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You can install LZ4 and bitshuffle through Conda if you are using h5py. I’m on travel at the moment, but I could probably come up with a set of instructions when I get back.
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<div>
<blockquote type="cite" class="">
<div class="">On Jun 24, 2016, at 3:06 PM, Andreas Förster <<a href="mailto:andreas.foerster@dectris.com" class="">andreas.foerster@dectris.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
Here are instructions for the Mac:
<div class=""><br class="">
</div>
<div class="">Homebrew</div>
<div class="">========</div>
<div class=""><span style="font-size: 12.8px;" class="">brew install hdf5 # install hdf5 library, might not be necessary<br class="">
</span><span style="font-size: 12.8px;" class="">brew install lz4 # install lz4 library<br class="">
</span><span style="font-size: 12.8px;" class="">git clone </span><a href="https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/master/LZ4" target="_blank" style="font-size: 12.8px;" class="">https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/master/LZ4</a><span style="font-size: 12.8px;" class=""> #
download hdf lz4 filter source<br class="">
</span><span style="font-size: 12.8px;" class="">cd LZ4 # change directory to lz4 source<br class="">
</span><span style="font-size: 12.8px;" class="">./configure # prepare the compilation<br class="">
</span><span style="font-size: 12.8px;" class="">make # compile<br class="">
</span><span style="font-size: 12.8px;" class="">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 class="">
</span><span style="font-size: 12.8px;" class="">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 class="">
</div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class="">Fink</span></div>
<div class=""><span style="font-size: 12.8px;" class="">===</span></div>
<div class="">I did that by emulating the source instructions below in fink.</div>
<div class=""><br class="">
</div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class="">For source junkies</span></div>
<div class=""><span style="font-size: 12.8px;" class="">==============</span></div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class="">download the latest versions of gcc, mpc, mpfr, gmp and isl</span><br style="font-size: 12.8px;" class="">
<a href="http://gcc.gnu.org/mirrors.html" target="_blank" style="font-size: 12.8px;" class="">http://gcc.gnu.org/mirrors.html</a><br style="font-size: 12.8px;" class="">
<a href="http://www.multiprecision.org/index.php?prog=mpc&page=download" target="_blank" style="font-size: 12.8px;" class="">http://www.multiprecision.org/index.php?prog=mpc&page=download</a><br style="font-size: 12.8px;" class="">
<a href="http://www.mpfr.org/mpfr-current/#download" target="_blank" style="font-size: 12.8px;" class="">http://www.mpfr.org/mpfr-current/#download</a><br style="font-size: 12.8px;" class="">
<a href="http://gmplib.org/" target="_blank" style="font-size: 12.8px;" class="">http://gmplib.org/</a><br style="font-size: 12.8px;" class="">
<a href="ftp://gcc.gnu.org/pub/gcc/infrastructure/" target="_blank" style="font-size: 12.8px;" class="">ftp://gcc.gnu.org/pub/gcc/infrastructure/</a><br style="font-size: 12.8px;" class="">
<br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">compile and install gmp, mofr, mpc and isl successively</span><br style="font-size: 12.8px;" class="">
<br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">to achieve that</span><br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">cd gmp* (or whatever package)</span><br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">mkdir build</span><br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">cd build</span><br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">../configure [with prefix, see list below]</span><br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">make -j 4</span><br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">sudo make </span><span style="font-size: 12.8px; background-color: rgb(255, 255, 255);" class="">install</span><br style="font-size: 12.8px;" class="">
<br style="font-size: 12.8px;" class="">
<span style="font-size: 12.8px;" class="">configure flags are</span>
<div style="font-size: 12.8px;" class="">gmp:<br class="">
--prefix=/usr/local/gcc-5.3.0 --with-gmp=/usr/local/gcc-5.3.0<br class="">
mpfr:<br class="">
--prefix=/usr/local/gcc-5.3.0 --with-gmp=/usr/local/gcc-5.3.0<br class="">
mpc:<br class="">
--prefix=/usr/local/gcc-5.3.0 --with-gmp=/usr/local/gcc-5.3.0 --with-mpfr=/usr/local/gcc-5.3.0<br class="">
