[Paraview] Error reading timeseries with spatial grid collection with XDMF
Nikolaos Beratlis
nikos.beratlis at gmail.com
Mon Nov 20 14:57:39 EST 2017
I tried reading them with XDMF 3 reader and it works fine.
Thank you for the suggestions.
Nikos
On Mon, Nov 20, 2017 at 2:14 PM, David E DeMarle <dave.demarle at kitware.com>
wrote:
> It might be that the reader doesn't like or want that both of your times
> are 0.0.
> ...
> <Time TimeType="Single" Value="0.0"/>
> ...
> <Time TimeType="Single" Value="0.0"/>
> ...
> but your third case doesn't fit that hypothesis.
>
> Otherwise your file looks ok at first glance. I'ld have to debug the
> reader on your data to figure out what is going wrong.
>
> David E DeMarle
> Kitware, Inc.
> Principal Engineer
> 21 Corporate Drive
> <https://maps.google.com/?q=21+Corporate+Drive+Clifton+Park,+NY+12065&entry=gmail&source=g>
> Clifton Park, NY 12065
> <https://maps.google.com/?q=21+Corporate+Drive+Clifton+Park,+NY+12065&entry=gmail&source=g>
> -8662
> Phone: 518-881-4909 <(518)%20881-4909>
>
> On Sun, Nov 12, 2017 at 11:15 PM, Joachim Pouderoux <
> joachim.pouderoux at kitware.com> wrote:
>
>> Nikos,
>>
>> It looks like you are using the Xdmf2 based reader.
>> Did you give a chance to the one based on Xdmf3?
>> What version of ParaView are you using?
>> Can you provide a full dataset we could use to reproduce the issue?
>>
>> Best,
>>
>>
>> *Joachim Pouderoux*, PhD
>>
>> *Technical Expert - Scientific Computing Team*
>> *Kitware SAS <http://www.kitware.fr>*
>>
>>
>> 2017-11-11 19:31 GMT+01:00 Nikolaos Beratlis <nikos.beratlis at gmail.com>:
>>
>>> Hi,
>>>
>>> I have a cartesian structured grid made of two sub-domains and a two
>>> snap shots in a time that I would like to read in Paraview. The data and
>>> grid files are stored in HDF5 file and I use a XDMF file to read them in a
>>> Paraview. The XDMF files looks like this:
>>>
>>> <?xml version="1.0" ?>
>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>> <Xdmf Version="2.2">
>>> <Domain Name="Bump">
>>> <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
>>>
>>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>>> <Time TimeType="Single" Value="0.0"/>
>>>
>>> <Grid GridType="Uniform" Name="GridZone0001">
>>> <Topology TopologyType="3DRectMesh" Dimensions=" 2 202 267"/>
>>> <Geometry GeometryType="VXVYVZ">
>>> <DataItem Dimensions=" 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> </DataItem>
>>> <DataItem Dimensions=" 202" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> </DataItem>
>>> <DataItem Dimensions=" 2" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> </DataItem>
>>> </Geometry>
>>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>>> <DataItem Dimensions=" 2 202 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> </DataItem>
>>> </Attribute>
>>> </Grid>
>>>
>>> <Grid GridType="Uniform" Name="GridZone0002">
>>> <Topology TopologyType="3DRectMesh" Dimensions=" 2 202 268"/>
>>> <Geometry GeometryType="VXVYVZ">
>>> <DataItem Dimensions=" 268" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>>> </DataItem>
>>> <DataItem Dimensions=" 202" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> </DataItem>
>>> <DataItem Dimensions=" 2" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>>> </DataItem>
>>> </Geometry>
>>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>>> <DataItem Dimensions=" 2 202 268" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0002
>>> </DataItem>
>>> </Attribute>
>>> </Grid>
>>> </Grid>
>>>
>>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>>> <Time TimeType="Single" Value="0.0"/>
>>>
>>> <Grid GridType="Uniform" Name="GridZone0001">
>>> <Topology TopologyType="3DRectMesh" Dimensions=" 2 202 267"/>
>>> <Geometry GeometryType="VXVYVZ">
>>> <DataItem Dimensions=" 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> </DataItem>
>>> <DataItem Dimensions=" 202" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> </DataItem>
>>> <DataItem Dimensions=" 2" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> </DataItem>
>>> </Geometry>
>>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>>> <DataItem Dimensions=" 2 202 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> </DataItem>
>>> </Attribute>
>>> </Grid>
>>>
>>> <Grid GridType="Uniform" Name="GridZone0002">
>>> <Topology TopologyType="3DRectMesh" Dimensions=" 2 202 268"/>
>>> <Geometry GeometryType="VXVYVZ">
>>> <DataItem Dimensions=" 268" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>>> </DataItem>
>>> <DataItem Dimensions=" 202" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> </DataItem>
>>> <DataItem Dimensions=" 2" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>>> </DataItem>
>>> </Geometry>
>>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>>> <DataItem Dimensions=" 2 202 268" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../Q_VPreg.h5sp.0002:/zone0002
>>> </DataItem>
>>> </Attribute>
>>> </Grid>
>>>
>>> </Grid>
>>>
>>> </Grid>
>>> </Domain>
>>> </Xdmf>
>>>
>>> The file is read in Paraview. When I advance in to the second instant in
>>> time I get the following error:
>>>
>>> Failed to read attribute data.
