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<div class="moz-cite-prefix">+1 <br>
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<div class="moz-cite-prefix">Clear use case for virtual data sets
and therefore HDF5 1.10.x<br>
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<div class="moz-cite-prefix">On 07/01/2019 15:25,
<a class="moz-txt-link-abbreviated" href="mailto:Jacob.Filik@Diamond.ac.uk">Jacob.Filik@Diamond.ac.uk</a> wrote:<br>
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi
Zbigniew,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I
think the only way you could do this would be to use the
virtual dataset (VDS) feature of HDF5, only available in the
1.10 release. This should allow you to create a “virtual”
stack from 4 separate images.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I
don’t this is a backwardly compatible feature though, so the
file may not be readable by applications using a pre-1.10
library version.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Kind
regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Jacob<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D">Dr
Jacob Filik</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D;background:white">Senior
Software Scientist</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D">Tel:
+441235 77 8690</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D">Diamond
Light Source Ltd.</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D">Diamond
House</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D">Harwell
Science & Innovation Campus</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D">Didcot</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D">Oxfordshire</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D">OX11
0DE</span><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"
lang="EN-US">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"
lang="EN-US"> NeXus
<a class="moz-txt-link-rfc2396E" href="mailto:nexus-bounces@shadow.nd.rl.ac.uk"><nexus-bounces@shadow.nd.rl.ac.uk></a>
<b>On Behalf Of </b>Zbigniew Reszela<br>
<b>Sent:</b> 07 January 2019 14:20<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:nexus@nexusformat.org">nexus@nexusformat.org</a><br>
<b>Subject:</b> [Nexus] HDF5 External Links in NeXus
files<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"-moz-fixed",serif">Hi
NeXus experts,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Let me illustrate it with an example. A scan involves just
one detector and provides 4 frames each of 1024x1024
shape.<br>
If the scan is configured to store the data in the master
file, this can be accessed in the following way:<br>
<br>
In [6]: f["entry1"]["measurement"]["twod01"]<br>
Out[6]: <HDF5 dataset "twod01": shape (4, 1024, 1024),
type "<f8"><br>
<br>
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:<br>
<br>
f = h5py.File("master.h5")<br>
f["entry1"]["measurement"]["twod01"] =
h5py.ExternalLink("slave.h5", "/data")<br>
<br>
then we can access the data from the master file:<br>
<br>
In [24]: f["entry1"]["measurement"]["twod01"]<br>
Out[24]: <HDF5 dataset "data": shape (4, 1024, 1024),
type "<u4"><br>
<br>
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.<br>
<br>
Thanks in advance for sharing your experience,<br>
<br>
Zbigniew Reszela<br>
(Alba Synchrotron) <o:p></o:p></span></p>
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