Introduction to Python Introduction to VTK Filip Malmberg filip

(1)

Filip Malmberg

filip _@cb.uu.se

(2)

IT Uppsala universitet

(3)

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.

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08-01-29 | #4

@ 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.

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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.

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08-01-29 | #6

@ 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).

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Python and VTK

• VTK is written in C++, but has bindings to Python, Java, Tcl ...

• In this course, we will use VTK with Python.

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08-01-29 | #8

@ 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.

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The Python language

• Variables and types

• Control structures

• Functions

• Classes

• File handling

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08-01-29 | #10

@ UU/IT

Variables

•All variables in Python are references

Variable Data

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Variable assignment

•A reference is created with=

^{a = 10}_{b = 20}

c = a + b

a 10

b 20

c 30

Creates the following situation:

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08-01-29 | #12

@ 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]

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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

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08-01-29 | #14

@ UU/IT

Datatypes

• Numbers

• Strings

• Boolean types

• Lists

• Tuples

• Others...

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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 = 9875628736L

>>> big_num.__class__

>>> pi_constant = 3.1415

>>> pi_constant.__class__

>>> z = complex(3.4, 8.35)

>>> z

(3.399999999+8.349999999j)

>>> z.__class__

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08-01-29 | #16

@ 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)

(0.576923072-0.384615381j)

>>> 2 / 3 0

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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 "<stdin>", line 1 s3 = "felaktigt'

SyntaxError: EOL while scanning ^ single-quoted string

>>> s4 = s1 + s2

>>> s4

'exempeltextexempeltext igen'

>>> s5 = str(3)

>>> s5

'3'>>> s5.__class__

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08-01-29 | #18

@ UU/IT

Boolean types

• The following expressions are false:

None False

The number 0

Every empty sequence Every empty mapping {}

• All other objects are defined to be true.

>>> a = True

>>> a.__class__

>>> a = 5 > 7

>>> a False

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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']

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08-01-29 | #20

@ 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']

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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

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08-01-29 | #22

@ UU/IT

Printing

• The Python command for writing text to the prompt is print.

>>> print "Hello"

Hello

>>> print "Hello", "world"

Hello world

>>> print 10+3 13

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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

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08-01-29 | #24

@ 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

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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

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08-01-29 | #26

@ UU/IT

for-loops

• Again, use indentation to

define a block of code.

>>> for i in range(10):

... print i

...0 12 34 56 78 9

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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

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08-01-29 | #28

@ 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.

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Executing Python programs

• Python files are executed using the python command.

• The search path to this program must be

• On windows, this is set by the system set.

variable PYTHONPATH.

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08-01-29 | #30

@ 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"

# a refers to a list a = [5, 2, 8, 5]

a.sort()

# a refers to a number again a = 10

a.sort()

$> python dynamic_binding.py 10 <type 'int'>

lkshjdglgv <type 'str'>

[5, 2, 8, 5] <type 'list'>

File "dynamic_binding.py", line 18, in<module>

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."

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Python is strongly typed

• No implicit type conversions

>>> a = 3

>>> b = '4'

>>> a + b

File "<stdin>", line 1, in

TypeError: unsupported operand type(s)

for +: 'int' and 'str'

>>> str(a) + b '34'>>> a + int(b) 7

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08-01-29 | #32

@ 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."

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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)

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08-01-29 | #34

@ 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.

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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.

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08-01-29 | #36

@ 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.

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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, "_")

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08-01-29 | #38

@ 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

(3, 573)

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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.

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08-01-29 | #40

@ 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

File "<stdin>", line 1, in <module>

NameError: name 'sys' is not defined

>>> import sys

>>> sys

>>> sys.version

'2.4.3 (#1, Dec 11 2006, 11:39:03) \n[GCC 4.1.1 20061130 (Red Hat 4.1.1-43)]'

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3 party modules

• Lots of freely available modules for:

– GUI:s

– Image Processing – Computer Graphics – Web development

– Numerical Computations

– ...

