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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: "Nicholas K. Sauter" <nksauter@lbl.gov>
- Date: Mon, 21 Jun 2010 08:51:01 -0700
- In-Reply-To: <4854F2500EA8C4478A508D2D92973E5206D6B5FA@EXCHANGE25.fed.cclrc.ac.uk>
- References: <4854F2500EA8C4478A508D2D92973E5206D6B5F9@EXCHANGE25.fed.cclrc.ac.uk><4C1F2B5C.30400@esrf.fr><4854F2500EA8C4478A508D2D92973E5206D6B5FA@EXCHANGE25.fed.cclrc.ac.uk>
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
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