numpy_pickle_utils.py

"""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 io
import sys
import warnings
import contextlib

from .compressor import _ZFILE_PREFIX
from .compressor import _COMPRESSORS

try:
    import numpy as np
except ImportError:
    np = None

Unpickler = pickle._Unpickler
Pickler = pickle._Pickler
xrange = range


try:
    # The python standard library can be built without bz2 so we make bz2
    # usage optional.
    # see https://github.com/scikit-learn/scikit-learn/issues/7526 for more
    # details.
    import bz2
except ImportError:
    bz2 = None

# Buffer size used in io.BufferedReader and io.BufferedWriter
_IO_BUFFER_SIZE = 1024 ** 2


def _is_raw_file(fileobj):
    """Check if fileobj is a raw file object, e.g created with open."""
    fileobj = getattr(fileobj, 'raw', fileobj)
    return isinstance(fileobj, io.FileIO)


def _get_prefixes_max_len():
    # Compute the max prefix len of registered compressors.
    prefixes = [len(compressor.prefix) for compressor in _COMPRESSORS.values()]
    prefixes += [len(_ZFILE_PREFIX)]
    return max(prefixes)


def _is_numpy_array_byte_order_mismatch(array):
    """Check if numpy array is having byte order mis-match"""
    return ((sys.byteorder == 'big' and
             (array.dtype.byteorder == '<' or
              (array.dtype.byteorder == '|' and array.dtype.fields and
               all(e[0].byteorder == '<'
                   for e in array.dtype.fields.values())))) or
            (sys.byteorder == 'little' and
             (array.dtype.byteorder == '>' or
              (array.dtype.byteorder == '|' and array.dtype.fields and
               all(e[0].byteorder == '>'
                   for e in array.dtype.fields.values())))))


def _ensure_native_byte_order(array):
    """Use the byte order of the host while preserving values

    Does nothing if array already uses the system byte order.
    """
    if _is_numpy_array_byte_order_mismatch(array):
        array = array.byteswap().newbyteorder('=')
    return array


###############################################################################
# Cache file utilities
def _detect_compressor(fileobj):
    """Return the compressor matching fileobj.

    Parameters
    ----------
    fileobj: file object

    Returns
    -------
    str in {'zlib', 'gzip', 'bz2', 'lzma', 'xz', 'compat', 'not-compressed'}
    """
    # Read the magic number in the first bytes of the file.
    max_prefix_len = _get_prefixes_max_len()
    if hasattr(fileobj, 'peek'):
        # Peek allows to read those bytes without moving the cursor in the
        # file whic.
        first_bytes = fileobj.peek(max_prefix_len)
    else:
        # Fallback to seek if the fileobject is not peekable.
        first_bytes = fileobj.read(max_prefix_len)
        fileobj.seek(0)

    if first_bytes.startswith(_ZFILE_PREFIX):
        return "compat"
    else:
        for name, compressor in _COMPRESSORS.items():
            if first_bytes.startswith(compressor.prefix):
                return name

    return "not-compressed"


def _buffered_read_file(fobj):
    """Return a buffered version of a read file object."""
    return io.BufferedReader(fobj, buffer_size=_IO_BUFFER_SIZE)


def _buffered_write_file(fobj):
    """Return a buffered version of a write file object."""
    return io.BufferedWriter(fobj, buffer_size=_IO_BUFFER_SIZE)


@contextlib.contextmanager
def _read_fileobject(fileobj, filename, mmap_mode=None):
    """Utility function opening the right fileobject from a filename.

    The magic number is used to choose between the type of file object to open:
    * regular file object (default)
    * zlib file object
    * gzip file object
    * bz2 file object
    * lzma file object (for xz and lzma compressor)

    Parameters
    ----------
    fileobj: file object
    compressor: str in {'zlib', 'gzip', 'bz2', 'lzma', 'xz', 'compat',
                        'not-compressed'}
    filename: str
        filename path corresponding to the fileobj parameter.
    mmap_mode: str
        memory map mode that should be used to open the pickle file. This
        parameter is useful to verify that the user is not trying to one with
        compression. Default: None.

