util_sparx.h

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00001 
00005 /*
00006  * Author: Pawel A.Penczek, 09/09/2006 (Pawel.A.Penczek@uth.tmc.edu)
00007  * Copyright (c) 2000-2006 The University of Texas - Houston Medical School
00008  *
00009  * This software is issued under a joint BSD/GNU license. You may use the
00010  * source code in this file under either license. However, note that the
00011  * complete EMAN2 and SPARX software packages have some GPL dependencies,
00012  * so you are responsible for compliance with the licenses of these packages
00013  * if you opt to use BSD licensing. The warranty disclaimer below holds
00014  * in either instance.
00015  *
00016  * This complete copyright notice must be included in any revised version of the
00017  * source code. Additional authorship citations may be added, but existing
00018  * author citations must be preserved.
00019  *
00020  * This program is free software; you can redistribute it and/or modify
00021  * it under the terms of the GNU General Public License as published by
00022  * the Free Software Foundation; either version 2 of the License, or
00023  * (at your option) any later version.
00024  *
00025  * This program is distributed in the hope that it will be useful,
00026  * but WITHOUT ANY WARRANTY; without even the implied warranty of
00027  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
00028  * GNU General Public License for more details.
00029  *
00030  * You should have received a copy of the GNU General Public License
00031  * along with this program; if not, write to the Free Software
00032  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
00033  *
00034  */
00035 
00040 #ifndef util__sparx_h__
00041 #define util__sparx_h__
00042 
00043 public:
00044 
00045 static int coveig(int n, float *covmat, float *eigval, float *eigvec);
00046 
00048 static Dict coveig_for_py(int ncov, const vector<float>& covmatpy);
00049 
00050 static void WTF(EMData* PROJ,vector<float> SS,float SNR,int K);
00051 
00052 static void WTM(EMData* PROJ, vector<float> SS,int DIAMETER,int NUMP);
00053 
00054 static Dict CANG(float PHI, float THETA, float PSI);
00055 
00056 static void BPCQ(EMData* B, EMData *CUBE,vector<float> DM);
00057 
00058 static vector<float> infomask(EMData* Vol, EMData* mask, bool);
00059 
00060 static void colreverse(float* beg, float* end, int nx);
00061 
00062 static void slicereverse(float* beg, float* end, int nx,int ny);
00063 
00098 static void cyclicshift(EMData* image, Dict params);
00099 
00100 static Dict im_diff(EMData* V1, EMData* V2, EMData* mask=0);
00101 
00114 static EMData* TwoDTestFunc(int Size, float p, float q,  float a, float b,
00115                    int flag=0, float alphaDeg=0); //PRB
00116 
00117 
00129 static void spline_mat(float *x, float *y, int n,  float *xq, float *yq, int m); //PRB
00130 
00143 static void spline(float *x, float *y, int n, float yp1, float ypn, float *y2);
00144   // PRB
00156 static void splint( float *xa, float *ya, float *y2a, int n,
00157                                      float *xq, float *yq, int m);
00158 
00159 
00170 static void Radialize(int *PermMatTr,  float * kValsSorted,
00171             float *weightofkvalsSorted, int Size, int *SizeReturned);
00172 
00173 
00174 
00175 class sincBlackman
00176 {
00177         protected:
00178                 int M; 
00179                 float fc; 
00180                 int ntable;
00181                 vector<float> sBtable;
00182                 virtual void build_sBtable(); 
00183                 float fltb;
00184         public:
00185                 sincBlackman(int M_, float fc_, int ntable_ = 1999);
00186                 virtual ~sincBlackman() {};
00187 
00188                 inline  float sBwin_tab(float x) const {
00189                         float xt;
00190                         if(x<0.0f) xt = -x*fltb+0.5f; else xt = x*fltb+0.5f;
00191                         return sBtable[ (int) xt];
00192                 }
00194                 int get_sB_size() const { return M; }
00195 };
00196 
00197 
00198 
00222 class KaiserBessel
00223 {
00224         protected:
00225                 float alpha, v, r; 
00226                 int N; 
00227                 int K; 
00228                 float vtable; 
00229                 int ntable;
00230                 vector<float> i0table;
00231                 float dtable; 
00232                 float alphar; 
00233                 float fac; 
00234                 float vadjust;
00235                 float facadj; 
00236                 virtual void build_I0table(); 
00237                 float fltb;
