#include <processor.h>
Inheritance diagram for EMAN::AutoMask3D2Processor:
Public Member Functions | |
virtual void | process_inplace (EMData *image) |
To process an image in-place. | |
virtual string | get_name () const |
Get the processor's name. | |
virtual string | get_desc () const |
Get the descrition of this specific processor. | |
virtual 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 = "mask.auto3d" |
radius | Pixel radius of a ball which is used to seed the flood filling operation | |
threshold | An isosurface threshold that suitably encases the mass | |
nshells | The number of dilation operations | |
nshellsgauss | number of Gaussian pixels to expand, following the dilation operations If true the result of the operation will produce the mask, not the masked volume |
Definition at line 5056 of file processor.h.
virtual string EMAN::AutoMask3D2Processor::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 5071 of file processor.h.
05072 { 05073 return "Tries to mask out only interesting density using something akin to a flood file approach."; 05074 }
virtual string EMAN::AutoMask3D2Processor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 5061 of file processor.h.
References NAME.
05062 { 05063 return NAME; 05064 }
virtual TypeDict EMAN::AutoMask3D2Processor::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 5076 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
05077 { 05078 TypeDict d; 05079 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 05080 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 05081 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 05082 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 05083 d.put("nshells", EMObject::INT, "The number of dilation operations"); 05084 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 05085 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 05086 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 05087 return d; 05088 }
static Processor* EMAN::AutoMask3D2Processor::NEW | ( | ) | [inline, static] |
Definition at line 5066 of file processor.h.
05067 { 05068 return new AutoMask3D2Processor(); 05069 }
void AutoMask3D2Processor::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 6597 of file processor.cpp.
References abs, EMAN::EMData::calc_n_highest_locations(), EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_ndim(), EMAN::EMData::get_size(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), ImageDimensionException, LOGWARN, EMAN::EMData::mult(), EMAN::Processor::params, EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), EMAN::EMData::set_size(), EMAN::EMData::set_value_at(), and EMAN::EMData::update().
06598 { 06599 if (!image) { 06600 LOGWARN("NULL Image"); 06601 return; 06602 } 06603 06604 if (image->get_ndim() != 3) { 06605 throw ImageDimensionException("This processor was only ever designed to work on 3D images."); 06606 } 06607 06608 /* 06609 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 06610 To get around this just use the return_mask parameter. 06611 string mask_output = params.set_default("write_mask", ""); 06612 if ( mask_output != "") { 06613 if (Util::is_file_exist(mask_output) ) throw InvalidParameterException("The mask output file name already exists. Please remove it if you don't need it."); 06614 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 06615 } 06616 */ 06617 06618 int radius=0; 06619 if (params.has_key("radius")) { 06620 radius = params["radius"]; 06621 } 06622 int nmaxseed=0; 06623 if (params.has_key("nmaxseed")) { 06624 nmaxseed = params["nmaxseed"]; 06625 } 06626 06627 float threshold=0.0; 06628 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 06629 else threshold=params["threshold"]; 06630 06631 int nshells = params["nshells"]; 06632 int nshellsgauss = params["nshellsgauss"]; 06633 int verbose=params.set_default("verbose",0); 06634 06635 int nx = image->get_xsize(); 06636 int ny = image->get_ysize(); 06637 int nz = image->get_zsize(); 06638 int nxy=nx*ny; 06639 06640 EMData *amask = new EMData(); 06641 amask->set_size(nx, ny, nz); 06642 06643 float *dat = image->get_data(); 06644 float *dat2 = amask->get_data(); 06645 int i,j,k; 06646 size_t l = 0; 06647 06648 // Seeds with the highest valued pixels 06649 if (nmaxseed>0) { 06650 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 06651 06652 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 06653 amask->set_value_at((*i).x,(*i).y,(*i).z,1.0); 06654 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 06655 } 06656 } 06657 06658 // Seeds with a sphere 06659 if (radius>0) { 06660 // start with an initial sphere 06661 for (k = -nz / 2; k < nz / 2; ++k) { 06662 for (j = -ny / 2; j < ny / 2; ++j) { 06663 for (i = -nx / 2; i < nx / 2; ++i,++l) { 06664 if (abs(k) > radius || abs(j) > radius || abs(i) > radius) continue; 06665 if ( (k * k + j * j + i * i) > (radius*radius) || dat[l] < threshold) continue; 06666 dat2[l] = 1.0f; 06667 } 06668 } 06669 } 06670 } 06671 06672 06673 // iteratively 'flood fills' the map... recursion would be better 06674 int done=0; 06675 int iter=0; 06676 while (!done) { 06677 iter++; 06678 done=1; 06679 if (verbose && iter%10==0) printf("%d iterations\n",iter); 06680 for (k=1; k<nz-1; ++k) { 06681 for (j=1; j<ny-1; ++j) { 06682 for (i=1; i<nx-1; ++i) { 06683 l=i+j*nx+k*nx*ny; 06684 if (dat2[l]) continue; 06685 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx]||dat2[l-nxy]||dat2[l+nxy])) { 06686 dat2[l]=1.0; 06687 done=0; 06688 } 06689 } 06690 } 06691 } 06692 } 06693 06694 amask->update(); 06695 06696 if (verbose) printf("extending mask\n"); 06697 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 06698 06699 bool return_mask = params.set_default("return_mask",false); 06700 if (return_mask) { 06701 // Yes there is probably a much more efficient way of getting the mask itself, but I am only providing a stop gap at the moment. 06702 memcpy(dat,dat2,image->get_size()*sizeof(float)); 06703 } else { 06704 image->mult(*amask); 06705 } 06706 06707 // EMAN2 policy is not to allow file io from with a processor 06708 //if (mask_output != "") { 06709 // amask->write_image(mask_output); 06710 //} 06711 06712 06713 delete amask; 06714 }
const string AutoMask3D2Processor::NAME = "mask.auto3d" [static] |