[Nexus] how to read files from Eiger?

[Herbert J. Bernstein]

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. 

  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
> 
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