[Paraview] XDMF Reader

David E DeMarle dave.demarle at kitware.com
Wed Sep 6 13:00:47 EDT 2017 

On Wed, Sep 6, 2017 at 12:47 PM, D Haley <mycae at gmx.com> wrote:
...

> Does paraview support CollectionType="Temporal"? [1]. If it is

important, I am using paraview 5.4.0
>
>
Yes.

Try putting the spatial collection inside the temporal one. Promote <Time=
Value="x"/> to the spatial collection.

<Xdmf>
  <Domain Name="Data">
     <Grid GridType="Collection" CollectionType="Tempoal">
       <Grid GridType="Collection" CollectionType="Spatial">
          <Time = 0>
          <Grid ... your existing temporal grid here >
       </Grid>
       <Grid GridType="Collection" CollectionType="Spatial">
          <Time = 1>
          <Grid ... your existing temporal grid here >
       </Grid>
       ...
     </Grid>
  </Domain>
</Xdmf>


>
> Thanks!
>
> [1]
> http://xdmf.org/index.php/XDMF_Model_and_Format#Uniform.
> 2C_Collection.2C_and_Tree
>
> On 06/09/17 14:18, David E DeMarle wrote:
> > Please reply-all to keep the mailing list on the thread so everyone can
> > contribute to the discussion and benefit from it.
> >
> > To make a multiblock from xdmf, enclose your grid inside of an
> > xdmfgridcollection like so:
> > <Xdmf>
> >   <Domain Name="Data">
> >      <Grid GridType="Collection" CollectionType="Spatial">
> >         <Grid ... your existing temporal grid here >
> >      </Grid>
> >   </Domain>
> > </Xdmf>
> >
> >
> > David E DeMarle
> > Kitware, Inc.
> > Principal Engineer
> > 21 Corporate Drive
> > Clifton Park, NY 12065-8662
> > Phone: 518-881-4909
> >
> > On Wed, Sep 6, 2017 at 9:05 AM, D Haley <mycae at gmx.com> wrote:
> >
> >> Hello,
> >>
> >> Thanks very much for the pointer. I'm looking around for multiblock file
> >> specifications - does such a thing exist, particularly for an XDMF+HDF5
> >> wrapper?
> >>
> >> I've found an example for .vtp [1], but I can't seem to find any
> >> specifications on what constitutes a .vtmb file. Subsequently I'm having
> >> trouble fully understanding what is and is not permitted.
> >>
> >>
> >> Thanks!
> >>
> >> [1] https://public.kitware.com/pipermail/paraview/2009-April/
> 011847.html
> >>
> >> On 06/09/17 10:44, David E DeMarle wrote:
> >>> Put the co-rect-mesh (image data) inside a grid collection
> (multiblock).
> >>>
> >>> Paraview's pipeline doesn't deal well with image data that changes
> >>> dimensions over time. This is not limited to xdmf. When inside a
> >>> multiblock, a different pipeline layer takes over and it works out.
> >>>
> >>> On Sep 6, 2017 5:09 AM, "D Haley" <mycae at gmx.com> wrote:
> >>>
> >>>>
> >>>> Dear Paraview List,
> >>>>
> >>>> I'm trying to read some HDF files, which contain dense voxel data. In
> my
> >>>> calculations, I write out the HDF and wrapper XDMF data to store
> >>>> timestep and other metadata.
> >>>>
> >>>> This all works fine, until I want to have 2 different voxel sizes at 2
> >>>> different timesteps (different number of voxels in each dimension).
> >>>>
> >>>> When loading up the data as a series of time-steps, everything works
> >>>> until I reach the first set of data from the new size. When loading
> the
> >>>> data, the values in the voxels seem to become invalid, and the
> bounding
> >>>> box around the data starts moving in the direction of (1,1,1).
> >>>>
> >>>> I can load each timestep individually correctly, it is just when I try
> >>>> to load the entire timeseries that it fails.
> >>>>
> >>>> Does anyone know a solution for this? I have raw voxel grids in the
> >>>> program that generates the data, so I need to wrap them in something
> to
> >>>> provide a timestep. I'd rather avoid having to interface with VTK, as
> >>>> the code I am working on does not have a VTK dependency - I'm just
> >>>> post-processing with paraview.
> >>>>
> >>>> I'm opening the series via:
> >>>> File->Open, then select the tree item data-..xmdf
> >>>>
> >>>> each file is written as:
> >>>>
> >>>> data-1.hdf.xmdf
> >>>> data-2.hdf.xmdf
> >>>> ....
> >>>>
> >>>> The XMDF files contain something like this
> >>>>
> >>>> Before problem timestep:
> >>>> ==========
> >>>> <?xml version="1.0" ?>
> >>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> >>>> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
> >>>> <Domain>
> >>>> <Grid Name="Data" GridType="Uniform">
> >>>> <Topology TopologyType="3DCORECTMesh" Dimensions="39 39 39"/>
> >>>> <Geometry GeometryType="ORIGIN_DXDYDZ">
> >>>> <DataItem Name="Origin" Dimensions="3" NumberType="Float"
> Precision="4"
> >>>> Format="XML">-1.26667 -1.26667 -1.26667</DataItem>
> >>>> <DataItem Name="Spacing" Dimensions="3" NumberType="Float"
> Precision="4"
> >>>> Format="XML">0.0666667 0.0666667 0.0666667</DataItem>
> >>>> </Geometry>
> >>>> <Attribute Name="second 0" AttributeType="Scalar" Center="Node">
> >>>> <DataItem Format="HDF" NumberType="Float" Precision="4" Dimensions="39
> >>>> 39 39">data-59.hdf:/voxels</DataItem></Attribute>
> >>>> </Grid>
> >>>> </Domain>
> >>>> </Xdmf>
> >>>> ==========
> >>>>
> >>>> After problem timestep:
> >>>> ==========
> >>>> <?xml version="1.0" ?>
> >>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> >>>> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
> >>>> <Domain>
> >>>> <Grid Name="Data" GridType="Uniform">
> >>>> <Topology TopologyType="3DCORECTMesh" Dimensions="31 31 31"/>
> >>>> <Geometry GeometryType="ORIGIN_DXDYDZ">
> >>>> <DataItem Name="Origin" Dimensions="3" NumberType="Float"
> Precision="4"
> >>>> Format="XML">-1 -1 -1</DataItem>
> >>>> <DataItem Name="Spacing" Dimensions="3" NumberType="Float"
> Precision="4"
> >>>> Format="XML">0.0666667 0.0666667 0.0666667</DataItem>
> >>>> </Geometry>
> >>>> <Attribute Name="second 0" AttributeType="Scalar" Center="Node">
> >>>> <DataItem Format="HDF" NumberType="Float" Precision="4" Dimensions="31
> >>>> 31 31">data-60.hdf:/voxels</DataItem></Attribute>
> >>>> </Grid>
> >>>> </Domain>
> >>>> </Xdmf>
> >>>> ==========
> >>>>
> >>>>
> >>>> Thanks!
> >>>> _______________________________________________
> >>>> Powered by www.kitware.com
> >>>>
> >>>> Visit other Kitware open-source projects at http://www.kitware.com/
> >>>> opensource/opensource.html
> >>>>
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> >>>>
> >>>
> >>
> >>
> >
>
>
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