brains:Building

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Contents 1 Building BRAINS 1.1 Prerequisites 1.2 Make a Sandbox Directory 1.3 Download the BRAINS Software 1.4 Build the BRAINS Software 1.5 Building BRAINS 64-bit on OS X 10.5 1.6 Platforms 2 Enabling Regression Testing Suite 3 How to Add a BRAINS Test Procedure 4 BRAINS Quality Dashboard

Building BRAINS

Prerequisites

You will need the following tools and libraries installed to build BRAINS

• git - Version 1.3 or greater
• cmake - Version 2.8.2 or greater
• Qt Development Environment - Version 4.7 or higher - Required only if you want to build the GUI.

Make a Sandbox Directory

This is the directory where you will download the source code, download images, and generated the resulting binaries

% mkdir /scratch/brains
% cd /scratch/brains

Download the BRAINS Software

• Beta release

% svn co https://www.nitrc.org/svn/brains/BRAINS/branches/BRAINS3_Release-1_0 BRAINS3

• Development version

% svn co https://www.nitrc.org/svn/brains/BRAINS/trunk BRAINS3 

To enable testing - Download the BRAINS Testing data

% svn checkout --username developername https://www.nitrc.org/svn/brainstestdata

Configuration Variables:

• Testing - By default this is set to ON. If you don't wish to build BRAINS3 tests, when you configure your build tree, set the following variables to be OFF
  • BRAINS_BUILD_TESTING
  • BUILD_TESTING
  • Slicer3_USE_VTK_DEBUG_LEAKS
• Python - By default this is set to ON. Presently you should set the following variables to be OFF.
  • Slicer3_BUILD_NUMPY
  • Slicer3_USE_PYTHON
  • Slicer3_USE_PYTHONQT
• Graphical User Interface (BRAINSTracerQt). Turn the following variables to ON
  • BRAINS_BUILD_GUI
  • BRAINS3_USE_QT
• Build Type - Debug or Release
  • CMAKE_BUILD_TYPE - For production use set to Release, Debug mode should only be used for development. You will see approximately a 4x speed increase building under Release mode.
• Installation Directory - Specify the location of the installed binaries using the CMake variable CMAKE_INSTALL_PREFIX

Build the BRAINS Software

Make a build directory and run CMake to configure it for building

% mkdir BRAINS3-build
% cd BRAINS3-build
% ccmake ../BRAINS3/SuperBuild

Ignorable warning message that occurs during make file generation:

Important CMake options:

• set the library path to allow the GenerateCLP program to find its required shared libraries.

% source ../BRAINS3/SuperBuild/setpath.sh

There is also a 'setpath.csh' script if you are running the C shell.

• run 'make' to generate all libraries and executables

% make

• on multiprocessor machines, you can speed up builds by running make in parallel

% make -j2 # for a dual core machine. -j4 for quad core, etc

Building BRAINS 64-bit on OS X 10.5

The default on OS X 10.5 is to build programs 32-bit. On OS X 10.6 the default is 64-bit. To build 64-bit on OS X, you need to set the CMake parameter CMAKE_OSX_ARCHITECTURES to "x86_64"

Platforms

The current build scripts has been tested on the following platforms

• Linux
  • Red Hat Enterprise Linux 5.5 -- 32 & 64 bit.
  • Ubuntu - 32 bit - 8.10
  • Ubuntu - 64 bit - 7.10
  • Ubuntu - 64 bit - 8.10

• Macintosh
  • Mac OS X - Intel - 10.5
  • Mac OS X - Intel - 10.6.x
  • Mac OS X - PPC - 10.5 - Deprecated -- will probably work, but we no longer have PPC Macs to test builds with. Note: need to set the environmental variable as described below
  • Mac OS X - 10.4 - Needs testing

 % export MACOSX_DEPLOYMENT_TARGET="10.4"

• Windows
  • MinGW - Needs testing
  • Visual Studio - Needs testing

Enabling Regression Testing Suite

1. Change directories to the location where you ran the BRAINS svn checkout
2. Checkout the regression testing suite
   • svn checkout --username developername https://www.nitrc.org/svn/brainstestdata
3. Add tests for recently developed regression testing suite

The results from the testing suite are posted on the BRAINS Dart Dashboard

How to Add a BRAINS Test Procedure

1. Create a file with the test in src/regressionmodule/module
   • The name of the procedure needs to match the file name
   • The procedure should take two inputs
     • pathToRegressionDir - Base directory for regression tsting data
     • dateString - Time stamp for test
   • Two global variables have been defined: MODULE_SUCCESS and MODULE_FAILURE. Your test should return one of these values depending on the status of your test
   • Convenience functions have been created for testing purposes
     • StartModule - Start module logging
     • StopModule - Stop module logging and return module status
     • ReportTestStatus - Report if a test passes or fails
     • CoreImageTest - test an image for specified parameters
2. Add the test procedure name to the CMakeLists.txt file in src/iplTclCmd
3. CMake will generate a wrapper script for testing the procedure
4. Quick test for testing new test

brains3 -b <Path-To-BRAINS-COMPILE>/<Platform>/DEBUG-build/BRAINS3-build/src/Testing/results/<Test>_wrapper.b2

BRAINS Quality Dashboard

BRAINS Dart Dashboard