#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 4977 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 4992 of file processor.h.
04993 { 04994 return "Tries to mask out only interesting density using something akin to a flood file approach."; 04995 }
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 4982 of file processor.h.
References NAME.
04983 { 04984 return NAME; 04985 }
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 4997 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
04998 { 04999 TypeDict d; 05000 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 05001 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 05002 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 05003 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 05004 d.put("nshells", EMObject::INT, "The number of dilation operations"); 05005 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 05006 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 05007 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 05008 return d; 05009 }
static Processor* EMAN::AutoMask3D2Processor::NEW | ( | ) | [inline, static] |
Definition at line 4987 of file processor.h.
04988 { 04989 return new AutoMask3D2Processor(); 04990 }
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 6376 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().
06377 { 06378 if (!image) { 06379 LOGWARN("NULL Image"); 06380 return; 06381 } 06382 06383 if (image->get_ndim() != 3) { 06384 throw ImageDimensionException("This processor was only ever designed to work on 3D images."); 06385 } 06386 06387 /* 06388 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 06389 To get around this just use the return_mask parameter. 06390 string mask_output = params.set_default("write_mask", ""); 06391 if ( mask_output != "") { 06392 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."); 06393 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 06394 } 06395 */ 06396 06397 int radius=0; 06398 if (params.has_key("radius")) { 06399 radius = params["radius"]; 06400 } 06401 int nmaxseed=0; 06402 if (params.has_key("nmaxseed")) { 06403 nmaxseed = params["nmaxseed"]; 06404 } 06405 06406 float threshold=0.0; 06407 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 06408 else threshold=params["threshold"]; 06409 06410 int nshells = params["nshells"]; 06411 int nshellsgauss = params["nshellsgauss"]; 06412 int verbose=params.set_default("verbose",0); 06413 06414 int nx = image->get_xsize(); 06415 int ny = image->get_ysize(); 06416 int nz = image->get_zsize(); 06417 int nxy=nx*ny; 06418 06419 EMData *amask = new EMData(); 06420 amask->set_size(nx, ny, nz); 06421 06422 float *dat = image->get_data(); 06423 float *dat2 = amask->get_data(); 06424 int i,j,k; 06425 size_t l = 0; 06426 06427 // Seeds with the highest valued pixels 06428 if (nmaxseed>0) { 06429 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 06430 06431 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 06432 amask->set_value_at((*i).x,(*i).y,(*i).z,1.0); 06433 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 06434 } 06435 } 06436 06437 // Seeds with a sphere 06438 if (radius>0) { 06439 // start with an initial sphere 06440 for (k = -nz / 2; k < nz / 2; ++k) { 06441 for (j = -ny / 2; j < ny / 2; ++j) { 06442 for (i = -nx / 2; i < nx / 2; ++i,++l) { 06443 if (abs(k) > radius || abs(j) > radius || abs(i) > radius) continue; 06444 if ( (k * k + j * j + i * i) > (radius*radius) || dat[l] < threshold) continue; 06445 dat2[l] = 1.0f; 06446 } 06447 } 06448 } 06449 } 06450 06451 06452 // iteratively 'flood fills' the map... recursion would be better 06453 int done=0; 06454 int iter=0; 06455 while (!done) { 06456 iter++; 06457 done=1; 06458 if (verbose && iter%10==0) printf("%d iterations\n",iter); 06459 for (k=1; k<nz-1; ++k) { 06460 for (j=1; j<ny-1; ++j) { 06461 for (i=1; i<nx-1; ++i) { 06462 l=i+j*nx+k*nx*ny; 06463 if (dat2[l]) continue; 06464 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx]||dat2[l-nxy]||dat2[l+nxy])) { 06465 dat2[l]=1.0; 06466 done=0; 06467 } 06468 } 06469 } 06470 } 06471 } 06472 06473 amask->update(); 06474 06475 if (verbose) printf("extending mask\n"); 06476 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 06477 06478 bool return_mask = params.set_default("return_mask",false); 06479 if (return_mask) { 06480 // 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. 06481 memcpy(dat,dat2,image->get_size()*sizeof(float)); 06482 } else { 06483 image->mult(*amask); 06484 } 06485 06486 // EMAN2 policy is not to allow file io from with a processor 06487 //if (mask_output != "") { 06488 // amask->write_image(mask_output); 06489 //} 06490 06491 06492 delete amask; 06493 }
const string AutoMask3D2Processor::NAME = "mask.auto3d" [static] |