Question

I have a 3D datastructure in C code that I want to visualize as boxes and points in 3D space. So I have a bunch of coordinates, some for points and some for boxes and I want to plot these in 3D to visualize the data structure. Anyone have experience doing anything similar to this? I started trying to use paraview. My plan being to generate a paraview statefile (xml-type file) and then just open it with paraview. The problem is those state files are massive and complex. To try and figure out the xml structure I was creating Boxes and Point sources in paraview and then looking at the state files it generated. It looks awful.

I just want to be able to say display a box with these coordinates and a point with these coordinates in a minimalistic way. Anyone have any ideas? Doesn’t have to be in C or paraview necessarily as I can output the coordinates and input in whatever to generate the final product. Python + Matlab would work just as well if it works.

Answer 1

So I figured out a nice compromise. I started with the git code as described here:

http://www.shocksolution.com/microfluidics-and-biotechnology/visualization/python-vtk-paraview/

It’s only one python file. The gist is the code there lets you give x,y,z positions and radius for points and outputs an XML file that is in VTK format. So to do the particles I just hand it the x,y,z positions and then a constant for the radius for all particles. Then I just make a spherical glyph on the datasets.

For the boxes I use the exact same code. For each box I still output x,y,z coordinates where the x,y,z values are the coordinates of the center of the box. Then for the “radius” parameter I use the edge length of the cube. This works because again in paraview I just glyph the datapoints for the boxes. I use the box glyph, and scale by scalar where the scalar is the radius. If you don’t orient the box glyphs and set the scalar factor to 1 you get the desired result. Here’s a simple example with everything uniform:

So I just output the coordinates in my C datastructure to CSV files and then in python pull in the files and use the code at the link and open the result with paraview. Here’s how I used the code at the link:

from vtktools import VTK_XML_Serial_Unstructured
import sys

if len(sys.argv) > 2:
    treeFile = sys.argv[1]
    bodyFile = sys.argv[2]
else:
    print 'No input files'
    exit(4)

x = []
y = []
z = []
r = []

f = open(treeFile, 'r')
for line in f:
    v = line.split(',')
    x.append(float(v[0].strip()))
    y.append(float(v[1].strip()))
    z.append(float(v[2].strip()))
    r.append(float(v[3].strip()))
f.close()

temp = treeFile.split('/')
if (len(temp) == 1):
    temp = temp[0]
else:
    temp = temp[-1]
tree_writer = VTK_XML_Serial_Unstructured()
tree_writer.snapshot(temp.split('.',1)[0] + '.vtu', x, y, z, [], [], [], [], [], [], r)
tree_writer.writePVD("octree.pvd")
x = []
y = []
z = []
r = []

f = open(bodyFile, 'r')
for line in f:
    v = line.split(',')
    x.append(float(v[0].strip()))
    y.append(float(v[1].strip()))
    z.append(float(v[2].strip()))
    r.append(float(v[3].strip()))
f.close()

temp = bodyFile.split('/')
if (len(temp) == 1):
    temp = temp[0]
else:
    temp = temp[-1]
body_writer = VTK_XML_Serial_Unstructured()
body_writer.snapshot(temp.split('.',1)[0] + '.vtu', x, y, z, [], [], [], [], [], [], r)
body_writer.writePVD("distribution.pvd")