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EMAN::FlattenBackgroundProcessor Class Reference

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

#include <processor.h>

Inheritance diagram for EMAN::FlattenBackgroundProcessor:

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Collaboration diagram for EMAN::FlattenBackgroundProcessor:

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List of all members.

Public Member Functions

void process_inplace (EMData *image)
 To process an image in-place.
string get_name () const
 Get the processor's name.
string get_desc () const
 Get the descrition of this specific processor.
TypeDict get_param_types () const
 Get processor parameter information in a dictionary.

Static Public Member Functions

ProcessorNEW ()

Static Public Attributes

const string NAME = "filter.flattenbackground"

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 3733 of file processor.h.


Member Function Documentation

string EMAN::FlattenBackgroundProcessor::get_desc  )  const [inline, virtual]
 

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 3748 of file processor.h.

03749                         {
03750                                 return "Flattens the background by subtracting the local mean";
03751                         }

string EMAN::FlattenBackgroundProcessor::get_name  )  const [inline, virtual]
 

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 3738 of file processor.h.

03739                         {
03740                                 return NAME;
03741                         }

TypeDict EMAN::FlattenBackgroundProcessor::get_param_types  )  const [inline, virtual]
 

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 3753 of file processor.h.

References EMAN::TypeDict::put().

03754                         {
03755                                 TypeDict d;
03756                                 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");
03757                                 d.put("radius", EMObject::INT, "The radius of circle/sphere that defines the local neighborhood. Exclusive of the mask argument");
03758                                 return d;
03759                         }

Processor* EMAN::FlattenBackgroundProcessor::NEW  )  [inline, static]
 

Definition at line 3743 of file processor.h.

03744                         {
03745                                 return new FlattenBackgroundProcessor();
03746                         }

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 2678 of file processor.cpp.

References EMAN::EMData::clip_inplace(), EMAN::EMData::convolute(), EMAN::EMData::get_edge_mean(), EMAN::EMData::get_ndim(), EMAN::EMData::get_value_at(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, InvalidParameterException, EMAN::EMData::mult(), nx, ny, EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::sub().

02679 {
02680 
02681         EMData* mask = params.set_default("mask",(EMData*)0);
02682         int radius = params.set_default("radius",0);
02683 
02684         if (radius != 0 && mask != 0) throw InvalidParameterException("Error - the mask and radius parameters are mutually exclusive.");
02685 
02686         if (mask == 0 && radius == 0) throw InvalidParameterException("Error - you must specify either the mask or the radius parameter.");
02687 
02688         // If the radius isn't 0, then turn the mask into the thing we want...
02689         bool deletemask = false;
02690         if (radius != 0) {
02691                 mask = new EMData;
02692                 int n = image->get_ndim();
02693                 if (n==1){
02694                         mask->set_size(2*radius+1);
02695                 } else if (n==2) {
02696                         mask->set_size(2*radius+1,2*radius+1);
02697                 }
02698                 else /*n==3*/ {
02699                         mask->set_size(2*radius+1,2*radius+1,2*radius+1);
02700                 }
02701                 // assuming default behavior is to make a circle/sphere with using the radius of the mask
02702                 mask->process_inplace("testimage.circlesphere");
02703         }
02704 
02705         // Double check that that mask isn't too big
02706         int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize();
02707         int nx = image->get_xsize(); int ny = image->get_ysize(); int nz = image->get_zsize();
02708         int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz;
02709         if (nz == 1) nzc = 1; // Sanity check
02710         if (ny == 1) nyc = 1; // Sanity check
02711 
02712         if ( mnx > nx || mny > ny || mnz > nz)
02713                 throw ImageDimensionException("Can not flatten using a mask that is larger than the image.");
02714 
02715         // Get the normalization factor
02716         float normfac = 0.0;
02717         for (int i=0; i<mask->get_xsize()*mask->get_ysize()*mask->get_zsize(); ++i){
02718                 normfac += mask->get_value_at(i);
02719         }
02720         // If the sum is zero the user probably doesn't understand that determining a measure of the mean requires
02721         // strictly positive numbers. The user has specified a mask that consists entirely of zeros, or the mask
02722         // has a mean of zero.
02723         if (normfac == 0) throw InvalidParameterException("Error - the pixels in the mask sum to zero. This breaks the flattening procedure");
02724         normfac = 1.0f/normfac;
02725 
02726         // The mask can now be automatically resized to the dimensions of the image
02727 //      bool undoclip = false;
02728 
02729         Region r;
02730         if (ny == 1) r = Region((mnx-nxc)/2,nxc);
02731         else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc);
02732         else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
02733         mask->clip_inplace(r,0);
02734 //      undoclip = true;
02735 //      if ( mnx < nx || mny < ny || mnz < nz) {
02736 //              Region r((mnx-nx)/2, (mny-ny)/2,(mnz-nz)/2,nx,ny,nz);
02737 //              mask->clip_inplace(r);
02738 //              undoclip = true;
02739 //      }
02740 
02741         Region r2;
02742         if (ny == 1) r2 = Region((nx-nxc)/2,nxc);
02743         else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc);
02744         else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc);
02745         image->clip_inplace(r2,image->get_edge_mean());
02746         // Finally do the convolution
02747         EMData* m = image->convolute(mask);
02748         // Normalize so that m is truly the local mean
02749         m->mult(normfac);
02750         // Before we can subtract, the mean must be phase shifted
02751         m->process_inplace("xform.phaseorigin.tocenter");
02752         // Subtract the local mean
02753 //      image->write_image("a.mrc");
02754 //      m->write_image("b.mrc");
02755         image->sub(*m); // WE'RE DONE!
02756         delete m;
02757 
02758         if (deletemask) {
02759                 delete mask;
02760         } else { // I clipped it inplace, so undo this clipping so the user gets back what the put in
02761                 Region r;
02762                 if (ny == 1) r = Region((nxc-mnx)/2,mnx);
02763                 else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny);
02764                 else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz);
02765                 mask->clip_inplace(r);
02766         }
02767 
02768         Region r3;
02769         if (ny == 1) r3 = Region((nxc-nx)/2,nx);
02770         else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny);
02771         else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz);
02772         image->clip_inplace(r3);
02773 //      if ( undoclip ) {
02774 //              Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz);
02775 //              mask->clip_inplace(r);
02776 //      }
02777 
02778 }


Member Data Documentation

const string FlattenBackgroundProcessor::NAME = "filter.flattenbackground" [static]
 

Definition at line 131 of file processor.cpp.


The documentation for this class was generated from the following files:
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