00001
00005
00006
00007
00008
00009
00010
00011
00012
00013
00014
00015
00016
00017
00018
00019
00020
00021
00022
00023
00024
00025
00026
00027
00028
00029
00030
00031
00032
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);
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_ns(EMData* circ1, EMData* circ2, vector<int> numr);
00558
00565 static EMData* Crosrng_msg(EMData* circ1, EMData* circ2, vector<int> numr);
00566
00573 static void Crosrng_msg_vec(EMData* circ1, EMData* circ2, vector<int> numr, float *q, float *t);
00574
00581 static EMData* Crosrng_msg_s(EMData* circ1, EMData* circ2, vector<int> numr);
00582
00589 static EMData* Crosrng_msg_m(EMData* circ1, EMData* circ2, vector<int> numr);
00590
00591 static vector<float> Crosrng_msg_vec_p(EMData* circ1, EMData* circ2, vector<int> numr );
00592 static void prb1d(double *b, int npoint, float *pos);
00593
00594 static void update_fav(EMData* ave,EMData* dat, float tot, int mirror, vector<int> numr);
00595 static void sub_fav(EMData* ave,EMData* dat, float tot, int mirror, vector<int> numr);
00596
00597
00598 static float ener(EMData* ave, vector<int> numr);
00599
00600 static float ener_tot(const vector<EMData*>& data, vector<int> numr, vector<float> tot);
00601
00603 static Dict min_dist_real(EMData* image, const vector<EMData*>& data);
00604
00606 static Dict min_dist_four(EMData* image, const vector<EMData*>& data);
00607
00614 static int k_means_cont_table_(int* group1, int* group2, int* stb, long int s1, long int s2, int flag);
00615
00616
00617
00618
00622 static void initial_prune(vector <vector <int*> > & Parts, int* dimClasses, int nParts, int K, int T);
00623
00627 static bool explore(vector <vector <int*> > & Parts, int* dimClasses, int nParts, int K, int T, int partref, int* curintx, int
00628 size_curintx, int* next, int size_next, int depth);
00629
00630
00631
00632
00637 static int generatesubmax(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int n_guesses, int LARGEST_CLASS);
00638
00642 static void search2(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* matchlist, int* costlist, int J);
00643
00644 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*
00645 costlist, int* curbranch);
00646
00651 static bool sanitycheck(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* output);
00652
00662 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,
00663 int branchfunc, int LIM);
00664
00665
00671 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,
00672 float stmult, int branchfunc, int LIM);
00673
00674 static int branch_factor_2(int* costlist, int* matchlist, int J, int T, int nParts, int curlevel, int max_branching, int LIM);
00675 static int branch_factor_3(int* costlist, int* matchlist, int J, int T, int nParts, int curlevel, int max_branching, int K, int LIM);
00676 static int branch_factor_4(int* costlist, int* matchlist, int J, int T, int nParts, int curlevel, int max_branching, float stmult);
00677
00678
00679
00680 static vector<double> cml_weights(const vector<float>& cml);
00681
00683 static vector<int> cml_line_insino(vector<float> Rot, int i_prj, int n_prj);
00684
00686 static vector<int> cml_line_insino_all(vector<float> Rot, vector<int> seq, int n_prj, int n_lines);
00687
00689 static vector<double> cml_init_rot(vector<float> Ori);
00690
00692 static vector<float> cml_update_rot(vector<float> Rot, int iprj, float nph, float th, float nps);
00693
00695 static vector<double> cml_line_in3d(vector<float> Ori, vector<int> seq, int nprj, int nlines);
00696
00698 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);
00699
00701 static double cml_disc(const vector<EMData*>& data, vector<int> com, vector<int> seq, vector<float> weights, int n_lines);
00702
00708 static void set_line(EMData* img, int posline, EMData* line, int offset, int length);
00709
00717 static void cml_prepare_line(EMData* sino, EMData* line, int ilf, int ihf, int pos_line, int nblines);
00718
00719
00720
00721
00722
00723
00724
00725
00726 static EMData* decimate(EMData* img, int x_step,int y_step=1,int z_step=1);
00727
00728 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);
00729
00730 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");
00731
00732 static vector<float> histogram(EMData* image, EMData* mask, int nbins = 128, float hmin =0.0f, float hmax = 0.0f );
00733
00734 static Dict histc(EMData *ref,EMData *img,EMData *mask);
