Reading VTK files in Python via python-vtk

by Forrest Sheng Bao http://fsbao.net

Update 2012-06-29: I just figured out a way to access polygons/cell using VTK's python binding. Check here: http://forrestbao.blogspot.com/2012/06/vtk-polygons-and-other-cells-as.html

Surprisingly, I noticed that there isn't a good document covering frequently-used functions of the Python module vtk (provided via python-vtk on Debian/Ubuntu Linux systems). So I decide to write a very simple one here, covering all functions that I have used.

Note:
  • This tutorial is for Python 2.X though slight changes can make it work with Python 3.X.
  • I assume you are familiar with VTK data format, thus you know what header, DATASET and POINT_DATA are.
  • Notations like In [123] or Out[123] are prompts in iPython (an interactive Python shell). They show a line of code and its output/effect, respectively. They should NOT appear in your code. And, when you use other Python interpreter/shell, you may not see it.
  • I did not use print function in iPython when showing something. But when you write a Python program, you need print to display.
Step 1: Set up the reader.
import vtk
reader = vtk.vtkDataSetReader()
reader.SetFileName("lh.sulc.fundi.from.pits.pial.vtk")
reader.ReadAllScalarsOn()  # Activate the reading of all scalars
reader.Update()

The reader is the top level object we use to access a VTK file. For example, you can know the header of a VTK file by
In [119]: reader.GetHeader()
Out[119]: 'Created by Mindboggle'

Step 2: Get data in DATASET block.

Again, reader is the top level. To get data in DATASET block, we need to call a method on reader.
data=reader.GetOutput()

We can know how many (not ``much'' here) data of each type are in the DATASET by the function GetNumberOf{VTK_Data_Type}(). For example, to know how may Points are there, we use:
In [11]: data.GetNumberOfPoints()
Out[11]: 128895

I used tab-completion function of iPython to find out all GetNumberOf{VTK_Data_Type}() for data:
data.GetNumberOfCells   data.GetNumberOfPolys
data.GetNumberOfLines   data.GetNumberOfStrips
data.GetNumberOfPieces  data.GetNumberOfVerts
data.GetNumberOfPoints  

After knowing the size of data of each type, we can access them. For example, to get the first point's coordinate, we can do this:
In [136]: data.GetPoint(0)
Out[136]: (-11.605026245117188, -97.47259521484375, 3.8222298622131348)

To access vertexes in the VERTICES block, it is a little different.
In [15]: data.GetNumberOfVerts()
Out[15]: 1L
In [18]: vt = data.GetVerts()
In [20]: vt.GetSize()
Out[20]: 56094L
In [23]: vt.GetData().GetValue(2)
Out[23]: 1091L
In [24]: vt.GetData().GetValue(3)
Out[24]: 1108L
Please note that some people, like myself, prefer to put all vertexes in one line, so the result of data.GetNumberOfVerts() and data.GetVerts().GetSize() look different. But it shouldn't bother you from using data.GetVerts().GetData().GetValue(x) to access them.

Step 3: get data in POINT_DATA/CELL_DATA block.

Data in POINT_DATA and CELL_DATA can be loaded via function GetPointData() and GetCellData(). For example,
d=data.GetPointData()

We will use loading a scalar array from POINT_DATA as an example below.
Vectors and tensors can be accessed in similar way by different functions.

All scalar arrays in a file can be viewed by:
In [140]: reader.GetNumberOfScalarsInFile() # get number of scalars
Out[140]: 5
In [141]: reader.GetScalarsNameInFile(1) # get scalar name string
Out[140]: curv

A scalar can be accessed by its name:
In [38]: array=d.GetArray('curv') # 'curv' is the scalar name
In [50]: array.GetValue(260957-260761+1)
Out[50]: 0.043181419372558594

In the end, you should see the following variables:
Variable   Type         Data/Info
---------------------------------
curv       vtkobject    vtkFloatArray (0x9e5cd38)<...>)\n  Array: 0x9f1a9a0\n\n
d          vtkobject    vtkPointData (0x9789b50)\<...>  PedigreeIds: (none)\n\n
data       vtkobject    vtkPolyData (0x9e6c650)\n<...>: 0\n  Ghost Level: 0\n\n
reader     vtkobject    vtkDataSetReader (0x9c431<...> InputStringLength: 0\n\n
vtk        module       < module 'vtk' from '/usr/<...>hon2.6/vtk/__init__.pyc'>

The end. Comments and questions are welcomed.

References:

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