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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 3686 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 3701 of file processor.h.

03702                         {
03703                                 return "Flattens the background by subtracting the local mean";
03704                         }

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 3691 of file processor.h.

03692                         {
03693                                 return NAME;
03694                         }

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 3706 of file processor.h.

References EMAN::TypeDict::put().

03707                         {
03708                                 TypeDict d;
03709                                 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");
03710                                 d.put("radius", EMObject::INT, "The radius of circle/sphere that defines the local neighborhood. Exclusive of the mask argument");
03711                                 return d;
03712                         }

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

Definition at line 3696 of file processor.h.

03697                         {
03698                                 return new FlattenBackgroundProcessor();
03699                         }

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 2600 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().

02601 {
02602 
02603         EMData* mask = params.set_default("mask",(EMData*)0);
02604         int radius = params.set_default("radius",0);
02605 
02606         if (radius != 0 && mask != 0) throw InvalidParameterException("Error - the mask and radius parameters are mutually exclusive.");
02607 
02608         if (mask == 0 && radius == 0) throw InvalidParameterException("Error - you must specify either the mask or the radius parameter.");
02609 
02610         // If the radius isn't 0, then turn the mask into the thing we want...
02611         bool deletemask = false;
02612         if (radius != 0) {
02613                 mask = new EMData;
02614                 int n = image->get_ndim();
02615                 if (n==1){
02616                         mask->set_size(2*radius+1);
02617                 } else if (n==2) {
02618                         mask->set_size(2*radius+1,2*radius+1);
02619                 }
02620                 else /*n==3*/ {
02621                         mask->set_size(2*radius+1,2*radius+1,2*radius+1);
02622                 }
02623                 // assuming default behavior is to make a circle/sphere with using the radius of the mask
02624                 mask->process_inplace("testimage.circlesphere");
02625         }
02626 
02627         // Double check that that mask isn't too big
02628         int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize();
02629         int nx = image->get_xsize(); int ny = image->get_ysize(); int nz = image->get_zsize();
02630         int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz;
02631         if (nz == 1) nzc = 1; // Sanity check
02632         if (ny == 1) nyc = 1; // Sanity check
02633 
02634         if ( mnx > nx || mny > ny || mnz > nz)
02635                 throw ImageDimensionException("Can not flatten using a mask that is larger than the image.");
02636 
02637         // Get the normalization factor
02638         float normfac = 0.0;
02639         for (int i=0; i<mask->get_xsize()*mask->get_ysize()*mask->get_zsize(); ++i){
02640                 normfac += mask->get_value_at(i);
02641         }
02642         // If the sum is zero the user probably doesn't understand that determining a measure of the mean requires
02643         // strictly positive numbers. The user has specified a mask that consists entirely of zeros, or the mask
02644         // has a mean of zero.
02645         if (normfac == 0) throw InvalidParameterException("Error - the pixels in the mask sum to zero. This breaks the flattening procedure");
02646         normfac = 1.0f/normfac;
02647 
02648         // The mask can now be automatically resized to the dimensions of the image
02649 //      bool undoclip = false;
02650 
02651         Region r;
02652         if (ny == 1) r = Region((mnx-nxc)/2,nxc);
02653         else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc);
02654         else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
02655         mask->clip_inplace(r,0);
02656 //      undoclip = true;
02657 //      if ( mnx < nx || mny < ny || mnz < nz) {
02658 //              Region r((mnx-nx)/2, (mny-ny)/2,(mnz-nz)/2,nx,ny,nz);
02659 //              mask->clip_inplace(r);
02660 //              undoclip = true;
02661 //      }
02662 
02663         Region r2;
02664         if (ny == 1) r2 = Region((nx-nxc)/2,nxc);
02665         else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc);
02666         else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc);
02667         image->clip_inplace(r2,image->get_edge_mean());
02668         // Finally do the convolution
02669         EMData* m = image->convolute(mask);
02670         // Normalize so that m is truly the local mean
02671         m->mult(normfac);
02672         // Before we can subtract, the mean must be phase shifted
02673         m->process_inplace("xform.phaseorigin.tocenter");
02674         // Subtract the local mean
02675 //      image->write_image("a.mrc");
02676 //      m->write_image("b.mrc");
02677         image->sub(*m); // WE'RE DONE!
02678         delete m;
02679 
02680         if (deletemask) {
02681                 delete mask;
02682         } else { // I clipped it inplace, so undo this clipping so the user gets back what the put in
02683                 Region r;
02684                 if (ny == 1) r = Region((nxc-mnx)/2,mnx);
02685                 else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny);
02686                 else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz);
02687                 mask->clip_inplace(r);
02688         }
02689 
02690         Region r3;
02691         if (ny == 1) r3 = Region((nxc-nx)/2,nx);
02692         else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny);
02693         else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz);
02694         image->clip_inplace(r3);
02695 //      if ( undoclip ) {
02696 //              Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz);
02697 //              mask->clip_inplace(r);
02698 //      }
02699 
02700 }


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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