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EMAN::RotationalAligner Class Reference
[a function or class that is CUDA enabled]

rotational alignment using angular correlation More...

#include <aligner.h>

Inheritance diagram for EMAN::RotationalAligner:

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Collaboration diagram for EMAN::RotationalAligner:

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List of all members.

Public Member Functions

virtual EMDataalign (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 EMDataalign (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

AlignerNEW ()
EMDataalign_180_ambiguous (EMData *this_img, EMData *to_img, int rfp_mode=0)

Static Public Attributes

const string NAME = "rotational"

Detailed Description

rotational alignment using angular correlation

Parameters:
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 218 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::RotationalAligner::align EMData this_img,
EMData to_img
const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 224 of file aligner.h.

References align().

00225                 {
00226                         return align(this_img, to_img, "dot", Dict());
00227                 }

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.

Parameters:
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.
Returns:
The aligned image.

Implements EMAN::Aligner.

Definition at line 301 of file aligner.cpp.

References align_180_ambiguous(), EMAN::EMData::cmp(), EMAN::EMData::get_attr(), EMAN::Transform::get_rotation(), InvalidParameterException, EMAN::EMData::process(), EMAN::EMData::set_attr(), and EMAN::Dict::set_default().

00303 {
00304         if (!to) throw InvalidParameterException("Can not rotational align - the image to align to is NULL");
00305         
00306 #ifdef EMAN2_USING_CUDA
00307         if(EMData::usecuda == 1) {
00308                 if(!this_img->cudarwdata) this_img->copy_to_cuda();
00309                 if(!to->cudarwdata) to->copy_to_cuda();
00310         }
00311 #endif
00312 
00313         // Perform 180 ambiguous alignment
00314         int rfp_mode = params.set_default("rfp_mode",0);
00315         EMData* rot_aligned = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode);
00316         Transform * tmp = rot_aligned->get_attr("xform.align2d");
00317         Dict rot = tmp->get_rotation("2d");
00318         float rotate_angle_solution = rot["alpha"];
00319         delete tmp;
00320 
00321         EMData *rot_align_180 = rot_aligned->process("math.rotate.180");
00322 
00323         // Generate the comparison metrics for both rotational candidates
00324         float rot_cmp = rot_aligned->cmp(cmp_name, to, cmp_params);
00325         float rot_180_cmp = rot_align_180->cmp(cmp_name, to, cmp_params);
00326 
00327         // Decide on the result
00328         float score = 0.0;
00329         EMData* result = NULL;
00330         if (rot_cmp < rot_180_cmp){
00331                 result = rot_aligned;
00332                 score = rot_cmp;
00333                 delete rot_align_180; rot_align_180 = 0;
00334         } else {
00335                 result = rot_align_180;
00336                 score = rot_180_cmp;
00337                 delete rot_aligned; rot_aligned = 0;
00338                 rotate_angle_solution = rotate_angle_solution-180.0f;
00339         }
00340 
00341 //      Transform* t = get_align_attr("xform.align2d",result);
00342 //      t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution));
00343         Transform tmp2(Dict("type","2d","alpha",rotate_angle_solution));
00344         result->set_attr("xform.align2d",&tmp2);
00345         return result;
00346 }

EMData * RotationalAligner::align_180_ambiguous EMData this_img,
EMData to_img,
int  rfp_mode = 0
[static]
 

Definition at line 253 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().

00253                                                                                             {
00254 
00255         // Make translationally invariant rotational footprints
00256         EMData* this_img_rfp, * to_rfp;
00257         if (rfp_mode == 0) {
00258                 this_img_rfp = this_img->make_rotational_footprint_e1();
00259                 to_rfp = to->make_rotational_footprint_e1();
00260         } else if (rfp_mode == 1) {
00261                 this_img_rfp = this_img->make_rotational_footprint();
00262                 to_rfp = to->make_rotational_footprint();
00263         } else if (rfp_mode == 2) {
00264                 this_img_rfp = this_img->make_rotational_footprint_cmc();
00265                 to_rfp = to->make_rotational_footprint_cmc();
00266         } else {
00267                 throw InvalidParameterException("rfp_mode must be 0,1 or 2");
00268         }
00269         int this_img_rfp_nx = this_img_rfp->get_xsize();
00270 
00271         // Do row-wise correlation, returning a sum.
00272         EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize());
00273         
00274         // Delete them, they're no longer needed
00275         delete this_img_rfp; this_img_rfp = 0;
00276         delete to_rfp; to_rfp = 0;
00277 
00278         // Now solve the rotational alignment by finding the max in the column sum
00279         float *data = cf->get_data();
00280         
00281         float peak = 0;
00282         int peak_index = 0;
00283         Util::find_max(data, this_img_rfp_nx, &peak, &peak_index);
00284 
00285         if( cf ) {
00286                 delete cf;
00287                 cf = 0;
00288         }
00289         float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx);
00290 
00291         // Return the result
00292         Transform tmp(Dict("type","2d","alpha",rot_angle));
00293         cf=this_img->process("xform",Dict("transform",(Transform*)&tmp));
00294 //      Transform* t = get_set_align_attr("xform.align2d",cf,this_img);
00295 //      Dict d("type","2d","alpha",rot_angle);
00296 //      t->set_rotation(d);
00297         cf->set_attr("xform.align2d",&tmp);
00298         return cf;
00299 }

virtual string EMAN::RotationalAligner::get_desc  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 234 of file aligner.h.

00235                 {
00236                         return "Performs rotational alignment,works accurately if the image is precentered, normally called internally in combination with translational and flip alignment";
00237                 }

virtual string EMAN::RotationalAligner::get_name  )  const [inline, virtual]
 

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns:
The Aligner's name.

Implements EMAN::Aligner.

Definition at line 229 of file aligner.h.

00230                 {
00231                         return NAME;
00232                 }

virtual TypeDict EMAN::RotationalAligner::get_param_types  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 246 of file aligner.h.

References EMAN::TypeDict::put().

00247                 {
00248                         TypeDict d;
00249                         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.");
00250                         return d;
00251                 }

Aligner* EMAN::RotationalAligner::NEW  )  [inline, static]
 

Definition at line 239 of file aligner.h.

00240                 {
00241                         return new RotationalAligner();
00242                 }


Member Data Documentation

const string RotationalAligner::NAME = "rotational" [static]
 

Definition at line 59 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Mon Mar 7 18:16:43 2011 for EMAN2 by  doxygen 1.3.9.1