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intbitset.pyx
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# $Id$
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007 CERN.
##
## CDS Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
## CDS Invenio is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with CDS Invenio; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
"""
Defines an intbitset data object to hold unordered sets of unsigned
integers with ultra fast set operations, implemented via bit vectors
and Python C extension to optimize speed and memory usage.
Emulates the Python built-in set class interface with some additional
specific methods such as its own fast dump and load marshalling
functions. Uses real bits to optimize memory usage, so may have
issues with endianness if you transport serialized bitsets between
various machine architectures.
"""
import zlib
from array import array
ctypedef unsigned long long int word_t
ctypedef unsigned char bool_t
ctypedef unsigned long long int Py_ssize_t
cdef extern from "Python.h":
object PyString_FromStringAndSize(char *s, Py_ssize_t len)
int PyObject_AsReadBuffer(object obj, void **buf, Py_ssize_t *buf_len)
cdef extern from "intbitset.h":
ctypedef struct IntBitSet:
int size
int allocated
word_t trailing_bits
int tot
word_t *bitset
int wordbytesize
int wordbitsize
IntBitSet *intBitSetCreate(int size, bool_t trailing_bits)
IntBitSet *intBitSetCreateFromBuffer(void *buf, int bufsize)
IntBitSet *intBitSetResetFromBuffer(IntBitSet *bitset, void *buf, int bufsize)
IntBitSet *intBitSetReset(IntBitSet *bitset)
void intBitSetDestroy(IntBitSet *bitset)
IntBitSet *intBitSetClone(IntBitSet *bitset)
int intBitSetGetSize(IntBitSet *bitset)
int intBitSetGetAllocated(IntBitSet *bitset)
int intBitSetGetTot(IntBitSet * bitset)
bool_t intBitSetIsInElem(IntBitSet *bitset, int elem)
void intBitSetAddElem(IntBitSet *bitset, int elem)
void intBitSetDelElem(IntBitSet *bitset, int elem)
bool_t intBitSetEmpty(IntBitSet *bitset)
IntBitSet *intBitSetUnion(IntBitSet *x, IntBitSet *y)
IntBitSet *intBitSetIntersection(IntBitSet *x, IntBitSet *y)
IntBitSet *intBitSetSub(IntBitSet *x, IntBitSet *y)
IntBitSet *intBitSetXor(IntBitSet *x, IntBitSet *y)
IntBitSet *intBitSetIUnion(IntBitSet *dst, IntBitSet *src)
IntBitSet *intBitSetIIntersection(IntBitSet *dst, IntBitSet *src)
IntBitSet *intBitSetISub(IntBitSet *x, IntBitSet *y)
IntBitSet *intBitSetIXor(IntBitSet *x, IntBitSet *y)
int intBitSetGetNext(IntBitSet *x, int last)
unsigned char intBitSetCmp(IntBitSet *x, IntBitSet *y)
cdef class intbitset:
"""
Defines an intbitset data object to hold unordered sets of
unsigned integers with ultra fast set operations, implemented via
bit vectors and Python C extension to optimize speed and memory
usage.
Emulates the Python built-in set class interface with some
additional specific methods such as its own fast dump and load
marshalling functions. Uses real bits to optimize memory usage,
so may have issues with endianness if you transport serialized
bitsets between various machine architectures.
"""
cdef IntBitSet *bitset
def __new__(self, rhs=0, int minsize=-1, object trailing_bits=0):
"""
Initialize intbitset.
* rhs can be:
- int/long for creating allocating empty intbitset that will hold at least
rhs elements, before being resized
- intbitset for cloning
- str for retrieving an intbitset that was dumped into a string
- array for retrieving an intbitset that was dumped into a string stored
in an array
- sequence made of integers for copying all the elements from the
sequence. If minsize is specified than it is initially allocated
enough space to hold up to minsize integers, otherwise the biggest
element of the sequence will be used.
* minsize is a suggested initial upper bound on the numbers that will be
stored, by looking at rhs a sequence of number.
* trailing_bits is 1, then the set will contain "all" the positive integers
after the biggest one added with rhs.
