[Nexus] how to read files from Eiger?

[Andreas Förster]

Dear Eugen and Herbert,

definitely agree with everything Herbert wrote.  Both LZ4 and bs-LZ4 should
be documented on the HDRMX website.

Best regards.


Andreas



On Fri, Jun 24, 2016 at 11:33 AM, Herbert J. Bernstein <yayahjb at gmail.com>
wrote:

> Dear Eugen,
>
>   The latest releases of the detector firmware support bitshuffle (as
> bslz4) which seems likely to eventually replace most uses of lz4 without
> bitshuffle, but right now there are a lot of pure lz4 images around.  The
> safest and simplest thing to do is to install both the bitsuffle and lz4
> filters.Then you can read any of the Eiger images from the filewriter
> interface.
>
>   Regards,
>     Herbert
>
> On Fri, Jun 24, 2016 at 4:05 AM, Eugen Wintersberger <
> eugen.wintersberger at desy.de> wrote:
>
>> 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>
>> <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
>>
>
>


-- 
<https://www.dectris.com>
Andreas Förster, Ph.D.
MX Application Scientist, Scientific Sales
Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email:
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