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

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. Goals for this lecture. Compile, compile, compile Learn how to use CMake Build ITK Compile several programs that use ITK

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

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  1. 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

  2. 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

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

  4. Getting help • Email the TA - Ken Rockot • kjr21@pitt.edu • Email Aaron Cois • cacois@pitt.edu • Email me - Damion Shelton • beowulf@cs.cmu.edu • Join the insight-users mailing list; instructions are at http://www.itk.org

  5. Getting help, cont. • Get help at Pitt • Stop by BEH 761 for Ken or Aaron • Get help at CMU • Damion’s 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 - don’t copy and paste stuff from friends • More so than other classes, you will be learning techniques that translate directly to the real world - don’t cheat yourself

  7. 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

  8. Assignments, cont. • Please interpret due dates as absolute, unless told otherwise • Really • We’re happy to spend time helping you debug code, but not at 11 pm the day before the assignment is due

  9. 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

  10. We can help you with • Windows & Linux: Everyone • MacOS: Damion and Ken • Sun, SGI, Cygwin: You’re on your own • If you’re going to have compiler problems, they’ll show up early in the course, so don’t procrastinate the first assignment

  11. What is ITK? • To clarify, ITK is a toolkit • It doesn’t “do” anything • You can’t “run” it • There isn’t an itk.exe file • Typically, you use ITK in conjunction with other toolkits to handle visualization and GUI interaction

  12. So, what’s 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, it’s easy to use (gasp!)

  13. 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

  14. You might be able to do… • Generic programming • Templates & templated classes • Partial specialization • The typedef & typename keywords • Revision control using CVS/SVN • Collaborative programming

  15. 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.

  16. Step 0 - Don’t panic! • There is substantial documentation on everything I’m 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

  17. Please DON’T wear yourself trying to write down all of the content of the following slides; they’ll be on the course web page • DO interrupt me and ask questions if something isn’t clear

  18. Step 1 • Get all of the code • Fortunately, we have CD’s for you • If you’re working on some particularly esoteric platform, it’s possible that you’re missing a binary version of CMake for your machine

  19. C++ Compiler gcc 2.95 – 3.2 Visual C++ 6.0 Visual .NET Intel 5.0 IRIX CC Borland 5.0 Mac OSX - gcc CMake www.cmake.org What do I need ?

  20. Cross platform development • ITK builds on a large combination of operating systems and platforms • Each compiler has it’s own input format; makefiles, workspaces, etc. • Q: How can you possibly coordinate builds on different platforms?

  21. 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

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

  23. 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

  24. Binary Tree Out Source Build ITK ITKb Recommended ! Common Common Algorithms Algorithms BasicFilter BasicFilter Numerics Numerics In Source Build IO IO In source vs. out source builds Source Tree

  25. 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

  26. Configure - Easy Start • Run CMake • Select the SOURCE directory • Select the BINARY directory

  27. Configure - Easy Start, cont.

  28. Configure - Easy Start, cont. • Disable BUILD_EXAMPLES • Disable BUILD_TESTING • Disable USE_FLTK • Disable USE_VTK • Disable ITK_WRAP_TCL

  29. Configure - Easy Start, cont. • Ignore CMAKE_CXX_FLAGS • Ignore DART_ROOT • Ignore ITK_DATA_ROOT • Ignore VW_RAW_DATA_PATH

  30. 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

  31. Build ITK

  32. 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

  33. Verify the Build Libraries will be found in: ITK_BINARY / bin / { Debug, Release}

  34. 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

  35. Building with gcc cont. Start in directory containing Insight mkdir InsightBin cd InsightBin ccmake ../Insight Edit CMake, reconfigure if needed make

  36. 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 don’t have anything executable

  37. 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

  38. 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

  39. How to build HelloWorld, cont. • Once CMake is happy, generate the makefile/project for your compiler • Build HelloWorld • Give it a try

  40. 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…

  41. 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

  42. 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 isn’t hard, but it may take some trial and error to discover everything you need • You don’t need to worry about this in the context of this class

  43. 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 - it’s a good habit to develop

  44. 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.).

  45. 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

  46. 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

  47. 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 you’re used to GUI’s

  48. 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

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