Welcome to the Insight Toolkit ITK Lecture 1 Getting Started

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Welcome to the Insight Toolkit!ITK Lecture 1 -
Getting Started

• Methods in Image Analysis
• CMU Robotics Institute 16-725
• U. Pitt Bioengineering 2630
• Spring Term, 2006

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Goals for this lecture

• Compile, compile, compile
• Learn how to use CMake
• Build ITK
• Compile several programs that use ITK
• Find documentation online
• Learn the quirks (if any) of the system you
  choose to use

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Online course access

• Distribution of lectures/homeworks/etc. will be
  handled via our lab web site
• http//www.vialab.org/methods_course/index.html

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Getting help

• Email the TA - Ken Rockot
• kjr21_at_pitt.edu
• Email Aaron Cois
• cacois_at_pitt.edu
• Email me - Damion Shelton
• beowulf_at_cs.cmu.edu
• Join the insight-users mailing list instructions
  are at http//www.itk.org

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Getting help, cont.

• Get help at Pitt
• Stop by BEH 761 for Ken or Aaron
• Get help at CMU
• Damions office is EDSH 214
• Email is usually the easiest contact method

6
Assignments

• Collaboration is encouraged unless told
  otherwise, feel free to discuss assignments with
  other students
• But please submit your own code - dont copy and
  paste stuff from friends
• More so than other classes, you will be learning
  techniques that translate directly to the real
  world - dont cheat yourself

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Grading of assignments

• Grading criteria
• Does it accomplish the specified task?
• Is it well commented? Follow the 6 month rule -
  if you leave for 6 months, you should be able to
  pick up where you left off.
• Many/most assignments will be pass-fail, with an
  opportunity to fix problems before final judgment
  is passed

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Assignments, cont.

• Please interpret due dates as absolute, unless
  told otherwise
• Really
• Were happy to spend time helping you debug code,
  but not at 11 pm the day before the assignment is
  due

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Computer requirements

• Windows, Linux, and Mac OS 10.2 work great,
  other platforms will work too
• Your own computer is preferable, but cluster
  machines will work
• Please be aware that ITK can consume a lot of
  disk space during the build process
• There is no reason to use one of the platforms
  over another, pick your favorite

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We can help you with

• Windows Linux Everyone
• MacOS Damion and Ken
• Sun, SGI, Cygwin Youre on your own
• If youre going to have compiler problems,
  theyll show up early in the course, so dont
  procrastinate the first assignment

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What is ITK?

• To clarify, ITK is a toolkit
• It doesnt do anything
• You cant run it
• There isnt an itk.exe file
• Typically, you use ITK in conjunction with other
  toolkits to handle visualization and GUI
  interaction

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So, whats it good for?

• ITK code is easy to add to existing C code
• It provides a variety of flexible data
  containers, and ways of processing / analyzing
  them
• You can do a lot in only a few lines of code
• Once you get used to it, its easy to use (gasp!)

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What we assume you can do

• Understand C syntax
• Classes
• Basic inheritance
• Standard flow control such as for, do, calling
  functions, etc.
• Pointers, dereferencing, passing by reference
• Work comfortably in the operating system of your
  choice, using the compiler of your choice

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You might be able to do

• Generic programming
• Templates templated classes
• Partial specialization
• The typedef typename keywords
• Revision control using CVS/SVN
• Collaborative programming

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You probably have not

• Used cross-platform make software (Jam, for
  example)
• Written C code that builds on multiple
  platforms
• Designed software using a data-flow architecture,
  worried about smart pointers, etc.

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Step 0 - Dont panic!

• There is substantial documentation on everything
  Im going to present here, and vastly more about
  things that we will never cover in this course
• http//www.itk.org/HTML/Documentation.htm
• You have a copy of the ITK Software Guide on the
  CD Ken made for you

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• Please DONT wear yourself trying to write down
  all of the content of the following slides
  theyll be on the course web page
• DO interrupt me and ask questions if something
  isnt clear

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Step 1

• Get all of the code
• Fortunately, we have CDs for you
• If youre working on some particularly esoteric
  platform, its possible that youre missing a
  binary version of CMake for your machine

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What do I need ?
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Cross platform development

• ITK builds on a large combination of operating
  systems and platforms
• Each compiler has its own input format
  makefiles, workspaces, etc.
• Q How can you possibly coordinate builds on
  different platforms?

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The answer CMake

• Cross platform tool to manage the build process
• Simplifies the build process
• Auto-configuration
• Easy access to external libraries
• Used by several other open source projects

www.cmake.org
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How CMake runs

• Write a CMakeLists.txt file describing your
  project in CMakes language
• Run CMake to generate an appropriate
  makefile/project/workspace for your compiler
• Compile as you normally would

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How CMake runs, cont.

