This tries to extract a single subunit from a symmetric structure. More...

#include <processor.h>

Inheritance diagram for EMAN::SegmentSubunitProcessor:

Collaboration diagram for EMAN::SegmentSubunitProcessor:

[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 = "segment.subunit"

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

This tries to extract a single subunit from a symmetric structure.

The borders between subunits may well be structurally ambiguous.

Parameters

sym	Symmetry of map
thr	Density threshold

Definition at line 7736 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::SegmentSubunitProcessor::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 7746 of file processor.h.

                {
                        return "This will attempt to mask out a single subunit from a symmetric structure. There may be some ambiguity at the intersection, so the result may not be unambiguous.";
                }

◆ get_name()

virtual string EMAN::SegmentSubunitProcessor::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 7741 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::SegmentSubunitProcessor::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 7756 of file processor.h.

                {
                        TypeDict d;
                        d.put("thr", EMObject::FLOAT, "Minimum density to consider for extraction");
                        d.put("sym", EMObject::STRING, "Symmetry");
//                      d.put("seed", EMObject::EMDATA, "An (optional) single level mask volume to use as a seed after symmetrizing");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 7751 of file processor.h.

                {
                        return new SegmentSubunitProcessor();
                }

◆ process_inplace()

void SegmentSubunitProcessor::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 7238 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        float thr = params["thr"];
        string symname=(string)params["sym"];
        Symmetry3D* sym = Factory<Symmetry3D>::get(symname);
        
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        if (ny == 1 || nz==1) {
                LOGERR("Error: segment.subunit works only in 3-D");
                return;
        }
 
        // there are other strategies which might allow us to avoid the extra copy, but this will have to do for now
        EMData *image1=new EMData(nx,ny,nz);
        image1->to_zero();
        EMData *image2=image->copy();
        
        // We're using image2 here temporarily to seed image1. We will reinitialize it when done
        image2->process_inplace("mask.sharp",Dict("inner_radius",(int)nz/5));           // we don't want to seed too close to the middle
        IntPoint ml=image2->calc_max_location();                // highest pixel value, now we symmetrize
 
        // Seed the multi-level mask
        int i=0;
        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;
                i++;
                Vec3f xf = t.transform(ml[0]-nx/2,ml[1]-ny/2,ml[2]-nz/2);
                image1->set_value_at((int)(xf[0]+nx/2),(int)(xf[1]+ny/2),(int)(xf[2]+nz/2),(float)i);
        }
        memcpy(image2->get_data(),image1->get_data(),image1->get_size()*sizeof(float)); // copy the seed from image 1 to image 2
        
        
                
        // We progressively lower the threshold, sort of like a very coarse watershed
        float max=(float)image->get_attr("maximum");
        float gap=max-thr;
        if (gap<=0) throw InvalidParameterException("SegmentSubunitProcessor: threshold must be < max value");
                
        for (int ti=0; ti<12; ti++) {
                float thr2=max-(ti+1)*gap/12.0;
                printf("threshold %1.4f\n",thr2);
                int change=1;
                while (change) {
                        change=0;
                        for (int z = 1; z < nz - 1; z++) {
                                for (int y = 1; y < ny - 1; y++) {
                                        for (int x = 1; x < nx - 1; x++) {
                                                // Skip the voxel if already part of a mask or if below threshold
                                                if (image1->get_value_at(x,y,z)>0 || image->get_value_at(x,y,z)<thr2) continue;
 
                                                // Note that this produces a directional bias in the case of ambiguous pixels
                                                // While this could be improved upon slightly, there can be truly ambiguous cases
                                                // and at least this method is deterministic
                                                if              (image1->get_value_at(x-1,y,z)>0) { image2->set_value_at_fast(x,y,z,image1->get_value_at(x-1,y,z)); change=1; }
                                                else if (image1->get_value_at(x+1,y,z)>0) { image2->set_value_at_fast(x,y,z,image1->get_value_at(x+1,y,z)); change=1; }
                                                else if (image1->get_value_at(x,y-1,z)>0) { image2->set_value_at_fast(x,y,z,image1->get_value_at(x,y-1,z)); change=1; }
                                                else if (image1->get_value_at(x,y+1,z)>0) { image2->set_value_at_fast(x,y,z,image1->get_value_at(x,y+1,z)); change=1; }
                                                else if (image1->get_value_at(x,y,z-1)>0) { image2->set_value_at_fast(x,y,z,image1->get_value_at(x,y,z-1)); change=1; }
                                                else if (image1->get_value_at(x,y,z+1)>0) { image2->set_value_at_fast(x,y,z,image1->get_value_at(x,y,z+1)); change=1; }
 
                                        }
                                }
                        }
                        memcpy(image1->get_data(),image2->get_data(),image1->get_size()*sizeof(float));
                }
//              char fs[20];
//              sprintf(fs,"lvl%d.hdf",ti);
//              image1->write_image(fs);
        }
        
//      image1->write_image("multilev.hdf");
//      image1->process_inplace("threshold.abovetozero",Dict("maxval",(float)1.01f));
//      image->mult(*image1);
 
        // our final return value is the multilevel mask
        memcpy(image->get_data(),image1->get_data(),image1->get_size()*sizeof(float));
        
        delete image1;
        delete image2;
        delete sym;
        image->update();
}

References EMAN::Factory< T >::get(), EMAN::Symmetry3D::get_syms(), InvalidParameterException, LOGERR, LOGWARN, EMAN::Processor::params, EMAN::Transform::transform(), x, and y.

Member Data Documentation

◆ NAME

const string SegmentSubunitProcessor::NAME = "segment.subunit"

static

Definition at line 7765 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