#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 304 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(). 00306 {
00307 if (!to) throw InvalidParameterException("Can not rotational align - the image to align to is NULL");
00308
00309 #ifdef EMAN2_USING_CUDA
00310 if(EMData::usecuda == 1) {
00311 //if(!this_img->getcudarwdata()) this_img->copy_to_cuda();
00312 //if(!to->getcudarwdata()) to->copy_to_cuda();
00313 }
00314 #endif
00315
00316 // Perform 180 ambiguous alignment
00317 int rfp_mode = params.set_default("rfp_mode",0);
00318 EMData* rot_aligned = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode);
00319 Transform * tmp = rot_aligned->get_attr("xform.align2d");
00320 Dict rot = tmp->get_rotation("2d");
00321 float rotate_angle_solution = rot["alpha"];
00322 delete tmp;
00323
00324 EMData *rot_align_180 = rot_aligned->process("math.rotate.180");
00325
00326 // Generate the comparison metrics for both rotational candidates
00327 float rot_cmp = rot_aligned->cmp(cmp_name, to, cmp_params);
00328 float rot_180_cmp = rot_align_180->cmp(cmp_name, to, cmp_params);
00329
00330 // Decide on the result
00331 float score = 0.0;
00332 EMData* result = NULL;
00333 if (rot_cmp < rot_180_cmp){
00334 result = rot_aligned;
00335 score = rot_cmp;
00336 delete rot_align_180; rot_align_180 = 0;
00337 } else {
00338 result = rot_align_180;
00339 score = rot_180_cmp;
00340 delete rot_aligned; rot_aligned = 0;
00341 rotate_angle_solution = rotate_angle_solution-180.0f;
00342 }
00343
00344 // Transform* t = get_align_attr("xform.align2d",result);
00345 // t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution));
00346 Transform tmp2(Dict("type","2d","alpha",rotate_angle_solution));
00347 result->set_attr("xform.align2d",&tmp2);
00348 return result;
00349 }
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Definition at line 256 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(). 00256 {
00257
00258 // Make translationally invariant rotational footprints
00259 EMData* this_img_rfp, * to_rfp;
00260 if (rfp_mode == 0) {
00261 this_img_rfp = this_img->make_rotational_footprint_e1();
00262 to_rfp = to->make_rotational_footprint_e1();
00263 } else if (rfp_mode == 1) {
00264 this_img_rfp = this_img->make_rotational_footprint();
00265 to_rfp = to->make_rotational_footprint();
00266 } else if (rfp_mode == 2) {
00267 this_img_rfp = this_img->make_rotational_footprint_cmc();
00268 to_rfp = to->make_rotational_footprint_cmc();
00269 } else {
00270 throw InvalidParameterException("rfp_mode must be 0,1 or 2");
00271 }
00272 int this_img_rfp_nx = this_img_rfp->get_xsize();
00273
00274 // Do row-wise correlation, returning a sum.
00275 EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize());
00276
00277 // Delete them, they're no longer needed
00278 delete this_img_rfp; this_img_rfp = 0;
00279 delete to_rfp; to_rfp = 0;
00280
00281 // Now solve the rotational alignment by finding the max in the column sum
00282 float *data = cf->get_data();
00283
00284 float peak = 0;
00285 int peak_index = 0;
00286 Util::find_max(data, this_img_rfp_nx, &peak, &peak_index);
00287
00288 if( cf ) {
00289 delete cf;
00290 cf = 0;
00291 }
00292 float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx);
00293
00294 // Return the result
00295 Transform tmp(Dict("type","2d","alpha",rot_angle));
00296 cf=this_img->process("xform",Dict("transform",(Transform*)&tmp));
00297 // Transform* t = get_set_align_attr("xform.align2d",cf,this_img);
00298 // Dict d("type","2d","alpha",rot_angle);
00299 // t->set_rotation(d);
00300 cf->set_attr("xform.align2d",&tmp);
00301 return cf;
00302 }
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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 59 of file aligner.cpp. |
1.3.9.1