3D Data visualization with Mayavi

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1 3D Data visualization with Mayavi Prabhu Ramachandran Department of Aerospace Engineering IIT Bombay SciPy.in 2012, December 27, IIT Bombay. Prabhu Ramachandran (IIT Bombay) Mayavi2 tutorial 1 / 53

2 In memory of John Hunter,

3 Kenneth Gonsalves,

4 and Raj Mathur.

5 Objectives At the end of this session you will be able to: 1 Use mlab effectively to visualize numpy array data of various kinds 2 Apply some of mayavi s advanced features

6 Outline 1 Quick introduction to Mayavi 2 mlab Prabhu Ramachandran (IIT Bombay) Mayavi2 tutorial 6 / 53

7 Outline 1 Quick introduction to Mayavi 2 mlab Prabhu Ramachandran (IIT Bombay) Mayavi2 tutorial 7 / 53

8 Overview of features

10 Live in your dialogs

11 Mayavi in applications

12 Exploring the documentation

13 Other features Easy customization Offscreen animations Automatic script generation Powerful command line options

14 Summary mayavi Uses VTK ( BSD license Linux, win32 and Mac OS X Highly scriptable Embed in Traits UIs (wxpython and PyQt4) Envisage Plugins Debian/Ubuntu/Fedora Pythonic 5

org) BSD license Linux, win32 and Mac OS X Highly

15 Outline 1 Quick introduction to Mayavi 2 mlab Prabhu Ramachandran (IIT Bombay) Mayavi2 tutorial 15 / 53

16 Overview Simple Convenient Full-featured Prabhu Ramachandran (IIT Bombay) Mayavi2 tutorial 16 / 53

17 Getting started Vanilla: $ ipython gui=wx with Pylab: $ ipython pylab=wx

18 Using mlab: >>> from enthought. mayavi import mlab Try these: >>> mlab. test_ <TAB> >>> mlab. test_contour3d ( ) >>> mlab. test_contour3d??

19 Exploring the view Mouse Keyboard Toolbar Mayavi icon 10

20 mlab plotting functions 0D data >>> from numpy import >>> t = l i nspace ( 0, 2 pi, 50) >>> u = cos ( t ) p i >>> x, y, z = s i n ( u ), cos ( u ), s i n ( t ) >>> mlab.points3d(x, y, z)

21 Changing how things look Clearing the view >>> mlab.clf() IPython is your friend! >>> mlab.points3d? Extra argument: Scalars Keyword arguments UI >>> mlab. points3d ( x, y, z, t, scale_mode= none )

22 Changing how things look Clearing the view >>> mlab.clf() IPython is your friend! >>> mlab.points3d? Extra argument: Scalars Keyword arguments UI >>> mlab. points3d ( x, y, z, t, scale_mode= none )

23 Changing how things look Clearing the view >>> mlab.clf() IPython is your friend! >>> mlab.points3d? Extra argument: Scalars Keyword arguments UI >>> mlab. points3d ( x, y, z, t, scale_mode= none )

24 1D data >>> mlab.plot3d(x, y, z, t ) Plots lines between the points

25 2D data >>> x, y = mgrid [ 3:3:100 j, 3:3:100 j ] >>> z = s i n ( x x + y y ) >>> mlab.surf(x, y, z) Assumes the points are rectilinear

26 2D data: mlab.mesh >>> mlab.mesh(x, y, z) Points needn t be regular >>> phi, t h e t a = numpy. mgrid [ 0 : p i :20 j,... 0:2 p i :20 j ] >>> x = s i n ( phi ) cos ( t h e t a ) >>> y = s i n ( phi ) s i n ( t h e t a ) >>> z = cos ( phi ) >>> mlab. mesh( x, y, z,... r e p r e s e n t a t i o n = wireframe )

27 3D data >>> x, y, z = o g r i d [ 5:5:64 j,... 5:5:64 j,... 5:5:64 j ] >>> mlab. contour3d ( x x y y + z z 2)

28 3D vector data: mlab.quiver3d >>> mlab. t e s t _ q u i v e r 3 d ( ) obj = mlab.quiver3d(x, y, z, u, v, w) 40

