#include <aligner.h>
Inheritance diagram for EMAN::RefineAlignerCG:
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 Public Attributes | |
static const string | NAME = "refinecg" |
Refines a preliminary 2D alignment to subpixel precision. Faster than 'refine', but requires better local minimum
xform.align2d | The Transform storing the starting guess. If unspecified the identity matrix is used | |
step | The initial increment used for stepping on the gradient. default=0.1 | |
precision | The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.02 | |
maxiter | The maximum number of iterations. default=12 | |
maxshift | 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 | |
stepscale | If set to any non-zero value, scale will be included in the alignment, and this will be the initial step. Images should be edgenormalized. If the scale goes beyond +-30% alignment will fail | |
verbose | This will cause debugging information to be printed on the screen for the iterative refinement. Larger numbers -> more info. default=0 |
Definition at line 1272 of file aligner.h.
virtual EMData* EMAN::RefineAlignerCG::align | ( | EMData * | this_img, | |
EMData * | to_img | |||
) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 1278 of file aligner.h.
References align().
01279 { 01280 return align(this_img, to_img, "sqeuclidean", Dict()); 01281 }
EMData * RefineAlignerCG::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 1802 of file aligner.cpp.
References EMAN::EMData::get_attr(), EMAN::EMData::get_xsize(), EMAN::Dict::has_key(), EMAN::Aligner::params, EMAN::EMData::process(), refalidf(), refalifdf(), refalifn(), refalifnfast(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_mirror(), EMAN::Transform::set_scale(), EMAN::Transform::set_trans(), status, t, and x.
Referenced by align().
01804 { 01805 01806 if (!to) { 01807 return 0; 01808 } 01809 01810 EMData *result; 01811 int mode = params.set_default("mode", 0); 01812 float saz = 0.0; 01813 float sdx = 0.0; 01814 float sdy = 0.0; 01815 float sscale = 1.0; 01816 bool mirror = false; 01817 Transform* t; 01818 if (params.has_key("xform.align2d") ) { 01819 t = params["xform.align2d"]; 01820 Dict params = t->get_params("2d"); 01821 saz = params["alpha"]; 01822 sdx = params["tx"]; 01823 sdy = params["ty"]; 01824 mirror = params["mirror"]; 01825 sscale = params["scale"]; 01826 } else { 01827 t = new Transform(); // is the identity 01828 } 01829 01830 // We do this to prevent the GSL routine from crashing on an invalid alignment 01831 if ((float)(this_img->get_attr("sigma"))==0.0 || (float)(to->get_attr("sigma"))==0.0) { 01832 result = this_img->process("xform",Dict("transform",t)); 01833 result->set_attr("xform.align2d",t); 01834 delete t; 01835 return result; 01836 } 01837 01838 float step = params.set_default("step",0.1f); 01839 float stepscale = params.set_default("stepscale",0.0f); 01840 01841 int np = 3; 01842 if (stepscale!=0.0) np++; 01843 Dict gsl_params; 01844 gsl_params["this"] = this_img; 01845 gsl_params["with"] = to; 01846 gsl_params["snr"] = params["snr"]; 01847 gsl_params["mirror"] = mirror; 01848 if (params.has_key("mask")) gsl_params["mask"]=params["mask"]; 01849 01850 const gsl_multimin_fdfminimizer_type *T = gsl_multimin_fdfminimizer_vector_bfgs; 01851 01852 gsl_vector *x = gsl_vector_alloc(np); 01853 gsl_vector_set(x, 0, sdx); 01854 gsl_vector_set(x, 1, sdy); 01855 gsl_vector_set(x, 2, saz); 01856 if (stepscale!