#include <processor.h>
Inheritance diagram for EMAN::AutoMask2DProcessor:
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 TypeDict | get_param_types () const |
Get processor parameter information in a dictionary. | |
virtual string | get_desc () const |
Get the descrition of this specific processor. | |
Static Public Member Functions | |
static Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "mask.auto2d" |
threshold | runs from ~ -2 to 2, negative numbers for dark protein and positive numbers for light protein (stain). | |
filter | is expressed as a fraction of the fourier radius. |
Definition at line 4938 of file processor.h.
virtual string EMAN::AutoMask2DProcessor::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 4967 of file processor.h.
virtual string EMAN::AutoMask2DProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 4943 of file processor.h.
References NAME.
04944 { 04945 return NAME; 04946 }
virtual TypeDict EMAN::AutoMask2DProcessor::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 4953 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
04954 { 04955 TypeDict d; 04956 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 04957 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 04958 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 04959 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 04960 d.put("nshells", EMObject::INT, "The number of dilation operations"); 04961 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 04962 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 04963 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 04964 return d; 04965 }
static Processor* EMAN::AutoMask2DProcessor::NEW | ( | ) | [inline, static] |
void AutoMask2DProcessor::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 5388 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::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().
05389 { 05390 if (!image) { 05391 LOGWARN("NULL Image"); 05392 return; 05393 } 05394 05395 if (image->get_ndim() != 2) { 05396 throw ImageDimensionException("This processor only supports 2D images."); 05397 } 05398 05399 /* 05400 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 05401 To get around this just use the return_mask parameter. 05402 string mask_output = params.set_default("write_mask", ""); 05403 if ( mask_output != "") { 05404 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."); 05405 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 05406 } 05407 */ 05408 05409 int radius=0; 05410 if (params.has_key("radius")) { 05411 radius = params["radius"]; 05412 } 05413 int nmaxseed=0; 05414 if (params.has_key("nmaxseed")) { 05415 nmaxseed = params["nmaxseed"]; 05416 } 05417 05418 float threshold=0.0; 05419 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 05420 else threshold=params["threshold"]; 05421 05422 05423 int nshells = params["nshells"]; 05424 int nshellsgauss = params["nshellsgauss"]; 05425 int verbose=params.set_default("verbose",0); 05426 05427 int nx = image->get_xsize(); 05428 int ny = image->get_ysize(); 05429 05430 EMData *amask = new EMData(); 05431 amask->set_size(nx, ny); 05432 05433 float *dat = image->get_data(); 05434 float *dat2 = amask->get_data(); 05435 int i,j; 05436 size_t l = 0; 05437 05438 if (verbose) printf("%f\t%f\t%f\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold); 05439 05440 // Seeds with the highest valued pixels 05441 if (nmaxseed>0) { 05442 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 05443 05444 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 05445 amask->set_value_at((*i).x,(*i).y,0,1.0); 05446 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 05447 } 05448 } 05449 05450 // Seeds with a circle 05451 if (radius>0) { 05452 // start with an initial circle 05453 l=0; 05454 for (j = -ny / 2; j < ny / 2; ++j) { 05455 for (i = -nx / 2; i < nx / 2; ++i,++l) { 05456 if ( abs(j) > radius || abs(i) > radius) continue; 05457 // if ( (j * j + i * i) > (radius*radius) || dat[l] < threshold) continue; // torn on the whole threshold issue here. Removing it prevents images from being totally masked out 05458 if ( (j * j + i * i) > (radius*radius) ) continue; 05459 dat2[l] = 1.0f; 05460 } 05461 } 05462 } 05463 05464 // iteratively 'flood fills' the map... recursion would be better 05465 int done=0; 05466 int iter=0; 05467 while (!done) { 05468 iter++; 05469 done=1; 05470 if (verbose && iter%10==0) printf("%d iterations\n",iter); 05471 for (j=1; j<ny-1; ++j) { 05472 for (i=1; i<nx-1; ++i) { 05473 l=i+j*nx; 05474 if (dat2[l]) continue; 05475 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) { 05476 dat2[l]=1.0; 05477 done=0; 05478 } 05479 } 05480 } 05481 } 05482 05483 amask->update(); 05484 05485 if (verbose) printf("extending mask\n"); 05486 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 05487 05488 bool return_mask = params.set_default("return_mask",false); 05489 if (return_mask) { 05490 // 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. 05491 memcpy(dat,dat2,image->get_size()*sizeof(float)); 05492 } else { 05493 image->mult(*amask); 05494 } 05495 05496 // EMAN2 policy is not to allow file io from with a processor 05497 //if (mask_output != "") { 05498 // amask->write_image(mask_output); 05499 //} 05500 05501 05502 delete amask; 05503 }
const string AutoMask2DProcessor::NAME = "mask.auto2d" [static] |