EMAN::ApplySymProcessor Class Reference

Applies a symmetry to a 3D model. More...

#include <processor.h>

Inheritance diagram for EMAN::ApplySymProcessor:

Collaboration diagram for EMAN::ApplySymProcessor:

Public Member Functions
virtual string	get_name () const
	Get the processor's name. More...
virtual void	process_inplace (EMData *image)
	To process an image in-place. More...
virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...
virtual TypeDict	get_param_types () const
	Get processor parameter information in a dictionary. More...
virtual string	get_desc () const
	Get the descrition of this specific processor. More...
Public Member Functions inherited from EMAN::Processor
virtual	~Processor ()
virtual void	process_list_inplace (vector< EMData * > &images)
	To process multiple images using the same algorithm. More...
virtual Dict	get_params () const
	Get the processor parameters in a key/value dictionary. More...
virtual void	set_params (const Dict &new_params)
	Set the processor parameters using a key/value dictionary. More...

Static Public Member Functions
static Processor *	NEW ()
Static Public Member Functions inherited from EMAN::Processor
static string	get_group_desc ()
	Get the description of this group of processors. More...
static void	EMFourierFilterInPlace (EMData *fimage, Dict params)
	Compute a Fourier-filter processed image in place. More...
static EMData *	EMFourierFilter (EMData *fimage, Dict params)
	Compute a Fourier-processor processed image without altering the original image. More...

Static Public Attributes
static const string	NAME = "xform.applysym"

Additional Inherited Members
Public Types inherited from EMAN::Processor
enum	fourier_filter_types {   TOP_HAT_LOW_PASS , TOP_HAT_HIGH_PASS , TOP_HAT_BAND_PASS , TOP_HOMOMORPHIC ,   GAUSS_LOW_PASS , GAUSS_HIGH_PASS , GAUSS_BAND_PASS , GAUSS_INVERSE ,   GAUSS_HOMOMORPHIC , BUTTERWORTH_LOW_PASS , BUTTERWORTH_HIGH_PASS , BUTTERWORTH_HOMOMORPHIC ,   KAISER_I0 , KAISER_SINH , KAISER_I0_INVERSE , KAISER_SINH_INVERSE ,   SHIFT , TANH_LOW_PASS , TANH_HIGH_PASS , TANH_HOMOMORPHIC ,   TANH_BAND_PASS , RADIAL_TABLE , CTF_ }
	Fourier filter Processor type enum. More...
Protected Attributes inherited from EMAN::Processor
Dict	params

Detailed Description

Applies a symmetry to a 3D model.

The model must be on aligned to its symmetry axis(via align3d or other mechanism)

Author

Steve Ludtke and John Flanagan

Date

June 2011

Parameters

sym	A string specifying the symmetry under which to do the alignment

Definition at line 2945 of file processor.h.

Member Function Documentation

get_desc()

virtual string EMAN::ApplySymProcessor::get_desc ( ) const

inlinevirtual

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns

The description of this processor.

Implements EMAN::Processor.

Definition at line 2970 of file processor.h.

                        {
                                return "Symmetry is imposed on a 2-D image (Cn only) or 3-D volume";
                        }

get_name()

virtual string EMAN::ApplySymProcessor::get_name ( ) const

inlinevirtual

Get the processor's name.

Each processor is identified by a unique name.

Returns

The processor's name.

Implements EMAN::Processor.

Definition at line 2948 of file processor.h.

                        {
                                return NAME;
                        }

References NAME.

get_param_types()

virtual TypeDict EMAN::ApplySymProcessor::get_param_types ( ) const

inlinevirtual

Get processor parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns

A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 2962 of file processor.h.

                        {
                                TypeDict d;
                                d.put("sym", EMObject::STRING, "The symmetry under which to do the alignment, Default=c1" );
                                d.put("averager", EMObject::STRING, "Name of an Averager to use. default=mean" );
                                return d;
                        }

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

NEW()

static Processor * EMAN::ApplySymProcessor::NEW ( )

inlinestatic

Definition at line 2953 of file processor.h.

                        {
                                return new ApplySymProcessor();
                        }

process()

EMData * ApplySymProcessor::process ( const EMData *const  image )

virtual

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.

Parameters

image

The image will be copied, actual process happen on copy of image.

Returns

the image processing result, may or may not be the same size of the input image

Reimplemented from EMAN::Processor.

Definition at line 1692 of file processor.cpp.

{
        string s=(string)params.set_default("sym","c1");
        if (s.length()<2) return image->copy();
        int n=atoi(s.c_str()+1);
        if ((s[0]=='c' || s[0]=='C') && n==1) return image->copy();
        
        Averager* imgavg = Factory<Averager>::get((string)params.set_default("averager","mean"));
 
        if (image->get_zsize()==1) {
                if (s[0]!='c' && s[0]!='C') throw ImageDimensionException("xform.applysym: Cn symmetry required for 2-D symmetrization");
                if (n<=0) throw InvalidValueException(n,"xform.applysym: Cn symmetry, n>0");
 
                for (int i=0; i<n; i++) {
                        Transform t(Dict("type","2d","alpha",(float)(i*360.0f/n)));
                        EMData* transformed = image->process("xform",Dict("transform",&t));
                        imgavg->add_image(transformed);
                        delete transformed;
                }
                EMData *ret=imgavg->finish();
                delete imgavg;
                return ret;
        }
 
        Symmetry3D* sym = Factory<Symmetry3D>::get((string)params.set_default("sym","c1"));
        vector<Transform> transforms = sym->get_syms();
 
        for(vector<Transform>::const_iterator trans_it = transforms.begin(); trans_it != transforms.end(); trans_it++) {
                Transform t = *trans_it;
                EMData* transformed = image->process("xform",Dict("transform",&t));
                imgavg->add_image(transformed);
                delete transformed;
        }
        EMData *ret=imgavg->finish();
        delete imgavg;
        return ret;
}

References EMAN::Averager::add_image(), EMAN::Averager::finish(), EMAN::Factory< T >::get(), EMAN::Symmetry3D::get_syms(), ImageDimensionException, InvalidValueException, EMAN::Processor::params, and EMAN::Dict::set_default().

Referenced by process_inplace().

process_inplace()

void ApplySymProcessor::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.

Parameters

image

The image to be processed.

Implements EMAN::Processor.

Definition at line 1730 of file processor.cpp.

{
        EMData *tmp=process(image);
        memcpy(image->get_data(),tmp->get_data(),(size_t)image->get_xsize()*image->get_ysize()*image->get_zsize()*sizeof(float));
        delete tmp;
        image->update();
        return;
}

References process().

Member Data Documentation

NAME

const string ApplySymProcessor::NAME = "xform.applysym"

static

Definition at line 2975 of file processor.h.

Referenced by get_name().

---

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

• processor.h
• processor.cpp