Build QUENCH

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[edit] Building QUENCH for Linux

Quench shares a lot of code with ConTrack. Therefore, in order to build Quench the steps below will also build ConTrack. Before running the build script have a look at the Linux build notes.

To build Quench:

  1. Create and navigate to an install folder in your terminal - for example, let's call it 'src'.
  2. Run the following commands:
wget https://white.stanford.edu/repos/StanfordTools-DWI/install/get_stanford_tools_dwi.sh --no-check-certificate
chmod 775 get_stanford_tools_dwi.sh
./get_stanford_tools_dwi.sh

If you get errors, you may not have some of the required packages. See the section below to make sure you have the appropriate software and libs.

Once your build is complete you can run the executable, which can be found here:

 /yourUniquePath/src/StanfordTools-DWI/quench/Quench

You can run this executable from any terminal if you place a link to it in your bin directory, or make an alias in your rc file.

[edit] Linux Build Notes

[edit] Required Packages and Libs

Using Synaptics (or apt-get) you will need to have these packages installed on Ubuntu to build Quench. The terms below are not exact - the version numbers can change and sometimes there will be a -dev attached to the name (to indicate development version). But you will need these packages in some form.

Required Software Packages for the Build:
  • Subversion (svn)
  • g++
  • autoconf
  • git
  • make
Libs needed to Run Quench (on most systems):
  • libvtk
  • libwxgtk (-dev)
  • libvtk-qt4
  • vtk-tcl
  • python-vtk
  • libgtk+2
  • libgtk (-dev)

We are all waiting and hoping for that magical time when Neurodebian incorporates itkGray and Quench.

Ubuntu

Packages can be installed using Synaptic or a command like:

 sudo apt-get install packageName

If the package name comes back as not found try:

 apt-cache search packageName

Fedora

Use yum:

 sudo yum install packageName
 sudo yum search packageName

[edit] Note for Ubuntu 14.04

Ubuntu 14.04 does not support libtiff4 library, which is used in Quench package. To install libtiff4 package in Ubuntu 14.04 system,

wget ftp.de.debian.org/debian/pool/main/t/tiff/libtiff4_3.9.4-5+squeeze10_amd64.deb
sudo dpkg -i libtiff4_3.9.4-5+squeeze10_amd64.deb
sudo apt-get install -f

[edit] Troubleshooting

With luck, the previous steps will have semi-automatically downloaded and installed these libraries as well as the Quench source code. If the script fails, you can use the links to download and install each library separately.

Quench source also can be obtained by using svn

 > svn checkout https://white.stanford.edu/repos/StanfordTools-DWI/quench

We are currently compiling Quench on Fedora Core 12, Kernel Release 2.6.32.16-141 with GCC 4.4.4.

[edit] Building QUENCH for Mac OS X

Installation for Mac OS X is similar to the Linux steps.

TODO (Tony is working on this): There are a few changes that need to be made to get_stanford_tools.sh to make it work for OS X.

  • wxWidgets needs "-arch" message on snow leopard
  • cmake needs to be called with -G mode and lets setup xcode for the Mac since it is nice.
  • Since we are already editing RAPID folder stuff, lets also get it to stop compiling the test app that never builds.
  • there needs to be a system recognition step in get_.sh for Mac versus linux.

  • [edit] To Build and Run QUENCH

    [edit] Troubleshooting

    We are currently compiling Quench on Mac OS 10.6.3 (Snow Leopard) with GCC 4.2.1.

    [edit] Building QUENCH for Windows

    It appears that the newest version of Quench, from Dec. 4th 2009, requires the driver series: msvcX100.dll (where X is p, r and c). These can be found on the web.

    It may be necessary to download the uSoft .NET framework under the development resources pulldown.

    We are checking with Tony and Shireesh about this.

    1. Download and unzip wxWidgets(2.8.10) to YOUR_WXWIDGETS_DIR

    Open YOUR_WXWIDGETS_DIR\build\msw\wx.dsw. Upgrade it to sln if asked by Visual Studio
    Build the 'Debug' and 'Release' Configuration

    2. Download and install CMake 3. Download VTK 5.2 source to YOUR_VTK_DIR

    a Goto YOUR_VTK_DIR and create build directory
    b Goto CMake install folder and run CMakeSetup.
    For source path specify YOUR_VTK_DIR
    For build path specify YOUR_VTK_DIR\build
    Click on Configure
    Uncheck BUILD_TESTING
    Click on Configure again
    Click on Generate
    c Goto YOUR_VTK_DIR\build and open VTK.sln
    Build debug and release version (Sleep)
    d Create an include folder in YOUR_VTK_DIR\build
    Search for all .h files in YOUR_VTK_DIRand copy it to YOUR_VTK_DIR\build\include

    4. Setup the include and lib paths in visual studio:

    Goto Tools->Options->Projects & Solutions->VC++ Directories
    From 'Show directories for' drop down list select 'Include files'
    Add the following paths to the bottom
    YOUR_WXWIDGETS_DIR\include
    YOUR_WXWIDGETS_DIR\include\msvc
    YOUR_VTK_DIR\Build\include
    YOUR_VTK_DIR\Build\utilities
    YOUR_VTK_DIR\vtk-5.2.1\Build\
    Select 'Library files' now and add the following paths
    YOUR_WXWIDGETS_DIR\lib\vc_lib
    Click on OK

    5. Checkout contrack using tortoise SVN to CONTRACK_DIR. Use this as the path https://simtk.org/svn/contrack
    6. Download RAPID. Extract it to CONTRACK_DIR\trunk folder

    Open CONTRACK_DIR\trunk\RAPID201\MSVC_Compile\RAPID201.dsw. Upgrade it to sln if asked by Visual Studio
    There is a bug in RAPID. Open RAPID_private.H and replace this line
    > friend RAPID_Collide(double R1[3][3], double T1[3], 
    
    with this
    > friend int RAPID_Collide(double R1[3][3], double T1[3], 
    
    Build Rapid

    7. Create folder Quench in CONTRACK_DIR\trunk

    Checkout quench to CONTRACK_DIR\trunk\Quench. Use this as the path https://white.stanford.edu/repos/vistasrc/quench
    Open CONTRACK_DIR\trunk\Quench\Projects\Quench\quench.sln
    In solution explorer, Right click on quench, choose properties
    In Configuration dropdown list(at top left) Select All configurations
    Goto Configuration properties->Linker->General
    Click on ... on the Additional Library Directories
    Replace C:\Program Files\vtk-5.2.1\Build\bin\$(ConfigurationName) with YOUR_VTK_DIR\Build\bin\$(ConfigurationName)
    Click OK
    Build Quench.

    This should complete the build process for QUENCH

    • To recover some disk space, search for *.obj, *.ncb, *.pch in wxWidgets and vtk folders and delete them.

    [edit] Troubleshooting

    [edit] API Documentation

    documentation

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