    Returns
    -------
        a file like object

    """
    # Detect if the fileobj contains compressed data.
    compressor = _detect_compressor(fileobj)

    if compressor == 'compat':
        # Compatibility with old pickle mode: simply return the input
        # filename "as-is" and let the compatibility function be called by the
        # caller.
        warnings.warn("The file '%s' has been generated with a joblib "
                      "version less than 0.10. "
                      "Please regenerate this pickle file." % filename,
                      DeprecationWarning, stacklevel=2)
        yield filename
    else:
        if compressor in _COMPRESSORS:
            # based on the compressor detected in the file, we open the
            # correct decompressor file object, wrapped in a buffer.
            compressor_wrapper = _COMPRESSORS[compressor]
            inst = compressor_wrapper.decompressor_file(fileobj)
            fileobj = _buffered_read_file(inst)

        # Checking if incompatible load parameters with the type of file:
        # mmap_mode cannot be used with compressed file or in memory buffers
        # such as io.BytesIO.
        if mmap_mode is not None:
            if isinstance(fileobj, io.BytesIO):
                warnings.warn('In memory persistence is not compatible with '
                              'mmap_mode "%(mmap_mode)s" flag passed. '
                              'mmap_mode option will be ignored.'
                              % locals(), stacklevel=2)
            elif compressor != 'not-compressed':
                warnings.warn('mmap_mode "%(mmap_mode)s" is not compatible '
                              'with compressed file %(filename)s. '
                              '"%(mmap_mode)s" flag will be ignored.'
                              % locals(), stacklevel=2)
            elif not _is_raw_file(fileobj):
                warnings.warn('"%(fileobj)r" is not a raw file, mmap_mode '
                              '"%(mmap_mode)s" flag will be ignored.'
                              % locals(), stacklevel=2)

        yield fileobj


def _write_fileobject(filename, compress=("zlib", 3)):
    """Return the right compressor file object in write mode."""
    compressmethod = compress[0]
    compresslevel = compress[1]

    if compressmethod in _COMPRESSORS.keys():
        file_instance = _COMPRESSORS[compressmethod].compressor_file(
            filename, compresslevel=compresslevel)
        return _buffered_write_file(file_instance)
    else:
        file_instance = _COMPRESSORS['zlib'].compressor_file(
            filename, compresslevel=compresslevel)
        return _buffered_write_file(file_instance)


# Utility functions/variables from numpy required for writing arrays.
# We need at least the functions introduced in version 1.9 of numpy. Here,
# we use the ones from numpy 1.10.2.
BUFFER_SIZE = 2 ** 18  # size of buffer for reading npz files in bytes


def _read_bytes(fp, size, error_template="ran out of data"):
    """Read from file-like object until size bytes are read.

    TODO python2_drop: is it still needed? The docstring mentions python 2.6
    and it looks like this can be at least simplified ...

    Raises ValueError if not EOF is encountered before size bytes are read.
    Non-blocking objects only supported if they derive from io objects.

    Required as e.g. ZipExtFile in python 2.6 can return less data than
    requested.

    This function was taken from numpy/lib/format.py in version 1.10.2.

    Parameters
    ----------
    fp: file-like object
    size: int
    error_template: str

    Returns
    -------
    a bytes object
        The data read in bytes.

    """
    data = bytes()
    while True:
        # io files (default in python3) return None or raise on
        # would-block, python2 file will truncate, probably nothing can be
        # done about that.  note that regular files can't be non-blocking
        try:
            r = fp.read(size - len(data))
            data += r
            if len(r) == 0 or len(data) == size:
                break
        except io.BlockingIOError:
            pass
    if len(data) != size:
        msg = "EOF: reading %s, expected %d bytes got %d"
        raise ValueError(msg % (error_template, size, len(data)))
    else:
        return data