EMAN::AutoMaskAsymUnit Class Reference

Tries to mask out only interesting density. More...

#include <processor.h>

Inheritance diagram for EMAN::AutoMaskAsymUnit:

Collaboration diagram for EMAN::AutoMaskAsymUnit:

Public Member Functions
virtual void	process_inplace (EMData *image)
	To process an image in-place. More...
virtual string	get_name () const
	Get the processor's name. 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 EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...
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 = "mask.asymunit"

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

Tries to mask out only interesting density.

Parameters

au	The asymmetric unit to mask, if -1 masks all asymmetric units but assigns each a unique value
sym	The symmetry type, for example, "tet"

Author

David Woolford

Date

February 2009

Definition at line 6830 of file processor.h.

Member Function Documentation

get_desc()

virtual string EMAN::AutoMaskAsymUnit::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 6854 of file processor.h.

                        {
                                return "Masks out a specific asymmetric unit of the given symmetry. If the au parameter is -1 will mask all asymmetric units, assigning the asymetric unit number to the masked area.";
                        }

get_name()

virtual string EMAN::AutoMaskAsymUnit::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 6835 of file processor.h.

                        {
                                return NAME;
                        }

References NAME.

get_param_types()

virtual TypeDict EMAN::AutoMaskAsymUnit::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 6845 of file processor.h.

                        {
                                TypeDict d;
                                d.put("symavg", EMObject::INT, "Cn symmetry only. If set, the mask for a single subunit will follow a linear falloff to the neighboring subunit. After applying, symmetrizing the map should produce a smooth symmetrized average of the masked subunit (and partially its two neighbors).");
                                d.put("au", EMObject::INT, "The asymmetric unit to mask out. If this is -1 will mask all asymmetric units, giving each a unique number.");
                                d.put("sym", EMObject::STRING, "The symmetry, for example, d7");
                                return d;
                        }

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

NEW()

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

inlinestatic

Definition at line 6840 of file processor.h.

                        {
                                return new AutoMaskAsymUnit();
                        }

process_inplace()

void AutoMaskAsymUnit::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 6702 of file processor.cpp.

                                                    {
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        int ox = nx/2;
        int oy = ny/2;
        int oz = nz/2;
 
        Symmetry3D* sym = Factory<Symmetry3D>::get((string)params["sym"]);
        int au = params.set_default("au",0);
        int symavg = params.set_default("symavg",0);
 
        if ((toupper(((string)params["sym"])[0])!='C' || au<0)&& symavg) throw InvalidParameterException("ERROR: symavg only works with Cn symmetry, and one au must be specified.");
        
        if (symavg) {
                for(int k = 0; k < nz; ++k ) {
                        for(int j = 0; j < ny; ++j ) {
                                for (int i = 0; i< nx; ++i) {
                                        float az=atan2(float(j-ny/2),float(i-nx/2));
                                        
                                }
                        }
                }
 
                delete sym;
        }
        
        float *d = image->get_data();
        for(int k = 0; k < nz; ++k ) {
                for(int j = 0; j < ny; ++j ) {
                        for (int i = 0; i< nx; ++i, ++d) {
                                //cout << i << " " << j << " " << k << endl;
                                Vec3f v(i-ox,j-oy,k-oz);
//                              v.normalize();
                                int a = sym->point_in_which_asym_unit(v);
                                if (au == -1) {
                                        *d = (float)a;
                                } else {
                                        if ( a == au ) *d = 1;
                                        else *d = 0;
                                }
                        }
                }
        }
 
        delete sym;
 
}

References EMAN::Factory< T >::get(), InvalidParameterException, LOGWARN, EMAN::Processor::params, EMAN::Symmetry3D::point_in_which_asym_unit(), and EMAN::Dict::set_default().

Member Data Documentation

NAME

const string AutoMaskAsymUnit::NAME = "mask.asymunit"

static

Definition at line 6859 of file processor.h.

Referenced by get_name().

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

• processor.h
• processor.cpp