00238         public:
00239                 KaiserBessel(float alpha_, int K, float r_,
00240                                      float v_, int N_, float vtable_=0.f,
00241                                          int ntable_ = 5999);
00242                 virtual ~KaiserBessel() {};
00244                 float I0table_maxerror();
00245                 vector<float> dump_table() {
00246                         return i0table;
00247                 }
00249                 virtual float sinhwin(float x) const;
00251                 virtual float i0win(float x) const;
00253                 inline float i0win_tab(float x) const {
00254                 /*float absx = fabs(x);
00255                         int loc = int(round(absx*fltb));
00256                         return i0table[loc];*/
00257                         float xt;
00258                         if(x<0.f) xt = -x*fltb+0.5f; else xt = x*fltb+0.5f;
00259                         return i0table[ (int) xt];
00260                         /*return i0table[ (int) (fabs(x)*fltb+0.5f)];
00261                                 if (absx > vtable) return 0.f;
00262                                 float loc = absx/dtable;
00263                                 return i0table[int(loc + 0.5f)]; */
00264                 }
00266                 int get_window_size() const { return K; }
00268                 class kbsinh_win {
00269                         KaiserBessel& kb;
00270                         public:
00271                         kbsinh_win(KaiserBessel& kb_) : kb(kb_) {}
00272                         float operator()(float x) const {
00273                                 return kb.sinhwin(x);
00274                         }
00275                         int get_window_size() const {return kb.get_window_size();}
00276                 };
00278                 kbsinh_win get_kbsinh_win() {
00279                         return kbsinh_win(*this);
00280                 }
00282                 class kbi0_win {
00283                         KaiserBessel& kb;
00284                         public:
00285                         kbi0_win(KaiserBessel& kb_) : kb(kb_) {}
00286                         float operator()(float x) const {
00287                                 return kb.i0win(x);
00288                         }
00289                         int get_window_size() const {return kb.get_window_size();}
00290                 };
00292                 kbi0_win get_kbi0_win() {
00293                         return kbi0_win(*this);
00294                 }
00295 };
00296 
00297 class FakeKaiserBessel : public KaiserBessel {
00298         public:
00299                 FakeKaiserBessel(float alpha, int K, float r_,
00300                                          float v_, int N_, float vtable_=0.f,
00301                                                  int ntable_ = 5999)
00302         : KaiserBessel(alpha, K, r_, v_, N_, vtable_, ntable_) {
00303                         build_I0table();
00304                 }
00305                 float sinhwin(float x) const;
00306                 float i0win(float x) const;
00307                 void build_I0table();
00308 };
00309 
00321                 static vector<float>
00322                 even_angles(float delta, float t1=0, float t2=90, float p1=0, float p2=359.999);
00323 
00324 
00377                 static float quadri(float x, float y, int nx, int ny, float* image);
00378 
00433                 static float quadri_background(float x, float y, int nx, int ny, float* image, int xnew, int ynew);
00434 
00435                 // Here counting is in C style, so coordinates of the pixel delx should be [0-nx-1]
00436                 /* Commented by Zhengfan Yang on 04/20/07
00437                 This function is written to replace get_pixel_conv(), which is too slow to use in practice.
00438                 I made the following changes to get_pixel_conv():
00439                 1. Use the same data passing scheme as quadri() and move the function from emdata_sparx.cpp to util_sparx.cpp
00440                 2. Reduce usage of i0win_tab (from 98 calls to 14 calls in 2D case, from 1029 calls to 21 calls in 3D case!)
00441                 3. Unfold the 'for' loop
00442                 4. Reduce the usage of multiplications through some bracketing (from 98 times to 57 times in 2D case, from 1029 times to 400 times in 3D case)
00443 
00444                 The shortcoming of this routine is that it only works for window size N=7. In case you want to use other window
00445                 size, say N=5, you can easily modify it by referring my code.
