[Imgcif-l] Pilatus 2M putative full CBF implementation

Nicholas Sauter nksauter at lbl.gov
Fri Jul 1 20:00:59 BST 2011 

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 at 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 at 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 at iucr.org [mailto:imgcif-l-bounces at 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 at 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)
> > >
> > >
> > >
> > >
> > >
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> > --
> > 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
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> 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.
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> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
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-- 
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

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