[Paraview] Paraview Not Reading Some Fields in Dataset
Tate Fanning
t8fanning at gmail.com
Wed Jan 31 11:07:46 EST 2018
I found a solution to the problem. The CFD code was writing the offsets
incorrectly. When I adjust them manually, Paraview can read the file just
fine.
This thread goes into a little more detail:
https://www.cfd-online.com/Forums/paraview/198220-paraview-not-reading-some-fields-dataset.html
On Tue, Jan 30, 2018 at 1:24 PM, Andy Bauer <andy.bauer at kitware.com> wrote:
> It looks like you have integer overflow (https://en.wikipedia.org/
> wiki/Integer_overflow). I'd suggest using a datatype with more precision
> and see if that fixes the issue.
>
> On Tue, Jan 30, 2018 at 3:15 PM, Tate Fanning <t8fanning at gmail.com> wrote:
>
>> I've output a vtu file from a CFD code. When trying to load the dataset
>> into Paraview I get the following errors:
>>
>> [CODE]Error reading uncompressed binary data header. Read 0 of 4 bytes.
>> ERROR: In C:\bbd\7cc78367\source-paraview\VTK\IO\XMLParser\vtkXMLDataParser.cxx,
>> line 609 vtkXMLDataParser (0000009CC7674520): Error reading uncompressed
>> binary data header. Read 0 of 4 bytes.
>>
>> Cannot read point data array "Cyl_Velocity" from PointData in piece 0.
>> The data array in the element may be too short. ERROR: In
>> C:\bbd\7cc78367\source-paraview\VTK\IO\XML\vtkXMLDataReader.cxx, line
>> 443 vtkXMLUnstructuredGridReader (0000009C837CFCE0): Cannot read point data
>> array "Cyl_Velocity" from PointData in piece 0. The data array in the
>> element may be too short.[/CODE]
>>
>> If I ask Paraview to not read the offending arrays, it reads the other
>> arrays in fine. From these errors, it seems the data file has some issues
>> with a few specific arrays.
>>
>> Upon inspection of the first part of the vtu file, the offending arrays
>> (Cyl_Velocity and Rel_Velocity) have negative offsets.
>>
>> [CODE]<VTKFile type="UnstructuredGrid" version="0.1"
>> byte_order="BigEndian">
>> <UnstructuredGrid>
>> <Piece NumberOfPoints=" 9855039" NumberOfCells=" 9523296">
>> <Points>
>> <DataArray type="Float64" Name="coordinates"
>> NumberOfComponents="3" format="appended" offset=" 0" />
>> </Points>
>> <Cells>
>> <DataArray type="Int32" Name="connectivity" format="appended"
>> offset=" 236520940" />
>> <DataArray type="Int32" Name="offsets" format="appended"
>> offset=" 541266416" />
>> <DataArray type="Int32" Name="types" format="appended" offset="
>> 579359604" />
>> </Cells>
>> <PointData>
>> <DataArray type="Float64" Name="rho" format="appended" offset="
>> 617452792" />
>> <DataArray type="Float64" Name="P" format="appended" offset="
>> 696293108" />
>> <DataArray type="Float64" Name="Phi" format="appended" offset="
>> 775133424" />
>> <DataArray type="Float64" Name="TKE" format="appended" offset="
>> 853973740" />
>> <DataArray type="Float64" Name="EPS" format="appended" offset="
>> 932814056" />
>> <DataArray type="Float64" Name="mut/mul" format="appended"
>> offset=" 1011654372" />
>> <DataArray type="Float64" Name="WDist" format="appended"
>> offset=" 1090494688" />
>> <DataArray type="Float64" Name="TimeStep" format="appended"
>> offset=" 1169335004" />
>> <DataArray type="Float64" Name="T" format="appended" offset="
>> 1248175320" />
>> <DataArray type="Float64" Name="Processor" format="appended"
>> offset=" 1327015636" />
>> <DataArray type="Float64" Name="Soundspeed" format="appended"
>> offset=" 1405855952" />
>> <DataArray type="Float64" Name="Lam.Visc" format="appended"
>> offset=" 1484696268" />
>> <DataArray type="Float64" Name="Yplusw" format="appended"
>> offset=" 1563536584" />
>> <DataArray type="Float64" Name="Qdotw" format="appended"
>> offset=" 1642376900" />
>> <DataArray type="Float64" Name="vort-x" format="appended"
>> offset=" 1721217216" />
>> <DataArray type="Float64" Name="vort-y" format="appended"
>> offset=" 1800057532" />
>> <DataArray type="Float64" Name="vort-z" format="appended"
>> offset=" 1878897848" />
>> <DataArray type="Float64" Name="helicity" format="appended"
>> offset=" 1957738164" />
>> <DataArray type="Float64" Name="Velocity" NumberOfComponents="3"
>> format="appended" offset=" 2036578480 <(203)%20657-8480>" />
>> <DataArray type="Float64" Name="Cyl_Velocity"
>> NumberOfComponents="3" format="appended" offset=" -2021867876" />
>> <DataArray type="Float64" Name="Rel_Velocity"
>> NumberOfComponents="3" format="appended" offset=" -1785346936" />
>> </PointData>
>> <CellData> </CellData>[/CODE]
>>
>> The CFD code also can output data files for a specific surface. When I
>> load one of those into Paraview, it has no issues with any data array in
>> that file, and everything works fine.
