Slicer3:Build Instructions

All-in-one Script to checkout and build Slicer3

To compile and build Slicer3, you need a set of development packages installed on your machine:

• pre-requisite material for Linux
• pre-requisite material for Windows
• pre-requisite material for Mac

There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. (Click here for background on getbuildtest and the experimental getbuildtest2 version).

Just do the following two commands (see for windows users below):

  svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3

  ./Slicer3/Scripts/getbuildtest.tcl

Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.

To run (all platforms):

./Slicer3-build/Slicer3

Note: the whole build environment takes about 2G of disk space.

Testing

Note also that getbuildtest will do an Experimental submission to the Slicer3 dashboard. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with

getbuildtest.tcl -t ""

Other options for the -t (--test-type) option are Nightly or Continuous (or any of the CTest options).

What does getbuildtest.tcl do?

This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.

Specifically, getbuildtest does the following steps:

• Refreshes Slicer3 svn
• Runs Scripts/genlib.tcl which does the following for each of the support libraries
  • does a cvs/svn checkout/update
  • runs cmake with the correct settings for use with Slicer3
  • runs make (or developer studio) to build the libraries
• Runs cmake on Slicer3
• Builds Slicer3
• Runs ctest on Slicer3
• (optionally) Runs CPack on Slicer3

Usage

Usage:

 usage: getbuildtest [options] [target]
   [target] is determined automatically if not specified
   [options] is one of the following:
    --help : prints this message and exits
    --clean : delete lib and build directories first
    -t --test-type : CTest test target
    --release : compile with optimization flags
    --update : does a cvs/svn update on each lib
    --pack : builds a distribution package (cpack)

Errors from getbuildtest

You will need to have your firewall configured to allow access to na-mic.org for cvs access through port 2401. Also you need 8081 for submitting to the dashboard.

Other errors might mean you don't have all the build tools (see next section).

If you want to generate a log of the build process, you can use a command like the following:

# for csh/tcsh:
./Scripts/getbuildtest.tcl |& tee build.log

or

# for sh/bash:
./Scripts/getbuildtest.tcl 2>&1 | tee build.log

Updating Your getbuildtest Build

There are a few options:

• you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)
• you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).
• you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.

The following command for unix machines will update, build, and launch the latest Slicer3:

svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)

getbuildtest on linux

To compile slicer and do development, be sure you have a complete set of development packages installed on your machine. The exact packages vary by distribution, but include:

• gcc
• gcc-c++
• libX11
• libX11-devel (libX11-dev on Ubuntu 7.04)
• libXt-devel (libXt-dev on Ubuntu)
• opengl/mesa (libgl1-mesa-dev on Ubuntu)

Ubuntu one line install:

sudo apt-get install subversion cvs tcl8.4 gcc g++ libX11-dev libXt-dev libxext-dev libgl1-mesa-dev libncurses5-dev tcsh

Also, be sure you have OpenGL and the GLX extension to X working. To check the installation, it is usually enough to confirm that the command

glxgears

runs with no errors.

getbuildtest on windows

The script should work fine on a properly configured windows environment. Current requirements are:

• Developer Studio 8 Visual C++ Express which is free from Microsoft - be sure to install the Platform SDK and follow the ridiculous manual steps to set up the paths see below.
• Developer Studio 9 Visual C++ Express Slicer:Build_Instructions:MSVS9
  • Other releases of visual studio also work (7 and 7.1)
  • If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically (you need to edit slicer_variables.tcl to point to the installation).
• Cygwin with the following packages
  • tcltk
  • svn
  • cvs
  • unzip
  • curl
• With Developers Studio and cygwin installed, you only need to do the svn checkout and getbuildtest script to get a fully working Slicer3 plus all the tools you need to develop new code.

Note: CMake and VTK will not work on a FAT formatted disk (use NTFS).

getbuildtest on Apple Mac OS X

For Mac OS 10.4.10 install the following from the OS disks (not installed by default on new machines):

• Xcode Tools (OS Disk 1, default window)
• X11: also on OS Disk 1, but you need to scroll down and find the Optional Installs installer and select X11 under Applications. See step-by-step instructions.
• X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg
• Subversion. Installation options here. Get the latest svn version for compatibility with the server and be sure your client includes SSL (so it can access https repositories).

