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

#include <processor.h>

Inheritance diagram for EMAN::AutoMask3DProcessor:

Collaboration diagram for EMAN::AutoMask3DProcessor:

[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.auto3d.thresh"

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

threshold1
threshold2

Definition at line 6906 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::AutoMask3DProcessor::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 6933 of file processor.h.

                {
                        return "Tries to mask out only interesting density";
                }

◆ get_name()

virtual string EMAN::AutoMask3DProcessor::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 6911 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::AutoMask3DProcessor::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 6921 of file processor.h.

                {
                        TypeDict d;
                        d.put("threshold1", EMObject::FLOAT, "High initial threshold for seeding.");
                        d.put("threshold2", EMObject::FLOAT, "Lower secondary threshold to define boundary.");
                        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.");
 
                        return d;
                }

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

◆ NEW()

static Processor * EMAN::AutoMask3DProcessor::NEW ( )

inlinestatic

Definition at line 6916 of file processor.h.

                {
                        return new AutoMask3DProcessor();
                }

◆ process_inplace()

void AutoMask3DProcessor::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 8486 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
        
 
        float sig = image->get_attr("sigma");
        float mean = image->get_attr("mean");
 
        float thr1 = params.set_default("threshold1",mean + sig * 2);
        float thr2 = params.set_default("threshold2",mean + sig * 1);
        
        EMData *mask=image->copy();
        mask->process_inplace("threshold.binary",Dict("value",thr1));
        
        EMData *mask2=image->copy();
        mask2->process_inplace("threshold.binary",Dict("value",thr2));
        float maskmean=mask->get_attr("mean");
        for (int i=0; i<1000; i++){
                mask->process_inplace("mask.addshells",Dict("nshells",2));
                mask->mult(*mask2);
                if (float(mask->get_attr("mean"))==maskmean) 
                        break;
                maskmean=mask->get_attr("mean");
//              printf("%d\t%f\n", i, maskmean);
        }
        
        
        // below copied from mask.auto3d
        int nshells = params["nshells"];
        int nshellsgauss = params["nshellsgauss"];
        
        mask->process_inplace("mask.addshells.gauss", Dict("val1", (int)(nshells+nshellsgauss/2),"val2",0));
        if (nshellsgauss>0) 
                mask->process_inplace("filter.lowpass.gauss", Dict("cutoff_abs", (float)(1.0f/(float)nshellsgauss)));
        
        mask->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.
                float *dat = image->get_data();
                float *dat2 = mask->get_data();
                memcpy(dat,dat2,image->get_size()*sizeof(float));
        } else {
                image->mult(*mask);
        }
 
        delete mask;
        delete mask2;
}

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

Member Data Documentation

◆ NAME

const string AutoMask3DProcessor::NAME = "mask.auto3d.thresh"

static

Definition at line 6938 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