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--></style></div><div data-marker="__QUOTED_TEXT__"><div style="font-family:'arial' , 'helvetica' , sans-serif;font-size:12pt;color:#000000"><div></div><div><div style="font-family:'arial' , 'helvetica' , sans-serif;font-size:12pt;color:#000000"><div><div style="font-family:'arial' , 'helvetica' , sans-serif;font-size:12pt;color:#000000"><div><div style="font-family:'arial' , 'helvetica' , sans-serif;font-size:12pt;color:#000000"><div><div style="font-family:'arial' , 'helvetica' , sans-serif;font-size:12pt;color:#000000"><div><div style="font-family:'arial' , 'helvetica' , sans-serif;font-size:12pt;color:#000000"><div>Dear Ray,<br></div><br><div>thank you for providing the tool.<br></div><br><div>I've just run the nxinspect on one of my file and I get unexpected warning i.e.<br></div><br><div>- This field is not defined in the base class NXtransformations</div><div> (but below NXtransformations we can create a field with any name)<br></div><br><div>- Axis ." not present in group "/scan/data"<br></div><div> (I thought '.' one of the possible values i.e.<br></div><div> '<span style="font-family:sans-serif" dir="ltr">The NXdata group attribute</span><span style="font-family:sans-serif" dir="ltr"> </span><span style="font-family:sans-serif" dir="ltr"><span class="highlight selected appended">axes</span> = . .</span><span style="font-family:sans-serif" dir="ltr"> </span><span style="font-family:sans-serif" dir="ltr">declares that both dimensions of the</span><span style="font-family:sans-serif" dir="ltr"> </span><span style="font-family:sans-serif" dir="ltr">data</span><span style="font-family:sans-serif" dir="ltr"> </span><span style="font-family:sans-serif" dir="ltr">field do not</span><br><span style="font-family:sans-serif" dir="ltr"> have associated dimension scales (plotting routines should use integer scaling for each axis).' </span>)<br></div><br><div>- Axis e" not present in group "/scan/data"<br></div><div> (if axes attribute contain a single string it is separated to single letters)<br></div><br><div>- NXcollection is an invalid class in NXcollection<br></div><div> (however in the documentation it is written that 'Anything (groups, fields, or attributes) placed in an <a href="https://manual.nexusformat.org/classes/base_classes/NXcollection.html#nxcollection" rel="nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer" target="_blank"><span class="std std-ref">NXcollection</span></a> group will not be validated.'</div><div> and NXcollection is a group so nesting of NXcollection should be allowed)<br></div><br><div> - NXcollection is an invalid class in NXroot<br></div><div> Is the NXcollection group really forbidden below NXroot? I saw some hdf5 multi-format files where NXcollection was used on the root level</div><div> to denote non-NeXus (meta)data. If NXcollection below in not allowed I would like to ask if it is possible to create HDF5 multiformat files<br></div><div> and how they should be create to be valid NeXus file?<br></div><div><br>Best regards,<br></div><div>Jan<br></div><br><hr id="zwchr"><div><b>From: </b>"Discussion forum for the NeXus data format" <nexus@shadow.nd.rl.ac.uk><br><b>To: </b>"Discussion forum for the NeXus data format" <nexus@shadow.isis.cclrc.ac.uk>, "Discussion forum for the NeXus data format" <nexus@nexusformat.org><br><b>Cc: </b>"Osborn, Raymond" <rosborn@anl.gov><br><b>Sent: </b>Tuesday, 17 September, 2024 15:03:22<br><b>Subject: </b>Re: [Nexus] Announcing beta-version of the NXvalidate Python package<br></div><br><div>
<div class="WordSection1">
<p class="MsoNormal">Hi Jens,</p>
<p class="MsoNormal">Thanks for the suggestion. Code maintenance is always an issue, but I had planned to issue a new release whenever there was an official NeXus release, which is not that frequent. I’m reluctant to complicate the installation process, but
I think we could achieve what you are requesting by allowing an option to point to another directory containing the definitions. That directory, for example, could be part of a cloned nexusformat git repository that the user can keep updated. I should be able
to implement that in the next few days.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">With regards,</p>
<p class="MsoNormal">Ray</p>
<div>
<div>
<p class="MsoNormal">-- <br>
Ray Osborn, Senior Scientist<br>
Materials Science Division<br>
Argonne National Laboratory<br>
Lemont, IL 60439, USA<br>
Phone: +1 (630) 252-9011<br>
Email: ROsborn@anl.gov</p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="color:black">From:
</span></b><span style="color:black">NeXus <nexus-bounces@shadow.nd.rl.ac.uk> on behalf of Jens Krüger via NeXus <nexus@shadow.nd.rl.ac.uk><br>
<b>Date: </b>Tuesday, September 17, 2024 at 1:29</span><span style="font-family:'arial' , sans-serif;color:black"> </span><span style="color:black">AM<br>
<b>To: </b>nexus@nexusformat.org <nexus@nexusformat.org><br>
<b>Cc: </b>Jens Krüger <Jens.Krueger@frm2.tum.de><br>
<b>Subject: </b>Re: [Nexus] Announcing beta-version of the NXvalidate Python package</span></p>
</div>
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<p class="MsoNormal"><span style="font-size:1pt;color:white">Hi Ray, thanks for the information about the nxinspect tool and the effort you put into this project. I have a question: Wouldn't it make sense to download all
the definitions from the nexusformat.</span><span style="font-size:1pt;font-family:'arial' , sans-serif;color:white"> </span><span style="font-size:1pt;color:white">org during the installation and use them locally</span></p>
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<pre style="white-space:pre-wrap"><span style="font-size:12pt;font-family:'arial' , sans-serif">Hi Ray,</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">thanks for the information about the nxinspect tool and the effort you </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">put into this project.</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">I have a question: Wouldn't it make sense to download all the </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">definitions from the nexusformat.org</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">during the installation and use them locally instead of put them into </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">the repo? I'm afraid,</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">that the sync between nexpy and nexusformat repos could be a big </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">challenge in the future.</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Best regards</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Jens</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Am 16.09.24 um 18:04 schrieb Osborn, Raymond via NeXus:</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> I am happy to announce that we have just issued the first beta-release of NXvalidate (<a href="https://urldefense.us/v3/__https:/github.com/nexpy/nxvalidate__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gtziFrBLA$" rel="nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer" target="_blank">https://urldefense.us/v3/__https://github.com/nexpy/nxvalidate__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gtziFrBLA$</a>), a new Python package used to inspect and validate NeXus files. It is currently available for installation on the PyPI server and the source code can be downloaded from Github. When it is more mature, it will be merged into the nexusformat package, with a GUI interface in NeXpy (<a href="https://urldefense.us/v3/__https:/nexpy.github.io/nexpy/__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gv42bvToA$" rel="nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer" target="_blank">https://urldefense.us/v3/__https://nexpy.github.io/nexpy/__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gv42bvToA$</a>). I hope to discuss this at the upcoming meeting of the NeXus International Advisory Committee and would welcome any feedback if you try it out before then. Please note that this is not a production release. Please post any issues to <a href="https://urldefense.us/v3/__https:/github.com/nexpy/nxvalidate/issues__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gsrqLSP2Q$" rel="nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer" target="_blank">https://urldefense.us/v3/__https://github.com/nexpy/nxvalidate/issues__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gsrqLSP2Q$</a>.