[Imgcif-l] Reading CBF files from Python

[Herbert J. Bernstein]

Dear Graeme and Jon,

   It sounds like you two have things under control.
Let me know you need anything.

   Regards,
     Herbert

=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya at dowling.edu
=====================================================

On Mon, 21 Jun 2010, Jon Wright wrote:

> 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
>
>
> [*** Terminated Message ***]
>