[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Reply to: [list | sender only]
Re: [Imgcif-l] Reading CBF files from Python
- To: <imgcif-l@iucr.org>
- Subject: Re: [Imgcif-l] Reading CBF files from Python
- From: <Graeme.Winter@Diamond.ac.uk>
- Date: Mon, 21 Jun 2010 10:26:42 +0100
- In-Reply-To: <4C1F2B5C.30400@esrf.fr>
- References: <4854F2500EA8C4478A508D2D92973E5206D6B5F9@EXCHANGE25.fed.cclrc.ac.uk><4C1F2B5C.30400@esrf.fr>
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 > 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 -- 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]
- Follow-Ups:
- Re: [Imgcif-l] Reading CBF files from Python (Nicholas K. Sauter)
- Re: [Imgcif-l] Reading CBF files from Python (Jon Wright)
- References:
- [Imgcif-l] Reading CBF files from Python (Graeme.Winter)
- Re: [Imgcif-l] Reading CBF files from Python (Jon Wright)
- Prev by Date: Re: [Imgcif-l] Reading CBF files from Python
- Next by Date: Re: [Imgcif-l] Reading CBF files from Python
- Prev by thread: Re: [Imgcif-l] Reading CBF files from Python
- Next by thread: Re: [Imgcif-l] Reading CBF files from Python
- Index(es):