</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Installation</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Released versions of nxvalidate can be installed using “pip install nxvalidate” and the source code can be downloaded from the NeXpy Git repository:</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> % git clone <a href="https://urldefense.us/v3/__http:/github.com/nexpy/nxvalidate.git__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gtz4Uru8A$" rel="nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer" target="_blank">https://urldefense.us/v3/__http://github.com/nexpy/nxvalidate.git__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gtz4Uru8A$</a></span><br></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Usage</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> The nxvalidate package provides a single command-line script.</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> % nxinspect -h</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> usage: nxinspect [-h] [-f FILENAME] [-p PATH] [-a [APPLICATION]]</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> [-b BASECLASS] [-i] [-w] [-e] [-v]</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Inspects and validates NeXus files.</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> options:</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -h, --help show this help message and exit</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -f FILENAME, --filename FILENAME</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> name of the NeXus file to be validated</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -p PATH, --path PATH</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> path to group to be validated in the NeXus file</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -b BASECLASS, --baseclass BASECLASS</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> name of the base class to be listed</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -a [APPLICATION], --application [APPLICATION]</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> validate the NeXus file against its application definition</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -i, --info output info messages in addition to warnings and errors</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -w, --warning output info messages in addition to warnings and errors</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -e, --error output info messages in addition to warnings and errors</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> -v, --version show program's version number and exit</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> N.B., the command is “nxinspect,” rather than “nxvalidate” to avoid confusion with the existing “cnxvalidate” application (<a href="https://urldefense.us/v3/__https:/github.com/nexusformat/cnxvalidate__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gtoRsqAFg$" rel="nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer nofollow noopener noreferrer" target="_blank">https://urldefense.us/v3/__https://github.com/nexusformat/cnxvalidate__;!!G_uCfscf7eWS!dBKs6J3MTRu8kT6R8Vfk1ILUz-I_1i71_Vh7ySBK_KpCdajICcg6uNBz-EHhHtwoin6wbp59N6si9gtoRsqAFg$</a>).</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Examples</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> 1. To compare the contents of a NeXus file with the base classes defined by the NeXus standard and print conflicting fields or groups, type:</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> % nxinspect -f <filename.nxs> -e</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> The --info, --warning and --error switches control how much information is output. The default is --warning.</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> 2. To check whether the contents of the NeXus file conform to the required contents of the application definition specified in the file, type:</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> % nxinspect -f <filename.nxs> -a</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> 3. To check whether the contents of the NeXus file conform to the required contents of an application definition file, type:</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> % nxinspect -f <filename.nxs> -a <application.nxdl.xml></span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> 4. To print the contents of a base class, type:</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> % nxinspect -b <base-class-name></span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> With regards,</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Ray Osborn</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> --</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Ray Osborn, Senior Scientist</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Materials Science Division</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Argonne National Laboratory</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Lemont, IL 60439, USA</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Phone: +1 (630) 252-9011</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> Email: ROsborn@anl.gov</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> _______________________________________________</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> NeXus mailing list</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">> NeXus@nexusformat.org</span></pre>
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<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">-- </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Dipl.-Phys. Jens Krüger</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Leiter Gruppe Instrumentsteuerung</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Head of Instrument control group</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Technische Universität München</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Forschungsneutronenquelle</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Heinz Maier-Leibnitz (FRM II)</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Lichtenberg-Str. 1</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">D-85748 Garching</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif"> </span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Tel: + 49 (0)89 289 14716</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">Fax: + 49 (0)89 289 14620</span></pre>
<pre><span style="font-size:12pt;font-family:'arial' , sans-serif">mailto: jens.krueger@frm2.tum.de</span></pre>
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