#include <aligner.h>
Inheritance diagram for EMAN::RTFSlowExhaustiveAligner:
Public Member Functions | |
virtual EMData * | align (EMData *this_img, EMData *to_img, const string &cmp_name, const Dict &cmp_params) 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_slow_exhaustive" |
This is very slow but can ensure localization of the global maximum
flip | Optional. This is the flipped version of the images that is being aligned. If specified it will be used for the handedness check, if not a flipped copy of the image will be made | |
maxshift | The maximum length of the detectable translational shift | |
transtep | The translation step to take when honing the alignment, which occurs after coarse alignment | |
angstep | The angular step (in degrees) to take in the exhaustive search for the solution angle. Typically very small i.e. 3 or smaller |
Definition at line 814 of file aligner.h.
virtual EMData* EMAN::RTFSlowExhaustiveAligner::align | ( | EMData * | this_img, | |
EMData * | to_img | |||
) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 819 of file aligner.h.
References align().
00820 { 00821 return align(this_img, to_img, "sqeuclidean", Dict()); 00822 }
EMData * RTFSlowExhaustiveAligner::align | ( | EMData * | this_img, | |
EMData * | to_img, | |||
const string & | cmp_name, | |||
const Dict & | cmp_params | |||
) | 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 1152 of file aligner.cpp.
References EMAN::EMConsts::deg2rad, EMAN::EMData::get_xsize(), InvalidParameterException, nx, EMAN::Aligner::params, EMAN::EMData::process(), EMAN::EMConsts::rad2deg, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), t, and v.
Referenced by align().
01154 { 01155 01156 EMData *flip = params.set_default("flip", (EMData *) 0); 01157 int maxshift = params.set_default("maxshift", -1); 01158 01159 EMData *flipped = 0; 01160 01161 bool delete_flipped = true; 01162 if (flip) { 01163 delete_flipped = false; 01164 flipped = flip; 01165 } 01166 else { 01167 flipped = to->process("xform.flip", Dict("axis", "x")); 01168 } 01169 01170 int nx = this_img->get_xsize(); 01171 01172 if (maxshift < 0) { 01173 maxshift = nx / 10; 01174 } 01175 01176 float angle_step = params.set_default("angstep", 0.0f); 01177 if ( angle_step == 0 ) angle_step = atan2(2.0f, (float)nx); 01178 else { 01179 angle_step *= (float)EMConsts::deg2rad; //convert to radians 01180 } 01181 float trans_step = params.set_default("transtep",1.0f); 01182 01183 if (trans_step <= 0) throw InvalidParameterException("transstep must be greater than 0"); 01184 if (angle_step <= 0) throw InvalidParameterException("angstep must be greater than 0"); 01185 01186 01187 Dict shrinkfactor("n",2); 01188 EMData *this_img_shrink = this_img->process("math.medianshrink",shrinkfactor); 01189 EMData *to_shrunk = to->process("math.medianshrink",shrinkfactor); 01190 EMData *flipped_shrunk = flipped->process("math.medianshrink",shrinkfactor); 01191 01192 int bestflip = 0; 01193 float bestdx = 0; 01194 float bestdy = 0; 01195 01196 float bestang = 0; 01197 float bestval = FLT_MAX; 01198 01199 int half_maxshift = maxshift / 2; 01200 01201 01202 for (int dy = -half_maxshift; dy <= half_maxshift; ++dy) { 01203 for (int dx = -half_maxshift; dx <= half_maxshift; ++dx) { 01204 if (hypot(dx, dy) <= maxshift) { 01205 for (float ang = -angle_step * 2.0f; ang <= (float)2 * M_PI; ang += angle_step * 4.0f) { 01206 EMData v(*this_img_shrink); 01207 Transform t(Dict("type","2d","alpha",static_cast<float>(ang*EMConsts::rad2deg))); 01208 t.set_trans((float)dx,(float)dy); 01209 v.transform(t); 01210 // v.rotate_translate(ang*EMConsts::rad2deg, 0.0f, 0.0f, (float)dx, (float)dy, 0.0f); 01211 01212 float lc = v.cmp(cmp_name, to_shrunk, cmp_params); 01213 01214 if (lc < bestval) { 01215 bestval = lc; 01216 bestang = ang; 01217 bestdx = (float)dx; 01218 bestdy = (float)dy; 01219 bestflip = 0; 01220 } 01221 01222 lc = v.cmp(cmp_name,flipped_shrunk , cmp_params); 01223 if (lc < bestval) { 01224 bestval = lc; 01225 bestang = ang; 01226 bestdx = (float)dx; 01227 bestdy = (float)dy; 01228 bestflip = 1; 01229 } 01230 } 01231 } 01232 } 01233 } 01234 01235 if( to_shrunk ) 01236 { 01237 delete to_shrunk; 01238 to_shrunk = 0; 01239 } 01240 if( flipped_shrunk ) 01241 { 01242 delete flipped_shrunk; 01243 flipped_shrunk = 0; 01244 } 01245 if( this_img_shrink ) 01246 { 01247 delete this_img_shrink; 01248 this_img_shrink = 0; 01249 } 01250 01251 bestdx *= 2; 01252 bestdy *= 2; 01253 bestval = FLT_MAX; 01254 01255 float bestdx2 = bestdx; 01256 float bestdy2 = bestdy; 01257 float bestang2 = bestang; 01258 01259 for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += trans_step) { 01260 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += trans_step) { 01261 if (hypot(dx, dy) <= maxshift) { 01262 for (float ang = bestang2 - angle_step * 6.0f; ang <= bestang2 + angle_step * 6.0f; ang += angle_step) { 01263 EMData v(*this_img); 01264 Transform t(Dict("type","2d","alpha",static_cast<float>(ang*EMConsts::rad2deg))); 01265 t.set_trans(dx,dy); 01266 v.transform(t); 01267 // v.rotate_translate(ang*EMConsts::rad2deg, 0.0f, 0.0f, (float)dx, (float)dy, 0.0f); 01268 01269 float lc = v.cmp(cmp_name, to, cmp_params); 01270 01271 if (lc < bestval) { 01272 bestval = lc; 01273 bestang = ang; 01274 bestdx = dx; 01275 bestdy = dy; 01276 bestflip = 0; 01277 } 01278 01279 lc = v.cmp(cmp_name, flipped, cmp_params); 01280 01281 if (lc < bestval) { 01282 bestval = lc; 01283 bestang = ang; 01284 bestdx = dx; 01285 bestdy = dy; 01286 bestflip = 1; 01287 } 01288 } 01289 } 01290 } 01291 } 01292 01293 if (delete_flipped) { delete flipped; flipped = 0; } 01294 01295 bestang *= (float)EMConsts::rad2deg; 01296 Transform t(Dict("type","2d","alpha",(float)bestang)); 01297 t.set_trans(bestdx,bestdy); 01298 01299 if (bestflip) { 01300 t.set_mirror(true); 01301 } 01302 01303 EMData* rslt = this_img->process("xform",Dict("transform",&t)); 01304 rslt->set_attr("xform.align2d",&t); 01305 01306 return rslt; 01307 }
virtual string EMAN::RTFSlowExhaustiveAligner::get_desc | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 828 of file aligner.h.
00829 { 00830 return "Experimental full 2D alignment with handedness check using more exhaustive search (not necessarily better than RTFBest)"; 00831 }
virtual string EMAN::RTFSlowExhaustiveAligner::get_name | ( | ) | const [inline, virtual] |
virtual TypeDict EMAN::RTFSlowExhaustiveAligner::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 838 of file aligner.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
00839 { 00840 TypeDict d; 00841 d.put("flip", EMObject::EMDATA,"Optional. This is the flipped version of the images that is being aligned. If specified it will be used for the handedness check, if not a flipped copy of the image will be made"); 00842 d.put("maxshift", EMObject::INT,"The maximum length of the detectable translational shift"); 00843 d.put("transtep", EMObject::FLOAT,"The translation step to take when honing the alignment, which occurs after coarse alignment"); 00844 d.put("angstep", EMObject::FLOAT,"The angular step (in degrees) to take in the exhaustive search for the solution angle. Typically very small i.e. 3 or smaller."); 00845 return d; 00846 }
static Aligner* EMAN::RTFSlowExhaustiveAligner::NEW | ( | ) | [inline, static] |
const string RTFSlowExhaustiveAligner::NAME = "rtf_slow_exhaustive" [static] |