#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 3655 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 3670 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 3660 of file processor.h.
References NAME.
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.
Reimplemented from EMAN::Processor.
Definition at line 3675 of file processor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and 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 }
static 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.
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(), EMAN::Processor::params, 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 }
const string FlattenBackgroundProcessor::NAME = "filter.flattenbackground" [static] |