[Imgcif-l] Reading CBF files from Python

[Nicholas K. Sauter]

Graeme,

The cctbx::cbflib_adaptbx has been optimized for decompression of 
Pilatus images--should be about 90 ms on newer Linux systems.  
Compression hasn't been tested but could potentially be optimized along 
similar lines. 

The code currently in cctbx::iotbx could be subclassed to read whatever 
CBF image you have--if you'd like to post your data somewhere I'll have 
a look.

Nick

On 6/21/2010 2:26 AM, Graeme.Winter at Diamond.ac.uk wrote:
> 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 at iucr.org [mailto:imgcif-l-bounces at 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 at 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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