339 lines
11 KiB
Python
339 lines
11 KiB
Python
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from __future__ import division, absolute_import, print_function
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import numpy as np
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from .numeric import uint8, ndarray, dtype
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from numpy.compat import long, basestring, is_pathlib_path
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__all__ = ['memmap']
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dtypedescr = dtype
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valid_filemodes = ["r", "c", "r+", "w+"]
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writeable_filemodes = ["r+", "w+"]
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mode_equivalents = {
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"readonly":"r",
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"copyonwrite":"c",
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"readwrite":"r+",
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"write":"w+"
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}
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class memmap(ndarray):
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"""Create a memory-map to an array stored in a *binary* file on disk.
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Memory-mapped files are used for accessing small segments of large files
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on disk, without reading the entire file into memory. NumPy's
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memmap's are array-like objects. This differs from Python's ``mmap``
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module, which uses file-like objects.
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This subclass of ndarray has some unpleasant interactions with
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some operations, because it doesn't quite fit properly as a subclass.
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An alternative to using this subclass is to create the ``mmap``
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object yourself, then create an ndarray with ndarray.__new__ directly,
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passing the object created in its 'buffer=' parameter.
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This class may at some point be turned into a factory function
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which returns a view into an mmap buffer.
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Delete the memmap instance to close.
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Parameters
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----------
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filename : str, file-like object, or pathlib.Path instance
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The file name or file object to be used as the array data buffer.
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dtype : data-type, optional
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The data-type used to interpret the file contents.
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Default is `uint8`.
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mode : {'r+', 'r', 'w+', 'c'}, optional
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The file is opened in this mode:
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+------+-------------------------------------------------------------+
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| 'r' | Open existing file for reading only. |
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+------+-------------------------------------------------------------+
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| 'r+' | Open existing file for reading and writing. |
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+------+-------------------------------------------------------------+
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| 'w+' | Create or overwrite existing file for reading and writing. |
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+------+-------------------------------------------------------------+
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| 'c' | Copy-on-write: assignments affect data in memory, but |
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| | changes are not saved to disk. The file on disk is |
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+------+-------------------------------------------------------------+
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Default is 'r+'.
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offset : int, optional
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In the file, array data starts at this offset. Since `offset` is
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measured in bytes, it should normally be a multiple of the byte-size
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of `dtype`. When ``mode != 'r'``, even positive offsets beyond end of
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file are valid; The file will be extended to accommodate the
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additional data. By default, ``memmap`` will start at the beginning of
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the file, even if ``filename`` is a file pointer ``fp`` and
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``fp.tell() != 0``.
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shape : tuple, optional
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The desired shape of the array. If ``mode == 'r'`` and the number
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of remaining bytes after `offset` is not a multiple of the byte-size
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of `dtype`, you must specify `shape`. By default, the returned array
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will be 1-D with the number of elements determined by file size
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and data-type.
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order : {'C', 'F'}, optional
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Specify the order of the ndarray memory layout:
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:term:`row-major`, C-style or :term:`column-major`,
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Fortran-style. This only has an effect if the shape is
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greater than 1-D. The default order is 'C'.
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Attributes
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----------
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filename : str or pathlib.Path instance
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Path to the mapped file.
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offset : int
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Offset position in the file.
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mode : str
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File mode.
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Methods
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-------
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flush
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Flush any changes in memory to file on disk.
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When you delete a memmap object, flush is called first to write
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changes to disk before removing the object.
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See also
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--------
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lib.format.open_memmap : Create or load a memory-mapped ``.npy`` file.
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Notes
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-----
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The memmap object can be used anywhere an ndarray is accepted.
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Given a memmap ``fp``, ``isinstance(fp, numpy.ndarray)`` returns
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``True``.
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Memory-mapped files cannot be larger than 2GB on 32-bit systems.
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When a memmap causes a file to be created or extended beyond its
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current size in the filesystem, the contents of the new part are
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unspecified. On systems with POSIX filesystem semantics, the extended
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part will be filled with zero bytes.
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Examples
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--------
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>>> data = np.arange(12, dtype='float32')
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>>> data.resize((3,4))
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This example uses a temporary file so that doctest doesn't write
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files to your directory. You would use a 'normal' filename.
