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ITUppsala universitet Introduction to Python Introduction to VTK Filip Malmberg

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1 ITUppsala universitet Introduction to Python Introduction to VTK Filip Malmberg

2 ITUppsala universitet Part 1: Introduction to Python

3 UU/IT | UU/IT What is Python? Dynamic, interpreted high-level language. Created in 1991 by Guido van Rossum. Design philosophy: Short development time is prioritized over excecution speed. Syntax similar to C++ or Java.

4 UU/IT | UU/IT 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.

5 UU/IT | UU/IT 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.

6 UU/IT | UU/IT 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 (www.swig.org).

7 UU/IT | UU/IT Python and VTK VTK is written in C++, but has bindings to Python, Java, Tcl... In this course, we will use VTK with Python.

8 UU/IT | UU/IT 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.

9 UU/IT | UU/IT The Python language Variables and types Control structures Functions Classes File handling

10 UU/IT | UU/IT Variables All variables in Python are references VariableData

11 UU/IT | UU/IT Variable names May contain english letters, numbers and underscores. Must not start with a number. Invalid names påskmust 1_varname varname 1 var&name Valid names varname vArNaMe1 var_name_1 _var_name

12 UU/IT | UU/IT Variable assignment A reference is created with= a = 10 b = 20 c = a + b a10 b20 c30 Creates the following situation:

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

14 UU/IT | UU/IT Datatypes Numbers Strings Boolean types Lists Tuples Others...

15 UU/IT | UU/IT Numbers Different kinds of numbers are represented by different classes: Integers (int)‏ Big integers (long)‏ Real numbers (float)‏ Complex numbers (complex)‏ >>> a = 10 >>> a.__class__ >>> big_num = L >>> big_num.__class__ >>> pi_constant = >>> pi_constant.__class__ >>> z = complex(3.4, 8.35)‏ >>> z ( j)‏ >>> z.__class__

16 UU/IT | UU/IT Operations on numbers The operations +, -, * and / work as usual. % - Remainder // - Integer division ** - Power abs(x)‏ int(x)‏ long(x)‏ float(x)‏ complex(a, b)‏ >>> a = 3.14 >>> b = 5 >>> c = b / a >>> c.__class__ >>> 5 // 2 2 >>> 5 // float(2)‏ 2.0 >>> 5 / float(2)‏ 2.5 >>> b / complex(6, 4)‏ ( j)‏ >>> 2 / 3 0

17 UU/IT | UU/IT Strings A string is a sequence of characters. A string is created using single or double quotes. >>> s1 = "exempeltext" >>> s2 = 'exempeltext igen' >>> s3 = "felaktigt' File " ", line 1 s3 = "felaktigt' ^ SyntaxError: EOL while scanning single-quoted string >>> s4 = s1 + s2 >>> s4 'exempeltextexempeltext igen' >>> s5 = str(3)‏ >>> s5 '3' >>> s5.__class__

18 UU/IT | UU/IT Boolean types The following expressions are false: None False The number 0 Every empty sequence Every empty mapping {} All other objects are (somewhat simplified)‏ defined to be true. >>> a = True >>> a.__class__ >>> a = 5 > 7 >>> a False

19 UU/IT | UU/IT 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']

20 UU/IT | UU/IT More on lists Individual element are accessed with an index within square brackets [index]. The first element has index 0. >>> list_2 [1, 'blandad', 'lista'] >>> list_2[1] 'blandad' >>> list_2[1] = "Nytt element" >>> list_2 [1, 'Nytt element', 'lista']

21 UU/IT | UU/IT 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 " ", line 1, in TypeError: 'tuple' object does not support item assignment

22 UU/IT | UU/IT Printing The Python command for writing text to the prompt is print. >>> print "Hello" Hello >>> print "Hello", "world" Hello world >>> print

23 UU/IT | UU/IT If-statements 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. >>> a = 10 >>> if a > 5:... print "The number is greater than 5"... The number is greater than 5

24 UU/IT | UU/IT 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 5

25 UU/IT | UU/IT 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 one"... elif a == 2:... print "a is two"... elif a == 3:... print "a is three"... else:... print "a is something else"... a is something else

26 UU/IT | UU/IT for-loops Again, use indentation to define a block of code. >>> for i in range(10):... print i

27 UU/IT | UU/IT 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)‏... 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=3

28 UU/IT | UU/IT 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.

29 UU/IT | UU/IT 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.

30 UU/IT | UU/IT Python is dynamically typed # -*- coding: utf-8 -*- # a refers to a number a = 1 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.sort() ‏ # a refers to a number again a = 10 a.sort()‏ $> python dynamic_binding.py 10 lkshjdglgv [5, 2, 8, 5] Traceback (most recent call last): File "dynamic_binding.py", line 18, in 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."

