numpy 1.9.3__zip → 1.10.0__zip

numpy-1.9.3/numpy/lib/format.py

@@ -1,771 +0,0 @@
-"""
-Define a simple format for saving numpy arrays to disk with the full
-information about them.
-
-The ``.npy`` format is the standard binary file format in NumPy for
-persisting a *single* arbitrary NumPy array on disk. The format stores all
-of the shape and dtype information necessary to reconstruct the array
-correctly even on another machine with a different architecture.
-The format is designed to be as simple as possible while achieving
-its limited goals.
-
-The ``.npz`` format is the standard format for persisting *multiple* NumPy
-arrays on disk. A ``.npz`` file is a zip file containing multiple ``.npy``
-files, one for each array.
-
-Capabilities
-------------
-
-- Can represent all NumPy arrays including nested record arrays and
-  object arrays.
-
-- Represents the data in its native binary form.
-
-- Supports Fortran-contiguous arrays directly.
-
-- Stores all of the necessary information to reconstruct the array
-  including shape and dtype on a machine of a different
-  architecture.  Both little-endian and big-endian arrays are
-  supported, and a file with little-endian numbers will yield
-  a little-endian array on any machine reading the file. The
-  types are described in terms of their actual sizes. For example,
-  if a machine with a 64-bit C "long int" writes out an array with
-  "long ints", a reading machine with 32-bit C "long ints" will yield
-  an array with 64-bit integers.
-
-- Is straightforward to reverse engineer. Datasets often live longer than
-  the programs that created them. A competent developer should be
-  able to create a solution in his preferred programming language to
-  read most ``.npy`` files that he has been given without much
-  documentation.
-
-- Allows memory-mapping of the data. See `open_memmep`.
-
-- Can be read from a filelike stream object instead of an actual file.
-
-- Stores object arrays, i.e. arrays containing elements that are arbitrary
-  Python objects. Files with object arrays are not to be mmapable, but
-  can be read and written to disk.
-
-Limitations
------------
-
-- Arbitrary subclasses of numpy.ndarray are not completely preserved.
-  Subclasses will be accepted for writing, but only the array data will
-  be written out. A regular numpy.ndarray object will be created
-  upon reading the file.
-
-.. warning::
-
-  Due to limitations in the interpretation of structured dtypes, dtypes
-  with fields with empty names will have the names replaced by 'f0', 'f1',
-  etc. Such arrays will not round-trip through the format entirely
-  accurately. The data is intact; only the field names will differ. We are
-  working on a fix for this. This fix will not require a change in the
-  file format. The arrays with such structures can still be saved and
-  restored, and the correct dtype may be restored by using the
-  ``loadedarray.view(correct_dtype)`` method.
-
-File extensions
----------------
-
-We recommend using the ``.npy`` and ``.npz`` extensions for files saved
-in this format. This is by no means a requirement; applications may wish
-to use these file formats but use an extension specific to the
-application. In the absence of an obvious alternative, however,
-we suggest using ``.npy`` and ``.npz``.
-
-Version numbering
------------------
-
-The version numbering of these formats is independent of NumPy version
-numbering. If the format is upgraded, the code in `numpy.io` will still
-be able to read and write Version 1.0 files.
-
-Format Version 1.0
-------------------
-
-The first 6 bytes are a magic string: exactly ``\\x93NUMPY``.
-
-The next 1 byte is an unsigned byte: the major version number of the file
-format, e.g. ``\\x01``.
-
-The next 1 byte is an unsigned byte: the minor version number of the file
-format, e.g. ``\\x00``. Note: the version of the file format is not tied
-to the version of the numpy package.
-
-The next 2 bytes form a little-endian unsigned short int: the length of
-the header data HEADER_LEN.
-
-The next HEADER_LEN bytes form the header data describing the array's
-format. It is an ASCII string which contains a Python literal expression
-of a dictionary. It is terminated by a newline (``\\n``) and padded with
-spaces (``\\x20``) to make the total length of
-``magic string + 4 + HEADER_LEN`` be evenly divisible by 16 for alignment
-purposes.