Remember to run getbuildtest from an xterm so the tests can access the X server.

configuration options

The file Slicer3/slicer_variables.tcl includes configuration options for which support libraries to use. You may want to change thes for testing or to get access to new functionality.

set ::SLICER_TAG "http://www.na-mic.org/svn/Slicer3/trunk"
set ::CMAKE_TAG "CMake-2-4-2"
set ::TEEM_TAG "Teem-1-9-0-patches"
set ::KWWidgets_TAG "HEAD"
set ::VTK_TAG "VTK-5-0"
set ::ITK_TAG ITK-3-0
set ::TCL_TAG "core-8-4-6"
set ::TK_TAG "core-8-4-6"
set ::ITCL_TAG "itcl-3-2-1"
set ::IWIDGETS_TAG "iwidgets-4-0-1"
set ::BLT_TAG "blt24z"
set ::SANDBOX_TAG "http://svn.na-mic.org/svn/NAMICSandBox/branches/Slicer-2-6"

For example, you may want a build against the ITK cvs head. Change the flag value and then run

getbuildtest.tcl --update 

which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use --clean.

Another useful option is to change your build type to include support debugging.

set ::VTK_BUILD_TYPE "RelWithDebInfo"

options are Debug, Release, or RelWithDebInfo. RelWithDebInfo is a compromise between speed and debuggability. If you are tracking down a tough C++ bug you will get better information in Debug mode. After changing this flag, you should run

getbuildtest.tcl --clean

to create a completely new build.

Manual checkout/build of Slicer3 and support libraries:

Prerequisite software

You need to get and build the following packages if you aren't using the getbuildtest script:

1. CMake (2.4.1 or later)
2. Tcl/Tk (8.4 or later)
3. incrTcl (3.2.1)
4. VTK 5.0
5. ITK 3.4
6. KWWidgets Slicer-3-0 tag
7. Teem (1.9.0)

Build Steps

Steps:

$ svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3
$ cvs -d :pserver:anoncvs@www.vtk.org:/cvsroot/VTK co VTK -r VTK-5-0
$ cvs -d :pserver:anoncvs@www.itk.org:/cvsroot/Insight co Insight -r ITK-3-4
$ cvs -d :pserver:anoncvs@www.kwwidgets.org:/cvsroot/KWWidgets co KWWidgets -r Slicer-3-0

Configure and build ITK

• BUILD_SHARED_LIBS ON
• CMAKE_SKIP_RPATH ON

Configure and build VTK

• All systems:
  • BUILD_SHARED_LIBS ON
  • CMAKE_SKIP_RPATH ON
  • VTK_WRAP_TCL ON
  • VTK_DEBUG_LEAKS ON

• MacOSX specific (Make sure to install X11):
  • VTK_USE_CARBON OFF
  • VTK_USE_X ON

• Note, those options should not appear, since they disapear since VTK5:
  • VTK_USE_HYBRID ON
  • VTK_USE_PATENTED ON

• Make sure that the TCL and TK path are set properly
  • TCL_* and TK_*

Configure and build KWWidgets

• You need to specify where your VTK build tree is.
• BUILD_SHARED_LIBS ON
• CMAKE_SKIP_RPATH ON

Build and Run Slicer3

Manually

1. Check out and build slicer3 (e.g. on linux)

 svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3
 mkdir Slicer3-build
 cd Slicer3-build
 ccmake ../Slicer3
 make

Again make sure to turn:

• BUILD_SHARED_LIBS ON
• CMAKE_SKIP_RPATH ON

Start slicer with the Slicer3 executable in your build directory.

SBuild

SBuild is a new, experimental build system for Slicer. It is based on getbuildtest2.tcl and genlib2.tcl, but rather than try to hid the gory details of building Slicer, SBuild attempts to expose a reasonable amount to the developer. The interface should be reasonably intuitive, but a brief walk through is useful. Click on the thumbnails for larger views. SBuild allows you to update and build just the portions of Slicer that you may require or want to build. Any of the required libraries may be specified to be build by SBuild, or to use an existing build. Existing libraries are not controlled by SBuild.

Adding new Libraries to SBuild

The default package of SBuild contains the minimal number of required libraries to build Slicer. Currently no optional libraries are installed. The procedure for providing an SBuild plugin is modestly complicated, but several good examples exist. All plugins go in SBuild.vfs/lib/SBuildPlugins. As an example, let's create a plugin called Mythical, contained in SBuild.vfs/lib/SBuildPlugins/Mythical.tcl.

In the Slicer3/Scripts/SBuild directory, run ./bootstrap run to run SBuild, and ./bootstrap build to build the Tcl Starkits.

