[Paraview] Assistance/Suggestion With Animating Relatively Small Datasets Over Many Timesteps
John.CTR.Mick at faa.gov
John.CTR.Mick at faa.gov
Thu Apr 12 09:10:01 EDT 2012
Samuel,
I just wanted to thank you for your advice! I am now in a situation
where I have migrated to using the EnSight File Format and am successfully
animating planetary trajectories in our solar system within the ParaView
environment. I would highly recommend the EnSight Gold File Format for
anybody in a similar situation, such as:
- Looking to animate scalars, vectors, and/or geometry over an
extremely long period of time
- In a situation where a file format still needs to be determined
- Desires keeping the number of files on disk to a minimum
If interested I'd be happy to share some of the simulations I have managed
to get out of ParaView.
Thank you again Samuel, the EnSight file format recommendation was a huge
assistance to my efforts! :)
-John
From:
Samuel Key <samuelkey at bresnan.net>
To:
John CTR Mick/ACT/CNTR/FAA at FAA
Date:
03/22/2012 04:47 PM
Subject:
Re: [Paraview] Assistance/Suggestion With Animating Relatively Small
Datasets Over Many Timesteps
John,
Try this document, attached
Use EnSight 'Gold' format; start on page 3 of the *.pdf file
Included is the EnSight file-format checker program; it does not check the
data just the file structure. Can be very helpful for quickly finding
something you missed in the file's format structure.
Included is the file 'resultsesg.f' that is my Fortran90/95 subroutine
(plus functions) for writing EnSight-formatted results. It is more
complicated than what you need but uses the EnSight's 'part' construct.
Start at line 955. (The coding before this is to write a time = 0.0 mesh
file for checking my program's input data with ParaView.)
Note that CBUFFER is always 80 characters no matter what you want to put
in the results file including a 'blank,' that is, nothing. The EnSight
reader expects an 80-character record at that position.
Regards,
Sam Key
On 3/22/2012 2:01 PM, John.CTR.Mick at faa.gov wrote:
Samuel,
Ah yes - I was hoping that another file format could make this
process much easier. I started looking a little at the file you provided
me - though I don't have much time at the moment to dig too deeply into
this - I wanted to send a quick thank-you for your response. The storage
schema presented by EnSight seems like it will dramatically reduce the
number of files, and storage requirements.
In your reply you mentioned attaching a "copy of the EnSight format
document". I did not see this in the e-mail, though I did find this:
http://www-vis.lbl.gov/NERSC/Software/ensight/doc/OnlineHelp/UM-C11.pdf
Is this the correct format document I should be referring to? If so - do
you recommend a particular casefile format to examine? This document
appears to cover several: EnSight Gold, EnSight6, and EnSight5.
My next step will be to decipher this format enough to create a
dataset that represents an unstructured grid of coordinate X,Y,Z points
with each point having a distinct velocity vector over my time span. If
you happen to have a concise example of one of referenced 'VARIABLE' files
- such as 'fmaego.data.nvel' - I believe that would help me greatly in
decoding the format quicker. Otherwise no worries, I already feel like
this is a much more tangible approach and appreciate the help you have
already offered!
Thank You Again,
John
From:
Samuel Key <samuelkey at bresnan.net>
To:
John CTR Mick/ACT/CNTR/FAA at FAA
Cc:
paraview at paraview.org
Date:
03/22/2012 02:06 PM
Subject:
Re: [Paraview] Assistance/Suggestion With Animating Relatively Small
Datasets Over Many Timesteps
John,
You might try the EnSight reader in ParaView. (I have used this format for
many multiple-part models with a common time history.) It takes a little
time to decipher the EnSight format but once you get it to work, it is
very easy after that. The primary concept to keep in mind is that each
part is an independently displayable graphics object. Each datum item
(scalar or vector values assigned to cells and points) is kept in a
separate file that contains all time steps. This storage scheme really
cuts down on the number of files.
Using the EnSight-format's part construct, you can use the Extract Block
filter to create a pipeline for each object, that is, do different
graphics operations on each part independently.
I have attached a typical EnSight 'case' file and a copy of the EnSight
format document. Using EnSight-formatted input gives in my opinion, easy
access to a wide selection of very useful filters.
Enjoy
On 3/22/2012 11:02 AM, John.CTR.Mick at faa.gov wrote:
First, thank you for the quick response I appreciate the input.
I took at look at the state file you provided, and my first thoughts are
suggesting that the Transform Filter may not provide exactly what I need.
In your example you are using the Animation Control to interpolate
parameters of the Transform Filter over time. However I don't believe
that any of the functions exposed
by the Transform filter will help me actually remove Points along with the
data in their associated Data Arrays.
In terms of viewing the "Information" tab in the Object Inspector - I have
a Dataset which has 2 Points, Several Arrays of Length 2 - and I would
like to create multiple filters; each
which would contain only 1 Point with Data Arrays of size 1.
Would it be helpful if I provided a state file with my test datasets?
From:
"Deij, Menno" <M.Deij at marin.nl>
To:
John CTR Mick/ACT/CNTR/FAA at FAA, "paraview at paraview.org"
<paraview at paraview.org>
Date:
03/22/2012 12:39 PM
Subject:
RE: [Paraview] Assistance/Suggestion With Animating Relatively Small
Datasets Over Many Timesteps
How about using a Transform Filter, possibly using scripting? Not sure if
that works with timesteps, but I suppose it can be done.
I made the following example for someone on the list recently, that shows
animation of a transformfilter:
http://markmail.org/download.xqy?id=wjep757breylvtao&number=1 (downloads a
state file)
dr. ir. Menno A. Deij
Software Engineer
Maritime Simulation Group
MARIN
2, Haagsteeg
E M.Deij at marin.nl
P.O. Box 28
T +31 317 49 39 11
6700 AA Wageningen
T +31 317 49 35 06
The Netherlands
I www.marin.nl
MARIN news: Exploratory study on the working principles of Energy Saving
Devices
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From: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org]
On Behalf Of John.CTR.Mick at faa.gov
Sent: Thursday, March 22, 2012 5:13 PM
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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