-
-The dictionary contains three keys:
-
-    "descr" : dtype.descr
-      An object that can be passed as an argument to the `numpy.dtype`
-      constructor to create the array's dtype.
-    "fortran_order" : bool
-      Whether the array data is Fortran-contiguous or not. Since
-      Fortran-contiguous arrays are a common form of non-C-contiguity,
-      we allow them to be written directly to disk for efficiency.
-    "shape" : tuple of int
-      The shape of the array.
-
-For repeatability and readability, the dictionary keys are sorted in
-alphabetic order. This is for convenience only. A writer SHOULD implement
-this if possible. A reader MUST NOT depend on this.
-
-Following the header comes the array data. If the dtype contains Python
-objects (i.e. ``dtype.hasobject is True``), then the data is a Python
-pickle of the array. Otherwise the data is the contiguous (either C-
-or Fortran-, depending on ``fortran_order``) bytes of the array.
-Consumers can figure out the number of bytes by multiplying the number
-of elements given by the shape (noting that ``shape=()`` means there is
-1 element) by ``dtype.itemsize``.
-
-Notes
------
-The ``.npy`` format, including reasons for creating it and a comparison of
-alternatives, is described fully in the "npy-format" NEP.
-
-"""
-from __future__ import division, absolute_import, print_function
-
-import numpy
-import sys
-import io
-import warnings
-from numpy.lib.utils import safe_eval
-from numpy.compat import asbytes, asstr, isfileobj, long, basestring
-
-if sys.version_info[0] >= 3:
-    import pickle
-else:
-    import cPickle as pickle
-
-MAGIC_PREFIX = asbytes('\x93NUMPY')
-MAGIC_LEN = len(MAGIC_PREFIX) + 2
-BUFFER_SIZE = 2**18  # size of buffer for reading npz files in bytes
-
-# difference between version 1.0 and 2.0 is a 4 byte (I) header length
-# instead of 2 bytes (H) allowing storage of large structured arrays
-
-def _check_version(version):
-    if version not in [(1, 0), (2, 0), None]:
-        msg = "we only support format version (1,0) and (2, 0), not %s"
-        raise ValueError(msg % (version,))
-
-def magic(major, minor):
-    """ Return the magic string for the given file format version.
-
-    Parameters
-    ----------
-    major : int in [0, 255]
-    minor : int in [0, 255]
-
-    Returns
-    -------
-    magic : str
-
-    Raises
-    ------
-    ValueError if the version cannot be formatted.
-    """
-    if major < 0 or major > 255:
-        raise ValueError("major version must be 0 <= major < 256")
-    if minor < 0 or minor > 255:
-        raise ValueError("minor version must be 0 <= minor < 256")
-    if sys.version_info[0] < 3:
-        return MAGIC_PREFIX + chr(major) + chr(minor)
-    else:
-        return MAGIC_PREFIX + bytes([major, minor])
-
-def read_magic(fp):
-    """ Read the magic string to get the version of the file format.
-
-    Parameters
-    ----------
-    fp : filelike object
-
-    Returns
-    -------
-    major : int
-    minor : int
-    """
-    magic_str = _read_bytes(fp, MAGIC_LEN, "magic string")
-    if magic_str[:-2] != MAGIC_PREFIX:
-        msg = "the magic string is not correct; expected %r, got %r"
-        raise ValueError(msg % (MAGIC_PREFIX, magic_str[:-2]))
-    if sys.version_info[0] < 3:
-        major, minor = map(ord, magic_str[-2:])
-    else:
-        major, minor = magic_str[-2:]
-    return major, minor
-
-def dtype_to_descr(dtype):
-    """
-    Get a serializable descriptor from the dtype.
-
-    The .descr attribute of a dtype object cannot be round-tripped through
-    the dtype() constructor. Simple types, like dtype('float32'), have
-    a descr which looks like a record array with one field with '' as
-    a name. The dtype() constructor interprets this as a request to give
-    a default name.  Instead, we construct descriptor that can be passed to
-    dtype().
