def test_empty_npz(tmpdir):
# Test for gh-9989
fname = os.path.join(tmpdir, "nothing.npz")
np.savez(fname)
with np.load(fname) as nps:
pass
def test_unicode_field_names(tmpdir):
# gh-7391
arr = np.array([
(1, 3),
(1, 2),
(1, 3),
(1, 2)
], dtype=[
('int', int),
(u'\N{CJK UNIFIED IDEOGRAPH-6574}\N{CJK UNIFIED IDEOGRAPH-5F62}', int)
])
fname = os.path.join(tmpdir, "unicode.npy")
with open(fname, 'wb') as f:
format.write_array(f, arr, version=(3, 0))
with open(fname, 'rb') as f:
arr2 = format.read_array(f)
assert_array_equal(arr, arr2)
# notifies the user that 3.0 is selected
with open(fname, 'wb') as f:
with assert_warns(UserWarning):
format.write_array(f, arr, version=None)
@pytest.mark.parametrize('dt, fail', [
(np.dtype({'names': ['a', 'b'], 'formats': [float, np.dtype('S3',
metadata={'some': 'stuff'})]}), True),
(np.dtype(int, metadata={'some': 'stuff'}), False),
(np.dtype([('subarray', (int, (2,)))], metadata={'some': 'stuff'}), False),
# recursive: metadata on the field of a dtype
(np.dtype({'names': ['a', 'b'], 'formats': [
float, np.dtype({'names': ['c'], 'formats': [np.dtype(int, metadata={})]})
]}), False)
])
@pytest.mark.skipif(IS_PYPY and sys.implementation.version <= (7, 3, 8),
reason="PyPy bug in error formatting")
def test_metadata_dtype(dt, fail):
# gh-14142
arr = np.ones(10, dtype=dt)
buf = BytesIO()
with assert_warns(UserWarning):
np.save(buf, arr)
buf.seek(0)
if fail:
with assert_raises(ValueError):
np.load(buf)