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""" Binary serialization
NPY format ==========
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 their 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 of ``len(magic string) + 2 + len(length) + HEADER_LEN`` be evenly divisible by 64 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``.
Format Version 2.0 ------------------
The version 1.0 format only allowed the array header to have a total size of 65535 bytes. This can be exceeded by structured arrays with a large number of columns. The version 2.0 format extends the header size to 4 GiB. `numpy.save` will automatically save in 2.0 format if the data requires it, else it will always use the more compatible 1.0 format.
The description of the fourth element of the header therefore has become: "The next 4 bytes form a little-endian unsigned int: the length of the header data HEADER_LEN."
Notes ----- The ``.npy`` format, including motivation for creating it and a comparison of alternatives, is described in the `"npy-format" NEP <https://www.numpy.org/neps/nep-0001-npy-format.html>`_, however details have evolved with time and this document is more current.
"""
asbytes, asstr, isfileobj, long, os_fspath )
# 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
msg = "we only support format version (1,0) and (2, 0), not %s" raise ValueError(msg % (version,))
""" 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. """ raise ValueError("major version must be 0 <= major < 256") raise ValueError("minor version must be 0 <= minor < 256") return MAGIC_PREFIX + chr(major) + chr(minor) else:
""" Read the magic string to get the version of the file format.
Parameters ---------- fp : filelike object
Returns ------- major : int minor : int """ msg = "the magic string is not correct; expected %r, got %r" raise ValueError(msg % (MAGIC_PREFIX, magic_str[:-2])) major, minor = map(ord, magic_str[-2:]) else:
""" 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.
""" # 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:
''' descr may be stored as dtype.descr, which is a list of (name, format, [shape]) tuples. Offsets are not explicitly saved, rather empty fields with name,format == '', '|Vn' are added as padding.
This function reverses the process, eliminating the empty padding fields. ''' # No padding removal needed
fields = [] offset = 0 for field in descr: if len(field) == 2: name, descr_str = field dt = descr_to_dtype(descr_str) else: name, descr_str, shape = field dt = numpy.dtype((descr_to_dtype(descr_str), shape))
# Ignore padding bytes, which will be void bytes with '' as name # Once support for blank names is removed, only "if name == ''" needed) is_pad = (name == '' and dt.type is numpy.void and dt.names is None) if not is_pad: fields.append((name, dt, offset))
offset += dt.itemsize
names, formats, offsets = zip(*fields) # names may be (title, names) tuples nametups = (n if isinstance(n, tuple) else (None, n) for n in names) titles, names = zip(*nametups) return numpy.dtype({'names': names, 'formats': formats, 'titles': titles, 'offsets': offsets, 'itemsize': offset})
""" 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['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.
""" 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 """ # Need to use repr here, since we eval these when reading
# Which version(s) we write depends on the total header size; v1 has a max of 65535 elif hlen + padlen_v2 < 2**32 and version in (None, (2, 0)): version = (2, 0) header_prefix = magic(2, 0) + struct.pack('<I', hlen + padlen_v2) topad = padlen_v2 else: msg = "Header length %s too big for version=%s" msg %= (hlen, version) raise ValueError(msg)
# 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 # ARRAY_ALIGN byte boundary. This supports memory mapping of dtypes # aligned up to ARRAY_ALIGN on systems like Linux where mmap() # offset must be page-aligned (i.e. the beginning of the file).
""" 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))
""" 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))
""" 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.
""" return _read_array_header(fp, version=(1, 0))
""" 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.
""" return _read_array_header(fp, version=(2, 0))
"""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.
""" else: from StringIO import StringIO
# adding newline as python 2.7.5 workaround token_type == tokenize.NAME and token_string == "L"): continue else: # removing newline (see above) as python 2.7.5 workaround
""" see read_array_header_1_0 """ # Read an unsigned, little-endian short int which has the length of the # header. elif version == (2, 0): hlength_type = '<I' 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 ARRAY_ALIGN byte # boundary. The keys are strings. # "shape" : tuple of int # "fortran_order" : bool # "descr" : dtype.descr except SyntaxError as e: msg = "Cannot parse header: %r\nException: %r" raise ValueError(msg % (header, e)) msg = "Header is not a dictionary: %r" raise ValueError(msg % d) msg = "Header does not contain the correct keys: %r" raise ValueError(msg % (keys,))
# Sanity-check the values. not numpy.all([isinstance(x, (int, long)) for x in d['shape']])): msg = "shape is not valid: %r" raise ValueError(msg % (d['shape'],)) msg = "fortran_order is not a valid bool: %r" raise ValueError(msg % (d['fortran_order'],)) except TypeError as e: msg = "descr is not a valid dtype descriptor: %r" raise ValueError(msg % (d['descr'],))
""" 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 allow_pickle : bool, optional Whether to allow writing pickled data. Default: True pickle_kwargs : dict, optional Additional keyword arguments to pass to pickle.dump, excluding 'protocol'. These are only useful when pickling objects in object arrays on Python 3 to Python 2 compatible format.
Raises ------ ValueError If the array cannot be persisted. This includes the case of allow_pickle=False and array being an object array. 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.
""" version) # this warning can be removed when 1.9 has aged enough warnings.warn("Stored array in format 2.0. It can only be" "read by NumPy >= 1.9", UserWarning, stacklevel=2)
buffersize = 0 else: # Set buffer size to 16 MiB to hide the Python loop overhead.
# 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. if not allow_pickle: raise ValueError("Object arrays cannot be saved when " "allow_pickle=False") if pickle_kwargs is None: pickle_kwargs = {} pickle.dump(array, fp, protocol=2, **pickle_kwargs) 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: array.tofile(fp) else: array, flags=['external_loop', 'buffered', 'zerosize_ok'], buffersize=buffersize, order='C'):
""" 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. allow_pickle : bool, optional Whether to allow reading pickled data. Default: True pickle_kwargs : dict Additional keyword arguments to pass to pickle.load. These are only useful when loading object arrays saved on Python 2 when using Python 3.
Returns ------- array : ndarray The array from the data on disk.
Raises ------ ValueError If the data is invalid, or allow_pickle=False and the file contains an object array.
""" count = 1 else:
# Now read the actual data. # The array contained Python objects. We need to unpickle the data. if not allow_pickle: raise ValueError("Object arrays cannot be loaded when " "allow_pickle=False") if pickle_kwargs is None: pickle_kwargs = {} try: array = pickle.load(fp, **pickle_kwargs) except UnicodeError as err: if sys.version_info[0] >= 3: # Friendlier error message raise UnicodeError("Unpickling a python object failed: %r\n" "You may need to pass the encoding= option " "to numpy.load" % (err,)) raise else: # 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.
# Use np.ndarray instead of np.empty since the latter does # not correctly instantiate zero-width string dtypes; see # https://github.com/numpy/numpy/pull/6430
# If dtype.itemsize == 0 then there's nothing more to read
count=read_count)
array.shape = shape[::-1] array = array.transpose() else:
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 or path-like 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 isfileobj(filename): raise ValueError("Filename must be a string or a path-like object." " 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(os_fspath(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, stacklevel=2) offset = fp.tell() finally: fp.close() else: # Read the header of the file first. fp = open(os_fspath(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
""" 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. """ # 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 except io.BlockingIOError: pass msg = "EOF: reading %s, expected %d bytes got %d" raise ValueError(msg % (error_template, size, len(data))) else: |