Introduction to VTK and Python. Filip Malmberg Uppsala universitet

Transcription

1 Introduction to VTK and Python Filip Malmberg IT Uppsala universitet

2 Todays lecture Introduction to the Visualization Toolkit (VTK) Some words about the assignments Introduction to Python #2

3 VTK The Visualization ToolKit What is VTK? What can VTK be used for? How to actually use VTK? #3

4 VTK The Visualization ToolKit Open source, freely available software for 3D computer graphics image processing visualization Managed by Kitware, Inc. Object-oriented design (C++) O High-level of abstraction Use C++, Tcl/Tk, Python, Java #4

5 True visualization system Techniques for visualizing scalar fields vector fields tensor fields Polygon reduction Mesh smoothing Image processing Your own algorithms #5

6 Additional features Parallel support message passing multi-threading Stereo support Integrates with Motif, Qt, Tcl/Tk, Python/Tk, X11, Windows,... Event handling 3D widgets #6

7 3D graphics Surface rendering Volume rendering Ray casting T Texture mapping (2D, 3D) Lights and cameras Textures Save render window to.png,.jpg,... ((useful for movie creation) #7

8 The Visualization Pipeline DATA Visualization algorithms FILTER MAPPING Interactive feedback DISPLAY #8

9 Objects Data objects e.g. vtkpolydata, vtkimagedata Process objects Source S objects (vtkreader, vtkspheresource) F Filter objects (vtkcontourfilter) M Mapper objects (vtkpolydatamapper) #9

10 7 basic VTK objects to render a scene vtkrenderwindow: manages a window on the display device vtkrenderer: coordinates the rendering process involving lights, cameras, and actors vtklight: a source of light to illuminate the scene vtkcamera: defines the view position, focal point, etc. vtkactor: represents an object rendered in the scene, both its properties and position in the world coordinate system vtkproperty: defines the appearance properties of an actor including colour, transparency, and lighting properties such as specular and diffuse. Also representational properties like wireframe and solid surface vtkmapper: the geometric representation for an actor. More than one actor may refer to the same mapper #10

11 Cube example #11

12 User interaction vtkrenderwindowinteractor allows the user to interact with the objects Try the following key presses w wireframe mode s surface mode j joystick mode t trackball mode button1 rotate button2 translate button3 scale r reset camera view e, q exit #12

13 Sphere example #13

14 VTK and C++ Build with CMake and your favorite compiler CMake generates makefiles or project files for your environment Use the resulting file(s) to build your executable Under Windows you can use Microsoft Visual C++ 8 Express Edition You have to install Tcl and/or Python to run vtk scripts #14

15 VTK resources Download Documentation Mailing lists Links FAQ, Search VTK Textbook VTK User s guide Mastering CMake #15

16 VTK Examples Really useful for getting started Available on the VTK webpage or in the VTK folder #16

17 VTK documentation #17

18 Summary + Free and open source Create graphics/visualization applications fairly fast Object oriented - easy to derive new classes Build applications using interpreted languages Tcl, Python, and Java Many (state-of-the-art) algorithms Heavily tested in real-world applications Large user base provides decent support Commercial support and consulting available #18

19 Summary Not a super-fast graphics engine due to portability and C++ dynamic binding you need a decent workstation Very large class hierarchy learning threshold might be steep #19

20 Computer exercises 2 assignments + 1 project on VTK #20

21 Computer exercises Work in pairs Examination Give a demonstration of your program Show source code Be able to answer questions about your work #21

22 Computer exercises UpUnet account, UU-LOCAL, password C VTK is installed in G:\Program\ACGV\VTK You need to set the proper paths, run the script in a command prompt G:\Program\ACGV\set_paths.bat #22

23 #23

24 What is Python? Dynamic, interpreted high-level language. Created in 1991 by Guido van Rossum. Design philosophy: Short development time is prioritized over execution speed. Syntax similar to C++ or Java #24

25 Facts about Python Portable, available for all common platforms. Python is Open Source and free to use, even for commercial applications. (Relatively) Easy to integrate with other languages, such as Java, C/C++, Fortran and.net. Designed for multiple paradigms. Both object oriented and procedural programming are possible #25

