[NeXus-committee] NXroot is required - or should be made so

Fri Aug 29 14:52:28 BST 2014

Herbert,

Am 29.08.2014 um 14:22 schrieb Herbert J. Bernstein <yayahjb at gmail.com>:

> Dear Mark,
> 
>  The reality is that an "HDF5 file" is not simply a file.  Using,
> say, fuse, you can easily write what you think is a separate HDF5
> file, but which is actually just a deeper node in a bigger HDF5 file,
> which is, itself a deeper
> node in a still larger HDF5 file, etc., so those "file attributes" we
> need with NXroots are, in the context of
> the overall HDF5 file, just attributes of a group somewhere deep down.
> 
>  I know most of us will work with an HDF5 file containing a single
> NeXus file and the root of the HDF5 file
> will be the root of the NeXus tree, but the facility that is
> supporting that HDF5 file could be doing so with
> a larger HDF5 file as the "real" container.
> 

Well, well. Actually I do not mind the NXroot attribute. But I do not want a NXroot group appearing somewhere 
in a HDF-5 NeXus file. It just belongs into a XML NeXus file. And I still think the documentation of NXroot is thus 
misleading.

Regards,

   Mark

>  Regards,
>    Herbert
> 
> On Fri, Aug 29, 2014 at 8:08 AM, Mark Könnecke <mark.koennecke at psi.ch> wrote:
>> 
>> Colleagues,
>> 
>> 
>> Am 29.08.2014 um 13:38 schrieb Herbert J. Bernstein <yayahjb at gmail.com>:
>> 
>>> Dear Colleagues,
>>> 
>>> This is actually a trickier and more subtle issue than it might at
>>> first appear. And HDF5 "file" is actually more like a file system in
>>> which it is perfectly legitimate to nest multiple HDF5 trees into a
>>> larger one.    More than one completely independent NeXus file could
>>> easily exist within the same overall HDF5 file serving as the file
>>> system.  What I would suggest is:
>>> 
>>> "The root of a NeXus file has the attribute NX_class="NXroot" as a
>>> node within an HDF5 file.  Most commonly, but not necessariiy, that
>>> node will also be the root of the containing HDF5 file.  If a NeXus
>>> file is started with an NXroot further down in the containing HDF5
>>> file, the nodes of the NeXus file will not refer to nodes outside
>>> NeXus file, except through the HDF5 external link mechanism, just as
>>> if they were is different files.“
>>> 
>> 
>> 
>> hold on, hold  on. As far as I remember there  are two reasons why NXroot actually exists:
>> 
>> * When we coded NeXus using XML as a file format, we actually physically needed it.
>> * Now, at the root level of a NeXus file we like to have some file attributes. In order to  make that available for validation somehow, NXroot
>>  was defined.
>> 
>> The use case of nesting multiple NeXus files in one hdf5 file was never agreed upon. This would require a strong argument why
>> we need this and a vote from the NIAC. And we already have NXentry for storing multiple data sets.
>> 
>> I thus suggest to change the documentation on NXroot that it exists for purely technical reasons, in order to validate
>> file attributes.
>> 
>> Regards,
>> 
>>    Mark
>> 
>> 
>> 
>>> Regards,
>>>   Herbert
>>> 
>>> On Thu, Aug 28, 2014 at 11:57 PM, Osborn, Raymond <rosborn at anl.gov> wrote:
>>>> Is this a ratified decision? I’m still not sure why this is necessary.
>>>> 
>>>> Ray
>>>> 
>>>> On Aug 28, 2014, at 11:23 AM, Pete Jemian <prjemian at gmail.com> wrote:
>>>> 
>>>> 
>>>> require that the attribute NX_class="NXroot" is assigned to the root of the
>>>> HDF5 file
>>>> 
>>>> On 8/28/2014 11:20 AM, Osborn, Raymond wrote:
>>>> 
>>>> I’m not sure I’m understanding this correspondence. NXroot is the root level
>>>> of the HDF5 file. When you read in the file, it might have some meaning as
>>>> the root of the file tree, but within the HDF5 file, it doesn’t exist as a
>>>> separate entity, so what does it mean to ‘require’ it?
>>>> 
>>>> Ray
>>>> 
>>>> 
>>>> On Aug 28, 2014, at 10:51 AM, Pete Jemian <prjemian at gmail.com> wrote:
>>>> 
>>>> yes
>>>> 
>>>> On 8/28/2014 10:50 AM, Joachim Wuttke wrote:
>>>> 
>>>> Shouldn't the manuscript describe best practice as of now,
>>>> regardless of compatibility issues?
>>>> 
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>>>> 
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>>>> 
>>>> --
>>>> Ray Osborn, Senior Scientist
>>>> Materials Science Division
>>>> Argonne National Laboratory
>>>> Argonne, IL 60439, USA
>>>> Phone: +1 (630) 252-9011
>>>> Email: ROsborn at anl.gov
>>>> 
>>>> 
>>>> 
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>>> 
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