Re: [Imgcif-l] CBF Format

[Harry Powell <harry@mrc-lmb.cam.ac.uk>]

Hi Herb

You've missed the point completely of what I wrote. _Of_course_ you could 
put the binary header in, but, to quote my last message -

>>so you can't just put the header information as it appears in the
>> native format and expect people to be able to read it by more-or-lessing
>> the file.

Perhaps I should have said "more" or "less" -ing, to make it plainer that 
I meant using the programs of those names to output the headers to the 
screen. As Charlie Brown used to say (and probably still does) - "good 
grief!"

> Dear Harry,
>
>  Actually, if you want the CCD header stictly
> as binary, rather than putting in an ASCII
> translation, you could do that as well, by
> putting it in as CBF binary section, just
> as we will be doing with thumbnails, but
> for debugging, a straight ASCII translation
> of the header before the reorganization
> into the imgCIF categories can be very useful.
>
>  Regards,
>    Herbert
>
> =====================================================
> 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 Thu, 13 Sep 2007, Harry Powell wrote:
>
>> Hi Herb
>>
>> not strictly true. The MarCCD headers are binary, Mar IP headers are
>> ASCII, so you can't just put the header information as it appears in the
>> native format and expect people to be able to read it by more-or-lessing
>> the file.
>>
>> Further to what I wrote yesterday, my experience of native MarCCD headers
>> is that they contain sufficient information to process the image (and
>> indeed full datasets) without reference to external files/lab books etc.
>> So if this information were to be written to a MarCCD CBF, that would be a
>> very good start.
>>
>>>  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
>>>>
>>>> _______________________________________________
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>>>> 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
>>
>>
>

Harry
-- 
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

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