#include <processor.h>
Inheritance diagram for EMAN::FlattenBackgroundProcessor:
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 | |
static Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "filter.flattenbackground" |
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 |
Definition at line 3731 of file processor.h.
string EMAN::FlattenBackgroundProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 3746 of file processor.h.
string EMAN::FlattenBackgroundProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 3736 of file processor.h.
References NAME.
03737 { 03738 return NAME; 03739 }
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.
Reimplemented from EMAN::Processor.
Definition at line 3751 of file processor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and EMAN::TypeDict::put().
03752 { 03753 TypeDict d; 03754 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"); 03755 d.put("radius", EMObject::INT, "The radius of circle/sphere that defines the local neighborhood. Exclusive of the mask argument"); 03756 return d; 03757 }
static Processor* EMAN::FlattenBackgroundProcessor::NEW | ( | ) | [inline, static] |
Definition at line 3741 of file processor.h.
03742 { 03743 return new FlattenBackgroundProcessor(); 03744 }
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.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 2672 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(), EMAN::Processor::params, EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::sub().
02673 { 02674 02675 EMData* mask = params.set_default("mask",(EMData*)0); 02676 int radius = params.set_default("radius",0); 02677 02678 if (radius != 0 && mask != 0) throw InvalidParameterException("Error - the mask and radius parameters are mutually exclusive."); 02679 02680 if (mask == 0 && radius == 0) throw InvalidParameterException("Error - you must specify either the mask or the radius parameter."); 02681 02682 // If the radius isn't 0, then turn the mask into the thing we want... 02683 bool deletemask = false; 02684 if (radius != 0) { 02685 mask = new EMData; 02686 int n = image->get_ndim(); 02687 if (n==1){ 02688 mask->set_size(2*radius+1); 02689 } else if (n==2) { 02690 mask->set_size(2*radius+1,2*radius+1); 02691 } 02692 else /*n==3*/ { 02693 mask->set_size(2*radius+1,2*radius+1,2*radius+1); 02694 } 02695 // assuming default behavior is to make a circle/sphere with using the radius of the mask 02696 mask->process_inplace("testimage.circlesphere"); 02697 } 02698 02699 // Double check that that mask isn't too big 02700 int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize(); 02701 int nx = image->get_xsize(); int ny = image->get_ysize(); int nz = image->get_zsize(); 02702 int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz; 02703 if (nz == 1) nzc = 1; // Sanity check 02704 if (ny == 1) nyc = 1; // Sanity check 02705 02706 if ( mnx > nx || mny > ny || mnz > nz) 02707 throw ImageDimensionException("Can not flatten using a mask that is larger than the image."); 02708 02709 // Get the normalization factor 02710 float normfac = 0.0; 02711 for (int i=0; i<mask->get_xsize()*mask->get_ysize()*mask->get_zsize(); ++i){ 02712 normfac += mask->get_value_at(i); 02713 } 02714 // If the sum is zero the user probably doesn't understand that determining a measure of the mean requires 02715 // strictly positive numbers. The user has specified a mask that consists entirely of zeros, or the mask 02716 // has a mean of zero. 02717 if (normfac == 0) throw InvalidParameterException("Error - the pixels in the mask sum to zero. This breaks the flattening procedure"); 02718 normfac = 1.0f/normfac; 02719 02720 // The mask can now be automatically resized to the dimensions of the image 02721 // bool undoclip = false; 02722 02723 Region r; 02724 if (ny == 1) r = Region((mnx-nxc)/2,nxc); 02725 else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc); 02726 else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc); 02727 mask->clip_inplace(r,0); 02728 // undoclip = true; 02729 // if ( mnx < nx || mny < ny || mnz < nz) { 02730 // Region r((mnx-nx)/2, (mny-ny)/2,(mnz-nz)/2,nx,ny,nz); 02731 // mask->clip_inplace(r); 02732 // undoclip = true; 02733 // } 02734 02735 Region r2; 02736 if (ny == 1) r2 = Region((nx-nxc)/2,nxc); 02737 else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc); 02738 else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc); 02739 image->clip_inplace(r2,image->get_edge_mean()); 02740 // Finally do the convolution 02741 EMData* m = image->convolute(mask); 02742 // Normalize so that m is truly the local mean 02743 m->mult(normfac); 02744 // Before we can subtract, the mean must be phase shifted 02745 m->process_inplace("xform.phaseorigin.tocenter"); 02746 // Subtract the local mean 02747 // image->write_image("a.mrc"); 02748 // m->write_image("b.mrc"); 02749 image->sub(*m); // WE'RE DONE! 02750 delete m; 02751 02752 if (deletemask) { 02753 delete mask; 02754 } else { // I clipped it inplace, so undo this clipping so the user gets back what the put in 02755 Region r; 02756 if (ny == 1) r = Region((nxc-mnx)/2,mnx); 02757 else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny); 02758 else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz); 02759 mask->clip_inplace(r); 02760 } 02761 02762 Region r3; 02763 if (ny == 1) r3 = Region((nxc-nx)/2,nx); 02764 else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny); 02765 else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz); 02766 image->clip_inplace(r3); 02767 // if ( undoclip ) { 02768 // Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz); 02769 // mask->clip_inplace(r); 02770 // } 02771 02772 }
const string FlattenBackgroundProcessor::NAME = "filter.flattenbackground" [static] |