"""Utilities for fast persistence of big data, with optional compression."""
# Author: Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# Copyright (c) 2009 Gael Varoquaux
# License: BSD Style, 3 clauses.
import pickle
import os
import sys
import warnings
try:
from pathlib import Path
except ImportError:
Path = None
from .compressor import lz4, LZ4_NOT_INSTALLED_ERROR
from .compressor import _COMPRESSORS, register_compressor, BinaryZlibFile
from .compressor import (ZlibCompressorWrapper, GzipCompressorWrapper,
BZ2CompressorWrapper, LZMACompressorWrapper,
XZCompressorWrapper, LZ4CompressorWrapper)
from .numpy_pickle_utils import Unpickler, Pickler
from .numpy_pickle_utils import _read_fileobject, _write_fileobject
from .numpy_pickle_utils import _read_bytes, BUFFER_SIZE
from .numpy_pickle_compat import load_compatibility
from .numpy_pickle_compat import NDArrayWrapper
# For compatibility with old versions of joblib, we need ZNDArrayWrapper
# to be visible in the current namespace.
# Explicitly skipping next line from flake8 as it triggers an F401 warning
# which we don't care.
from .numpy_pickle_compat import ZNDArrayWrapper # noqa
from ._compat import _basestring, PY3_OR_LATER
from .backports import make_memmap
# Register supported compressors
register_compressor('zlib', ZlibCompressorWrapper())
register_compressor('gzip', GzipCompressorWrapper())
register_compressor('bz2', BZ2CompressorWrapper())
register_compressor('lzma', LZMACompressorWrapper())
register_compressor('xz', XZCompressorWrapper())
register_compressor('lz4', LZ4CompressorWrapper())
###############################################################################
# Utility objects for persistence.
class NumpyArrayWrapper(object):
"""An object to be persisted instead of numpy arrays.
This object is used to hack into the pickle machinery and read numpy
array data from our custom persistence format.
More precisely, this object is used for:
* carrying the information of the persisted array: subclass, shape, order,
dtype. Those ndarray metadata are used to correctly reconstruct the array
with low level numpy functions.
* determining if memmap is allowed on the array.
* reading the array bytes from a file.
* reading the array using memorymap from a file.
* writing the array bytes to a file.
Attributes
----------
subclass: numpy.ndarray subclass
Determine the subclass of the wrapped array.
shape: numpy.ndarray shape
Determine the shape of the wrapped array.
order: {'C', 'F'}
Determine the order of wrapped array data. 'C' is for C order, 'F' is
for fortran order.
dtype: numpy.ndarray dtype
Determine the data type of the wrapped array.
allow_mmap: bool
Determine if memory mapping is allowed on the wrapped array.
Default: False.
"""
def __init__(self, subclass, shape, order, dtype, allow_mmap=False):
"""Constructor. Store the useful information for later."""
self.subclass = subclass
self.shape = shape
self.order = order
self.dtype = dtype
self.allow_mmap = allow_mmap
def write_array(self, array, pickler):
"""Write array bytes to pickler file handle.
This function is an adaptation of the numpy write_array function
available in version 1.10.1 in numpy/lib/format.py.
"""
# Set buffer size to 16 MiB to hide the Python loop overhead.
buffersize = max(16 * 1024 ** 2 // array.itemsize, 1)
if array.dtype.hasobject:
# We contain Python objects so we cannot write out the data
# directly. Instead, we will pickle it out with version 2 of the
# pickle protocol.
pickle.dump(array, pickler.file_handle, protocol=2)
else:
for chunk in pickler.np.nditer(array,
flags=['external_loop',
'buffered',
'zerosize_ok'],
buffersize=buffersize,
order=self.order):
pickler.file_handle.write(chunk.tostring('C'))
def read_array(self, unpickler):
"""Read array from unpickler file handle.
This function is an adaptation of the numpy read_array function
available in version 1.10.1 in numpy/lib/format.py.
"""
if len(self.shape) == 0:
count = 1
else:
# joblib issue #859: we cast the elements of self.shape to int64 to
# prevent a potential overflow when computing their product.
shape_int64 = [unpickler.np.int64(x) for x in self.shape]
count = unpickler.np.multiply.reduce(shape_int64)
# Now read the actual data.
if self.dtype.hasobject:
# The array contained Python objects. We need to unpickle the data.
array = pickle.load(unpickler.file_handle)
else:
if (not PY3_OR_LATER and
unpickler.np.compat.isfileobj(unpickler.file_handle)):
# In python 2, gzip.GzipFile is considered as a file so one
# can use numpy.fromfile().
# For file objects, use np.fromfile function.
# This function is faster than the memory-intensive
# method below.
array = unpickler.np.fromfile(unpickler.file_handle,
dtype=self.dtype, count=count)
else:
# This is not a real file. We have to read it the
# memory-intensive way.
# crc32 module fails on reads greater than 2 ** 32 bytes,
# breaking large reads from gzip streams. Chunk reads to
# BUFFER_SIZE bytes to avoid issue and reduce memory overhead
# of the read. In non-chunked case count < max_read_count, so
# only one read is performed.
max_read_count = BUFFER_SIZE // min(BUFFER_SIZE,
self.dtype.itemsize)
array = unpickler.np.empty(count, dtype=self.dtype)
for i in range(0, count, max_read_count):
read_count = min(max_read_count, count - i)
read_size = int(read_count * self.dtype.itemsize)
data = _read_bytes(unpickler.file_handle,
read_size, "array data")
array[i:i + read_count] = \
unpickler.np.frombuffer(data, dtype=self.dtype,
count=read_count)
del data
if self.order == 'F':
array.shape = self.shape[::-1]
array = array.transpose()
else:
array.shape = self.shape
return array
def read_mmap(self, unpickler):
"""Read an array using numpy memmap."""
offset = unpickler.file_handle.tell()
if unpickler.mmap_mode == 'w+':
unpickler.mmap_mode = 'r+'
marray = make_memmap(unpickler.filename,
dtype=self.dtype,
shape=self.shape,
order=self.order,
mode=unpickler.mmap_mode,
offset=offset)
# update the offset so that it corresponds to the end of the read array
unpickler.file_handle.seek(offset + marray.nbytes)
return marray
def read(self, unpickler):
"""Read the array corresponding to this wrapper.
