[Nexus] how to read files from Eiger?

Fri Jun 24 13:51:22 BST 2016

HI Pete

We use these files & filters in dials via h5py and within our build it *generally* just works {there are exceptions which we are looking in to} including on macs

That said, we compile in the extensions into the distro so the users do not need to worry - for MX this is *very important*

For Eiger data sets the data may just be too big to transmogrify effectively

Cheerio Graeme

From: NeXus [mailto:nexus-bounces at nexusformat.org] On Behalf Of Jemian, Pete R.
Sent: 24 June 2016 13:45
To: Eugen Wintersberger; Herbert J. Bernstein; Discussion forum for the NeXus data format
Cc: Richter, Tobias (ESS,RAL,LSCI); rsweet at bnl.gov; jjakoncic at bnl.gov; andreas.foerster at dectris.com
Subject: Re: [Nexus] how to read files from Eiger?

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.

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 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.

Pete

Sent from a device with a dreadfully small screen

-------- Original message --------
From: Eugen Wintersberger <eugen.wintersberger at desy.de<mailto:eugen.wintersberger at desy.de>>
Date: 6/24/2016 3:05 AM (GMT-06:00)
To: "Jemian, Pete R." <jemian at anl.gov<mailto:jemian at anl.gov>>, "Herbert J. Bernstein" <yayahjb at gmail.com<mailto:yayahjb at gmail.com>>, Discussion forum for the NeXus data format <nexus at nexusformat.org<mailto:nexus at nexusformat.org>>
Cc: Tobias.Richter at diamond.ac.uk<mailto:Tobias.Richter at diamond.ac.uk>, jjakoncic at bnl.gov<mailto:jjakoncic at bnl.gov>, andreas.foerster at dectris.com<mailto:andreas.foerster at dectris.com>, rsweet at bnl.gov<mailto: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><mailto: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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