#include <aligner.h>
Inheritance diagram for EMAN::RotationalAligner:
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 | |
Aligner * | NEW () |
EMData * | align_180_ambiguous (EMData *this_img, EMData *to_img, int rfp_mode=0) |
Static Public Attributes | |
const string | NAME = "rotational" |
rfp_mode | Either 0,1 or 2. A temporary flag for testing the rotational foot print. O is the original eman1 way. 1 is just using calc_ccf without padding. 2 is using calc_mutual_correlation without padding |
Definition at line 218 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 224 of file aligner.h. References align(). 00225 { 00226 return align(this_img, to_img, "dot", Dict()); 00227 }
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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 309 of file aligner.cpp. References align_180_ambiguous(), EMAN::EMData::cmp(), EMAN::EMData::get_attr(), EMAN::Transform::get_rotation(), InvalidParameterException, EMAN::EMData::process(), EMAN::EMData::set_attr(), and EMAN::Dict::set_default(). 00311 { 00312 if (!to) throw InvalidParameterException("Can not rotational align - the image to align to is NULL"); 00313 00314 #ifdef EMAN2_USING_CUDA 00315 if(EMData::usecuda == 1) { 00316 //if(!this_img->getcudarwdata()) this_img->copy_to_cuda(); 00317 //if(!to->getcudarwdata()) to->copy_to_cuda(); 00318 } 00319 #endif 00320 00321 // Perform 180 ambiguous alignment 00322 int rfp_mode = params.set_default("rfp_mode",0); 00323 EMData* rot_aligned = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode); 00324 Transform * tmp = rot_aligned->get_attr("xform.align2d"); 00325 Dict rot = tmp->get_rotation("2d"); 00326 float rotate_angle_solution = rot["alpha"]; 00327 delete tmp; 00328 00329 EMData *rot_align_180 = rot_aligned->process("math.rotate.180"); 00330 00331 // Generate the comparison metrics for both rotational candidates 00332 float rot_cmp = rot_aligned->cmp(cmp_name, to, cmp_params); 00333 float rot_180_cmp = rot_align_180->cmp(cmp_name, to, cmp_params); 00334 00335 // Decide on the result 00336 float score = 0.0; 00337 EMData* result = NULL; 00338 if (rot_cmp < rot_180_cmp){ 00339 result = rot_aligned; 00340 score = rot_cmp; 00341 delete rot_align_180; rot_align_180 = 0; 00342 } else { 00343 result = rot_align_180; 00344 score = rot_180_cmp; 00345 delete rot_aligned; rot_aligned = 0; 00346 rotate_angle_solution = rotate_angle_solution-180.0f; 00347 } 00348 00349 // Transform* t = get_align_attr("xform.align2d",result); 00350 // t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution)); 00351 Transform tmp2(Dict("type","2d","alpha",rotate_angle_solution)); 00352 result->set_attr("xform.align2d",&tmp2); 00353 return result; 00354 }
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Definition at line 261 of file aligner.cpp. References EMAN::EMData::calc_ccfx(), data, EMAN::Util::find_max(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), InvalidParameterException, EMAN::EMData::make_rotational_footprint(), EMAN::EMData::make_rotational_footprint_cmc(), EMAN::EMData::make_rotational_footprint_e1(), EMAN::EMData::process(), and EMAN::EMData::set_attr(). Referenced by EMAN::RotateTranslateAligner::align(), and align(). 00261 { 00262 00263 // Make translationally invariant rotational footprints 00264 EMData* this_img_rfp, * to_rfp; 00265 if (rfp_mode == 0) { 00266 this_img_rfp = this_img->make_rotational_footprint_e1(); 00267 to_rfp = to->make_rotational_footprint_e1(); 00268 } else if (rfp_mode == 1) { 00269 this_img_rfp = this_img->make_rotational_footprint(); 00270 to_rfp = to->make_rotational_footprint(); 00271 } else if (rfp_mode == 2) { 00272 this_img_rfp = this_img->make_rotational_footprint_cmc(); 00273 to_rfp = to->make_rotational_footprint_cmc(); 00274 } else { 00275 throw InvalidParameterException("rfp_mode must be 0,1 or 2"); 00276 } 00277 int this_img_rfp_nx = this_img_rfp->get_xsize(); 00278 00279 // Do row-wise correlation, returning a sum. 00280 EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize()); 00281 00282 // Delete them, they're no longer needed 00283 delete this_img_rfp; this_img_rfp = 0; 00284 delete to_rfp; to_rfp = 0; 00285 00286 // Now solve the rotational alignment by finding the max in the column sum 00287 float *data = cf->get_data(); 00288 00289 float peak = 0; 00290 int peak_index = 0; 00291 Util::find_max(data, this_img_rfp_nx, &peak, &peak_index); 00292 00293 if( cf ) { 00294 delete cf; 00295 cf = 0; 00296 } 00297 float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx); 00298 00299 // Return the result 00300 Transform tmp(Dict("type","2d","alpha",rot_angle)); 00301 cf=this_img->process("xform",Dict("transform",(Transform*)&tmp)); 00302 // Transform* t = get_set_align_attr("xform.align2d",cf,this_img); 00303 // Dict d("type","2d","alpha",rot_angle); 00304 // t->set_rotation(d); 00305 cf->set_attr("xform.align2d",&tmp); 00306 return cf; 00307 }
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Implements EMAN::Aligner. Definition at line 234 of file aligner.h. 00235 { 00236 return "Performs rotational alignment,works accurately if the image is precentered, normally called internally in combination with translational and flip alignment"; 00237 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 229 of file aligner.h. 00230 {
00231 return NAME;
00232 }
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Implements EMAN::Aligner. Definition at line 246 of file aligner.h. References EMAN::TypeDict::put(). 00247 { 00248 TypeDict d; 00249 d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print. O is the original eman1 way. 1 is just using calc_ccf without padding. 2 is using calc_mutual_correlation without padding."); 00250 return d; 00251 }
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Definition at line 239 of file aligner.h. 00240 { 00241 return new RotationalAligner(); 00242 }
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Definition at line 60 of file aligner.cpp. |