MorphoGraphX installation

MorphoGraphX uses CMake. After creating a build directory and configuring CMake, select the different AddOns for inclusion in the build 
by checking the BUILD_<AddOn> lines.

After configuring with CMake, type "make" and then make package.  

To get the process documentation, select BUILD_DOXYGEN and also type "make doc". Selecting BUILD_DOXYGEN with typing "make doc" will
result in an error.

It is possible to compile with Cuda, TBB, or OMP as the backend for Thrust. Cuda requires an nVidia graphics card. Be sure the
THRUST_DEVICE_SYSTEM variable is set correctly in CMake.

In order to use processes from the Insight Toolkit (ITK) the ITK package must be installed.

Depending on the distro and the AddOns selected, most of the required packages are:
libtbb-dev libtiff-dev libboost-all-dev cimg-dev libgsl-dev libqt5opengl5-dev ocl-icd-opencl-dev libtriangle-dev libtet1.5-dev libcgal-dev
libeigen3-dev doxygen r-cran-rinside libqt5svg5-dev libhdf5-dev

Notes:

- if you have anaconda installed, you make need to rename it, search for such locations in CMake and if found remove the entries and after 
removing anaconda configure CMake again.
- if it finds python 3, change them to 2.7, which you may have to install.
- for hdf5, you need to link /usr/lib/x86.../hsdf5/serial/libhdf5.so /usr/lib/libhdf5.so
- for hdf5 on Ubuntu 18, you need a different version of ITK, and an updated version of HDF5
- for R to work, you need to install r-cran-rinside r-cran-ggplot2 libqt5svg5-dev libfontconfig1-dev and in R install.packages("svglite")
- to compile the CNN AddOn, you will need to build libtorch and change the CMake to point to the libraries there, you may also require libmkl
