[Paraview] XDMF Reader

Wed Sep 6 12:47:35 EDT 2017

Dear David,

Thanks very much for the help - this does indeed work if I use a spatial
grid collectiontype.

However if I change this to a temporal type (whether or not I include
<Time Value="x" /> in each sub-grid), then I do not end up with a
frame-by-frame animation, as I was hoping for. I simply end up with the
first grid shown, and the rest do not contain any data - there is only
one frame shown globally.

Does paraview support CollectionType="Temporal"? [1]. If it is
important, I am using paraview 5.4.0

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
>>>>
>>>> Please keep messages on-topic and check the ParaView Wiki at:
>>>> http://paraview.org/Wiki/ParaView
>>>>
>>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/paraview
>>>>
>>>
>>
>>
> 