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########################################################################
#
# License: MIT
# Created: September 22, 2010
# Author: Francesc Alted - faltet@gmail.com
#
########################################################################
import os
import sys
from distutils.version import LooseVersion
try:
import cPickle as pickle
except ImportError:
import pickle
from blosc import blosc_extension as _ext
import blosc
if sys.version_info[0] < 3:
int_ = (int, long)
else:
int_ = (int,)
def detect_number_of_cores():
"""
detect_number_of_cores()
Detect the number of cores in this system.
Returns
-------
out : int
The number of cores in this system.
"""
# Linux, Unix and MacOS:
if hasattr(os, "sysconf"):
if "SC_NPROCESSORS_ONLN" in os.sysconf_names:
# Linux & Unix:
ncpus = os.sysconf("SC_NPROCESSORS_ONLN")
if isinstance(ncpus, int) and ncpus > 0:
return ncpus
else: # OSX:
return int(os.popen2("sysctl -n hw.ncpu")[1].read())
# Windows:
if "NUMBER_OF_PROCESSORS" in os.environ:
ncpus = int(os.environ["NUMBER_OF_PROCESSORS"])
if ncpus > 0:
return ncpus
return 1 # Default
def set_nthreads(nthreads):
"""
set_nthreads(nthreads)
Set the number of threads to be used during Blosc operation.
Parameters
----------
nthreads : int
The number of threads to be used during Blosc operation.
Returns
-------
out : int
The previous number of used threads.
Raises
------
ValueError
If nthreads is larger that the maximum number of threads blosc can use.
Notes
-----
The number of threads for Blosc is the maximum number of cores
detected on your machine (via `detect_number_of_cores`). In some
cases Blosc gets better results if you set the number of threads
to a value slightly below than your number of cores.
Examples
--------
Set the number of threads to 2 and then to 1:
>>> oldn = blosc.set_nthreads(2)
>>> blosc.set_nthreads(1)
2
"""
if nthreads > blosc.MAX_THREADS:
raise ValueError("the number of threads cannot be larger than %d" %
blosc.MAX_THREADS)
return _ext.set_nthreads(nthreads)
def set_blocksize(blocksize):
"""set_blocksize(blocksize)
Force the use of a specific blocksize. If 0, an automatic
blocksize will be used (the default).
Notes
-----
This is a low-level function and is recommened for expert users only.
Examples
--------
>>> blosc.set_blocksize(512)
"""
_ext.set_blocksize(blocksize)
def compressor_list():
"""
compressor_list()
Returns a list of compressors available in C library.
Parameters
----------
None
Returns
-------
out : list
The list of names.
"""
return _ext.compressor_list().split(',')
def code_to_name(code):
"""
code_to_name(code)
Return the compressor name of a compressor code.
Parameters
----------
code : int
The compressor code.
Returns
-------
out : str
The compressor name.
"""
return _ext.code_to_name(code)
def name_to_code(name):
"""
name_to_code(name)
Return the compressor code of a compressor name.
Parameters
----------
name : str
The compressor name.
Returns
-------
out : int
The compressor code.
"""
return _ext.name_to_code(name)
def clib_info(cname):
"""
clib_info(cname)
Return info for compression libraries in C library.
Parameters
----------
cname : str
The compressor name.
Returns
-------
out : tuple
The associated library name and version.
"""
return _ext.clib_info(cname)
def get_clib(bytesobj):
"""
get_clib(bytesobj)
Return the name of the compression library for Blosc `bytesobj` buffer.
Parameters
----------
bytesobj : str / bytes
The compressed buffer.
Returns
-------
out : str
The name of the compression library.
"""
_check_bytesobj(bytesobj)
return _ext.get_clib(bytesobj)
def free_resources():
"""
free_resources()
Free possible memory temporaries and thread resources.
Returns
-------
out : None
Notes
-----
Blosc maintain a pool of threads waiting for work as well as some
temporary space. You can use this function to release these
resources when you are not going to use Blosc for a long while.
