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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);
00116
00117
00129 static void spline_mat(float *x, float *y, int n, float *xq, float *yq, int m);
00130
00143 static void spline(float *x, float *y, int n, float yp1, float ypn, float *y2);
00144
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
00255
00256
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
00261
00262
00263
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
00436
00437
00438
00439
00440
00441
00442
00443
00444
00445
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
00450
00451
00452
00453
00454
00455
00456
00457
00458
00459
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
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
00500
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
00504
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
00508
00509
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
00526
00527
00528
00529
00530
00531
00532
00533
00534
00535
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
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
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
00679
00680
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
00721
00722
00723
00724
00725
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
00741
00742
00743
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
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
00764
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
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
00782
00783
00784
00785 static EMData* madn_scalar(EMData* img, EMData* img1, float scalar);
00786
00787 static EMData* mult_scalar(EMData* img, float scalar);
00788
00789 static EMData* addn_img(EMData* img, EMData* img1);
00790
00791 static EMData* subn_img(EMData* img, EMData* img1);
00792
00793 static EMData* muln_img(EMData* img, EMData* img1);
00794
00795 static EMData* divn_img(EMData* img, EMData* img1);
00796
00797 static EMData* divn_filter(EMData* img, EMData* img1);
00798
00799
00800 static void mad_scalar(EMData* img, EMData* img1, float scalar);
00801
00802 static void mul_scalar(EMData* img, float scalar);
00803
00804 static void add_img(EMData* img, EMData* img1);
00805
00806 static void add_img_abs(EMData* img, EMData* img1);
00807
00808 static void add_img2(EMData* img, EMData* img1);
00809
00810 static void sub_img(EMData* img, EMData* img1);
00811
00812 static void mul_img(EMData* img, EMData* img1);
00813
00814 static void div_img(EMData* img, EMData* img1);
00815
00816 static void div_filter(EMData* img, EMData* img1);
00817
00818 static EMData* pack_complex_to_real(EMData* img);
00819 private:
00820 static float ang_n(float peakp, string mode, int maxrin);
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
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
00924
00925
00926
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
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
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
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__