Re: [Imgcif-l] CBF - Adding binary proprietary format header dump

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

Hi Jon & Justin

Having the header information duplicated like this might be useful in  
the early stages of development, but I really don't see that having  
it as a MIME encoded binary is terribly helpful - an ASCII  
transcription would be much more useful for users.


> Justin,
>
> Some users might have concerns that they "get the same results"  
> with the
> new file format, so that having the old headers in the files would  
> make
> it easier to check on that. Certainly we would be interested to have
> access to writing information to the new headers with current cameras
> and the linux device server. Currently things can be encoded into the
> "file_comments" and "dataset_comments", and are then decoded again  
> later
> (if not by mosflm).
>
> Retaining the original header will be useful for developers who are
> further downstream, and work in other fields than mosflm.
>
> It would also be useful if there is a way to arrange things so that
> simple minded file readers find the x-ray image first, rather than
> getting confused by finding the header instead. Just in case some  
> people
> start at the top of file and move down looking for the first mime  
> header.
>
> Best wishes,
>
> Jon
>
>
>
> harry powell wrote:
>> Hi Justin
>>
>> If you want to keep the Mar header items, why not just keep on
>> writing Mar format images (which are well-supported by all the major
>> integration programs)?
>>
>> As a developer, I think I would prefer you to write all the Mar
>> header items as CIF header items, if you want to write CBFs. If the
>> imgCIF items don't exist, tell the community and I'm sure they could
>> be accommodated.
>>
>> Mosflm will _only_ read the imgCIF header items and ignore any
>> comments or non-image MIME components (why on earth would I spend
>> time writing code to read both kinds of header item from an image
>> file when the imgCIF headers are supposed to be definitive?), and my
>> understanding is that XDS doesn't read the CBF or Mar header items in
>> any case. I don't know about d*Trek or HKL...
>>
>> On 24 Sep 2007, at 20:51, Justin Anderson wrote:
>>
>>> Hi Harry, thanks for the reply.
>>>
>>> We were wanting to dump in our binary header so that we could  
>>> read it
>>> directly in to the marccd program and be able to recover the entire
>>> original header that way (regardless of which of our header items  
>>> are
>>> mapped to CIF header fields).
>>>
>>> What were your concerns with having it in the file?
>>>
>>> Regards,
>>>
>>> Justin
>>>
>>>
>>> On 09/24/2007 02:38 PM, harry powell wrote:
>>>> Hi
>>>>
>>>> I don't understand why you'd want to add the binary header, to be
>>>> honest. I can see why you might want to have the contents of the
>>>> header as an ASCII comment section - but I think this should  
>>>> just be
>>>> a check while developing the file format.
>>>>
>>>> Could you elaborate why you'd want it there?
>>>>
>>>>> Hello everyone,
>>>>>
>>>>> We here would, in fact, like to add our binary header to the CBF
>>>>> file.
>>>>> Should that just go into an additional binary section, with MIME
>>>>> header
>>>>> and all of that?  If so, is there any recommendation as to how we
>>>>> can
>>>>> refer to it in the CIF headers so that I can distinguish  
>>>>> between the
>>>>> binary image data and our binary header data?  My inclination  
>>>>> is to
>>>>> add
>>>>> the ".header_convention" column to my "_array_data" loop and fill
>>>>> it in
>>>>> with "RAY_1.0" or something like that for the our binary header  
>>>>> and
>>>>> with
>>>>>   an empty value "" for the image data.
>>>>>
>>>>> e.g. :
>>>>>
>>>>> loop_
>>>>> _array_data.array_id
>>>>> _array_data.binary_id
>>>>> _array_data.header_convention
>>>>> _array_data.data
>>>>>   ARRAY1 1 RAY_1.0
>>>>> ;
>>>>> --CIF-BINARY-FORMAT-SECTION--
>>>>> <<MIME header for Rayonix binary header dump>>
>>>>> <<Rayonix binary header dump>>
>>>>> --CIF-BINARY-FORMAT-SECTION----
>>>>> ;
>>>>>   ARRAY2 2
>>>>> ;
>>>>> --CIF-BINARY-FORMAT-SECTION--
>>>>> <<MIME header for image binary data>>
>>>>> <<Image binary data>>
>>>>> --CIF-BINARY-FORMAT-SECTION----
>>>>> ;
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Regards,
>>>>>
>>>>> -- 
>>>>> 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
>>>> Harry
>>> _______________________________________________
>>> imgcif-l mailing list
>>> imgcif-l@iucr.org
>>> http://scripts.iucr.org/mailman/listinfo/imgcif-l
>>
>> Harry
>
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Harry
-- 
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH




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