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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 3655 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 3670 of file processor.h.

03671                         {
03672                                 return "Flattens the background by subtracting the local mean";
03673                         }

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 3660 of file processor.h.

03661                         {
03662                                 return NAME;
03663                         }

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 3675 of file processor.h.

References EMAN::TypeDict::put().

03676                         {
03677                                 TypeDict d;
03678                                 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");
03679                                 d.put("radius", EMObject::INT, "The radius of circle/sphere that defines the local neighborhood. Exclusive of the mask argument");
03680                                 return d;
03681                         }

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

Definition at line 3665 of file processor.h.

03666                         {
03667                                 return new FlattenBackgroundProcessor();
03668                         }

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 2665 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().

02666 {
02667 
02668         EMData* mask = params.set_default("mask",(EMData*)0);
02669         int radius = params.set_default("radius",0);
02670 
02671         if (radius != 0 && mask != 0) throw InvalidParameterException("Error - the mask and radius parameters are mutually exclusive.");
02672 
02673         if (mask == 0 && radius == 0) throw InvalidParameterException("Error - you must specify either the mask or the radius parameter.");
02674 
02675         // If the radius isn't 0, then turn the mask into the thing we want...
02676         bool deletemask = false;
02677         if (radius != 0) {
02678                 mask = new EMData;
02679                 int n = image->get_ndim();
02680                 if (n==1){
02681                         mask->set_size(2*radius+1);
02682                 } else if (n==2) {
02683                         mask->set_size(2*radius+1,2*radius+1);
02684                 }
02685                 else /*n==3*/ {
02686                         mask->set_size(2*radius+1,2*radius+1,2*radius+1);
02687                 }
02688                 // assuming default behavior is to make a circle/sphere with using the radius of the mask
02689                 mask->process_inplace("testimage.circlesphere");
02690         }
02691 
02692         // Double check that that mask isn't too big
02693         int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize();
02694         int nx = image->get_xsize(); int ny = image->get_ysize(); int nz = image->get_zsize();
02695         int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz;
02696         if (nz == 1) nzc = 1; // Sanity check
02697         if (ny == 1) nyc = 1; // Sanity check
02698 
02699         if ( mnx > nx || mny > ny || mnz > nz)
02700                 throw ImageDimensionException("Can not flatten using a mask that is larger than the image.");
02701 
02702         // Get the normalization factor
02703         float normfac = 0.0;
02704         for (int i=0; i<mask->get_xsize()*mask->get_ysize()*mask->get_zsize(); ++i){
02705                 normfac += mask->get_value_at(i);
02706         }
02707         // If the sum is zero the user probably doesn't understand that determining a measure of the mean requires
02708         // strictly positive numbers. The user has specified a mask that consists entirely of zeros, or the mask
02709         // has a mean of zero.
02710         if (normfac == 0) throw InvalidParameterException("Error - the pixels in the mask sum to zero. This breaks the flattening procedure");
02711         normfac = 1.0f/normfac;
02712 
02713         // The mask can now be automatically resized to the dimensions of the image
02714 //      bool undoclip = false;
02715 
02716         Region r;
02717         if (ny == 1) r = Region((mnx-nxc)/2,nxc);
02718         else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc);
02719         else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
02720         mask->clip_inplace(r,0);
02721 //      undoclip = true;
02722 //      if ( mnx < nx || mny < ny || mnz < nz) {
02723 //              Region r((mnx-nx)/2, (mny-ny)/2,(mnz-nz)/2,nx,ny,nz);
02724 //              mask->clip_inplace(r);
02725 //              undoclip = true;
02726 //      }
02727 
02728         Region r2;
02729         if (ny == 1) r2 = Region((nx-nxc)/2,nxc);
02730         else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc);
02731         else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc);
02732         image->clip_inplace(r2,image->get_edge_mean());
02733         // Finally do the convolution
02734         EMData* m = image->convolute(mask);
02735         // Normalize so that m is truly the local mean
02736         m->mult(normfac);
02737         // Before we can subtract, the mean must be phase shifted
02738         m->process_inplace("xform.phaseorigin.tocenter");
02739         // Subtract the local mean
02740 //      image->write_image("a.mrc");
02741 //      m->write_image("b.mrc");
02742         image->sub(*m); // WE'RE DONE!
02743         delete m;
02744 
02745         if (deletemask) {
02746                 delete mask;
02747         } else { // I clipped it inplace, so undo this clipping so the user gets back what the put in
02748                 Region r;
02749                 if (ny == 1) r = Region((nxc-mnx)/2,mnx);
02750                 else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny);
02751                 else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz);
02752                 mask->clip_inplace(r);
02753         }
02754 
02755         Region r3;
02756         if (ny == 1) r3 = Region((nxc-nx)/2,nx);
02757         else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny);
02758         else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz);
02759         image->clip_inplace(r3);
02760 //      if ( undoclip ) {
02761 //              Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz);
02762 //              mask->clip_inplace(r);
02763 //      }
02764 
02765 }


Member Data Documentation

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

Definition at line 136 of file processor.cpp.


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