Source code for tables.filters

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#
# License: BSD
# Created: 2007-02-23
# Author: Ivan Vilata i Balaguer - ivan at selidor dot net
#
# $Id$
#
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"""Functionality related with filters in a PyTables file."""

# Imports
# =======
import warnings
import numpy

from . import utilsextension, blosc_compressor_list, blosc_compcode_to_compname
from .exceptions import FiltersWarning
from distutils.version import LooseVersion

import tables
from tables.req_versions import min_blosc_bitshuffle_version

blosc_version = LooseVersion(tables.which_lib_version("blosc")[1])


# Public variables
# ================
__docformat__ = 'reStructuredText'
"""The format of documentation strings in this module."""

all_complibs = ['zlib', 'lzo', 'bzip2', 'blosc']
all_complibs += ['blosc:%s' % cname for cname in blosc_compressor_list()]


"""List of all compression libraries."""

foreign_complibs = ['szip']
"""List of known but unsupported compression libraries."""

default_complib = 'zlib'
"""The default compression library."""


# Private variables
# =================
_shuffle_flag = 0x1
_fletcher32_flag = 0x2
_rounding_flag = 0x4
_bitshuffle_flag = 0x8


# Classes
# =======
[docs]class Filters: """Container for filter properties. This class is meant to serve as a container that keeps information about the filter properties associated with the chunked leaves, that is Table, CArray, EArray and VLArray. Instances of this class can be directly compared for equality. Parameters ---------- complevel : int Specifies a compression level for data. The allowed range is 0-9. A value of 0 (the default) disables compression. complib : str Specifies the compression library to be used. Right now, 'zlib' (the default), 'lzo', 'bzip2' and 'blosc' are supported. Additional compressors for Blosc like 'blosc:blosclz' ('blosclz' is the default in case the additional compressor is not specified), 'blosc:lz4', 'blosc:lz4hc', 'blosc:snappy', 'blosc:zlib' and 'blosc:zstd' are supported too. Specifying a compression library which is not available in the system issues a FiltersWarning and sets the library to the default one. shuffle : bool Whether or not to use the *Shuffle* filter in the HDF5 library. This is normally used to improve the compression ratio. A false value disables shuffling and a true one enables it. The default value depends on whether compression is enabled or not; if compression is enabled, shuffling defaults to be enabled, else shuffling is disabled. Shuffling can only be used when compression is enabled. bitshuffle : bool Whether or not to use the *BitShuffle* filter in the Blosc library. This is normally used to improve the compression ratio. A false value disables bitshuffling and a true one enables it. The default value is disabled. fletcher32 : bool Whether or not to use the *Fletcher32* filter in the HDF5 library. This is used to add a checksum on each data chunk. A false value (the default) disables the checksum. least_significant_digit : int If specified, data will be truncated (quantized). In conjunction with enabling compression, this produces 'lossy', but significantly more efficient compression. For example, if *least_significant_digit=1*, data will be quantized using ``around(scale*data)/scale``, where ``scale = 2**bits``, and bits is determined so that a precision of 0.1 is retained (in this case bits=4). Default is *None*, or no quantization. .. note:: quantization is only applied if some form of compression is enabled Examples -------- This is a small example on using the Filters class:: import numpy import tables fileh = tables.open_file('test5.h5', mode='w') atom = Float32Atom() filters = Filters(complevel=1, complib='blosc', fletcher32=True) arr = fileh.create_earray(fileh.root, 'earray', atom, (0,2), "A growable array", filters=filters) # Append several rows in only one call arr.append(numpy.array([[1., 2.], [2., 3.], [3., 4.]], dtype=numpy.float32)) # Print information on that enlargeable array print("Result Array:") print(repr(arr)) fileh.close() This enforces the use of the Blosc library, a compression level of 1 and a Fletcher32 checksum filter as well. See the output of this example:: Result Array: /earray (EArray(3, 2), fletcher32, shuffle, blosc(1)) 'A growable array' type = float32 shape = (3, 2) itemsize = 4 nrows = 3 extdim = 0 flavor = 'numpy' byteorder = 'little' .. rubric:: Filters attributes .. attribute:: fletcher32 Whether the *Fletcher32* filter is active or not. .. attribute:: complevel The compression level (0 disables compression). .. attribute:: complib The compression filter used (irrelevant when compression is not enabled). .. attribute:: shuffle Whether the *Shuffle* filter is active or not. .. attribute:: bitshuffle Whether the *BitShuffle* filter is active or not (Blosc only). """ @property def shuffle_bitshuffle(self): """Encode NoShuffle (0), Shuffle (1) and BitShuffle (2) filters.""" if (self.shuffle and self.bitshuffle): raise ValueError( "Shuffle and BitShuffle cannot be active at the same time") if not (self.shuffle or self.bitshuffle): return 0 if self.shuffle: return 1 if self.bitshuffle: return 2 @classmethod def _from_leaf(cls, leaf): # Get a dictionary with all the filters parent = leaf._v_parent filters_dict = utilsextension.get_filters(parent._v_objectid, leaf._v_name) if filters_dict is None: filters_dict = {} # not chunked # Keyword arguments are all off kwargs = dict(complevel=0, shuffle=False, bitshuffle=False, fletcher32=False, least_significant_digit=None, _new=False) for (name, values) in filters_dict.items(): if name == 'deflate': name = 'zlib' if name in all_complibs: kwargs['complib'] = name if name == "blosc": kwargs['complevel'] = values[4] if values[5] == 1: # Shuffle filter is internal to blosc kwargs['shuffle'] = True elif values[5] == 2: # Shuffle filter is internal to blosc kwargs['bitshuffle'] = True # From Blosc 1.3 on, parameter 6 is used for the compressor if len(values) > 6: cname = blosc_compcode_to_compname(values[6]) kwargs['complib'] = "blosc:%s" % cname else: kwargs['complevel'] = values[0] elif name in foreign_complibs: kwargs['complib'] = name kwargs['complevel'] = 1 # any nonzero value will do elif name in ['shuffle', 'fletcher32']: kwargs[name] = True return cls(**kwargs) @classmethod def _unpack(cls, packed): """Create a new `Filters` object from a packed version. >>> Filters._unpack(0) Filters(complevel=0, shuffle=False, bitshuffle=False, fletcher32=False, least_significant_digit=None) >>> Filters._unpack(0x101) Filters(complevel=1, complib='zlib', shuffle=False, bitshuffle=False, fletcher32=False, least_significant_digit=None) >>> Filters._unpack(0x30109) Filters(complevel=9, complib='zlib', shuffle=True, bitshuffle=False, fletcher32=True, least_significant_digit=None) >>> Filters._unpack(0x3010A) Traceback (most recent call last): ... ValueError: compression level must be between 0 and 9 >>> Filters._unpack(0x1) Traceback (most recent call last): ... ValueError: invalid compression library id: 0 """ kwargs = {'_new': False} # Byte 0: compression level. kwargs['complevel'] = complevel = packed & 0xff packed >>= 8 # Byte 1: compression library id (0 for none). if complevel > 0: complib_id = int(packed & 0xff) if not (0 < complib_id <= len(all_complibs)): raise ValueError("invalid compression library id: %d" % complib_id) kwargs['complib'] = all_complibs[complib_id - 1] packed >>= 8 # Byte 2: parameterless filters. kwargs['shuffle'] = packed & _shuffle_flag kwargs['bitshuffle'] = packed & _bitshuffle_flag kwargs['fletcher32'] = packed & _fletcher32_flag has_rounding = packed & _rounding_flag packed >>= 8 # Byte 3: least significant digit. if has_rounding: kwargs['least_significant_digit'] = numpy.int8(packed & 0xff) else: kwargs['least_significant_digit'] = None return cls(**kwargs) def _pack(self): """Pack the `Filters` object into a 64-bit NumPy integer.""" packed = numpy.int64(0) # Byte 3: least significant digit. if self.least_significant_digit is not None: #assert isinstance(self.least_significant_digit, numpy.int8) packed |= self.least_significant_digit packed <<= 8 # Byte 2: parameterless filters. if self.shuffle: packed |= _shuffle_flag if self.bitshuffle: packed |= _bitshuffle_flag if self.fletcher32: packed |= _fletcher32_flag if self.least_significant_digit: packed |= _rounding_flag packed <<= 8 # Byte 1: compression library id (0 for none). if self.complevel > 0: packed |= all_complibs.index(self.complib) + 1 packed <<= 8 # Byte 0: compression level. packed |= self.complevel return packed def __init__(self, complevel=0, complib=default_complib, shuffle=True, bitshuffle=False, fletcher32=False, least_significant_digit=None, _new=True): if not (0 <= complevel <= 9): raise