VTK ParaView tutorial

Jean M. Favre, Cscs

Description

ParaView Python InterfaceUsage on the Horus and Rigi clusters31-07-2009Dr. Jean M. FavreData Analysis and Visualization GroupParaView at CSCS paraview and pvbatch can run in a single or multi-cpusession The “standard” version called paraview, will run interactively, i.e. with a graphics OpenGL window. This is intended to do exploratory visualization, and to prepare a visualization script. ParaView should be run on horus. The “batch-oriented” tool called pvbatch, will run without user’s interaction. It can execute a hand-written python script, or reload a script generated with paraview, and save images to disk. pvbatch uses offscreen-rendering and the Mesa3D rendering library. Pvbatch should be run on rigi.Reloading a script paraview can reload a script with the command File->Load State pvbatch can reload the same script with the commandfrom paraview.simple import *servermanager.Connect()servermanager.LoadState('/users/jfavre/state.pvsm')N.B. if necessary, load your plugin before your stateState files should not be hand-edited.Reloading the coloredSphere example paraview (interactive) can reload the stateFile->Load State (select file)/apps-vis/ParaView3BatchExamples/coloredSphere.pvsmor pvbatch can execute the python script/apps-vis/ParaView3BatchExamples/coloredSphere.0.py (which itself reloads the state and writes an image)All the above was tested in serial and parallel mode with ParaView version 3.6, on horus and rigiRunning ...

Informations

• Publié par: Orra
• Nombre de lectures: 164
• Langue: English

Extrait

ParaView Python Interface Usage on the Horus and Rigi clusters

31-07-2009

Dr. Jean M. Favre

Data Analysis and Visualization Group

ParaView at CSCS

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paraview and pvbatch can run in a single or multi-cpu session

The “standard” version called p  araview , will run interactively, i.e. with a graphics OpenGL window. This is intended to do exploratory visualization, and to prepare a visualization script. ParaView should be run on horus .

The “batch-oriented” tool called pvbatch , will run without user’s interaction. It can execute a hand-written python script, or reload a script generated with paraview , and save images to disk. pvbatch uses offscreen-rendering and the Mesa3D rendering library. Pvbatch should be run on rigi .

Reloading a script

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paraview can reload a script with the command File->Load State

pvbatch can reload the same script with the command

from paraview.simple import * servermanager.Connect() servermanager.LoadState('/users/jfavre/state.pvsm')

N.B. if necessary, load your plugin before your state State files should not be hand-edited.

Reloading the coloredSphere example

 paraview (interactive) can reload the state File->Load State (select file)

or

/apps-vis/ParaView3BatchExamples/coloredSphere.pvsm

execute the  / ( p a w v p h b p i a c s t h - c   v i i t h s s / c e P l a f a   n r r e a l V o i a e d w s 3  t B h a e t   c s   h t p a E t y x e t   h a a o m n n p   l s e c s r / i c pt oloredSphere.0.py  d writes an image)

All the above was tested in serial and parallel mode with ParaView version 3.6, on horus and rigi

Running pvbatch on rigi

N.B. Because of MPI compilation, please note that we must use a different path for the rigi pvbatch executable:

/apps-csvis/Paraview3BuildMesa/bin/pvbatch 

Example to run with 4 cpus on rigi:

you will need to submit a job via the OpenPBS Pro scheduler.

See /apps-vis/Paraview3BatchExamples/coloredSphere.sh

make your own copy, edit the path to write the image, and submit as:

qsub coloredSphere.sh

Example: /apps-vis/ParaView3BatchExamples/coloredSphere.0.py

from paraview.simple import * sm = servermanager sm.Connect() sphere = Sphere() sphere.ThetaResolution = 100 sphere.PhiResolution = 100 pidscal = ProcessIdScalars(sphere) view = sm.CreateRenderView() rep = Show(pidscal, view) nbprocs = sm.ActiveConnection.GetNumberOfDataPartitions

lt = MakeBlueToRedLT(0, nbprocs-1) lt.NumberOfTableValues = nbprocs

rep.LookupTable = lt rep.ColorAttributeType = 'POINT_DATA' rep.ColorArrayName = "ProcessId"  

bar = CreateScalarBar(LookupTable=lt, Title=“PID”) view.Representations.append(bar)

view.ResetCamera() view.StillRender() view.WriteImage("/project/csvis/ParaViewTests/Sphere.0.png","vtkPNGWriter")

Problem: Run the same ParaView visualization for multiple files

While running paraview, get the python interface. Find all files

Tools-> Python Shell

import glob, string

files = glob.glob(“/scratch/user/file*.dat”) files.sort()

# Find the source object

file = FindSource(“name”)

for f in files: file.FileName = f view.StillRender()

Run the same visualization for multiple files

If your data reader is time-aware, then AnimateReader() will animate. The execution is run on-demand by the view.

Problem: it always start at the beginning and runs to the end with a fixed increment. You can change that and do your own start, end, and time increment.

tsteps = reader.TimestepValues start = 0 i = start incr = 1 while i < len(tsteps): view.ViewTime = tsteps[i] view.StillRender() imgfile = “/scratch/images/image.%03d.png” %i view.WriteImage(imgfile, “vtkPNGWriter”,1) i = i + incr

Run the same visualization for multiple files

how do we update the pipeline objects?

must find the names of the objects to be modified

view = servermanager.GetRenderView()

#assume you created a pipeline and read a file called file.000.dat #using the GUI Open menu # the object called 'file.000.dat' shows in the pipeline viewer

reader = FindSource('file.000.dat') # reader can now be updated reader.Filename = files[i] view.StillRender()

impo rfmop ra .sostr)( h5”) file (“files*.bolbolgselig =  tr sg f in grtb,lo PdulL.aogaremrnaerve t() s nnecr.Coeganamrevres * trpoimlempsiw.ieav deea : r es NaleFir.  rof 0 =i lif ni f a() v amer Stiliew. v f ei em = esCt.weR "/= erusjfs/reav neRl(red gmi ) elifical/dssf.%03d.pP/orejtc/siBMode  ,elifgmi(egamIeitWrw.ie i v % " ng 1

another example script.py with pvbatch

i  + )1 =i r", ritePNGW"vtk /'suig(nfjvare/srojere/PBioMcts/l/lacideiBZHTEbialicedoM inugPl SM s.'o r ) aeed r =osurces.BioH5(FileemaNif =[sel d )]0 = 3 ltfis.er(ID3r) ds eade = rnput aDatre.siftlfs =erltFicefaurtSSe =dip )3d = tupnI( .Process filters(snIup tdIcSlara w ieCr=  ds= ) v sf iVre)(weetaedneR

Images for cube fea s0?.mesh.h5: _ _