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<p>Hi everyone,</p>
<p>As Benjamin commented, at recent NFDI workshop I heard about
alternative file formats to fulfill some features that hdf5 may
lack as slice read/write performance, read-write-many capabilities
and convenient reading. <br>
</p>
<p>We don't have a lot of experience with hdf5 and it might be that
some of these features can be covered with an hdf5 virtual layer
or other means.</p>
<p>I have the impression that NeXus file format will become the
standard in PaNosc/ExPands european projects and we are working on
the integration of NeXus files in our data analysis workflows.</p>
<p>Our question to the community is precisely to know your
experience with hdf5, it's limitations, as well as to survey if
there is interest for a join effort to investigate how hdf5
compares with other file format as zarr, adios or even exdir.</p>
<p>Thank you for your invitation to next meeting on April 26th. I
would have join but I have an other appointment at that time. Any
how, someone else from Alba will join.<br>
</p>
<p>Kind regards,</p>
<p> Gabriel</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 7/4/22 21:42, Osborn, Raymond via
NeXus wrote:<br>
</div>
<blockquote type="cite"
cite="mid:D8EBE0C6-5639-4F71-9407-3A13CB5455B5@anl.gov">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi everyone,
<div class="">NeXus was originally both a standard for defining
how data should be organized in files and a unified API for
reading and writing those files, irrespective of the physical
file format, HDF4, HDF5, or XML. Thanks mainly to the work that
Mark Koennecke put into the C-API, it achieved both goals
seamlessly. I think it was a remarkable technical achievement.
To some extent, the two components were independent of each
other, but not entirely. For example, HDF4 did not allow group
attributes, so for a long time, they were not part of the
definitions. Now that HDF4 is obsolete, the NeXus definitions
have evolved to use more and more of the features that HDF5
provides, many of which have become an essential part of the
standard. </div>
<div class=""><br class="">
</div>
<div class="">I think there are therefore two questions that need
to be clarified, preferably before we next meet. The first is
whether the proposed alternative physical file formats will
allow the same type of hierarchical data organization and
features that have now become part of the standard. If they
didn’t, this would probably be a deal-breaker, unless there is a
way of interfacing, say, regular HDF5 NeXus files to the new
file formats, in much the same way that HDF5 handles external
links. </div>
<div class=""><br class="">
</div>
<div class="">The second is whether there is a need to revive the
API to handle the new formats, so that we are not faced with the
situation that Tobias warned about with a large fraction of the
user community unable to read such files. The reason the API
became deprecated is, in my view, that we have depended too much
on one or two people (i.e., Mark in the case of the C-API) to
take all the responsibility for maintaining it, so that
supporting new HDF5 features, such as virtual data sets or even
variable-length-strings, fell entirely on them. While an
increasing number of facilities have become dependent on NeXus,
very few of them, if any, have committed resources to
maintaining it, so it has become an activity that many of us
squeeze in when we have free time from our other
responsibilities. If facilities like Alba, and presumably
others, feel that they are being held back by technical
limitations of HDF5, then it might be necessary to rethink the
NeXus support model, so that API development is revived by being
integrated into other facility software development projects,
such as Mantid or Dials. It would probably save the facilities
money in the long term, but it would require NeXus to be less of
a part-time activity. Or we need to encourage more people to
contribute, in the way the more successful open-source projects
are run. I would certainly welcome additional support for the
Python API for the same reasons.</div>
<div class=""><br class="">
</div>
<div class="">With best regards,</div>
<div class="">Ray</div>
<div class="">
<div class="">
<div class="">-- <br class="">
Ray Osborn, Senior Scientist<br class="">
Materials Science Division<br class="">
Argonne National Laboratory<br class="">
Argonne, IL 60439, USA<br class="">
Phone: +1 (630) 252-9011<br class="">
<a href="mailto:ROsborn@anl.gov" class=""
moz-do-not-send="true">Email: ROsborn@anl.gov</a><br
class="">
<br class="">
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 7, 2022, at 12:16 PM, Watts Benjamin
(PSI) via NeXus <<a
href="mailto:nexus@shadow.nd.rl.ac.uk"
class="moz-txt-link-freetext" moz-do-not-send="true">nexus@shadow.nd.rl.ac.uk</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr"
style="font-style: normal; font-variant-caps: normal;
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text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration: none;
font-size: 12pt; font-family: Calibri, Helvetica,
sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;"
class="">Hi Tobias,</div>
<div style="margin-top: 0px; margin-bottom: 0px;"
class=""> I agree that we have spent the past
decade recommending HDF5, but at the same time we
have been saying that NeXus is about the
organisation of data within the container, not the
container file format itself. I can see that you
feel surprised by the sudden discussion of other
file formats, just as I was surprised to hear the
community talking about it at the recent NFDI
workshop. I am only advocating for discussion and I
would like to hear your input.<span
class="Apple-converted-space"> </span><span
class="">I agree that multiple backends will
introduce higher support requirements that NeXus
doesn't currently have resources for.</span><span
class="Apple-converted-space"> </span>Your
preference for NeXus referring to a (small) defined
set of file formats is a valid view point and I
agree that there are practicalities to consider. I
view the next telco as just the restart of an old
discussion and nothing can really change until a
proposal is brought to a NIAC meeting (and
