How to Build ShapeWorks from Source?

If you encounter problems, have questions, or need help, please contact <shapeworks-dev-support@sci.utah.edu>.

Minimum Requirements

Linux

  • CMake 3.11 (provided by conda below if not already installed)
  • GCC 7.5.0
  • Qt 5.9.8 (optional for GUI components)

Mac

  • CMake 3.11 (provided by conda below if not already installed)
  • Clang 10.0.0
  • Qt 5.9.8 (optional for GUI components)

Windows

  • CMake 3.11 (provided by conda below if not already installed)
  • MSVC 2019
  • Qt 5.9.8 (optional for GUI components)

Clone source

To clone the ShapeWorks source:

$ git clone https://github.com/SCIInstitute/ShapeWorks
See How to Contribute? for more details on git commands.

Install dependencies

Linux and Mac

Anaconda

We use Anaconda (conda) to install many dependencies required for both building and running ShapeWorks. Conda [sub]environments do not affect a machine's global setup in any way, do not require sudo to install, and are only available at the user level when activated.

To install conda and the dependencies it provides (currently requires either bash or zsh shell), run: 

$ source conda_installs.sh

ShapeWorks uses git-lfs to store image data for testing. If git-lfs was not already installed before cloning ShapeWorks, please use the following commands to get this data:

$ git lfs fetch
$ git lfs install
$ git lfs checkout

Activate shapeworks environment

Each time you build or use ShapeWorks from the command line, you must first activate its environment using the conda activate shapeworks command on the terminal.

Qt5

Download and install the latest version of Qt5, selecting the LGPL (free) license (at least version 5.10 required).

After installing Qt5, add the directory containing qmake.exe to your PATH. See Adding to PATH Environment Variable for help with this.

Example qmake directory Linux: /opt/Qt5.14.0/5.14.0/gcc_64/bin

VXL, VTK, ITK, Eigen and OpenVDB

These dependencies can be installed using the build_dependencies.sh script.

Use $ ./build_dependencies.sh --help for more details on the available options.

Note

If you get an error that looks like this:

which: no qmake in (...) 
For GUI applications, please make sure at least version $QT_MIN_VER of Qt5 is installed and that its qmake is in the path.
Download Qt5 from: https://download.qt.io/archive/qt/

Make sure you added Qt to your path as explained in the Qt5 installation step.

Important

If you decide to build ITK yourself and you would like to use the ShapeWorks GUI applications, ITK must be built with VTK.

Windows

CMake

Download and install [CMake]
Download and install [Visual Studio 2019]

Anaconda

Download and install [Anaconda].

Important

It is recommended not to add Anaconda to your PATH and not to register Anaconda as your default Python.

Using the Anaconda Prompt, run conda_installs.bat

Qt5

Download and install the latest version of Qt5, selecting the LGPL (free) license (at least version 5.10 required).

After installing Qt5, add the directory containing qmake.exe to your PATH. See Adding to PATH Environment Variable for help with this.

Example qmake directory: D:\Qt\5.14.0\winrt_x64_msvc2017\bin

VXL, VTK, ITK, Eigen and OpenVDB

These dependencies can be installed using the build_dependencies.sh script. Use an msys shell (e.g., git bash) to do this on Windows.

Use $ ./build_dependencies.sh --help for more details on the available build_dependencies options.

Important

If you get an error that says: which: no qmake in (...)
Make sure you added Qt to your path as explained in the Qt5 installation step.

Important

If you decide to build ITK yourself and you would like to use the ShapeWorks GUI applications, ITK must be built with VTK.

Configure and Build

Linux & Mac

Make a build directory and use cmake to configure your build:

mkdir build
cd build
cmake <options> ..
There is a CMake GUI to see and change any of the options: - On OSX/Linux, you can use the GUI by running ccmake instead of cmake.