00446                 */
00447                 static float get_pixel_conv_new(int nx, int ny, int nz, float delx, float dely, float delz, float* data, Util::KaiserBessel& kb);
00448 
00449                 // Here counting is in C style, so coordinates of the pixel delx should be [0-nx-1]
00450                 /* Commented by Zhengfan Yang on 04/20/07
00451                 This function is written to replace get_pixel_conv(), which is too slow to use in practice.
00452                 I made the following changes to get_pixel_conv():
00453                 1. Use the same data passing scheme as quadri() and move the function from emdata_sparx.cpp to util_sparx.cpp
00454                 2. Reduce usage of i0win_tab (from 98 calls to 14 calls in 2D case, from 1029 calls to 21 calls in 3D case!)
00455                 3. Unfold the 'for' loop
00456                 4. Reduce the usage of multiplications through some bracketing (from 98 times to 57 times in 2D case, from 1029 times to 400 times in 3D case)
00457 
00458                 The shortcoming of this routine is that it only works for window size N=7. In case you want to use other window
00459                 size, say N=5, you can easily modify it by referring my code.
00460                 */
00461         static float get_pixel_conv_new_background(int nx, int ny, int nz, float delx, float dely, float delz, float* data, Util::KaiserBessel& kb, int xnew, int ynew);
00462 
00463                 static std::complex<float> extractpoint2(int nx, int ny, float nuxnew, float nuynew, EMData *fimage, Util::KaiserBessel& kb);
00464 
00465                 /*static float quadris(float x, float y, int nx, int ny, float* image);*/
00466                 static float bilinear(float xold, float yold, int nsam, int nrow, float* xim);
00467 
00468 
00477                 static float triquad(float r, float s, float t, float* fdata);
00478 
00486                 class Gaussian {
00487                         float sigma;
00488                         float rttwopisigma;
00489                         float twosigma2;
00490                         public:
00491                         Gaussian(float sigma_ = 1.0) : sigma(sigma_) {
00492                                 rttwopisigma = sqrtf(static_cast<float>(twopi)*sigma);
00493                                 twosigma2 = 2*sigma*sigma;
00494                         }
00495                         inline float operator()(float x) const {
00496                                 return exp(-x*x/(twosigma2))/rttwopisigma;
00497                         }
00498                 };
00499         /*static void alrq(float *xim,  int nsam , int nrow , int *numr,
00500                              float *circ, int lcirc, int nring, char mode);*/
00501         static EMData* Polar2D(EMData* image, vector<int> numr, string mode);
00502         static EMData* Polar2Dm(EMData* image, float cns2, float cnr2, vector<int> numr, string cmode);
00503         /*static void alrq_ms(float *xim, int    nsam, int  nrow, float cns2, float cnr2,
00504                             int  *numr, float *circ, int lcirc, int  nring, char  mode);*/
00505         static void alrl_ms(float *xim, int    nsam, int  nrow, float cns2, float cnr2,
00506                             int  *numr, float *circ, int lcirc, int  nring, char  mode);
00507         /*static void alrq_msi(EMData* image,float cns2, float cnr2,
00508                            int  *numr, float *circ, int lcirc, int  nring, char  mode, Util::KaiserBessel&
00509                                                kb);*/
00510         static EMData* Polar2Dmi(EMData* image, float cns2, float cnr2, vector<int> numr, string cmode, Util::KaiserBessel& kb);
00511 
00512         static void  fftr_q(float  *xcmplx, int nv);
00513         static void  fftr_d(double *xcmplx, int nv);
00514         static void  fftc_q(float  *br, float  *bi, int ln, int ks);
00515         static void  fftc_d(double *br, double *bi, int ln, int ks);
00516 
00518         static void  Frngs(EMData* circ, vector<int> numr);
00519         static void  Normalize_ring(EMData* ring, const vector<int>& numr);
00520 
00522         static void  Frngs_inv(EMData* circ, vector<int> numr);
00523 
00524         /*
00525                 A little notes about different Crosrng:
00526                 Basically, they all do cross-correlation function to two images in polar coordinates
00527                 Crosrng_e is the original one
00528                 Crosrng_ew is the one that you could apply weights to different rings
00529                 Crosrng_ms assumes the user already apply weights to circ1, it also returns both
00530                            straight and mirrored positions simultaneously.
