A "dust removal" filter which will remove above threshold densities smaller than a given size. More...

#include <processor.h>

Inheritance diagram for EMAN::AutoMaskDustProcessor:

Collaboration diagram for EMAN::AutoMaskDustProcessor:

[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 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.dust3d"

Protected Attributes
EMData *	mask

EMData *	image

Protected Attributes inherited from EMAN::Processor
Dict	params

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...

Detailed Description

A "dust removal" filter which will remove above threshold densities smaller than a given size.

Parameters

voxels
threshold

Definition at line 6866 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::AutoMaskDustProcessor::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 6890 of file processor.h.

                {
                        return "A dust removal filter which will remove above threshold densities smaller than a given size";
                }

◆ get_name()

virtual string EMAN::AutoMaskDustProcessor::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 6871 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::AutoMaskDustProcessor::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 6881 of file processor.h.

                {
                        TypeDict d;
                        d.put("threshold", EMObject::FLOAT,"Only considers densities above the threshold");
                        d.put("voxels", EMObject::INT,"If a connected mass is smaller than this many voxels it is removed");
                        d.put("verbose", EMObject::INT, "Level of verbosity, 0 default. 1 will print each non-excluded zone");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 6876 of file processor.h.

                {
                        return new AutoMaskDustProcessor();
                }

◆ process_inplace()

void AutoMaskDustProcessor::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 8542 of file processor.cpp.

{
        if (!imagein) {
                LOGWARN("NULL Image");
                return;
        }
        image=imagein;
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        int verbose=params.set_default("verbose",0);
        unsigned int voxels=params.set_default("voxels",27);
        float threshold=params.set_default("threshold",1.5);
 
        mask = new EMData();
        mask->set_size(nx, ny, nz);
        mask->to_one();
 
        for (int zz = 0; zz < nz; zz++) {
                for (int yy = 0; yy < ny; yy++) {
                        for (int xx = 0; xx < nx; xx++) {
                                if (image->get_value_at(xx,yy,zz)>threshold && mask->get_value_at(xx,yy,zz)==1.0) {
                                        vector<Vec3i> pvec;
                                        pvec.push_back(Vec3i(xx,yy,zz));
                                        for (uint i=0; i<pvec.size(); i++) {
                                                // Duplicates will occur the way the algorithm is constructed, so we eliminate them as we encounter them
                                                if (mask->sget_value_at(pvec[i])==0.0f) {
                                                        pvec.erase(pvec.begin()+i);
                                                        i--;
                                                        continue;
                                                }
 
                                                // mask out the points in the volume
                                                mask->set_value_at(pvec[i],0.0f);
 
                                                int x=pvec[i][0];
                                                int y=pvec[i][1];
                                                int z=pvec[i][2];
                                                // Any neighboring values above threshold we haven't already set get added to the list
                                                if (image->sget_value_at(x-1,y,z)>threshold && mask->get_value_at(x-1,y,z)==1.0) pvec.push_back(Vec3i(x-1,y,z));
                                                if (image->sget_value_at(x+1,y,z)>threshold && mask->get_value_at(x+1,y,z)==1.0) pvec.push_back(Vec3i(x+1,y,z));
                                                if (image->sget_value_at(x,y-1,z)>threshold && mask->get_value_at(x,y-1,z)==1.0) pvec.push_back(Vec3i(x,y-1,z));
                                                if (image->sget_value_at(x,y+1,z)>threshold && mask->get_value_at(x,y+1,z)==1.0) pvec.push_back(Vec3i(x,y+1,z));
                                                if (image->sget_value_at(x,y,z-1)>threshold && mask->get_value_at(x,y,z-1)==1.0) pvec.push_back(Vec3i(x,y,z-1));
                                                if (image->sget_value_at(x,y,z+1)>threshold && mask->get_value_at(x,y,z+1)==1.0) pvec.push_back(Vec3i(x,y,z+1));
                                        }
 
                                        // If the blob is too big, then we don't mask it out after all, but we set the value
                                        // to 2.0 so we know the voxels have already been examined, and don't check them again
                                        if (pvec.size()>voxels) {
                                                if (verbose) printf("%d\t%d\t%d\tvoxels: %d\n",xx,yy,zz,(int)pvec.size());
                                                for (uint i=0; i<pvec.size(); i++) mask->set_value_at(pvec[i],2.0);
                                        }
                                }
                        }
                }
        }
 
        mask->process_inplace("threshold.binary",Dict("value",0.5));
 
        // Now we expand the mask by 1 pixel and blur the edge
        mask->mult(-1.0f);
        mask->add(1.0f);
        mask->process_inplace("mask.addshells",Dict("nshells",2));              // expand by 1 shell
        mask->process_inplace("filter.lowpass.gauss",Dict("cutoff_abs",0.25f));
        mask->mult(-1.0f);
        mask->add(1.0f);
        mask->update();
 
        // apply the mask
        image->mult(*mask);
        if (verbose>1) mask->write_image("mask.hdf", 0, EMUtil::IMAGE_HDF);
 
        delete mask;
}

References image, EMAN::EMUtil::IMAGE_HDF, LOGWARN, mask, EMAN::Processor::params, EMAN::Dict::set_default(), x, and y.

Member Data Documentation

◆ image

EMData* EMAN::AutoMaskDustProcessor::image

protected

Definition at line 6899 of file processor.h.

Referenced by process_inplace().

◆ mask

EMData* EMAN::AutoMaskDustProcessor::mask

protected

Definition at line 6898 of file processor.h.

Referenced by process_inplace().

◆ NAME

const string AutoMaskDustProcessor::NAME = "mask.dust3d"

static

Definition at line 6895 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

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process_inplace()

Member Data Documentation

◆ image

◆ mask

◆ NAME