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

Hi Jon,

Thanks - I see that this is bundled with cctbx and Labelit, which was
awesome. However it seems that the modules from pycbf aren't available
as standard :o(  - I am slightly hamstrung by the fact that I use the
cctbx python, so having access to other python extensions presents a
problem. However I *really need* cctbx :o) - xia2 won't work without it
now.

My rate limiting step right now is the reading and writing of the byte
offset compression. I am going to guess that if I messed with the python
paths and such I should be able to find your implementation. Do you have
a method in there which will allow me to just pack and unpack the
byte_offset compressed regions?

This is the data in question:

###CBF: Version July 2008 generated by XDS

data_FRAME.cbf

_array_data.header_convention "XDS special"
_array_data.header_contents
;
;

_array_data.data
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
     conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size:   9450352
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
X-Binary-Number-of-Elements:   9437184
X-Binary-Size-Fastest-Dimension:    3072
X-Binary-Size-Second-Dimension:    3072
(massive binary blob)

The bit which is causing me problems is that the cbflib adaptor raises
an exception as most of the "proper" cbf stuff (i.e. the CIF) is not
present. Erk.

Any suggestions will be pounced apon!

Many thanks,

Graeme 

-----Original Message-----
From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On
Behalf Of Jon Wright
Sent: 21 June 2010 10:06
To: The Crystallographic Binary File and its imgCIF application to image
data
Subject: Re: [Imgcif-l] Reading CBF files from Python

Hi Graeme,

There is a swig based python binding included with CBFlib in the pycbf
subfolder. It should work for reading files (see pycbf_test1.py). 
Further work was needed for writing. Let me know if you run into
problems. Improvements are most welcome.

Best

Jon

Graeme.Winter@Diamond.ac.uk wrote:
> Hi Folks,
>  
> Does anyone know if CBF images can be read from Python? I coded up 
> something in Python to do this but it's a spot slow to say the least. 
> My interest is partly in reading the cbf "image" files calculated by 
> XDS to explain what it has been up to. I could code something up in 
> 'c' or a bridge to CBFlib but that would be hardish to maintain, so a 
> solution using existing Python libraries would suit me better.
>  
> I looked quickly at PyCIFrw but this appears to be mostly about the 
> CIF side of things rather than the MIME encoded chunks. Please correct

> me if I am wrong. I also tried iotbx.detectors.cbf.CBFImage but hit an

> exception which probably relates to this being more of a picture than 
> a diffraction image.
>  
> Thanks,
>  
> Graeme
>  
> Dr. Graeme Winter
> Software and MX Support Scientist
> Diamond Light Source
>  
> +44 1235 778091 (work)
> +44 7786 662784 (work mobile)
>  
>  
> 
> 
> 

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