[Paraview] XDMF Reader

Wed Sep 6 09:18:20 EDT 2017

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!
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