#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 | ||||
static Processor * | NEW () | |||
Static Public Attributes | ||||
static 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 1429 of file processor.h.
void EMAN::SymAlignProcessor::assert_valid_aspect | ( | const vector< int > & | translation, | |
const EMData *const | image | |||
) | const [private] |
Check that the particular aspect is valid
ImageDimensionException | if the image is not 1,2 or 3D. |
Region EMAN::SymAlignProcessor::get_clip_region | ( | vector< int > & | translation, | |
const EMData *const | image | |||
) | const [private] |
Get the clip region that will achieve the desired translation
ImageDimensionException | if the image is not 1,2 or 3D. |
translation | the amount by which to translate | |
image | the image that will eventually used for the translation operation |
virtual string EMAN::SymAlignProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 1458 of file processor.h.
01459 { 01460 return "The image is centered and rotated to the standard orientation for the specified symmetry"; 01461 }
virtual string EMAN::SymAlignProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 1432 of file processor.h.
References NAME.
01433 { 01434 return NAME; 01435 }
virtual TypeDict EMAN::SymAlignProcessor::get_param_types | ( | ) | const [inline, virtual] |
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 1446 of file processor.h.
References EMAN::EMObject::FLOAT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.
01447 { 01448 TypeDict d; 01449 d.put("sym", EMObject::STRING, "The symmetry under which to do the alignment, Default=c1" ); 01450 d.put("delta", EMObject::FLOAT,"Angle the separates points on the sphere. This is exclusive of the \'n\' paramater. Default is 10"); 01451 d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10"); 01452 d.put("lphi", EMObject::FLOAT,"Lower bound for phi. Default it 0"); 01453 d.put("uphi", EMObject::FLOAT,"Upper bound for phi. Default it 359.9"); 01454 d.put("avger", EMObject::STRING, "The sort of averager to use, Default=mean" ); 01455 return d; 01456 }
static Processor* EMAN::SymAlignProcessor::NEW | ( | ) | [inline, static] |
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.
image | The image will be copied, actual process happen on copy of image. |
Reimplemented from EMAN::Processor.
Definition at line 874 of file processor.cpp.
References EMAN::Averager::add_image(), EMAN::Averager::finish(), EMAN::Symmetry3D::gen_orientations(), EMAN::EMData::get_attr(), EMAN::Symmetry3D::get_symmetries(), EMAN::Processor::params, phi, EMAN::EMData::process(), EMAN::Dict::set_default(), and t.
00875 { 00876 00877 // Set parms 00878 float dphi = params.set_default("dphi",10.f); 00879 float lphi = params.set_default("lphi",0.0f); 00880 float uphi = params.set_default("uphi",359.9f); 00881 00882 Dict d; 00883 d["inc_mirror"] = true; 00884 d["delta"] = params.set_default("delta",10.f); 00885 00886 //Genrate points on a sphere in an asymmetric unit 00887 Symmetry3D* sym = Factory<Symmetry3D>::get((string)params.set_default("sym","c1")); 00888 vector<Transform> transforms = sym->gen_orientations((string)params.set_default("orientgen","eman"),d); 00889 00890 //Genrate symmetry related orritenations 00891 vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]); 00892 00893 float bestquality = 0.0f; 00894 EMData* bestimage; 00895 for(vector<Transform>::const_iterator trans_it = transforms.begin(); trans_it != transforms.end(); trans_it++) { 00896 Dict tparams = trans_it->get_params("eman"); 00897 Transform t(tparams); 00898 for( float phi = lphi; phi < uphi; phi += dphi ) { 00899 tparams["phi"] = phi; 00900 t.set_rotation(tparams); 00901 00902 //Get the averagaer 00903 Averager* imgavg = Factory<Averager>::get((string)params.set_default("avger","mean")); 00904 //Now make the averages 00905 for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) { 00906 Transform sympos = t*(*it); 00907 EMData* transformed = image->process("xform",Dict("transform",&sympos)); 00908 imgavg->add_image(transformed); 00909 delete transformed; 00910 } 00911 00912 EMData* symptcl=imgavg->finish(); 00913 delete imgavg; 00914 //See which average is the best 00915 float quality = symptcl->get_attr("sigma"); 00916 if(quality > bestquality) { 00917 bestquality = quality; 00918 bestimage = symptcl; 00919 } else { 00920 delete symptcl; 00921 } 00922 } 00923 } 00924 return bestimage; 00925 }
void SymAlignProcessor::process_inplace | ( | EMData * | image | ) | [virtual] |
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.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 927 of file processor.cpp.
const string SymAlignProcessor::NAME = "xform.symalign" [static] |