#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 | |
static Aligner * | NEW () |
static EMData * | align_180_ambiguous (EMData *this_img, EMData *to_img, int rfp_mode=0) |
Static Public Attributes | |
static 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.
virtual EMData* EMAN::RotationalAligner::align | ( | EMData * | this_img, | |
EMData * | to_img | |||
) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 224 of file aligner.h.
References align().
00225 { 00226 return align(this_img, to_img, "dot", Dict()); 00227 }
EMData * RotationalAligner::align | ( | EMData * | this_img, | |
EMData * | to_img, | |||
const string & | cmp_name = "dot" , |
|||
const Dict & | cmp_params = Dict() | |||
) | 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 304 of file aligner.cpp.
References align_180_ambiguous(), EMAN::EMData::cmp(), EMAN::EMData::get_attr(), EMAN::Transform::get_rotation(), InvalidParameterException, EMAN::Aligner::params, EMAN::EMData::process(), EMAN::EMData::set_attr(), and EMAN::Dict::set_default().
Referenced by align().
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 }
EMData * RotationalAligner::align_180_ambiguous | ( | EMData * | this_img, | |
EMData * | to_img, | |||
int | rfp_mode = 0 | |||
) | [static] |
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 }
virtual string EMAN::RotationalAligner::get_desc | ( | ) | const [inline, virtual] |
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 }
virtual string EMAN::RotationalAligner::get_name | ( | ) | const [inline, virtual] |
virtual TypeDict EMAN::RotationalAligner::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 246 of file aligner.h.
References EMAN::EMObject::INT, and 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 }
static Aligner* EMAN::RotationalAligner::NEW | ( | ) | [inline, static] |
const string RotationalAligner::NAME = "rotational" [static] |