Lecture 2

A brief overview of simple Python

and more advanced C++
Methods in Medical Image Analysis - Spring 2022
16-725 (CMU RI) : BioE 2630 (Pitt)
Dr. John Galeotti

Based in part on Damion Shelton’s slides from 2006

This work by John Galeotti and Damion Shelton, © 2004-2022, was made possible in part by NIH NLM contract#
HHSN276201000580P, and is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this
license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 171 2nd Street, Suite 300, San 1
Francisco, California, 94105, USA. Permissions beyond the scope of this license may be available by emailing [email protected].
The most recent version of these slides may be accessed online via http://itk.galeotti.net/
Goals for this lecture

 C++ vs. Python

 Brief Python Introduction
 Overview of object-oriented programming
 Inheritance & polymorphism
 Public / private / protected derivation
 Overview of generic programming
 templates
 templated classes
 specialization
 typedef & typename keywords
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Disclaimer

 Some of you will definitely know more about

Python than I do.
 Some of you may know more about object
oriented programming than what I will present
(or what I remember)
 We will not discuss the more esoteric
inheritance methods, such as friend classes

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Reference & Review Material
 Books
 C++ How to Program - Deitel & Deitel
 Teach Yourself C++ in 21 Days - Liberty
 Using the STL: The C++ Standard Template Library - Robson
 Design Patterns; Elements of Reusable Object-Oriented
Software - Gamma et al.
 Websites
 http://docs.python.org/tutorial/
 http://docs.python.org/reference/index.html
 http://www.cppreference.com/
 I use this one more than the rest.
 http://www.cplusplus.com/doc/tutorial/
 http://www.sgi.com/tech/stl/table_of_contents.html
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C++ vs. Python
 C++
 Compile and Link
 Low-level language (but standardized higher-level libraries available)
 Writing code takes longer
 Code runs very fast
 Python
 Interpreted
 Very high level language
 Writing code is quick and easy
 Python code runs more slowly, but…
 Python can call precompiled C/C++ Libraries
 Best of both worlds
 So ITK could should execute at full compiled speed, even when called
from Python.
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Formatting note

 In general, I will try to format code in a fixed-

width font as follows:
this->IsSome(code);
 However, not all code that I present could
actually be executed (the above, for instance)

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Python Example Code
(Take notes as needed!)
# Everything on a line after a # is a comment
# Warning: Indentation matters in Python!
import SimpleITK as sitk # use sitk as the module name

input = sitk.ReadImage( "images/cthead1.jpg" )

output = sitk.SmoothingRecursiveGaussian ( input , 2.0 )
sitk.Show( output )

image = sitk.Image( 256,256, sitk.sitkFloat32 )

image[160,160]= 99.9 # [] allows direct pixel access
sitk.Show( sitk.Add( output, image) )

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Python Example Code
(Take notes as needed!)
# Continuing from the previous slide...

imagevolume = sitk.Image( 192,192,32, sitk.sitkInt16 )

# Change image to use the matching pixel type
image = sitk.Cast( image, imagevolume.GetPixelIDValue() )
# Copy over the previous pixel value of 99
imagevolume.SetPixel ( 64,64,0, image.GetPixel(160,160) )

sliceNum = 1
while sliceNum < 31: # indention must match!
pixelValue = 16 + 4*sliceNum
imagevolume[96,96,sliceNum] = pixelValue
print(pixelValue)
sliceNum = sliceNum+1

sitk.Show( imagevolume, "VolTitle" ) 10

 Python Example Code:
sitk.ImageViewer(): The object-oriented alternative

image_viewer = sitk.ImageViewer()
image_viewer.SetTitle(’VolTitle’)

# Now run ImageViewer using the default image viewer:

image_viewer.Execute(imagevolume)

# Change viewer program, then display again:

image_viewer.SetApplication(
'/Applications/ITK-SNAP.app/Contents/MacOS/ITK-SNAP')
image_viewer.Execute(imagevolume)

