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Re: [Imgcif-l] Adding references to external files to imgCIF

Thanks for the support Herbert. Does anybody have any concerns orimprovements to the data names that I sent originally? If not, I guess Iwill write up some formal dictionary definitions for your consideration.
James.
On Wed, 13 Feb 2019 at 21:39, Herbert J. Bernstein <yayahjb@gmail.com>wrote:
> Dear Colleagues,>>   Since 2012 NIAC and COMCIFS have worked cooperatively to make imgCIF/CBF> and NeXus/HDF5 fully interoperable.  This is very> far along, e.g.with NeXus/HDF5 NXtransformations having been added to> NeXus/HDF5 to carry the same information as imgCIF/CBF AXIS.> What James has suggested will allow imgcif/CBF to carry the same dataset> structure information as is conveyed in the external links of> an Eiger dataset, which divides the collected data into a master file with> the metadata and a set of datafiles.  This structural division> may not be important for some smaller datasets with only a few hundred to> a few thousand frames, but can be very important in> handling datasets with more frames than that that are encountered in> serial crystallography.  Even for the smaller datasets this approach can> help to solve a problem for archives and facilities that need to store> metadata in a relational database while the data itself has been parked in> raw file systems, non-relational databases, zenodo, etc.  As with almost> all of CIF, imgCIF/CBF metadata maps very easily and directly> into relational tables, while putting NeXus/HDF5 metadata into a> relational database first requires exactly the same sort of transformations> as we have already designed to map NeXus/HDF5 metadata into imgCIF/CBF> To me it seems that James' suggestion is not a reinvention> of this particular wheel, but may be an important step in avoiding> reinvention of the wheel.  This may avoid a lot of unnecessary> transformation> of huge quantities of raw data in serial crystallography while making the> metadata more accessible.>>   I would suggest giving James' suggestion serious consideration.>>   Regards,>     Herbert> while putting>> On Wed, Feb 13, 2019 at 4:02 AM James Hester <jamesrhester@gmail.com>> wrote:>>> Dear Graeme,>>>> The context of this is the idea that a single imgCIF file could be>> generated from a collection of raw image files (in whatever format,>> whether>> HDF5, or ADSC, or Bruker, or Rigaku, etc.) which would contain the>> metadata>> pertaining to that collection. In such a situation, some way of referring>> to the raw frames from within the imgCIF file is required.>>>> I agree that a perfectly reasonable approach is not to generate any new>> file at all, and simply to access the metadata directly in whatever format>> happens to be there. This was my initial impulse as well and it took me a>> while to understand that the actual proposal was to create an imgCIF file,>> rather than just use imgCIF datanames for specification purposes.  From a>> semantic point of view both amount to the same thing so my only real>> motivation here is to add an image linking facility to imgCIF so that the>> "generate a summary metadata file" approach is possible.>>>> Could we just copy the HDF5 way of referring to objects in other HDF5>> files>> as a quick solution?>>>> all the best,>> James.>>>> On Wed, 13 Feb 2019 at 19:03, Graeme.Winter@Diamond.ac.uk <>> Graeme.Winter@diamond.ac.uk> wrote:>>>> > Dear James,>> >>> > On the face of it, this looks a lot to me like a reinvention of HDF5 ->> > perhaps with specific semantics - and there is already a (complete?)>> > mapping from imgCIF to HDF5 / NeXus>> >>> > Have I missed something? No offence meant, trying to understand the>> shape>> > of the problem you are trying to solve>> >>> > Thanks & best wishes Graeme>> >>> > > On 13 Feb 2019, at 05:15, James Hester <jamesrhester@gmail.com>>> wrote:>> > >>> > > Dear All,>> > >>> > > Recent Commdat discussion revealed a desire to reference external>> images>> > > from within an imgCIF file. This would allow the metadata for a>> dataset>> > to>> > > be held within a single imgCIF file, while the frames themselves>> remain>> > > separate. This avoids the impracticality of navigating through an>> > enormous>> > > mulit-frame imgCIF file in order to extract a relatively compact>> amount>> > of>> > > information.