Flattens the background by subtracting the local mean. More...

#include <processor.h>

Inheritance diagram for EMAN::FlattenBackgroundProcessor:

Collaboration diagram for EMAN::FlattenBackgroundProcessor:

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Public Member Functions
void	process_inplace (EMData *image)
	To process an image in-place. More...

string	get_name () const
	Get the processor's name. More...

string	get_desc () const
	Get the descrition of this specific processor. More...

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 = "filter.flattenbackground"

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

Flattens the background by subtracting the local mean.

Parameters

map	an EMData object that defines the extent of the local neighbourhood - will be used for convolution
radius	exclusive of the mask parameter, this defines the radius of a circle/sphere that will be used for local mean subtraction

Author: David Woolford

Date: April 2008

Definition at line 5276 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::FlattenBackgroundProcessor::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 5291 of file processor.h.

                        {
                                return "Flattens the background by subtracting the local mean";
                        }

◆ get_name()

string EMAN::FlattenBackgroundProcessor::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 5281 of file processor.h.

                        {
                                return NAME;
                        }

References NAME.

◆ get_param_types()

TypeDict EMAN::FlattenBackgroundProcessor::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 5296 of file processor.h.

                        {
                                TypeDict d;
                                d.put("mask", EMObject::EMDATA, "A mask the defines the local neighborhood that will be used to find the local mean. Exclusive of the radius argument");
                                d.put("radius", EMObject::INT, "The radius of circle/sphere that defines the local neighborhood. Exclusive of the mask argument");
                                return d;
                        }

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

◆ NEW()

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

inlinestatic

Definition at line 5286 of file processor.h.

                        {
                                return new FlattenBackgroundProcessor();
                        }

◆ process_inplace()

void FlattenBackgroundProcessor::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 3622 of file processor.cpp.

{
 
        EMData* mask = params.set_default("mask",(EMData*)0);
        int radius = params.set_default("radius",0);
 
        if (radius != 0 && mask != 0) throw InvalidParameterException("Error - the mask and radius parameters are mutually exclusive.");
 
        if (mask == 0 && radius == 0) throw InvalidParameterException("Error - you must specify either the mask or the radius parameter.");
 
        // If the radius isn't 0, then turn the mask into the thing we want...
        bool deletemask = false;
        if (radius != 0) {
                mask = new EMData;
                int n = image->get_ndim();
                if (n==1){
                        mask->set_size(2*radius+1);
                } else if (n==2) {
                        mask->set_size(2*radius+1,2*radius+1);
                }
                else /*n==3*/ {
                        mask->set_size(2*radius+1,2*radius+1,2*radius+1);
                }
                // assuming default behavior is to make a circle/sphere with using the radius of the mask
                mask->process_inplace("testimage.circlesphere");
        }
 
        // Double check that that mask isn't too big
        int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize();
        int nx = image->get_xsize(); int ny = image->get_ysize(); int nz = image->get_zsize();
        int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz;
        if (nz == 1) nzc = 1; // Sanity check
        if (ny == 1) nyc = 1; // Sanity check
 
        if ( mnx > nx || mny > ny || mnz > nz)
                throw ImageDimensionException("Can not flatten using a mask that is larger than the image.");
 
        // Get the normalization factor
        float normfac = 0.0;
        for (int i=0; i<mask->get_xsize()*mask->get_ysize()*mask->get_zsize(); ++i){
                normfac += mask->get_value_at(i);
        }
        // If the sum is zero the user probably doesn't understand that determining a measure of the mean requires
        // strictly positive numbers. The user has specified a mask that consists entirely of zeros, or the mask
        // has a mean of zero.
        if (normfac == 0) throw InvalidParameterException("Error - the pixels in the mask sum to zero. This breaks the flattening procedure");
        normfac = 1.0f/normfac;
 
        // The mask can now be automatically resized to the dimensions of the image
//      bool undoclip = false;
 
        Region r;
        if (ny == 1) r = Region((mnx-nxc)/2,nxc);
        else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc);
        else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
        mask->clip_inplace(r,0);
//      undoclip = true;
//      if ( mnx < nx || mny < ny || mnz < nz) {
//              Region r((mnx-nx)/2, (mny-ny)/2,(mnz-nz)/2,nx,ny,nz);
//              mask->clip_inplace(r);
//              undoclip = true;
//      }
 
        Region r2;
        if (ny == 1) r2 = Region((nx-nxc)/2,nxc);
        else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc);
        else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc);
        image->clip_inplace(r2,image->get_edge_mean());
        // Finally do the convolution
        EMData* m = image->convolute(mask);
        // Normalize so that m is truly the local mean
        m->mult(normfac);
        // Before we can subtract, the mean must be phase shifted
        m->process_inplace("xform.phaseorigin.tocenter");
        // Subtract the local mean
//      image->write_image("a.mrc");
//      m->write_image("b.mrc");
        image->sub(*m); // WE'RE DONE!
        delete m;
 
        if (deletemask) {
                delete mask;
        } else { // I clipped it inplace, so undo this clipping so the user gets back what the put in
                Region r;
                if (ny == 1) r = Region((nxc-mnx)/2,mnx);
                else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny);
                else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz);
                mask->clip_inplace(r);
        }
 
        Region r3;
        if (ny == 1) r3 = Region((nxc-nx)/2,nx);
        else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny);
        else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz);
        image->clip_inplace(r3);
//      if ( undoclip ) {
//              Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz);
//              mask->clip_inplace(r);
//      }
 
}

References EMAN::EMData::clip_inplace(), EMAN::EMData::convolute(), ImageDimensionException, InvalidParameterException, EMAN::Processor::params, and EMAN::Dict::set_default().

Member Data Documentation

◆ NAME

const string FlattenBackgroundProcessor::NAME = "filter.flattenbackground"

static

Definition at line 5304 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