>>
>> Upon inspection of the first part of a single surface vtu file with no
>> issues, no array has a negative offset.
>>
>> [CODE] <VTKFile type="UnstructuredGrid" version="0.1"
>> byte_order="BigEndian">
>> <UnstructuredGrid>
>> <Piece NumberOfPoints=" 176025" NumberOfCells=" 174528">
>> <Points>
>> <DataArray type="Float64" Name="coordinates"
>> NumberOfComponents="3" format="appended" offset=" 0" />
>> </Points>
>> <Cells>
>> <DataArray type="Int32" Name="connectivity" format="appended"
>> offset=" 4224604" />
>> <DataArray type="Int32" Name="offsets" format="appended"
>> offset=" 7017056" />
>> <DataArray type="Int32" Name="types" format="appended" offset="
>> 7715172" />
>> </Cells>
>> <PointData>
>> <DataArray type="Float64" Name="rho" format="appended" offset="
>> 8413288" />
>> <DataArray type="Float64" Name="P" format="appended" offset="
>> 9821492" />
>> <DataArray type="Float64" Name="Phi" format="appended" offset="
>> 11229696" />
>> <DataArray type="Float64" Name="TKE" format="appended" offset="
>> 12637900" />
>> <DataArray type="Float64" Name="EPS" format="appended" offset="
>> 14046104" />
>> <DataArray type="Float64" Name="mut/mul" format="appended"
>> offset=" 15454308" />
>> <DataArray type="Float64" Name="WDist" format="appended"
>> offset=" 16862512" />
>> <DataArray type="Float64" Name="TimeStep" format="appended"
>> offset=" 18270716" />
>> <DataArray type="Float64" Name="T" format="appended" offset="
>> 19678920" />
>> <DataArray type="Float64" Name="Processor" format="appended"
>> offset=" 21087124" />
>> <DataArray type="Float64" Name="Soundspeed" format="appended"
>> offset=" 22495328" />
>> <DataArray type="Float64" Name="Lam.Visc" format="appended"
>> offset=" 23903532" />
>> <DataArray type="Float64" Name="Yplusw" format="appended"
>> offset=" 25311736" />
>> <DataArray type="Float64" Name="Qdotw" format="appended"
>> offset=" 26719940" />
>> <DataArray type="Float64" Name="vort-x" format="appended"
>> offset=" 28128144" />
>> <DataArray type="Float64" Name="vort-y" format="appended"
>> offset=" 29536348" />
>> <DataArray type="Float64" Name="vort-z" format="appended"
>> offset=" 30944552" />
>> <DataArray type="Float64" Name="helicity" format="appended"
>> offset=" 32352756" />
>> <DataArray type="Float64" Name="Velocity" NumberOfComponents="3"
>> format="appended" offset=" 33760960" />
>> <DataArray type="Float64" Name="Cyl_Velocity"
>> NumberOfComponents="3" format="appended" offset=" 37985564" />
>> <DataArray type="Float64" Name="Rel_Velocity"
>> NumberOfComponents="3" format="appended" offset=" 42210168" />
>> </PointData>
>> <CellData> </CellData>[/CODE]
>>
>> So I think the offset sign is relevant to my problem, but I don't really
>> know what it means or how to fix it. Does anyone know what I can do to fix
>> my data set, or at least know what the underlying problem is?
>>
>> Thank you.
>>
>> --
>> *Tate Fanning*
>> Ph.D. Candidate
>> Turbomachinery Research Lab
>> BYU Mechanical Engineering
>> 360-953-7457 <(360)%20953-7457>
>> t8fanning at gmail.com
>>
>>
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>
--
*Tate Fanning*
Ph.D. Candidate
Turbomachinery Research Lab
BYU Mechanical Engineering
360-953-7457
t8fanning at gmail.com
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