31 UU/IT | UU/IT Python is strongly typed No implicit type conversions >>> a = 3 >>> b = '4' >>> a + b Traceback (most recent call last): File " ", line 1, in TypeError: unsupported operand type(s)‏ for +: 'int' and 'str' >>> str(a) + b '34' >>> a + int(b)‏ 7

32 UU/IT | UU/IT 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. $> python function_01.py Detta skrivs först. Detta skrivs inuti funktionen Detta skrivs efter metodanropet. # function_01.py def function_a(): print "Detta skrivs inuti funktionen." print "Detta skrivs först." function_a() # Funktionen anropas print "Detta skrivs efter metodanropet."

33 UU/IT | UU/IT Function arguments We communicate with functions by specifying arguments in the function call. $> python function_02.py Hello Maja. You are 23 years old. Hello Pelle. You are 31 years old. # function_02.py def greeting(name, age): print """Hello %s. You are %i years old.""" % (name, age)‏ greeting("Maja", 23)‏ greeting("Pelle", 31)‏

34 UU/IT | UU/IT Default arguments Default arguments can be used to avoid having to specify all arguments. # function_03.py def greeting(name, age=20): print """Hej %s. Du är %i år gammal.""" % (name, age)‏ greeting("Maja", 23)‏ greeting("Pelle")‏ $> python function_03.py Hej Maja. Du är 23 år gammal. Hej Pelle. Du är 20 år gammal.

35 UU/IT | UU/IT 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, age)‏ greeting()‏ greeting("Pelle")‏ greeting(45) # Gives the wrong result $> python function_04.py Hello Unknown. You are 20 years old. Hello Pelle. You are 20 years old. Hello 45. You are 20 years old.

36 UU/IT | UU/IT Arguments by name The solution is to give arguments by name. # function_05.py def greeting(name="Okänd", age=20): print """Hej %s. Du är %i år gammal.""" % (name, age)‏ greeting()‏ greeting("Pelle") # Still works greeting(name="Pelle") # Eqvivalent greeting(age=45) # Gives the right result greeting("Maja", 33)‏ greeting(name = "Maja", age = 33) # Eqvivalent $> python function_05.py Hej Okänd. Du är 20 år gammal. Hej Pelle. Du är 20 år gammal. Hej Okänd. Du är 45 år gammal. Hej Maja. Du är 33 år gammal.

37 UU/IT | UU/IT 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 = ["Detta", "är", "inte", "så", "meningsfullt"] print my_own_join(my_text_pieces, "_")‏ $> python return_values_01.py Detta_är_inte_så_meningsfullt.

38 UU/IT | UU/IT Multiple return values Python allows any number of return values. # return_values_03.py def min_max(seq): return min(seq), max(seq)‏ a = [3, 573, 234, 24] minimum, maximum = min_max(a)‏ print minimum, maximum result = min_max(a)‏ print result print result.__class__ $> python return_values_03.py (3, 573)‏

39 UU/IT | UU/IT 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.

40 UU/IT | UU/IT 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 " ", line 1, in NameError: name 'sys' is not defined >>> import sys >>> sys >>> sys.version '2.4.3 (#1, Dec , 11:39:03) \n[GCC (Red Hat )]'

41 UU/IT | UU/IT 3 rd party modules Lots of freely available modules for: –GUI:s –Image Processing –Computer Graphics –Web development –Numerical Computations –...

42 UU/IT | UU/IT The VTK module  VTK in python is implemented as a Module >>> import vtk

43 UU/IT | UU/IT 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 anObject=MyClass()‏ anObject.printNumber()‏

44 UU/IT | UU/IT 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 anObject=MyClass()‏ anObject.printNumber()‏

45 UU/IT | UU/IT 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.

46 UU/IT | UU/IT Private variables, cont. Under the hood, private variables are hidden by textually replacing the name “__member” with “_classname__member” # -*- coding: utf-8 -*- # io_01.py class MyClass: __MyNumber=10 #private variable #Now we use the class anObject=MyClass()‏ print anObject.__MyNumber #This won't work print anObject._MyClass__MyNumber #This will work, but is usually a bad idea

47 UU/IT | UU/IT File I/O in python Files are opened with the open statement # -*- coding: utf-8 -*- # io_01.py f = open("newfile.txt", "r") # Öppna filen print f.read() # Läs in hela filen “r” -read only “w”- write only “r+” - read and write “a” - append data at the end of the file “b”- binary file

48 UU/IT | UU/IT Reading parts of a file # -*- coding: utf-8 -*- # io_01.py f = open("newfile.txt")‏ for row in f.readlines(): print row, f.close()‏ f = open("newfile.txt")‏ print f.read(8)‏ print f.read(5)‏ $> python io_02.py Detta är textrad 1. Detta är textrad 2. Detta är textrad 3. Detta är textrad 4. Detta är text