# Change the viewer command, to also pass arguments:

# (use ITK-SNAP's -z option to open the image in zoomed mode)
image_viewer.SetCommand(
'/Applications/ITK-SNAP.app/Contents/MacOS/ITK-SNAP -z
2’) 11
Credit: excerpted from https://simpleitk.readthedocs.io/en/v1.2.4/Examples/ImageViewing/Documentation.html
List of SimpleITK Pixel Types

 The definitive list of SimpleITK pixel types is in its

source code
 SimpleITK’s source code must be downloaded separately
 Look at the bottom of this file:
 SimpleITK/Code/Common/include/sitkPixelIDValues.h
 Warning: Not every compilation of SimpleITK
supports all of these pixel types.
 The source code has recommendations for how to check that
a given type is available, etc.

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Don’t freak out about what’s next

 Most students in the class only loosely use

most of the following C++ material.
 Most students will do all or most of their
programming in Python, with only simple
object-oriented programming.
 Most students only need a limited
understanding of what follows, so they can
occasionally make sense of ITK’s C++
documentation (in cases where the Python
documentation isn’t as good).
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Object-oriented programming

 Identify functional units in your design

 Write classes to implement these functional
units
 Preferably as “black boxes”
 Separate functionality as much as possible to
promote code re-use

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Class membership

 Classes have member variables and methods

 ITK names class member variables with the “m_”
prefix, as in “m_VariableName”
 Class members are 1 of 3 types
 Public
 Private
 Protected

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Public membership

 Everyone can access the member

 The rest of the world
 The class itself
 Child classes
 You should avoid making member variables
public, in order to prevent undesired
modification.
 A black box shouldn’t have openings!

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Private membership

 Only the class itself can access the member

 It’s not visible to the rest of the world
 Child classes can’t access it either

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Protected membership

 The middle ground between public and private

 The outside world can’t access it… but derived
classes can

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ITK and membership

 In ITK, member variables are almost always

private
 There are public accessor functions that allow
the rest of the world to get and set the value of
the private member
 This ensures that the class knows when the
value of a variable changes

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 Why do it this way?

 Consider a filter class—if someone changes a

variable in the filter, it should re-run itself the next
time the user asks for output
 If nothing has changed, it doesn’t waste time
running again
 Accessor functions set a “modified flag” to notify
the framework when things have changed
 More on this in another lecture

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Inheritance in a nutshell

 Pull common functionality into a base class

 Implement specific/unique functionality in
derived classes
 Don’t re-invent the wheel!
 Base classes = parents
 Derived classes = children

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Overloading

 If a child class re-implements a function from

the base class, it “overloads” the function
 You can use this to change the behavior of a
function in the child class, while preserving the
global interface

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 An example of inheritance in a
graphical drawing program

Shape
Polygon
Triangle
Quadrilateral
Rectangle
Trapezoid
Rhombus
Pentagon
ConicSection
Ellipse
Circle
Parabola
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An example of ITK inheritance
itk::DataObject
itk::ImageBase< VImageDimension >
itk::Image< TPixel, VImageDimension>

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C++ Namespaces

 Namespaces solve the problem of classes that

have the same name
 E.g., ITK contains an Array class, perhaps your
favorite add-on toolkit does too
 You can avoid conflicts by creating your own
namespace around code
namespace itk { code }

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 C++ Namespaces, cont.

 Within a given namespace, you refer to other

classes in the same namespace by their name only,
e.g. inside the itk namespace Array means “use
the ITK array”
 Outside of the namespace, you use the itk:: prefix,
e.g. itk::Array
 Only code which is part of ITK itself should be
inside the itk namespace
 At minimum, you’re always in the global
namespace
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C++ Namespaces, cont.

 Note that code within the itk namespace

should refer to code outside of the namespace
explicitly
 E.g. use std::cout instead of cout

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C++ Virtual functions

 Want to enforce a consistent interface across a

set of child classes?
 Virtual functions allow a base class to declare
functions that “might” or “must” be in its child
classes
 The “=0” declaration means that the function
must be implemented in a child class
 Because it is not implemented in the base class
 Virtual functions that are implemented in the
base class can still be overridden by child classes
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C++ Virtual functions, cont.