Examples
--------
>>> blosc.free_resources()
>>>
"""
_ext.free_resources()
def _check_shuffle(shuffle):
if shuffle not in [blosc.NOSHUFFLE, blosc.SHUFFLE, blosc.BITSHUFFLE]:
raise ValueError("shuffle can only be one of NOSHUFFLE, SHUFFLE"
" and BITSHUFFLE.")
if (shuffle == blosc.BITSHUFFLE and
LooseVersion(blosc.blosclib_version) < LooseVersion("1.8.0")):
raise ValueError("You need C-Blosc 1.8.0 or higher for using"
" BITSHUFFLE.")
def _check_clevel(clevel):
if not 0 <= clevel <= 9:
raise ValueError("clevel can only be in the 0-9 range.")
def _check_cname(cname):
list_cnames = compressor_list()
if cname not in list_cnames:
raise ValueError("cname can only be one of: %s, not '%s'" %
(list_cnames, cname))
def _check_typesize(typesize):
if not 1 <= typesize <= blosc.MAX_TYPESIZE:
raise ValueError("typesize can only be in the 1-%d range." %
blosc.MAX_TYPESIZE)
def _check_bytesobj(bytesobj):
if not isinstance(bytesobj, bytes):
raise TypeError("only string (2.x) or bytes (3.x) objects "
"supported as input")
def _check_input_length(input_name, input_len):
if input_len > blosc.MAX_BUFFERSIZE:
raise ValueError("%s cannot be larger than %d bytes" %
(input_name, blosc.MAX_BUFFERSIZE))
def _check_address(address):
if not isinstance(address, int_):
raise TypeError("only int or long objects are supported as address")
def compress(bytesobj, typesize=8, clevel=9, shuffle=blosc.SHUFFLE,
cname='blosclz'):
"""compress(bytesobj[, typesize=8, clevel=9, shuffle=blosc.SHUFFLE, cname='blosclz']])
Compress bytesobj, with a given type size.
Parameters
----------
bytesobj : bytes-like object (supporting the buffer interface)
The data to be compressed.
typesize : int
The data type size.
clevel : int (optional)
The compression level from 0 (no compression) to 9
(maximum compression). The default is 9.
shuffle : int (optional)
The shuffle filter to be activated. Allowed values are
blosc.NOSHUFFLE, blosc.SHUFFLE and blosc.BITSHUFFLE. The
default is blosc.SHUFFLE.
cname : string (optional)
The name of the compressor used internally in Blosc. It can be
any of the supported by Blosc ('blosclz', 'lz4', 'lz4hc',
'snappy', 'zlib', 'zstd' and maybe others too). The default is
'blosclz'.
Returns
-------
out : str / bytes
The compressed data in form of a Python str / bytes object.
Raises
------
TypeError
If bytesobj doesn't support the buffer interface.
ValueError
If bytesobj is too long.
If typesize is not within the allowed range.
If clevel is not within the allowed range.
If cname is not a valid codec.
Examples
--------
>>> import array
>>> a = array.array('i', range(1000*1000))
>>> a_bytesobj = a.tostring()
>>> c_bytesobj = blosc.compress(a_bytesobj, typesize=4)
>>> len(c_bytesobj) < len(a_bytesobj)
True
"""
_check_input_length('bytesobj', len(bytesobj))
_check_typesize(typesize)
_check_shuffle(shuffle)
_check_clevel(clevel)
_check_cname(cname)
return _ext.compress(bytesobj, typesize, clevel, shuffle, cname)
def compress_ptr(address, items, typesize=8, clevel=9, shuffle=blosc.SHUFFLE,
cname='blosclz'):
"""compress_ptr(address, items[, typesize=8, clevel=9, shuffle=blosc.SHUFFLE, cname='blosclz']])
Compress the data at address with given items and typesize.
Parameters
----------
address : int or long
the pointer to the data to be compressed
items : int
The number of items (of typesize) to be compressed.
typesize : int
The data type size.
clevel : int (optional)
The compression level from 0 (no compression) to 9
(maximum compression). The default is 9.
shuffle : int (optional)
The shuffle filter to be activated. Allowed values are
blosc.NOSHUFFLE, blosc.SHUFFLE and blosc.BITSHUFFLE. The
default is blosc.SHUFFLE.
cname : string (optional)
The name of the compressor used internally in Blosc. It can be
any of the supported by Blosc ('blosclz', 'lz4', 'lz4hc',
'snappy', 'zlib', 'zstd' and maybe others too). The default is
'blosclz'.
Returns
-------
out : str / bytes
The compressed data in form of a Python str / bytes object.
Raises
------
TypeError
If address is not of type int or long.
ValueError
If items * typesize is larger than the maximum allowed buffer size.
If typesize is not within the allowed range.
If clevel is not within the allowed range.
If cname is not within the supported compressors.
Notes
-----
This function can be used anywhere that a memory address is available in
Python. For example the Numpy "__array_interface__['data'][0]" construct,
or when using the ctypes modules.