00531                 Crosrng_msg differs from the previous ones in that it returns the cross-correlation
00532                             function entirely instead of the peak value and position, thus makes it
00533                             possible to use the gridding method to determine the peak position
00534                 Crosrng_msg_s is same as Crosrng_msg except that it only checks straight position
00535                 Crosrng_msg_m is same as Crosrng_msg except that it only checks mirrored position
00536           */
00537         static Dict Crosrng_e(EMData* circ1, EMData* circ2, vector<int> numr, int neg);
00538         static Dict Crosrng_ew(EMData* circ1, EMData* circ2, vector<int> numr, vector<float> w, int neg);
00539 
00540         static Dict Crosrng_ms(EMData* circ1, EMData* circ2, vector<int> numr);
00541         static Dict Crosrng_ms_delta(EMData* circ1, EMData* circ2, vector<int> numr, float delta_start, float delta);
00542 
00548         static Dict Crosrng_sm_psi(EMData* circ1, EMData* circ2, vector<int> numr, float psi, int flag);
00549 
00556         static Dict Crosrng_psi_0_180(EMData* circ1, EMData* circ2, vector<int> numr, float psi_max);
00557         static Dict Crosrng_psi_0_180_no_mirror(EMData* circ1, EMData* circ2, vector<int> numr, float psi_max);
00558         static Dict Crosrng_ns(EMData* circ1, EMData* circ2, vector<int> numr);
00559 
00566         static EMData* Crosrng_msg(EMData* circ1, EMData* circ2, vector<int> numr);
00567 
00574         static void Crosrng_msg_vec(EMData* circ1, EMData* circ2, vector<int> numr, float *q, float *t);
00575 
00582         static EMData* Crosrng_msg_s(EMData* circ1, EMData* circ2, vector<int> numr);
00583 
00590         static EMData* Crosrng_msg_m(EMData* circ1, EMData* circ2, vector<int> numr);
00591 
00592         static vector<float> Crosrng_msg_vec_p(EMData* circ1, EMData* circ2, vector<int> numr );
00593         static void  prb1d(double *b, int npoint, float *pos);
00594 
00595         static void update_fav(EMData* ave,EMData* dat, float tot, int mirror, vector<int> numr);
00596         static void sub_fav(EMData* ave,EMData* dat, float tot, int mirror, vector<int> numr);
00597 
00598         // helper functions for ali2d_ra
00599         static float ener(EMData* ave, vector<int> numr);
00600 
00601         static float ener_tot(const vector<EMData*>& data, vector<int> numr, vector<float> tot);
00602 
00604         static Dict min_dist_real(EMData* image, const vector<EMData*>& data);
00605 
00607         static Dict min_dist_four(EMData* image, const vector<EMData*>& data);
00608 
00615         static int k_means_cont_table_(int* group1, int* group2, int* stb, long int s1, long int s2, int flag);
00616 
00617         // branch and bound matching algorithm
00618 
00619         
00623         static void initial_prune(vector <vector <int*> > & Parts, int* dimClasses, int nParts, int K, int T);
00624 
00628         static bool explore(vector <vector <int*> > & Parts, int* dimClasses, int nParts, int K, int T, int partref, int* curintx, int
00629                         size_curintx, int* next, int size_next, int depth);
00630 
00631         
00632         
00633 
00638         static int generatesubmax(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int n_guesses, int LARGEST_CLASS);
00639 
00643         static void search2(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* matchlist, int* costlist, int J);
00644         
00645         static void explore2(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* curintx, int size_curintx, int* next, int size_next, int depth, int J, int* matchlist, int*
00646 costlist, int* curbranch);
00647         
00652         static bool sanitycheck(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* output);
00653 
00663         static vector<int> bb_enumerateMPI_(int* argParts, int* dimClasses, int nParts, int K, int T, int n_guesses, int LARGEST_CLASS, int J, int max_branching, float stmult,
00664         int branchfunc, int LIM);
00665 
00666         
00672         static int* branchMPI(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int curlevel,int n_guesses, int LARGEST_CLASS, int J, int max_branching,
