[Paraview] Using JOIN to load images from Many HDF files.

[John Hammonds]

Marcus,

The HDF data that I am working with is currently collected using the 
NeXus data format (http://www.nexusformat.org/).  Some of the data that 
is collected has all of the data in one big file and others have the 
data in separate files.  For the case that all of the data is in one big 
file, XDMF actually works pretty smoothly once you get over the initial 
hurdles.  For the case that the data is in different files, I had the 
issues that I described.  Note that I have also looked the last couple 
of days on loading Tiff images (for another beamline here 
www.aps.anl.gov) using Binary instead of HDF. This went pretty smoothly 
except that the XDMF pages do not mention that you can use Short as the 
NumberType for 16 bit data. Eventually I tried it and it fixed my 
loading issues.

Note that we also have some Tomography beamlines here.  Their data is 
captured in a similar but different HDF format (can't see to find the 
link at the moment).

John
On 7/11/2014 2:42 PM, Marcus D. Hanwell wrote:
> On Fri, Jul 11, 2014 at 10:51 AM, John Hammonds <JPHammonds at anl.gov> wrote:
>> I tried posting this to the XDMF mailing list and have received no response.
>> Hoping someone here can help...
>>
>> I have a number of images(a few hundred) , each collected in an individual
>> HDF file, that I am trying to read into Paraview using a XDMF file.  I have
>> found that I can use JOIN to do this but it seems that I need to nest the
>> JOINs.  The nesting seems to be due to some limit on the number of things
>> that can be referenced in the JOIN.  I seem to be limited to ten items in
>> the join list.  All of this has me building some odd Join files due to the
>> way things are joined at each level.  I am wondering if I am missing
>> something that would make this a lot simpler.  Esp since I seem to have
>> trouble when large sets are not the same size.  I am including a working
>> XDMF file an example of one of the HDF files for reference.
>>
> How is your data produced? We are developing a custom ParaView
> application, and as part of that we are adding some new readers to VTK
> to support S/TEM tomography using an HDF5-based format. The spec is
> here,
>
> http://emdatasets.lbl.gov/spec/
>
> It would be great to understand your needs, and whether some of this
> development work could be tweaked in order to address a wider range of
> experimental data that might help your user community. If XDMF is one
> path, then we should also look more closely at supporting that too.
>
> Thanks,
>
> Marcus

-- 
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John Hammonds
Software Services Group
Advanced Photon Source
Argonne National Laboratory
JPHammonds at anl.gov