isl:<br class="">
--prefix=/usr/local/gcc-5.3.0 --with-gmp-prefix=/usr/local/gcc-5.3.0<br class="">
<br class="">
</div>
<div style="font-size: 12.8px;" class="">then install gcc:<br class="">
cd gcc*<br class="">
mkdir build && cd build<br class="">
../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 class="">
(takes 1 h)<br class="">
make -j 4<br class="">
sudo make <span class="">install</span><br class="">
<br class="">
get bitshuffle:<br class="">
clone <a href="https://github.com/kiyo-masui/bitshuffle.git" target="_blank" class="">https://github.com/kiyo-masui/bitshuffle.git</a><br class="">
cd bitshuffle<br class="">
<br class="">
modify INCLUDE_DIRS and LIBRARY_DIRS in setup.py to point to gcc-5.3.0:<br class="">
vi setup.py<br class="">
modify:<br class="">
if sys.platform == 'darwin':<br class="">
pass<br class="">
# putting here both macports and homebrew paths will generate<br class="">
# "ld: warning: dir not found" at the linking phase<br class="">
#INCLUDE_DIRS += ['/opt/local/include'] # macports<br class="">
#LIBRARY_DIRS += ['/opt/local/lib'] # macports<br class="">
#INCLUDE_DIRS += ['/usr/local/include'] # homebrew<br class="">
#LIBRARY_DIRS += ['/usr/local/lib'] # homebrew<br class="">
elif sys.platform.startswith('freebsd'):<br class="">
pass<br class="">
#INCLUDE_DIRS += ['/usr/local/include'] # homebrew<br class="">
#LIBRARY_DIRS += ['/usr/local/lib'] # homebrew<br class="">
INCLUDE_DIRS += ['/usr/local/gcc-5.3.0/include'] # gcc 5.3<br class="">
LIBRARY_DIRS += ['/usr/local/gcc-5.3.0/lib'] # gcc 5.3<br class="">
<br class="">
pip <span class="">install</span> .<br class="">
<br class="">
easy as this :)</div>
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<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class="">Best regards.</span></div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class="">Andreas</span></div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
<div class=""><span style="font-size: 12.8px;" class=""><br class="">
</span></div>
</div>
<div class="gmail_extra" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<br class="">
<div class="gmail_quote">On Fri, Jun 24, 2016 at 1:51 PM, Eugen Wintersberger<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:eugen.wintersberger@desy.de" target="_blank" class="">eugen.wintersberger@desy.de</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">
<div bgcolor="#FFFFFF" text="#000000" class="">
<p class="">Hi Pete<br class="">
</p>
<span class=""><br class="">
<div class="">On 06/24/16 14:45, Jemian, Pete R. wrote:<br class="">
</div>
<blockquote type="cite" class="">
<div class="">Eugen</div>
<div class=""><br class="">
</div>
<div class="">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 class="">
<blockquote type="cite" class="">
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">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<span class="Apple-converted-space"> </span><br class="">
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 class="">
<br class="">
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 class="">
<blockquote type="cite" class="">
<div class=""><br class="">
</div>
<div class="">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)<span class="Apple-converted-space"> </span><br class="">
things are a bit more complicated. My personal suggestions to users is to use Linux for analysis whenever possible.<span class="Apple-converted-space"> </span><br class="">
<br class="">
I am on vacation next week but will add the LZ4+BitShuffle filter immediately when I am back ;) Promissed ;)<br class="">
<br class="">
regards<span class="HOEnZb"><font color="#888888" class=""><br class="">
Eugen</font></span>
<div class="">
<div class="h5"><br class="">
<blockquote type="cite" class="">
<div class=""><br class="">
</div>
<div class="">Pete</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div style="font-size: 10px; color: rgb(87, 87, 87);" class=""><br class="">
</div>
<div style="font-size: 10px; color: rgb(87, 87, 87);" class="">Sent from a device with a dreadfully small screen</div>
</div>
<br class="">
<br class="">
-------- Original message --------<br class="">
From: Eugen Wintersberger<span class="Apple-converted-space"> </span><a href="mailto:eugen.wintersberger@desy.de" target="_blank" class=""><eugen.wintersberger@desy.de></a><span class="Apple-converted-space"> </span><br class="">
Date: 6/24/2016 3:05 AM (GMT-06:00)<span class="Apple-converted-space"> </span><br class="">