00673         float stmult, int branchfunc, int LIM);
00674 
00675         static int branch_factor_2(int* costlist, int* matchlist, int J, int T, int nParts, int curlevel, int max_branching, int LIM);
00676         static int branch_factor_3(int* costlist, int* matchlist, int J, int T, int nParts, int curlevel, int max_branching, int K, int LIM);
00677         static int branch_factor_4(int* costlist, int* matchlist, int J, int T, int nParts, int curlevel, int max_branching, float stmult);
00678         // new code common-lines
00679 
00680         //helper function for the weights calculation by Voronoi to Cml
00681         static vector<double> cml_weights(const vector<float>& cml);
00682 
00684         static vector<int> cml_line_insino(vector<float> Rot, int i_prj, int n_prj);
00685 
00687         static vector<int> cml_line_insino_all(vector<float> Rot, vector<int> seq, int n_prj, int n_lines);
00688 
00690         static vector<double> cml_init_rot(vector<float> Ori);
00691 
00693         static vector<float> cml_update_rot(vector<float> Rot, int iprj, float nph, float th, float nps);
00694 
00696         static vector<double> cml_line_in3d(vector<float> Ori, vector<int> seq, int nprj, int nlines);
00697 
00699         static vector<double> cml_spin_psi(const vector<EMData*>& data, vector<int> com, vector<float> weights, int iprj, vector<int> iw, int n_psi, int d_psi, int n_prj);
00700 
00702         static double cml_disc(const vector<EMData*>& data, vector<int> com, vector<int> seq, vector<float> weights, int n_lines);
00703 
00709         static void set_line(EMData* img, int posline, EMData* line, int offset, int length);
00710 
00718         static void cml_prepare_line(EMData* sino, EMData* line, int ilf, int ihf, int pos_line, int nblines);
00719 
00720         /* Decimates the image with respect to the image center.
00721          * (i.e) the center of the original image is kept the same
00722          * and then the initial start pixel is calculated with respect to the
00723          * center of the image
00724          * @params(image, x-pixel, y-pixel,z-pixel)
00725          * works for all 3 dimensions
00726         **/
00727         static EMData* decimate(EMData* img, int x_step,int y_step=1,int z_step=1);
00728 
00729         static EMData* window(EMData* img,int new_nx ,int new_ny=1, int new_nz=1, int x_offset=0, int y_offset=0, int z_offset=0);
00730 
00731         static EMData* pad(EMData* img, int new_nx, int new_ny=1, int new_nz=1, int x_offset=0, int y_offset=0, int z_offset=0, char *params="average");
00732 
00733         static vector<float> histogram(EMData* image, EMData* mask, int nbins = 128, float hmin =0.0f, float hmax = 0.0f );
00734 
00735         static Dict histc(EMData *ref,EMData *img,EMData *mask);
00736 
00737         static float hist_comp_freq(float PA,float PB,size_t size_img, int hist_len, EMData *img, vector<float> ref_freq_hist, EMData *mask, float ref_h_diff, float ref_h_min);
00738 
00739 
00740         /* The unit in the ctf function: dz: Angstrom, cs: CM  Ps: Angstrom, Voltage: Kv,dza: Angstrom, azz: degree wgh: None unit. b_factor: Angstrom^2
00741          The CTF function takes form of   *sin(-quadpi*(dz*lambda*ak^2-cs*lambda^3*ak^4/2.)-wgh)*exp(-b_factor*ak^2)*sign
00742           * sign can be set as +1 or -1 . The unit of frequency ak is 1/Angstrom
00743                   Attention: Envelope function in power spectrum has a form of exp(-b_factor*ak^2)
00744                                           */
00745         static float   tf(float dzz, float ak, float voltage = 300.0f, float cs = 2.0f, float wgh = 0.1f, float b_factor = 0.0f, float sign = -1.0f);
00746         static EMData *compress_image_mask(EMData* image, EMData* mask);
00747 
00749         static EMData *reconstitute_image_mask(EMData *image,EMData *mask);
00750 
00751         static vector<float> merge_peaks(vector<float> peak1, vector<float> peak2,float p_size);
00752         static vector<float> pw_extract(vector<float>pw, int n, int iswi,float ps);
00753         static vector<float> call_cl1(long int *k,long int *n, float *ps, long int *iswi, float *pw, float *q2, double *q, double *x, double *res, double *cu, double *s, long int *iu);
