#include <processor.h>
Inheritance diagram for EMAN::SymAlignProcessor:


Public Member Functions | |
| virtual string | get_name () const |
| Get the processor's name. | |
| virtual void | process_inplace (EMData *image) |
| To process an image in-place. | |
| virtual EMData * | process (const EMData *const image) |
| To proccess an image out-of-place. | |
| virtual TypeDict | get_param_types () const |
| Get processor parameter information in a dictionary. | |
| virtual string | get_desc () const |
| Get the descrition of this specific processor. | |
Static Public Member Functions | |
| Processor * | NEW () |
Static Public Attributes | |
| const string | NAME = "xform.symalign" |
Private Member Functions | |
| void | assert_valid_aspect (const vector< int > &translation, const EMData *const image) const |
| Check that the particular aspect is valid. | |
| Region | get_clip_region (vector< int > &translation, const EMData *const image) const |
| Get the clip region that will achieve the desired translation. | |
| sym | A string specifying the symmetry under which to do the alignment |
Definition at line 1525 of file processor.h.
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Check that the particular aspect is valid.
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Get the clip region that will achieve the desired translation.
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 1554 of file processor.h. 01555 {
01556 return "The image is centered and rotated to the standard orientation for the specified symmetry";
01557 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 1528 of file processor.h. 01529 {
01530 return NAME;
01531 }
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Get processor parameter information in a dictionary. Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.
Reimplemented from EMAN::Processor. Definition at line 1542 of file processor.h. References EMAN::TypeDict::put(). 01543 {
01544 TypeDict d;
01545 d.put("sym", EMObject::STRING, "The symmetry under which to do the alignment, Default=c1" );
01546 d.put("delta", EMObject::FLOAT,"Angle the separates points on the sphere. This is exclusive of the \'n\' paramater. Default is 10");
01547 d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10");
01548 d.put("lphi", EMObject::FLOAT,"Lower bound for phi. Default it 0");
01549 d.put("uphi", EMObject::FLOAT,"Upper bound for phi. Default it 359.9");
01550 d.put("avger", EMObject::STRING, "The sort of averager to use, Default=mean" );
01551 return d;
01552 }
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Definition at line 1533 of file processor.h. 01534 {
01535 return new SymAlignProcessor();
01536 }
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To proccess an image out-of-place. For those processors which can only be processed out-of-place, override this function to give the right behavior.
Reimplemented from EMAN::Processor. Definition at line 880 of file processor.cpp. References EMAN::Averager::add_image(), EMAN::Averager::finish(), EMAN::Symmetry3D::gen_orientations(), EMAN::Factory< T >::get(), EMAN::EMData::get_attr(), EMAN::FactoryBase::get_params(), EMAN::Symmetry3D::get_symmetries(), phi, EMAN::EMData::process(), EMAN::Dict::set_default(), EMAN::Transform::set_rotation(), and t. 00881 {
00882
00883 // Set parms
00884 float dphi = params.set_default("dphi",10.f);
00885 float lphi = params.set_default("lphi",0.0f);
00886 float uphi = params.set_default("uphi",359.9f);
00887
00888 Dict d;
00889 d["inc_mirror"] = true;
00890 d["delta"] = params.set_default("delta",10.f);
00891
00892 //Genrate points on a sphere in an asymmetric unit
00893 Symmetry3D* sym = Factory<Symmetry3D>::get((string)params.set_default("sym","c1"));
00894 vector<Transform> transforms = sym->gen_orientations((string)params.set_default("orientgen","eman"),d);
00895
00896 //Genrate symmetry related orritenations
00897 vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]);
00898
00899 float bestquality = 0.0f;
00900 EMData* bestimage = 0;
00901 for(vector<Transform>::const_iterator trans_it = transforms.begin(); trans_it != transforms.end(); trans_it++) {
00902 Dict tparams = trans_it->get_params("eman");
00903 Transform t(tparams);
00904 for( float phi = lphi; phi < uphi; phi += dphi ) {
00905 tparams["phi"] = phi;
00906 t.set_rotation(tparams);
00907
00908 //Get the averagaer
00909 Averager* imgavg = Factory<Averager>::get((string)params.set_default("avger","mean"));
00910 //Now make the averages
00911 for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
00912 Transform sympos = t*(*it);
00913 EMData* transformed = image->process("xform",Dict("transform",&sympos));
00914 imgavg->add_image(transformed);
00915 delete transformed;
00916 }
00917
00918 EMData* symptcl=imgavg->finish();
00919 delete imgavg;
00920 //See which average is the best
00921 float quality = symptcl->get_attr("sigma");
00922 if(quality > bestquality) {
00923 bestquality = quality;
00924 bestimage = symptcl;
00925 } else {
00926 delete symptcl;
00927 }
00928 }
00929 }
00930 return bestimage;
00931 }
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To process an image in-place. For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.
Implements EMAN::Processor. Definition at line 933 of file processor.cpp. 00934 {
00935 cout << "Not implemented yet" << endl;
00936 }
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Definition at line 89 of file processor.cpp. |
1.3.9.1