"""
cdef Py_ssize_t size
cdef void *buf
cdef int elem
cdef int i
cdef int last
cdef int remelem
msg = "Error"
self.bitset = NULL
if type(rhs) in (int, long):
if rhs < 0:
raise ValueError, "rhs can't be negative"
self.bitset = intBitSetCreate(rhs, trailing_bits)
elif type(rhs) is intbitset:
self.bitset = intBitSetClone((<intbitset>rhs).bitset)
elif type(rhs) in (str, array):
try:
if type(rhs) is array:
rhs = rhs.tostring()
tmp = zlib.decompress(rhs)
if PyObject_AsReadBuffer(tmp, &buf, &size) < 0:
raise Exception, "Buffer error!!!"
self.bitset = intBitSetCreateFromBuffer(buf, size)
except Exception, msg:
raise ValueError, "rhs is corrupted: %s" % msg
elif hasattr(rhs, '__iter__'):
try:
if minsize > -1:
self.bitset = intBitSetCreate(minsize, trailing_bits)
else:
if rhs:
self.bitset = intBitSetCreate(int(max(rhs)), trailing_bits)
else:
self.bitset = intBitSetCreate(0, trailing_bits)
if trailing_bits:
last = 0
for elem in rhs:
if int(elem) < 0:
raise ValueError, "Negative numbers, not allowed"
for remelem from last <= remelem < elem:
intBitSetDelElem(self.bitset, remelem)
last = elem + 1
else:
for elem in rhs:
if int(elem) < 0:
raise ValueError, "Negative numbers, not allowed"
intBitSetAddElem(self.bitset, elem)
except Exception, msg:
raise ValueError, "retrieving integers from rhs is impossible: %s" \
% msg
else:
raise TypeError, "rhs is of unknown type %s" % type(rhs)
def __dealloc__(self):
if self.bitset:
intBitSetDestroy(self.bitset)
def __contains__(self, int elem):
if elem < 0:
raise ValueError, "Negative numbers, not allowed"
return intBitSetIsInElem(self.bitset, elem) != 0
def __cmp__(self, intbitset rhs not None):
raise TypeError, "cannot compare intbitset using cmp()"
def __richcmp__(self, intbitset rhs not None, int op):
cdef short unsigned int tmp
tmp = intBitSetCmp((<intbitset>self).bitset, rhs.bitset)
if op == 0: # <
return tmp == 1
if op == 1: # <=
return tmp <= 1
if op == 2: # ==
return tmp == 0
if op == 3: # !=
return tmp > 0
if op == 4: # >
return tmp == 2
if op == 5: # >=
return tmp in (0, 2)
def __len__(self):
return intBitSetGetTot(self.bitset)
def __hash__(self):
return hash(PyString_FromStringAndSize(<char *>self.bitset.bitset, wordbytesize * (intBitSetGetTot(self.bitset) / wordbitsize + 1)))
def __nonzero__(self):
return not intBitSetEmpty(self.bitset)
def __iadd__(self, rhs):
cdef int elem
if isinstance(rhs, (int, long)):
if int(rhs) < 0:
raise ValueError, "Negative numbers, not allowed"
intBitSetAddElem(self.bitset, rhs)
elif isinstance(rhs, intbitset):
intBitSetIUnion(self.bitset, (<intbitset> rhs).bitset)
else:
for elem in rhs:
if int(elem) < 0:
raise ValueError, "Negative numbers, not allowed"
intBitSetAddElem(self.bitset, elem)
return self
def __isub__(self, rhs):
cdef int elem
if isinstance(rhs, (int, long)):
if int(rhs) < 0:
raise ValueError, "Negative numbers, not allowed"
intBitSetDelElem(self.bitset, rhs)
elif isinstance(rhs, intbitset):
intBitSetISub(self.bitset, (<intbitset> rhs).bitset)
else:
for elem in rhs:
if int(elem) < 0:
raise ValueError, "Negative numbers, not allowed"
intBitSetDelElem(self.bitset, elem)
return self
def __deepcopy__(self, memo):
return intbitset(self)
def __del__(self, int elem):
if int(elem) < 0:
raise ValueError, "Negative numbers, not allowed"
intBitSetDelElem(self.bitset, elem)
def __and__(self, intbitset rhs not None):
ret = intbitset()
intBitSetDestroy((<intbitset>ret).bitset)
(<intbitset>ret).bitset = intBitSetIntersection((<intbitset> self).bitset, rhs.bitset)
return ret
def __or__(self, intbitset rhs not None):
ret = intbitset()
intBitSetDestroy((<intbitset>ret).bitset)
(<intbitset>ret).bitset = intBitSetUnion((<intbitset> self).bitset, rhs.bitset)
return ret
def __xor__(self, intbitset rhs not None):
ret = intbitset()
intBitSetDestroy((<intbitset>ret).bitset)
(<intbitset>ret).bitset = intBitSetXor((<intbitset> self).bitset, rhs.bitset)
return ret
def __sub__(self, intbitset rhs not None):
ret = intbitset()
intBitSetDestroy((<intbitset>ret).bitset)
(<intbitset>ret).bitset = intBitSetSub((<intbitset> self).bitset, rhs.bitset)
