Jon’s Project Blog

I reviewed paraview about two years ago, and I more or less lambasted it for not being very well documented and that the mailing list was not as responsive to “beginners” questions as one might imagine. Some of the examples on the wiki also did not work back then. I have been quietly monitoring and occasionally evaluating paraview to see how it has been improving. In one of the recent versions this year, they actually released the user guide/handbook, which contains some useful information. The file reader formats have greatly improved and a lot of the features rival that of tecplot, which is not free.

While my research lab recently acquired Abaqus, all of my dissertation code is in the Finite Element Analysis Program (FEAP) from Berkeley. It was written mainly by Robert Taylor (one of the Godfathers of finite elements) and by Sanjay Govindjee. It is a pretty good code, and is written mainly in Fortran/C. Unfortunately, while it includes some sophisticated numerical schemes and efficient solvers, it does not provide much in terms of pre- and post-processing for finite elements. In the past we used Ansys to generate meshes, and manipulated the boundary conditions by hand. However, we have since then, obtained patient-specific heart meshes, and the number of nodes is much larger and the geometry/numbering is not so obvious.

Fortunately, paraview has some powerful selection filters and tools available. Unfortunately, after each selection the number of elements and nodes is renumbered. Paraview actually keeps track of the global id’s but for some reason it is filtered out from the spreadsheet view by default. However this can be changed easily. To use paraview as a pre-processor, the idea is to use successive “Extract Selection” filters after using the “Fustrum” or “Surface” selection tool for nodes/elements in the Selection Toolbar. One should think of it as taking the original mesh, and then slicing or cutting away the parts that are not of interest until you are left with only what you want. Lastly, in the selection explorer, you can also select “Invert Selection”, which effectively allows you to select the portion you want to “cut-away” from the mesh.

The following are instructions to perform this pre-processing selection using paraview.

1. If not already done, go to Preferences > Charts. Then delete the line that says “vtkOriginalIds” that is in the “hidden” list. This will show the “vtkOriginalIds” value in the spreadsheet view and allow you to “Save Data” on each “Extract Selection”, such that one will get a mapping from vtkOriginalIds to the renumbered fields.
2. Use the provided selection tools, and “Extract Selection” successively until you arrive at the selection you want.
3. Click on each “Extract Selection” filter and click on File > Save Data. Select a filename, and make sure to specify either Point/Cell/Field data so you save the proper mapping.
4. Next you can use the following python script to get the proper mapping using 0-index numbering (paraview indexing). The script takes in a list of “Extraction Selection” csv files and an outputfilename for the global id mapping.

import os,sys
 
def parse(args):
    extractions, outputfile = map(open,args[:-1]),open(args[-1],"w")
 
    ids = []
    newids = []
 
    for extraction in extractions:
        origids = []
        for line in (extraction.readlines())[1:]:
            orig= line.split(",")[0]
            origids.append(int(orig))
 
        # if ids is filled map rewrite ids accor
        if len(ids) > 0:
           for id in range(len(origids)):
               origids[id] = ids[origids[id]]
 
        ids = origids
 
    for id in ids:
        outputfile.write("%d\n" % (id))
 
    outputfile.close()      
 
if __name__=="__main__":
    parse(sys.argv[1:])

For those of you that use tecplot, you know that while the interface is fairly straightforward and the resulting visuals look pretty good, tecplot has one major flaw. The animations are generated in with essentially the MSRLE codec from a decade ago. The codec’s color palette generally cannot handle continuous color flooding  in tecplot; if you try to open it up on other machines or convert them to say flash video or mp4, you will find that the the colors are all messed up. Sometimes the frame size in tecplot causes the video to not display correctly.

So to fix this issue, I found out that the swf output actually works correctly. Modifying the previous pbox2avi script, I created a tecplot specific script to generate mpeg’s or whatever else ffmpeg can spit out. The script is pretty much a more rudimentary version of pbox2avi.py.

Requirements: swftools, ffmpeg

Download tecplot2mpeg.py.

As usual the code for the script is below:

# Copyright 2010 Jonathan Wong
# python script to convert SWF files generated from tecplot to mpeg
 
#requires swfextract
 
import commands,sys,re,math
 
def parse(filename):
#check filename for .swf extension
if not filename.find('.swf'): # not a comprehensive check
return
 
fileprefix = filename[0:filename.find('.swf')]
commands.getstatusoutput("rm %s.mpeg" % (fileprefix,))
 
#open file
status, output = commands.getstatusoutput("swfextract %s" % (filename,))
 
print output
 
#find "JPEGs: ID(s)"
slide_identifier = "PNGs: ID(s)"
start=output.find(slide_identifier)
slide_extract=[]
if start:
start += len(slide_identifier)+1
slide_end = output.find("[-f]",start)
print start,slide_end
slide_extract=output[start:slide_end-2].replace(" ","")
 
# now extract all the data
print "swfextract %s -P -p %s" % (filename,slide_extract)
 
slides = slide_extract.split(",")
digits = 1 + int(math.log10(int(slides[-1])))
 
for slide in slides:
print "Processing frame: %d" % (int(int(slide)/2)+1,)
print ("swfextract %%s -p %%s & mv output.png %s%%0%dd.png" % (fileprefix,digits,)) % (filename,slide,int(int(slide)/2)+1)
status, output = commands.getstatusoutput(("swfextract %%s -p %%s && mv output.png %s%%0%dd.png" % (fileprefix,digits,)) % (filename,slide,int(int(slide)/2)+1))
 
status, output = commands.getstatusoutput("ffmpeg -f image2 -i %s%%04d.png -b 600k %s.mpeg && rm %s*.png" % (fileprefix,fileprefix,fileprefix))
return slide_extract
 
if __name__=="__main__":
slides=parse(sys.argv[1])