A small R package to pull in handy routines from openCV (and eventually vlfeat and scikit-image) for processing of 3D surfaces, typically obtained from a 3D microscope. Though this library is independent of the x3pr R package for basic x3p data format handeling, we are designing it with the x3p format in mind.

• Under heavy development. Current capabilities:

  • Interactive 3D surface and point plotting
  • Hole detection
  • Hole filling
  • Inner and outer rectangular region of interest (ROI) cropping
  • Inner and outer circular region of interest (ROI) cropping
  • Surface data bitdepth conversion
  • Surface resizing
  • 2D filtering (multiple types: blur, gaussian, sobel, wavelet)
  • 2D FFT magnitudes with plots
  • 2D CCF
  • 2D polynomial (form) fitting up to 5th degree
  • Python interface via boost.python

• The package requies that openCV, python, boost, vlfeat (the C library. The MATLAB parts are not necessary) are installed. It is currently being developed with openCV 2.4.11, but we will change over to 3.0 soon.

• We have only tested this on OSX and some compiler/linker flags are unique to our programming enviornment. Take a look at /src/Makvars if you want to begin to figure out how to compile for your enviornment (though we don't recommend that yet, and probably won't for a while. The package is under heavy development.) It should compile in Linux with clang installed and some fiddeling with the compiler/linker flags in Makevars. Compiling with gcc should only take a little extra coaxing. We intend that this package will work with Windows, OSX and Linux, but that is still some time in the future.