Importantly, the user is responsible for making sure that the memory
address is valid and that the memory pointed to is contiguous. Passing a
non-valid address has a high likelihood of crashing the interpreter by
segfault.
Examples
--------
>>> import numpy
>>> items = 7
>>> np_array = numpy.arange(items)
>>> c = blosc.compress_ptr(np_array.__array_interface__['data'][0], \
items, np_array.dtype.itemsize)
>>> d = blosc.decompress(c)
>>> np_ans = numpy.fromstring(d, dtype=np_array.dtype)
>>> (np_array == np_ans).all()
True
>>> import ctypes
>>> typesize = 8
>>> data = [float(i) for i in range(items)]
>>> Array = ctypes.c_double * items
>>> a = Array(*data)
>>> c = blosc.compress_ptr(ctypes.addressof(a), items, typesize)
>>> d = blosc.decompress(c)
>>> import struct
>>> ans = [struct.unpack('d', d[i:i+typesize])[0] \
for i in range(0, items*typesize, typesize)]
>>> data == ans
True
"""
_check_address(address)
if items < 0:
raise ValueError("items cannot be negative")
length = items * typesize
_check_input_length('length', length)
_check_typesize(typesize)
_check_shuffle(shuffle)
_check_clevel(clevel)
_check_cname(cname)
return _ext.compress_ptr(address, length, typesize, clevel, shuffle, cname)
def decompress(bytesobj, as_bytearray=False):
"""decompress(bytesobj)
Decompresses a bytesobj compressed object.
Parameters
----------
bytesobj : str / bytes
The data to be decompressed.
as_bytearray : bool, optional
If this flag is True then the return type will be a bytearray object
instead of a bytesobject.
Returns
-------
out : str / bytes or bytearray
The decompressed data in form of a Python str / bytes object.
If as_bytearray is True then this will be a bytearray object, otherwise
this will be a str/ bytes object.
Raises
------
TypeError
If bytesobj is not of type bytes or string.
Examples
--------
>>> import array
>>> a = array.array('i', range(1000*1000))
>>> a_bytesobj = a.tostring()
>>> c_bytesobj = blosc.compress(a_bytesobj, typesize=4)
>>> a_bytesobj2 = blosc.decompress(c_bytesobj)
>>> a_bytesobj == a_bytesobj2
True
>>> b"" == blosc.decompress(blosc.compress(b"", 1))
True
>>> b"1"*7 == blosc.decompress(blosc.compress(b"1"*7, 8))
True
>>> type(blosc.decompress(blosc.compress(b"1"*7, 8),
... as_bytearray=True)) is bytearray
True
"""
return _ext.decompress(bytesobj, as_bytearray)
def decompress_ptr(bytesobj, address):
"""decompress_ptr(bytesobj, address)
Decompresses a bytesobj compressed object into the memory at address.
Parameters
----------
bytesobj : str / bytes
The data to be decompressed.
address : int or long
the pointer to the data to be compressed
Returns
-------
nbytes : int
the number of bytes written to the buffer
Raises
------
TypeError
If bytesobj is not of type bytes or string.
If address is not of type int or long.
Notes
-----
This function can be used anywhere that a memory address is available in
Python. For example the Numpy "__array_interface__['data'][0]" construct,
or when using the ctypes modules.
Importantly, the user is responsible for making sure that the memory
address is valid and that the memory pointed to is contiguous and can be
written to. Passing a non-valid address has a high likelihood of crashing
the interpreter by segfault.
Examples
--------
>>> import numpy
>>> items = 7
>>> np_array = numpy.arange(items)
>>> c = blosc.compress_ptr(np_array.__array_interface__['data'][0], \
items, np_array.dtype.itemsize)
>>> np_ans = numpy.empty(items, dtype=np_array.dtype)
>>> nbytes = blosc.decompress_ptr(c, np_ans.__array_interface__['data'][0])
>>> (np_array == np_ans).all()
True
>>> nbytes == items * np_array.dtype.itemsize
True
>>> import ctypes
>>> typesize = 8
>>> data = [float(i) for i in range(items)]
>>> Array = ctypes.c_double * items
>>> in_array = Array(*data)
>>> c = blosc.compress_ptr(ctypes.addressof(in_array), items, typesize)
>>> out_array = ctypes.create_string_buffer(items*typesize)
>>> nbytes = blosc.decompress_ptr(c, ctypes.addressof(out_array))
>>> import struct
>>> ans = [struct.unpack('d', out_array[i:i+typesize])[0] \
for i in range(0, items*typesize, typesize)]
>>> data == ans
True
>>> nbytes == items * typesize
True
"""
_check_bytesobj(bytesobj)
_check_address(address)
return _ext.decompress_ptr(bytesobj, address)
def pack_array(array, clevel=9, shuffle=blosc.SHUFFLE, cname='blosclz'):
"""pack_array(array[, clevel=9, shuffle=blosc.SHUFFLE, cname='blosclz']])
Pack (compress) a NumPy array.