26 What is Python good for? Internet applications, good support for HTTP, FTP, SMTP and CGI. Integrating components written in a low-level language, glue code. Portable system tools, same commands on each platform. Compare with dir (Windows) and ls (Linux). Portable GUI:s. Database handling. Projects where time of development is more important than speed of execution #26

27 What is Python not good for? Tasks where performance is critical. Such tasks can be implemented in C/C++ modules using tools such as SWIG ( #27

28 Python and VTK VTK is written in C++, but has bindings to Python, Java, Tcl... In this course, we will use VTK with Python #28

29 The Python prompt Can be used to execute individual Python commands interactively. The prompt has a memory which is kept until the prompt is closed. Start the prompt by typing python in a terminal #29

30 The Python language Variables and types Control structures Functions Classes File handling #30

31 Variables All variables in Python are references Variable Data #31

32 Variable names May contain english letters, numbers and underscores. Must not start with a number. Valid names Invalid names varname varname1 var_name_1 _var_name påskmust 1_varname varname 1 var&name #32

33 Variable assignment A reference is created with= a = 10 b = 20 c = a + b Creates the following situation: a 10 b 20 c #33

34 More on references Multiple references: Many variables can refer to the same object. list_a list_b list_c [1, 2, 3] >>> >>> >>> >>> >>> >>> [1, list = [1, 2, 3] list_a = [1, 2, 3] list_b = list_a list_c = list_b list_c[2] = 78 list_a 2, 78] Reference counting: An object is deleted automatically when no variables refer to it #34

35 Datatypes Numbers Strings Boolean types Lists Tuples Others #35

36 Numbers Different kinds of numbers are represented by different classes: I Integers (int) Big integers (long) B Real numbers (float) R Complex numbers (complex) C >>> a = 10 >>> a. class <type 'int'> >>> big_num = L >>> big_num. class <type 'long'> >>> pi_constant = >>> pi_constant. class <type 'float'> >>> z = complex(3.4, 8.35) > >>> z ( ( j) >>> z. class <type 'complex'> #36

37 Operations on numbers The operations +, -, * and / work as usual. % - Remainder // - Integer division ** - Power abs(x) a i int(x) l long(x) f float(x) ccomplex(a, b) >>> a = 3.14 >>> b = 5 >>> c = b / a >>> c. class <type 'float'> >>> 5 // 2 2 >>> 5 // float(2) > 2.0 >>> 5 / float(2) > 2.5 >>> b / complex(6, 4) > ( ( j) >>> 2 / #37

38 Strings A string is a sequence of characters. A string is created using single or double quotes. >>> s1 = "a correct example" >>> s2 = 'another correct example' >>> s3 = "not correct' File "<stdin>", line 1 s3 = "not correct' ^ SyntaxError: EOL while scanning single-quoted string >>> s4 = s1 + s2 >>> s4 'a correct exampleanother correct example' >>> s5 = str(3) > >>> s5 '3' >>> s5. class <type 'str'> #38

39 Boolean types The following expressions are false: None False The number 0 Every empty sequence Every empty mapping {} All other objects are (somewhat s simplified) defined to be true. >>> a = True >>> a. class <type 'bool'> >>> a = 5 > 7 >>> a False #39

40 Lists Lists are containers with an arbitrary number of elements. The elements can be any Python object. A single list can contain objects of many different types. >>> list = [1, 2, 3] >>> list [1, 2, 3] >>> list_2 = [1, "mixed", "li"+"st"] >>> list_2 [1, 'mixed', 'list'] #40

41 More on lists Individual element are accessed with an index within square brackets [index]. The first element has index 0. >>> list_2 [1, 'mixed', 'list'] >>> list_2[1] 'mixed' >>> list_2[1] = "New element" >>> list_2 [1, 'New element', 'list'] #41

42 Tuples Tuples are static lists. Tuples have better performance than lists, but are less flexible. > >>> tuple_1 = (1, 2, 3) >>> tuple_2 = (1, "mixed") > >>> tuple_2[1] 'mixed' >>> tuple_2[1] = "New element" Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: 'tuple' object does not support item assignment #42

