[vtkusers] Explicit numbering of nodes for Xdmf/h5

[Andrew Parker]

Hey George,

In this instance I'm going the other way.  My application knows the
NodeLabels, but it's paraview that I need to get to understand that they
are not-contiguously implicitly numbered.  Paraview is assuming an implicit
zero-based ordering when it reads the node positions in, and I want a way
to tell it that actually these nodes have an explicit label/number, and not
to go for zero-based, but instead to use this number when relating to the
topology information.  I need to be able to write out as per my demo file
so that paraview can read it in.  I'm trying to do this in a way that means
my code does not have to renumber the nodes - this would be a problem for
me and I'd really like to avoid that.  Do you know if it would be possible
doing it the way I suggested in my previous post?  Do any of the xdmf2
developers have some thoughts/comments on this?

Cheers,
Andy


On 24 November 2013 21:24, George Zagaris <george.zagaris at kitware.com>wrote:

> I am not very familiar with xdmf/h5, so I could be way off, but couldn't
> you add a node-attribute array to your mesh (just like you add the
> velocities), which would store the "NodeLabels"? That way, the geometry
> would still be read in using the local, contiguous numbering, 0-N, but your
> application can infer the "NodeLabels", explicitly by accessing the
> node-attribute array. Does this help?
>
> Best,
> George
>
>
> On Sat, Nov 23, 2013 at 12:13 PM, Andrew Parker <
> andy.john.parker at googlemail.com> wrote:
>
>> All,
>>
>> In an effort to spark some comments I thought I'd try to provide a small
>> example for what I want to do in case my previous post (below) was unclear.
>>  Below is a valid xdmf file that paraview understands for a plane.
>>
>> <?xml version="1.0"?>
>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd">
>> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
>>   <Domain>
>>     <Grid GridType="Uniform">
>>       <Topology TopologyType="Quadrilateral" Dimensions="1">
>>         <DataItem Dimensions="1 4" NumberType="Int" Precision="8"
>> Format="XML">
>>            0 1 3 2
>> </DataItem>
>>       </Topology>
>>       <Geometry GeometryType="XYZ">
>>         <DataItem Dimensions="4 3" NumberType="Float" Precision="4"
>> Format="XML">
>>   -0.5 -0.5 0
>>   0.5 -0.5 0
>>   -0.5 0.5 0
>>   0.5 0.5 0
>> </DataItem>
>>       </Geometry>
>>     </Grid>
>>   </Domain>
>> </Xdmf>
>>
>> ---  Now, what I want to do is to allow for the fact that the nodes
>> defining this plane, may happen to be labelled 300, 20, 22, 80 instead of
>> 0->3.  The key point being that there is still only 4 nodes, not 300 in the
>> file for which I only need 4 to define the geom, but need to write out 300
>> to all for the 0-based implicit ordering.  Therefore, I'd like a section in
>> the geom part of the xmf file to qualify this numbering.  It doesn't bother
>> me if they're subsequently renumbered inside paraview/vtk, only that I
>> don't have to, as this is a simplistic version of something more
>> complicated.  So to be verbose, it should now look like:
>>
>> <?xml version="1.0"?>
>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd">
>> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
>>   <Domain>
>>     <Grid GridType="Uniform">
>>       <Topology TopologyType="Quadrilateral" Dimensions="1">
>>         <DataItem Dimensions="1 4" NumberType="Int" Precision="8"
>> Format="XML">
>>           * 300 20 22 80 *
>> </DataItem>
>>       </Topology>
>>       <Geometry GeometryType="*XYZ_Explicit*">
>>         <DataItem Dimensions="4 3" NumberType="Float" Precision="4"
>> Format="XML">
>> *   20 -0.5 -0.5 0 *
>>  *   22 0.5 -0.5 0 *
>> *   80 -0.5 0.5 0 *
>> *   300 0.5 0.5 0 *
>>  </DataItem>
>>       </Geometry>
>>     </Grid>
>>   </Domain>
>> </Xdmf>
>>
>> Can this be done, or could this be done in the future?  Am I being daft
>> and there is an easy way to do this?
>>
>> Cheers again,
>> Andy
>>
>>
>> On 22 November 2013 17:19, Andrew Parker <andy.john.parker at googlemail.com
>> > wrote:
>>
>>> All,
>>>
>>> Hopefully this is a simple question.  I'm using xdmf with h5 files to
>>> store my mesh and view via paraview.  However, due to a recent change in my
>>> code, I now want to be able to specify "NodeNumber XPosition YPosition
>>> ZPosition" as a tuple for each node/point position in the mesh (it's
>>> unstructured) so that I can explicitly number the nodes.  Currently I do
>>> something like:
>>>
>>> <Geometry Type= "X_Y_Z">
>>> <DataItem Name="VX" NumberType="Float" Dimensions="1660" Precision="8"
>>> Format="HDF">
>>> points.h5:/Mesh/Xposition/
>>> </DataItem>
>>> <DataItem Name="VY" NumberType="Float" Dimensions="1660" Precision="8"
>>> Format="HDF">
>>> points.h5:/Mesh/Yposition/
>>> </DataItem>
>>> <DataItem Name="VZ" NumberType="Float" Dimensions="1660" Precision="8"
>>> Format="HDF">
>>> points.h5:/Mesh/Zposition/
>>> </DataItem>
>>> </Geometry>
>>>
>>> But this assume that the first x, y, and z in the file are meant to be
>>> for node 0, and node 0 is referenced in the topology section.  Now what I
>>> want to do is to be able to define for each x, y, z tuple the specific node
>>> number that those positions refer to. So explicit numbering rather than
>>> implicit numbering.  Can this be done with xdmf, I assume it can?  If not a
>>> massive amount of renumbering is needed.....
>>>
>>> Any help really appreciated.
>>>
>>> Cheers,
>>> Andy
>>>
>>
>>
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