#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 5011 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 5026 of file processor.h.
05027 { 05028 return "Tries to mask out only interesting density using something akin to a flood file approach."; 05029 }
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 5016 of file processor.h.
References NAME.
05017 { 05018 return NAME; 05019 }
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 5031 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
05032 { 05033 TypeDict d; 05034 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 05035 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 05036 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 05037 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 05038 d.put("nshells", EMObject::INT, "The number of dilation operations"); 05039 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 05040 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 05041 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 05042 return d; 05043 }
static Processor* EMAN::AutoMask3D2Processor::NEW | ( | ) | [inline, static] |
Definition at line 5021 of file processor.h.
05022 { 05023 return new AutoMask3D2Processor(); 05024 }
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 6525 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().
06526 { 06527 if (!image) { 06528 LOGWARN("NULL Image"); 06529 return; 06530 } 06531 06532 if (image->get_ndim() != 3) { 06533 throw ImageDimensionException("This processor was only ever designed to work on 3D images."); 06534 } 06535 06536 /* 06537 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 06538 To get around this just use the return_mask parameter. 06539 string mask_output = params.set_default("write_mask", ""); 06540 if ( mask_output != "") { 06541 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."); 06542 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 06543 } 06544 */ 06545 06546 int radius=0; 06547 if (params.has_key("radius")) { 06548 radius = params["radius"]; 06549 } 06550 int nmaxseed=0; 06551 if (params.has_key("nmaxseed")) { 06552 nmaxseed = params["nmaxseed"]; 06553 } 06554 06555 float threshold=0.0; 06556 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 06557 else threshold=params["threshold"]; 06558 06559 int nshells = params["nshells"]; 06560 int nshellsgauss = params["nshellsgauss"]; 06561 int verbose=params.set_default("verbose",0); 06562 06563 int nx = image->get_xsize(); 06564 int ny = image->get_ysize(); 06565 int nz = image->get_zsize(); 06566 int nxy=nx*ny; 06567 06568 EMData *amask = new EMData(); 06569 amask->set_size(nx, ny, nz); 06570 06571 float *dat = image->get_data(); 06572 float *dat2 = amask->get_data(); 06573 int i,j,k; 06574 size_t l = 0; 06575 06576 // Seeds with the highest valued pixels 06577 if (nmaxseed>0) { 06578 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 06579 06580 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 06581 amask->set_value_at((*i).x,(*i).y,(*i).z,1.0); 06582 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 06583 } 06584 } 06585 06586 // Seeds with a sphere 06587 if (radius>0) { 06588 // start with an initial sphere 06589 for (k = -nz / 2; k < nz / 2; ++k) { 06590 for (j = -ny / 2; j < ny / 2; ++j) { 06591 for (i = -nx / 2; i < nx / 2; ++i,++l) { 06592 if (abs(k) > radius || abs(j) > radius || abs(i) > radius) continue; 06593 if ( (k * k + j * j + i * i) > (radius*radius) || dat[l] < threshold) continue; 06594 dat2[l] = 1.0f; 06595 } 06596 } 06597 } 06598 } 06599 06600 06601 // iteratively 'flood fills' the map... recursion would be better 06602 int done=0; 06603 int iter=0; 06604 while (!done) { 06605 iter++; 06606 done=1; 06607 if (verbose && iter%10==0) printf("%d iterations\n",iter); 06608 for (k=1; k<nz-1; ++k) { 06609 for (j=1; j<ny-1; ++j) { 06610 for (i=1; i<nx-1; ++i) { 06611 l=i+j*nx+k*nx*ny; 06612 if (dat2[l]) continue; 06613 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx]||dat2[l-nxy]||dat2[l+nxy])) { 06614 dat2[l]=1.0; 06615 done=0; 06616 } 06617 } 06618 } 06619 } 06620 } 06621 06622 amask->update(); 06623 06624 if (verbose) printf("extending mask\n"); 06625 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 06626 06627 bool return_mask = params.set_default("return_mask",false); 06628 if (return_mask) { 06629 // 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. 06630 memcpy(dat,dat2,image->get_size()*sizeof(float)); 06631 } else { 06632 image->mult(*amask); 06633 } 06634 06635 // EMAN2 policy is not to allow file io from with a processor 06636 //if (mask_output != "") { 06637 // amask->write_image(mask_output); 06638 //} 06639 06640 06641 delete amask; 06642 }
const string AutoMask3D2Processor::NAME = "mask.auto3d" [static] |