accepted).</div>
<div style="margin-top: 0px; margin-bottom: 0px;"
class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;"
class="">Cheers,</div>
<div style="margin-top: 0px; margin-bottom: 0px;"
class="">Ben<br class="">
</div>
</div>
<hr tabindex="-1" style="caret-color: rgb(0, 0, 0);
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<span style="caret-color: rgb(0, 0, 0); font-family:
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inline !important;" class=""></span>
<div id="divRplyFwdMsg" dir="ltr" style="caret-color:
rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration:
none;" class="">
<font style="font-size: 11pt;" class="" face="Calibri,
sans-serif"><b class="">From:</b><span
class="Apple-converted-space"> </span>Tobias
Richter <<a href="mailto:Tobias.Richter@ess.eu"
class="moz-txt-link-freetext"
moz-do-not-send="true">Tobias.Richter@ess.eu</a>><br
class="">
<b class="">Sent:</b><span
class="Apple-converted-space"> </span>Thursday, 7
April 2022 6:23:43 PM<br class="">
<b class="">To:</b><span
class="Apple-converted-space"> </span>Discussion
forum for the NeXus data format;
<a href="mailto:nexus@nexusformat.org"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus@nexusformat.org</a><br
class="">
<b class="">Cc:</b><span
class="Apple-converted-space"> </span>Watts
Benjamin (PSI); Alexander Debus; Nicolas Soler;
Franz Pöschel; Emilio Centeno Ortiz<br class="">
<b class="">Subject:</b><span
class="Apple-converted-space"> </span>Re: [Nexus]
HDF5 as NeXus file format</font>
<div class=""> </div>
</div>
<div style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<div class="WordSection1" style="page: WordSection1;">
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class="">Hi all,<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class="">According to this discussion from a
decade ago HDF5 is singled out as the only
preferred physical file format:<span
class="Apple-converted-space"> </span><a
href="https://www.nexusformat.org/NIAC2012"
style="color: blue; text-decoration:
underline;" class="moz-txt-link-freetext"
moz-do-not-send="true">https://www.nexusformat.org/NIAC2012</a><o:p
class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<ul style="margin-bottom: 0cm;" class="" type="disc">
<li class="MsoNormal" style="margin: 0cm;
font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(81, 81, 81);
background-color: white; background-position:
initial initial; background-repeat: initial
initial;">
<span style="font-size: 13.5pt; font-family:
"PT Sans", sans-serif;" class="">NeXus
guiding statements:<o:p class=""></o:p></span>
<ul style="margin-bottom: 0cm;" class=""
type="circle">
<li class="MsoNormal" style="margin: 0cm;
font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(81, 81, 81);
background-color: white;
background-position: initial initial;
background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family:
"PT Sans", sans-serif;" class="">The
main focus of the NeXus community is to
further develop the dictionaries, base
classes and application definitions.<o:p
class=""></o:p></span></li>
<li class="MsoNormal" style="margin: 0cm;
font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(81, 81, 81);
background-color: white;
background-position: initial initial;
background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family:
"PT Sans", sans-serif;" class="">The
NIAC is a forum for resolving issues.<o:p
class=""></o:p></span></li>
<li class="MsoNormal" style="margin: 0cm;
font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(81, 81, 81);
background-color: white;
background-position: initial initial;
background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family:
"PT Sans", sans-serif;" class="">The
NIAC acts as a custodian for NeXus:
definitions, examples, documentation,
reference implementations.<o:p class=""></o:p></span></li>
<li class="MsoNormal" style="margin: 0cm;
font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(81, 81, 81);
background-color: white;
background-position: initial initial;
background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family:
"PT Sans", sans-serif;" class="">NeXus
can be mapped to different physical file
formats:<o:p class=""></o:p></span>
<ul style="margin-bottom: 0cm;" class=""
type="square">
<li class="MsoNormal" style="margin: 0cm;
font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(81, 81, 81);
background-color: white;
background-position: initial initial;
background-repeat: initial initial;">
<span style="font-size: 13.5pt;
font-family: "PT Sans",
sans-serif;" class="">HDF5 is the
preferred physical file format.<o:p
class=""></o:p></span></li>
<li class="MsoNormal" style="margin: 0cm;
font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(81, 81, 81);
background-color: white;
background-position: initial initial;
background-repeat: initial initial;">
<span style="font-size: 13.5pt;
font-family: "PT Sans",
sans-serif;" class="">NeXus-XML is the
currently supported ASCII file format.<o:p
class=""></o:p></span></li>
</ul>
</li>
</ul>
</li>
</ul>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class="">Technically you can map into
different backends. Yes. XML is still sort of
supported. At the time it was requested that
other options would get the official blessing
(YAML being specifically asked for) but for
practical exchange between facilities the
consensus was to stick with HDF5.<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class="">There no longer is a recommended or
fully maintained abstraction layer (like NAPI)
to do an on the fly translation between
backends. Who would be in charge of defining how
the “official” mapping into sqlite or whatever
would look like? How many backends can the
community commit to support in the long run?<o:p
class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class="">When tools that are currently
developed/supported/maintained to “read”
NeXus/HDF5 fail to work with what gets handed
out, we are in a worse situation than we are
now. Note: What facilities do internally for
performance optimisations or other reasons could
be different, if it stays internal. But I am
clearly a lot less open minded about producing
non-HDF5 files with a “NeXus” label than Ben.
