ToMassCenterProcessor centers image at center of mass, ignores old dx, dy. More...

#include <processor.h>

Inheritance diagram for EMAN::ToMassCenterProcessor:

Collaboration diagram for EMAN::ToMassCenterProcessor:

[legend]

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 string	get_desc () const
	Get the descrition of this specific processor. More...

virtual TypeDict	get_param_types () const
	Get processor parameter information in a dictionary. 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 = "xform.centerofmass"

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

ToMassCenterProcessor centers image at center of mass, ignores old dx, dy.

Parameters

int_shift_only set to 1 only shift by integer, no interpolation

Definition at line 7126 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::ToMassCenterProcessor::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 7141 of file processor.h.

                {
                        return "ToMassCenterProcessor centers image at center of mass, with a threshold. Only values higher than the threshold are considered.";
                }

◆ get_name()

virtual string EMAN::ToMassCenterProcessor::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 7131 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::ToMassCenterProcessor::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 7146 of file processor.h.

                {
                        TypeDict d;
                        d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation");
                        d.put("threshold", EMObject::FLOAT, "Only values larger than the threshold are included in the center of mass computation. Default is 0.");
                        d.put("powercenter", EMObject::INT, "If set, squares pixel values before computing the center. The threshold is with respect to the squared values.");
//                      d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 7136 of file processor.h.

                {
                        return new ToMassCenterProcessor();
                }

◆ process_inplace()

void ToMassCenterProcessor::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 7423 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        int int_shift_only = params.set_default("int_shift_only",1);
        int powercenter = params.set_default("powercenter",0);
        float threshold = params.set_default("threshold",0.0f);
//      int positive = params.set_default("positive",0);
 
        if ((float)image->get_attr("sigma")==0.0f) return;              // Can't center a constant valued image
        if (threshold>(float)image->get_attr("maximum")) {
                printf("Warning, centering threshold %1.2f, but image max %1.2f. Adjusting.",threshold,(float)image->get_attr("maximum"));
                threshold=(float)image->get_attr("mean")+(float)image->get_attr("sigma");
        }
 
        EMData *tmp = 0;
        if (powercenter) { tmp=image; image=tmp->process("math.squared"); }  // yes, I know, not very efficient
        FloatPoint com = image->calc_center_of_mass(threshold);
        if (powercenter) { delete image; image=tmp; }
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        if (int_shift_only) {
                int dx = -(floor(com[0] + 0.5f) - nx / 2);
                int dy = -(floor(com[1] + 0.5f) - ny / 2);
                int dz = 0;
                if (nz > 1) {
                        dz = -(floor(com[2] + 0.5f) - nz / 2);
                }
                if (abs(dx)>=nx-1 || abs(dy)>=ny-1 || abs(dz)>=nz) {
                        printf("ERROR, center of mass outside image\n");
                }
                else {
                        image->translate(dx, dy, dz);
 
                        Transform t;
                        t.set_trans((float)dx,(float)dy,(float)dz);
 
                        if (nz > 1) {
                                image->set_attr("xform.align3d",&t);
                        } else {
                                image->set_attr("xform.align2d",&t);
                        }
                }
        }
        else {
                float dx = -(com[0] - nx / 2);
                float dy = -(com[1] - ny / 2);
                float dz = 0;
                if (nz > 1) {
                        dz = -(com[2] - nz / 2);
                }
                if (fabs(dx)>=nx-1 || fabs(dy)>=ny-2 || fabs(dz)>=nz) {
                        printf("ERROR, center of mass outside image\n");
                }
                else {
                        image->translate(dx, dy, dz);
 
                        Transform t;
                        t.set_trans(dx,dy,dz);
 
                        if (nz > 1) {
                                image->set_attr("xform.align3d",&t);
                        } else {
                                image->set_attr("xform.align2d",&t);
                        }
                }
        }
}

References LOGWARN, EMAN::Processor::params, EMAN::Dict::set_default(), EMAN::Transform::set_trans(), and EMAN::EMData::translate().

Member Data Documentation

◆ NAME

const string ToMassCenterProcessor::NAME = "xform.centerofmass"

static

Definition at line 7156 of file processor.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process_inplace()

Member Data Documentation

◆ NAME