>>>
>>> Paraview shows data from the first subset (zone0001), it can't read the
>>> data from the second subset (zone0002).
>>>
>>>
>>> When I read only on instant in time like this:
>>>
>>> <?xml version="1.0" ?>
>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>> <Xdmf Version="2.2">
>>> <Domain Name="Bump">
>>> <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
>>>
>>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>>> <Time TimeType="Single" Value="0.0"/>
>>>
>>> <Grid GridType="Uniform" Name="GridZone0001">
>>> <Topology TopologyType="3DRectMesh" Dimensions=" 2 202 267"/>
>>> <Geometry GeometryType="VXVYVZ">
>>> <DataItem Dimensions=" 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> </DataItem>
>>> <DataItem Dimensions=" 202" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> </DataItem>
>>> <DataItem Dimensions=" 2" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> </DataItem>
>>> </Geometry>
>>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>>> <DataItem Dimensions=" 2 202 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> </DataItem>
>>> </Attribute>
>>> </Grid>
>>>
>>> <Grid GridType="Uniform" Name="GridZone0002">
>>> <Topology TopologyType="3DRectMesh" Dimensions=" 2 202 268"/>
>>> <Geometry GeometryType="VXVYVZ">
>>> <DataItem Dimensions=" 268" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>>> </DataItem>
>>> <DataItem Dimensions=" 202" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> </DataItem>
>>> <DataItem Dimensions=" 2" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>>> </DataItem>
>>> </Geometry>
>>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>>> <DataItem Dimensions=" 2 202 268" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0002
>>> </DataItem>
>>> </Attribute>
>>> </Grid>
>>> </Grid>
>>>
>>> </Grid>
>>> </Domain>
>>> </Xdmf>
>>>
>>> the file is read successfully and no errors show up.
>>>
>>> Also when I read two time instants but with only one subset (zone0001)
>>> Paraview doesn't throw any errors.
>>>
>>> <?xml version="1.0" ?>
>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>> <Xdmf Version="2.2">
>>> <Domain Name="Bump">
>>> <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
>>>
>>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>>> <Time TimeType="Single" Value="0.0"/>
>>>
>>> <Grid GridType="Uniform" Name="GridZone0001">
>>> <Topology TopologyType="3DRectMesh" Dimensions=" 2 202 267"/>
>>> <Geometry GeometryType="VXVYVZ">
>>> <DataItem Dimensions=" 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> </DataItem>
>>> <DataItem Dimensions=" 202" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> </DataItem>
>>> <DataItem Dimensions=" 2" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> </DataItem>
>>> </Geometry>
>>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>>> <DataItem Dimensions=" 2 202 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> </DataItem>
>>> </Attribute>
>>> </Grid>
>>>
>>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>>> <Time TimeType="Single" Value="0.0"/>
>>>
>>> <Grid GridType="Uniform" Name="GridZone0001">
>>> <Topology TopologyType="3DRectMesh" Dimensions=" 2 202 267"/>
>>> <Geometry GeometryType="VXVYVZ">
>>> <DataItem Dimensions=" 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> </DataItem>
>>> <DataItem Dimensions=" 202" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> </DataItem>
>>> <DataItem Dimensions=" 2" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> </DataItem>
>>> </Geometry>
>>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>>> <DataItem Dimensions=" 2 202 267" NumberType="Float" Precision="4"
>>> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> </DataItem>
>>> </Attribute>
>>> </Grid>
>>>
>>> </Grid>
>>>
>>> </Grid>
>>> </Domain>
>>> </Xdmf>
>>>
>>>
>>> Does anyone see the problem in the code?
>>>
>>> Kind regards,
>>>
>>> Nikos
>>>
>>>
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>>
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>>
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>>
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>>
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