43 Printing The Python command for writing text to the prompt is print. >>> print "Hello" Hello >>> print "Hello", "world" Hello world >>> print #43

44 If-statements >>> a = 10 >>> if a > 5:... print "The number is greater than 5"... The number is greater than 5 Note the indentation! In Python, indentation is used to control which block a statement belongs to. A colon indicates that a new block of code begins #44

45 else >>> a = 10 >>> if a < 5:... print "a is less than 5"... else:... print "a is greater than or equal to 5"... a is greater than or equal to #45

46 Multiple choices Multiple choices are handled with elif. Many languages have a case-statement for handling multiple choices. This was deemed redundant by the Python developers. >>> a = 10 >>> if a == 1:... print "a is... elif a == 2:... print "a is... elif a == 3:... print "a is... else:... print "a is... a is something else one" two" three" something else" #46

47 for-loops Again, use indentation to define a block of code. >>> for i in range(10):... print i #47

48 Nested loops >>> for i in range(2):... for j in range(3):... for k in range(4):... print "i=%i, j=%i, k=%i" % (i, j, k) p... i=0, j=0, k=0 i=0, j=0, k=1 i=0, j=0, k=2 i=0, j=0, k=3 i=0, j=1, k=0 i=0, j=1, k=1... i=1, j=1, k=2 i=1, j=1, k=3 i=1, j=2, k=0 i=1, j=2, k=1 i=1, j=2, k=2 i=1, j=2, k= #48

49 Beyond the Python prompt The python prompt is not suited for larger programs. Python programs are stored in regular text files. Commonly the filenames end with.py, but this is not required #49

50 Executing Python programs Python files are executed using the python command. The search path to this program must be set. On windows, this is set by the system variable PYTHONPATH #50

51 Python is dynamically typed # -*- coding: utf-8 -*# a refers to a number a = 10 print a, a. class # a refers to a string a = "lkshjdglgv" print a, a. class # a refers to a list a = [5, 2, 8, 5] print a, a. class a a.sort() # a refers to a number again a = 10 a a.sort() $> python dynamic_binding.py 10 <type 'int'> lkshjdglgv <type 'str'> [5, 2, 8, 5] <type 'list'> Traceback (most recent call last): File "dynamic_binding.py", line 18, in <module> a a.sort() AttributeError: 'int' object has no attribute 'sort' Duck Typing: "when I see a bird that walks like a duck and swims like a duck and quacks like a duck, I call that bird a duck." #51

52 Python is strongly typed No implicit type conversions >>> a = 3 >>> b = '4' >>> a + b Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: unsupported operand t type(s) for +: 'int' and 'str' >>> str(a) + b '34' >>> a + int(b) > #52

53 Functions in Python A function is create using the reserved word def followed by the function name and a colon. The rules for function names are the same as for variable names. # function_01.py def function_a(): print "This is printed within function_a." $> python function_01.py This is printed first. This is printed within function_a. This is printed after the function call. print "This is printed first." function_a() # Function call print "This is printed after the function call." #53

54 Function arguments We communicate with functions by specifying arguments in the function call. # function_02.py def greeting(name, age): print """Hello %s. You are %i years old.""" % (name, age) ( g greeting("lisa", 23) greeting("erik", 31) g $> python function_02.py Hello Lisa. You are 23 years old. Hello Erik. You are 31 years old #54

55 Default arguments Default arguments can be used to avoid having to specify all arguments. # function_03.py def greeting(name, age=20): print """Hello %s. You are %i years old.""" % (name, age) ( g greeting("lisa", 23) g greeting("erik") $> python function_03.py Hello Lisa. You are 23 years old. Hello Erik. You are 20 years old #55

56 Order of arguments Problems with many arguments: Arguments must be given in the order given in the function defintion. # function_04.py def greeting(name="unknown", age=20): print """Hello %s. You are %i years old.""" % (name, a age) greeting() g g greeting("erik") greeting(45) # Gives the wrong result $> python function_04.py Hello Unknown. You are 20 years old. Hello Erik. You are 20 years old. Hello 45. You are 20 years old #56