29 3D vector data: mlab.flow >>> x, y, z = mgrid [ 2:3, 2:3, 2:3] >>> r = s q r t ( x 2 + y 2 + z 4) >>> u = y s i n ( r ) / ( r ) >>> v = x s i n ( r ) / ( r ) >>> w = z e r o s _ l i k e ( z ) >>> obj = mlab. flow ( x, y, z, u, v, w, seedtype= plane ) >>> obj. stream_tracer. i n t e g r a t o r _ t y p e = \ runge_kutta45

30 Exercise: Lorenz equation dx dt dy dt dz dt = s(y x) = rx y xz = xy bz Let s = 10, r = 28, b = 8./3. Region of interest x, y, z = mgrid [ 50:50:20 j, 50:50:20 j, 10:60:20 j ] Use mlab.quiver3d

31 mlab. quiver3d ( x, y, z, u, v, w, s c a l e _ f a c t o r =0.01, mask_points =5) mlab. show ( ) Solution def lorenz ( x, y, z, s =10., r =28., b = 8. / 3. ) : u = s ( y x ) v = r x y x z w = x y b z return u, v, w x, y, z = mgrid [ 50:50:20 j, 50:50:20 j, 10:60:20 j ] u, v, w = lorenz ( x, y, z )

32 Issues and solutions Basic visualization: not very useful Tweak parameters: mask_points, scale_factor Explore parameters on UI mlab.flow is a lot better! Good visualization involves work 50

33 Other utility functions gcf: get current figure savefig, figure axes, outline title, xlabel, ylabel, zlabel colorbar, scalarbar, vectorbar show: Standalone mlab scripts Others, see UG

34 Can we do more? Yes!

35 quiver3d ( x, y, z, u, v, w, s c a l e _ f a c t o r =0.01, mask_points =5)

36 Looking inside

37 The pipeline 60

38 Mayavi Engine TVTK Scene Source Filter ModuleManager Lookup tables List of Modules

39 Changing the pipeline On UI Right click on node drag drop Script Or use mlab.pipeline Example: mlab.pipeline. outline () obj.remove()

40 Exercise >>> mlab. t e s t _ q u i v e r 3 d ( ) Hide vectors, add a Vector Cut Plane >>> mlab. t e s t _ f l o w ( ) Add a Vector Cut Plane Can also use the Lorenz example

41 Exercise >>> mlab. t e s t _ q u i v e r 3 d ( ) Hide vectors, add a Vector Cut Plane >>> mlab. t e s t _ f l o w ( ) Add a Vector Cut Plane Can also use the Lorenz example

42 Surprised?

43 So what is the problem?

44 Points?

45 Curve?

46 Surface?

47 Interior of sphere?

48 Datasets Quiver v/s Flow 75

49 Recap mlab gets you started Pipeline and data flow Datasets are important

50 Changing the pipeline On UI Right click on node drag drop Script Or use mlab.pipeline Example: mlab.pipeline. outline () obj.remove()

51 mlab and Mayavi2? mlab is just a thin layer over the Mayavi OO API mlab commands return mayavi objects

52 Exercise 1 Start with flow for the Lorenz system 2 Now extract the vector norm (use a filter) 3 Plot iso-contours of this 4 Figure out how to do this from the UI and mlab.pipeline 85 Prabhu Ramachandran (IIT Bombay) Mayavi2 tutorial 49 / 53

53 So how do you make a fancier script? Use script recording Demo

54 So how do you make a fancier script? Use script recording Demo

55 Animating data >>> s = mlab. flow ( x, y, z, u, v, w) >>> s. mlab_source. u = u z mlab_source.set: multiple attributes If you change the shape of the arrays use the reset method

56 Setting the view >>> p r i n t mlab. view ( ) >>> mlab. view ( azimuth=none, e l e v a t i o n =None, distance=none, f o c a l p o i n t =None ) 100

57 Thank you!

Material for tutorial. Twitter: prabhu_r. Slides: http://goo.gl/5u7pv. Demos: http://goo.gl/mc0ea. www.enthought.com/~prabhu/m2_tutorial.

Material for tutorial. Twitter: prabhu_r. Slides: http://goo.gl/5u7pv. Demos: http://goo.gl/mc0ea. www.enthought.com/~prabhu/m2_tutorial. Material for tutorial Twitter: prabhu_r Slides: http://goo.gl/5u7pv www.enthought.com/~prabhu/m2_tutorial.pdf Demos: http://goo.gl/mc0ea www.enthought.com/~prabhu/demos.zip 3D Data visualization with Mayavi