Converting VTK structured grids to matrices

Tags: programming, research

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I recently had to convert several structured grids in VTK format for further processing. Since I could not find any other code for doing this, here is my quick and dirty approach:

#!/usr/bin/env python3

from PIL import Image

import numpy
import os
import re
import sys

reDimensions = re.compile( r'DIMENSIONS\s+(\d+)\s+(\d+)\s+(\d+)' )
reSpacing    = re.compile( r'SPACING\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)' )
rePointData  = re.compile( r'POINT_DATA\s+(\d+)' )
reTableData  = re.compile( r'(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)' )

for filename in sys.argv[1:]:
    with open( filename ) as f:
        width  = 0
        height = 0
        depth  = 0

        data = None # Contains matrix data
        ii   = 0    # Current data index for filling matrix

        # Stores only those coordinates (given as an x and y position)
        # that are nonzero. This permits to match adjacent time steps
        # in a very concise and sparse manner.
        nonZero = list()

        for line in f:
            if reDimensions.match(line):
                result = reDimensions.match(line)
                width  = int( )
                height = int( )
                depth  = int( )

                assert width * height * depth > 0, "Invalid dimensions"

                data = numpy.zeros( (height,width) )
            elif reSpacing.match(line):
                result = reSpacing.match(line)
                sx     =
                sy     =
                sz     =

                # TODO: I am ignoring the spacing, hence I am only
                # able to load uniform rectilinear grids.
                assert sx == sy and sy == sz, "Invalid spacing"
            elif rePointData.match(line):
                result = rePointData.match(line)
                num    = int( )

                assert num == width * height * depth, "Inconsistent dimensions"
            elif reTableData.match(line):
                result = reTableData.match(line) 
                d      = (u,v,w) = (
                                    float( ),
                                    float( ),
                                    float( )

                for k in range(0,3):
                    ix     = ii % width
                    iy     = ii // width 
                    ii     = ii + 1

                    if d[k] > 0:
                        nonZero.append( (ix,iy) )

                    data[iy][ix] = d[k]

    # TODO: `data` is now a matrix corresponding to the dimensions of
    # the original grid.Do something with it...

    # Store non-zero coordinates

    outputCoordinates = "/tmp/"\
             + os.path.splitext( os.path.basename(filename) )[0]\
             + ".txt"

    with open(outputCoordinates, "w") as g:
        for (x,y) in nonZero:
            print("%d\t%d" % (x,y), file=g)

    # Store image

    outputImage =   "/tmp/"\
             + os.path.splitext( os.path.basename(filename) )[0]\
             + ".png"

The code from above iterates over a list of VTK files (assumed to be in ASCII format) that contains POINT_DATA, i.e. a scalar value for each grid cell. Provided that the grid follows uniform spacing, the code is capable of parsing it and stores the POINT_DATA values in a numpy matrix. Moreover, the list of non-zero coordinates of the matrix is written to /tmp, along with a pixel-based image of grid. Both outputs are highly useful for debugging and understanding the input.

Feel free to do more with this code—I am hereby releasing it into the public domain.