#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. |