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

• To: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
• Subject: Re: [Imgcif-l] Reading CBF files from Python
• From: "Nicholas K. Sauter" <nksauter@lbl.gov>
• Date: Sat, 03 Jul 2010 21:03:43 -0700
• In-Reply-To: <4854F2500EA8C4478A508D2D92973E5206D6B655@EXCHANGE25.fed.cclrc.ac.uk>
• References: <4854F2500EA8C4478A508D2D92973E5206D6B5F9@EXCHANGE25.fed.cclrc.ac.uk><4C1F2B5C.30400@esrf.fr><4854F2500EA8C4478A508D2D92973E5206D6B5FA@EXCHANGE25.fed.cclrc.ac.uk><4C1F8A65.2020504@lbl.gov><4854F2500EA8C4478A508D2D92973E5206D6B604@EXCHANGE25.fed.cclrc.ac.uk><4C224E02.1060304@lbl.gov><4854F2500EA8C4478A508D2D92973E5206D6B610@EXCHANGE25.fed.cclrc.ac.uk><4854F2500EA8C4478A508D2D92973E5206D6B655@EXCHANGE25.fed.cclrc.ac.uk>

All,

OK, Graeme Winter's compress/uncompress routines are now checked in to 
the open source Computational Crystallography Toolbox, 
http://cctbx.sf.net.  They use the CBF byte-offset algorithm to convert 
an integer array to compressed string and vice versa.

A Python unit test to excercise the entire cycle is at 
cctbx_sources/cbflib_adaptbx/excercise_compression.py

Herbert---
You were right:  reading the entire compressed file directly into a 
memory buffer allows the decompression routine to operate much faster, 
compared with getc() or a smaller buffer.  2Kx2K files compress & 
uncompress in about 50 ms...faster than anything else I've seen!

Nick Sauter

Graeme.Winter@Diamond.ac.uk wrote:
> Hi Folks,
>
> In case anyone is interested, I coded up a pretty simple implementation
> of the byte offset compression and decompression in C++, with the
> interface
>
>   vector<char> compress(vector<int> data)
>   vector<int> uncompress(vector<char> packed)
>
> It could be useful for people wanting to "edit" images, which is what I
> had in mind. It's finding it's way into cctbx (thanks Nick!) but I will
> be happy to mail it out if anyone would like it.
>
> Best wishes,
>
> Graeme
>
>
>   
>   

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• References:
  • [Imgcif-l] Reading CBF files from Python (Graeme.Winter)
  • Re: [Imgcif-l] Reading CBF files from Python (Jon Wright)
  • Re: [Imgcif-l] Reading CBF files from Python (Graeme.Winter)
  • Re: [Imgcif-l] Reading CBF files from Python (Nicholas K. Sauter)
  • Re: [Imgcif-l] Reading CBF files from Python (Graeme.Winter)
  • Re: [Imgcif-l] Reading CBF files from Python (Nicholas K. Sauter)
  • Re: [Imgcif-l] Reading CBF files from Python (Graeme.Winter)
  • Re: [Imgcif-l] Reading CBF files from Python (Graeme.Winter)

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