Compressive Second Harmonic Generation Imaging

3D Coherent second harmonic generation imaging based on wirtinger flow based phase retrieval from phase coded aperture patterns, followed by solving a regularized linear inverse problem.

Installation and use:

• Install fftw2 as follows: Download fftw-2.1.5.tar.gz from www.fftw.org Unpack fftw2:

  tar -xzvf fftw-2.1.5.tar.gz 
  

  Install as follows:

  cd fftw-2.1.5
  ./configure
  make 
  sudo make install
  

  The above process should work correctly on Mac OS. For linux, you might need to replace make with make CFLAGS="-fPIC" in order to install fftw2 correctly.

• Then install the included curvelab package as follows:

  Enter /Curvelab/. Edit makefile.opt for specify the directory in which fftw is installed. Create libraries using

  make lib
  

  Test using

  make test
  

• Enter /Curvelab/fdct3d/src/.

  Check if 3d curvelet transform is working fine in C++:

  make test
  ./test options
  

  In setup.py, set FFTW to the path to the fftw installation directory. (same as the one used previously). Install the python package which wraps fdct3d using cython:

  bash installer.sh cython
  

  For testing, run functions from the file test.py.