[Nexus] Nexpy

[Pete Jemian]

relevant documentation in the manual:

*Design* chapter:
http://download.nexusformat.org/doc/html/design.html#index-13

Details of the XML Schema:
http://download.nexusformat.org/doc/html/nxdl_desc.html#index-1

On Wed, Jun 14, 2017 at 8:12 AM, Osborn, Raymond <rosborn at anl.gov> wrote:

> Steve,
> The NeXus format has, since its inception, had the concept that there is a
> parent object for each link, defined by the attribute ‘target’, even though
> linked data are stored in HDF5 files as hard links. NeXpy, or rather the
> underlying nexusformat API, is designed to make that association clear,
> whereas h5py makes no such distinction. I’m not sure if there is even a way
> for h5py to tell what groups an object has been added to without checking
> object ids.
>
> If you have a recent version of NeXpy installed, you can open the example
> file, ‘chopper.nxs’, from the Help menu. I will use it to discuss why I
> believe it handles links appropriately. In ‘chopper.nxs’, the data group
> contains two links. Here are edited selections from the file tree:
>
> entry:NXentry
>   data:NXdata
>     polar_angle -> /entry/instrument/detector/polar_angle
>   instrument:NXinstrument
>     detector:NXdetector
>       polar_angle = float32(148)
>         @target = '/entry/instrument/detector/polar_angle'
>
> So ‘/entry/data/polar_angle’ and ‘/entry/instrument/detector/polar_angle’
> are both paths to the same HDF5 object, but the parent object is deemed by
> the NeXus format to be the latter, as specified by its target attribute.
> NeXpy chooses to display the other instance, in ‘/entry/data’ as a link to
> make this clear.
>
> >>> chopper.entry.data.polar_angle
> NXlink('/entry/instrument/detector/polar_angle')
> >>> chopper.entry.instrument.detector.polar_angle
> NXfield(array([  -7.19999981,   -6.5999999 ,   -6.        , ...,
>  116.3999939 ,
>         116.99999237,  117.59999084], dtype=float32))
>
> If you want to know what the parent object is, you can use the NXlink’s
> ‘nxlink’ attribute, which returns the parent.
>
> >>> chopper.entry.data.polar_angle.nxlink
> NXfield(array([  -7.19999981,   -6.5999999 ,   -6.        , ...,
>  116.3999939 ,
>         116.99999237,  117.59999084], dtype=float32))
>
> Within the NeXpy GUI, you can right-click on the link, which has a chain
> link icon by it, to display the parent. There is no way to do this in a
> generic HDF5 viewer.
>
> In practice, the fact that ‘/entry/data/polar_angle’ is an NXlink object
> should make no difference in your use of the data. For example, you can
> check its dtype or shape, and use fields in arithmetic expressions on
> either the parent or the link.
>
> >>> chopper.entry.data.polar_angle + 100.0
> NXfield(array([  92.80000305,   93.40000153,   94.        , ...,
>  216.3999939 ,
>         217.        ,  217.59999084], dtype=float32))
> >>> chopper.entry.instrument.detector.polar_angle + 100.0
> NXfield(array([  92.80000305,   93.40000153,   94.        , ...,
>  216.3999939 ,
>         217.        ,  217.59999084], dtype=float32))
>
> I think this is the right way to handle links. In h5py, you could update a
> dataset’s value without knowing that it has the side effect of changing its
> value in another group. In NeXpy, the existence of the link is clear but it
> shouldn’t impede your use of its values or attributes. I would welcome
> further comments if you think these are not the right calls.
>
> With best regards,
> Ray
>
> On Jun 14, 2017, at 6:13 AM, steve.collins at diamond.ac.uk wrote:
>
> Hello,
>
> I’d like to subscribe to this email list. I’m not sure if it is
> appropriate to ask a technical question here, but here is one anyway (I
> hope it’s OK):
>
> I have a question about the Python Nexusformat/NeXpy nxload method.
>
> I seem to have problems reading data entries that have been defined using
> links. That is, the method returns an NXlink object rather than the actual
> data:
>
> n.entry1.default.ic1monitor
> Out[143]: NXlink('['/entry1/instrument/ic1monitor/ic1monitor']')
>
> If I use h5py directly then I get the dataset:
>
> h['/entry1/default/ic1monitor']
> Out[144]: <HDF5 dataset "ic1monitor": shape (10001,), type "<f8">
>
> Is this expected or am I doing something wrong? I read in the manual that
> all data are specified via links so there is no distinction between the
> 'original' data and a link. Is that right?
>
> Thank you for your help.
>
> Regards,
> Steve Collins (Diamond Light Source)
>
> P.S. I can send you the data files and Python code of course, if that
> helps.
>
>
> --
> Ray Osborn, Senior Scientist
> Materials Science Division
> Argonne National Laboratory
> Argonne, IL 60439, USA
> Phone: +1 (630) 252-9011 <(630)%20252-9011>
> Email: ROsborn at anl.gov
>
>
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