[Nexus] HDF5 as NeXus file format

[Tobias Richter]

Hi all,

According to this discussion from a decade ago HDF5 is singled out as the only preferred physical file format: https://www.nexusformat.org/NIAC2012


  *   NeXus guiding statements:
     *   The main focus of the NeXus community is to further develop the dictionaries, base classes and application definitions.
     *   The NIAC is a forum for resolving issues.
     *   The NIAC acts as a custodian for NeXus: definitions, examples, documentation, reference implementations.
     *   NeXus can be mapped to different physical file formats:
        *   HDF5 is the preferred physical file format.
        *   NeXus-XML is the currently supported ASCII file format.

Technically you can map into different backends. Yes. XML is still sort of supported. At the time it was requested that other options would get the official blessing (YAML being specifically asked for) but for practical exchange between facilities the consensus was to stick with HDF5.

There no longer is a recommended or fully maintained abstraction layer (like NAPI) to do an on the fly translation between backends. Who would be in charge of defining how the “official” mapping into sqlite or whatever would look like? How many backends can the community commit to support in the long run?

When tools that are currently developed/supported/maintained to “read” NeXus/HDF5 fail to work with what gets handed out, we are in a worse situation than we are now. Note: What facilities do internally for performance optimisations or other reasons could be different, if it stays internal. But I am clearly a lot less open minded about producing non-HDF5 files with a “NeXus” label than Ben. Maybe I missed some decisions that were taken lately in this direction or we’re no longer interested in being able to read each other’s files. Should either be the case, I’ll be quiet.

Best wishes,
Tobias


From: NeXus <nexus-bounces at shadow.nd.rl.ac.uk> on behalf of "Watts Benjamin (PSI) via NeXus" <nexus at shadow.nd.rl.ac.uk>
Reply to: Discussion forum for the NeXus data format <nexus at shadow.nd.rl.ac.uk>
Date: Thursday, 7 April 2022 at 17:10
To: "nexus at nexusformat.org" <nexus at nexusformat.org>
Cc: Benjamin Watts <benjamin.watts at psi.ch>, Alexander Debus <a.debus at hzdr.de>, Nicolas Soler <nsoler at cells.es>, Franz Pöschel <f.poeschel at hzdr.de>, Emilio Centeno Ortiz <ecenteno at cells.es>
Subject: Re: [Nexus] HDF5 as NeXus file format


Hi Gabriel,

   NeXus is officially not dependent on HDF5 and we are definitely open minded about implementing the NeXus data format on file formats other than HDF5. We plan to discuss such issues at our next teleconference<https://www.nexusformat.org/Telco_20220426.html> on April 26th and I invite you to join us. Are there specific container file formats that you are interested in?



Cheers,

Ben

________________________________
From: NeXus <nexus-bounces at shadow.nd.rl.ac.uk> on behalf of Gabriel Jover Manas via NeXus <nexus at shadow.nd.rl.ac.uk>
Sent: Thursday, 7 April 2022 4:47 PM
To: nexus at nexusformat.org
Cc: Gabriel Jover Manas; Nicolas Soler; Emilio Centeno Ortiz
Subject: [Nexus] HDF5 as NeXus file format

Dear NeXus Users Community,

Last NFDI NeXus Workshop was a great opportunity to meet the community and learn from the experience of other scientists and institutions.

Here at ALBA we are working on the integration of NeXus files in our data analysis workflows.

In this scope we are interested on investigating alternatives to hdf5 as NeXus file format, in terms of slice read/write performance, read-write-many capabilities and convenient reading.

Would the community be open to decoupling the data format (NeXus) from the file format (HDF5)?
Is there already any effort in the community in this direction?
Is anyone else also interested?



Best regards,

Gabriel


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Gabriel Jover-Mañas

Scientific Data Management
Computing Division



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