00754         static vector<float> lsfit(long int *ks,long int *n, long int *klm2d, long int *iswi, float *q1,double *q, double *x, double *res, double *cu, double *s,long int *iu);
00755         static void cl1(long int *k, long int *l, long int *m, long int *n, long int *klm2d,double *q, double *x, double *res, double *cu, long
00756         int *iu, double *s);
00757         static float eval(char * images,EMData * img, vector<int> S,int N, int K,int size);
00758 
00759         /*  VORONOI DIAGRAM */
00760         static vector<double> vrdg(const vector<float>& ph, const vector<float>& th);
00761         static void hsortd(double *theta,double *phi,int *key,int len,int option);
00762         static void voronoidiag(double *theta,double *phi,double* weight,int n);
00763         /*static void angstep(double* thetast,int len);*/
00764         /*static void voronoi(double *phi,double *theta,double *weight,int lenw,int low,int medium,int nt,int last);*/
00765         static void voronoi(double *phi,double *theta,double *weight, int nt);
00766         static void disorder2(double *x,double *y,int *key,int len);
00767         static void ang_to_xyz(double *x,double *y,double *z,int len);
00768         static void flip23(double *x,double *y,double *z,int *key,int k,int len);
00769         struct tmpstruct{
00770                 double theta1,phi1;
00771                 int key1;
00772                 };
00773         static bool cmp1(tmpstruct tmp1,tmpstruct tmp2);
00774         static bool cmp2(tmpstruct tmp1,tmpstruct tmp2);
00775         /**********************************************************/
00776         /* ######### STRIDPACK USED COMMANDS FOR VORONOI #########################*/
00777         static int trmsh3_(int *n0, double *tol, double *x, double *y, double *z__, int *n, int *list, int *lptr,
00778                int *lend, int *lnew, int *indx, int *lcnt, int *near__, int *next, double *dist, int *ier);
00779         static double areav_(int *k, int *n, double *x, double *y, double *z__, int *list, int *lptr, int *lend, int *ier);
00780         /**********************************************************/
00781         /* ######### STRIDPACK USED COMMANDS FOR VORONOI #########################*/
00782 
00783     /*  Various operation on images */
00784         /* out = img + scalar * img1  */
00785         static EMData* madn_scalar(EMData* img, EMData* img1, float scalar);
00786         /* out = scalar * img  */
00787         static EMData* mult_scalar(EMData* img, float scalar);
00788         /* out = img + img1  */
00789         static EMData* addn_img(EMData* img, EMData* img1);
00790         /* out = img - img1  */
00791         static EMData* subn_img(EMData* img, EMData* img1);
00792         /* out = img * img1  */
00793         static EMData* muln_img(EMData* img, EMData* img1);
00794         /* out = img / img1  */
00795         static EMData* divn_img(EMData* img, EMData* img1);
00796         /* img /= Re(img1) with zero check  */
00797         static EMData* divn_filter(EMData* img, EMData* img1);
00798 
00799         /* img += scalar * img1 */
00800         static void mad_scalar(EMData* img, EMData* img1, float scalar);
00801         /* img *= scalar  */
00802         static void mul_scalar(EMData* img, float scalar);
00803         /* img += img1  */
00804         static void add_img(EMData* img, EMData* img1);
00805         /* img += abs(img1)  */
00806         static void add_img_abs(EMData* img, EMData* img1);
00807         /* img += img1**2  */
00808         static void add_img2(EMData* img, EMData* img1);
00809         /* img -= img1  */
00810         static void sub_img(EMData* img, EMData* img1);
00811         /* img *= img1  */
00812         static void mul_img(EMData* img, EMData* img1);
00813         /* img /= img1  */
00814         static void div_img(EMData* img, EMData* img1);
00815         /* img /= Re(img1) with zero check  */
00816         static void div_filter(EMData* img, EMData* img1);
00817         /* pack absolute values of complex image into  real image with addition of Friedel part  */
00818         static EMData* pack_complex_to_real(EMData* img);
00819 private:
00820         static float ang_n(float peakp, string mode, int maxrin); //this function is used by apmq()
