#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 562 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 568 of file aligner.h. References align(). 00569 { 00570 return align(this_img, to_img, "sqeuclidean", Dict()); 00571 }
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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 1023 of file aligner.cpp. References 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. 01025 { 01026 01027 if (!to) { 01028 return 0; 01029 } 01030 01031 int mode = params.set_default("mode", 0); 01032 float saz = 0.0; 01033 float sdx = 0.0; 01034 float sdy = 0.0; 01035 bool mirror = false; 01036 Transform* t; 01037 if (params.has_key("xform.align2d") ) { 01038 t = params["xform.align2d"]; 01039 Dict params = t->get_params("2d"); 01040 saz = params["alpha"]; 01041 sdx = params["tx"]; 01042 sdy = params["ty"]; 01043 mirror = params["mirror"]; 01044 01045 } else { 01046 t = new Transform(); // is the identity 01047 } 01048 01049 int np = 3; 01050 Dict gsl_params; 01051 gsl_params["this"] = this_img; 01052 gsl_params["with"] = to; 01053 gsl_params["snr"] = params["snr"]; 01054 gsl_params["mirror"] = mirror; 01055 01056 01057 01058 const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex; 01059 gsl_vector *ss = gsl_vector_alloc(np); 01060 01061 float stepx = params.set_default("stepx",1.0f); 01062 float stepy = params.set_default("stepy",1.0f); 01063 // Default step is 5 degree - note in EMAN1 it was 0.1 radians 01064 float stepaz = params.set_default("stepaz",5.0f); 01065 01066 gsl_vector_set(ss, 0, stepx); 01067 gsl_vector_set(ss, 1, stepy); 01068 gsl_vector_set(ss, 2, stepaz); 01069 01070 gsl_vector *x = gsl_vector_alloc(np); 01071 gsl_vector_set(x, 0, sdx); 01072 gsl_vector_set(x, 1, sdy); 01073 gsl_vector_set(x, 2, saz); 01074 01075 Cmp *c = 0; 01076 01077 gsl_multimin_function minex_func; 01078 if (mode == 2) { 01079 minex_func.f = &refalifnfast; 01080 } 01081 else { 01082 c = Factory < Cmp >::get(cmp_name, cmp_params); 01083 gsl_params["cmp"] = (void *) c; 01084 minex_func.f = &refalifn; 01085 } 01086 01087 minex_func.n = np; 01088 minex_func.params = (void *) &gsl_params; 01089 01090 gsl_multimin_fminimizer *s = gsl_multimin_fminimizer_alloc(T, np); 01091 gsl_multimin_fminimizer_set(s, &minex_func, x, ss); 01092 01093 int rval = GSL_CONTINUE; 01094 int status = GSL_SUCCESS; 01095 int iter = 1; 01096 01097 float precision = params.set_default("precision",0.04f); 01098 int maxiter = params.set_default("maxiter",28); 01099 01100 // printf("Refine sx=%1.2f sy=%1.2f sa=%1.2f prec=%1.4f maxit=%d\n",stepx,stepy,stepaz,precision,maxiter); 01101 // 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)); 01102 01103 while (rval == GSL_CONTINUE && iter < maxiter) { 01104 iter++; 01105 status = gsl_multimin_fminimizer_iterate(s); 01106 if (status) { 01107 break; 01108 } 01109 rval = gsl_multimin_test_size(gsl_multimin_fminimizer_size(s), precision); 01110 } 01111 01112 int maxshift = params.set_default("maxshift",-1); 01113 01114 if (maxshift <= 0) { 01115 maxshift = this_img->get_xsize() / 4; 01116 } 01117 float fmaxshift = static_cast<float>(maxshift); 01118 EMData *result; 01119 if ( fmaxshift >= fabs((float)gsl_vector_get(s->x, 0)) && fmaxshift >= fabs((float)gsl_vector_get(s->x, 1)) ) 01120 { 01121 // 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)); 01122 Transform tsoln(Dict("type","2d","alpha",(float)gsl_vector_get(s->x, 2))); 01123 tsoln.set_mirror(mirror); 01124 tsoln.set_trans((float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1)); 01125 result = this_img->process("xform",Dict("transform",&tsoln)); 01126 result->set_attr("xform.align2d",&tsoln); 01127 } else { // The refine aligner failed - this shift went beyond the max shift 01128 // 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)); 01129 result = this_img->process("xform",Dict("transform",t)); 01130 result->set_attr("xform.align2d",t); 01131 } 01132 01133 delete t; 01134 t = 0; 01135 01136 gsl_vector_free(x); 01137 gsl_vector_free(ss); 01138 gsl_multimin_fminimizer_free(s); 01139 01140 if ( c != 0 ) delete c; 01141 return result; 01142 }
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Implements EMAN::Aligner. Definition at line 578 of file aligner.h. 00579 { 00580 return "Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision."; 00581 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 573 of file aligner.h. 00574 {
00575 return NAME;
00576 }
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Implements EMAN::Aligner. Definition at line 588 of file aligner.h. References EMAN::TypeDict::put(). 00589 { 00590 TypeDict d; 00591 00592 d.put("mode", EMObject::INT, "Currently unused"); 00593 d.put("xform.align2d", EMObject::TRANSFORM, "The Transform storing the starting guess. If unspecified the identity matrix is used"); 00594 d.put("stepx", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 1"); 00595 d.put("stepy", EMObject::FLOAT, "The y increment used to create the starting simplex. Default is 1"); 00596 d.put("stepaz", EMObject::FLOAT, "The rotational increment used to create the starting simplex. Default is 5"); 00597 d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04."); 00598 d.put("maxiter", EMObject::INT,"The maximum number of iterations that can be performed by the Simplex minimizer"); 00599 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."); 00600 return d; 00601 }
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Definition at line 583 of file aligner.h. 00584 { 00585 return new RefineAligner(); 00586 }
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Definition at line 62 of file aligner.cpp. |