Maybe I missed some decisions that were taken
lately in this direction or we’re no longer
interested in being able to read each other’s
files. Should either be the case, I’ll be quiet.<o:p
class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class="">Best wishes,<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class="">Tobias<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="border-style: solid none none;
border-top-width: 1pt; border-top-color: rgb(181,
196, 223); padding: 3pt 0cm 0cm;" class="">
<div style="margin: 0cm 0cm 0cm 36pt; font-size:
11pt; font-family: Calibri, sans-serif;"
class="">
<b class=""><span style="font-size: 12pt;"
class="">From:<span
class="Apple-converted-space"> </span></span></b><span
style="font-size: 12pt;" class="">NeXus <<a
href="mailto:nexus-bounces@shadow.nd.rl.ac.uk"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus-bounces@shadow.nd.rl.ac.uk</a>>
on behalf of "Watts Benjamin (PSI) via NeXus"
<<a href="mailto:nexus@shadow.nd.rl.ac.uk"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus@shadow.nd.rl.ac.uk</a>><br
class="">
<b class="">Reply to:<span
class="Apple-converted-space"> </span></b>Discussion
forum for the NeXus data format <<a
href="mailto:nexus@shadow.nd.rl.ac.uk"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus@shadow.nd.rl.ac.uk</a>><br
class="">
<b class="">Date:<span
class="Apple-converted-space"> </span></b>Thursday,
7 April 2022 at 17:10<br class="">
<b class="">To:<span
class="Apple-converted-space"> </span></b>"<a
href="mailto:nexus@nexusformat.org"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus@nexusformat.org</a>"
<<a href="mailto:nexus@nexusformat.org"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus@nexusformat.org</a>><br
class="">
<b class="">Cc:<span
class="Apple-converted-space"> </span></b>Benjamin
Watts <<a
href="mailto:benjamin.watts@psi.ch"
class="moz-txt-link-freetext"
moz-do-not-send="true">benjamin.watts@psi.ch</a>>,
Alexander Debus <<a
href="mailto:a.debus@hzdr.de"
class="moz-txt-link-freetext"
moz-do-not-send="true">a.debus@hzdr.de</a>>,
Nicolas Soler <<a
href="mailto:nsoler@cells.es"
class="moz-txt-link-freetext"
moz-do-not-send="true">nsoler@cells.es</a>>,
Franz Pöschel <<a
href="mailto:f.poeschel@hzdr.de"
class="moz-txt-link-freetext"
moz-do-not-send="true">f.poeschel@hzdr.de</a>>,
Emilio Centeno Ortiz <<a
href="mailto:ecenteno@cells.es"
class="moz-txt-link-freetext"
moz-do-not-send="true">ecenteno@cells.es</a>><br
class="">
<b class="">Subject:<span
class="Apple-converted-space"> </span></b>Re:
[Nexus] HDF5 as NeXus file format<o:p class=""></o:p></span></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0cm 36pt; font-size:
11pt; font-family: Calibri, sans-serif;"
class="">
<o:p class=""> </o:p></div>
</div>
<div id="divtagdefaultwrapper" class="">
<div style="margin-top: 0px; margin-bottom: 0px;
margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class="">Hi Gabriel,<o:p
class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;
margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class=""> NeXus is
officially not dependent on HDF5 and we are
definitely open minded about implementing the
NeXus<span class="Apple-converted-space"> </span><i
class="">data format</i><span
class="Apple-converted-space"> </span>on<span
class="Apple-converted-space"> </span><i
class="">file formats</i><span
class="Apple-converted-space"> </span>other
than HDF5. We plan to discuss such issues at
our<span class="Apple-converted-space"> </span><a
href="https://www.nexusformat.org/Telco_20220426.html" style="color:
blue; text-decoration: underline;" class=""
moz-do-not-send="true">next teleconference</a><span
class="Apple-converted-space"> </span>on
April 26th and I invite you to join us. Are
there specific container file formats that you
are interested in?<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;
margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class=""><o:p
class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;
margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class="">Cheers,<o:p
class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;
margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class="">Ben<o:p
class=""></o:p></span></div>
