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Re: [Imgcif-l] Reading CBF files from Python

Hi Nick,

You are of course correct - I was trying to think about this in 'C' terms - however it also occurs to me that the char * is a NULL terminated string... the API below would be broken then :o)

So strCompressedImage = compress(integerArray) and the inverse with flex_ints would be correct. And much cleaner.

I didn't think byte offset worked with anything other than integers? I would be aiming for compression and decompression of integer maps much faster than my python implementation, which is clearly not hard!

How does this sound? I could see that this would be more generally useful...

Best wishes,

Graeme




-----Original Message-----
From: imgcif-l-bounces@iucr.org on behalf of Nicholas K. Sauter
Sent: Thu 6/24/2010 7:54 PM
To: The Crystallographic Binary File and its imgCIF application to image data
Subject: Re: [Imgcif-l] Reading CBF files from Python

Hi Graeme,

What would be the overall goal here?  Normally within CCTBX, the return
values and argument values are Python types, so instead of char * and
unsigned short * we use Python string and scitbx.flex_int.  It may be
possible to wrap raw pointers with Boost Python such that they are
treated opaquely by Python, but we don't usually use this procedure.

Then again, cctbx::cbflib_adaptbx specializes the byte offset
compression (optimized_byte_offset) so that integer arrays can be
compressed extra fast, above what is possible with the generic low-level
routine.

Are we aiming here to compress non-integer types, mixing of multiple
types, better performance, or something else?

Best,
Nick


Graeme.Winter@Diamond.ac.uk wrote:
> Hi Nick,
>
> Many thanks - this is rather quicker than my pure Python implementation
> (just over two orders of magnitude!)
>
> Would it be straightforward to boost the lower level compression /
> decompression routines? It's not clear from the cbflib docs that these
> would be easily extracted - for instance:
>
>  char * compressed = cbf_byte_offset_compress(unsigned short * array,
> int nx, int ny)
>
>  - and -
>
>  unsigned short * array = cbf_byte_offset_decompress(char * compressed,
> int nx, int ny)
>
> Are not really exported in a stand alone fashion?
>
> Still - this is *much* better than what I have right now.
>
> Best wishes,
>
> Graeme
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