Hamming Distance

[godavemon]

I need to calculate the Hamming Distance of two integers. The hamming
distance is the number of bits in two integers that don't match. I
thought there'd be a function in math or scipy but i haven't been able
to find one. This is my function but it seems like there should be a
faster way. I do this computation many times and speed up is
important.

def hamdist( a, b , bits = 32):
def _hamdist( x, bits):
if bits:
return (x & 1) + _hamdist(x >1, bits-1)
return x & 1
return _hamdist( a ^ b, bits)


Another alternative would be to convert the XOR to a binary string and
count the # of 1's.

Which would be fastest? Are there better alternatives?

Thanks!

[Raymond Hettinger]

Re: Hamming Distance

On Jun 19, 4:27 pm, godavemon <davefow...@gma il.comwrote:

I need to calculate the Hamming Distance of two integers.  The hamming
distance is the number of bits in two integers that don't match.  I
thought there'd be a function in math or scipy but i haven't been able
to find one.  This is my function but it seems like there should be a
faster way.  I do this computation many times and speed up is
important.

The simplest speed-up is to break the inputs into n-length blocks and
then look them up in an n-by-n table.

Also, re-write your function to use iteration instead of recursion
(the latter is *very* expensive in Python).

The fastest way is to write a C function or use Pyrex.


Raymond

[John Machin]

Re: Hamming Distance

On Jun 20, 9:27 am, godavemon <davefow...@gma il.comwrote:

I need to calculate the Hamming Distance of two integers. The hamming
distance is the number of bits in two integers that don't match. I
thought there'd be a function in math or scipy but i haven't been able
to find one. This is my function but it seems like there should be a
faster way. I do this computation many times and speed up is
important.
>
def hamdist( a, b , bits = 32):
def _hamdist( x, bits):
if bits:
return (x & 1) + _hamdist(x >1, bits-1)
return x & 1
return _hamdist( a ^ b, bits)
>
Another alternative would be to convert the XOR to a binary string and

Isn't it a "binary string" already?

count the # of 1's.

My guess is that counting the 1-bits in (a ^ b) would be hard to beat,
and that a recursive function is just not in the race.

>
Which would be fastest?

Implement both and time them.

Are there better alternatives?

I doubt it.

BTW one presumes that your integers are non-negative ...

HTH

Cheers,
John

[Mensanator]

Re: Hamming Distance

On Jun 19, 6:27 pm, godavemon <davefow...@gma il.comwrote:

I need to calculate the Hamming Distance of two integers.  The hamming
distance is the number of bits in two integers that don't match.  I
thought there'd be a function in math or scipy but i haven't been able
to find one.  This is my function but it seems like there should be a
faster way.  I do this computation many times and speed up is
important.
>
def hamdist( a, b , bits = 32):
    def _hamdist( x, bits):
        if bits:
            return (x & 1) + _hamdist(x >1, bits-1)
        return x & 1
    return _hamdist( a ^ b, bits)
>
Another alternative would be to convert the XOR to a binary string and
count the # of 1's.
>
Which would be fastest?  Are there better alternatives?

Yep, use the gmpy module.

>>import gmpy
>>help(gmpy.ham dist)

Help on built-in function hamdist in module gmpy:
hamdist(...)
hamdist(x,y): returns the Hamming distance (number of bit-
positions
where the bits differ) between x and y. x and y must be mpz, or
else
get coerced to mpz.

>>gmpy.hamdist( 15,6)

2

>>gmpy.hamdist( 2**177149,10**5 3330)

61877

>>gmpy.hamdist( 2**177149-1,10**53330)

115285

>
Thanks!

[Robert Kern]

Re: Hamming Distance

godavemon wrote:

I need to calculate the Hamming Distance of two integers. The hamming
distance is the number of bits in two integers that don't match. I
thought there'd be a function in math or scipy but i haven't been able
to find one. This is my function but it seems like there should be a
faster way. I do this computation many times and speed up is
important.
>
def hamdist( a, b , bits = 32):
def _hamdist( x, bits):
if bits:
return (x & 1) + _hamdist(x >1, bits-1)
return x & 1
return _hamdist( a ^ b, bits)
>
>
Another alternative would be to convert the XOR to a binary string and
count the # of 1's.
>
Which would be fastest? Are there better alternatives?