-
-    Parameters
-    ----------
-    dtype : dtype
-        The dtype of the array that will be written to disk.
-
-    Returns
-    -------
-    descr : object
-        An object that can be passed to `numpy.dtype()` in order to
-        replicate the input dtype.
-
-    """
-    if dtype.names is not None:
-        # This is a record array. The .descr is fine.  XXX: parts of the
-        # record array with an empty name, like padding bytes, still get
-        # fiddled with. This needs to be fixed in the C implementation of
-        # dtype().
-        return dtype.descr
-    else:
-        return dtype.str
-
-def header_data_from_array_1_0(array):
-    """ Get the dictionary of header metadata from a numpy.ndarray.
-
-    Parameters
-    ----------
-    array : numpy.ndarray
-
-    Returns
-    -------
-    d : dict
-        This has the appropriate entries for writing its string representation
-        to the header of the file.
-    """
-    d = {}
-    d['shape'] = array.shape
-    if array.flags.c_contiguous:
-        d['fortran_order'] = False
-    elif array.flags.f_contiguous:
-        d['fortran_order'] = True
-    else:
-        # Totally non-contiguous data. We will have to make it C-contiguous
-        # before writing. Note that we need to test for C_CONTIGUOUS first
-        # because a 1-D array is both C_CONTIGUOUS and F_CONTIGUOUS.
-        d['fortran_order'] = False
-
-    d['descr'] = dtype_to_descr(array.dtype)
-    return d
-
-def _write_array_header(fp, d, version=None):
-    """ Write the header for an array and returns the version used
-
-    Parameters
-    ----------
-    fp : filelike object
-    d : dict
-        This has the appropriate entries for writing its string representation
-        to the header of the file.
-    version: tuple or None
-        None means use oldest that works
-        explicit version will raise a ValueError if the format does not
-        allow saving this data.  Default: None
-    Returns
-    -------
-    version : tuple of int
-        the file version which needs to be used to store the data
-    """
-    import struct
-    header = ["{"]
-    for key, value in sorted(d.items()):
-        # Need to use repr here, since we eval these when reading
-        header.append("'%s': %s, " % (key, repr(value)))
-    header.append("}")
-    header = "".join(header)
-    # Pad the header with spaces and a final newline such that the magic
-    # string, the header-length short and the header are aligned on a
-    # 16-byte boundary.  Hopefully, some system, possibly memory-mapping,
-    # can take advantage of our premature optimization.
-    current_header_len = MAGIC_LEN + 2 + len(header) + 1  # 1 for the newline
-    topad = 16 - (current_header_len % 16)
-    header = header + ' '*topad + '\n'
-    header = asbytes(_filter_header(header))
-
-    if len(header) >= (256*256) and version == (1, 0):
-        raise ValueError("header does not fit inside %s bytes required by the"
-                         " 1.0 format" % (256*256))
-    if len(header) < (256*256):
-        header_len_str = struct.pack('<H', len(header))
-        version = (1, 0)
-    elif len(header) < (2**32):
-        header_len_str = struct.pack('<I', len(header))
-        version = (2, 0)
-    else:
-        raise ValueError("header does not fit inside 4 GiB required by "
-                         "the 2.0 format")
-
-    fp.write(magic(*version))
-    fp.write(header_len_str)
-    fp.write(header)
-    return version
-
-def write_array_header_1_0(fp, d):
-    """ Write the header for an array using the 1.0 format.
-
-    Parameters
-    ----------
-    fp : filelike object
-    d : dict
-        This has the appropriate entries for writing its string
-        representation to the header of the file.
-    """
-    _write_array_header(fp, d, (1, 0))
-
-
-def write_array_header_2_0(fp, d):
-    """ Write the header for an array using the 2.0 format.
-        The 2.0 format allows storing very large structured arrays.
-
-    .. versionadded:: 1.9.0
-
-    Parameters
-    ----------
-    fp : filelike object
-    d : dict
-        This has the appropriate entries for writing its string
-        representation to the header of the file.