>> > >>> > > As a starting proposal, I suggest we extend the _array_data category>> with>> > > the following three datanames:>> > >>> > > (1) _array_data.external_format    A value drawn from an enumerated>> list>> > of>> > > formats (e.g. "SMV","HDF5","Bruker"). The definition for each>> enumerated>> > > value would explain how to interpret _array_data.internal_path>> > > (2) _array_data.location_url           A URI for the file containing>> the>> > > image. A relative URL is relative to the location of the imgCIF file>> > > (3) _array_data.internal_path        A format-specific string>> describing>> > > the location of the frame within the file identified by>> > > _array_data.location_uri, interpreted according to the value given in>> > > _array_data.external_format>> > >>> > > So for a multi-frame HDF5 file buried in a subdirectory of the>> location>> > > referenced with a DOI, with appropriate definitions of the path>> notation:>> > >>> > > loop_>> > > _array_data.array_id>> > > _array_data.binary_id>> > > _array_data.external_format>> > > _array_data.location_uri>> > > _array_data.internal_path>> > > 1 1 NXMX doi:x.y.z>> directory/run/masterfilename:/entry1/detector/data[0]>> > > 1 2 NXMX doi:x.y.z>> directory/run/masterfilename:/entry1/detector/data[1]>> > > ...>> > >>> > > Or for a bunch of single-frame files generated by an ADSC detector in>> the>> > > same directory as the imgCIF file>> > >>> > > _array_data.array_id>> > > _array_data.binary_id>> > > _array_data.external_format>> > > _array_data.location_uri>> > > 1 1 ADSC ./tartaric.001>> > > 1 2 ADSC ./tartaric.002>> > > 1 3 ADSC ./tartaric.003>> > > ...>> > >>> > > The imgCIF data items describing the structure of the data array would>> > > refer to the data after it has been provided by the format. The form>> in>> > > which it is provided should be specified in the definition of each>> value>> > of>> > > "_array_data.external_format".  So, for example, the various>> compression>> > > methods in HDF5 would be invisible if the data as returned are>> specified>> > to>> > > be an array of Reals.>> > >>> > > From the point of view of initial data validation, it would be>> sufficient>> > > to check that all referenced files are accessible, and that the>> provided>> > > locations exist.>> > >>> > > Thoughts?>> > > James.>> > >>> > > -->> > > T +61 (02) 9717 9907>> > > F +61 (02) 9717 3145>> > > M +61 (04) 0249 4148>> > > _______________________________________________>> > > imgcif-l mailing list>> > > imgcif-l@iucr.org>> > > http://mailman.iucr.org/cgi-bin/mailman/listinfo/imgcif-l>> >>> >>> > -->> > This e-mail and any attachments may contain confidential, copyright and>> or>> > privileged material, and are for the use of the intended addressee>> only. If>> > you are not the intended addressee or an authorised recipient of the>> > addressee please notify us of receipt by returning the e-mail and do not>> > use, copy, retain, distribute or disclose the information in or>> attached to>> > the e-mail.>> > Any opinions expressed within this e-mail are those of the individual>> and>> > not necessarily of Diamond Light Source Ltd.>> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any>> > attachments are free from viruses and we cannot accept liability for any>> > damage which you may sustain as a result of software viruses which may>> be>> > transmitted in or with the message.>> > Diamond Light Source Limited (company no. 4375679). Registered in>> England>> > and Wales with its registered office at Diamond House, Harwell Science>> and>> > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom>> >>> >>>>> -->> T +61 (02) 9717 9907>> F +61 (02) 9717 3145>> M +61 (04) 0249 4148>> _______________________________________________>> imgcif-l mailing list>> imgcif-l@iucr.org>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/imgcif-l>>>
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