00821 public:
00822 
00828         static vector<float> multiref_polar_ali_2d(EMData* image, const vector< EMData* >& crefim,
00829                 float xrng, float yrng, float step, string mode,
00830                 vector< int >numr, float cnx, float cny);
00831 
00832         /* In this version, we return a list of peaks for all reference images */
00833         static vector<float> multiref_polar_ali_2d_peaklist(EMData* image, const vector< EMData* >& crefim,
00834                 float xrng, float yrng, float step, string mode,
00835                 vector< int >numr, float cnx, float cny);
00836 
00837         static vector<int> assign_groups(const vector<float>& d, int nref, int nima);
00838 
00844         static vector<float> multiref_polar_ali_2d_delta(EMData* image, const vector< EMData* >& crefim,
00845                 float xrng, float yrng, float step, string mode,
00846                 vector< int >numr, float cnx, float cny, float delta_start, float delta);
00847 
00853         static vector<float> multiref_polar_ali_2d_nom(EMData* image, const vector< EMData* >& crefim,
00854                 float xrng, float yrng, float step, string mode,
00855                 vector< int >numr, float cnx, float cny);
00856 
00862         static vector<float> multiref_polar_ali_2d_local(EMData* image, const vector< EMData* >& crefim,
00863                 float xrng, float yrng, float step, float ant, string mode,
00864                 vector< int >numr, float cnx, float cny);
00865 
00872         static vector<float> multiref_polar_ali_helical(EMData* image, const vector< EMData* >& crefim,
00873                 float xrng, float yrng, float step, float psi_max, string mode,
00874                 vector< int >numr, float cnx, float cny, int ynumber=-1);
00875         static vector<float> multiref_polar_ali_helical_local(EMData* image, const vector< EMData* >& crefim,
00876                 float xrng, float yrng, float step, float ant, float psi_max, string mode,
00877                 vector< int >numr, float cnx, float cny, int ynumber=-1);
00878         static vector<float> multiref_polar_ali_helical_90(EMData* image, const vector< EMData* >& crefim,
00879                 float xrng, float yrng, float step, float psi_max, string mode,
00880                 vector< int >numr, float cnx, float cny, int ynumber=-1);
00881         static vector<float> multiref_polar_ali_helical_90_local(EMData* image, const vector< EMData* >& crefim,
00882                 float xrng, float yrng, float step, float ant, float psi_max, string mode,
00883                 vector< int >numr, float cnx, float cny, int ynumber=-1);
00884 
00890         static vector<float> multiref_polar_ali_2d_local_psi(EMData* image, const vector< EMData* >& crefim,
00891                 float xrng, float yrng, float step, float ant, float psi_max, string mode,
00892                 vector< int >numr, float cnx, float cny);
00893 
00901         static void multiref_peaks_ali2d(EMData* image, EMData* crefim,
00902                 float xrng, float yrng, float step, string mode,
00903                 vector< int >numr, float cnx, float cny, EMData* peaks, EMData* peakm);
00904 
00912         static void multiref_peaks_compress_ali2d(EMData* image, EMData* crefim, float xrng, float yrng,
00913              float step, string mode, vector<int>numr, float cnx, float cny, EMData *peaks, EMData *peakm,
00914              EMData *peaks_compress, EMData *peakm_compress);
00915 
00920         static vector<float> ali2d_ccf_list(EMData* image, EMData* crefim, float xrng, float yrng,
00921              float step, string mode, vector<int>numr, float cnx, float cny, double T);
00922      /*
00923         static void multiref_peaks_ali(EMData* image, const vector< EMData* >& crefim,
00924                 float xrng, float yrng, float step, string mode,
00925                 vector< int >numr, float cnx, float cny, EMData* peaks, EMData* peakm,
00926                     int nphi, int ntheta);
00927 */
00928         static vector<float> twoD_fine_ali(EMData* image, EMData *refim, EMData* mask, float ang, float sxs, float sys);
00929 
00930         static vector<float> twoD_fine_ali_G(EMData* image, EMData *refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sxs, float sys);