I think this works:

In [26]: hexbits = {'0': 0,
....: '1': 1,
....: '2': 1,
....: '3': 2,
....: '4': 1,
....: '5': 2,
....: '6': 2,
....: '7': 3,
....: '8': 1,
....: '9': 2,
....: 'A': 2,
....: 'B': 3,
....: 'C': 2,
....: 'D': 3,
....: 'E': 3,
....: 'F': 4}

In [28]: def hamming(a, b):
....: return sum(hexbits[h] for h in hex(a^b)[2:])
....:

In [29]: hamming(1,1)
Out[29]: 0

In [30]: hamming(1,2)
Out[30]: 2

In [31]: hamming(2,2)
Out[31]: 0

In [32]: hamming(2,3)
Out[32]: 1


This might be a wee faster, I haven't timed it:

sum(map(h.get, hex(a^b)[2:]))

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

[Matimus]

Re: Hamming Distance

On Jun 19, 4:27 pm, godavemon <davefow...@gma il.comwrote:

I need to calculate the Hamming Distance of two integers.  The hamming
distance is the number of bits in two integers that don't match.  I
thought there'd be a function in math or scipy but i haven't been able
to find one.  This is my function but it seems like there should be a
faster way.  I do this computation many times and speed up is
important.
>
def hamdist( a, b , bits = 32):
    def _hamdist( x, bits):
        if bits:
            return (x & 1) + _hamdist(x >1, bits-1)
        return x & 1
    return _hamdist( a ^ b, bits)
>
Another alternative would be to convert the XOR to a binary string and
count the # of 1's.
>
Which would be fastest?  Are there better alternatives?
>
Thanks!

I see no good reason to use recursion for this type of thing. Here are
some of my attempts:

from math import log

def yours(a, b , bits = 32):
def _hamdist( x, bits):
if bits:
return (x & 1) + _hamdist(x >1, bits-1)
return x & 1
return _hamdist(a ^ b, bits)


def simple(a, b, bits=32):
x = a ^ b
return sum((x >i & 1) for i in xrange(bits))

def lazy(a, b, bits=32):
x = (a ^ b) & ((1 << bits) - 1)
tot = 0
while x:
tot += x & 1
x >>= 1
return tot

def fancy(a, b, bits=32):
x = (a ^ b) & ((1 << bits) - 1)
tot = 0
while x:
tot += 1
x ^= 1 << int(log(x, 2))
return tot

test_vals = (
((0xffffffff, 0), 32),
((0,0), 0),
((1,0), 1),
((0x80000000, 0), 1),
((0x55555555, 0), 16)
)

def test(f):
test_vals = (
((0xffffffff, 0), 32), # ALL
((0,0), 0), # None
((1,0), 1), # First
((0x80000000, 0), 1), # Last
((0x55555555, 0), 16), # Every Other
((0xffff, 0), 16), # First Half
((0xffff0000, 0), 16), # Last Half
)
for i, (args, exp) in enumerate(test_vals):
if f(*args) != exp:
return 0
return 1

if __name__ == "__main__":
for f in (yours, simple, lazy, fancy):
if not test(f):
print "%s failed"%f.__name__

The python module `timeit` is handy for testing speed:

python -mtimeit -s"from hamdist import *" "test(yours )"
10000 loops, best of 3: 95.1 usec per loop

python -mtimeit -s"from hamdist import *" "test(simpl e)"
10000 loops, best of 3: 65.3 usec per loop

python -mtimeit -s"from hamdist import *" "test(lazy) "
10000 loops, best of 3: 59.8 usec per loop

python -mtimeit -s"from hamdist import *" "test(fancy )"
10000 loops, best of 3: 77.2 usec per loop

Even the ridiculous `fancy` version beat the recursive version.

Matt

[Raymond Hettinger]

Re: Hamming Distance

Non-recursive, 8-bit block table lookup version:

def ham(a, b, ht=[hamdist(a,0) for a in range(256)]):
x = a ^ b
dist = 0
while x:
dist += ht[x & 255]
x >>= 8
return dist

Raymond

[godavemon]

Re: Hamming Distance

Awesome! Thanks a lot.

