Bit substring search

[Kris Kennaway]

I am trying to parse a bit-stream file format (bzip2) that does not have
byte-aligned record boundaries, so I need to do efficient matching of
bit substrings at arbitrary bit offsets.

Is there a package that can do this? This one comes close:

http://ilan.schnell-web.net/prog/bitarray/

but it only supports single bit substring match.

Kris

[bearophileHUGS]

Kris Kennaway:

I am trying to parse a bit-stream file format (bzip2) that does not have
byte-aligned record boundaries, so I need to do efficient matching of
bit substrings at arbitrary bit offsets.
Is there a package that can do this?

You may take a look at Hachoir or some other modules:
http://hachoir.org/wiki/hachoir-core
http://pypi.python.org/pypi/construct/2.00
http://pypi.python.org/pypi/FmtRW/20040603
Etc. More:
http://pypi.python.org/pypi?%3Aactio...ch&term=binary

Bye,
bearophile

[Kris Kennaway]

be************@ lycos.com wrote:

Kris Kennaway:

>I am trying to parse a bit-stream file format (bzip2) that does not have
byte-aligned record boundaries, so I need to do efficient matching of
bit substrings at arbitrary bit offsets.
Is there a package that can do this?

You may take a look at Hachoir or some other modules:
http://hachoir.org/wiki/hachoir-core
http://pypi.python.org/pypi/construct/2.00

Thanks. hachoir also comes close, but it also doesnt seem to be able to
match substrings at a bit level (e.g. the included bzip2 parser just
reads the header and hands the entire file off to libbzip2 to extract
data from).

construct exports a bit stream but it's again pure python and matching
substrings will be slow. It will need C support to do that efficiently.

http://pypi.python.org/pypi/FmtRW/20040603
Etc. More:
http://pypi.python.org/pypi?%3Aactio...ch&term=binary

Unfortunately I didnt find anything else useful here yet :(

Kris

[bearophileHUGS]

Kris Kennaway:

Unfortunately I didnt find anything else useful here yet :(

I see, I'm sorry, I have found hachoir quite nice in the past. Maybe
there's no really efficient way to do it with Python, but you can
create a compiled extension, so you can see if it's fast enough for
your purposes.
To create such extension you can:
- One thing that requires very little time is to create an extension
with ShedSkin, once installed it just needs Python code.
- Cython (ex-Pyrex) too may be okay, but it's a bit trikier on Windows
machines.
- Using Pyd to create a D extension for Python is often the faster way
I have found to create extensions. I need just few minutes to create
them this way. But you need to know a bit of D.
- Then, if you want you can write a C extension, but if you have not
done it before you may need some hours to make it work.

Bye,
bearophile

[Kris Kennaway]

be************@ lycos.com wrote:

Kris Kennaway:

>Unfortunatel y I didnt find anything else useful here yet :(

I see, I'm sorry, I have found hachoir quite nice in the past. Maybe
there's no really efficient way to do it with Python, but you can
create a compiled extension, so you can see if it's fast enough for
your purposes.
To create such extension you can:
- One thing that requires very little time is to create an extension
with ShedSkin, once installed it just needs Python code.
- Cython (ex-Pyrex) too may be okay, but it's a bit trikier on Windows
machines.
- Using Pyd to create a D extension for Python is often the faster way
I have found to create extensions. I need just few minutes to create
them this way. But you need to know a bit of D.
- Then, if you want you can write a C extension, but if you have not
done it before you may need some hours to make it work.

Thanks for the pointers, I think a C extension will end up being the way
to go, unless someone has beaten me to it and I just haven't found it yet.

Kris

[Kris Kennaway]

Scott David Daniels wrote:

Kris Kennaway wrote:

>Thanks for the pointers, I think a C extension will end up being the
way to go, unless someone has beaten me to it and I just haven't found
it yet.

Depending on the pattern length you are targeting, it may be fastest to
increase the out-of-loop work. For a 40-bit string, build an 8-target
Aho-Corasick machine, and at each match check the endpoints. This will
only work well if 40 bits is at the low end of what you are hunting for.

Thanks, I wasn't aware of Aho-Corasick.

Kris