To: "Jemian, Pete R."<span class="Apple-converted-space"> </span><a href="mailto:jemian@anl.gov" target="_blank" class=""><jemian@anl.gov></a>, "Herbert J. Bernstein"<span class="Apple-converted-space"> </span><a href="mailto:yayahjb@gmail.com" target="_blank" class=""><yayahjb@gmail.com></a>,
Discussion forum for the NeXus data format<span class="Apple-converted-space"> </span><a href="mailto:nexus@nexusformat.org" target="_blank" class=""><nexus@nexusformat.org></a><span class="Apple-converted-space"> </span><br class="">
Cc:<span class="Apple-converted-space"> </span><a href="mailto:Tobias.Richter@diamond.ac.uk" target="_blank" class="">Tobias.Richter@diamond.ac.uk</a>,<span class="Apple-converted-space"> </span><a href="mailto:jjakoncic@bnl.gov" target="_blank" class="">jjakoncic@bnl.gov</a>,<span class="Apple-converted-space"> </span><a href="mailto:andreas.foerster@dectris.com" target="_blank" class="">andreas.foerster@dectris.com</a>,<span class="Apple-converted-space"> </span><a href="mailto:rsweet@bnl.gov" target="_blank" class="">rsweet@bnl.gov</a><span class="Apple-converted-space"> </span><br class="">
Subject: Re: [Nexus] how to read files from Eiger?<span class="Apple-converted-space"> </span><br class="">
<br class="">
<div class="">
<p class="">Hi Pete,</p>
<p class="">On which Linux systems do you want to read the files. For Ubuntu 14.04 and Debian 8 we have packages available.<span class="Apple-converted-space"> </span><br class="">
</p>
<div class="">On 06/23/16 19:27, Pete Jemian wrote:<br class="">
</div>
<blockquote type="cite" class="">Very helpful. Thanks for the quick turnaround.<span class="Apple-converted-space"> </span><br class="">
Now I go off in a corner with an internet connection for quiet time ...<span class="Apple-converted-space"> </span><br class="">
<br class="">
On 6/23/2016 12:25 PM, Herbert J. Bernstein wrote:<span class="Apple-converted-space"> </span><br class="">
<blockquote type="cite" class="">Dear Pete,<span class="Apple-converted-space"> </span><br class="">
<br class="">
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.<span class="Apple-converted-space"> </span><br class="">
</blockquote>
</blockquote>
For the current files BittShuffle is not required. Most probably required for latter releases of the detector?<br class="">
<br class="">
regards<br class="">
Eugen<br class="">
<blockquote type="cite" class="">
<blockquote type="cite" class=""><br class="">
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" class="">HDRMX.medsbio.org</a>. There is a link for the hdrmx-bb list on the page. Please
post comments, questions and suggestions there.<span class="Apple-converted-space"> </span><br class="">
<br class="">
Regards,<span class="Apple-converted-space"> </span><br class="">
Herbert<span class="Apple-converted-space"> </span><br class="">
<br class="">
Sent from my iPad<span class="Apple-converted-space"> </span><br class="">
<br class="">
<blockquote type="cite" class="">On Jun 23, 2016, at 12:48, Pete Jemian<span class="Apple-converted-space"> </span><a href="mailto:prjemian@gmail.com" target="_blank" class=""><prjemian@gmail.com></a><span class="Apple-converted-space"> </span>wrote:<span class="Apple-converted-space"> </span><br class="">
<br class="">
<br class="">
We have received a linked fileset from an Eiger 1M Anderson want to read it.<span class="Apple-converted-space"> </span><br class="">
Cannot seem to progress past knowing that there is data.<span class="Apple-converted-space"> </span><br class="">
Here is an excerpt from h5dump (version 1.8.16):<span class="Apple-converted-space"> </span><br class="">
<br class="">
DATASET "data" {<span class="Apple-converted-space"> </span><br class="">
DATATYPE H5T_STD_U32LE<span class="Apple-converted-space"> </span><br class="">
DATASPACE SIMPLE { ( 1, 1065, 1030 ) / ( H5S_UNLIMITED, 1065, 1030 ) }<span class="Apple-converted-space"> </span><br class="">
DATA {h5dump error: unable to print data<span class="Apple-converted-space"> </span><br class="">
<br class="">
}<span class="Apple-converted-space"> </span><br class="">
ATTRIBUTE "image_nr_high" {<span class="Apple-converted-space"> </span><br class="">
DATATYPE H5T_STD_I32LE<span class="Apple-converted-space"> </span><br class="">
DATASPACE SCALAR<span class="Apple-converted-space"> </span><br class="">
DATA {<span class="Apple-converted-space"> </span><br class="">
(0): 1<span class="Apple-converted-space"> </span><br class="">
}<span class="Apple-converted-space"> </span><br class="">
}<span class="Apple-converted-space"> </span><br class="">
