#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 3692 of file processor.h.
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 3707 of file processor.h.
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3697 of file processor.h. References NAME. 03698 { 03699 return NAME; 03700 }
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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 3712 of file processor.h. References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and EMAN::TypeDict::put(). 03713 { 03714 TypeDict d; 03715 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"); 03716 d.put("radius", EMObject::INT, "The radius of circle/sphere that defines the local neighborhood. Exclusive of the mask argument"); 03717 return d; 03718 }
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Definition at line 3702 of file processor.h. 03703 { 03704 return new FlattenBackgroundProcessor(); 03705 }
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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 2697 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(), get_xsize(), 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(). 02698 { 02699 02700 EMData* mask = params.set_default("mask",(EMData*)0); 02701 int radius = params.set_default("radius",0); 02702 02703 if (radius != 0 && mask != 0) throw InvalidParameterException("Error - the mask and radius parameters are mutually exclusive."); 02704 02705 if (mask == 0 && radius == 0) throw InvalidParameterException("Error - you must specify either the mask or the radius parameter."); 02706 02707 // If the radius isn't 0, then turn the mask into the thing we want... 02708 bool deletemask = false; 02709 if (radius != 0) { 02710 mask = new EMData; 02711 int n = image->get_ndim(); 02712 if (n==1){ 02713 mask->set_size(2*radius+1); 02714 } else if (n==2) { 02715 mask->set_size(2*radius+1,2*radius+1); 02716 } 02717 else /*n==3*/ { 02718 mask->set_size(2*radius+1,2*radius+1,2*radius+1); 02719 } 02720 // assuming default behavior is to make a circle/sphere with using the radius of the mask 02721 mask->process_inplace("testimage.circlesphere"); 02722 } 02723 02724 // Double check that that mask isn't too big 02725 int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize(); 02726 int nx = image->get_xsize(); int ny = image->get_ysize(); int nz = image->get_zsize(); 02727 int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz; 02728 if (nz == 1) nzc = 1; // Sanity check 02729 if (ny == 1) nyc = 1; // Sanity check 02730 02731 if ( mnx > nx || mny > ny || mnz > nz) 02732 throw ImageDimensionException("Can not flatten using a mask that is larger than the image."); 02733 02734 // Get the normalization factor 02735 float normfac = 0.0; 02736 for (int i=0; i<mask->get_xsize()*mask->get_ysize()*mask->get_zsize(); ++i){ 02737 normfac += mask->get_value_at(i); 02738 } 02739 // If the sum is zero the user probably doesn't understand that determining a measure of the mean requires 02740 // strictly positive numbers. The user has specified a mask that consists entirely of zeros, or the mask 02741 // has a mean of zero. 02742 if (normfac == 0) throw InvalidParameterException("Error - the pixels in the mask sum to zero. This breaks the flattening procedure"); 02743 normfac = 1.0f/normfac; 02744 02745 // The mask can now be automatically resized to the dimensions of the image 02746 // bool undoclip = false; 02747 02748 Region r; 02749 if (ny == 1) r = Region((mnx-nxc)/2,nxc); 02750 else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc); 02751 else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc); 02752 mask->clip_inplace(r,0); 02753 // undoclip = true; 02754 // if ( mnx < nx || mny < ny || mnz < nz) { 02755 // Region r((mnx-nx)/2, (mny-ny)/2,(mnz-nz)/2,nx,ny,nz); 02756 // mask->clip_inplace(r); 02757 // undoclip = true; 02758 // } 02759 02760 Region r2; 02761 if (ny == 1) r2 = Region((nx-nxc)/2,nxc); 02762 else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc); 02763 else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc); 02764 image->clip_inplace(r2,image->get_edge_mean()); 02765 // Finally do the convolution 02766 EMData* m = image->convolute(mask); 02767 // Normalize so that m is truly the local mean 02768 m->mult(normfac); 02769 // Before we can subtract, the mean must be phase shifted 02770 m->process_inplace("xform.phaseorigin.tocenter"); 02771 // Subtract the local mean 02772 // image->write_image("a.mrc"); 02773 // m->write_image("b.mrc"); 02774 image->sub(*m); // WE'RE DONE! 02775 delete m; 02776 02777 if (deletemask) { 02778 delete mask; 02779 } else { // I clipped it inplace, so undo this clipping so the user gets back what the put in 02780 Region r; 02781 if (ny == 1) r = Region((nxc-mnx)/2,mnx); 02782 else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny); 02783 else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz); 02784 mask->clip_inplace(r); 02785 } 02786 02787 Region r3; 02788 if (ny == 1) r3 = Region((nxc-nx)/2,nx); 02789 else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny); 02790 else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz); 02791 image->clip_inplace(r3); 02792 // if ( undoclip ) { 02793 // Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz); 02794 // mask->clip_inplace(r); 02795 // } 02796 02797 }
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Definition at line 3720 of file processor.h. Referenced by get_name(). |