[Nexus] HDF5 External Links in NeXus files

[Pete Jemian]

Also, this minor change,

--- NXScan
+++ NXentry

On Mon, Jan 7, 2019, 8:19 AM Zbigniew Reszela <zreszela at cells.es wrote:

> Hi NeXus experts,
>
> I'm not sure if your list is for this kind of questions. If not, could you
> please advice where to look for help and forgive me this message.
>
> We would like to write a HDF5 file, let's call it the master file, with
> multiple NXScan entries. The scan can be configured so the detector's data
> are directly stored in the master file or the detector's data are stored in
> a separate file(s), let's call it the slave file(s). In the later case, in
> the master file, we would like to use the HDF5 external links to the slave
> file(s). The idea is to provide as transparent as possible (between these
> two saving modalities) access to the data.
>
> Let me illustrate it with an example. A scan involves just one detector
> and provides 4 frames each of 1024x1024 shape.
> If the scan is configured to store the data in the master file, this can
> be accessed in the following way:
>
> In [6]: f["entry1"]["measurement"]["twod01"]
> Out[6]: <HDF5 dataset "twod01": shape (4, 1024, 1024), type "<f8">
>
> If the scan is configured to store the detector's data in the slave file
> (all 4 frames in one dataset) and we use the following code to insert the
> external link:
>
> f = h5py.File("master.h5")
> f["entry1"]["measurement"]["twod01"] = h5py.ExternalLink("slave.h5",
> "/data")
>
> then we can access the data from the master file:
>
> In [24]: f["entry1"]["measurement"]["twod01"]
> Out[24]: <HDF5 dataset "data": shape (4, 1024, 1024), type "<u4">
>
> My question is how to create the external links (or use some alternative
> solution) if the detector's data are stored in multiple files, for example
> 1 frame per file (4 slave files in total), or 2 frame per file (2 slave
> files in total). Here we would like to maintain the way of accessing all
> the scan frames with the f["entry1"]["measurement"]["twod01"] syntax.
>
> Thanks in advance for sharing your experience,
>
> Zbigniew Reszela
> (Alba Synchrotron)
>
>
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