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

#include <processor.h>

Inheritance diagram for EMAN::AutoMask3D2Processor:

Collaboration diagram for EMAN::AutoMask3D2Processor:

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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 = "mask.auto3d"

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

radius	Pixel radius of a ball which is used to seed the flood filling operation
threshold	An isosurface threshold that suitably encases the mass
nshells	The number of dilation operations
nshellsgauss	number of Gaussian pixels to expand, following the dilation operations @return_mask If true the result of the operation will produce the mask, not the masked volume

Definition at line 6948 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::AutoMask3D2Processor::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 6963 of file processor.h.

                {
                        return "This will mask a 3-D volume using a 'flood filling' approach. It begins with a seed generated either as a sphere with \
specified 'radius' or with the 'nmaxseed' highest values. It then includes any mass connected to the seed with value higher than 'threshold'.\
Next, the mask is expanded by 'nshells'+'nshellsgauss'/2 voxels. Finally a gaussian low-pass filter is applied with a width of 'nshellsgauss'.";
                }

◆ get_name()

virtual string EMAN::AutoMask3D2Processor::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 6953 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::AutoMask3D2Processor::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 6970 of file processor.h.

                {
                        TypeDict d;
                        d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. ");
                        d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses.");
                        d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass.");
                        d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma");
                        d.put("nshells", EMObject::INT, "Number of 1-voxel shells to expand the mask by.");
                        d.put("nshellsgauss", EMObject::INT, "Width in voxels of a Gaussian decay at the edge of the mask.");
                        d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume.");
                        d.put("verbose", EMObject::INT, "How verbose to be (stdout)");
                        return d;
                }

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

◆ NEW()

static Processor * EMAN::AutoMask3D2Processor::NEW ( )

inlinestatic

Definition at line 6958 of file processor.h.

                {
                        return new AutoMask3D2Processor();
                }

◆ process_inplace()

void AutoMask3D2Processor::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 8621 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        if (image->get_ndim() != 3) {
                throw ImageDimensionException("This processor was only ever designed to work on 3D images.");
        }
 
        /*
         The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor
         To get around this just use the return_mask parameter.
        string mask_output = params.set_default("write_mask", "");
        if ( mask_output != "") {
                if (Util::is_file_exist(mask_output) ) throw InvalidParameterException("The mask output file name already exists. Please remove it if you don't need it.");
                if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized");
        }
        */
 
        int radius=0;
        if (params.has_key("radius")) {
                radius = params["radius"];
        }
        int nmaxseed=0;
        if (params.has_key("nmaxseed")) {
                nmaxseed = params["nmaxseed"];
        }
 
        float threshold=0.0;
        if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"];
        else threshold=params["threshold"];
 
        int nshells = params["nshells"];
        int nshellsgauss = params["nshellsgauss"];
        int verbose=params.set_default("verbose",0);
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
        int nxy=nx*ny;
 
        EMData *amask = new EMData();
        amask->set_size(nx, ny, nz);
 
        float *dat = image->get_data();
        float *dat2 = amask->get_data();
        int i,j,k;
        size_t l = 0;
 
        // Seeds with the highest valued pixels
        if (nmaxseed>0) {
                vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed);
 
                for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) {
                        amask->set_value_at((*i).x,(*i).y,(*i).z,1.0);
                        if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value);
                }
        }
 
        // Seeds with a sphere
        if (radius>0) {
                // start with an initial sphere
                for (k = -nz / 2; k < nz / 2; ++k) {
                        for (j = -ny / 2; j < ny / 2; ++j) {
                                for (i = -nx / 2; i < nx / 2; ++i,++l) {
                                        if (abs(k) > radius || abs(j) > radius || abs(i) > radius) continue;
                                        if ( (k * k + j * j + i * i) > (radius*radius) || dat[l] < threshold) continue;
                                        dat2[l] = 1.0f;
                                }
                        }
                }
        }
 
 
        // iteratively 'flood fills' the map... recursion would be better
        int done=0;
        int iter=0;
        while (!done) {
                iter++;
                done=1;
                if (verbose && iter%10==0) printf("%d iterations\n",iter);
                for (k=1; k<nz-1; ++k) {
                        for (j=1; j<ny-1; ++j) {
                                for (i=1; i<nx-1; ++i) {
                                        l=i+j*nx+k*nx*ny;
                                        if (dat2[l]) continue;
                                        if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx]||dat2[l-nxy]||dat2[l+nxy])) {
                                                dat2[l]=1.0;
                                                done=0;
                                        }
                                }
                        }
                }
        }
 
        amask->update();
 
        if (verbose) printf("expanding mask\n");
        amask->process_inplace("mask.addshells.gauss", Dict("val1", (int)(nshells+nshellsgauss/2),"val2",0));
        if (verbose) printf("filtering mask\n");
        if (nshellsgauss>0) amask->process_inplace("filter.lowpass.gauss", Dict("cutoff_abs", (float)(1.0f/(float)nshellsgauss)));
        amask->process_inplace("threshold.belowtozero", Dict("minval",(float)0.002));   // this makes the value exactly 0 beyond ~2.5 sigma
 
        bool return_mask = params.set_default("return_mask",false);
        if (return_mask) {
                // Yes there is probably a much more efficient way of getting the mask itself, but I am only providing a stop gap at the moment.
                dat = image->get_data();
                dat2 = amask->get_data();
                memcpy(dat,dat2,image->get_size()*sizeof(float));
        } else {
                image->mult(*amask);
        }
 
        // EMAN2 policy is not to allow file io from with a processor
        //if (mask_output != "") {
        //      amask->write_image(mask_output);
        //}
 
 
        delete amask;
}

References EMAN::Dict::has_key(), ImageDimensionException, LOGWARN, EMAN::Processor::params, and EMAN::Dict::set_default().

Member Data Documentation

◆ NAME

const string AutoMask3D2Processor::NAME = "mask.auto3d"

static

Definition at line 6984 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