Introduction to Python and VTK

Transcription

1 Introduction to Python and VTK Scientific Visualization, HT 2013 Lecture 2 Johan Nysjö Centre for Image analysis Swedish University of Agricultural Sciences Uppsala University

2 2 About me PhD student in Computerized Image Analysis (since 2011) Developing methods and tools for interactive analysis of medical 3D (volume) images Research interests include image analysis, visualization, computer graphics, haptics, and GPGPU programming

3 3 Python (TBD)

4 4 What I use Python for Medical image analysis Graphics programming (PyOpenGL) Scientific visualization (VTK) GPGPU programming (PyOpenCL) High-performance computing (NumPy and SciPy) Scripting experiments for my PhD research Plotting things (Matplotlib)

5 5 VTK

6 6 VTK Open source, freely available C++ toolkit for visualization 3D computer graphics image processing (often combined with ITK) Managed by Kitware Inc. Object-oriented design High level of abstraction (compared to, e.g., OpenGL) Bindings/wrappers to Tcl/Tk, Python, and Java

7 Some examples of what you can do with VTK Creating visualizations of scalar, vector, and tensor fields volume data (e.g., 3D CT or MRI scans) Mesh and polygon processing Image analysis (2D and 3D images) Isosurface extraction Implementing your own algorithms 7

8 8 And more Surface rendering Volume rendering Ray casting Texture mapping (slice based) Lights and cameras Textures Save render window to.png,.jpg, (useful for creating short movies)

9 9 Volume rendering

10 Rendering graphical 3D models (imported from.stl,.ply,.obj, etc) Flat shading 10

11 11 Lighting and shading Source:

12 VTK is heavily object-oriented (and a bit over-designed...) 12

13 13 Rendering performance VTK has decent rendering performance and is good for rapid prototyping of 3D visualizations and applications but is not as optimized for rendering large complex 3D scenes (i.e., scenes with millions of polygons and dynamic content) as, e.g., dedicated game engines or scene-graph APIs Also, VTK does not support more advanced (per-pixel) lighting models out of the box

14 14 The visualization pipeline To visualize your data in VTK, you normally set up a pipeline like this: source/reader filter mapper actor renderer renderwindow interactor

15 15 Sources VTK provides various source classes that can be used to construct simple geometric objects like spheres, cubes, cones, cylinders, etc... Examples: vtkspheresource, vtkcubesource, vtkconesource, source/reader filter mapper actor renderer renderwindow interactor

16 16 Readers Reader classes reads data from file You can, e.g., use the vtkstructuredpointsreader to read volumetric image data or use the vtkstlreader to read a 3D model (polygon mesh) from a.stl file source/reader filter mapper actor renderer renderwindow interactor

17 17 Filters Filters a VTK classes that receive data, modify it in some way, and return the modified data as output to be used in the next step in the pipeline For instance, you can use filters to select data of a particular size, strength, intensity, etc You can also use filters to, e.g, process polygon meshes source/reader filter mapper actor renderer renderwindow interactor

18 18 Mappers vtkmapper is an abstract class to specify interface between data and graphics primitives Subclasses of vtkmapper map data through a lookup table and control the creation of rendering primitives that interface to the graphics library The mapping can be controlled by supplying a lookup table and specifying a scalar range to map data through vtkpolydatamapper is a class that maps polygonal data (vtkpolydata) to graphics primitives vtkpolydatamapper serves as a superclass for device-specific polydata mappers that do the actual mapping

19 19 Actors vtkactor is used to represent an entity in a rendering scene It inherits functions related to the actor's position and orientation from vtkprop The actor also has scaling and maintains a reference to the defining geometry (i.e., the mapper), rendering properties, and possibly a texture map source/reader filter mapper actor renderer renderwindow interactor

20 20 Renderer Rendering is the process of converting graphics primitives (points, lines, triangles, etc), a specification for lights, and a camera view into an 2D image that can be displayed on the screen The vtkrenderer class control the rendering process for actors and scenes VTK uses OpenGL for rendering source/reader filter mapper actor renderer renderwindow interactor

21 21 Render window The vtkrenderwindow class creates a window for renderers to draw into source/reader filter mapper actor renderer renderwindow interactor

22 22 Interactors The vtkrenderwindowinteractor class provides platform-independent window interaction via the mouse or keyboard Allows you to select (or, in computer graphics speak, pick) actors, rotate/zoom/pan the camera, etc Also handles time events source/reader filter mapper actor renderer renderwindow interactor

23 Example 1: A simple 3D scene 23

24 24 Pipeline for the cube example

25 25 Source code cube.py Included in the.zip file containing the source code and datasets for Assignment 1 You can download it from the course webpage on Studentportalen

26 Example 2: Earthquake data 26

27 Visualizing the quakes with sphere glyphs 27

28 28 Sphere glyphs Strength Position

29 29 Colormaps

30 30 Colormaps

31 31 Colormaps

32 Example 2: Air currents 32

33 33 Arrow glyphs, first try

34 34 Arrow glyphs, first try Direction and speed

35 35 Cut planes

36 36 Cut planes Direction and speed

37 37 Arrow glyphs, second try

38 38 Arrow glyphs, second try Direction and speed

39 39 Streamtubes

40 40 Streamtubes Direction and speed Seeds (starting points)

41 Example 3: Medical 3D data 41

42 42 Outline

43 43 Outline Volume image

44 44 Multi-planar reformatting (MPR)

45 45 Multi-planar reformatting (MPR) Volume image

46 46 Surface rendering

47 47 Surface rendering Segmented volume image

48 48 Combined visualization

49 49 Conclusions VTK contains thousands of classes and might seem a bit intimidating at first... The pipeline is typically however, one can create useful visualizations with just a few of them source/reader filter mapper actor renderer renderwindow interactor Use VTK's example programs as templates when you write new programs!

50 50 Resources

51 51 More resources Anders has created a couple of nice VTK tutorials. You can find a link to them on the course webpage in Studentportalen. You will find these tutorials very useful when solving the assignments. Maybe too useful... but don't worry, I was kind enough to add some extra work into the assignments this year so you should be kept busy :-)

52 52 About the assignments There will be two assignments and one project The lab sessions will be in PC-lab 1312 and 1313 We encourage you to work in groups of 2 You are supposed to present your solutions to us (Johan and Anders) during the lab session (or at the next lab session). You don't have to hand in the code. VTK will be installed on the lab PCs (we are currently upgrading it) but I highly recommend you to install Python and VTK on your own computers

53 53 Installing VTK on Linux Normally included in the package repository. For instance, on Ubuntu you can install VTK and the Python-wrapper by just typing sudo apt-get install libvtk5-dev python-vtk Also fairly easy to build VTK from scratch. You need GCC, CMake, + some extra dependencies Finally, you can install VTK via the Python distributions EPD (which recently changed name to Enthought Canopy) and Anaconda (see next slide)

54 54 Installing VTK on Windows Don't bother compiling it yourself (unless you have plenty of time to spare) Install it via one of the following Python distributions: Enthought Python Distribution (EPD). You can apply for a free academic license here Anaconda (VTK is available in the package repository) pythonxy (Warning! will override existing Python installations) I will add more detailed installation instructions on Studentportalen

55 55 Installing VTK on Mac Install it via EPD or Anaconda (see previous slide). Previously, VTK was not included in the 64-bit Mac version of EPD (might have changed), so you might have to go for the 32-bit version Expect to spend some long hours in front of the compiler if you try to build it yourself...

56 56 See you on the first lab on Monday!