EMAN::ToCenterProcessor Class Reference

ToCenterProcessor centers image, ignores old dx, dy. More...

#include <processor.h>

Inheritance diagram for EMAN::ToCenterProcessor:

Collaboration diagram for EMAN::ToCenterProcessor:

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.center"

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

ToCenterProcessor centers image, ignores old dx, dy.

Definition at line 7090 of file processor.h.

Member Function Documentation

get_desc()

virtual string EMAN::ToCenterProcessor::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 7105 of file processor.h.

                {
                        return "Centers similar to the way a human would, by identifying the shape of the object and centering its sillouette. May be inaccurate if sillouette cannot be clearly identified. ";
                }

get_name()

virtual string EMAN::ToCenterProcessor::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 7095 of file processor.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

virtual TypeDict EMAN::ToCenterProcessor::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 7110 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("positive", EMObject::INT, "uses only densities >0 for the calculatton");
                        return d;
                }

NEW()

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

inlinestatic

Definition at line 7100 of file processor.h.

                {
                        return new ToCenterProcessor();
                }

process_inplace()

void ToCenterProcessor::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 7331 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        if ((float)image->get_attr("sigma")==0.0f) return;              // Can't center a constant valued image
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        // Preprocess a copy of the image to better isolate the "bulk" of the object
        float gmw=(nx/16)>5?nx/16:5;            // gaussian mask width
        EMData *image2=image->process("filter.highpass.gauss",Dict("cutoff_pixels",nx<50?nx/10:5));             // clear out large scale gradients
        image2->process_inplace("normalize.circlemean",Dict("radius",ny/2-4));
        image2->process_inplace("mask.gaussian",Dict("inner_radius",nx/2-gmw,"outer_radius",gmw/1.3));  // get rid of peripheral garbage
        image2->process_inplace("math.squared");                // exaggerate stronger density and includes strong negative density
        image2->process_inplace("filter.lowpass.gauss",Dict("cutoff_abs",0.05));                                                // get rid of peripheral garbage
        image2->process_inplace("normalize.circlemean",Dict("radius",ny/2-6));
 
        // We compute a histogram so we can decide on a good threshold value
        float hmin=(float)image2->get_attr("mean");
        float hmax=(float)image2->get_attr("mean")+(float)image2->get_attr("sigma")*4.0;
        vector <float> hist = image2->calc_hist( 100,hmin,hmax);
        double tot=0;
        int i;
        for (i=99; i>=0; i--) {
                tot+=hist[i];
                if (tot>nx*ny*nz/10) break;             // find a threshold encompassing a specific fraction of the total area/volume
        }
        float thr=(i*hmax+(99-i)*hmin)/99.0;            // this should now be a threshold encompasing ~1/10 of the area in the image
//      printf("mean %f   sigma %f       thr %f\n",(float)image2->get_attr("mean"),(float)image2->get_attr("sigma"),thr);
 
        // threshold so we are essentially centering the object silhouette
        image2->process_inplace("threshold.belowtozero",Dict("minval",thr));
//      image2->process_inplace("threshold.binary",Dict("value",thr));
//      image2->write_image("dbg1.hdf",-1);
 
        EMData *image3;
        if (nz==1) image3=image2->process("mask.auto2d",Dict("radius",nx/10,"threshold",thr*0.9,"nmaxseed",5));
        else image3=image2->process("mask.auto3d",Dict("radius",nx/10,"threshold",thr*0.9,"nmaxseed",5));
 
        // if the mask failed, we revert to the thresholded, but unmasked image
        if (nz==1 && (float)image3->get_attr("sigma")==0) {
                delete image3;
                image3=image2->process("math.linearpyramid");
                image3->add(9.0f);              // we comress the pyramid from .9-1
                image3->mult(0.9f);
                image3->process_inplace("mask.auto2d",Dict("threshold",0.5,"nmaxseed",5));      // should find seed points with a central bias
//              image3->write_image("dbg3.hdf",-1);
        }
 
        image3->process_inplace("threshold.binary",Dict("value",thr));
 
        if ((float)image3->get_attr("sigma")==0) delete image3;
        else {
                delete image2;
                image2=image3;
        }
 
//      image2->write_image("dbg2.hdf",-1);
        FloatPoint com = image2->calc_center_of_mass(0.5);
        delete image2;
 
        // actual centering is int translate 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);
                }
        }
 
 
}

References EMAN::EMData::calc_hist(), LOGWARN, EMAN::Transform::set_trans(), and EMAN::EMData::translate().

Member Data Documentation

NAME

const string ToCenterProcessor::NAME = "xform.center"

static

Definition at line 7119 of file processor.h.

Referenced by get_name().

---

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

• processor.h
• processor.cpp