On Jun 19, 5:00 pm, Mensanator <mensana...@aol .comwrote:

On Jun 19, 6:27 pm, godavemon <davefow...@gma il.comwrote:
>
>
>

I need to calculate the Hamming Distance of two integers. The hamming
distance is the number of bits in two integers that don't match. I
thought there'd be a function in math or scipy but i haven't been able
to find one. This is my function but it seems like there should be a
faster way. I do this computation many times and speed up is
important.

>

def hamdist( a, b , bits = 32):
def _hamdist( x, bits):
if bits:
return (x & 1) + _hamdist(x >1, bits-1)
return x & 1
return _hamdist( a ^ b, bits)

>

Another alternative would be to convert the XOR to a binary string and
count the # of 1's.

>

Which would be fastest? Are there better alternatives?

>
Yep, use the gmpy module.
>

>import gmpy
>help(gmpy.hamd ist)

>
Help on built-in function hamdist in module gmpy:
hamdist(...)
hamdist(x,y): returns the Hamming distance (number of bit-
positions
where the bits differ) between x and y. x and y must be mpz, or
else
get coerced to mpz.
>

>gmpy.hamdist(1 5,6)

2

>gmpy.hamdist(2 **177149,10**53 330)

61877

>gmpy.hamdist(2 **177149-1,10**53330)

>
115285
>
>
>

Thanks!

[godavemon]

Re: Hamming Distance

Great thanks!

On Jun 19, 5:37 pm, Matimus <mccre...@gmail .comwrote:

On Jun 19, 4:27 pm, godavemon <davefow...@gma il.comwrote:
>
>
>

I need to calculate the Hamming Distance of two integers. The hamming
distance is the number of bits in two integers that don't match. I
thought there'd be a function in math or scipy but i haven't been able
to find one. This is my function but it seems like there should be a
faster way. I do this computation many times and speed up is
important.

>

def hamdist( a, b , bits = 32):
def _hamdist( x, bits):
if bits:
return (x & 1) + _hamdist(x >1, bits-1)
return x & 1
return _hamdist( a ^ b, bits)

>

Another alternative would be to convert the XOR to a binary string and
count the # of 1's.

>

Which would be fastest? Are there better alternatives?

>

Thanks!

>
I see no good reason to use recursion for this type of thing. Here are
some of my attempts:
>

from math import log
>
def yours(a, b , bits = 32):
     def _hamdist( x, bits):
         if bits:
             return (x & 1) + _hamdist(x >1, bits-1)
         return x & 1
     return _hamdist(a ^ b, bits)
>
def simple(a, b, bits=32):
    x = a ^ b
    return sum((x >i & 1) for i in xrange(bits))
>
def lazy(a, b, bits=32):
    x = (a ^ b) & ((1 << bits) - 1)
    tot = 0
    while x:
        tot += x & 1
        x >>= 1
    return tot
>
def fancy(a, b, bits=32):
    x = (a ^ b) & ((1 << bits) - 1)
    tot = 0
    while x:
        tot += 1
        x ^= 1 << int(log(x, 2))
    return tot
>
test_vals = (
        ((0xffffffff, 0), 32),
        ((0,0), 0),
        ((1,0), 1),
        ((0x80000000, 0), 1),
        ((0x55555555, 0), 16)
        )
>
def test(f):
    test_vals = (
            ((0xffffffff, 0), 32), # ALL
            ((0,0), 0), # None
            ((1,0), 1), # First
            ((0x80000000, 0), 1), # Last
            ((0x55555555, 0), 16), # Every Other
            ((0xffff, 0), 16), # First Half
            ((0xffff0000, 0), 16), # Last Half
            )
    for i, (args, exp) in enumerate(test_vals):
        if f(*args) != exp:
            return 0
    return 1
>
if __name__ == "__main__":
    for f in (yours, simple, lazy, fancy):
        if not test(f):
            print "%s failed"%f.__name__

>
The python module `timeit` is handy for testing speed:
>
python -mtimeit -s"from hamdist import *" "test(yours )"
10000 loops, best of 3: 95.1 usec per loop
>
python -mtimeit -s"from hamdist import *" "test(simpl e)"
10000 loops, best of 3: 65.3 usec per loop
>
python -mtimeit -s"from hamdist import *" "test(lazy) "
10000 loops, best of 3: 59.8 usec per loop
>
python -mtimeit -s"from hamdist import *" "test(fancy )"
10000 loops, best of 3: 77.2 usec per loop
>
Even the ridiculous `fancy` version beat the recursive version.
>
Matt