Use the unpickler to get all information to correctly read the array.
Parameters
----------
unpickler: NumpyUnpickler
Returns
-------
array: numpy.ndarray
"""
# When requested, only use memmap mode if allowed.
if unpickler.mmap_mode is not None and self.allow_mmap:
array = self.read_mmap(unpickler)
else:
array = self.read_array(unpickler)
# Manage array subclass case
if (hasattr(array, '__array_prepare__') and
self.subclass not in (unpickler.np.ndarray,
unpickler.np.memmap)):
# We need to reconstruct another subclass
new_array = unpickler.np.core.multiarray._reconstruct(
self.subclass, (0,), 'b')
return new_array.__array_prepare__(array)
else:
return array
###############################################################################
# Pickler classes
class NumpyPickler(Pickler):
"""A pickler to persist big data efficiently.
The main features of this object are:
* persistence of numpy arrays in a single file.
* optional compression with a special care on avoiding memory copies.
Attributes
----------
fp: file
File object handle used for serializing the input object.
protocol: int, optional
Pickle protocol used. Default is pickle.DEFAULT_PROTOCOL under
python 3, pickle.HIGHEST_PROTOCOL otherwise.
"""
dispatch = Pickler.dispatch.copy()
def __init__(self, fp, protocol=None):
self.file_handle = fp
self.buffered = isinstance(self.file_handle, BinaryZlibFile)
# By default we want a pickle protocol that only changes with
# the major python version and not the minor one
if protocol is None:
protocol = (pickle.DEFAULT_PROTOCOL if PY3_OR_LATER
else pickle.HIGHEST_PROTOCOL)
Pickler.__init__(self, self.file_handle, protocol=protocol)
# delayed import of numpy, to avoid tight coupling
try:
import numpy as np
except ImportError:
np = None
self.np = np
def _create_array_wrapper(self, array):
"""Create and returns a numpy array wrapper from a numpy array."""
order = 'F' if (array.flags.f_contiguous and
not array.flags.c_contiguous) else 'C'
allow_mmap = not self.buffered and not array.dtype.hasobject
wrapper = NumpyArrayWrapper(type(array),
array.shape, order, array.dtype,
allow_mmap=allow_mmap)
return wrapper
def save(self, obj):
"""Subclass the Pickler `save` method.
This is a total abuse of the Pickler class in order to use the numpy
persistence function `save` instead of the default pickle
implementation. The numpy array is replaced by a custom wrapper in the
pickle persistence stack and the serialized array is written right
after in the file. Warning: the file produced does not follow the
pickle format. As such it can not be read with `pickle.load`.
"""
if self.np is not None and type(obj) in (self.np.ndarray,
self.np.matrix,
self.np.memmap):
if type(obj) is self.np.memmap:
# Pickling doesn't work with memmapped arrays
obj = self.np.asanyarray(obj)
# The array wrapper is pickled instead of the real array.
wrapper = self._create_array_wrapper(obj)
Pickler.save(self, wrapper)
# A framer was introduced with pickle protocol 4 and we want to
# ensure the wrapper object is written before the numpy array
# buffer in the pickle file.
# See https://www.python.org/dev/peps/pep-3154/#framing to get
# more information on the framer behavior.
if self.proto >= 4:
self.framer.commit_frame(force=True)
# And then array bytes are written right after the wrapper.
wrapper.write_array(obj, self)
return
return Pickler.save(self, obj)
class NumpyUnpickler(Unpickler):
"""A subclass of the Unpickler to unpickle our numpy pickles.
Attributes
----------
mmap_mode: str
The memorymap mode to use for reading numpy arrays.
file_handle: file_like
File object to unpickle from.
filename: str
Name of the file to unpickle from. It should correspond to file_handle.
This parameter is required when using mmap_mode.
np: module
Reference to numpy module if numpy is installed else None.
"""
dispatch = Unpickler.dispatch.copy()
def __init__(self, filename, file_handle, mmap_mode=None):
# The next line is for backward compatibility with pickle generated
# with joblib versions less than 0.10.
self._dirname = os.path.dirname(filename)
self.mmap_mode = mmap_mode
self.file_handle = file_handle
# filename is required for numpy mmap mode.
self.filename = filename
self.compat_mode = False
Unpickler.__init__(self, self.file_handle)
try:
import numpy as np
except ImportError:
np = None
self.np = np
def load_build(self):
"""Called to set the state of a newly created object.
We capture it to replace our place-holder objects, NDArrayWrapper or
NumpyArrayWrapper, by the array we are interested in. We
replace them directly in the stack of pickler.
NDArrayWrapper is used for backward compatibility with joblib <= 0.9.
"""
Unpickler.load_build(self)
# For backward compatibility, we support NDArrayWrapper objects.
if isinstance(self.stack[-1], (NDArrayWrapper, NumpyArrayWrapper)):
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