EMAN::AutoMask2DProcessor Class Reference

Attempts to automatically mask out the particle, excluding other particles in the box, etc. More...

#include <processor.h>

Inheritance diagram for EMAN::AutoMask2DProcessor:

Collaboration diagram for EMAN::AutoMask2DProcessor:

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.auto2d"

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

Attempts to automatically mask out the particle, excluding other particles in the box, etc.

Parameters

threshold	runs from ~ -2 to 2, negative numbers for dark protein and positive numbers for light protein (stain).
filter	is expressed as a fraction of the fourier radius.

Definition at line 6786 of file processor.h.

Member Function Documentation

get_desc()

virtual string EMAN::AutoMask2DProcessor::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 6815 of file processor.h.

                {
                        return "2D version of mask.auto3d";
                }

get_name()

virtual string EMAN::AutoMask2DProcessor::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 6791 of file processor.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

virtual TypeDict EMAN::AutoMask2DProcessor::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 6801 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, "The number of dilation operations");
                        d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations");
                        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::AutoMask2DProcessor::NEW ( )

inlinestatic

Definition at line 6796 of file processor.h.

                {
                        return new AutoMask2DProcessor();
                }

process_inplace()

void AutoMask2DProcessor::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 6757 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        if (image->get_ndim() != 2) {
                throw ImageDimensionException("This processor only supports 2D 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=params.set_default("radius",0);
        int nmaxseed=params.set_default("nmaxseed",0);
 
        float threshold=0.0;
        if (params.has_key("sigma") || !params.has_key("threshold")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"];
        else threshold=params["threshold"];
 
 
        int nshells = params.set_default("nshells",0);
        int nshellsgauss = params.set_default("nshellsgauss",0);
        int verbose=params.set_default("verbose",0);
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
 
        EMData *amask = new EMData();
        amask->set_size(nx, ny);
 
        float *dat = image->get_data();
        float *dat2 = amask->get_data();
        int i,j;
        size_t l = 0;
 
        if (verbose) printf("%f\t%f\t%f\t%d\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold,nmaxseed);
 
        // Seeds with the highest valued pixels
        if (nmaxseed>0) {
                EMData *peaks=image->process("mask.onlypeaks",Dict("npeaks",0));                // only find true peak values (pixels surrounded by lower values)
                vector<Pixel> maxs=peaks->calc_n_highest_locations(nmaxseed);
                delete peaks;
 
                for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) {
                        if ((*i).x==0 || (*i).y==0 ) continue;          // generally indicates a failed peak search, and regardless we don't really want edges
                        amask->set_value_at((*i).x,(*i).y,0,1.0);
                        if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value);
                }
        }
 
        // Seeds with a circle
        if (radius>0) {
                // start with an initial circle
                l=0;
                for (j = -ny / 2; j < ny / 2; ++j) {
                        for (i = -nx / 2; i < nx / 2; ++i,++l) {
                                if ( abs(j) > radius || abs(i) > radius) continue;
                                if ( (j * j + i * i) > (radius*radius) || dat[l] < threshold) continue;         // torn on the whole threshold issue here. Removing it prevents images from being totally masked out
                                if ( (j * j + i * i) > (radius*radius) ) 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 (j=1; j<ny-1; ++j) {
                        for (i=1; i<nx-1; ++i) {
                                l=i+j*nx;
                                if (dat2[l]) continue;
                                if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) {
                                        dat2[l]=1.0;
                                        done=0;
                                }
                        }
                }
        }
 
        amask->update();
 
        if (verbose) printf("extending mask\n");
        if (nshells>0 || nshellsgauss>0) amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss));
 
        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.
                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 AutoMask2DProcessor::NAME = "mask.auto2d"

static

Definition at line 6820 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