Re: [Imgcif-l] CBF Format

["Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>]

Dear Harry,

  Actually you can have your miniCBF header and full
header, too, even for MAR.  If you look at the
file converted_flat_orig.cbf in the CBFlib data
files kit, you will see;

_diffrn_frame_data.id FRAME1
_diffrn_frame_data.detector_element_id ELEMENT1
_diffrn_frame_data.array_id ARRAY1
_diffrn_frame_data.binary_id 1
_diffrn_frame_data.details
;
 DETECTOR = MAR 345;
 PIXEL SIZE = 0.15 0.15;
 WAVELENGTH = 1.080000;
 DISTANCE = 240;
 OSCILLATION AXIS = PHI;
 PHI = 0;
 OSCILLATION RANGE = 1;
 PROGRAM = mar345 Version 0.8.6;
 DATE = Thu Dec  4 10:23:48 1997;
 SCANNER = 26;
 FORMAT = 2300  PCK 5290000;
 HIGH = 155;
 PIXEL = LENGTH 150  HEIGHT 150;
 OFFSET = ROFF 5.000  TOFF 0.000;
 MULTIPLIER = 1.000;
 GAIN = 1.000;
 RESOLUTION = 1.761;
 PHI.. = START 0.000  END 1.000  OSC 1;
 OMEGA = START 0.000  END 0.000  OSC 0;
 CHI = 0.000;
 TWOTHETA = 0.000;
 CENTER = X 1150.000  Y 1150.000;
 MODE = TIME;
 EXPOSURE TIME = 20.00;
 COUNTS = START 19.35 END 19.29  NMEAS 9;
 COUNTS.. = MIN 19.27  MAX 19.38;
 COUNTS.... = AVE 19.30  SIG 0.03;
 INTENSITY = MIN 1  MAX 249051  AVE 207.8  SIG 951.09;
 HISTOGRAM = START 0  END 2023  MAX 28307;
 GENERATOR = ROTATINGANODE  kV 10.0  mA 20.0;
 MONOCHROMATOR = GRAPHITE  POLAR 0.000;
 COLLIMATOR = WIDTH 0.30  HEIGHT 0.30;
;

I added this to extra copy of header information
to the output of convert_image when I was working
with Chris on the ADSC header.  I proved so
useful there, that I put it in for MAR as
well and would suggest it for all detectors.

=====================================================
 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 Wed, 12 Sep 2007, Harry Powell wrote:

> Hi
>
> I'd like to concur with Nick. As far as Mosflm is concerned, the miniCBF
> is not a CBF. In my opinion, it should not be called "anything" CBF.
> Developers of some other integration programs have been rather less polite
> (privately) in their descriptions of the miniCBF.
>
> My understanding is that the miniCBF was developed for the Pilatus
> detector for processing with XDS - which does not use image header
> information except for the image size and compression algorithm (and it
> gets these from the MIME part).
>
> If you include the CIF fields that are present in images from the ADSCs at
> Diamond, you will not be going far wrong - see an example header at
>
>  	http://www.mrc-lmb.cam.ac.uk/harry/herb.header
>
> (this is a file I prepared for Herb a little while ago, and not linked to,
> so you need to use this URL). Note that it also includes the normal ADSC
> header information as a properly-formed CIF comment (i.e. free text
> delimited by ";" on lines on their own), but this is not parsed by Mosflm.
> MarCCD headers, being binary encoded, would probably not be usefully
> reproduced in the CBF header!
>
> The beamline and data acquisition staff at Diamond expect all their PX
> area detectors to write CBFs in the same form with the same header
> information as proper CIF items; the image compression algorithm is up to
> the detector manufacturer, as long as it is one of those supported by
> CBFlib.
>
> >From a personal point of view, I think it would be really nice if all CBFs
> (at least in the same field) conformed to the same format!
>
> > Thanks for working on CBF support for the Mar CCD.  The image processing
> > program LABELIT expects full CBF, not miniCBF.  The MIME area is not
> > parsed.  You are correct in identifying the "non-optional" data items.
> > This is as far as my expertise goes...it would be quite helpful if some
> > Mar datasets written in CBF format were to be made available.  The most
> > useful test cases would be those where the direct beam is offset from
> > the detector center, but not at a 45- or 90-degree position angle.  Full
> > datasets would be most useful.
> >
> > Nick Sauter
> >
> > Justin Anderson wrote:
> >
> >> Hello everyone,
> >>
> >> My name is Justin Anderson with Rayonix (formerly MarUSA).  I have been
> >> given the task of adding CBF format support to the marccd program.  I
> >> was hoping you could help me with a few questions that have arisen.  I
> >> truly appreciate it.
> >>
> >> Now for the questions...
> >>
> >> 1)  Are miniCBF files meant to be read by imaging programs such as
> >> marccd or are they expected to be converted to full CBF format first?
> >>
> >> 2)  What is the minimum set of fields that is necessary for an official
> >> miniCBF and CBF file?  In the "Simple Example Header" in section 2 of
> >> the Draft Format
> >> (http://www.iucr.org/iucr-top/cif/cbf/cbf_definition.html) it does
> >> mention at one point that "the above" data items are optional.  Does
> >> that imply that the items below are required?
> >>
> >> 3)  Some items can exist in both the header area and the MIME area.  One
> >> such example is the image size (e.g. fastest and second-fastest number
> >> of pixels).  When reading a CBF file, should I expect to get that
> >> information from the MIME, the CBF header area or would it be found in both?
> >>
> >> I appreciate any help you can give me.
> >>
> >>
> >>
> >> Justin Anderson                    Rayonix, LLC (Formerly Mar USA)
> >> Software Engineer                  justin@rayonix.com
> >> 1880 Oak Ave. Ste. 120             Evanston, IL, USA 60201
> >> 877.627.9729                       847.869.1548
> >>
> >> _______________________________________________
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> >> imgcif-l@iucr.org
> >> http://scripts.iucr.org/mailman/listinfo/imgcif-l
> >>
> >>
> >
> > --
> > Nicholas K. Sauter, Ph.D.
> > Lawrence Berkeley National Laboratory
> > 1 Cyclotron Road
> > Berkeley, CA 94720
> >
> > nksauter@lbl.gov
> > Voice: 510-486-5713
> > Fax: 510-486-5909
> > _______________________________________________
> > imgcif-l mailing list
> > imgcif-l@iucr.org
> > http://scripts.iucr.org/mailman/listinfo/imgcif-l
> >
>
> Harry
> --
> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
> Road, Cambridge, CB2 2QH
>
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