#include <aligner.h>
Inheritance diagram for EMAN::RTFExhaustiveAligner:
Public Member Functions | |
virtual EMData * | align (EMData *this_img, EMData *to_img, const string &cmp_name="dot", const Dict &cmp_params=Dict()) const |
To align 'this_img' with another image passed in through its parameters. | |
virtual EMData * | align (EMData *this_img, EMData *to_img) const |
virtual string | get_name () const |
Get the Aligner's name. | |
virtual string | get_desc () const |
virtual TypeDict | get_param_types () const |
Static Public Member Functions | |
static Aligner * | NEW () |
Static Public Attributes | |
static const string | NAME = "rtf_exhaustive" |
slow
flip | ||
maxshift | Maximum translation in pixels |
Definition at line 770 of file aligner.h.
virtual EMData* EMAN::RTFExhaustiveAligner::align | ( | EMData * | this_img, | |
EMData * | to_img | |||
) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 775 of file aligner.h.
References align().
00776 { 00777 return align(this_img, to_img, "sqeuclidean", Dict()); 00778 }
EMData * RTFExhaustiveAligner::align | ( | EMData * | this_img, | |
EMData * | to_img, | |||
const string & | cmp_name = "dot" , |
|||
const Dict & | cmp_params = Dict() | |||
) | const [virtual] |
To align 'this_img' with another image passed in through its parameters.
The alignment uses a user-given comparison method to compare the two images. If none is given, a default one is used.
this_img | The image to be compared. | |
to_img | 'this_img" is aligned with 'to_img'. | |
cmp_name | The comparison method to compare the two images. | |
cmp_params | The parameter dictionary for comparison method. |
Implements EMAN::Aligner.
Definition at line 905 of file aligner.cpp.
References EMAN::Util::calc_best_fft_size(), EMAN::EMData::calc_ccfx(), EMAN::EMData::calc_max_index(), EMAN::EMData::cmp(), EMAN::EMData::copy(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), InvalidParameterException, ny, EMAN::Aligner::params, EMAN::EMData::process(), EMAN::EMConsts::rad2deg, EMAN::EMData::rotate_x(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), t, and EMAN::EMData::unwrap().
Referenced by align().
00907 { 00908 EMData *flip = params.set_default("flip", (EMData *) 0); 00909 int maxshift = params.set_default("maxshift", this_img->get_xsize()/8); 00910 if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2"); 00911 00912 int ny = this_img->get_ysize(); 00913 int xst = (int) floor(2 * M_PI * ny); 00914 xst = Util::calc_best_fft_size(xst); 00915 00916 Dict d("n",2); 00917 EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d); 00918 00919 int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2; 00920 EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true); 00921 if( to_shrunk_unwrapped ) 00922 { 00923 delete to_shrunk_unwrapped; 00924 to_shrunk_unwrapped = 0; 00925 } 00926 to_shrunk_unwrapped = tmp; 00927 00928 EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy(); 00929 EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true); 00930 EMData *to_unwrapped_copy = to_unwrapped->copy(); 00931 00932 bool delete_flipped = true; 00933 EMData *flipped = 0; 00934 if (flip) { 00935 delete_flipped = false; 00936 flipped = flip; 00937 } 00938 else { 00939 flipped = to->process("xform.flip", Dict("axis", "x")); 00940 } 00941 EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d); 00942 tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true); 00943 if( to_shrunk_flipped_unwrapped ) 00944 { 00945 delete to_shrunk_flipped_unwrapped; 00946 to_shrunk_flipped_unwrapped = 0; 00947 } 00948 to_shrunk_flipped_unwrapped = tmp; 00949 EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy(); 00950 EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true); 00951 EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy(); 00952 00953 if (delete_flipped && flipped != 0) { 00954 delete flipped; 00955 flipped = 0; 00956 } 00957 00958 EMData *this_shrunk_2 = this_img->process("math.medianshrink",d); 00959 00960 float bestval = FLT_MAX; 00961 float bestang = 0; 00962 int bestflip = 0; 00963 float bestdx = 0; 00964 float bestdy = 0; 00965 00966 int half_maxshift = maxshift / 2; 00967 00968 int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift; 00969 for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) { 00970 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) { 00971 #ifdef _WIN32 00972 if (_hypot(dx, dy) <= half_maxshift) { 00973 #else 00974 if (hypot(dx, dy) <= half_maxshift) { 00975 #endif 00976 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true); 00977 EMData *uwc = uw->copy(); 00978 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped); 00979 00980 uwc->rotate_x(a->calc_max_index()); 00981 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params); 00982 if (cm < bestval) { 00983 bestval = cm; 00984 bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize()); 00985 bestdx = (float)dx; 00986 bestdy = (float)dy; 