ITK/Release 4/Modularization/Prototype/Tutorial

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Overview

  • Toy modular ITK design

This tutorial demonstrates the prototype of modularized ITK with a toy example containing seven modules required to build Nrrd image I/O programs.

The seven library modules are: 

 * itk-vnl (a subset of numeric libraries of VXL),
 * itksys (a system supporting library),
 * itk-common (core classes, macro definitions, typedefs, and other software constructs central to ITK),
 * itk-io-common (classes that support the reading and writing of data),
 * nrrdio (third-party library of nrrd image IO),
 * itk-io-nrrd (itk wrapper of nrrdio).
 * itk-zlib (zlib library wrapped up for nirrdio)


  • CMake prototyping

To enable ITK developers download and configure the whole modularized ITK package, we have prototyped several CMake packaging strategies. The major challenge is to manage dependencies between the modules. Two approaches have been proposed so far and are demonstrated in this tutorial.

One method uses "add_subdirectory" to include ITK modules in correct order according to their dependencies. Git submodule [1] is used to obtain all the modules all together with version controls. Here we refer this approach as "itk-complete" approach (Method A), which is designed for ITK developers. Another approach is to use the state-of-the-art cmake function "add_export_project" to automate the process of pulling selected modules from their repositories. Users can select the specific modules they need for their applications from the cmake gui. We refer to this second approach as "itk-optional" approach (Method B).

Requirements

  • A computer with a network connection ( windows and linux platforms only at the moment)
  • A build environment (gcc / VS)
  • CMake 2.8.2 installed([2])
  • Git 1.7.x.x installed ([3])

Build and test toy modular ITK

Module-by-module

The repositories of the seven modules in the toy modular ITK are listed as follows. They can be build separately with manually specified (via cmake gui) paths for their required depending modules. 

#itk-vnl
  git://kwsource.kitwarein.com/itk/itk-vnl.git

#itksys
 git://kwsource.kitwarein.com/itk/itksys.git

#itk-zlib
 git://kwsource.kitwarein.com/itk/itk-zlib.git

#nrrdio
  git://kwsource.kitwarein.com/itk/nrrdio.git

#itk-common
 git://kwsource.kitwarein.com/itk/itk-common.git

#itk-io-common
 git://kwsource.kitwarein.com/itk/itk-io-common.git

#itk-io-nrrd
 git://kwsource.kitwarein.com/itk/itk-io-nrrd.git

CTest results of those modules can be found on the dashboard: 

http://www.cdash.org/CDash/index.php?project=Insight#ITKv4_Modularization

Method A: itk-complete

Download the itk-complete superproject package to the source directory (/src) using Git : 

git clone git://kwsource.kitwarein.com/itk/itk-complete.git

In the created itk-complete directory: ".gitsubmodule" file contains all submodules' urls; "itk-depends" module contains the dependencies among the modules and cmake codes to configure the superproject according to the dependencies. You will also see empty directories created for the seven modules.

Download toy modular ITK modules using git submodule : 

# enter the itk-complete directory 
cd itk-complete

# add the submodule repository URLs
git submodule init

# clone the repositories and check out the commits specified in the superproject
git submodule update

Now you have all the source codes ready for building the toy modular ITK.

Build itk-complete project in the build directory (/bin): 

#CMake configure and generate
cd /bin/itk-complete
ccmake /src/itk-complete

#compile
make

Till now you have successfully build the modular ITK project from source codes. Their dependencies are automatically configured according to the predefined dependencies in the package.

Test itk-complete with an example application: 

 # get the test package app-itk-complete
 git clone git://kwsource.kitwarein.com/itk/app-itk-complete.git
 
 # cmake configure and generate
 cd /bin/app-itk-complete
 ccmake /src/app-itk-complete

 # build and test
 make test

Two tests in the application are both related to nrrd image IO. The "itkNrrdVectorImageReadWriteTest" tests with a vector nrrd input image which is automatically downloaded from MIDAS database at the testing time (Test with MIDAS data).

Method B: itk-optional

Download the itk-optional package using Git to the source directory (/src): 

git clone git://kwsource.kitwarein.com/itk/itk-optional.git

Download the dependency module : 

# download to the itk-optional directory 
cd itk-optional
git clone git://kwsource.kitwarein.com/itk/itk-depends.git

Build itk-optional project in the build directory (/bin): 

#CMake configure and generate
cd /bin/itk-optional
ccmake /src/itk-optional



#compile
make

You will notice the modules are downloaded (as external projects) at the build time. The source codes are downloaded to the default binary directory where you build the project.


Test itk-complete with an example application: 

 # get the test package app-itk-optional
 git clone git://kwsource.kitwarein.com/itk/app-itk-optional.git
 
 cd /bin/app-itk-optional
 ccmake /src/app-itk-optional
 
 make test

Tests with MIDAS data

The testing data in this tutorial are all stored remotely in MIDAS. 

http://midas.kitware.com/

CMake command "midas_ctest" automatically obtain the data from MIDAS server according to a key file associate with the data. In order to use midas_test command, "MIDAS.cmake" needs to be included in the test cmake scripts.

Reference

 https://git.wiki.kernel.org/index.php/GitSubmoduleTutorial
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