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Re: [dddwg] To contribute to Open Science using Zenodo Ifound quite straightforward
- To: James Hester <jamesrhester@gmail.com>, "IUCr Working Group on Diffraction data Deposition" <dddwg@iucr.org>
- Subject: Re: [dddwg] To contribute to Open Science using Zenodo Ifound quite straightforward
- From: Christopher Thomas Chantler <chantler@unimelb.edu.au>
- Date: Wed, 28 Sep 2016 05:12:10 +0000
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Terrific idea James ;)
------------------------------------------------------------
Christopher Chantler, Professor, FAIP
Editor-in-Chief, Radiation Physics and Chemistry
Chair, International IUCr Commission on XAFS
President, International Radiation Physics Society
School of Physics, University of Melbourne
Parkville Victoria 3010 Australia
+61-3-83445437 FAX +61-3-93474783
From: dddwg [dddwg-bounces@iucr.org] on behalf of James Hester [jamesrhester@gmail.com]
Sent: Wednesday, 28 September 2016 3:08 PM To: IUCr Working Group on Diffraction data Deposition Subject: Re: [dddwg] To contribute to Open Science using Zenodo I found quite straightforward Dear All:
Now, it is always possible to split a data transfer specification into the metadata component and the file-format-specific component (as scientific facts do not depend on the format in which they are expressed). It follows that the good metadata work of imgCIF
can be distilled from the imgCIF standard and appropriate locations created in nxMX (or any other format containing the appropriate data primitives). My forthcoming paper that grew out of the Roving workshop demonstrates how this would be done for imgCIF and
an earlier version of nxMX - the software demonstration is on Zenodo via Github, although may be a little opaque without the paper to refer to (http://doi.org/10.5281/zenodo.154459).Our Rovinj DDDWG discussions centered around getting some sort of standard set of metadata for single images, and now a few years later we find ourselves talking about standard metadata for complete experiments! As Graeme says, this is covered comprehensively by imgCIF, which can describe a set of images from quite complex experiments, involving multiple detectors consisting of multiple modules of varying geometry and scan directions, multiple and coupled sample rotation axes, and probably a few other 'multiples' as well. As far as I can tell nxMX is gradually expanding towards the same level of coverage (I see that multiple detector modules have recently(?) been defined in nxMX). The problem with imgCIF has been (and Herbert or Graeme might have more insight into this) that the community/detector manufacturers were looking for something that described a single (binary) image, and imgCIF appeared too complex (thus imgCBF). Additionally, simply concatenating 720 images into a text file as imgCIF envisages is perhaps not the most efficient file structure for retrieval of the data and I assume that binary formats such as HDF5 would work better. The human-readable definitions corresponding to the above list are embedded in a CIF dictionary but it is a matter of a few minutes to write software to bring the names and the human-readable definitions together. If this
group is interested, I can probably whip something up and post it.
James.
On 28 September 2016 at 02:18, <Graeme.Winter@diamond.ac.uk> wrote:
Kamil -- T +61 (02) 9717 9907
F +61 (02) 9717 3145 M +61 (04) 0249 4148 |
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- References:
- [dddwg] To contribute to Open Science using Zenodo I found quitestraightforward (John Helliwell)
- Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward (Coles S.J.)
- Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward (Kamil Dziubek)
- Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward (Coles S.J.)
- Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward (Kamil Dziubek)
- Re: [dddwg] To contribute to Open Science using Zenodo Ifound quite straightforward (Graeme.Winter)
- Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward (James Hester)
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