49 UU/IT | UU/IT Writing to a file # -*- coding: utf-8 -*- # io_03.py f = open("newfile.txt", "w")‏ f.write(str(3) + "\n")‏ f.write(str([1,2,3]) + "\n")‏ f.write(str({"name":"Kalle"}) + "\n")‏ f.close()‏ f = open("newfile.txt", "a")‏ f.write("Denna rad läggs till.")‏ f.close()‏ f = open("newfile.txt")‏ print f.read()‏ f.close()‏ $> python io_03.py 3 [1, 2, 3] {'name': 'Kalle'} Denna rad läggs till.

50 UU/IT | UU/IT That's it! Now you know the basics of Python More info:

51 ITUppsala universitet Part 2: Introduction to VTK

52 UU/IT | UU/IT  What is VTK?  What can VTK be used for?  How to actually use VTK? VTK – The Visualization ToolKit

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

54 UU/IT | UU/IT True visualization system  Techniques for visualizing scalar fields vector fields tensor fields  Polygon reduction  Mesh smoothing  Image processing  Your own algorithms

55 UU/IT | UU/IT Additional features  Parallel support message passing multi-threading  Stereo support  Integrates with Motif, Qt, Tcl/Tk, Python/Tk, X11, Windows,...  Event handling  3D widgets

56 UU/IT | UU/IT 3D graphics  Surface rendering  Volume rendering Ray casting Texture mapping (2D, 3D)‏  Lights and cameras  Textures  Save render window to.png,.jpg,... (useful for movie creation)‏

57 UU/IT | UU/IT Data Representation  Collection of cells & points  Cells specify topology Shape such as triangle, tetrahedron  Points specify geometry Point coordinates assigned to a topology  Data attributes Data associated with topology or geometry

58 UU/IT | UU/IT Data attributes assigned to points or cells  Scalar  Vector magnitude and direction  Normal a vector of magnitude 1 used for lighting  Texture coordinate mapping data points into a texture space  Tensor

59 UU/IT | UU/IT Visualization of attributes  Scalar fields Color Mapping  vtkLookupTable  vtkScalarsToColors  vtkColorTransferFunction Contouring  vtkContourFilter  vtkMarchingCubes

60 UU/IT | UU/IT Visualization of attributes  Vector fields Glyphs  vtkGlyph3D Streamlines/points/tubes  vtkStreamer  vtkStreamLine  vtkStreamPoints

61 UU/IT | UU/IT Visualization of attributes  Tensor fields vtkTensor vtkTensorGlyph

62 UU/IT | UU/IT The Visualization Pipeline DATA FILTERMAPPING DISPLAY Visualization algorithms Interactive feedback

63 UU/IT | UU/IT Objects  Data objects e.g. vtkPolyData, vtkImageData  Process objects Source objects (vtkReader, vtkSphereSource)‏ Filter objects (vtkContourFilter)‏ Mapper objects (vtkPolyDataMapper)‏

64 UU/IT | UU/IT 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

65 UU/IT | UU/IT Cube example 0/

66 UU/IT | UU/IT User interaction  vtkRenderWindowInteractor allows the user to interact with the objects  Try the following key presses w wireframe modes surface mode j joystick modet trackball mode button1 rotatebutton2 translate button3 scaler reset camera view e, q exit

67 UU/IT | UU/IT Sphere example 0/

68 UU/IT | UU/IT 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++ Express Edition  You have to install Tcl and/or Python to run vtk scripts

69 UU/IT | UU/IT VTK resources  Download Documentation Mailing lists Links FAQ, Search  VTK Textbook VTK User’s guide Mastering CMake

70 UU/IT | UU/IT VTK Examples  Really useful for getting started  Available on the VTK webpage or in the VTK folder.

71 UU/IT | UU/IT VTK documentation

72 UU/IT | UU/IT Summary +  Free and open source  Create graphics/visualization applications fairly fast  Object oriented - easy to derive new classes  Build applications using “interpretive” 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

73 UU/IT | UU/IT 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

74 UU/IT | UU/IT Computer exercises  2 assignments on VTK

75 UU/IT | UU/IT Computer exercises  One project on VTK

76 UU/IT | UU/IT Computer exercises  Deadline is next lab session Give a demonstration of your program Show source code Be able to answer questions

77 UU/IT | UU/IT Computer exercises  Lab 1 Wednesday September 8 13:15-17:00 P1312D, P1313D Basics of VTK  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

78 ITUppsala universitet Introduction to Python Introduction to VTK Filip Malmberg


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