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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">HI Pete<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">We use these files & filters in dials via h5py and within our build it *<b>generally</b>* just works {there are exceptions which we are looking in to} including
on macs<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">That said, we compile in the extensions into the distro so the users do not need to worry – for MX this is *<b>very important</b>*<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">For Eiger data sets the data may just be too big to transmogrify effectively<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">Cheerio Graeme<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>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> NeXus [mailto:nexus-bounces@nexusformat.org]
<b>On Behalf Of </b>Jemian, Pete R.<br>
<b>Sent:</b> 24 June 2016 13:45<br>
<b>To:</b> Eugen Wintersberger; Herbert J. Bernstein; Discussion forum for the NeXus data format<br>
<b>Cc:</b> Richter, Tobias (ESS,RAL,LSCI); rsweet@bnl.gov; jjakoncic@bnl.gov; andreas.foerster@dectris.com<br>
<b>Subject:</b> Re: [Nexus] how to read files from Eiger?<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">Eugen<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">First off, I (representing the user who asked me about this) want to read that file with the HDF5 plugin in IgorPro on a Mac.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Adding the compression library to this toolset is not trivial. I must persuade the 3rd party developer of that plugin to make this addition.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I also want to read that file with the h5py package in python on mac, Windows, and Linux.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">We are on the leading edge here but our users have already begun to struggle with reading these files. Until the compression filters are part of common installations, a converter tool is needed.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Pete<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;color:#575757"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;color:#575757">Sent from a device with a dreadfully small screen<o:p></o:p></span></p>
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<br>
-------- Original message --------<br>
From: Eugen Wintersberger <<a href="mailto:eugen.wintersberger@desy.de">eugen.wintersberger@desy.de</a>>
<br>
Date: 6/24/2016 3:05 AM (GMT-06:00) <br>
To: "Jemian, Pete R." <<a href="mailto:jemian@anl.gov">jemian@anl.gov</a>>, "Herbert J. Bernstein" <<a href="mailto:yayahjb@gmail.com">yayahjb@gmail.com</a>>, Discussion forum for the NeXus data format <<a href="mailto:nexus@nexusformat.org">nexus@nexusformat.org</a>>
<br>
Cc: <a href="mailto:Tobias.Richter@diamond.ac.uk">Tobias.Richter@diamond.ac.uk</a>,
<a href="mailto:jjakoncic@bnl.gov">jjakoncic@bnl.gov</a>, <a href="mailto:andreas.foerster@dectris.com">
andreas.foerster@dectris.com</a>, <a href="mailto:rsweet@bnl.gov">rsweet@bnl.gov</a>
<br>
Subject: Re: [Nexus] how to read files from Eiger? <o:p></o:p></p>
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<p>Hi Pete,<o:p></o:p></p>
<p>On which Linux systems do you want to read the files. For Ubuntu 14.04 and Debian 8 we have packages available.
<o:p></o:p></p>
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<p class="MsoNormal">On 06/23/16 19:27, Pete Jemian wrote:<o:p></o:p></p>
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<p class="MsoNormal">Very helpful. Thanks for the quick turnaround. <br>
Now I go off in a corner with an internet connection for quiet time ... <br>
<br>
On 6/23/2016 12:25 PM, Herbert J. Bernstein wrote: <br>
<br>
<o:p></o:p></p>
<p class="MsoNormal">Dear Pete, <br>
<br>
This is a solvable problem, but requires some preliminary software installations. First, be sure your HDF5 kit is reasonably recent and has filter plugin support. Then pickup and install both the LZ4 and BitShuffle filters. Now make sure HDF5_PLUGIN_PATH
is defined to point to the directory containing the filter libraries. Then h5dump should be able to handle the Eiger files.
<o:p></o:p></p>
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<p class="MsoNormal">For the current files BittShuffle is not required. Most probably required for latter releases of the detector?<br>
<br>
regards<br>
Eugen<br>
<br>
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<p class="MsoNormal"><br>
Eugen is gathering the filters on github. I am gathering other software and links to test data and templates at HDRMX.medsbio.org. There is a link for the hdrmx-bb list on the page. Please post comments, questions and suggestions there.
<br>
<br>
Regards, <br>
Herbert <br>
<br>
Sent from my iPad <br>
<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">On Jun 23, 2016, at 12:48, Pete Jemian
<a href="mailto:prjemian@gmail.com"><prjemian@gmail.com></a> wrote: <br>
<br>
<br>
We have received a linked fileset from an Eiger 1M Anderson want to read it. <br>
Cannot seem to progress past knowing that there is data. <br>
Here is an excerpt from h5dump (version 1.8.16): <br>
<br>
DATASET "data" { <br>
DATATYPE H5T_STD_U32LE <br>
DATASPACE SIMPLE { ( 1, 1065, 1030 ) / ( H5S_UNLIMITED, 1065, 1030 ) }
<br>
DATA {h5dump error: unable to print data <br>
<br>
} <br>
ATTRIBUTE "image_nr_high" { <br>
DATATYPE H5T_STD_I32LE <br>
DATASPACE SCALAR <br>
DATA { <br>
(0): 1 <br>
} <br>
} <br>
ATTRIBUTE "image_nr_low" { <br>
DATATYPE H5T_STD_I32LE <br>
DATASPACE SCALAR <br>
DATA { <br>
(0): 1 <br>
} <br>
} <br>
} <br>
<br>
It's the error: "h5dump error: unable to print data" <br>
<br>
Is this the case where we have the wrong version of the HDF5 libraries? <br>
Is there a tool to render such files compatible with the 1.8 libraries? <br>
If so, where is that tool? <br>
<br>
Pete <br>
<br>
_______________________________________________ <br>
NeXus mailing list <br>
<a href="mailto:NeXus@nexusformat.org">NeXus@nexusformat.org</a> <br>
<a href="http://lists.nexusformat.org/mailman/listinfo/nexus">http://lists.nexusformat.org/mailman/listinfo/nexus</a>
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <br>
Dr. Eugen Wintersberger <br>
<br>
FS-EC <br>
DESY <br>
Notkestr. 85 <br>
D-22607 Hamburg <br>
Germany <br>
<br>
E-Mail: <a href="mailto:eugen.wintersberger@desy.de">eugen.wintersberger@desy.de</a>
<br>
Telefon: +49-40-8998-1917 <o:p></o:p></p>
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