00735
00736 static float hist_comp_freq(float PA,float PB,int size_img, int hist_len, EMData *img, vector<float> ref_freq_hist, EMData *mask, float ref_h_diff, float ref_h_min);
00737
00738
00739
00740
00741
00742
00743
00744 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);
00745 static EMData *compress_image_mask(EMData* image, EMData* mask);
00746
00748 static EMData *reconstitute_image_mask(EMData *image,EMData *mask);
00749
00750 static vector<float> merge_peaks(vector<float> peak1, vector<float> peak2,float p_size);
00751 static vector<float> pw_extract(vector<float>pw, int n, int iswi,float ps);
00752 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);
00753 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);
00754 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
00755 int *iu, double *s);
00756 static float eval(char * images,EMData * img, vector<int> S,int N, int K,int size);
00757
00758
00759 static vector<double> vrdg(const vector<float>& ph, const vector<float>& th);
00760 static void hsortd(double *theta,double *phi,int *key,int len,int option);
00761 static void voronoidiag(double *theta,double *phi,double* weight,int n);
00762
00763
00764 static void voronoi(double *phi,double *theta,double *weight, int nt);
00765 static void disorder2(double *x,double *y,int *key,int len);
00766 static void ang_to_xyz(double *x,double *y,double *z,int len);
00767 static void flip23(double *x,double *y,double *z,int *key,int k,int len);
00768 struct tmpstruct{
00769 double theta1,phi1;
00770 int key1;
00771 };
00772 static bool cmp1(tmpstruct tmp1,tmpstruct tmp2);
00773 static bool cmp2(tmpstruct tmp1,tmpstruct tmp2);
00774
00775
00776 static int trmsh3_(int *n0, double *tol, double *x, double *y, double *z__, int *n, int *list, int *lptr,
00777 int *lend, int *lnew, int *indx, int *lcnt, int *near__, int *next, double *dist, int *ier);
00778 static double areav_(int *k, int *n, double *x, double *y, double *z__, int *list, int *lptr, int *lend, int *ier);
00779
00780
00781
00782
00783
00784 static EMData* madn_scalar(EMData* img, EMData* img1, float scalar);
00785
00786 static EMData* mult_scalar(EMData* img, float scalar);
00787
00788 static EMData* addn_img(EMData* img, EMData* img1);
00789
00790 static EMData* subn_img(EMData* img, EMData* img1);
00791
00792 static EMData* muln_img(EMData* img, EMData* img1);
00793
00794 static EMData* divn_img(EMData* img, EMData* img1);
00795
00796 static EMData* divn_filter(EMData* img, EMData* img1);
00797
00798
00799 static void mad_scalar(EMData* img, EMData* img1, float scalar);
00800
00801 static void mul_scalar(EMData* img, float scalar);
00802
00803 static void add_img(EMData* img, EMData* img1);
00804
00805 static void add_img_abs(EMData* img, EMData* img1);
00806
00807 static void add_img2(EMData* img, EMData* img1);
00808
00809 static void sub_img(EMData* img, EMData* img1);
00810
00811 static void mul_img(EMData* img, EMData* img1);
00812
00813 static void div_img(EMData* img, EMData* img1);
00814
00815 static void div_filter(EMData* img, EMData* img1);
00816
00817 static EMData* pack_complex_to_real(EMData* img);
00818 private:
00819 static float ang_n(float peakp, string mode, int maxrin);
00820 public:
00821
00827 static vector<float> multiref_polar_ali_2d(EMData* image, const vector< EMData* >& crefim,
00828 float xrng, float yrng, float step, string mode,
00829 vector< int >numr, float cnx, float cny);
00830
00831
00832 static vector<float> multiref_polar_ali_2d_peaklist(EMData* image, const vector< EMData* >& crefim,
00833 float xrng, float yrng, float step, string mode,
00834 vector< int >numr, float cnx, float cny);
00840 static vector<float> multiref_polar_ali_2d_delta(EMData* image, const vector< EMData* >& crefim,
00841 float xrng, float yrng, float step, string mode,
00842 vector< int >numr, float cnx, float cny, float delta_start, float delta);
00843
00849 static vector<float> multiref_polar_ali_2d_nom(EMData* image, const vector< EMData* >& crefim,
00850 float xrng, float yrng, float step, string mode,
00851 vector< int >numr, float cnx, float cny);
00852
00858 static vector<float> multiref_polar_ali_2d_local(EMData* image, const vector< EMData* >& crefim,
00859 float xrng, float yrng, float step, float ant, string mode,
00860 vector< int >numr, float cnx, float cny);
00861
