#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 3476 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 3491 of file processor.h. 03492 { 03493 return "Flattens the background by subtracting the local mean"; 03494 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3481 of file processor.h. 03482 {
03483 return NAME;
03484 }
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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 3496 of file processor.h. References EMAN::TypeDict::put(). 03497 { 03498 TypeDict d; 03499 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"); 03500 d.put("radius", EMObject::INT, "The radius of circle/sphere that defines the local neighborhood. Exclusive of the mask argument"); 03501 return d; 03502 }
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Definition at line 3486 of file processor.h. 03487 { 03488 return new FlattenBackgroundProcessor(); 03489 }
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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 2545 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(). 02546 { 02547 02548 EMData* mask = params.set_default("mask",(EMData*)0); 02549 int radius = params.set_default("radius",0); 02550 02551 if (radius != 0 && mask != 0) throw InvalidParameterException("Error - the mask and radius parameters are mutually exclusive."); 02552 02553 if (mask == 0 && radius == 0) throw InvalidParameterException("Error - you must specify either the mask or the radius parameter."); 02554 02555 // If the radius isn't 0, then turn the mask into the thing we want... 02556 bool deletemask = false; 02557 if (radius != 0) { 02558 mask = new EMData; 02559 int n = image->get_ndim(); 02560 if (n==1){ 02561 mask->set_size(2*radius+1); 02562 } else if (n==2) { 02563 mask->set_size(2*radius+1,2*radius+1); 02564 } 02565 else /*n==3*/ { 02566 mask->set_size(2*radius+1,2*radius+1,2*radius+1); 02567 } 02568 // assuming default behavior is to make a circle/sphere with using the radius of the mask 02569 mask->process_inplace("testimage.circlesphere"); 02570 } 02571 02572 // Double check that that mask isn't too big 02573 int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize(); 02574 int nx = image->get_xsize(); int ny = image->get_ysize(); int nz = image->get_zsize(); 02575 int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz; 02576 if (nz == 1) nzc = 1; // Sanity check 02577 if (ny == 1) nyc = 1; // Sanity check 02578 02579 if ( mnx > nx || mny > ny || mnz > nz) 02580 throw ImageDimensionException("Can not flatten using a mask that is larger than the image."); 02581 02582 // Get the normalization factor 02583 float normfac = 0.0; 02584 for (int i=0; i<mask->get_xsize()*mask->get_ysize()*mask->get_zsize(); ++i){ 02585 normfac += mask->get_value_at(i); 02586 } 02587 // If the sum is zero the user probably doesn't understand that determining a measure of the mean requires 02588 // strictly positive numbers. The user has specified a mask that consists entirely of zeros, or the mask 02589 // has a mean of zero. 02590 if (normfac == 0) throw InvalidParameterException("Error - the pixels in the mask sum to zero. This breaks the flattening procedure"); 02591 normfac = 1.0f/normfac; 02592 02593 // The mask can now be automatically resized to the dimensions of the image 02594 // bool undoclip = false; 02595 02596 Region r; 02597 if (ny == 1) r = Region((mnx-nxc)/2,nxc); 02598 else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc); 02599 else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc); 02600 mask->clip_inplace(r,0); 02601 // undoclip = true; 02602 // if ( mnx < nx || mny < ny || mnz < nz) { 02603 // Region r((mnx-nx)/2, (mny-ny)/2,(mnz-nz)/2,nx,ny,nz); 02604 // mask->clip_inplace(r); 02605 // undoclip = true; 02606 // } 02607 02608 Region r2; 02609 if (ny == 1) r2 = Region((nx-nxc)/2,nxc); 02610 else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc); 02611 else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc); 02612 image->clip_inplace(r2,image->get_edge_mean()); 02613 // Finally do the convolution 02614 EMData* m = image->convolute(mask); 02615 // Normalize so that m is truly the local mean 02616 m->mult(normfac); 02617 // Before we can subtract, the mean must be phase shifted 02618 m->process_inplace("xform.phaseorigin.tocenter"); 02619 // Subtract the local mean 02620 // image->write_image("a.mrc"); 02621 // m->write_image("b.mrc"); 02622 image->sub(*m); // WE'RE DONE! 02623 delete m; 02624 02625 if (deletemask) { 02626 delete mask; 02627 } else { // I clipped it inplace, so undo this clipping so the user gets back what the put in 02628 Region r; 02629 if (ny == 1) r = Region((nxc-mnx)/2,mnx); 02630 else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny); 02631 else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz); 02632 mask->clip_inplace(r); 02633 } 02634 02635 Region r3; 02636 if (ny == 1) r3 = Region((nxc-nx)/2,nx); 02637 else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny); 02638 else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz); 02639 image->clip_inplace(r3); 02640 // if ( undoclip ) { 02641 // Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz); 02642 // mask->clip_inplace(r); 02643 // } 02644 02645 }
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Definition at line 125 of file processor.cpp. |