=0.0) gsl_vector_set(x,3,1.0); 01857 01858 Cmp *c = 0; 01859 01860 gsl_multimin_function_fdf minex_func; 01861 if (mode == 2) { 01862 minex_func.f = &refalifnfast; 01863 } 01864 else { 01865 c = Factory < Cmp >::get(cmp_name, cmp_params); 01866 gsl_params["cmp"] = (void *) c; 01867 minex_func.f = &refalifn; 01868 } 01869 01870 minex_func.df = &refalidf; 01871 minex_func.fdf = &refalifdf; 01872 minex_func.n = np; 01873 minex_func.params = (void *) &gsl_params; 01874 01875 gsl_multimin_fdfminimizer *s = gsl_multimin_fdfminimizer_alloc(T, np); 01876 gsl_multimin_fdfminimizer_set(s, &minex_func, x, step, 0.001f); 01877 01878 int rval = GSL_CONTINUE; 01879 int status = GSL_SUCCESS; 01880 int iter = 1; 01881 01882 float precision = params.set_default("precision",0.02f); 01883 int maxiter = params.set_default("maxiter",12); 01884 int verbose = params.set_default("verbose",0); 01885 01886 // printf("Refine sx=%1.2f sy=%1.2f sa=%1.2f prec=%1.4f maxit=%d\n",stepx,stepy,stepaz,precision,maxiter); 01887 // 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)); 01888 01889 while (rval == GSL_CONTINUE && iter < maxiter) { 01890 iter++; 01891 status = gsl_multimin_fdfminimizer_iterate(s); 01892 if (status) { 01893 break; 01894 } 01895 rval = gsl_multimin_test_gradient (s->gradient, precision); 01896 // if (verbose>2) printf("GSL %d. %1.3f %1.3f %1.3f %1.3f\n",iter,gsl_vector_get(s->x,0),gsl_vector_get(s->x,1),gsl_vector_get(s->x,2),s->gradient[0]); 01897 } 01898 01899 int maxshift = params.set_default("maxshift",-1); 01900 01901 if (maxshift <= 0) { 01902 maxshift = this_img->get_xsize() / 4; 01903 } 01904 float fmaxshift = static_cast<float>(maxshift); 01905 if ( fmaxshift >= fabs((float)gsl_vector_get(s->x, 0)) && fmaxshift >= fabs((float)gsl_vector_get(s->x, 1)) && (stepscale==0 || (((float)gsl_vector_get(s->x, 3))<1.3 && ((float)gsl_vector_get(s->x, 3))<0.7)) ) 01906 { 01907 if (verbose>0) printf(" Refine good (%d) %1.2f %1.2f %1.1f\n",iter,(float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1),(float)gsl_vector_get(s->x, 2)); 01908 Transform tsoln(Dict("type","2d","alpha",(float)gsl_vector_get(s->x, 2))); 01909 tsoln.set_mirror(mirror); 01910 tsoln.set_trans((float)gsl_vector_get(s->x, 0),(float)gsl_vector_get(s->x, 1)); 01911 if (stepscale!=0.0) tsoln.set_scale((float)gsl_vector_get(s->x, 3)); 01912 result = this_img->process("xform",Dict("transform",&tsoln)); 01913 result->set_attr("xform.align2d",&tsoln); 01914 } else { // The refine aligner failed - this shift went beyond the max shift 01915 if (verbose>1) 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)); 01916 result = this_img->process("xform",Dict("transform",t)); 01917 result->set_attr("xform.align2d",t); 01918 } 01919 01920 delete t; 01921 t = 0; 01922 01923 gsl_vector_free(x); 01924 gsl_multimin_fdfminimizer_free(s); 01925 01926 if (c != 0) delete c; 01927 return result; 01928 }
virtual string EMAN::RefineAlignerCG::get_desc | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 1288 of file aligner.h.
01289 { 01290 return "Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision."; 01291 }
virtual string EMAN::RefineAlignerCG::get_name | ( | ) | const [inline, virtual] |
virtual TypeDict EMAN::RefineAlignerCG::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 1298 of file aligner.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::TRANSFORM.
01299 { 01300 TypeDict d; 01301 01302 d.put("mode", EMObject::INT, "Currently unused"); 01303 d.put("xform.align2d", EMObject::TRANSFORM, "The Transform storing the starting guess. If unspecified the identity matrix is used"); 01304 d.put("step", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 0.1"); 01305 d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.02."); 01306 d.put("maxiter", EMObject::INT,"The maximum number of iterations that can be performed by the Simplex minimizer. default=12"); 01307 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."); 01308 d.put("stepscale", EMObject::FLOAT, "If set to any non-zero value, scale will be included in the alignment. Images should be edgenormalized. If the scale goes beyond +-30% alignment will fail."); 01309 d.put("mask", EMObject::EMDATA, "A mask to be applied to the image being aligned prior to each similarity comparison."); 01310 d.put("verbose", EMObject::INT, "This will cause debugging information to be printed on the screen for the iterative refinement. Larger numbers -> more info. default=0"); 01311 return d; 01312 }
static Aligner* EMAN::RefineAlignerCG::NEW | ( | ) | [inline, static] |
const string RefineAlignerCG::NAME = "refinecg" [static] |