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

Dear James,
An index could be very useful but there seem to be some practical problems to overcome:
- How should this handle different frame formats?- Does it pull in detailed external_format binary descriptions?- What if frames are using proprietary compression?
With HDF the it seems the library accepts binary data described by a set of "External Storage Properties" and takes care of reading this data too. As it only arrived in h5py in the last release (2.9, Dec 2018) it is something I look forwards to trying out soon. So far I do not know if you can have compression and things like ascii overflow tables. If anyone can share examples it would help me to learn to use it.
Not sure this message helps... if you leave out the need to read the data then everything would be simplified, but then what is the index going to be used for ?
All the best,

PS: and many thanks for pycifrw !

On 13/02/2019 10:01, James Hester 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>>>>> 
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