#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 1164 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().
01166 { 01167 01168 EMData *flip = params.set_default("flip", (EMData *) 0); 01169 int maxshift = params.set_default("maxshift", -1); 01170 01171 EMData *flipped = 0; 01172 01173 bool delete_flipped = true; 01174 if (flip) { 01175 delete_flipped = false; 01176 flipped = flip; 01177 } 01178 else { 01179 flipped = to->process("xform.flip", Dict("axis", "x")); 01180 } 01181 01182 int nx = this_img->get_xsize(); 01183 01184 if (maxshift < 0) { 01185 maxshift = nx / 10; 01186 } 01187 01188 float angle_step = params.set_default("angstep", 0.0f); 01189 if ( angle_step == 0 ) angle_step = atan2(2.0f, (float)nx); 01190 else { 01191 angle_step *= (float)EMConsts::deg2rad; //convert to radians 01192 } 01193 float trans_step = params.set_default("transtep",1.0f); 01194 01195 if (trans_step <= 0) throw InvalidParameterException("transstep must be greater than 0"); 01196 if (angle_step <= 0) throw InvalidParameterException("angstep must be greater than 0"); 01197 01198 01199 Dict shrinkfactor("n",2); 01200 EMData *this_img_shrink = this_img->process("math.medianshrink",shrinkfactor); 01201 EMData *to_shrunk = to->process("math.medianshrink",shrinkfactor); 01202 EMData *flipped_shrunk = flipped->process("math.medianshrink",shrinkfactor); 01203 01204 int bestflip = 0; 01205 float bestdx = 0; 01206 float bestdy = 0; 01207 01208 float bestang = 0; 01209 float bestval = FLT_MAX; 01210 01211 int half_maxshift = maxshift / 2; 01212 01213 01214 for (int dy = -half_maxshift; dy <= half_maxshift; ++dy) { 01215 for (int dx = -half_maxshift; dx <= half_maxshift; ++dx) { 01216 if (hypot(dx, dy) <= maxshift) { 01217 for (float ang = -angle_step * 2.0f; ang <= (float)2 * M_PI; ang += angle_step * 4.0f) { 01218 EMData v(*this_img_shrink); 01219 Transform t(Dict("type","2d","alpha",static_cast<float>(ang*EMConsts::rad2deg))); 01220 t.set_trans((float)dx,(float)dy); 01221 v.transform(t); 01222 // v.rotate_translate(ang*EMConsts::rad2deg, 0.0f, 0.0f, (float)dx, (float)dy, 0.0f); 01223 01224 float lc = v.cmp(cmp_name, to_shrunk, cmp_params); 01225 01226 if (lc < bestval) { 01227 bestval = lc; 01228 bestang = ang; 01229 bestdx = (float)dx; 01230 bestdy = (float)dy; 01231 bestflip = 0; 01232 } 01233 01234 lc = v.cmp(cmp_name,flipped_shrunk , cmp_params); 01235 if (lc < bestval) { 01236 bestval = lc; 01237 bestang = ang; 01238 bestdx = (float)dx; 01239 bestdy = (float)dy; 01240 bestflip = 1; 01241 } 01242 } 01243 } 01244 } 01245 } 01246 01247 if( to_shrunk ) 01248 { 01249 delete to_shrunk; 01250 to_shrunk = 0; 01251 } 01252 if( flipped_shrunk ) 01253 { 01254 delete flipped_shrunk; 01255 flipped_shrunk = 0; 01256 } 01257 if( this_img_shrink ) 01258 { 01259 delete this_img_shrink; 01260 this_img_shrink = 0; 01261 } 01262 01263 bestdx *= 2; 01264 bestdy *= 2; 01265 bestval = FLT_MAX; 01266 01267 float bestdx2 = bestdx; 01268 float bestdy2 = bestdy; 01269 float bestang2 = bestang; 01270 01271 for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += trans_step) { 01272 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += trans_step) { 01273 if (hypot(dx, dy) <= maxshift) { 01274 for (float ang = bestang2 - angle_step * 6.0f; ang <= bestang2 + angle_step * 6.0f; ang += angle_step) { 01275 EMData v(*this_img); 01276 Transform t(Dict("type","2d","alpha",static_cast<float>(ang*EMConsts::rad2deg))); 01277 t.set_trans(dx,dy); 01278 v.transform(t); 01279 // v.rotate_translate(ang*EMConsts::rad2deg, 0.0f, 0.0f, (float)dx, (float)dy, 0.0f); 01280 01281 float lc = v.cmp(cmp_name, to, cmp_params); 01282 01283 if (lc < bestval) { 01284 bestval = lc; 01285 bestang = ang; 01286 bestdx = dx; 01287 bestdy = dy; 01288 bestflip = 0; 01289 } 01290 01291 lc = v.cmp(cmp_name, flipped, cmp_params); 01292 01293 if (lc < bestval) { 01294 bestval = lc; 01295 bestang = ang; 01296 bestdx = dx; 01297 bestdy = dy; 01298 bestflip = 1; 01299 } 01300 } 01301 } 01302 } 01303 } 01304 01305 if (delete_flipped) { delete flipped; flipped = 0; } 01306 01307 bestang *= (float)EMConsts::rad2deg; 01308 Transform t(Dict("type","2d","alpha",(float)bestang)); 01309 t.set_trans(bestdx,bestdy); 01310 01311 if (bestflip) { 01312 t.set_mirror(true); 01313 } 01314 01315 EMData* rslt = this_img->process("xform",Dict("transform",&t)); 01316 rslt->set_attr("xform.align2d",&t); 01317 01318 return rslt; 01319 }
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] |