#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=2) |
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 285 of file aligner.h.
virtual EMData* EMAN::RotationalAligner::align | ( | EMData * | this_img, | |
EMData * | to_img | |||
) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 291 of file aligner.h.
References align().
00292 { 00293 return align(this_img, to_img, "dot", Dict()); 00294 }
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 434 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().
00436 { 00437 if (!to) throw InvalidParameterException("Can not rotational align - the image to align to is NULL"); 00438 00439 #ifdef EMAN2_USING_CUDA 00440 if(EMData::usecuda == 1) { 00441 //if(!this_img->getcudarwdata()) this_img->copy_to_cuda(); 00442 //if(!to->getcudarwdata()) to->copy_to_cuda(); 00443 } 00444 #endif 00445 00446 // Perform 180 ambiguous alignment 00447 int rfp_mode = params.set_default("rfp_mode",2); 00448 EMData* rot_aligned = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode); 00449 Transform * tmp = rot_aligned->get_attr("xform.align2d"); 00450 Dict rot = tmp->get_rotation("2d"); 00451 float rotate_angle_solution = rot["alpha"]; 00452 delete tmp; 00453 00454 EMData *rot_align_180 = rot_aligned->process("math.rotate.180"); 00455 00456 // Generate the comparison metrics for both rotational candidates 00457 float rot_cmp = rot_aligned->cmp(cmp_name, to, cmp_params); 00458 float rot_180_cmp = rot_align_180->cmp(cmp_name, to, cmp_params); 00459 00460 // Decide on the result 00461 float score = 0.0; 00462 EMData* result = NULL; 00463 if (rot_cmp < rot_180_cmp){ 00464 result = rot_aligned; 00465 score = rot_cmp; 00466 delete rot_align_180; rot_align_180 = 0; 00467 } else { 00468 result = rot_align_180; 00469 score = rot_180_cmp; 00470 delete rot_aligned; rot_aligned = 0; 00471 rotate_angle_solution = rotate_angle_solution-180.0f; 00472 } 00473 00474 // Transform* t = get_align_attr("xform.align2d",result); 00475 // t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution)); 00476 Transform tmp2(Dict("type","2d","alpha",rotate_angle_solution)); 00477 result->set_attr("xform.align2d",&tmp2); 00478 return result; 00479 }
EMData * RotationalAligner::align_180_ambiguous | ( | EMData * | this_img, | |
EMData * | to_img, | |||
int | rfp_mode = 2 | |||
) | [static] |
Definition at line 386 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().
00386 { 00387 00388 // Make translationally invariant rotational footprints 00389 EMData* this_img_rfp, * to_rfp; 00390 if (rfp_mode == 0) { 00391 this_img_rfp = this_img->make_rotational_footprint_e1(); 00392 to_rfp = to->make_rotational_footprint_e1(); 00393 } else if (rfp_mode == 1) { 00394 this_img_rfp = this_img->make_rotational_footprint(); 00395 to_rfp = to->make_rotational_footprint(); 00396 } else if (rfp_mode == 2) { 00397 this_img_rfp = this_img->make_rotational_footprint_cmc(); 00398 to_rfp = to->make_rotational_footprint_cmc(); 00399 } else { 00400 throw InvalidParameterException("rfp_mode must be 0,1 or 2"); 00401 } 00402 int this_img_rfp_nx = this_img_rfp->get_xsize(); 00403 00404 // Do row-wise correlation, returning a sum. 00405 EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize()); 00406 00407 // Delete them, they're no longer needed 00408 delete this_img_rfp; this_img_rfp = 0; 00409 delete to_rfp; to_rfp = 0; 00410 00411 // Now solve the rotational alignment by finding the max in the column sum 00412 float *data = cf->get_data(); 00413 00414 float peak = 0; 00415 int peak_index = 0; 00416 Util::find_max(data, this_img_rfp_nx, &peak, &peak_index); 00417 00418 if( cf ) { 00419 delete cf; 00420 cf = 0; 00421 } 00422 float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx); 00423 00424 // Return the result 00425 Transform tmp(Dict("type","2d","alpha",rot_angle)); 00426 cf=this_img->process("xform",Dict("transform",(Transform*)&tmp)); 00427 // Transform* t = get_set_align_attr("xform.align2d",cf,this_img); 00428 // Dict d("type","2d","alpha",rot_angle); 00429 // t->set_rotation(d); 00430 cf->set_attr("xform.align2d",&tmp); 00431 return cf; 00432 }
virtual string EMAN::RotationalAligner::get_desc | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 301 of file aligner.h.
00302 { 00303 return "Performs rotational alignment,works accurately if the image is precentered, normally called internally in combination with translational and flip alignment"; 00304 }
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 313 of file aligner.h.
References EMAN::EMObject::INT, and EMAN::TypeDict::put().
00314 { 00315 TypeDict d; 00316 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."); 00317 return d; 00318 }
static Aligner* EMAN::RotationalAligner::NEW | ( | ) | [inline, static] |
const string RotationalAligner::NAME = "rotational" [static] |