[Imgcif-l] Reading CBF files from Python

[Jon Wright]

Hi Graeme,

To use the binding the wrapper needs to be compiled, which should just 
mean typing "python setup.py build" in the pycbf subfolder. Then you 
just need to drop pycbf.py and _pycbf.so somewhere on your python path 
(import sys; print sys.path). The binding runs entirely via calls to 
CBFlib, so if there is something useful in there, it should be possible 
to include it. Herbert can probably help more for knowing where to look.

If you can send an example image off-list I'll try to take a look

Best

Jon

Graeme.Winter at Diamond.ac.uk wrote:
> 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 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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