The first section of Mythical.tcl provides some housekeeping details:

package provide SBuildPlugins 1.0 

lappend ::SBuild(Plugins) Mythical 

set ::Plugin(Mythical,Type) "optional"
set ::Plugin(Mythical,Order) 100
set ::Plugin(Mythical,CanUseUserBuild) 1

The Mythical plugin must append itself to ::SBuild(Plugins) to register, and declares itself optional, builds in order 100, and can use user provided builds.

Each plugin must provide several Tcl procs to do various functions. The naming convention is PluginName-Function-Architecture. In this example PluginName is Mythical. SBuild first looks for the -Architecture variant, and failing, calls the PluginName-Function. For instance, Mythical-Update is the Tcl proc that updates the source for Mythical, while Mythical-Build-Windows is a specialization for Windows. The important functions are: Update, Configure, Build, and ConfigureSlicer. The ConfigureSlicer function may append a CMake argument to be used when Slicer is configured. If external packages are allowed, the ConfigureExternal function is called. ConfigureExternal usually looks for libraries and sets a LibPath to be used to configure Slicer. Examples of these functions are shown below.

# Here is where we would add lines to the main Slicer3 configuration
proc Mythical-Setup {} {
  global SBuild
}

# How do we setup for an external build
proc Mythical-ConfigureExternal {} {
  global SBuild
  set SBuild(Mythical,LibPath) [file dirname [FindFile $::SBuild(Mythical,ExternalBuildPath) [list libMythicalCommon* MythicalCommon*.lib MythicalCommon*.dll]]]
}

# Add a line to Slicer's CMake command
proc Mythical-ConfigureSlicer {} {
  global Plugin SBuild Slicer
  set dir [file join $SBuild(SlicerLibDir) Insight-build]
  if { $SBuild(Mythical,UseExternalBuild) } {
    set dir $SBuild(Mythical,ExternalBuildPath)
  }
  Debug "setting Mythical_DIR to $dir"
  lappend Slicer(CMakeArguments) -DMythical_DIR:FILEPATH=$dir
}

# How do we update Mythical?
proc Mythical-Update {} {
  Debug "Checking out Mythical"
  global SBuild Plugin
  file mkdir Insight
  ExecuteCommand $SBuild(SVNCommand) co http://www.mythical.org/svn/Mythical/trunk Mythical
}

# Configure to build
proc Mythical-Configure {} {
  Debug "Configure Mythical"
  global SBuild Plugin
  file mkdir Mythical-build
  cd Mythical-build
  ExecuteCommand $SBuild(CMake) \
    -G$SBuild(Generator) \
    -DCMAKE_CXX_COMPILER:STRING=$::SBuild(CompilerPath)/$SBuild(Compiler) \
    -DCMAKE_CXX_COMPILER_FULLPATH:FILEPATH=$::SBuild(CompilerPath)/$SBuild(Compiler) \
    -DBUILD_SHARED_LIBS:BOOL=ON \
    -DCMAKE_SKIP_RPATH:BOOL=ON \
    -DBUILD_EXAMPLES:BOOL=OFF \
    -DBUILD_TESTING:BOOL=OFF \
    -DCMAKE_BUILD_TYPE:STRING=$::SBuild(BuildType) \
    -DCMAKE_CXX_FLAGS_DEBUG:STRING=$::SBuild(CMakeCXXFlagsDebug) \
    ../Insight
}

# How do we build on windows?
proc Mythical-Build-Windows {} {
  global SBuild
  cd Insight-build
  ExecuteCommand $SBuild(Make) Mythical.SLN /build  $SBuild(BuildType)
}

# How do we build on other Makefile-based systems?
proc Mythical-Build {} {
  Debug "Building Mythical"
  global SBuild
  cd Insight-build
  eval ExecuteCommand $SBuild(Make) $SBuild(ParallelMake)
}

# Clean up Mythical (nothing for the moment).
proc Mythical-Clean {} {
  Debug "Cleaning Mythical"
}

Links

• http://www.na-mic.org/Wiki/index.php/Slicer3
• http://www.na-mic.org/websvn/listing.php?repname=Slicer3
• Howto integrate Slicer3 into Eclipse

Information on Free Microsoft C++ Compiler on Windows

Be sure to follow all the steps on Microsoft link. Yes it means you need to download the compiler and sdk.

• http://msdn.microsoft.com/vstudio/express/visualc/usingpsdk/