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]orOut[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
printfunction in iPython when showing something. But when you write a Python program, you needprintto display.
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 byIn [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]: 1108LPlease 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:
No comments:
Post a Comment