#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 1152 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. 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 }
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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. |
1.3.9.1