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Re: [Imgcif-l] Pilatus 2M putative full CBF implementation
- To: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
- Subject: Re: [Imgcif-l] Pilatus 2M putative full CBF implementation
- From: Nicholas Sauter <nksauter@lbl.gov>
- Date: Fri, 1 Jul 2011 12:00:59 -0700
- In-Reply-To: <A9A5AB5D578E0D4E9F681A8ACA77D0D70F9476@EXCHMBX01.fed.cclrc.ac.uk>
- References: <13999B6FC038EB44B067771E3CFBD091097228@EXCHMBX01.fed.cclrc.ac.uk><BANLkTikxTHsNtFYuSLBsQOduHtv0r2ZFyg@mail.gmail.com><A9A5AB5D578E0D4E9F681A8ACA77D0D70F9476@EXCHMBX01.fed.cclrc.ac.uk>
Alan, I didn't realize the files could be read both ways. I can force Labelit to read the files in one format or the other; I still get correct autoindexing, but the lattice results are slightly different numerically. In trying to track this down, I printed out the relevant parameters from both types of read. Beam centers differ by 4 microns. File reads give similar timings on our Intel Xeon; 19.9 ms for CBF-format; 19.5 ms for Pilatus format. Trying this many times and in different orders, it consistently takes about 0.2 - 0.5 ms longer to read the CBF-format. Nick P.S. Here's the complete cctbx/Python script I used, plus the output: ##### Python script run in CCTBX environment: from iotbx.detectors import CBFImage, PilatusImage import pprint def compare(file): C = CBFImage(file) P = PilatusImage(file); P.readHeader() print "As a CBF-format image:" pprint.pprint(C.parameters) print "As a Pilatus-format image:" pprint.pprint(P.parameters) def benchmark(file): from libtbx.development.timers import Timer T = Timer("CBF-format") for x in xrange(1000): C = CBFImage(file); C.read() T = Timer("Pilatus-format") for x in xrange(1000): P = PilatusImage(file); P.read() del T assert P.linearintdata==C.linearintdata if __name__=="__main__": import sys compare(file=sys.argv[1]) benchmark(file=sys.argv[1]) As a CBF-format image: {'BEAM_CENTER_X': 144.3900000000025, 'BEAM_CENTER_Y': 126.08000000000216, 'CCD_IMAGE_SATURATION': 590314.0, 'DETECTOR_SN': 0, 'DISTANCE': 155.02, 'OSC_RANGE': 0.05, 'OSC_START': 0.0, 'PIXEL_SIZE': 0.17200000000000001, 'SIZE1': 1679, 'SIZE2': 1475, 'TWOTHETA': 0.0, 'WAVELENGTH': 0.9173} As a Pilatus-format image: {'BEAM_CENTER_X': 144.394, 'BEAM_CENTER_Y': 126.08460000000001, 'CCD_IMAGE_SATURATION': 590314, 'DETECTOR_SN': 'PILATUS 2M S/N 24-0107 Diamond', 'DISTANCE': 155.0, 'DISTANCE_UNITS': 'm', 'OSC_RANGE': 0.05, 'OSC_START': 0.0, 'PIXEL_SIZE': 0.17200000000000001, 'PIXEL_SIZE_UNITS': 'm', 'SIZE1': 1679, 'SIZE2': 1475, 'WAVELENGTH': 0.9173} start timing Pilatus-format start timing CBF-format time for Pilatus-format: CPU, 18.950s; elapsed, 19.278s time for CBF-format: CPU, 19.240s; elapsed, 19.568s On Fri, Jul 1, 2011 at 12:50 AM, <Alun.Ashton@diamond.ac.uk> wrote: > Thanks Nick, > > Out of interest, and for the record, are you reading the 'full' CIF header > in these CBF files, or the embedded 'miniCBF' header. And is there any > slowdown if it's the 'full' CIF header? > > Alun > ___________________________________________________________ > Alun Ashton, alun.ashton@diamond.ac.uk Tel: +44 1235 778404 > Scientific Software Team Leader, http://www.diamond.ac.uk/ > Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K. > > > > -----Original Message----- > > From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On > > Behalf Of Nicholas Sauter > > Sent: 30 June 2011 19:42 > > To: The Crystallographic Binary File and its imgCIF application to > > image data > > Subject: Re: [Imgcif-l] Pilatus 2M putative full CBF implementation > > > > Graeme, > > > > The new dataset looks good in terms of the indexing process with > > LABELIT. > > > > Cheers, > > Nick > > > > On Thu, Jun 30, 2011 at 8:44 AM, <Graeme.Winter@diamond.ac.uk> wrote: > > > > > Dear people interested in imgCIF, > > > > > > As you will no doubt know, we have been battling for a while to get > > to > > > generating full cbf images from our detectors. We have now reached a > > > milestone - full cbf images from Pilatus instruments which cbflib > > recognises > > > and can read, and that can be processed with our automated software. > > > However, we felt that it would be important to make these data > > available for > > > review among CIF experts to ensure that there are no real boo boo's > > in > > > there. > > > > > > So, a full Pilatus2M image data set can be found from: > > > > > > ftp://ftpanon.diamond.ac.uk/GraemeWinter/CBF/Pilatus2M/C.tar.bz2 > > > > > > which appears to process well using xia2 / XDS, which relies on pycbf > > now > > > included in cctbx to read the image headers and is currently an > > unreleased > > > version. It is unreleased for a good reason: the assumptions which > > define > > > the CIF in the images here are the same set of assumptions used in > > > understanding them, though the headers are based on those from an > > ADSC Q315 > > > so should be good. If you are keen though you can get the bleeding > > edge code > > > from sourceforge. > > > > > > The axes described are the "canonical" rather than true ones i.e. > > they are > > > where we would ideally like everything to be rather than where > > everything is > > > actually measured to be - the latter will be a refinement at some > > point in > > > the future. > > > > > > What would I like? People to download this, unpack it and critique > > the > > > headers which are contained therein. > > > > > > For people who are interested in the how, you will also find a .cif > > file in > > > the tarball - this was generated by GDA from a metatemplate using > > some > > > Python code and is used by the "camserver" program to compose the > > full cbf > > > image. Any errors in the CIF are therefore my fault in composing this > > > template and need fixing! > > > > > > Thanks in advance and best wishes, > > > > > > Graeme > > > > > > Dr. Graeme Winter > > > Senior Software Scientist > > > Diamond Light Source > > > > > > +44 1235 778091 (work) > > > +44 7786 662784 (work mobile) > > > > > > > > > > > > > > > > > > -- > > > > > > 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 > > > > > > > > > > > -- > > Nicholas K. Sauter, Ph. D. > > Computer Staff Scientist/Engineer > > Physical BioSciences Division > > Lawrence Berkeley National Laboratory > > 1 Cyclotron Rd., Bldg. 64R0121 > > Berkeley, CA 94720-8118 > > (510) 486-5713 > > _______________________________________________ > > 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 > -- Nicholas K. Sauter, Ph. D. Computer Staff Scientist/Engineer Physical BioSciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713 _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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- References:
- [Imgcif-l] Pilatus 2M putative full CBF implementation (Graeme.Winter)
- Re: [Imgcif-l] Pilatus 2M putative full CBF implementation (Nicholas Sauter)
- Re: [Imgcif-l] Pilatus 2M putative full CBF implementation (Alun.Ashton)
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