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
00627 static void bb_enumerate_(int* Parts, int* classDims, int nParts, int nClasses, int T, int n_guesses, int* levels);
00628
00632 static void initial_prune(vector <vector <int*> > & Parts, int* dimClasses, int nParts, int K, int T);
00633
00637 static bool explore(vector <vector <int*> > & Parts, int* dimClasses, int nParts, int K, int T, int partref, int* curintx, int
00638 size_curintx, int* next, int size_next, int depth);
00639
00640 static int* branch(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* Levels, int nLevels, int curlevel, int n_guesses);
00641
00649 static int findTopLargest(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* matchlist, int max_num_matches, int*
00650 costlist, int n_guesses);
00651
00656 static int generatesubmax(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int n_guesses);
00657
00661 static void search2(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int newT, int* curmax);
00662
00663 static int* explore2(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int newT, int* curintx, int size_curintx, int* next, int
00664 size_next, int depth);
00665
00670 static bool sanitycheck(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* output);
00671
00681 static vector<int> bb_enumerateMPI_(int* argParts, int* dimClasses, int nParts, int K, int T, int nTop, int n_guesses, bool doMPI, int* Levels);
00682
00688 static vector<int> branchMPIpy_(int* argParts, int* dimClasses, int nParts, int K, int T, int* Levels, int nLevels, int n_guesses, int nFirst, int* firstmatches);
00689
00695 static int* branchMPI(int* argParts, int* Indices, int* dimClasses, int nParts, int K, int T, int* Levels, int nLevels, int curlevel,int n_guesses, int nFirst, int* firstmatches);
00696
00697
00698
00699
00700 static vector<double> cml_weights(const vector<float>& cml);
00701
00703 static vector<int> cml_line_insino(vector<float> Rot, int i_prj, int n_prj);
00704
00706 static vector<int> cml_line_insino_all(vector<float> Rot, vector<int> seq, int n_prj, int n_lines);
00707
00709 static vector<double> cml_init_rot(vector<float> Ori);
00710
00712 static vector<float> cml_update_rot(vector<float> Rot, int iprj, float nph, float th, float nps);
00713
00715 static vector<double> cml_line_in3d(vector<float> Ori, vector<int> seq, int nprj, int nlines);
00716
00718 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);
00719
00721 static double cml_disc(const vector<EMData*>& data, vector<int> com, vector<int> seq, vector<float> weights, int n_lines);
00722
00728 static void set_line(EMData* img, int posline, EMData* line, int offset, int length);
00729
00737 static void cml_prepare_line(EMData* sino, EMData* line, int ilf, int ihf, int pos_line, int nblines);
00738
00739
00740
00741
00742
00743
00744
00745
00746 static EMData* decimate(EMData* img, int x_step,int y_step=1,int z_step=1);
00747
00748 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);
00749
00750 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");
00751
00752 static vector<float> histogram(EMData* image, EMData* mask, int nbins = 128, float hmin =0.0f, float hmax = 0.0f );
00753
00754 static Dict histc(EMData *ref,EMData *img,EMData *mask);
00755
00756 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);
00757
00758
00759
00760
00761
00762
00763
00764 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);
00765 static EMData *compress_image_mask(EMData* image, EMData* mask);
00766
00768 static EMData *reconstitute_image_mask(EMData *image,EMData *mask);
00769
00770 static vector<float> merge_peaks(vector<float> peak1, vector<float> peak2,float p_size);
00771 static vector<float> pw_extract(vector<float>pw, int n, int iswi,float ps);
00772 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);
00773 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);
00774 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
00775 int *iu, double *s);
00776 static float eval(char * images,EMData * img, vector<int> S,int N, int K,int size);
00777
00778
00779 static vector<double> vrdg(const vector<float>& ph, const vector<float>& th);
00780 static void hsortd(double *theta,double *phi,int *key,int len,int option);
00781 static void voronoidiag(double *theta,double *phi,double* weight,int n);
00782
00783
00784 static void voronoi(double *phi,double *theta,double *weight, int nt);
00785 static void disorder2(double *x,double *y,int *key,int len);
00786 static void ang_to_xyz(double *x,double *y,double *z,int len);
00787 static void flip23(double *x,double *y,double *z,int *key,int k,int len);
00788 struct tmpstruct{
00789 double theta1,phi1;
00790 int key1;
00791 };
00792 static bool cmp1(tmpstruct tmp1,tmpstruct tmp2);
00793 static bool cmp2(tmpstruct tmp1,tmpstruct tmp2);
00794
00795
00796 static int trmsh3_(int *n0, double *tol, double *x, double *y, double *z__, int *n, int *list, int *lptr,
00797 int *lend, int *lnew, int *indx, int *lcnt, int *near__, int *next, double *dist, int *ier);
00798 static double areav_(int *k, int *n, double *x, double *y, double *z__, int *list, int *lptr, int *lend, int *ier);
00799
00800
00801
00802
00803
00804 static EMData* madn_scalar(EMData* img, EMData* img1, float scalar);
00805
00806 static EMData* mult_scalar(EMData* img, float scalar);
00807