<p class="MsoNormal" style="margin: 0cm 0cm 12pt
36pt; font-size: 11pt; font-family: Calibri,
sans-serif;">
<span style="font-size: 12pt;" class=""><o:p
class=""> </o:p></span></p>
<div class="">
<div class="MsoNormal" style="margin: 0cm 0cm
0cm 36pt; font-size: 11pt; font-family:
Calibri, sans-serif; text-align: center;"
align="center">
<span style="font-size: 12pt;" class="">
<hr class="" width="100%" size="0"
align="center">
</span></div>
<div id="divRplyFwdMsg" class="">
<div style="margin: 0cm 0cm 0cm 36pt;
font-size: 11pt; font-family: Calibri,
sans-serif;" class="">
<b class=""><span style="" class="">From:</span></b><span
style="" class=""><span
class="Apple-converted-space"> </span>NeXus
<<a
href="mailto:nexus-bounces@shadow.nd.rl.ac.uk"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus-bounces@shadow.nd.rl.ac.uk</a>>
on behalf of Gabriel Jover Manas via NeXus
<<a
href="mailto:nexus@shadow.nd.rl.ac.uk"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus@shadow.nd.rl.ac.uk</a>><br
class="">
<b class="">Sent:</b><span
class="Apple-converted-space"> </span>Thursday,
7 April 2022 4:47 PM<br class="">
<b class="">To:</b><span
class="Apple-converted-space"> </span><a
href="mailto:nexus@nexusformat.org"
class="moz-txt-link-freetext"
moz-do-not-send="true">nexus@nexusformat.org</a><br
class="">
<b class="">Cc:</b><span
class="Apple-converted-space"> </span>Gabriel
Jover Manas; Nicolas Soler; Emilio Centeno
Ortiz<br class="">
<b class="">Subject:</b><span
class="Apple-converted-space"> </span>[Nexus]
HDF5 as NeXus file format</span><span
style="font-size: 12pt;" class=""><o:p
class=""></o:p></span></div>
<div class="">
<div style="margin: 0cm 0cm 0cm 36pt;
font-size: 11pt; font-family: Calibri,
sans-serif;" class="">
<span style="font-size: 12pt;" class=""> <o:p
class=""></o:p></span></div>
</div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0cm 36pt;
font-size: 11pt; font-family: Calibri,
sans-serif;" class="">
<span style="font-size: 12pt;" class="">Dear
NeXus Users Community,<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom:
0px; margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class="">Last
NFDI NeXus Workshop was a great
opportunity to meet the community and
learn from the experience of other
scientists and institutions.<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom:
0px; margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class="">Here at
ALBA we are working on the integration of
NeXus files in our data analysis
workflows.<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom:
0px; margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class="">In this
scope we are interested on investigating
alternatives to hdf5 as NeXus file format,
in terms of slice read/write performance,
read-write-many capabilities and
convenient reading.<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom:
0px; margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class="">Would
the community be open to decoupling the
data format (NeXus) from the file format
(HDF5)?<br class="">
Is there already any effort in the
community in this direction?<br class="">
Is anyone else also interested?<o:p
class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom:
0px; margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class=""><o:p
class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom:
0px; margin-left: 36pt;" class=""><span
style="font-size: 12pt;" class="">Best
regards,<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom:
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style="font-size: 12pt;" class="">Gabriel<o:p
class=""></o:p></span></div>
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class="moz-txt-link-freetext" moz-do-not-send="true">https://lists.nexusformat.org/mailman/listinfo/nexus</a></span></div>
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<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
NeXus mailing list
<a class="moz-txt-link-abbreviated" href="mailto:NeXus@nexusformat.org">NeXus@nexusformat.org</a>
<a class="moz-txt-link-freetext" href="https://lists.nexusformat.org/mailman/listinfo/nexus">https://lists.nexusformat.org/mailman/listinfo/nexus</a>
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