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>>> from tempfile import mkdtemp
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>>> import os.path as path
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>>> filename = path.join(mkdtemp(), 'newfile.dat')
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Create a memmap with dtype and shape that matches our data:
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>>> fp = np.memmap(filename, dtype='float32', mode='w+', shape=(3,4))
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>>> fp
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memmap([[ 0., 0., 0., 0.],
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[ 0., 0., 0., 0.],
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[ 0., 0., 0., 0.]], dtype=float32)
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Write data to memmap array:
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>>> fp[:] = data[:]
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>>> fp
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memmap([[ 0., 1., 2., 3.],
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[ 4., 5., 6., 7.],
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[ 8., 9., 10., 11.]], dtype=float32)
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>>> fp.filename == path.abspath(filename)
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True
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Deletion flushes memory changes to disk before removing the object:
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>>> del fp
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Load the memmap and verify data was stored:
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>>> newfp = np.memmap(filename, dtype='float32', mode='r', shape=(3,4))
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>>> newfp
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memmap([[ 0., 1., 2., 3.],
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[ 4., 5., 6., 7.],
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[ 8., 9., 10., 11.]], dtype=float32)
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Read-only memmap:
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>>> fpr = np.memmap(filename, dtype='float32', mode='r', shape=(3,4))
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>>> fpr.flags.writeable
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False
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Copy-on-write memmap:
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>>> fpc = np.memmap(filename, dtype='float32', mode='c', shape=(3,4))
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>>> fpc.flags.writeable
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True
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It's possible to assign to copy-on-write array, but values are only
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written into the memory copy of the array, and not written to disk:
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>>> fpc
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memmap([[ 0., 1., 2., 3.],
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[ 4., 5., 6., 7.],
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[ 8., 9., 10., 11.]], dtype=float32)
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>>> fpc[0,:] = 0
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>>> fpc
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memmap([[ 0., 0., 0., 0.],
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[ 4., 5., 6., 7.],
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[ 8., 9., 10., 11.]], dtype=float32)
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File on disk is unchanged:
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>>> fpr
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memmap([[ 0., 1., 2., 3.],
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[ 4., 5., 6., 7.],
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[ 8., 9., 10., 11.]], dtype=float32)
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Offset into a memmap:
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>>> fpo = np.memmap(filename, dtype='float32', mode='r', offset=16)
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>>> fpo
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memmap([ 4., 5., 6., 7., 8., 9., 10., 11.], dtype=float32)
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"""
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__array_priority__ = -100.0
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def __new__(subtype, filename, dtype=uint8, mode='r+', offset=0,
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shape=None, order='C'):
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# Import here to minimize 'import numpy' overhead
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import mmap
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import os.path
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try:
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mode = mode_equivalents[mode]
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except KeyError:
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if mode not in valid_filemodes:
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raise ValueError("mode must be one of %s" %
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(valid_filemodes + list(mode_equivalents.keys())))
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if hasattr(filename, 'read'):
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fid = filename
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own_file = False
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elif is_pathlib_path(filename):
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fid = filename.open((mode == 'c' and 'r' or mode)+'b')
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own_file = True
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else:
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fid = open(filename, (mode == 'c' and 'r' or mode)+'b')
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own_file = True
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if (mode == 'w+') and shape is None:
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raise ValueError("shape must be given")
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fid.seek(0, 2)
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flen = fid.tell()
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descr = dtypedescr(dtype)
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_dbytes = descr.itemsize
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if shape is None:
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bytes = flen - offset
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if (bytes % _dbytes):
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fid.close()
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raise ValueError("Size of available data is not a "
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"multiple of the data-type size.")
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size = bytes // _dbytes
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shape = (size,)
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else:
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if not isinstance(shape, tuple):
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shape = (shape,)
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size = 1
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for k in shape:
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size *= k
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bytes = long(offset + size*_dbytes)
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if mode == 'w+' or (mode == 'r+' and flen < bytes):
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fid.seek(bytes - 1, 0)
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fid.write(b'\0')
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fid.flush()
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if mode == 'c':
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acc = mmap.ACCESS_COPY
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elif mode == 'r':
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acc = mmap.ACCESS_READ
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else:
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acc = mmap.ACCESS_WRITE
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start = offset - offset % mmap.ALLOCATIONGRANULARITY
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bytes -= start
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array_offset = offset - start
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mm = mmap.mmap(fid.fileno(), bytes, access=acc, offset=start)
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self = ndarray.__new__(subtype, shape, dtype=descr, buffer=mm,
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offset=array_offset, order=order)
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self._mmap = mm
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self.offset = offset
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self.mode = mode
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if isinstance(filename, basestring):
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self.filename = os.path.abspath(filename)
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elif is_pathlib_path(filename):
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self.filename = filename.resolve()
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# py3 returns int for TemporaryFile().name
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elif (hasattr(filename, "name") and
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isinstance(filename.name, basestring)):
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self.filename = os.path.abspath(filename.name)
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# same as memmap copies (e.g. memmap + 1)
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else:
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self.filename = None
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if own_file:
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fid.close()
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return self
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def __array_finalize__(self, obj):
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if hasattr(obj, '_mmap') and np.may_share_memory(self, obj):
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self._mmap = obj._mmap
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self.filename = obj.filename
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self.offset = obj.offset
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self.mode = obj.mode
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else:
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self._mmap = None
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self.filename = None
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self.offset = None
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self.mode = None
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def flush(self):
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"""
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Write any changes in the array to the file on disk.
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For further information, see `memmap`.
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Parameters
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----------
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None
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See Also
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--------
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memmap
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"""
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if self.base is not None and hasattr(self.base, 'flush'):
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self.base.flush()
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def __array_wrap__(self, arr, context=None):
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arr = super(memmap, self).__array_wrap__(arr, context)
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# Return a memmap if a memmap was given as the output of the
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# ufunc. Leave the arr class unchanged if self is not a memmap
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# to keep original memmap subclasses behavior
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if self is arr or type(self) is not memmap:
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return arr
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# Return scalar instead of 0d memmap, e.g. for np.sum with
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# axis=None
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if arr.shape == ():
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return arr[()]
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# Return ndarray otherwise
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return arr.view(np.ndarray)
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def __getitem__(self, index):
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res = super(memmap, self).__getitem__(index)
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if type(res) is memmap and res._mmap is None:
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return res.view(type=ndarray)
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return res
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