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IT Uppsala universitet
Part 1: Introduction to Python
UU/IT
08-01-29 | #3@ 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.
UU/IT
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.
UU/IT
08-01-29 | #5@ 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.
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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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08-01-29 | #7@ 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.
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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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08-01-29 | #9@ UU/IT
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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08-01-29 | #11@ UU/IT
Variable assignment
•A reference is created with= a = 10b = 20c = 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]
UU/IT
08-01-29 | #13@ UU/IT
Variable names
•May contain english letters, numbers and underscores.
• Must not start with a number.
Invalid names
påskmust1_varnamevarname 1var&name
Valid names
varnamevArNaMe1var_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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08-01-29 | #15@ 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__<type 'int'>>>> big_num = 9875628736L>>> big_num.__class__<type 'long'>>>> pi_constant = 3.1415>>> pi_constant.__class__<type 'float'>>>> z = complex(3.4, 8.35)>>> z(3.399999999+8.349999999j)>>> z.__class__<type 'complex'>
UU/IT
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__<type 'float'>>>> 5 // 22>>> 5 // float(2)2.0>>> 5 / float(2)2.5>>> b / complex(6, 4)(0.576923072-0.384615381j)>>> 2 / 30
UU/IT
08-01-29 | #17@ 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 "<stdin>", line 1s3 = "felaktigt'
^SyntaxError: EOL while scanningsingle-quoted string>>> s4 = s1 + s2>>> s4'exempeltextexempeltext igen'>>> s5 = str(3)>>> s5'3'>>> s5.__class__<type 'str'>
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08-01-29 | #18@ UU/IT
Boolean types
• The following expressions are false:NoneFalseThe number 0Every empty sequenceEvery empty mapping {}• All other objects are defined to
be true.
>>> a = True>>> a.__class__<type 'bool'>>>> a = 5 > 7>>> aFalse
UU/IT
08-01-29 | #19@ 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']
UU/IT
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']
UU/IT
08-01-29 | #21@ 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 "<stdin>", line 1, in <module>TypeError: 'tuple' object does not support itemassignment
UU/IT
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+313
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08-01-29 | #23@ 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
UU/IT
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
UU/IT
08-01-29 | #25@ 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
UU/IT
08-01-29 | #26@ UU/IT
for-loops
• Again, use indentation to define a block of code. >>> for i in range(10):
... print i
...0123456789
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08-01-29 | #27@ 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=0i=0, j=0, k=1i=0, j=0, k=2i=0, j=0, k=3i=0, j=1, k=0i=0, j=1, k=1...i=1, j=1, k=2i=1, j=1, k=3i=1, j=2, k=0i=1, j=2, k=1i=1, j=2, k=2i=1, j=2, k=3
UU/IT
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.
UU/IT
08-01-29 | #29@ 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.
UU/IT
08-01-29 | #30@ UU/IT
Python is dynamically typed# -*- coding: utf-8 -*-# a refers to a numbera = 1print a, a.__class__
# a refers to a stringa = "lkshjdglgv"print a, a.__class__
# a refers to a lista = [5, 2, 8, 5]print a, a.__class__a.sort()
# a refers to a number againa = 10a.sort()
$> python dynamic_binding.py10 <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.sort()AttributeError: 'int' object has noattribute '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."
UU/IT
08-01-29 | #31@ UU/IT
Python is strongly typed
• No implicit type conversions
>>> a = 3>>> b = '4'>>> a + bTraceback (most recent call last):
File "<stdin>", line 1, in <module>TypeError: unsupported operand type(s)for +: 'int' and 'str'>>> str(a) + b'34'>>> a + int(b)7
UU/IT
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.pyDetta skrivs först.Detta skrivs inuti funktionenDetta skrivs efter metodanropet.
# function_01.py
def function_a():print "Detta skrivs
inuti funktionen."
print "Detta skrivs först."function_a() # Funktionen anropasprint "Detta skrivs efter metodanropet."
UU/IT
08-01-29 | #33@ UU/IT
Function arguments
•We communicate with functions by specifying arguments in the function call.
