[Nexus] HDF5 External Links in NeXus files

[Zbigniew Reszela]

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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