-    """
-    _write_array_header(fp, d, (2, 0))
-
-def read_array_header_1_0(fp):
-    """
-    Read an array header from a filelike object using the 1.0 file format
-    version.
-
-    This will leave the file object located just after the header.
-
-    Parameters
-    ----------
-    fp : filelike object
-        A file object or something with a `.read()` method like a file.
-
-    Returns
-    -------
-    shape : tuple of int
-        The shape of the array.
-    fortran_order : bool
-        The array data will be written out directly if it is either
-        C-contiguous or Fortran-contiguous. Otherwise, it will be made
-        contiguous before writing it out.
-    dtype : dtype
-        The dtype of the file's data.
-
-    Raises
-    ------
-    ValueError
-        If the data is invalid.
-
-    """
-    _read_array_header(fp, version=(1, 0))
-
-def read_array_header_2_0(fp):
-    """
-    Read an array header from a filelike object using the 2.0 file format
-    version.
-
-    This will leave the file object located just after the header.
-
-    .. versionadded:: 1.9.0
-
-    Parameters
-    ----------
-    fp : filelike object
-        A file object or something with a `.read()` method like a file.
-
-    Returns
-    -------
-    shape : tuple of int
-        The shape of the array.
-    fortran_order : bool
-        The array data will be written out directly if it is either
-        C-contiguous or Fortran-contiguous. Otherwise, it will be made
-        contiguous before writing it out.
-    dtype : dtype
-        The dtype of the file's data.
-
-    Raises
-    ------
-    ValueError
-        If the data is invalid.
-
-    """
-    _read_array_header(fp, version=(2, 0))
-
-
-def _filter_header(s):
-    """Clean up 'L' in npz header ints.
-
-    Cleans up the 'L' in strings representing integers. Needed to allow npz
-    headers produced in Python2 to be read in Python3.
-
-    Parameters
-    ----------
-    s : byte string
-        Npy file header.
-
-    Returns
-    -------
-    header : str
-        Cleaned up header.
-
-    """
-    import tokenize
-    if sys.version_info[0] >= 3:
-        from io import StringIO
-    else:
-        from StringIO import StringIO
-
-    tokens = []
-    last_token_was_number = False
-    for token in tokenize.generate_tokens(StringIO(asstr(s)).read):
-        token_type = token[0]
-        token_string = token[1]
-        if (last_token_was_number and
-                token_type == tokenize.NAME and
-                token_string == "L"):
-            continue
-        else:
-            tokens.append(token)
-        last_token_was_number = (token_type == tokenize.NUMBER)
-    return tokenize.untokenize(tokens)
-
-
-def _read_array_header(fp, version):
-    """
-    see read_array_header_1_0
-    """
-    # Read an unsigned, little-endian short int which has the length of the
-    # header.
-    import struct
-    if version == (1, 0):
-        hlength_str = _read_bytes(fp, 2, "array header length")
-        header_length = struct.unpack('<H', hlength_str)[0]
-        header = _read_bytes(fp, header_length, "array header")
-    elif version == (2, 0):
-        hlength_str = _read_bytes(fp, 4, "array header length")
-        header_length = struct.unpack('<I', hlength_str)[0]
-        header = _read_bytes(fp, header_length, "array header")
-    else:
-        raise ValueError("Invalid version %r" % version)
-
-    # The header is a pretty-printed string representation of a literal
-    # Python dictionary with trailing newlines padded to a 16-byte
-    # boundary. The keys are strings.
-    #   "shape" : tuple of int
-    #   "fortran_order" : bool
-    #   "descr" : dtype.descr
-    header = _filter_header(header)
-    try:
-        d = safe_eval(header)
-    except SyntaxError as e:
-        msg = "Cannot parse header: %r\nException: %r"
-        raise ValueError(msg % (header, e))
-    if not isinstance(d, dict):
-        msg = "Header is not a dictionary: %r"
-        raise ValueError(msg % d)
-    keys = sorted(d.keys())
-    if keys != ['descr', 'fortran_order', 'shape']:
-        msg = "Header does not contain the correct keys: %r"
-        raise ValueError(msg % (keys,))
-
-    # Sanity-check the values.