ValueError("compression level must be between 0 and 9") if _new and complevel > 0: # These checks are not performed when loading filters from disk. if complib not in all_complibs: raise ValueError( "compression library ``%s`` is not supported; " "it must be one of: %s" % (complib, ", ".join(all_complibs))) if utilsextension.which_lib_version(complib) is None: warnings.warn("compression library ``%s`` is not available; " "using ``%s`` instead" % (complib, default_complib), FiltersWarning) complib = default_complib # always available complevel = int(complevel) complib = str(complib) shuffle = bool(shuffle) bitshuffle = bool(bitshuffle) fletcher32 = bool(fletcher32) if least_significant_digit is not None: least_significant_digit = numpy.int8(least_significant_digit) if complevel == 0: # Override some inputs when compression is not enabled. complib = None # make it clear there is no compression shuffle = False # shuffling and not compressing makes no sense least_significant_digit = None elif complib not in all_complibs: # Do not try to use a meaningful level for unsupported libs. complevel = -1 self.complevel = complevel """The compression level (0 disables compression).""" self.complib = complib """The compression filter used (irrelevant when compression is not enabled). """ self.shuffle = shuffle """Whether the *Shuffle* filter is active or not.""" self.bitshuffle = bitshuffle """Whether the *BitShuffle* filter is active or not.""" if (self.complib and self.bitshuffle and not self.complib.startswith('blosc')): raise ValueError( "BitShuffle can only be used inside Blosc") if self.shuffle and self.bitshuffle: # BitShuffle has priority in case both are specified self.shuffle = False if self.bitshuffle and blosc_version < min_blosc_bitshuffle_version: raise ValueError( "This Blosc library does not have support for the bitshuffle " "filter. Please update to Blosc >= %s" % \ min_blosc_bitshuffle_version) self.fletcher32 = fletcher32 """Whether the *Fletcher32* filter is active or not.""" self.least_significant_digit = least_significant_digit """The least significant digit to which data shall be truncated.""" def __repr__(self): args, complevel = [], self.complevel if complevel >= 0: # meaningful compression level args.append('complevel=%d' % complevel) if complevel != 0: # compression enabled (-1 or > 0) args.append('complib=%r' % self.complib) args.append('shuffle=%s' % self.shuffle) args.append('bitshuffle=%s' % self.bitshuffle) args.append('fletcher32=%s' % self.fletcher32) args.append( 'least_significant_digit=%s' % self.least_significant_digit) return '{}({})'.format(self.__class__.__name__, ', '.join(args)) def __str__(self): return repr(self) def __eq__(self, other): if not isinstance(other, self.__class__): return False for attr in self.__dict__: if getattr(self, attr) != getattr(other, attr): return False return True # XXX: API incompatible change for PyTables 3 line # Overriding __eq__ blocks inheritance of __hash__ in 3.x # def __hash__(self): # return hash((self.__class__, self.complevel, self.complib, # self.shuffle, self.bitshuffle, self.fletcher32))
[docs] def copy(self, **override): """Get a copy of the filters, possibly overriding some arguments. Constructor arguments to be overridden must be passed as keyword arguments. Using this method is recommended over replacing the attributes of an instance, since instances of this class may become immutable in the future:: >>> filters1 = Filters() >>> filters2 = filters1.copy() >>> filters1 == filters2 True >>> filters1 is filters2 False >>> filters3 = filters1.copy(complevel=1) #doctest: +ELLIPSIS Traceback (most recent call last): ... ValueError: compression library ``None`` is not supported... >>> filters3 = filters1.copy(complevel=1, complib='zlib') >>> print(filters1) Filters(complevel=0, shuffle=False, bitshuffle=False, fletcher32=False, least_significant_digit=None) >>> print(filters3) Filters(complevel=1, complib='zlib', shuffle=False, bitshuffle=False, fletcher32=False, least_significant_digit=None) >>> filters1.copy(foobar=42) Traceback (most recent call last): ... TypeError: __init__() got an unexpected keyword argument 'foobar' """ newargs = self.__dict__.copy() newargs.update(override) return self.__class__(**newargs)
# Main part # ========= def _test(): """Run ``doctest`` on this module.""" import doctest doctest.testmod() if __name__ == '__main__': _test()