<div dir="ltr">Here are instructions for the Mac:<div><br></div><div>Homebrew</div><div>========</div><div><span style="font-size:12.8px">brew install hdf5 # install hdf5 library, might not be necessary<br></span><span style="font-size:12.8px">brew install lz4 # install lz4 library<br></span><span style="font-size:12.8px">git clone </span><a href="https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/master/LZ4" style="font-size:12.8px" target="_blank">https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/master/LZ4</a><span style="font-size:12.8px"> # download hdf lz4 filter source<br></span><span style="font-size:12.8px">cd LZ4 # change directory to lz4 source<br></span><span style="font-size:12.8px">./configure # prepare the compilation<br></span><span style="font-size:12.8px">make # compile<br></span><span style="font-size:12.8px">This should produce the file ./plugins/lib/libh5lz4.dylib. Copy this file into your hdf5 plugin folder e.g. cp libh5lz4.dylib /usr/local/hdf5/lib/plugin/.<br></span><span style="font-size:12.8px">Now, the decompression in hdf5 should work. Please keep in mind that the directories and files might differ for your system installation and must be modified accordingly. It might be necessary to supply the h5 and lz4 installation path to the configure command ( e.g. ../configure --with-hdf5=/temp/hdf5 --with-lz4lib=/temp/lz4).</span><br></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Fink</span></div><div><span style="font-size:12.8px">===</span></div><div>I did that by emulating the source instructions below in fink.</div><div><br></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">For source junkies</span></div><div><span style="font-size:12.8px">==============</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">download the latest versions of gcc, mpc, mpfr, gmp and isl</span><br style="font-size:12.8px"><a href="http://gcc.gnu.org/mirrors.html" style="font-size:12.8px" target="_blank">http://gcc.gnu.org/mirrors.html</a><br style="font-size:12.8px"><a href="http://www.multiprecision.org/index.php?prog=mpc&page=download" style="font-size:12.8px" target="_blank">http://www.multiprecision.org/index.php?prog=mpc&page=download</a><br style="font-size:12.8px"><a href="http://www.mpfr.org/mpfr-current/#download" style="font-size:12.8px" target="_blank">http://www.mpfr.org/mpfr-current/#download</a><br style="font-size:12.8px"><a href="http://gmplib.org/" style="font-size:12.8px" target="_blank">http://gmplib.org/</a><br style="font-size:12.8px"><a href="ftp://gcc.gnu.org/pub/gcc/infrastructure/" style="font-size:12.8px" target="_blank">ftp://gcc.gnu.org/pub/gcc/infrastructure/</a><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">compile and install gmp, mofr, mpc and isl successively</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">to achieve that</span><br style="font-size:12.8px"><span style="font-size:12.8px">cd gmp* (or whatever package)</span><br style="font-size:12.8px"><span style="font-size:12.8px">mkdir build</span><br style="font-size:12.8px"><span style="font-size:12.8px">cd build</span><br style="font-size:12.8px"><span style="font-size:12.8px">../configure [with prefix, see list below]</span><br style="font-size:12.8px"><span style="font-size:12.8px">make -j 4</span><br style="font-size:12.8px"><span style="font-size:12.8px">sudo make </span><span style="font-size:12.8px;background-color:rgb(255,255,255)">install</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">configure flags are</span><div style="font-size:12.8px">gmp:<br>--prefix=/usr/local/gcc-5.3.0 --with-gmp=/usr/local/gcc-5.3.0<br>mpfr:<br>--prefix=/usr/local/gcc-5.3.0 --with-gmp=/usr/local/gcc-5.3.0<br>mpc:<br>--prefix=/usr/local/gcc-5.3.0 --with-gmp=/usr/local/gcc-5.3.0 --with-mpfr=/usr/local/gcc-5.3.0<br>isl:<br>--prefix=/usr/local/gcc-5.3.0 --with-gmp-prefix=/usr/local/gcc-5.3.0<br><br></div><div style="font-size:12.8px">then install gcc:<br>cd gcc*<br>mkdir build && cd build<br>../configure --prefix=/usr/local/gcc-5.3.0 --enable-checking=release --with-gmp=/usr/local/gcc-5.3.0 --with-mpfr=/usr/local/gcc-5.3.0 --with-mpc=/usr/local/gcc-5.3.0 --enable-languages=c,c++,fortran --with-isl=/usr/local/gcc-5.3.0 --program-suffix=-5.3.0<br>(takes 1 h)<br>make -j 4<br>sudo make <span>install</span><br><br>get bitshuffle:<br>clone <a href="https://github.com/kiyo-masui/bitshuffle.git" target="_blank">https://github.com/kiyo-masui/bitshuffle.git</a><br>cd bitshuffle<br><br>modify INCLUDE_DIRS and LIBRARY_DIRS in setup.py to point to gcc-5.3.0:<br>vi setup.py<br>modify:<br>if sys.platform == 'darwin':<br> pass<br> # putting here both macports and homebrew paths will generate<br> # "ld: warning: dir not found" at the linking phase<br> #INCLUDE_DIRS += ['/opt/local/include'] # macports<br> #LIBRARY_DIRS += ['/opt/local/lib'] # macports<br> #INCLUDE_DIRS += ['/usr/local/include'] # homebrew<br> #LIBRARY_DIRS += ['/usr/local/lib'] # homebrew<br>elif sys.platform.startswith('freebsd'):<br> pass<br> #INCLUDE_DIRS += ['/usr/local/include'] # homebrew<br> #LIBRARY_DIRS += ['/usr/local/lib'] # homebrew<br>INCLUDE_DIRS += ['/usr/local/gcc-5.3.0/include'] # gcc 5.3<br>LIBRARY_DIRS += ['/usr/local/gcc-5.3.0/lib'] # gcc 5.3<br><br>pip <span>install</span> .<br><br>easy as this :)</div></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Best regards.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Andreas</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px"><br></span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 24, 2016 at 1:51 PM, Eugen Wintersberger <span dir="ltr"><<a href="mailto:eugen.wintersberger@desy.de" target="_blank">eugen.wintersberger@desy.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p>Hi Pete<br>
</p><span class="">
<br>
<div>On 06/24/16 14:45, Jemian, Pete R.
wrote:<br>
</div>
<blockquote type="cite">
<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></span>
Unfortunately I do not have a Mac test environment here ;)<span class=""><br>
<blockquote 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></span>
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.<span class=""><br>
<blockquote 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></span>
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<span class="HOEnZb"><font color="#888888"><br>
Eugen</font></span><div><div class="h5"><br>
<blockquote type="cite">
<div><br>
</div>
<div>Pete</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<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 href="mailto:eugen.wintersberger@desy.de" target="_blank"><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" target="_blank"><jemian@anl.gov></a>, "Herbert J.
Bernstein" <a href="mailto:yayahjb@gmail.com" target="_blank"><yayahjb@gmail.com></a>, Discussion forum for the
NeXus data format <a href="mailto:nexus@nexusformat.org" target="_blank"><nexus@nexusformat.org></a>
<br>
Cc: <a href="mailto:Tobias.Richter@diamond.ac.uk" target="_blank">Tobias.Richter@diamond.ac.uk</a>, <a href="mailto:jjakoncic@bnl.gov" target="_blank">jjakoncic@bnl.gov</a>,
<a href="mailto:andreas.foerster@dectris.com" target="_blank">andreas.foerster@dectris.com</a>, <a href="mailto:rsweet@bnl.gov" target="_blank">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>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
<a href="http://HDRMX.medsbio.org" target="_blank">HDRMX.medsbio.org</a>. 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 href="mailto:prjemian@gmail.com" target="_blank">
<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" target="_blank">NeXus@nexusformat.org</a>
<br>
<a href="http://lists.nexusformat.org/mailman/listinfo/nexus" target="_blank">http://lists.nexusformat.org/mailman/listinfo/nexus</a>
<br>
<br>
</blockquote>
</blockquote>
<br>
</blockquote>
<br>
<div>-- <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" target="_blank">
eugen.wintersberger@desy.de</a> <br>
Telefon: <a href="tel:%2B49-40-8998-1917" value="+494089981917" target="_blank">+49-40-8998-1917</a> <br>
</div>
</div>
</blockquote>
<br>
<div>-- <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" target="_blank">eugen.wintersberger@desy.de</a> <br>
Telefon: <a href="tel:%2B49-40-8998-1917" value="+494089981917" target="_blank">+49-40-8998-1917</a> <br>