00868 static vector<float> multiref_polar_ali_helical(EMData* image, const vector< EMData* >& crefim,
00869 float xrng, float yrng, float step, float psi_max, string mode,
00870 vector< int >numr, float cnx, float cny, int ynumber=-1);
00871
00877 static vector<float> multiref_polar_ali_2d_local_psi(EMData* image, const vector< EMData* >& crefim,
00878 float xrng, float yrng, float step, float ant, float psi_max, string mode,
00879 vector< int >numr, float cnx, float cny);
00880
00888 static void multiref_peaks_ali2d(EMData* image, EMData* crefim,
00889 float xrng, float yrng, float step, string mode,
00890 vector< int >numr, float cnx, float cny, EMData* peaks, EMData* peakm);
00891
00899 static void multiref_peaks_compress_ali2d(EMData* image, EMData* crefim, float xrng, float yrng,
00900 float step, string mode, vector<int>numr, float cnx, float cny, EMData *peaks, EMData *peakm,
00901 EMData *peaks_compress, EMData *peakm_compress);
00902
00907 static vector<float> ali2d_ccf_list(EMData* image, EMData* crefim, float xrng, float yrng,
00908 float step, string mode, vector<int>numr, float cnx, float cny, double T);
00909
00910
00911
00912
00913
00914
00915 static vector<float> twoD_fine_ali(EMData* image, EMData *refim, EMData* mask, float ang, float sxs, float sys);
00916
00917 static vector<float> twoD_fine_ali_G(EMData* image, EMData *refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sxs, float sys);
00918
00919 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);
00920
00921 static vector<float> twoD_fine_ali_SD(EMData* image, EMData *refim, EMData* mask, float ang, float sxs, float sys);
00922
00923 static float ccc_images(EMData *, EMData *, EMData *, float , float , float );
00924
00925 static vector<float> twoD_fine_ali_SD_G(EMData* image, EMData *refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sxs, float sys);
00926
00927 static float ccc_images_G(EMData* image, EMData* refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sx, float sy);
00928
00929 static EMData* move_points(EMData* img, float qprob, int ri, int ro);
00930
00931 static EMData* get_biggest_cluster( EMData* mg );
00932
00933
00934 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);
00935
00936 static inline int mono(int k1, int k2) {
00937 #ifdef _WIN32
00938 int mk = _cpp_max(k1,k2);
00939 return _cpp_min(k1,k2) + mk*(mk-1)/2;
00940 #else
00941 int mk = std::max(k1,k2);
00942 return std::min(k1,k2) + mk*(mk-1)/2;
00943 #endif //_WIN32
00944 }
00945
00946 static inline int nint180(float arg) {
00947 int res = int(arg + 180.5) - 180;
00948 return res;
00949 }
00950
00951 static inline float mean(float *x, int n) {
00952 float s = 0.0f;
00953 for (int i=0; i<n; i++) s+=x[i];
00954 return s/static_cast<float>(n);
00955 }
00956
00957 static inline float var(float *x, int n) {
00958 float s = 0.0f;
00959 float m = mean(x, n);
00960 for (int i=0; i<n; i++) s += (x[i]-m)*(x[i]-m);
00961 return s/static_cast<float>(n);
00962 }
00963
00964 static inline void rot_shift(float x, float y, float alpha, float x0, float y0, float* x1, float *y1) {
00965 float cosi = cos(alpha/180.0f*M_PI);
00966 float sini = sin(alpha/180.0f*M_PI);
00967 *x1 = x*cosi+y*sini+x0;
00968 *y1 = -x*sini+y*cosi+y0;
00969 }
00970
00971 static vector<float> multi_align_error(vector<float> args, vector<float> all_ali_params);
00972 static float multi_align_error_func(double* x, vector<float> all_ali_params, int nima, int num_ali);
00973 static void multi_align_error_dfunc(double* x, vector<float> all_ali_params, int nima, int num_ali, double* g);
00974
00975 static vector<float> cluster_pairwise(EMData* d, int K, float T, float F);
00976
00977 static vector<float> cluster_equalsize(EMData* d);
00978 static vector<float> vareas(EMData* d);
00979
00985 static EMData* get_slice(EMData *vol, int dim, int index);
00986
00987 static void image_mutation(EMData *img, float mutation_rate);
00988
00990 static void array_mutation(float* list, int len_list, float mutation_rate, float min_val, float max_val, int K, int is_mirror);
00991
00992 static vector<float> list_mutation(vector<float> list, float mutation_rate, float min_val, float max_val, int K, int is_mirror);
00993
00994
00995
00996 static inline float restrict1(float x, int nx) {
00997 while ( x < 0.0f ) x += nx;
00998 while ( x >= (float)(nx) ) x -= nx;
00999 return x;
01000 }
01001
01002 #endif //util__sparx_h__