cSIM with speckle in Python3

This is a Python3 implementation of coherent structured illumination microscopy algorithm with speckle
cSIM_speckle_simulation.ipynb: Jupyter notebook for creating simulation data for cSIM processing
Preprocess.ipynb: Jupyter notebook for generating appropriate exp dataset for optimization
cSIM_main.ipynb: Jupyter notebook for main optimization algorithm to process dataset
cSIM_func.py: Processing functions with numpy implementation
cSIM_func_af.py: Processing functions with arrayfire implementation
dftregistration.py: DFT registration python code translated by [1] to python from original MATLAB code in [2]
zernfun.py: Zernike polynomial generation function translated from original MATLAB code in [3]

[1] https://github.com/keflavich/image_registration
[2] Manuel Guizar-Sicairos, Samuel T. Thurman, and James R. Fienup, "Efficient subpixel image registration algorithms," Opt. Lett. 33, 156-158 (2008).
[3] https://www.mathworks.com/matlabcentral/fileexchange/7687-zernike-polynomials

Environment requirement

Python 3.6, ArrayFire

1. Follow http://arrayfire.org/docs/index.htm for ArrayFire installation
2. Follow https://github.com/arrayfire/arrayfire-python to install ArrayFire Python and set the path to the libraries

Data download

You can find sample experiment data from here: TBD