00987 bestflip = 0; 00988 } 00989 00990 00991 if( a ) 00992 { 00993 delete a; 00994 a = 0; 00995 } 00996 if( uw ) 00997 { 00998 delete uw; 00999 uw = 0; 01000 } 01001 if( uwc ) 01002 { 01003 delete uwc; 01004 uwc = 0; 01005 } 01006 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true); 01007 uwc = uw->copy(); 01008 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped); 01009 01010 uwc->rotate_x(a->calc_max_index()); 01011 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params); 01012 if (cm < bestval) { 01013 bestval = cm; 01014 bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize()); 01015 bestdx = (float)dx; 01016 bestdy = (float)dy; 01017 bestflip = 1; 01018 } 01019 01020 if( a ) 01021 { 01022 delete a; 01023 a = 0; 01024 } 01025 01026 if( uw ) 01027 { 01028 delete uw; 01029 uw = 0; 01030 } 01031 if( uwc ) 01032 { 01033 delete uwc; 01034 uwc = 0; 01035 } 01036 } 01037 } 01038 } 01039 if( this_shrunk_2 ) 01040 { 01041 delete this_shrunk_2; 01042 this_shrunk_2 = 0; 01043 } 01044 if( to_shrunk_unwrapped ) 01045 { 01046 delete to_shrunk_unwrapped; 01047 to_shrunk_unwrapped = 0; 01048 } 01049 if( to_shrunk_unwrapped_copy ) 01050 { 01051 delete to_shrunk_unwrapped_copy; 01052 to_shrunk_unwrapped_copy = 0; 01053 } 01054 if( to_shrunk_flipped_unwrapped ) 01055 { 01056 delete to_shrunk_flipped_unwrapped; 01057 to_shrunk_flipped_unwrapped = 0; 01058 } 01059 if( to_shrunk_flipped_unwrapped_copy ) 01060 { 01061 delete to_shrunk_flipped_unwrapped_copy; 01062 to_shrunk_flipped_unwrapped_copy = 0; 01063 } 01064 bestdx *= 2; 01065 bestdy *= 2; 01066 bestval = FLT_MAX; 01067 01068 float bestdx2 = bestdx; 01069 float bestdy2 = bestdy; 01070 // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental 01071 // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this 01072 // algorithm 01073 for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) { 01074 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) { 01075 01076 #ifdef _WIN32 01077 if (_hypot(dx, dy) <= maxshift) { 01078 #else 01079 if (hypot(dx, dy) <= maxshift) { 01080 #endif 01081 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true); 01082 EMData *uwc = uw->copy(); 01083 EMData *a = uw->calc_ccfx(to_unwrapped); 01084 01085 uwc->rotate_x(a->calc_max_index()); 01086 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params); 01087 01088 if (cm < bestval) { 01089 bestval = cm; 01090 bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize()); 01091 bestdx = dx; 01092 bestdy = dy; 01093 bestflip = 0; 01094 } 01095 01096 if( a ) 01097 { 01098 delete a; 01099 a = 0; 01100 } 01101 if( uw ) 01102 { 01103 delete uw; 01104 uw = 0; 01105 } 01106 if( uwc ) 01107 { 01108 delete uwc; 01109 uwc = 0; 01110 } 01111 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true); 01112 uwc = uw->copy(); 01113 a = uw->calc_ccfx(to_flip_unwrapped); 01114 01115 uwc->rotate_x(a->calc_max_index()); 01116 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params); 01117 01118 if (cm < bestval) { 01119 bestval = cm; 01120 bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize()); 01121 bestdx = dx; 01122 bestdy = dy; 01123 bestflip = 1; 01124 } 01125 01126 if( a ) 01127 { 01128 delete a; 01129 a = 0; 01130 } 01131 if( uw ) 01132 { 01133 delete uw; 01134 uw = 0; 01135 } 01136 if( uwc ) 01137 { 01138 delete uwc; 01139 uwc = 0; 01140 } 01141 } 01142 } 01143 } 01144 if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;} 01145 if( to_shrunk_unwrapped ) { delete to_shrunk_unwrapped; to_shrunk_unwrapped = 0;} 01146 if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; } 01147 if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; } 01148 if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;} 01149 01150 bestang *= (float)EMConsts::rad2deg; 01151 Transform t(Dict("type","2d","alpha",(float)bestang)); 01152 t.set_pre_trans(Vec2f(-bestdx,-bestdy)); 01153 if (bestflip) { 01154 t.set_mirror(true); 01155 } 01156 01157 EMData* ret = this_img->process("xform",Dict("transform",&t)); 01158 ret->set_attr("xform.align2d",&t); 01159 01160 return ret; 01161 }
virtual string EMAN::RTFExhaustiveAligner::get_desc | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 785 of file aligner.h.
00786 { 00787 return "Experimental full 2D alignment with handedness check using semi-exhaustive search (not necessarily better than RTFBest)"; 00788 }
virtual string EMAN::RTFExhaustiveAligner::get_name | ( | ) | const [inline, virtual] |
virtual TypeDict EMAN::RTFExhaustiveAligner::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 795 of file aligner.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and EMAN::TypeDict::put().
00796 { 00797 TypeDict d; 00798 00799 d.put("flip", EMObject::EMDATA); 00800 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00801 return d; 00802 }
static Aligner* EMAN::RTFExhaustiveAligner::NEW | ( | ) | [inline, static] |
const string RTFExhaustiveAligner::NAME = "rtf_exhaustive" [static] |