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08-01-29 | #42

@ UU/IT

The VTK module

 VTK in python is implemented as a Module

>>> import vtk

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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:

MyNumber=10

def printNumber(self):

print 'The number is ',MyNumber

#Now we use the class anObject=MyClass() anObject.printNumber()

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08-01-29 | #44

@ 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.

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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

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08-01-29 | #46

@ 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

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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 text

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08-01-29 | #48

@ 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.

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That's it!

• Now you know the basics of Python

• More info: www.python.org

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IT Uppsala universitet

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 What is VTK?

 What can VTK be used for?

 How to actually use VTK?

VTK – The Visualization ToolKit

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08-01-29 | #52

@ 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

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True visualization system

 Techniques for visualizing

• scalar fields

• vector fields

• tensor fields

 Polygon reduction

 Mesh smoothing

 Image processing

 Your own algorithms

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08-01-29 | #54

@ 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

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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)

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08-01-29 | #56

@ 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

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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

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08-01-29 | #58

@ UU/IT

Visualization of attributes

 Scalar fields

• Color Mapping

 vtkLookupTable

 vtkScalarsToColors

 vtkColorTransferFunction

• Contouring

 vtkContourFilter

 vtkMarchingCubes

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Visualization of attributes

 Vector fields

• Glyphs

 vtkGlyph3D

• Streamlines/points/tubes

 vtkStreamer

 vtkStreamLine

 vtkStreamPoints

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08-01-29 | #60

@ UU/IT

Visualization of attributes

 Tensor fields

• vtkTensor

• vtkTensorGlyph

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The Visualization Pipeline

DATA

FILTER MAPPING

Visualization algorithms

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08-01-29 | #62

@ UU/IT

Objects

 Data objects

• e.g. vtkPolyData, vtkImageData

 Process objects

• Source objects (vtkReader, vtkSphereSource)

• Filter objects (vtkContourFilter)

• Mapper objects (vtkPolyDataMapper)

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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

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08-01-29 | #64

@ UU/IT

Cube example

http://www.it.uu.se/edu/course/homepage/vetvis/ht11/

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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

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08-01-29 | #66

@ UU/IT

Sphere example

http://www.it.uu.se/edu/course/homepage/vetvis/ht11/

(67)

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

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08-01-29 | #68

@ UU/IT

VTK resources

 www.vtk.org

• Download

• Documentation

• Mailing lists

• Links

• FAQ, Search

 www.kitware.com

• VTK Textbook

• VTK User’s guide

• Mastering CMake

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VTK Examples

 Really useful for getting started

 Available on the VTK webpage or in the VTK

folder.

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08-01-29 | #70

@ UU/IT

VTK documentation

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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

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08-01-29 | #72

@ 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

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Computer exercises

 2 assignments on VTK

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08-01-29 | #74

@ UU/IT

Computer exercises

 One project on VTK

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Computer exercises

 Deadline is next lab session

• Give a demonstration of your program

• Show source code

• Be able to answer questions

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08-01-29 | #76

@ UU/IT

Computer exercises

 Lab 1

Wednesday September 7 13:15-17:00 P1312D, P1313D

Basics of VTK

 UpUnet account, UU-LOCAL, password C

 VTK 5.0.0 is installed in

• G:\Program\ACGV\VTK-5.0.0

 You need to set the proper paths, run the script in a command prompt

• G:\Program\ACGV\set_paths.bat

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Introduction to Python Introduction to VTK Filip Malmberg filip

Filip Malmberg

filip @cb.uu.se

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.

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.

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.

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).

Python and VTK

• VTK is written in C++, but has bindings to Python, Java, Tcl ...

• In this course, we will use VTK with Python.

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.

The Python language

• Variables and types

• Control structures

• Functions

• Classes

• File handling

Variables

•All variables in Python are references

Variable Data

Variable assignment

•A reference is created with=

a 10

b 20

c 30

Creates the following situation:

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

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

Datatypes

• Numbers

• Strings

• Boolean types

• Lists

• Tuples

• Others...

Numbers

•Different kinds of

numbers are represented by different classes:

Integers (int)

Big integers (long) Real numbers (float)

Complex numbers (complex)

Operations on numbers

filip _@cb.uu.se