Transcript Matlab Tricks

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
 [email protected]
 Email Aaron Cois
 [email protected]
 Email me - Damion Shelton
 [email protected]
 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
 Damion’s office is EDSH 214
 Email is usually the easiest contact
method
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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
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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
 We’re 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
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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
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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
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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!)
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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 - 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
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
 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
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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
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What do I need ?
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
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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?
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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 CMake’s 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
Out
Source Build
ITK
Binary Tree
ITKb
Common
Common
Algorithms
Algorithms
BasicFilter
BasicFilter
Numerics
IO
In
Source
Build
Numerics
IO
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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 don’t 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-ofsource 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:
1. Writing some code
2. Writing a CMakeLists.txt file
3. Running CMake
4. Building your code
5. Rinse, repeat
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An aside: how to use ITK with
existing 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
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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 - it’s 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 you’re used to GUI’s
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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
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