57 Arguments by name The solution is to give arguments by name. # function_05.py def greeting(name="unknown", age=20): print """Hello %s. You are %i years old.""" % (name, age) p greeting() g greeting("erik") # Still works greeting(name="erik") # Eqvivalent greeting(age=45) # Gives the right result greeting("lisa", 33) g greeting(name = "Lisa", age = 33) # Eqvivalent $> python function_05.py Hello Unknown. You are 20 years old. Hello Erik. You are 20 years old. Hello Erik. You are 20 years old. Hello Unknown. You are 45 years old. Hello Lisa. You are 33 years old. Hello Lisa. You are 33 years old #57

58 Return values The return statement is used to return a value from a function. # return_values_01.py def my_own_join(texts, separator=" "): s = "" for text in texts: s += text + separator s = s[:-len(separator)] + "." return s my_text_pieces = ["This", "is", "not", "very", "meaningful"] print my_own_join(my_text_pieces, "_") p $> python return_values_01.py This is not very meaningful #58

59 Multiple return values Python allows any number of return values. # return_values_03.py def min_max(seq): return min(seq), max(seq) r a = [3, 573, 234, 24] minimum, maximum = min_max(a) m print minimum, maximum result = min_max(a) r print result print result. class $> python return_values_03.py (3, 573) ( <type 'tuple'> #59

60 Modules When writing larger programs, it is not practical to keep all code in the same file. In python Modules offer a way to separate large programs into smaller units. Modules are also used to organize functions and variables into namespaces #60

61 Standard modules Python has a number of standard modules that are always available for import. Modules are imported with the import-statement. >>> sys Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'sys' is not defined >>> import sys >>> sys <module 'sys' (built-in)> >>> sys.version '2.4.3 (#1, Dec , 11:39:03) \n[gcc (Red Hat )]' #61

62 3rd party modules Lots of freely available modules for: GUI:s Image Processing Computer Graphics Web development Numerical Computations #62

63 The VTK module VTK in python is implemented as a Module >>> import vtk #63

64 Object oriented programming Python is originally a procedural language, with added support for object orientation. Classes are defined using the class keyword: # -*- coding: utf-8 -*# io_01.py class MyClass MyNumer=10 def printnumber(self): print 'The number is ',MyNumber #Now we use the class a anobject=myclass() a anobject.printnumber() #64

65 Object oriented programming Python is originally a procedural language, with added support for object orientation. Classes are defined using the class keyword: # -*- coding: utf-8 -*# io_01.py class MyClass: MyNumer=10 def printnumber(self): print 'The number is ',MyNumber #Now we use the class a anobject=myclass() a anobject.printnumber() #65

66 Private variables Python has limited support for private class variables. Variable names starting with two underscores ( ) are considered private. If you really want to, it is still possible to access those variables from outside the class #66

67 File I/O in python Files are opened with the open statement # -*- coding: utf-8 -*# io_01.py f = open("newfile.txt", "r") # Open a file print f.read() # Read the whole file r -read only w - write only r+ - read and write a - append data at the end of the file b - binary file #67

68 Reading parts of a file # -*- coding: utf-8 -*# io_02.py f = open("newfile.txt") for row in f.readlines(): print row, f.close() f f = open("newfile.txt") print f.read(8) p print f.read(5) p $> python io_02.py This is line 1. This is line 2. This is line 3. This is line 4. This is line #68

69 Writing to a file # -*- coding: utf-8 -*# io_03.py f = open("newfile.txt", "w") f.write(str(3) + "\n") f f.write(str([1,2,3]) + "\n") f f.write(str({"name":"kalle"}) + "\n") f f f.close() f = open("newfile.txt", "a") f.write("this line is appended.") f f f.close() f = open("newfile.txt") print f.read() p f f.close() $> python io_03.py 3 [1, 2, 3] {'name': 'Kalle'} This line is appended #69

70 That's it! Now you know the basics of Python More info: #70