 You can specify (and use) a virtual function

without knowing how it will be implemented in
child classes
 This allows for polymorphism
 For example:
virtual void DrawSelf() = 0;

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 C++ Example of polymorphism in a
graphical drawing program

Shape: DrawSelf() = 0;
Polygon: int vertices; DrawSelf() connects vertices with line segments
Triangle: vertices=3
Quadrilateral: vertices=4
Rectangle
Trapezoid
Rhombus
Pentagon: vertices=5
ConicSection
Ellipse: DrawSelf() uses semimajor and semiminor axes
Circle: forces length semiminor axis = length semimajor
Parabola

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Generic programming

 Generic programming encourages:

 Writing code without reference to a specific data
type (float, int, etc.)
 Designing code in the most “abstract” manner
possible
 Why?
 Trades a little extra design time for greatly improved
re-usability

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Image example

 Images are usually stored as arrays of a

particular data type
 e.g. unsigned char[256*256]
 It’s convenient to wrap this array inside an
image class (good object oriented design)
 Allowing the user to change the image size is
easy with dynamically allocated arrays

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Image example, cont.

 Unfortunately, changing the data type is not so

easy
 Typically you make a design choice and live with
it (most common)
 Or, you’re forced to implement a double class, a
float class, an int class, and so on (less
common, can be complicated)
 This is the interface used by SimpleITK, but…
 SimpleITK usually automates type selection to make
your life easier
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Templates to the rescue

 Templates provide a way out of the data type

quandary
 ITK uses templates extensively
 SimpleITK relies on ITK, and SimpleITK’s automated
type functionality depends on ITK’s templated nature
 If you’re familiar with macros, you can think of
templates as macros on steroids
 With templates, you design classes to handle an
arbitrary “type”

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 Anatomy of a templated class

template <typename TPixel, unsigned

int VImageDimension=2>
class ITK_TEMPLATE_EXPORT Image :
public ImageBase<VImageDimension>

Template keyword, the < >’s enclose template

parameters

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Anatomy of a templated class

template <typename TPixel, unsigned

int VImageDimension=2>
class ITK_TEMPLATE_EXPORT Image :
public ImageBase<VImageDimension>

TPixel is a class (of some sort)

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Anatomy of a templated class

template <typename TPixel, unsigned

int VImageDimension=2>
class ITK_TEMPLATE_EXPORT Image :
public ImageBase<VImageDimension>

VImageDimension is an unsigned int,

with a default value of 2

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Anatomy of a templated class

template <typename TPixel, unsigned

int VImageDimension=2>
class ITK_TEMPLATE_EXPORT Image :
public ImageBase<VImageDimension>

Image is the name of this class

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Anatomy of a templated class

template <typename TPixel, unsigned

int VImageDimension=2>
class ITK_TEMPLATE_EXPORT Image :
public ImageBase<VImageDimension>

Image is derived from ImageBase in a

public manner

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Specialization

 When you specify all of the template

parameters, you “fully specialize” the class
 In the previous example,
ImageBase<VImageDimension> specializes
the base class by specifying its template
parameter.
 Note that the VImageDimension parameter is
actually “passed through” from Image’s
template parameters

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Derivation from templated classes

 You must specify all template parameters of the

base class
 The template parameters of the base class may
or may not be linked to template parameters of
the derived class
 You can derive a non-templated class from a
templated one if you want to (by hard coding
all of the template parameters)

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Partial specialization

 C++ also allows partial specialization

 For example, you write an Image class that
must be 3D, but still templates the pixel type
(or vice-versa)

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 Templated class instances

 To create an instance of a templated class, you must

fully specialize it
 E.g.
itk::Image<int, 3> myImage;
Creates a 3D image of integers
(not quite true, but we can pretend it does until we cover smart pointers)