return ret
def __iand__(self, intbitset rhs not None):
intBitSetIIntersection(self.bitset, rhs.bitset)
return self
def __ior__(self, intbitset rhs not None):
intBitSetIUnion(self.bitset, rhs.bitset)
return self
def __ixor__(self, intbitset rhs not None):
intBitSetIXor(self.bitset, rhs.bitset)
return self
def __repr__(self):
cdef int last
cdef int maxelem
if self.bitset.trailing_bits:
maxelem = (intBitSetGetSize(self.bitset)) * wordbitsize
ret = "intbitset(["
last = -1
while last < maxelem:
last = intBitSetGetNext(self.bitset, last)
ret = ret + '%i, ' % last
if ret.endswith(", "):
ret = ret[:-2]
ret = ret + '], trailing_bits=True)'
return ret
else:
ret = "intbitset(["
last = -1
while last >= -1:
last = intBitSetGetNext(self.bitset, last)
ret = ret + '%i, ' % last
ret = ret[:-len('-2, ')]
if ret.endswith(', '):
ret = ret[:-2]
ret = ret + '])'
return ret
def __str__(self):
cdef int tot
tot = intBitSetGetTot(self.bitset)
if tot < 0:
begin_list = self.to_sorted_list(0, 10)
ret = "intbitset(["
for n in begin_list:
ret = ret + '%i, ' % n
ret = ret + "...])"
return ret
elif tot > 10:
begin_list = self.to_sorted_list(0, 5)
end_list = self.to_sorted_list(tot - 5, tot)
ret = "intbitset(["
for n in begin_list:
ret = ret + '%i, ' % n
ret = ret + "..., "
for n in end_list:
ret = ret + '%i, ' % n
ret = ret[:-2]
ret = ret + '])'
return ret
else:
return self.__repr__()
## Buffer interface
#def __getreadbuffer__(self, int i, void **p):
#if i != 0:
#return -1
#p[0] = (<intbitset >self).bitset
#return (<intbitset >self).size * wordbytesize
#def __getwritebuffer__(self, int i, void **p):
#if i != 0:
#raise SystemError
#p[0] = (<intbitset >self).bitset
#return (<intbitset >self).size * wordbytesize
#def __getsegcount__(self, int *p):
#if p != NULL:
#p[0] = (<intbitset >self).size * wordbytesize
#return 1
#def __getcharbuffer__(self, int i, char **p):
#if i != 0:
#return -1
#p[0] = <char *> (<intbitset >self).bitset
#return (<intbitset >self).size * wordbytesize
# Iterator interface
def __iter__(self):
if self.bitset.trailing_bits:
raise OverflowError, "It's impossible to iterate over an infinite set."
return intbitset_iterator(self)
# Customized interface
def add(self, int elem):
"""Add an element to a set.
This has no effect if the element is already present."""
if int(elem) < 0:
raise ValueError, "Negative numbers, not allowed"
intBitSetAddElem(self.bitset, elem)
def clear(self):
intBitSetReset(self.bitset)
def difference(intbitset self, intbitset rhs):
"""Return the difference of two intbitsets as a new set.
(i.e. all elements that are in this intbitset but not the other.)
"""
return self.__sub__(rhs)
def difference_update(self, intbitset rhs):
"""Remove all elements of another set from this set."""
self.__isub__(rhs)
def discard(self, int elem):
"""Remove an element from a intbitset if it is a member.
If the element is not a member, do nothing."""
intBitSetDelElem(self.bitset, elem)
def intersection(self, intbitset rhs):
"""Return the intersection of two intbitsets as a new set.
(i.e. all elements that are in both intbitsets.)
"""
return self.__and__(rhs)
def intersection_update(self, intbitset rhs):
"""Update a intbitset with the intersection of itself and another."""
self.__iand__(rhs)
def union(self, intbitset rhs):
"""Return the union of two intbitsets as a new set.
(i.e. all elements that are in either intbitsets.)
"""
return self.__or__(rhs)
def union_update(self, intbitset rhs):
"""Update a intbitset with the union of itself and another."""
self.__ior__(rhs)
def issubset(self, intbitset rhs):
"""Report whether another set contains this set."""
return self.__le__(rhs)
def issuperset(self, intbitset rhs):
"""Report whether this set contains another set."""
return self.__ge__(rhs)
def symmetric_difference(self, intbitset rhs):
"""Return the symmetric difference of two sets as a new set.
(i.e. all elements that are in exactly one of the sets.)
"""
return self.__xor__(rhs)
def symmetric_difference_update(self, intbitset rhs):
"""Update an intbitset with the symmetric difference of itself and another.
