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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: Wed, 23 Jun 2010 11:13:54 -0700
• In-Reply-To: <4854F2500EA8C4478A508D2D92973E5207CD5958@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><4C20DB8C.8020507@lbl.gov><4854F2500EA8C4478A508D2D92973E5207CD5958@EXCHANGE25.fed.cclrc.ac.uk>

Graeme,

Just found this myself.  The trick is adding the following line to the 
top of the file:

from scitbx.array_family import flex

Note to self:  reorganize the cbflib_adaptbx so that this import is done 
transparently.

Nick

Graeme.Winter@Diamond.ac.uk wrote:
> Hi Nick,
>
> Not sure I have things built quite right then:
>
> [gw56@ws050 tmp]$ labelit.python 
> Python 2.6.5 (r265_cci:79063, Jun  2 2010, 06:13:15) 
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>   
>>>> from cbflib_ext import MiniCBFAdaptor
>>>> a = MiniCBFAdaptor("image.cbf")
>>>> r = a.optimized_read_data(3072, 3072)
>>>>         
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> TypeError: No to_python (by-value) converter found for C++ type: scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10u> > >
>
> However, API's such as this would be just the ticket. The tricky thing about the compression will of course be constructing all of the rest of the CBF structure around 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)

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