• This is not unlike the configure-make process you
  may be familiar with from various Unix systems
• But it works with many compilers
• CMakeLists.txt files are easy to perform revision
  control on

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In source vs. out source builds
Source Tree
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Why use two trees?

• Keeps your source and binary code separate
• Minimizes the amount of damage you can do to your
  CVS tree
• ITK is found in the /Insight folder
• We suggest that you build it in the /InsightBin
  folder

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Configure - Easy Start

• Run CMake
• Select the SOURCE directory
• Select the BINARY directory

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Configure - Easy Start, cont.
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Configure - Easy Start, cont.

• Disable BUILD_EXAMPLES
• Disable BUILD_TESTING
• Disable USE_FLTK
• Disable USE_VTK
• Disable ITK_WRAP_TCL

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Configure - Easy Start, cont.

• Ignore CMAKE_CXX_FLAGS
• Ignore DART_ROOT
• Ignore ITK_DATA_ROOT
• Ignore VW_RAW_DATA_PATH

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Configuring and Generating

• Each time you change an option or options you may
  need to configure CMake again
• If the generate option (OK under Windows) is
  not presented, you definitely need to hit
  configure again
• If any of the options are highlighted in red, you
  need to reconfigure

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Build ITK
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Build ITK

• Open ITK.dsw in the Binary Directory
• Select ALL_BUILD project
• Build it - it takes about 15 minutes on a
  P3-1000, but your mileage may vary

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Verify the Build

• Libraries will be found in
• ITK_BINARY / bin / Debug, Release

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Building with gcc

• Order of operations is the same
• Differences
• Run the ccmake executable, which uses a curses
  TUI, the options are identical
• Run make instead of Visual Studio
• Think of CMake as replacing the ./configure
  step you may be used to

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Building with gcc cont.

• Start in directory containing Insight
• mkdir InsightBin
• cd InsightBin
• ccmake ../Insight
• Edit CMake, reconfigure if needed
• make

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Now what?

• At this point, you should have two things
• A directory containing a bunch of source code
  (e.g. /Insight)
• A directory containing the built ITK libraries
  (e.g. /InsightBin)
• As mentioned earlier, you dont have anything
  executable

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Building an application

• ITK comes with a simple application you can build
  in order to test the ITK libraries out of
  source (I.e. not built inside ITK)
• It can be found in
• /Insight/Examples/Installation

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How to build HelloWorld

• Copy rename the Installation directory
  somewhere outside of the Insight directory
• Run CMake on HelloWorld
• Remember the source/binary distinction and use
  HelloWorldBin as your build location
• CMake should automatically find ITK
• if not, edit the ITK_DIR option

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How to build HelloWorld, cont.

• Once CMake is happy, generate the
  makefile/project for your compiler
• Build HelloWorld
• Give it a try

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More examples

• You can turn on the Examples option in CMake,
  which will build all of the examples for you
• Or you can copy the examples out-of-source and
  build them like you did HelloWorld
• These examples link into ITK Software Guide read
  the chapter, poke the code and see what happens

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Workflow thoughts

• You should get used to the idea of
• Writing some code
• Writing a CMakeLists.txt file
• Running CMake
• Building your code
• Rinse, repeat

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An aside how to use ITK withexisting
applications

• Your app probably does not use CMake
• In this case, you need to link to the ITK
  libraries explicitly and include the appropriate
  source directories
• This isnt hard, but it may take some trial and
  error to discover everything you need
• You dont need to worry about this in the context
  of this class

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Revision control with CVS

• Revision control software allows you to store
  incremental changes to software
• You will be expected to use CVS to manage your
  homework assignments
• I encourage you to use revision control on your
  code outside of this class as well - its a good
  habit to develop

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CVS terms

• Server - what it sounds like
• Module - a group of files that can be accessed on
  the server
• User - each module has associated users, with
  varying levels of access (read only, read/write,
  etc.).

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CVS terms, cont.

• Checkout - Download a fresh copy of a module from
  the server to your computer
• Update - Sync your copy of a module with the
  server copy much faster than a checkout
• Commit - Merge changes made to your local copy
  with the server

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CVS setup

• The CVS server for this course is
• cvs.vialab.org
• You will each have a module, based on your email
  Ken will tell you about this
• Only you and the instructors will have access to
  this module
• Later, there may be group modules for the final
  project

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CVS setup, cont.

• I prefer to use a GUI wrapper for CVS
• http//www.wincvs.org
• Versions are available for Windows, Mac, and
  Linux
• Windows users can use Explorer integration via
  http//www.tortoisecvs.org/
• Command line works fine too, but may be more
  awkward if youre used to GUIs

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ITK Documentation

• Most of the ITK documentation is generated
  automatically from source comments using Doxygen
• Please familiarize yourself with the various
  means of navigating the Doxygen documentation
  online
• http//www.itk.org/Doxygen/html/index.html