00808 static EMData* addn_img(EMData* img, EMData* img1);
00809
00810 static EMData* subn_img(EMData* img, EMData* img1);
00811
00812 static EMData* muln_img(EMData* img, EMData* img1);
00813
00814 static EMData* divn_img(EMData* img, EMData* img1);
00815
00816 static EMData* divn_filter(EMData* img, EMData* img1);
00817
00818
00819 static void mad_scalar(EMData* img, EMData* img1, float scalar);
00820
00821 static void mul_scalar(EMData* img, float scalar);
00822
00823 static void add_img(EMData* img, EMData* img1);
00824
00825 static void add_img_abs(EMData* img, EMData* img1);
00826
00827 static void add_img2(EMData* img, EMData* img1);
00828
00829 static void sub_img(EMData* img, EMData* img1);
00830
00831 static void mul_img(EMData* img, EMData* img1);
00832
00833 static void div_img(EMData* img, EMData* img1);
00834
00835 static void div_filter(EMData* img, EMData* img1);
00836
00837 static EMData* pack_complex_to_real(EMData* img);
00838 private:
00839 static float ang_n(float peakp, string mode, int maxrin);
00840 public:
00841
00847 static vector<float> multiref_polar_ali_2d(EMData* image, const vector< EMData* >& crefim,
00848 float xrng, float yrng, float step, string mode,
00849 vector< int >numr, float cnx, float cny);
00850
00856 static vector<float> multiref_polar_ali_2d_delta(EMData* image, const vector< EMData* >& crefim,
00857 float xrng, float yrng, float step, string mode,
00858 vector< int >numr, float cnx, float cny, float delta_start, float delta);
00859
00865 static vector<float> multiref_polar_ali_2d_nom(EMData* image, const vector< EMData* >& crefim,
00866 float xrng, float yrng, float step, string mode,
00867 vector< int >numr, float cnx, float cny);
00868
00874 static vector<float> multiref_polar_ali_2d_local(EMData* image, const vector< EMData* >& crefim,
00875 float xrng, float yrng, float step, float ant, string mode,
00876 vector< int >numr, float cnx, float cny);
00877
00884 static vector<float> multiref_polar_ali_helical(EMData* image, const vector< EMData* >& crefim,
00885 float xrng, float yrng, float step, float psi_max, string mode,
00886 vector< int >numr, float cnx, float cny);
00887
00893 static vector<float> multiref_polar_ali_2d_local_psi(EMData* image, const vector< EMData* >& crefim,
00894 float xrng, float yrng, float step, float ant, float psi_max, string mode,
00895 vector< int >numr, float cnx, float cny);
00896
00904 static void multiref_peaks_ali2d(EMData* image, EMData* crefim,
00905 float xrng, float yrng, float step, string mode,
00906 vector< int >numr, float cnx, float cny, EMData* peaks, EMData* peakm);
00907
00915 static void multiref_peaks_compress_ali2d(EMData* image, EMData* crefim, float xrng, float yrng,
00916 float step, string mode, vector<int>numr, float cnx, float cny, EMData *peaks, EMData *peakm,
00917 EMData *peaks_compress, EMData *peakm_compress);
00918
00923 static vector<float> ali2d_ccf_list(EMData* image, EMData* crefim, float xrng, float yrng,
00924 float step, string mode, vector<int>numr, float cnx, float cny, double T);
00925
00926
00927
00928
00929
00930
00931 static vector<float> twoD_fine_ali(EMData* image, EMData *refim, EMData* mask, float ang, float sxs, float sys);
00932
00933 static vector<float> twoD_fine_ali_G(EMData* image, EMData *refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sxs, float sys);
00934
00935 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);
00936
00937 static vector<float> twoD_fine_ali_SD(EMData* image, EMData *refim, EMData* mask, float ang, float sxs, float sys);
00938
00939 static float ccc_images(EMData *, EMData *, EMData *, float , float , float );
00940
00941 static vector<float> twoD_fine_ali_SD_G(EMData* image, EMData *refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sxs, float sys);
00942
00943 static float ccc_images_G(EMData* image, EMData* refim, EMData* mask, Util::KaiserBessel& kb, float ang, float sx, float sy);
00944
00945 static EMData* move_points(EMData* img, float qprob, int ri, int ro);
00946
00947 static EMData* get_biggest_cluster( EMData* mg );
00948
00949
00950 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);
00951
00952 static inline int mono(int k1, int k2) {
00953 #ifdef _WIN32
00954 int mk = _cpp_max(k1,k2);
00955 return _cpp_min(k1,k2) + mk*(mk-1)/2;
00956 #else
00957 int mk = std::max(k1,k2);
00958 return std::min(k1,k2) + mk*(mk-1)/2;
00959 #endif //_WIN32
00960 }
00961
00962 static inline int nint180(float arg) {
00963 int res = int(arg + 180.5) - 180;
00964 return res;
00965 }
00966
00967 static vector<float> cluster_pairwise(EMData* d, int K, float T, float F);
00968
00969 static vector<float> cluster_equalsize(EMData* d);
00970 static vector<float> vareas(EMData* d);
00971
00977 static EMData* get_slice(EMData *vol, int dim, int index);
00978
00979 static void image_mutation(EMData *img, float mutation_rate);
00980
00982 static void array_mutation(float* list, int len_list, float mutation_rate, float min_val, float max_val, int K, int is_mirror);
00983
00984 static vector<float> list_mutation(vector<float> list, float mutation_rate, float min_val, float max_val, int K, int is_mirror);
00985
00986
00987
00988 static inline float restrict1(float x, int nx) {
00989 while ( x < 0.0f ) x += nx;
00990 while ( x >= (float)(nx) ) x -= nx;
00991 return x;
00992 }
00993
00994 #endif //util__sparx_h__