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Re: [Imgcif-l] Reading CBF files from Python
- To: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
- Subject: Re: [Imgcif-l] Reading CBF files from Python
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Mon, 21 Jun 2010 07:31:53 -0400 (EDT)
- In-Reply-To: <4C1F3784.6060107@esrf.fr>
- References: <4854F2500EA8C4478A508D2D92973E5206D6B5F9@EXCHANGE25.fed.cclrc.ac.uk><4C1F2B5C.30400@esrf.fr><4854F2500EA8C4478A508D2D92973E5206D6B5FA@EXCHANGE25.fed.cclrc.ac.uk><4C1F3784.6060107@esrf.fr>
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@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@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@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 > > > [*** Terminated Message ***] > _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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- [Imgcif-l] Reading CBF files from Python (Graeme.Winter)
- Re: [Imgcif-l] Reading CBF files from Python (Jon Wright)
- Re: [Imgcif-l] Reading CBF files from Python (Graeme.Winter)
- Re: [Imgcif-l] Reading CBF files from Python (Jon Wright)
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