<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<p>Hi Pete<br>
</p>
<br>
<div class="moz-cite-prefix">On 06/24/16 14:45, Jemian, Pete R.
wrote:<br>
</div>
<blockquote
cite="mid:3x3ffr71c0c52kn0suavte8h.1466772308156@email.android.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div>Eugen</div>
<div><br>
</div>
<div>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.</div>
</blockquote>
Unfortunately I do not have a Mac test environment here ;)<br>
<blockquote
cite="mid:3x3ffr71c0c52kn0suavte8h.1466772308156@email.android.com"
type="cite">
<div><br>
</div>
<div>Adding the compression library to this toolset is not
trivial. I must persuade the 3rd party developer of that plugin
to make this addition.</div>
<div><br>
</div>
<div>I also want to read that file with the h5py package in python
on mac, Windows, and Linux.</div>
</blockquote>
We are currently testing an MSI package for Windows here. On Linux
everything is easy. For Debian and Ubuntu we have packages which
also set <br>
the correct environment variables. We tried to use all kinds of
software to access the data which works fine on Linux once the
package is installed.<br>
<br>
For Windows we have seen that with the current build (Windows 7) at
least Matlab R2016 and Anaconda Python 3.5 work flawlessly with the
plugin.<br>
<blockquote
cite="mid:3x3ffr71c0c52kn0suavte8h.1466772308156@email.android.com"
type="cite">
<div><br>
</div>
<div>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.</div>
</blockquote>
The point is simply that as long as you are on a Linux system
everything is fine. At least on Windows (I have no experience with
Mac) <br>
things are a bit more complicated. My personal suggestions to users
is to use Linux for analysis whenever possible. <br>
<br>
I am on vacation next week but will add the LZ4+BitShuffle filter
immediately when I am back ;) Promissed ;)<br>
<br>
regards<br>
Eugen<br>
<blockquote
cite="mid:3x3ffr71c0c52kn0suavte8h.1466772308156@email.android.com"
type="cite">
<div><br>
</div>
<div>Pete</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div id="composer_signature">
<div style="font-size:85%; color:#575757"><br>
</div>
<div style="font-size:85%; color:#575757">Sent from a device
with a dreadfully small screen</div>
</div>
<br>
<br>
-------- Original message --------<br>
From: Eugen Wintersberger <a class="moz-txt-link-rfc2396E" 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 class="moz-txt-link-rfc2396E" href="mailto:jemian@anl.gov"><jemian@anl.gov></a>, "Herbert J.
Bernstein" <a class="moz-txt-link-rfc2396E" href="mailto:yayahjb@gmail.com"><yayahjb@gmail.com></a>, Discussion forum for the
NeXus data format <a class="moz-txt-link-rfc2396E" href="mailto:nexus@nexusformat.org"><nexus@nexusformat.org></a>
<br>
Cc: <a class="moz-txt-link-abbreviated" href="mailto:Tobias.Richter@diamond.ac.uk">Tobias.Richter@diamond.ac.uk</a>, <a class="moz-txt-link-abbreviated" href="mailto:jjakoncic@bnl.gov">jjakoncic@bnl.gov</a>,
<a class="moz-txt-link-abbreviated" href="mailto:andreas.foerster@dectris.com">andreas.foerster@dectris.com</a>, <a class="moz-txt-link-abbreviated" href="mailto:rsweet@bnl.gov">rsweet@bnl.gov</a>
<br>
Subject: Re: [Nexus] how to read files from Eiger? <br>
<br>
<div>
<p>Hi Pete,</p>
<p>On which Linux systems do you want to read the files. For
Ubuntu 14.04 and Debian 8 we have packages available.
<br>
</p>
<div class="moz-cite-prefix">On 06/23/16 19:27, Pete Jemian
wrote:<br>
</div>
<blockquote type="cite">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>
<blockquote type="cite">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.
<br>
</blockquote>
</blockquote>
For the current files BittShuffle is not required. Most probably
required for latter releases of the detector?<br>
<br>
regards<br>
Eugen<br>
<blockquote type="cite">
<blockquote type="cite"><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>
<blockquote type="cite">On Jun 23, 2016, at 12:48, Pete
Jemian <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
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 moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:NeXus@nexusformat.org">NeXus@nexusformat.org</a>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://lists.nexusformat.org/mailman/listinfo/nexus">http://lists.nexusformat.org/mailman/listinfo/nexus</a>
<br>
<br>
</blockquote>
</blockquote>
<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
Dr. Eugen Wintersberger <br>
<br>
FS-EC <br>
DESY <br>
Notkestr. 85 <br>
D-22607 Hamburg <br>
Germany <br>
<br>
E-Mail: <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:eugen.wintersberger@desy.de">
eugen.wintersberger@desy.de</a> <br>
Telefon: +49-40-8998-1917 <br>
</div>
</div>
</blockquote>
<br>
<div class="moz-signature">-- <br>
Dr. Eugen Wintersberger <br>
<br>
FS-EC <br>
DESY <br>
Notkestr. 85 <br>
D-22607 Hamburg <br>
Germany <br>
<br>
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:eugen.wintersberger@desy.de">eugen.wintersberger@desy.de</a> <br>
Telefon: +49-40-8998-1917 <br>
</div>
</body>
</html>