00931 
00932         static vector<float> twoD_to_3D_ali(EMData* volft, Util::KaiserBessel& kb, EMData *refim, EMData* mask, float phi, float theta, float psi, float sxs, float sxy);
00933 
00934         static vector<float> twoD_fine_ali_SD(EMData* image, EMData *refim, EMData* mask, float ang, float sxs, float sys);
00935 
00936         static float ccc_images(EMData *, EMData *, EMData *, float , float , float );
00937 
00938         static vector<float> twoD_fine_ali_SD_G(EMData* image, EMData *refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sxs, float sys);
00939 
00940         static float ccc_images_G(EMData* image, EMData* refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sx, float sy);
00941 
00942         static EMData* move_points(EMData* img,  float qprob, int ri, int ro);
00943 
00944         static EMData* get_biggest_cluster( EMData* mg );
00945 
00946         //static EMData* ctf_img(int nx, int ny, int nz, float dz, float ps, float voltage=300.0f,float cs=2.0f,float wgh=0.1f,float b_factor=0.0f,float dza=0.0f,float azz=0.0f,float sign=-1.0f);
00947         static EMData* ctf_img(int nx, int ny, int nz, float dz, float ps, float voltage,float cs,float wgh,float b_factor,float dza,float azz,float sign);
00948 
00949         static inline int mono(int k1, int k2) {
00950 #ifdef _WIN32
00951                 int  mk = _cpp_max(k1,k2);
00952                 return  _cpp_min(k1,k2) + mk*(mk-1)/2;
00953 #else
00954                 int  mk = std::max(k1,k2);
00955                 return  std::min(k1,k2) + mk*(mk-1)/2;
00956 #endif  //_WIN32
00957         }
00958 
00959         static inline int nint180(float arg) {
00960             int res = int(arg + 180.5) - 180;
00961             return res;
00962         }
00963         
00964         static inline float mean(float *x, int n) {
00965                 float s = 0.0f;
00966                 for (int i=0; i<n; i++) s+=x[i];
00967                 return s/static_cast<float>(n);
00968         }
00969 
00970         static inline float var(float *x, int n) {
00971                 float s = 0.0f;
00972                 float m = mean(x, n);
00973                 for (int i=0; i<n; i++) s += (x[i]-m)*(x[i]-m);
00974                 return s/static_cast<float>(n);
00975         }
00976         
00977         static inline void rot_shift(float x, float y, float alpha, float x0, float y0, float* x1, float *y1) {
00978                 float cosi = cos(alpha/180.0f*M_PI);
00979                 float sini = sin(alpha/180.0f*M_PI);
00980                 *x1 = x*cosi+y*sini+x0;
00981                 *y1 = -x*sini+y*cosi+y0;
00982         }
00983         
00984         static vector<float> multi_align_error(vector<float> args, vector<float> all_ali_params);
00985         static float multi_align_error_func(double* x, vector<float> all_ali_params, int nima, int num_ali);
00986         static void multi_align_error_dfunc(double* x, vector<float> all_ali_params, int nima, int num_ali, double* g);
00987         
00988         static vector<float> cluster_pairwise(EMData* d, int K, float T, float F);
00989         //static vector<float> cluster_equalsize(EMData* d, int m);
00990         static vector<float> cluster_equalsize(EMData* d);
00991         static vector<float> vareas(EMData* d);
00992 
00998         static EMData* get_slice(EMData *vol, int dim, int index);
00999 
01000         static void image_mutation(EMData *img, float mutation_rate);
01001 
01003         static void array_mutation(float* list, int len_list, float mutation_rate, float min_val, float max_val, int K, int is_mirror);
01004 
01005         static vector<float> list_mutation(vector<float> list, float mutation_rate, float min_val, float max_val, int K, int is_mirror);
01006         /*
01007                         To restrict the value to [0, nx)
01008         */
01009         static inline float restrict1(float x, int nx) {
01010                 while ( x < 0.0f )        x += nx;
01011                 while ( x >= (float)(nx) )  x -= nx;
01012                 return x;
01013         }
01014 
01015 #endif  //util__sparx_h__

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