ATTRIBUTE "image_nr_low" {<span class="Apple-converted-space"> </span><br class="">
DATATYPE H5T_STD_I32LE<span class="Apple-converted-space"> </span><br class="">
DATASPACE SCALAR<span class="Apple-converted-space"> </span><br class="">
DATA {<span class="Apple-converted-space"> </span><br class="">
(0): 1<span class="Apple-converted-space"> </span><br class="">
}<span class="Apple-converted-space"> </span><br class="">
}<span class="Apple-converted-space"> </span><br class="">
}<span class="Apple-converted-space"> </span><br class="">
<br class="">
It's the error: "h5dump error: unable to print data"<span class="Apple-converted-space"> </span><br class="">
<br class="">
Is this the case where we have the wrong version of the HDF5 libraries?<span class="Apple-converted-space"> </span><br class="">
Is there a tool to render such files compatible with the 1.8 libraries?<span class="Apple-converted-space"> </span><br class="">
If so, where is that tool?<span class="Apple-converted-space"> </span><br class="">
<br class="">
Pete<span class="Apple-converted-space"> </span><br class="">
<br class="">
_______________________________________________<span class="Apple-converted-space"> </span><br class="">
NeXus mailing list<span class="Apple-converted-space"> </span><br class="">
<a href="mailto:NeXus@nexusformat.org" target="_blank" class="">NeXus@nexusformat.org</a><span class="Apple-converted-space"> </span><br class="">
<a href="http://lists.nexusformat.org/mailman/listinfo/nexus" target="_blank" class="">http://lists.nexusformat.org/mailman/listinfo/nexus</a><span class="Apple-converted-space"> </span><br class="">
<br class="">
</blockquote>
</blockquote>
<br class="">
</blockquote>
<br class="">
<div class="">--<span class="Apple-converted-space"> </span><br class="">
Dr. Eugen Wintersberger<span class="Apple-converted-space"> </span><br class="">
<br class="">
FS-EC<span class="Apple-converted-space"> </span><br class="">
DESY<span class="Apple-converted-space"> </span><br class="">
Notkestr. 85<span class="Apple-converted-space"> </span><br class="">
D-22607 Hamburg<span class="Apple-converted-space"> </span><br class="">
Germany<span class="Apple-converted-space"> </span><br class="">
<br class="">
E-Mail:<span class="Apple-converted-space"> </span><a href="mailto:eugen.wintersberger@desy.de" target="_blank" class="">eugen.wintersberger@desy.de</a><span class="Apple-converted-space"> </span><br class="">
Telefon:<span class="Apple-converted-space"> </span><a href="tel:%2B49-40-8998-1917" value="+494089981917" target="_blank" class="">+49-40-8998-1917</a><span class="Apple-converted-space"> </span><br class="">
</div>
</div>
</blockquote>
<br class="">
<div class="">--<span class="Apple-converted-space"> </span><br class="">
Dr. Eugen Wintersberger<span class="Apple-converted-space"> </span><br class="">
<br class="">
FS-EC<span class="Apple-converted-space"> </span><br class="">
DESY<span class="Apple-converted-space"> </span><br class="">
Notkestr. 85<span class="Apple-converted-space"> </span><br class="">
D-22607 Hamburg<span class="Apple-converted-space"> </span><br class="">
Germany<span class="Apple-converted-space"> </span><br class="">
<br class="">
E-Mail:<span class="Apple-converted-space"> </span><a href="mailto:eugen.wintersberger@desy.de" target="_blank" class="">eugen.wintersberger@desy.de</a><span class="Apple-converted-space"> </span><br class="">
Telefon:<span class="Apple-converted-space"> </span><a href="tel:%2B49-40-8998-1917" value="+494089981917" target="_blank" class="">+49-40-8998-1917</a><span class="Apple-converted-space"> </span><br class="">
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
<br clear="all" class="">
<div class=""><br class="">
</div>
--<span class="Apple-converted-space"> </span><br class="">
<div class="gmail_signature" data-smartmail="gmail_signature"><a href="https://www.dectris.com/" target="_blank" class=""></a>
<div class=""><span style="font-family: Verdana; font-size: large;" class="">Andreas Förster, Ph.D.</span></div>
<div class=""><font face="Verdana" size="1" class=""><span style="color: rgb(128, 128, 128);" class="">MX Application Scientist, Scientific Sales</span></font></div>
<div class=""><span style="white-space: pre;" class=""></span></div>
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</blockquote>
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<br 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="">
Email: <a href="mailto:ROsborn@anl.gov" class="">ROsborn@anl.gov</a><br class="">
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