[Imgcif-l] Fwd: Re: Nexus / cbf roundtrip
Herbert J. Bernstein
yaya at bernstein-plus-sons.com
Mon Oct 3 16:22:30 BST 2011
Dear Graeme,
There is no problem putting every part of a CIF or of multiples
CIFS into HDF5, but it then does not conform to the formal NeXus
definitions, simply
because NeXus does not have a full set of definitions for the PX
experiment yet. If we flesh out the NeXus definitions and add some
links back into the CIF tables, we should be OK. The problem is not
technical, but social -- getting agreement among all parties on the
definitions so that people will be able to read what other write.
Regards,
Herbert
At 10:30 AM -0400 10/3/11, Herbert J. Bernstein wrote:
>From: <Graeme.Winter at Diamond.ac.uk>
>To: <imgcif-l at iucr.org>
>Date: Mon, 3 Oct 2011 14:28:56 +0000
>Reply-To: The Crystallographic Binary File and its imgCIF
>application to image data <imgcif-l at iucr.org>
>
>Dear Herbert,
>
>If I may clarify: the intermediate "NeXus format" state - is the
>description of the rotation axes in there incomplete, i.e. not as
>well structured as the CIF? Or (as it sounds) is it simply that the
>contents of the imgCIF file are copied into NeXus, but that the
>resulting file is hard to interpret as NeXus?
>
>Also, was it possible to copy the information in several imgCIF
>files into a single NeXus? I gather that in principle it should be.
>
>Many thanks,
>
>Graeme
>
>
>-----Original Message-----
>From: imgcif-l-bounces at iucr.org [mailto:imgcif-l-bounces at iucr.org]
>On Behalf Of Herbert J. Bernstein
>Sent: 03 October 2011 12:10
>To: The Crystallographic Binary File and its imgCIF application to image data
>Subject: Re: [Imgcif-l] Nexus / cbf roundtrip
>
>Dear Colleagues,
>
> An imgCIF file can be placed into an HDF5 file (via NeXus) and
>recovered accurately. Starting the trip the other way is a
>more complex journey because there is not yet an agreed statement
>of the representation of a PX experiment in NeXus. For example,
>the issue of the best handling of the nests of axes is still
>to be resolved. There is also the more general issue of
>how best to represent the entire tree structure of HDF5
>(for NeXus) as relational tables (for CIF), but I expect that
>will fall out very naturally if we focus on the PX experiment.
>
> I would be very happy to participate in working out the
>details. If there is interest, I would suggest starting with
>the nests of axes.
>
> 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 at dowling.edu
>=====================================================
>
>On Mon, 3 Oct 2011, Graeme.Winter at Diamond.ac.uk wrote:
>
>> Return-path: <imgcif-l-bounces at iucr.org>
>> From: <Graeme.Winter at Diamond.ac.uk>
>> To: <imgcif-l at iucr.org>
>> Thread-Topic: Nexus / cbf roundtrip
>> Thread-Index: AcyBpo1rUTk8svcRRS6YJfqVOila5w==
>> Date: Mon, 3 Oct 2011 08:29:22 +0000
>> Message-ID:
>><13999B6FC038EB44B067771E3CFBD0911319E2 at EXCHMBX03.fed.cclrc.ac.uk>
>> Subject: [Imgcif-l] Nexus / cbf roundtrip
>> X-BeenThere: imgcif-l at iucr.org
>> X-Mailman-Version: 2.1.9
>
>> Hi Folks,
>>
>> Not wishing to open any kind of pot of worms, but recently someone asked
>> about interoperability between nexus and cbf files. Are there tools out
>> there which will export a set of cbf files to a nexus file and (most
>> importantly) invert this to recover the original cbf files?
>>
>> If so, how are the derived nexus files defined? It seems to me at the
>> moment that the nexus file descriptions give a less sophisticated
>> language for describing diffraction experiments.
>>
>> Many thanks,
>>
>> Graeme
>>
>> Dr. Graeme Winter
>> Senior Software Scientist
>> Diamond Light Source
>>
>> +44 1235 778091 (work)
>> +44 7786 662784 (work mobile)
>>
>>
>>
>>
>>
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>Diamond Light Source Ltd. cannot guarantee that this e-mail or any
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=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Brookhaven Campus, B111B
1300 William Floyd Parkway, Shirley, NY, 11967
+1-631-244-1328
Lab: +1-631-244-1935
Cell: +1-631-428-1397
yaya at dowling.edu
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