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

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


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 214 of file aligner.h.


Member Function Documentation

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 234 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().

00236 {
00237         if (!to) throw InvalidParameterException("Can not rotational align - the image to align to is NULL");
00238 
00239         // Perform 180 ambiguous alignment
00240         int rfp_mode = params.set_default("rfp_mode",0);
00241         EMData* rot_aligned = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode);
00242         Transform * tmp = rot_aligned->get_attr("xform.align2d");
00243         Dict rot = tmp->get_rotation("2d");
00244         float rotate_angle_solution = rot["alpha"];
00245         delete tmp;
00246 
00247         EMData *rot_align_180 = rot_aligned->process("math.rotate.180");
00248 
00249         // Generate the comparison metrics for both rotational candidates
00250         float rot_cmp = rot_aligned->cmp(cmp_name, to, cmp_params);
00251         float rot_180_cmp = rot_align_180->cmp(cmp_name, to, cmp_params);
00252         // Decide on the result
00253         float score = 0.0;
00254         EMData* result = NULL;
00255         if (rot_cmp < rot_180_cmp){
00256                 result = rot_aligned;
00257                 score = rot_cmp;
00258                 delete rot_align_180; rot_align_180 = 0;
00259         } else {
00260                 result = rot_align_180;
00261                 score = rot_180_cmp;
00262                 delete rot_aligned; rot_aligned = 0;
00263                 rotate_angle_solution = rotate_angle_solution-180.0f;
00264         }
00265 
00266 //      Transform* t = get_align_attr("xform.align2d",result);
00267 //      t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution));
00268         Transform tmp2(Dict("type","2d","alpha",rotate_angle_solution));
00269         result->set_attr("xform.align2d",&tmp2);
00270         return result;
00271 }

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

Implements EMAN::Aligner.

Definition at line 220 of file aligner.h.

References align().

00221                 {
00222                         return align(this_img, to_img, "", Dict());
00223                 }

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 225 of file aligner.h.

00226                 {
00227                         return "rotational";
00228                 }

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

Implements EMAN::Aligner.

Definition at line 230 of file aligner.h.

00231                 {
00232                         return "Performs rotational alignment,works accurately if the image is precentered, normally called internally in combination with translational and flip alignment";
00233                 }

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

Definition at line 235 of file aligner.h.

00236                 {
00237                         return new RotationalAligner();
00238                 }

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

Definition at line 187 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().

00187                                                                                             {
00188 
00189         // Make translationally invariant rotational footprints
00190         EMData* this_img_rfp, * to_rfp;
00191         if (rfp_mode == 0) {
00192                 this_img_rfp = this_img->make_rotational_footprint_e1();
00193                 to_rfp = to->make_rotational_footprint_e1();
00194         } else if (rfp_mode == 1) {
00195                 this_img_rfp = this_img->make_rotational_footprint();
00196                 to_rfp = to->make_rotational_footprint();
00197         } else if (rfp_mode == 2) {
00198                 this_img_rfp = this_img->make_rotational_footprint_cmc();
00199                 to_rfp = to->make_rotational_footprint_cmc();
00200         } else {
00201                 throw InvalidParameterException("rfp_mode must be 0,1 or 2");
00202         }
00203         int this_img_rfp_nx = this_img_rfp->get_xsize();
00204 
00205         // Do row-wise correlation, returning a sum.
00206         EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize());
00207 
00208         // Delete them, they're no longer needed
00209         delete this_img_rfp; this_img_rfp = 0;
00210         delete to_rfp; to_rfp = 0;
00211 
00212         // Now solve the rotational alignment by finding the max in the column sum
00213         float *data = cf->get_data();
00214         float peak = 0;
00215         int peak_index = 0;
00216         Util::find_max(data, this_img_rfp_nx, &peak, &peak_index);
00217 
00218         if( cf ) {
00219                 delete cf;
00220                 cf = 0;
00221         }
00222         float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx);
00223 
00224         // Return the result
00225         Transform tmp(Dict("type","2d","alpha",rot_angle));
00226         cf=this_img->process("math.transform",Dict("transform",(Transform*)&tmp));
00227 //      Transform* t = get_set_align_attr("xform.align2d",cf,this_img);
00228 //      Dict d("type","2d","alpha",rot_angle);
00229 //      t->set_rotation(d);
00230         cf->set_attr("xform.align2d",&tmp);
00231         return cf;
00232 }

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

Implements EMAN::Aligner.

Definition at line 242 of file aligner.h.

References EMAN::EMObject::INT, and EMAN::TypeDict::put().

00243                 {
00244                         TypeDict d;
00245                         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.");
00246                         return d;
00247                 }


The documentation for this class was generated from the following files:

Generated on Sat Nov 21 02:20:14 2009 for EMAN2 by  doxygen 1.5.6