#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 5017 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 5032 of file processor.h.
05033 { 05034 return "Tries to mask out only interesting density using something akin to a flood file approach."; 05035 }
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 5022 of file processor.h.
References NAME.
05023 { 05024 return NAME; 05025 }
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 5037 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
05038 { 05039 TypeDict d; 05040 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 05041 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 05042 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 05043 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 05044 d.put("nshells", EMObject::INT, "The number of dilation operations"); 05045 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 05046 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 05047 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 05048 return d; 05049 }
static Processor* EMAN::AutoMask3D2Processor::NEW | ( | ) | [inline, static] |
Definition at line 5027 of file processor.h.
05028 { 05029 return new AutoMask3D2Processor(); 05030 }
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 6483 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().
06484 { 06485 if (!image) { 06486 LOGWARN("NULL Image"); 06487 return; 06488 } 06489 06490 if (image->get_ndim() != 3) { 06491 throw ImageDimensionException("This processor was only ever designed to work on 3D images."); 06492 } 06493 06494 /* 06495 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 06496 To get around this just use the return_mask parameter. 06497 string mask_output = params.set_default("write_mask", ""); 06498 if ( mask_output != "") { 06499 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."); 06500 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 06501 } 06502 */ 06503 06504 int radius=0; 06505 if (params.has_key("radius")) { 06506 radius = params["radius"]; 06507 } 06508 int nmaxseed=0; 06509 if (params.has_key("nmaxseed")) { 06510 nmaxseed = params["nmaxseed"]; 06511 } 06512 06513 float threshold=0.0; 06514 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 06515 else threshold=params["threshold"]; 06516 06517 int nshells = params["nshells"]; 06518 int nshellsgauss = params["nshellsgauss"]; 06519 int verbose=params.set_default("verbose",0); 06520 06521 int nx = image->get_xsize(); 06522 int ny = image->get_ysize(); 06523 int nz = image->get_zsize(); 06524 int nxy=nx*ny; 06525 06526 EMData *amask = new EMData(); 06527 amask->set_size(nx, ny, nz); 06528 06529 float *dat = image->get_data(); 06530 float *dat2 = amask->get_data(); 06531 int i,j,k; 06532 size_t l = 0; 06533 06534 // Seeds with the highest valued pixels 06535 if (nmaxseed>0) { 06536 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 06537 06538 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 06539 amask->set_value_at((*i).x,(*i).y,(*i).z,1.0); 06540 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 06541 } 06542 } 06543 06544 // Seeds with a sphere 06545 if (radius>0) { 06546 // start with an initial sphere 06547 for (k = -nz / 2; k < nz / 2; ++k) { 06548 for (j = -ny / 2; j < ny / 2; ++j) { 06549 for (i = -nx / 2; i < nx / 2; ++i,++l) { 06550 if (abs(k) > radius || abs(j) > radius || abs(i) > radius) continue; 06551 if ( (k * k + j * j + i * i) > (radius*radius) || dat[l] < threshold) continue; 06552 dat2[l] = 1.0f; 06553 } 06554 } 06555 } 06556 } 06557 06558 06559 // iteratively 'flood fills' the map... recursion would be better 06560 int done=0; 06561 int iter=0; 06562 while (!done) { 06563 iter++; 06564 done=1; 06565 if (verbose && iter%10==0) printf("%d iterations\n",iter); 06566 for (k=1; k<nz-1; ++k) { 06567 for (j=1; j<ny-1; ++j) { 06568 for (i=1; i<nx-1; ++i) { 06569 l=i+j*nx+k*nx*ny; 06570 if (dat2[l]) continue; 06571 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx]||dat2[l-nxy]||dat2[l+nxy])) { 06572 dat2[l]=1.0; 06573 done=0; 06574 } 06575 } 06576 } 06577 } 06578 } 06579 06580 amask->update(); 06581 06582 if (verbose) printf("extending mask\n"); 06583 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 06584 06585 bool return_mask = params.set_default("return_mask",false); 06586 if (return_mask) { 06587 // 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. 06588 memcpy(dat,dat2,image->get_size()*sizeof(float)); 06589 } else { 06590 image->mult(*amask); 06591 } 06592 06593 // EMAN2 policy is not to allow file io from with a processor 06594 //if (mask_output != "") { 06595 // amask->write_image(mask_output); 06596 //} 06597 06598 06599 delete amask; 06600 }
const string AutoMask3D2Processor::NAME = "mask.auto3d" [static] |