RvtkStatismo is an R-package aiming to integrate Statismo (a C++ library to calculate and modify statistical shape models) using vtkStandardMeshRepresenter and thus also includes some functionality of the VTK library.

Install prerequisites

• Linux: Install VTK (headers and library), CMake, HDF5 libraries and R build environment and of course statismo

On Ubuntu (14.04/14.10/15.04), this can be easily accomplished by:

sudo apt-add-repository ppa:zarquon42/ppa
sudo apt-get update
sudo apt-get install statismo r-base-dev

• OS X * Install R, XCODE and cmake, run the following lines in your terminal:

 git clone https://github.com/statismo/statismo.git
 mkdir build && cd build
 cmake ../statismo/superbuild 
 make ## make a coffee or go for lunch

There are two ways to tell R, where the libraries reside:

1. Dirty solution. Copy the libs to where R can find them:

   cp INSTALL/lib/libvtk* INSTALL/lib/libboost* INSTALL/lib/libhdf5* /Library/Frameworks/R.framework/Resources/lib
    

2. In OS X Yosemite there seems no way to set the environment variable DYLD_LIBRARY_PATH globally, so we create a file ~/Library/LaunchAgents/statismo.plistcontaining the following xml code (of course replacing the path with yours):

   <?xml version="1.0" encoding="UTF-8"?>
   <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
   <plist version="1.0">
   <dict>
     <key>Label</key>
     <string>my.startup</string>
     <key>ProgramArguments</key>
     <array>
       <string>sh</string>
       <string>-c</string>
       <string>
       launchctl setenv DYLD_LIBRARY_PATH /Users/myuser/statismo/build/INSTALL/lib
      </string>
   
     </array>
     <key>RunAtLoad</key>
     <true/>
   </dict>
   </plist>

   Now logout and login again.

   To use RvtkStatismo in a console you need to run (works for one session only):

   export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/Users/myuser/statismo/build/INSTALL/lib
   

   To make this permanent add this command to your ~/.bash_profile (create it if it does not exist).

• Windows: SUCKS BIG TIME!! install CMake and MinGW (including MSYS) and make sure the respective paths are included in the PATH variable). Then download VTK source code and build it. If you build VTK static libraries, the R-package will be portable.

Install R-dependencies: Issue the following command in your R-terminal:

install.packages(c("Rcpp","Morpho","RcppEigen"))

Installation of the R-package "RvtkStatismo" - using devtools (this automatically installs the required R-packages)

Install devtools

from within R (Ubuntu/Debian users will have to install libcurl4-gnutls-dev beforehand):

install.packages("devtools")

Install RvtkStatismo

Run the following command in R:

require(devtools)
install_github("zarquon42b/RvtkStatismo", local=FALSE)

Installation of the-R package from source

1. Download tarball (and extract) or clone using git

2. (optional) go to RvtkStatismo/src and customize cmake parameters (using ccmake or cmake-gui), such as VTK or Statismo installation paths.

3. within the base directory of RvtkStatismo run:

    R CMD INSTALL .