$> python function_02.pyHello Maja. You are23 years old.Hello Pelle. You are31 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)
UU/IT
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.pyHej Maja. Du är23 år gammal.Hej Pelle. Du är20 år gammal.
UU/IT
08-01-29 | #35@ 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.pyHello Unknown. You are 20 years old.Hello Pelle. You are 20 years old.Hello 45. You are 20 years old.
UU/IT
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 worksgreeting(name="Pelle") # Eqvivalentgreeting(age=45) # Gives the right resultgreeting("Maja", 33)greeting(name = "Maja", age = 33) # Eqvivalent
$> python function_05.pyHej Okänd. Du är 20 år gammal.Hej Pelle. 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.Hej Maja. Du är 33 år gammal.
UU/IT
08-01-29 | #37@ 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 + separators = s[:-len(separator)] + "."
return s
my_text_pieces = ["Detta", "är", "inte","så", "meningsfullt"]print my_own_join(my_text_pieces, "_")
$> python return_values_01.pyDetta_är_inte_så_meningsfullt.
UU/IT
08-01-29 | #38@ UU/IT
Multiple return values
• Python allows any number of return values.
# return_values_03.pydef min_max(seq):
return min(seq), max(seq)
a = [3, 573, 234, 24]minimum, maximum = min_max(a)print minimum, maximumresult = min_max(a)print resultprint result.__class__
$> python return_values_03.py3 573(3, 573)<type 'tuple'>
UU/IT
08-01-29 | #39@ 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.
UU/IT
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.
>>> sysTraceback (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 2006, 11:39:03) \n[GCC 4.1.1 20061130 (Red Hat 4.1.1-43)]'
UU/IT
08-01-29 | #41@ UU/IT
3rd 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
UU/IT
08-01-29 | #43@ 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:MyNumber=10def printNumber(self):
print 'The number is ',MyNumber
#Now we use the classanObject=MyClass()anObject.printNumber()
UU/IT
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.
UU/IT
08-01-29 | #45@ 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 classanObject=MyClass()print anObject.__MyNumber #This won't workprint anObject._MyClass__MyNumber #This will work, but is usually a bad idea
UU/IT
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 filenprint 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
UU/IT
08-01-29 | #47@ 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.pyDetta är textrad 1.Detta är textrad 2.Detta är textrad 3.Detta är textrad 4.Detta är text
UU/IT
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.py3[1, 2, 3]{'name': 'Kalle'}Denna rad läggs till.
UU/IT
08-01-29 | #49@ UU/IT
That's it!
• Now you know the basics of Python• More info: www.python.org
IT Uppsala universitet
Part 2: Introduction to VTK
UU/IT
08-01-29 | #51@ UU/IT
What is VTK? What can VTK be used for? How to actually use VTK?
VTK – The Visualization ToolKit
UU/IT
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
UU/IT
08-01-29 | #53@ UU/IT
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
UU/IT
08-01-29 | #55@ 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)
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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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08-01-29 | #57@ 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
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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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08-01-29 | #59@ UU/IT
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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08-01-29 | #61@ UU/IT
The Visualization Pipeline
DATA
FILTER MAPPING
DISPLAY
Visualization algorithms
Interactive feedback
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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)
UU/IT
08-01-29 | #63@ 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
UU/IT
08-01-29 | #64@ UU/IT
Cube example
http://www.it.uu.se/edu/course/homepage/vetvis/ht11/
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08-01-29 | #65@ UU/IT
User interaction vtkRenderWindowInteractor
• allows the user to interact with the objects
Try the following key presses w wireframe mode s surface modej joystick mode t trackball modebutton1 rotate button2 translate button3 scale r reset camera viewe, q exit
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08-01-29 | #66@ UU/IT
Sphere example
http://www.it.uu.se/edu/course/homepage/vetvis/ht11/
UU/IT
08-01-29 | #67@ 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
UU/IT
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
UU/IT
08-01-29 | #69@ UU/IT
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
UU/IT
08-01-29 | #71@ 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
UU/IT
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
UU/IT
08-01-29 | #73@ UU/IT
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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08-01-29 | #75@ UU/IT
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, P1313DBasics 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
