#include <aligner.h>
Inheritance diagram for EMAN::RefineAligner:
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 () |
Static Public Attributes | |
const string | NAME = "refine" |
Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision.
Definition at line 750 of file aligner.h.
|
Implements EMAN::Aligner. Definition at line 756 of file aligner.h. References align(). 00757 { 00758 return align(this_img, to_img, "sqeuclidean", Dict()); 00759 }
|
|
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 1200 of file aligner.cpp. References EMAN::EMData::get_attr(), EMAN::Transform::get_params(), EMAN::EMData::get_xsize(), EMAN::Dict::has_key(), EMAN::Cmp::params, EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), status, t, and x. 01202 { 01203 01204 if (!to) { 01205 return 0; 01206 } 01207 01208 EMData *result; 01209 int mode = params.set_default("mode", 0); 01210 float saz = 0.0; 01211 float sdx = 0.0; 01212 float sdy = 0.0; 01213 bool mirror = false; 01214 Transform* t; 01215 if (params.has_key("xform.align2d") ) { 01216 t = params["xform.align2d"]; 01217 Dict params = t->get_params("2d"); 01218 saz = params["alpha"]; 01219 sdx = params["tx"]; 01220 sdy = params["ty"]; 01221 mirror = params["mirror"]; 01222 01223 } else { 01224 t = new Transform(); // is the identity 01225 } 01226 01227 // We do this to prevent the GSL routine from crashing on an invalid alignment 01228 if ((float)(this_img->get_attr("sigma"))==0.0 || (float)(to->get_attr("sigma"))==0.0) { 01229 result = this_img->process("xform",Dict("transform",t)); 01230 result->set_attr("xform.align2d",t); 01231 delete t; 01232 return result; 01233 } 01234 01235 int np = 3; 01236 Dict gsl_params; 01237 gsl_params["this"] = this_img; 01238 gsl_params["with"] = to; 01239 gsl_params["snr"] = params["snr"]; 01240 gsl_params["mirror"] = mirror; 01241 01242 01243 01244 const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex; 01245 gsl_vector *ss = gsl_vector_alloc(np); 01246 01247 float stepx = params.set_default("stepx",1.0f); 01248 float stepy = params.set_default("stepy",1.0f); 01249 // Default step is 5 degree - note in EMAN1 it was 0.1 radians 01250 float stepaz = params.set_default("stepaz",5.0f); 01251 01252 gsl_vector_set(ss, 0, stepx); 01253 gsl_vector_set(ss, 1, stepy); 01254 gsl_vector_set(ss, 2, stepaz); 01255 01256 gsl_vector *x = gsl_vector_alloc(np); 01257 gsl_vector_set(x, 0, sdx); 01258 gsl_vector_set(x, 1, sdy); 01259 gsl_vector_set(x, 2, saz); 01260 01261 Cmp *c = 0; 01262 01263 gsl_multimin_function minex_func; 01264 if (mode == 2) { 01265 minex_func.f = &refalifnfast; 01266 } 01267 else { 01268 c = Factory < Cmp >::get(cmp_name, cmp_params); 01269 gsl_params["cmp"] = (void *) c; 01270 minex_func.f = &refalifn; 01271 } 01272 01273 minex_func.n = np; 01274 minex_func.params = (void *) &gsl_params; 01275 01276 gsl_multimin_fminimizer *s = gsl_multimin_fminimizer_alloc(T, np); 01277 gsl_multimin_fminimizer_set(s, &minex_func, x, ss); 01278 01279 int rval = GSL_CONTINUE; 01280 int status = GSL_SUCCESS; 01281 int iter = 1; 01282 01283 float precision = params.set_default("precision",0.04f); 01284 int maxiter = params.set_default("maxiter",28); 01285 01286 // printf("Refine sx=%1.2f sy=%1.2f sa=%1.2f prec=%1.4f maxit=%d\n",stepx,stepy,stepaz,precision,maxiter); 01287 // printf("%1.2f %1.2f %1.1f ->",(float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1),(float)gsl_vector_get(s->x, 2)); 01288 01289 while (rval == GSL_CONTINUE && iter < maxiter) { 01290 iter++; 01291 status = gsl_multimin_fminimizer_iterate(s); 01292 if (status) { 01293 break; 01294 } 01295 rval = gsl_multimin_test_size(gsl_multimin_fminimizer_size(s), precision); 01296 } 01297 01298 int maxshift = params.set_default("maxshift",-1); 01299 01300 if (maxshift <= 0) { 01301 maxshift = this_img->get_xsize() / 4; 01302 } 01303 float fmaxshift = static_cast<float>(maxshift); 01304 if ( fmaxshift >= fabs((float)gsl_vector_get(s->x, 0)) && fmaxshift >= fabs((float)gsl_vector_get(s->x, 1)) ) 01305 { 01306 // printf(" Refine good %1.2f %1.2f %1.1f\n",(float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1),(float)gsl_vector_get(s->x, 2)); 01307 Transform tsoln(Dict("type","2d","alpha",(float)gsl_vector_get(s->x, 2))); 01308 tsoln.set_mirror(mirror); 01309 tsoln.set_trans((float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1)); 01310 result = this_img->process("xform",Dict("transform",&tsoln)); 01311 result->set_attr("xform.align2d",&tsoln); 01312 } else { // The refine aligner failed - this shift went beyond the max shift 01313 // printf(" Refine Failed %1.2f %1.2f %1.1f\n",(float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1),(float)gsl_vector_get(s->x, 2)); 01314 result = this_img->process("xform",Dict("transform",t)); 01315 result->set_attr("xform.align2d",t); 01316 } 01317 01318 delete t; 01319 t = 0; 01320 01321 gsl_vector_free(x); 01322 gsl_vector_free(ss); 01323 gsl_multimin_fminimizer_free(s); 01324 01325 if ( c != 0 ) delete c; 01326 return result; 01327 }
|
|
Implements EMAN::Aligner. Definition at line 766 of file aligner.h. 00767 { 00768 return "Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision."; 00769 }
|
|
Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 761 of file aligner.h. 00762 {
00763 return NAME;
00764 }
|
|
Implements EMAN::Aligner. Definition at line 776 of file aligner.h. References EMAN::TypeDict::put(). 00777 { 00778 TypeDict d; 00779 00780 d.put("mode", EMObject::INT, "Currently unused"); 00781 d.put("xform.align2d", EMObject::TRANSFORM, "The Transform storing the starting guess. If unspecified the identity matrix is used"); 00782 d.put("stepx", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 1"); 00783 d.put("stepy", EMObject::FLOAT, "The y increment used to create the starting simplex. Default is 1"); 00784 d.put("stepaz", EMObject::FLOAT, "The rotational increment used to create the starting simplex. Default is 5"); 00785 d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04."); 00786 d.put("maxiter", EMObject::INT,"The maximum number of iterations that can be performed by the Simplex minimizer"); 00787 d.put("maxshift", EMObject::INT,"Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution."); 00788 return d; 00789 }
|
|
Definition at line 771 of file aligner.h. 00772 { 00773 return new RefineAligner(); 00774 }
|
|
Definition at line 66 of file aligner.cpp. |