Parameters
----------
array : ndarray
The NumPy array to be packed.
clevel : int (optional)
The compression level from 0 (no compression) to 9
(maximum compression). The default is 9.
shuffle : int (optional)
The shuffle filter to be activated. Allowed values are
blosc.NOSHUFFLE, blosc.SHUFFLE and blosc.BITSHUFFLE. The
default is blosc.SHUFFLE.
cname : string (optional)
The name of the compressor used internally in Blosc. It can be
any of the supported by Blosc ('blosclz', 'lz4', 'lz4hc',
'snappy', 'zlib', 'zstd' and maybe others too). The default is
'blosclz'.
Returns
-------
out : str / bytes
The packed array in form of a Python str / bytes object.
Raises
------
TypeError
If array does not quack like a numpy ndarray.
ValueError
If array.itemsize * array.size is larger than the maximum allowed
buffer size.
If typesize is not within the allowed range.
If clevel is not within the allowed range.
If cname is not within the supported compressors.
Examples
--------
>>> import numpy
>>> a = numpy.arange(1e6)
>>> parray = blosc.pack_array(a)
>>> len(parray) < a.size*a.itemsize
True
"""
if not (hasattr(array, 'dtype') and hasattr(array, 'shape')):
# This does not quack like an ndarray
raise TypeError(
"only NumPy ndarray objects supported as input")
itemsize = array.itemsize
_check_input_length('array size', array.size*itemsize)
_check_typesize(array.itemsize)
_check_shuffle(shuffle)
_check_clevel(clevel)
_check_cname(cname)
# Use the fastest pickle available
pickled_array = pickle.dumps(array, pickle.HIGHEST_PROTOCOL)
# ... and compress the pickle
packed_array = compress(pickled_array, itemsize, clevel, shuffle, cname)
return packed_array
def unpack_array(packed_array):
"""unpack_array(packed_array)
Unpack (decompress) a packed NumPy array.
Parameters
----------
packed_array : str / bytes
The packed array to be decompressed.
Returns
-------
out : ndarray
The decompressed data in form of a NumPy array.
Raises
------
TypeError
If packed_array is not of type bytes or string.
Examples
--------
>>> import numpy
>>> a = numpy.arange(1e6)
>>> parray = blosc.pack_array(a)
>>> len(parray) < a.size*a.itemsize
True
>>> a2 = blosc.unpack_array(parray)
>>> numpy.alltrue(a == a2)
True
"""
_check_bytesobj(packed_array)
# First decompress the pickle
pickled_array = _ext.decompress(packed_array, False)
# ... and unpickle
array = pickle.loads(pickled_array)
return array
# For the load tests protocol:
# http://docs.python.org/2/library/unittest.html#load-tests-protocol
def load_tests(loader, tests, pattern):
import doctest
tests.addTests(doctest.DocTestSuite())
return tests
def print_versions():
"""Print all the versions of software that python-blosc relies on."""
import platform
print("-=" * 38)
print("python-blosc version: %s" % blosc.__version__)
print("Blosc version: %s" % blosc.blosclib_version)
print("Compressors available: %s" % blosc.cnames)
print("Compressor library versions:")
for clib in sorted(blosc.clib_versions.keys()):
print(" %s: %s" % (clib, blosc.clib_versions[clib]))
print("Python version: %s" % sys.version)
(sysname, nodename, release, version, machine, processor) = platform.uname()
print("Platform: %s-%s-%s (%s)" % (sysname, release, machine, version))
if sysname == "Linux":
print("Linux dist: %s" % " ".join(platform.linux_distribution()[:-1]))
if not processor:
processor = "not recognized"
print("Processor: %s" % processor)
print("Byte-ordering: %s" % sys.byteorder)
print("Detected cores: %s" % blosc.ncores)
print("Number of threads to use by default: %s" % blosc.nthreads)
print("-=" * 38)
if __name__ == '__main__':
# test myself
import doctest
print_versions()
nfail, ntests = doctest.testmod()
if nfail == 0:
print("All %d tests passed successfully!" % ntests)
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