#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 | |
Aligner * | NEW () |
Static Public Attributes | |
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.
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Implements EMAN::Aligner. Definition at line 819 of file aligner.h. References align(). 00820 { 00821 return align(this_img, to_img, "sqeuclidean", Dict()); 00822 }
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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.
Implements EMAN::Aligner. Definition at line 1151 of file aligner.cpp. References EMAN::EMData::cmp(), EMAN::EMData::get_xsize(), InvalidParameterException, nx, EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_mirror(), EMAN::Transform::set_trans(), t, EMAN::EMData::transform(), and v. 01153 { 01154 01155 EMData *flip = params.set_default("flip", (EMData *) 0); 01156 int maxshift = params.set_default("maxshift", -1); 01157 01158 EMData *flipped = 0; 01159 01160 bool delete_flipped = true; 01161 if (flip) { 01162 delete_flipped = false; 01163 flipped = flip; 01164 } 01165 else { 01166 flipped = to->process("xform.flip", Dict("axis", "x")); 01167 } 01168 01169 int nx = this_img->get_xsize(); 01170 01171 if (maxshift < 0) { 01172 maxshift = nx / 10; 01173 } 01174 01175 float angle_step = params.set_default("angstep", 0.0f); 01176 if ( angle_step == 0 ) angle_step = atan2(2.0f, (float)nx); 01177 else { 01178 angle_step *= (float)EMConsts::deg2rad; //convert to radians 01179 } 01180 float trans_step = params.set_default("transtep",1.0f); 01181 01182 if (trans_step <= 0) throw InvalidParameterException("transstep must be greater than 0"); 01183 if (angle_step <= 0) throw InvalidParameterException("angstep must be greater than 0"); 01184 01185 01186 Dict shrinkfactor("n",2); 01187 EMData *this_img_shrink = this_img->process("math.medianshrink",shrinkfactor); 01188 EMData *to_shrunk = to->process("math.medianshrink",shrinkfactor); 01189 EMData *flipped_shrunk = flipped->process("math.medianshrink",shrinkfactor); 01190 01191 int bestflip = 0; 01192 float bestdx = 0; 01193 float bestdy = 0; 01194 01195 float bestang = 0; 01196 float bestval = FLT_MAX; 01197 01198 int half_maxshift = maxshift / 2; 01199 01200 01201 for (int dy = -half_maxshift; dy <= half_maxshift; ++dy) { 01202 for (int dx = -half_maxshift; dx <= half_maxshift; ++dx) { 01203 if (hypot(dx, dy) <= maxshift) { 01204 for (float ang = -angle_step * 2.0f; ang <= (float)2 * M_PI; ang += angle_step * 4.0f) { 01205 EMData v(*this_img_shrink); 01206 Transform t(Dict("type","2d","alpha",static_cast<float>(ang*EMConsts::rad2deg))); 01207 t.set_trans((float)dx,(float)dy); 01208 v.transform(t); 01209 // v.rotate_translate(ang*EMConsts::rad2deg, 0.0f, 0.0f, (float)dx, (float)dy, 0.0f); 01210 01211 float lc = v.cmp(cmp_name, to_shrunk, cmp_params); 01212 01213 if (lc < bestval) { 01214 bestval = lc; 01215 bestang = ang; 01216 bestdx = (float)dx; 01217 bestdy = (float)dy; 01218 bestflip = 0; 01219 } 01220 01221 lc = v.cmp(cmp_name,flipped_shrunk , cmp_params); 01222 if (lc < bestval) { 01223 bestval = lc; 01224 bestang = ang; 01225 bestdx = (float)dx; 01226 bestdy = (float)dy; 01227 bestflip = 1; 01228 } 01229 } 01230 } 01231 } 01232 } 01233 01234 if( to_shrunk ) 01235 { 01236 delete to_shrunk; 01237 to_shrunk = 0; 01238 } 01239 if( flipped_shrunk ) 01240 { 01241 delete flipped_shrunk; 01242 flipped_shrunk = 0; 01243 } 01244 if( this_img_shrink ) 01245 { 01246 delete this_img_shrink; 01247 this_img_shrink = 0; 01248 } 01249 01250 bestdx *= 2; 01251 bestdy *= 2; 01252 bestval = FLT_MAX; 01253 01254 float bestdx2 = bestdx; 01255 float bestdy2 = bestdy; 01256 float bestang2 = bestang; 01257 01258 for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += trans_step) { 01259 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += trans_step) { 01260 if (hypot(dx, dy) <= maxshift) { 01261 for (float ang = bestang2 - angle_step * 6.0f; ang <= bestang2 + angle_step * 6.0f; ang += angle_step) { 01262 EMData v(*this_img); 01263 Transform t(Dict("type","2d","alpha",static_cast<float>(ang*EMConsts::rad2deg))); 01264 t.set_trans(dx,dy); 01265 v.transform(t); 01266 // v.rotate_translate(ang*EMConsts::rad2deg, 0.0f, 0.0f, (float)dx, (float)dy, 0.0f); 01267 01268 float lc = v.cmp(cmp_name, to, cmp_params); 01269 01270 if (lc < bestval) { 01271 bestval = lc; 01272 bestang = ang; 01273 bestdx = dx; 01274 bestdy = dy; 01275 bestflip = 0; 01276 } 01277 01278 lc = v.cmp(cmp_name, flipped, cmp_params); 01279 01280 if (lc < bestval) { 01281 bestval = lc; 01282 bestang = ang; 01283 bestdx = dx; 01284 bestdy = dy; 01285 bestflip = 1; 01286 } 01287 } 01288 } 01289 } 01290 } 01291 01292 if (delete_flipped) { delete flipped; flipped = 0; } 01293 01294 bestang *= (float)EMConsts::rad2deg; 01295 Transform t(Dict("type","2d","alpha",(float)bestang)); 01296 t.set_trans(bestdx,bestdy); 01297 01298 if (bestflip) { 01299 t.set_mirror(true); 01300 } 01301 01302 EMData* rslt = this_img->process("xform",Dict("transform",&t)); 01303 rslt->set_attr("xform.align2d",&t); 01304 01305 return rslt; 01306 }
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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 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 823 of file aligner.h. 00824 {
00825 return NAME;
00826 }
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Implements EMAN::Aligner. Definition at line 838 of file aligner.h. References 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 }
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Definition at line 833 of file aligner.h. 00834 { 00835 return new RTFSlowExhaustiveAligner(); 00836 }
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Definition at line 72 of file aligner.cpp. |