#include <aligner.h>


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 217 of file aligner.h.
| 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 254 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().
00256 { 00257 if (!to) throw InvalidParameterException("Can not rotational align - the image to align to is NULL"); 00258 00259 // Perform 180 ambiguous alignment 00260 int rfp_mode = params.set_default("rfp_mode",0); 00261 EMData* rot_aligned = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode); 00262 Transform * tmp = rot_aligned->get_attr("xform.align2d"); 00263 Dict rot = tmp->get_rotation("2d"); 00264 float rotate_angle_solution = rot["alpha"]; 00265 delete tmp; 00266 00267 EMData *rot_align_180 = rot_aligned->process("math.rotate.180"); 00268 00269 // Generate the comparison metrics for both rotational candidates 00270 float rot_cmp = rot_aligned->cmp(cmp_name, to, cmp_params); 00271 float rot_180_cmp = rot_align_180->cmp(cmp_name, to, cmp_params); 00272 // Decide on the result 00273 float score = 0.0; 00274 EMData* result = NULL; 00275 if (rot_cmp < rot_180_cmp){ 00276 result = rot_aligned; 00277 score = rot_cmp; 00278 delete rot_align_180; rot_align_180 = 0; 00279 } else { 00280 result = rot_align_180; 00281 score = rot_180_cmp; 00282 delete rot_aligned; rot_aligned = 0; 00283 rotate_angle_solution = rotate_angle_solution-180.0f; 00284 } 00285 00286 // Transform* t = get_align_attr("xform.align2d",result); 00287 // t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution)); 00288 Transform tmp2(Dict("type","2d","alpha",rotate_angle_solution)); 00289 result->set_attr("xform.align2d",&tmp2); 00290 return result; 00291 }
| virtual EMData* EMAN::RotationalAligner::align | ( | EMData * | this_img, | |
| EMData * | to_img | |||
| ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 223 of file aligner.h.
References align().
00224 { 00225 return align(this_img, to_img, "", Dict()); 00226 }
| virtual string EMAN::RotationalAligner::get_name | ( | ) | const [inline, virtual] |
| virtual string EMAN::RotationalAligner::get_desc | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 233 of file aligner.h.
00234 { 00235 return "Performs rotational alignment,works accurately if the image is precentered, normally called internally in combination with translational and flip alignment"; 00236 }
| static Aligner* EMAN::RotationalAligner::NEW | ( | ) | [inline, static] |
| EMData * RotationalAligner::align_180_ambiguous | ( | EMData * | this_img, | |
| EMData * | to_img, | |||
| int | rfp_mode = 0 | |||
| ) | [static] |
Definition at line 207 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().
00207 { 00208 00209 // Make translationally invariant rotational footprints 00210 EMData* this_img_rfp, * to_rfp; 00211 if (rfp_mode == 0) { 00212 this_img_rfp = this_img->make_rotational_footprint_e1(); 00213 to_rfp = to->make_rotational_footprint_e1(); 00214 } else if (rfp_mode == 1) { 00215 this_img_rfp = this_img->make_rotational_footprint(); 00216 to_rfp = to->make_rotational_footprint(); 00217 } else if (rfp_mode == 2) { 00218 this_img_rfp = this_img->make_rotational_footprint_cmc(); 00219 to_rfp = to->make_rotational_footprint_cmc(); 00220 } else { 00221 throw InvalidParameterException("rfp_mode must be 0,1 or 2"); 00222 } 00223 int this_img_rfp_nx = this_img_rfp->get_xsize(); 00224 00225 // Do row-wise correlation, returning a sum. 00226 EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize()); 00227 00228 // Delete them, they're no longer needed 00229 delete this_img_rfp; this_img_rfp = 0; 00230 delete to_rfp; to_rfp = 0; 00231 00232 // Now solve the rotational alignment by finding the max in the column sum 00233 float *data = cf->get_data(); 00234 float peak = 0; 00235 int peak_index = 0; 00236 Util::find_max(data, this_img_rfp_nx, &peak, &peak_index); 00237 00238 if( cf ) { 00239 delete cf; 00240 cf = 0; 00241 } 00242 float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx); 00243 00244 // Return the result 00245 Transform tmp(Dict("type","2d","alpha",rot_angle)); 00246 cf=this_img->process("xform",Dict("transform",(Transform*)&tmp)); 00247 // Transform* t = get_set_align_attr("xform.align2d",cf,this_img); 00248 // Dict d("type","2d","alpha",rot_angle); 00249 // t->set_rotation(d); 00250 cf->set_attr("xform.align2d",&tmp); 00251 return cf; 00252 }
| virtual TypeDict EMAN::RotationalAligner::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 245 of file aligner.h.
References EMAN::EMObject::INT, and EMAN::TypeDict::put().
00246 { 00247 TypeDict d; 00248 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."); 00249 return d; 00250 }
const string RotationalAligner::NAME = "rotational" [static] |
1.5.6