-    if (not isinstance(d['shape'], tuple) or
-            not numpy.all([isinstance(x, (int, long)) for x in d['shape']])):
-        msg = "shape is not valid: %r"
-        raise ValueError(msg % (d['shape'],))
-    if not isinstance(d['fortran_order'], bool):
-        msg = "fortran_order is not a valid bool: %r"
-        raise ValueError(msg % (d['fortran_order'],))
-    try:
-        dtype = numpy.dtype(d['descr'])
-    except TypeError as e:
-        msg = "descr is not a valid dtype descriptor: %r"
-        raise ValueError(msg % (d['descr'],))
-
-    return d['shape'], d['fortran_order'], dtype
-
-def write_array(fp, array, version=None):
-    """
-    Write an array to an NPY file, including a header.
-
-    If the array is neither C-contiguous nor Fortran-contiguous AND the
-    file_like object is not a real file object, this function will have to
-    copy data in memory.
-
-    Parameters
-    ----------
-    fp : file_like object
-        An open, writable file object, or similar object with a
-        ``.write()`` method.
-    array : ndarray
-        The array to write to disk.
-    version : (int, int) or None, optional
-        The version number of the format. None means use the oldest
-        supported version that is able to store the data.  Default: None
-
-    Raises
-    ------
-    ValueError
-        If the array cannot be persisted.
-    Various other errors
-        If the array contains Python objects as part of its dtype, the
-        process of pickling them may raise various errors if the objects
-        are not picklable.
-
-    """
-    _check_version(version)
-    used_ver = _write_array_header(fp, header_data_from_array_1_0(array),
-                                   version)
-    # this warning can be removed when 1.9 has aged enough
-    if version != (2, 0) and used_ver == (2, 0):
-        warnings.warn("Stored array in format 2.0. It can only be"
-                      "read by NumPy >= 1.9", UserWarning)
-
-    # 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, fp, protocol=2)
-    elif array.flags.f_contiguous and not array.flags.c_contiguous:
-        if isfileobj(fp):
-            array.T.tofile(fp)
-        else:
-            for chunk in numpy.nditer(
-                    array, flags=['external_loop', 'buffered', 'zerosize_ok'],
-                    buffersize=buffersize, order='F'):
-                fp.write(chunk.tobytes('C'))
-    else:
-        if isfileobj(fp):
-            array.tofile(fp)
-        else:
-            for chunk in numpy.nditer(
-                    array, flags=['external_loop', 'buffered', 'zerosize_ok'],
-                    buffersize=buffersize, order='C'):
-                fp.write(chunk.tobytes('C'))
-
-
-def read_array(fp):
-    """
-    Read an array from an NPY file.
-
-    Parameters
-    ----------
-    fp : file_like object
-        If this is not a real file object, then this may take extra memory
-        and time.
-
-    Returns
-    -------
-    array : ndarray
-        The array from the data on disk.
-
-    Raises
-    ------
-    ValueError
-        If the data is invalid.
-
-    """
-    version = read_magic(fp)
-    _check_version(version)
-    shape, fortran_order, dtype = _read_array_header(fp, version)
-    if len(shape) == 0:
-        count = 1
-    else:
-        count = numpy.multiply.reduce(shape)
-
-    # Now read the actual data.
-    if dtype.hasobject:
-        # The array contained Python objects. We need to unpickle the data.
-        array = pickle.load(fp)
-    else:
-        if isfileobj(fp):
-            # We can use the fast fromfile() function.