</div>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><a href="https://www.dectris.com" target="_blank"></a><div><span style="font-family:Verdana;font-size:large">Andreas Förster, Ph.D.</span></div><div><font face="Verdana" size="1"><span style="color:rgb(128,128,128)">MX Application Scientist, Scientific Sales</span></font></div><div><span style="white-space:pre"> </span></div><div><font color="#808080" size="1"><font face="Verdana">Phone: </font></font><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">+41 56 500 2100</span><font color="#808080" size="1"><font face="Verdana"> </font><span style="font-family:Arial,Helvetica,sans-serif;line-height:14px">|</span><span style="font-family:Verdana"> Direct</span><span style="font-family:Verdana">:</span><span style="font-family:Verdana"> </span></font><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">+41 56 500 2176</span><font color="#808080" size="1"><span style="font-family:Verdana"> </span><span style="font-family:Arial,Helvetica,sans-serif;line-height:14px">|</span><span style="font-family:Verdana"> </span><font style="font-family:Verdana">Email:</font><span style="font-family:Verdana"> <a href="mailto:andreas.foerster@dectris.com" target="_blank">andreas.foerster@dectris.com</a></span></font></div><div><span style="font-size:x-small;color:rgb(128,128,128);font-family:Verdana">DECTRIS Ltd. </span><span style="font-size:x-small;color:rgb(128,128,128);font-family:Verdana;line-height:14px">|</span><span style="font-size:x-small;color:rgb(128,128,128);font-family:Verdana;line-height:14px"> Taefernweg 1</span><span style="font-size:x-small;color:rgb(128,128,128);font-family:Verdana;line-height:14px"> </span><span style="font-size:x-small;color:rgb(128,128,128);font-family:Verdana;line-height:14px">| 5405 Baden-Daettwil</span><span style="font-size:x-small;color:rgb(128,128,128);font-family:Verdana;line-height:14px"> </span><font style="font-size:x-small;color:rgb(128,128,128);font-family:Verdana;line-height:14px">| Switz</font><font size="1"><font face="Verdana"><font style="color:rgb(128,128,128);line-height:14px">erland</font><span style="color:rgb(128,128,128);line-height:14px"> </span><font style="color:rgb(128,128,128);line-height:14px">| </font></font><a href="https://www.dectris.com" target="_blank"><font face="Verdana">www.dectris.com</font></a></font></div><div><font size="1"><font style="color:rgb(128,128,128);font-family:Verdana;line-height:14px"><br></font></font></div><div><div><a href="https://www.linkedin.com/company/5067919" target="_blank"><img src="https://www.dectris.com/tl_files/root/signatur/linkein-ico1.png" alt="LinkedIn" style="width:15px;height:15px;margin-left:400px;float:left"></a></div></div><div> <a href="https://www.facebook.com/pages/Dectris-Ltd/623855944369304" target="_blank"><img src="https://www.dectris.com/tl_files/root/signatur/facebook-ico1.png" alt="facebook" style="width:15px;height:15px"></a> <a href="https://twitter.com/DECTRIS_News" target="_blank"><img src="https://www.dectris.com/tl_files/root/signatur/twitter-ico1.png" style="width:15px;height:15px"></a></div><div><br></div><div><br></div><div><img src="https://www.dectris.com/tl_files/root/signatur/dectris_plus%20slogan.png" style="float:left;height:30px;width:262px;margin-left:195px"></div><div><font face="Verdana" color="#808080" size="1"><br></font></div><div><font face="Verdana" color="#808080" size="1"><br></font></div><div><font face="Verdana" color="#808080" size="1"><br></font></div><div><font face="Verdana" color="#808080" size="1">Confidentiality Note: This message is intended only for the use of the named </font></div><div><font face="Verdana" color="#808080" size="1">recipient(s) </font><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">and may contain confidential and/or privileged information. </span><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">If you </span></div><div><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">are not the intended </span><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">recipient, please contact the sender and delete </span><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">the message.</span></div><div><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">Any unauthorized use of </span><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">the information contained in this </span><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small">message is prohibited.</span></div><div><span style="color:rgb(128,128,128);font-family:Verdana;font-size:x-small"><br></span></div><div><font face="Verdana" color="#808080" size="1"><br></font></div></div>
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