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

Graeme,

I've checked in code to cctbx.sf.net that does a basic read and write of 
your image data.  Example python script is attached.  The headers in the 
output file are not binary identical to the input, but the data itself 
is identical.

Nick

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


from scitbx.array_family import flex #mandatory import for cbflib_ext
from cbflib_ext import MiniCBFAdaptor,CBFWriteAdaptor

initial_file = "/net/sunbird/raid1/sauter/rawdata/gw/special_picture/image.cbf"
target_file = "target.cbf"

initial_adaptor = MiniCBFAdaptor(initial_file)
initial_rawdata = initial_adaptor.optimized_read_data()

write_adaptor = CBFWriteAdaptor(target_file)
write_adaptor.write_data(initial_rawdata)

del initial_adaptor
del write_adaptor

target_adaptor = MiniCBFAdaptor(target_file)
target_rawdata = target_adaptor.optimized_read_data()

assert initial_rawdata.size() == target_rawdata.size()
assert initial_rawdata == target_rawdata
import os; os.remove(target_file)
print "OK"

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