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Re: [Imgcif-l] CBF Format
- To: Harry Powell <harry@mrc-lmb.cam.ac.uk>
- Subject: Re: [Imgcif-l] CBF Format
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Wed, 12 Sep 2007 17:46:01 -0400 (EDT)
- Cc: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
- In-Reply-To: <Pine.LNX.4.64.0709122208150.14234@ls1.lmb.internal>
- References: <46E8433B.7080908@rayonix.com> <46E850F9.5010003@lbl.gov><Pine.LNX.4.64.0709122208150.14234@ls1.lmb.internal>
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 > >> > >> _______________________________________________ > >> imgcif-l mailing list > >> 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 > > _______________________________________________ > 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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