Options

If you used the build_dependencies.sh script above, the prefix for all dependencies is the same. Otherwise, the specific paths to VTK, VXL, ITK, and Eigen3 are all required.

Required (if you used build_dependencies.sh):

  -DCMAKE_PREFIX_PATH=<dependencies install path>

Required (otherwise):

  -DVXL_DIR=<vxl cmake path>           (contains VXLConfig.cmake)
  -DVTK_DIR=<vtk cmake path>           (contains VTKConfig.cmake)
  -DITK_DIR=<itk cmake path>           (contains ITKConfig.cmake)
  -DEigen3_DIR=<eigen3 cmake path>     (contains Eigen3Config.cmake)
  -DOpenVDB_DIR=<openvdb cmake path>   (contains FindOpenVDB.cmake)

Optional: 

  -G<generator>                       default: Unix Makefiles (ex: -GXCode or -G"Visual Studio 16 2019" -Ax64)  
  -DBuild_Studio=[OFF|ON]             default: OFF
  -DBuild_View2=[OFF|ON]              default: OFF
  -DBuild_Post=[OFF|ON]               default: OFF
  -DCMAKE_INSTALL_PREFIX=<path>       default: ./install
  -DCMAKE_BUILD_TYPE=[Debug|Release]  default: Release (only required is default generator is used)
See Examples below for common values of the variables.

Building

  • Makefiles:
    • make -j<num_procs> where num_procs is the number of parallel processes, say 8.
    • You might need to build using cmake --build . -j 16 to pass parallel flags to dependent projects (e.g., vtk)
  • XCode project: open ShapeWorks.xcodeproj and build from there.

Before running Examples/Python scripts

Add the ShapeWorks and dependency binaries to the path:
$ export PATH=/path/to/shapeworks/build/bin:/path/to/dependencies/bin:$PATH

Examples

OSX example that builds dependencies separately, then generates an XCode project for ShapeWorks: 

$ ./build_dependencies.sh
mkdir build
cd build
cmake -DCMAKE_PREFIX_PATH="${PWD}/../dependencies/install" -DBuild_Post:BOOL=ON -DBuild_View2:BOOL=ON -DBuild_Studio:BOOL=ON -DUSE_OPENMP=OFF -Wno-dev -Wno-deprecated -GXcode ..
open ShapeWorks.xcodeproj

Windows

Use the cmake from the Anaconda Prompt with shapeworks env activated to configure and generate project files for your preferred build system (e.g., Visual Studio 16 2019).

Options

Required:

  -DCMAKE_PREFIX_PATH=<qt cmake path>  (This is different from qmake path in the Install Qt5 step
  -DVXL_DIR=<vxl cmake path>           (contains VXLConfig.cmake)
  -DVTK_DIR=<vtk cmake path>           (contains VTKConfig.cmake)
  -DITK_DIR=<itk cmake path>           (contains ITKConfig.cmake)
  -DEigen3_DIR=<eigen cmake path>      (contains Eigen3Config.cmake)
  -DOpenVDB_DIR=<openvdb cmake path>   (contains FindOpenVDB.cmake)
Optional: 
  -D Build_Studio=[OFF|ON]             default: OFF
  -D Build_View2=[OFF|ON]              default: OFF
  -D Build_Post=[OFF|ON]               default: ON
  -D CMAKE_INSTALL_PREFIX=<path>       default: ./install
  -D CMAKE_BUILD_TYPE=[Debug|Release]

Examples

An example that builds dependencies separately then generates a Visual Studio project for ShapeWorks:

> conda activate shapeworks
> ./build_dependencies.sh --build-dir=../dependencies --install-dir=../dependencies
> mkdir build
> cd build
> cmake -G"Visual Studio 16 2019" -Ax64 -DVXL_DIR=../dependencies/vxl/build -DCMAKE_PREFIX_PATH=../dependencies -DBuild_Post:BOOL=ON -DBuild_View2:BOOL=ON -DBuild_Studio:BOOL=ON ..