Reading a .vtk file with python

问题

I've been given a legacy format vtk file (I think its an unstructured grid) and I'd like to read it in with python and output a .npy file instead, since I know how to deal with that.

The file is a dump from ATHENA and so has density, velocity, magnetic field along with the coordinates.

I'm very much a procedural programmer, so all these objects are confusing...

回答1:

Here is the solution that I came up with, the trick was turning on ReadAllVectorsOn().

import numpy
from vtk import vtkStructuredPointsReader
from vtk.util import numpy_support as VN

reader = vtkStructuredPointsReader()
reader.SetFileName(filename)
reader.ReadAllVectorsOn()
reader.ReadAllScalarsOn()
reader.Update()

data = reader.GetOutput()

dim = data.GetDimensions()
vec = list(dim)
vec = [i-1 for i in dim]
vec.append(3)

u = VN.vtk_to_numpy(data.GetCellData().GetArray('velocity'))
b = VN.vtk_to_numpy(data.GetCellData().GetArray('cell_centered_B'))

u = u.reshape(vec,order='F')
b = b.reshape(vec,order='F')

x = zeros(data.GetNumberOfPoints())
y = zeros(data.GetNumberOfPoints())
z = zeros(data.GetNumberOfPoints())

for i in range(data.GetNumberOfPoints()):
        x[i],y[i],z[i] = data.GetPoint(i)

x = x.reshape(dim,order='F')
y = y.reshape(dim,order='F')
z = z.reshape(dim,order='F')

回答2:

meshio (a project of mine) knows the VTK format, so you could simply

pip install meshio

and then

import meshio
mesh = meshio.read('file.vtk')
# mesh.points, mesh.cells, ...

回答3:

Here's a script that reads polygon data into numpy arrays from a VTK file using the VTK Python SDK:

import sys

import numpy
import vtk

reader = vtk.vtkPolyDataReader()
reader.SetFileName(sys.argv[1])
reader.Update()

polydata = reader.GetOutput()

for i in range(polydata.GetNumberOfCells()):
   pts = polydata.GetCell(i).GetPoints()    
   np_pts = numpy.array([pts.GetPoint(i) for i in range(pts.GetNumberOfPoints())])
   print np_pts

回答4:

Have you tried using paraview? (http://www.paraview.org/) It can give you a visual idea of what is going on behind the scenes and can output the file in a number of different ways. I would suggest this as I don't have a clue what your data is like. http://www.vtk.org/Wiki/VTK/Examples/Python may also have an example that may fit the bill for you. Personally, I'd have a play with paraview and go from there.

回答5:

It should be mentioned that in its latest release, the yt project http://yt-project.org/ includes support for ATHENA, meaning that by all means this is way to analyze the simulation data using python.

回答6:

Here's a short snippet for reading points from legacy VTK files:

import numpy as np
import vtk

filename = 'model.vtk'

reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(filename)
reader.Update()

points = np.array( reader.GetOutput().GetPoints().GetData() )

The variable points is an (N,2) or (N,3) array, where N is the number of points.

来源：https://stackoverflow.com/questions/11727822/reading-a-vtk-file-with-python

标签

python

vtk