SH Alignment

This is a software library for alignment of two 3D volumes which is super fast and accurate. It is written in Python and C.
For detail, please check paper "Fast and Accurate Reference-free Alignment of Subtomograms", Y. Chen, S. Pfeffer, T. Hrabe, J. Schuller. F. Foerster, Journal of Structural Biology, 2013.

Except for Numpy/Scipy and FFTW3 (the migration from 2 to 3 is done!), the prerequisites of this software are two other libraries: "frm" from Situs (http://situs.biomachina.org/) and "SpharmonicKit" (http://www.cs.dartmouth.edu/~geelong/sphere/). Both of the source codes are slightly modified/debugged and already included here.
It might also depend on one other library in the furture: "NFFT" (http://www-user.tu-chemnitz.de/~potts/nfft/), which helps to improve the accuracy of interpolation in the Fourier space. It is not mandatory, and thus the source code is not included.

This library is stand-alone and does not depend on PyTom anymore, which makes the integration into other softwares really easily. Please check the test folder for a simple example to use it. Otherwise, if you want to use it for (massive) subtomogram alignment in cryoelectron tomography, PyTom library (http://sourceforge.net/projects/pytom/) is strongly recommanded.

COMPILE:
1. run: python compile.py (followed by --help to see other possible arguments)
2. if the compilation finishes successfully, set the LD_LIBRARY_PATH/DYLD_LIBRARY_PATH and PYTHONPATH printed at the end


COPYRIGHT:
Yuxiang Chen (chenyxkk@googlemail.com), 2012-2013
