[Nexus] how to read files from Eiger?
Eugen Wintersberger
eugen.wintersberger at desy.de
Fri Jun 24 13:51:45 BST 2016
Hi Pete
On 06/24/16 14:45, Jemian, Pete R. wrote:
> Eugen
>
> 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.
Unfortunately I do not have a Mac test environment here ;)
>
> Adding the compression library to this toolset is not trivial. I must
> persuade the 3rd party developer of that plugin to make this addition.
>
> I also want to read that file with the h5py package in python on mac,
> Windows, and Linux.
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
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.
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.
>
> 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.
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)
things are a bit more complicated. My personal suggestions to users is
to use Linux for analysis whenever possible.
I am on vacation next week but will add the LZ4+BitShuffle filter
immediately when I am back ;) Promissed ;)
regards
Eugen
>
> Pete
>
>
>
>
> Sent from a device with a dreadfully small screen
>
>
> -------- Original message --------
> From: Eugen Wintersberger <eugen.wintersberger at desy.de>
> Date: 6/24/2016 3:05 AM (GMT-06:00)
> To: "Jemian, Pete R." <jemian at anl.gov>, "Herbert J. Bernstein"
> <yayahjb at gmail.com>, Discussion forum for the NeXus data format
> <nexus at nexusformat.org>
> Cc: Tobias.Richter at diamond.ac.uk, jjakoncic at bnl.gov,
> andreas.foerster at dectris.com, rsweet at bnl.gov
> Subject: Re: [Nexus] how to read files from Eiger?
>
> Hi Pete,
>
> On which Linux systems do you want to read the files. For Ubuntu 14.04
> and Debian 8 we have packages available.
>
> On 06/23/16 19:27, Pete Jemian wrote:
>> Very helpful. Thanks for the quick turnaround.
>> Now I go off in a corner with an internet connection for quiet time ...
>>
>> On 6/23/2016 12:25 PM, Herbert J. Bernstein wrote:
>>> Dear Pete,
>>>
>>> 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.
> For the current files BittShuffle is not required. Most probably
> required for latter releases of the detector?
>
> regards
> Eugen
>>>
>>> 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.
>>>
>>> Regards,
>>> Herbert
>>>
>>> Sent from my iPad
>>>
>>>> On Jun 23, 2016, at 12:48, Pete Jemian <prjemian at gmail.com> wrote:
>>>>
>>>>
>>>> We have received a linked fileset from an Eiger 1M Anderson want
>>>> to read it.
>>>> Cannot seem to progress past knowing that there is data.
>>>> Here is an excerpt from h5dump (version 1.8.16):
>>>>
>>>> DATASET "data" {
>>>> DATATYPE H5T_STD_U32LE
>>>> DATASPACE SIMPLE { ( 1, 1065, 1030 ) / ( H5S_UNLIMITED,
>>>> 1065, 1030 ) }
>>>> DATA {h5dump error: unable to print data
>>>>
>>>> }
>>>> ATTRIBUTE "image_nr_high" {
>>>> DATATYPE H5T_STD_I32LE
>>>> DATASPACE SCALAR
>>>> DATA {
>>>> (0): 1
>>>> }
>>>> }
>>>> ATTRIBUTE "image_nr_low" {
>>>> DATATYPE H5T_STD_I32LE
>>>> DATASPACE SCALAR
>>>> DATA {
>>>> (0): 1
>>>> }
>>>> }
>>>> }
>>>>
>>>> It's the error: "h5dump error: unable to print data"
>>>>
>>>> Is this the case where we have the wrong version of the HDF5
>>>> libraries?
>>>> Is there a tool to render such files compatible with the 1.8
>>>> libraries?
>>>> If so, where is that tool?
>>>>
>>>> Pete
>>>>
>>>> _______________________________________________
>>>> NeXus mailing list
>>>> NeXus at nexusformat.org
>>>> http://lists.nexusformat.org/mailman/listinfo/nexus
>>>>
>>
>
> --
> Dr. Eugen Wintersberger
>
> FS-EC
> DESY
> Notkestr. 85
> D-22607 Hamburg
> Germany
>
> E-Mail: eugen.wintersberger at desy.de
> Telefon: +49-40-8998-1917
--
Dr. Eugen Wintersberger
FS-EC
DESY
Notkestr. 85
D-22607 Hamburg
Germany
E-Mail: eugen.wintersberger at desy.de
Telefon: +49-40-8998-1917
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