[Paraview] Assistance/Suggestion With Animating Relatively Small Datasets Over Many Timesteps

Thu Mar 22 16:56:53 EDT 2012

I would stick to the CSV file if you've got all the information you need inside it

... but instead of using a table to points filter, create your own custom filter which takes the CSV table as input, and outputs just a small polydata object which has the current positions (+scalars) encoded for the given time.

All you need to do is create a RequestData function which looks at UPDATE_TIME, and fetches the corresponding rows/columns for each planet/point for that time and adds them to the output.

For added fun, you can export a multi-block dataset, and/or have a treeview which allows you to enable/disable certain planets/points. This way you can

Reader -> ExtractPlanetFilter1 ->Render (use textureA)
                    ExtractPlanetFilter2->Render (use tectureB)

[Or other combinations with ExtractBlockFilter if you use multiblock ].

The Reader would simply subclass polydataalgorithm, but take a vtkTable as input. Couple of hours work is all you'd need and you can leave the data in its current form.

$0.02

JB

From: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org] On Behalf Of John.CTR.Mick at faa.gov
Sent: 22 March 2012 17:13
To: paraview at paraview.org
Subject: [Paraview] Assistance/Suggestion With Animating Relatively Small Datasets Over Many Timesteps

     This is my first experience posting to the ParaView Mailing List; as well as my first project I am exploring with ParaView.  I hope I am posting this question to the correct audience.

     I am attempting to create an animation of our Solar System - at an extremely high update interval - perhaps plotting the position and velocity of significant solar system bodies over 165 Earth years at
a one day interval.  Initially I thought I would be able to work with CSV files to define a dataset which includes time, positional coordinates, and velocity vectors.  While testing this approach I managed to use the TableToPoints filter to create a visualization of a sample dataset; but I was not able to sequence over the individual timesteps.  So in effect you see all the positions a particular planet was at for the entire duration of the dataset.

I created a video of this test and made it available online:
     http://www.youtube.com/watch?v=XLPxx-2Zc9Q

     Next I thought perhaps the CSV format was a little too general for what I needed, so I read the VTK file format document and migrated over to the XML VTK format.  It seems like there is no way to define time sequenced data natively within the file format itself?  ParaView expects the user to break the timesteps into individual files - with a numeric indicator in the filename to define the sequence.  If I were to take this approach, I could be looking at creating nearly 500,000 individual files to represent the entire duration of time I'm interested in plotting.  I feel like there must be a better way to do this.

     As a small improvement I thought I could at least combine all of the unique solar system bodies (Earth, Sun, etc.), into a single timestep file such as this:
          (filename: timeseries_2455562.vtu)

<?xml version="1.0"?>
<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" compressor="vtkZLibDataCompressor">
  <UnstructuredGrid>
    <Piece NumberOfPoints="2" NumberOfCells="2">
      <PointData Vectors="Velocity" Scalars="Radius">
        <DataArray Name="Time" type="Float32" format="ascii">2455562 2455562</DataArray>
        <DataArray Name="Radius" type="Float32" format="ascii">6371 696000</DataArray>
        <DataArray Name="Velocity" type="Float32" NumberOfComponents="3" format="ascii">
          -2.982651603443954E+01 -5.304542013817379E+00 -7.226846229160870E-04
          0 0 0
        </DataArray>
      </PointData>
      <Points>
        <DataArray type="Float32" NumberOfComponents="3" format="ascii">
          -2.567030301930377E+07 1.448508985971261E+08 -3.607762965630511E+03
          0 0 0
        </DataArray>
      </Points>
      <Cells>
        <DataArray Name="connectivity" type="Int32" format="ascii">0 1</DataArray>
        <DataArray Name="offsets" type="Int32" format="ascii">1 2</DataArray>
        <DataArray Name="types" type="UInt8" format="ascii">1 1</DataArray>
      </Cells>
    </Piece>
  </UnstructuredGrid>
</VTKFile>

The idea of this approach was to list all of the scalars and vectors for each corresponding body in a single file.  In this example the first listed scalar, vector, or coordinate point, is the Earth while the second set of values indicates the Sun's data.  By combining the bodies into a single file I could reduce the 500,000 files required down to some 60,000 files....still undesirable but better.

However I would also like to segment the Points once inside the ParaView environment; so I can create a distinct pipeline for each body in the dataset.  One application for this would be to allow different Glyph rendering rules for the Sun and the Earth so I can make the Sun...have a Sun texture - and the Earth an Earth texture.

After experimenting with this for awhile I found myself trying to implement a Programmable Filter.  The filter would take the Unstructured Grid for the given timestep, and given an index, extract the Point, Scalar, and Vector data from its input - then set only those values to the Output Unstructured Grid.  I currently have a script that looks something like this:

# CELLID 0 = EARTH
cellId = 0

# Obtain References To Input/Output Data
gridI = self.GetUnstructuredGridInput()
gridO = self.GetUnstructuredGridOutput()
dataI = self.GetInput()
dataO = self.GetOutput()
scalarI = dataI.GetPointData().GetScalars()
vectorI = dataI.GetPointData().GetVectors()

# Initialize Local Storage Arrays
newVector = vtk.vtkFloatArray()
newVector.SetName(vectorI.GetName())
newVector.SetNumberOfComponents(3)
newScalar = vtk.vtkFloatArray()
newScalar.SetName(scalarI.GetName())
newPoint = vtk.vtkPoints()
newPoint.SetNumberOfPoints(1)
newCell = vtk.vtkCellArray()

# Lookup CellId References
idCell = gridI.GetCell(cellId)
idCellType = gridI.GetCellType(cellId)
idPoint = gridI.GetPoints().GetPoint(cellId)
idScalar = scalarI.GetTuple(cellId)
idVector = vectorI.GetTuple(cellId)

# Populate New Local Cell Array with CellId Cell
newCell.InsertNextCell(idCell)

# Populate New Local Point Array With CellId Point
newPoint.SetPoint(0, idPoint)

# Populate New Local Scalars with CellId Scalar Tuples
newScalar.InsertNextTuple(idScalar)

# Populate New Local Vectors with CellID Vector Tuples
newVector.InsertNextTuple(idVector)

# Copy Local Cells, Scalars, Vectors, and Points Into Output Pipeline Data
gridO.SetPoints(newPoint)
gridO.SetCells(idCellType, newCell)
dataO.GetPointData().SetScalars(newScalar)
dataO.GetPointData().SetVectors(newVector)

The filter does achieve the desired effect for the cellID 0 - but when I switch the value of cellID to 1 (which should refer to the Sun's index) ParaView crashes hard - where I assume I am missing something, possibly requesting something out of bounds in memory.

I've been struggling with this problem for a little while now and thought to share my progress here; hopefully there is somebody out there with a little more insight that could help guide me towards either a conclusion with this implementation or a suggestion for a better approach.

Essentially - How can one give ParaView Point and Velocity vectors over a vast sequence of time without creating potentially hundreds of thousands of files on disc?  Does this Programmable Filter seem like a reasonable approach?  Is there a native feature I am missing that does this already?  Is there some other file format other than VTK I could use to have ParaView understand this format of data?

Any thoughts, comments, or questions will be greatly appreciated.  :)

Thanks,
     John
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