"""
self.__ixor__(rhs)
# Dumping & Loading
def fastdump(self):
"""Return a compressed string representation suitable to be saved
somewhere."""
cdef Py_ssize_t size
size = intBitSetGetSize((<intbitset> self).bitset)
tmp = PyString_FromStringAndSize(<char *>self.bitset.bitset, ( size + 1) * wordbytesize)
tmp2 = zlib.compress(tmp)
return tmp2
def fastload(self, object strdump):
"""Load a compressed string representation produced by a previous call
to the fastdump method into the current intbitset. The previous content
will be replaced."""
cdef Py_ssize_t size
cdef void *buf
buf = NULL
size = 0
try:
if type(strdump) is array:
strdump = strdump.tostring()
# tmp needed to not be garbage collected
tmp = zlib.decompress(strdump)
if PyObject_AsReadBuffer(tmp, &buf, &size) < 0:
raise Exception
intBitSetResetFromBuffer((<intbitset> self).bitset, buf, size)
except:
raise ValueError, "strdump is corrupted"
return self
def copy(self):
"""Return a shallow copy of a set."""
return intbitset(self)
def pop(self):
"""Remove and return an arbitrary set element."""
cdef int ret
ret = intBitSetGetNext(self.bitset, -1)
if ret < 0:
raise KeyError, "pop from an empty intbitset"
intBitSetDelElem(self.bitset, ret)
return ret
def remove(self, int elem):
"""Remove an element from a set; it must be a member.
If the element is not a member, raise a KeyError.
"""
if int(elem) < 0:
raise ValueError, "Negative numbers, not allowed"
if intBitSetIsInElem(self.bitset, elem):
intBitSetDelElem(self.bitset, elem)
else:
raise KeyError, elem
def strbits(self):
"""Return a string of 0s and 1s representing the content in memory
of the intbitset.
"""
cdef int i
cdef int last
if (<intbitset> self).bitset.trailing_bits:
raise OverflowError, "It's impossible to print an infinite set."
last = 0
ret = ''
for i in self:
ret = ret + '0'*(i-last)+'1'
last = i+1
return ret
def update_with_signs(self, rhs):
"""Given a dictionary rhs whose keys are integers, remove all the integers
whose value are less than 0 and add every integer whose value is 0 or more"""
cdef int value
try:
for value, sign in rhs.items():
if int(value) < 0:
raise ValueError, "Negative numbers, not allowed"
if sign < 0:
intBitSetDelElem(self.bitset, value)
else:
intBitSetAddElem(self.bitset, value)
except AttributeError:
raise TypeError, "rhs should be a valid dictionary with integers keys and integer values"
def get_size(self):
return intBitSetGetSize(self.bitset)
def get_allocated(self):
return intBitSetGetAllocated(self.bitset)
def get_sorted_element(self, int index):
"""Return element at position index in the sorted representation of the
set. Note that index must be less than len(self)"""
cdef int l
cdef int last
cdef int i
l = intBitSetGetTot(self.bitset)
if index < 0:
if self.bitset.trailing_bits:
raise OverflowError, "It's impossible to retrieve a negative item from an infinite set."
index = index + l
if 0 <= index < l:
last = intBitSetGetNext(self.bitset, -1)
for i from 0 <= i < index:
last = intBitSetGetNext(self.bitset, last)
else:
raise IndexError, "intbitset index out of range"
return last
def to_sorted_list(self, int i, int j):
"""Return a sublist of the sorted representation of the set.
Note, negative indices are not supported."""
cdef int l
cdef int last
cdef int cnt
if self.bitset.trailing_bits:
raise OverflowError, "It's impossible to retrieve a list from an infinite set."
l = intBitSetGetTot(self.bitset)
if i == 0 and j == -1:
return intbitset(self)
ret = intbitset()
if i < 0:
i = i + l
if j < 0:
j = j + l
if i >= l:
i = l
if j >= l:
j = l
last = -1
for cnt from 0 <= cnt < i:
last = intBitSetGetNext(self.bitset, last)
for cnt from i <= cnt < j:
last = intBitSetGetNext(self.bitset, last)
intBitSetAddElem((<intbitset> ret).bitset, last)
return ret
cdef class intbitset_iterator:
cdef int last
cdef IntBitSet *bitset
def __new__(self, intbitset bitset not None):
self.last = -1
self.bitset = bitset.bitset
def __next__(self):
self.last = intBitSetGetNext((<intbitset_iterator>self).bitset, self.last)
if self.last < 0:
self.last = -2
raise StopIteration
return self.last
def __iter__(self):
return self

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