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 using shorthand type names

 One consequence of templates is that the names of a

fully defined type may be quite long
 E.g., this might be a legal type:
itk::Image<itk::MyObject<3, double>,
3>

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 using shorthand type names

 You can create a short-hand “alias” for our user-

defined type with the using keyword:

using 3DIntImageType = itk::Image<int, 3>;

3DIntImageType myImage;
3DIntImageType anotherImage;

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 Fun with using

 using types can themselves be global members of

classes and accessed as such
using OutputType = itk::Image<double, 3>;
OutputType::Pointer im = filter1.GetOutput();
 In template classes, member using aliases are often
defined in terms of template parameters—no problem!
This is quite handy.
using InputType = itk::Image<TPixel, 3>;

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Naming of templates and using

 ITK uses the following conventions:

 Template parameters are indicated by T (for type) or
V (for value). E.g. TPixel means “the type of the
pixel” and VImageDimension means “value
template parameter image dimension”
 Defined types (created with using) are named as
FooType. E.g. CharImage5DType

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Be careful

 If you’re careless in naming classes, template

arguments, typedefs, aliases, and member
variables (with the “m_” prefix), then it can be
quite difficult to tell them apart!
 Don’t write a new language using typedefs.
 Remember to comment well and don’t use
obscure names
 e.g. BPType is bad, BoundaryPointType is good

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Typenames
 typename exists to “optionally” help the compiler
 Different compilers handle it differently
 In general, you can take it to mean that you are
promising the compiler that what follows is some sort of
valid type, even if the compiler can’t see that yet
 Example of when to use and not use typename:
 using PixelType = Tpixel;
 // template parameter names don’t need typename
 using Superclass = ImageBase<VImageDimension>;
 // direct class names don’t need typename either

 using PointType = typename Superclass::PointType

;
 // do use typename when referring to an alias
defined inside another alias
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For more on “typename”
 https://en.wikipedia.org/wiki/Typename

 http://blogs.msdn.com/slippman/archive/2004/08/11/212768.aspx

 https://en.cppreference.com/w/cpp/language/dependent_name
 https://en.cppreference.com/w/cpp/language/type_alias

 Note: typename is handled differently in different C++ standards.

ITKv5 is compliant with C++11.

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.hxx, .cxx, .h

 ITK uses three standard file extensions, and so

should you:
 .h files indicate a class header file
 .cxx indicates either
 executable code (an example, test, demo, etc.)
 a non-templated class implementation
 .hxx indicates a templated class implementation
 Like a .cxx file, but it can’t be compiled by itself because it
does not specify its template parameter values
 FYI, previous versions of ITK used .txx instead of .hxx

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Did this all make sense?
 If not, you probably want to sick to Python or C++ SimpleITK

 If you want to use full C++ ITK (not required for this class):
 It’s ok if you’re a little rusty on the details, etc.
 It’s helpful if you have seen and used some of this stuff before.
 If this is mostly new to you:
 Understand that neither I nor the TA will teach you how to do basic
programming in Python or C++
 You should probably use mostly SimpleITK
 Beware that SimpleITK lacks many of ITK’s more advanced features, including several
types of registration and the ability to tweak less frequently used parameters.
 If you don’t know how to write and compile C++ programs, then I recommend
using Python!
 CMU 15-112: https://www.cs.cmu.edu/~112/
 http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-189-a-gentle-introduction-to-
programming-using-python-january-iap-2011/
 You could also take a class on C++
 http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-s096-introduction-to-c-and-c-
january-iap-2013/

52
Final advice

 If you run across something in ITK you don’t

understand, don’t panic
 Be careful not to confuse typedefs with classes
 Error messages can be quite long with templates and will take
time to get used to
 Email for help sooner rather than later
 Learning the style of C++ used by native ITK is at least
half the battle to writing native ITK Code
 Remember, if you just need to use common ITK
functionality, then SimpleITK is usually the way to go!
 https://simpleitk.org/doxygen/v2_0/html/Filter_Coverage.html

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