#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 | |
Processor * | NEW () |
Static Public Attributes | |
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 3733 of file processor.h.
|
Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 3748 of file processor.h. 03749 { 03750 return "Flattens the background by subtracting the local mean"; 03751 }
|
|
Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3738 of file processor.h. 03739 {
03740 return NAME;
03741 }
|
|
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 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 }
|
|
Definition at line 3743 of file processor.h. 03744 { 03745 return new FlattenBackgroundProcessor(); 03746 }
|
|
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.
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 }
|
|
Definition at line 131 of file processor.cpp. |