Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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

Hi Nick,

Thanks, I will put it somewhere useful. Would it be straightforward to
have these C++ methods boosted to Python to perhaps read in a string of
the compressed image, return a flex array of integers and the inverse?
This would make them directly available in a most convenient manner!

Image at: http://www.ccp4.ac.uk/xia/image.cbf

Best wishes,

Graeme

-----Original Message-----
From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On
Behalf Of Nicholas K. Sauter
Sent: 21 June 2010 16:51
To: The Crystallographic Binary File and its imgCIF application to image
data
Subject: Re: [Imgcif-l] Reading CBF files from Python

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@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@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)
>>  
>>  
>>
>>
>>
>>     
>
> _______________________________________________
> imgcif-l mailing list
> imgcif-l@iucr.org
> http://scripts.iucr.org/mailman/listinfo/imgcif-l
>
>   
_______________________________________________
imgcif-l mailing list
imgcif-l@iucr.org
http://scripts.iucr.org/mailman/listinfo/imgcif-l

-- 
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
 



_______________________________________________
imgcif-l mailing list
imgcif-l@iucr.org
http://scripts.iucr.org/mailman/listinfo/imgcif-l

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.

Useful links