-            array = numpy.fromfile(fp, dtype=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, dtype.itemsize)
-
-            array = numpy.empty(count, dtype=dtype)
-            for i in range(0, count, max_read_count):
-                read_count = min(max_read_count, count - i)
-                read_size = int(read_count * dtype.itemsize)
-                data = _read_bytes(fp, read_size, "array data")
-                array[i:i+read_count] = numpy.frombuffer(data, dtype=dtype,
-                                                         count=read_count)
-
-        if fortran_order:
-            array.shape = shape[::-1]
-            array = array.transpose()
-        else:
-            array.shape = shape
-
-    return array
-
-
-def open_memmap(filename, mode='r+', dtype=None, shape=None,
-                fortran_order=False, version=None):
-    """
-    Open a .npy file as a memory-mapped array.
-
-    This may be used to read an existing file or create a new one.
-
-    Parameters
-    ----------
-    filename : str
-        The name of the file on disk.  This may *not* be a file-like
-        object.
-    mode : str, optional
-        The mode in which to open the file; the default is 'r+'.  In
-        addition to the standard file modes, 'c' is also accepted to mean
-        "copy on write."  See `memmap` for the available mode strings.
-    dtype : data-type, optional
-        The data type of the array if we are creating a new file in "write"
-        mode, if not, `dtype` is ignored.  The default value is None, which
-        results in a data-type of `float64`.
-    shape : tuple of int
-        The shape of the array if we are creating a new file in "write"
-        mode, in which case this parameter is required.  Otherwise, this
-        parameter is ignored and is thus optional.
-    fortran_order : bool, optional
-        Whether the array should be Fortran-contiguous (True) or
-        C-contiguous (False, the default) if we are creating a new file in
-        "write" mode.
-    version : tuple of int (major, minor) or None
-        If the mode is a "write" mode, then this is the version of the file
-        format used to create the file.  None means use the oldest
-        supported version that is able to store the data.  Default: None
-
-    Returns
-    -------
-    marray : memmap
-        The memory-mapped array.
-
-    Raises
-    ------
-    ValueError
-        If the data or the mode is invalid.
-    IOError
-        If the file is not found or cannot be opened correctly.
-
-    See Also
-    --------
-    memmap
-
-    """
-    if not isinstance(filename, basestring):
-        raise ValueError("Filename must be a string.  Memmap cannot use"
-                         " existing file handles.")
-
-    if 'w' in mode:
-        # We are creating the file, not reading it.
-        # Check if we ought to create the file.
-        _check_version(version)
-        # Ensure that the given dtype is an authentic dtype object rather
-        # than just something that can be interpreted as a dtype object.
-        dtype = numpy.dtype(dtype)
-        if dtype.hasobject:
-            msg = "Array can't be memory-mapped: Python objects in dtype."
-            raise ValueError(msg)
-        d = dict(
-            descr=dtype_to_descr(dtype),
-            fortran_order=fortran_order,
-            shape=shape,
-        )
-        # If we got here, then it should be safe to create the file.
-        fp = open(filename, mode+'b')
-        try:
-            used_ver = _write_array_header(fp, d, version)
-            # this warning can be removed when 1.9 has aged enough
-            if version != (2, 0) and used_ver == (2, 0):
-                warnings.warn("Stored array in format 2.0. It can only be"
-                              "read by NumPy >= 1.9", UserWarning)
-            offset = fp.tell()
-        finally:
-            fp.close()
-    else:
-        # Read the header of the file first.
-        fp = open(filename, 'rb')
-        try:
-            version = read_magic(fp)
-            _check_version(version)
-
-            shape, fortran_order, dtype = _read_array_header(fp, version)
-            if dtype.hasobject:
-                msg = "Array can't be memory-mapped: Python objects in dtype."
-                raise ValueError(msg)
-            offset = fp.tell()
-        finally:
-            fp.close()
-
-    if fortran_order:
-        order = 'F'
-    else:
-        order = 'C'
-
-    # We need to change a write-only mode to a read-write mode since we've
-    # already written data to the file.
-    if mode == 'w+':
-        mode = 'r+'
-
-    marray = numpy.memmap(filename, dtype=dtype, shape=shape, order=order,
-        mode=mode, offset=offset)
-
-    return marray
-
-
-def _read_bytes(fp, size, error_template="ran out of data"):
-    """
-    Read from file-like object until size bytes are read.
-    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.
-    """
-    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