EMAN2
pca.h
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00001 /*
00002  * Author: Chao Yang
00003  * Copyright (c) 2000-2006
00004  *
00005  * This software is issued under a joint BSD/GNU license. You may use the
00006  * source code in this file under either license. However, note that the
00007  * complete EMAN2 and SPARX software packages have some GPL dependencies,
00008  * so you are responsible for compliance with the licenses of these packages
00009  * if you opt to use BSD licensing. The warranty disclaimer below holds
00010  * in either instance.
00011  *
00012  * This complete copyright notice must be included in any revised version of the
00013  * source code. Additional authorship citations may be added, but existing
00014  * author citations must be preserved.
00015  *
00016  * This program is free software; you can redistribute it and/or modify
00017  * it under the terms of the GNU General Public License as published by
00018  * the Free Software Foundation; either version 2 of the License, or
00019  * (at your option) any later version.
00020  *
00021  * This program is distributed in the hope that it will be useful,
00022  * but WITHOUT ANY WARRANTY; without even the implied warranty of
00023  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
00024  * GNU General Public License for more details.
00025  *
00026  * You should have received a copy of the GNU General Public License
00027  * along with this program; if not, write to the Free Software
00028  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
00029  *
00030  */
00031 
00032 //#ifndef sparx__pca_h__
00033 //#define sparx__pca_h__
00034 
00035 #include "emdata.h"
00036 
00037 namespace EMAN {
00038    class PCA {
00039       public: 
00040          vector<float>   singular_vals;        // singular values
00041          vector<EMData*> eigenimages; // eigenimages
00042 
00043          // pca in core
00044          int dopca(vector <EMData*> imgstack, EMData *mask);
00045          int dopca(vector <EMData*> imgstack, EMData *mask, int nvec);
00046          int dopca_lan(vector <EMData*> imgstack, EMData *mask, int nvec);
00047 
00048          // pca out of core
00049          int dopca_ooc(const string &filename_in, const string &filename_out, 
00050                        const string &lanscratch,  EMData *mask, int nvec);
00051 
00052          // Lanczos factorization (used by dopca_lan)
00053          int Lanczos(vector <EMData*> imgstack, int *maxiter, 
00054                      float  *diag, float *subdiag, float *V, float *beta);
00055 
00056          // Lanczos factorization out-of-core (used by dopca_ooc)
00057          int Lanczos_ooc(string const& filename_in, int *kstep, 
00058                          float  *diag, float *subdiag, 
00059                          string const& lanscratch, float  *beta);
00060 
00061          // retrieve singular vectors and values
00062          vector<float>   get_vals();
00063          vector<EMData*> get_vecs();
00064 
00065          // flush singular values and vectors
00066          void clear();
00067    };
00068 }
00069 
00070 //#endif //sparx__pca_h__