#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 4942 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 4957 of file processor.h.
04958 { 04959 return "Tries to mask out only interesting density using something akin to a flood file approach."; 04960 }
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 4947 of file processor.h.
References NAME.
04948 { 04949 return NAME; 04950 }
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 4962 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
04963 { 04964 TypeDict d; 04965 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 04966 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 04967 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 04968 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 04969 d.put("nshells", EMObject::INT, "The number of dilation operations"); 04970 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 04971 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 04972 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 04973 return d; 04974 }
static Processor* EMAN::AutoMask3D2Processor::NEW | ( | ) | [inline, static] |
Definition at line 4952 of file processor.h.
04953 { 04954 return new AutoMask3D2Processor(); 04955 }
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 6411 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().
06412 { 06413 if (!image) { 06414 LOGWARN("NULL Image"); 06415 return; 06416 } 06417 06418 if (image->get_ndim() != 3) { 06419 throw ImageDimensionException("This processor was only ever designed to work on 3D images."); 06420 } 06421 06422 /* 06423 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 06424 To get around this just use the return_mask parameter. 06425 string mask_output = params.set_default("write_mask", ""); 06426 if ( mask_output != "") { 06427 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."); 06428 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 06429 } 06430 */ 06431 06432 int radius=0; 06433 if (params.has_key("radius")) { 06434 radius = params["radius"]; 06435 } 06436 int nmaxseed=0; 06437 if (params.has_key("nmaxseed")) { 06438 nmaxseed = params["nmaxseed"]; 06439 } 06440 06441 float threshold=0.0; 06442 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 06443 else threshold=params["threshold"]; 06444 06445 int nshells = params["nshells"]; 06446 int nshellsgauss = params["nshellsgauss"]; 06447 int verbose=params.set_default("verbose",0); 06448 06449 int nx = image->get_xsize(); 06450 int ny = image->get_ysize(); 06451 int nz = image->get_zsize(); 06452 int nxy=nx*ny; 06453 06454 EMData *amask = new EMData(); 06455 amask->set_size(nx, ny, nz); 06456 06457 float *dat = image->get_data(); 06458 float *dat2 = amask->get_data(); 06459 int i,j,k; 06460 size_t l = 0; 06461 06462 // Seeds with the highest valued pixels 06463 if (nmaxseed>0) { 06464 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 06465 06466 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 06467 amask->set_value_at((*i).x,(*i).y,(*i).z,1.0); 06468 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 06469 } 06470 } 06471 06472 // Seeds with a sphere 06473 if (radius>0) { 06474 // start with an initial sphere 06475 for (k = -nz / 2; k < nz / 2; ++k) { 06476 for (j = -ny / 2; j < ny / 2; ++j) { 06477 for (i = -nx / 2; i < nx / 2; ++i,++l) { 06478 if (abs(k) > radius || abs(j) > radius || abs(i) > radius) continue; 06479 if ( (k * k + j * j + i * i) > (radius*radius) || dat[l] < threshold) continue; 06480 dat2[l] = 1.0f; 06481 } 06482 } 06483 } 06484 } 06485 06486 06487 // iteratively 'flood fills' the map... recursion would be better 06488 int done=0; 06489 int iter=0; 06490 while (!done) { 06491 iter++; 06492 done=1; 06493 if (verbose && iter%10==0) printf("%d iterations\n",iter); 06494 for (k=1; k<nz-1; ++k) { 06495 for (j=1; j<ny-1; ++j) { 06496 for (i=1; i<nx-1; ++i) { 06497 l=i+j*nx+k*nx*ny; 06498 if (dat2[l]) continue; 06499 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx]||dat2[l-nxy]||dat2[l+nxy])) { 06500 dat2[l]=1.0; 06501 done=0; 06502 } 06503 } 06504 } 06505 } 06506 } 06507 06508 amask->update(); 06509 06510 if (verbose) printf("extending mask\n"); 06511 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 06512 06513 bool return_mask = params.set_default("return_mask",false); 06514 if (return_mask) { 06515 // 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. 06516 memcpy(dat,dat2,image->get_size()*sizeof(float)); 06517 } else { 06518 image->mult(*amask); 06519 } 06520 06521 // EMAN2 policy is not to allow file io from with a processor 06522 //if (mask_output != "") { 06523 // amask->write_image(mask_output); 06524 //} 06525 06526 06527 delete amask; 06528 }
const string AutoMask3D2Processor::NAME = "mask.auto3d" [static] |