#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 4886 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 4901 of file processor.h.
04902 { 04903 return "Tries to mask out only interesting density using something akin to a flood file approach."; 04904 }
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 4891 of file processor.h.
References NAME.
04892 { 04893 return NAME; 04894 }
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 4906 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
04907 { 04908 TypeDict d; 04909 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 04910 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 04911 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 04912 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 04913 d.put("nshells", EMObject::INT, "The number of dilation operations"); 04914 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 04915 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 04916 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 04917 return d; 04918 }
static Processor* EMAN::AutoMask3D2Processor::NEW | ( | ) | [inline, static] |
Definition at line 4896 of file processor.h.
04897 { 04898 return new AutoMask3D2Processor(); 04899 }
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 6409 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().
06410 { 06411 if (!image) { 06412 LOGWARN("NULL Image"); 06413 return; 06414 } 06415 06416 if (image->get_ndim() != 3) { 06417 throw ImageDimensionException("This processor was only ever designed to work on 3D images."); 06418 } 06419 06420 /* 06421 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 06422 To get around this just use the return_mask parameter. 06423 string mask_output = params.set_default("write_mask", ""); 06424 if ( mask_output != "") { 06425 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."); 06426 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 06427 } 06428 */ 06429 06430 int radius=0; 06431 if (params.has_key("radius")) { 06432 radius = params["radius"]; 06433 } 06434 int nmaxseed=0; 06435 if (params.has_key("nmaxseed")) { 06436 nmaxseed = params["nmaxseed"]; 06437 } 06438 06439 float threshold=0.0; 06440 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 06441 else threshold=params["threshold"]; 06442 06443 int nshells = params["nshells"]; 06444 int nshellsgauss = params["nshellsgauss"]; 06445 int verbose=params.set_default("verbose",0); 06446 06447 int nx = image->get_xsize(); 06448 int ny = image->get_ysize(); 06449 int nz = image->get_zsize(); 06450 int nxy=nx*ny; 06451 06452 EMData *amask = new EMData(); 06453 amask->set_size(nx, ny, nz); 06454 06455 float *dat = image->get_data(); 06456 float *dat2 = amask->get_data(); 06457 int i,j,k; 06458 size_t l = 0; 06459 06460 // Seeds with the highest valued pixels 06461 if (nmaxseed>0) { 06462 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 06463 06464 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 06465 amask->set_value_at((*i).x,(*i).y,(*i).z,1.0); 06466 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 06467 } 06468 } 06469 06470 // Seeds with a sphere 06471 if (radius>0) { 06472 // start with an initial sphere 06473 for (k = -nz / 2; k < nz / 2; ++k) { 06474 for (j = -ny / 2; j < ny / 2; ++j) { 06475 for (i = -nx / 2; i < nx / 2; ++i,++l) { 06476 if (abs(k) > radius || abs(j) > radius || abs(i) > radius) continue; 06477 if ( (k * k + j * j + i * i) > (radius*radius) || dat[l] < threshold) continue; 06478 dat2[l] = 1.0f; 06479 } 06480 } 06481 } 06482 } 06483 06484 06485 // iteratively 'flood fills' the map... recursion would be better 06486 int done=0; 06487 int iter=0; 06488 while (!done) { 06489 iter++; 06490 done=1; 06491 if (verbose && iter%10==0) printf("%d iterations\n",iter); 06492 for (k=1; k<nz-1; ++k) { 06493 for (j=1; j<ny-1; ++j) { 06494 for (i=1; i<nx-1; ++i) { 06495 l=i+j*nx+k*nx*ny; 06496 if (dat2[l]) continue; 06497 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx]||dat2[l-nxy]||dat2[l+nxy])) { 06498 dat2[l]=1.0; 06499 done=0; 06500 } 06501 } 06502 } 06503 } 06504 } 06505 06506 amask->update(); 06507 06508 if (verbose) printf("extending mask\n"); 06509 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 06510 06511 bool return_mask = params.set_default("return_mask",false); 06512 if (return_mask) { 06513 // 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. 06514 memcpy(dat,dat2,image->get_size()*sizeof(float)); 06515 } else { 06516 image->mult(*amask); 06517 } 06518 06519 // EMAN2 policy is not to allow file io from with a processor 06520 //if (mask_output != "") { 06521 // amask->write_image(mask_output); 06522 //} 06523 06524 06525 delete amask; 06526 }
const string AutoMask3D2Processor::NAME = "mask.auto3d" [static] |