#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 4936 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 4965 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 4941 of file processor.h.
References NAME.
04942 { 04943 return NAME; 04944 }
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 4951 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
04952 { 04953 TypeDict d; 04954 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 04955 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 04956 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 04957 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 04958 d.put("nshells", EMObject::INT, "The number of dilation operations"); 04959 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 04960 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 04961 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 04962 return d; 04963 }
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 5382 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().
05383 { 05384 if (!image) { 05385 LOGWARN("NULL Image"); 05386 return; 05387 } 05388 05389 if (image->get_ndim() != 2) { 05390 throw ImageDimensionException("This processor only supports 2D images."); 05391 } 05392 05393 /* 05394 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 05395 To get around this just use the return_mask parameter. 05396 string mask_output = params.set_default("write_mask", ""); 05397 if ( mask_output != "") { 05398 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."); 05399 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 05400 } 05401 */ 05402 05403 int radius=0; 05404 if (params.has_key("radius")) { 05405 radius = params["radius"]; 05406 } 05407 int nmaxseed=0; 05408 if (params.has_key("nmaxseed")) { 05409 nmaxseed = params["nmaxseed"]; 05410 } 05411 05412 float threshold=0.0; 05413 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 05414 else threshold=params["threshold"]; 05415 05416 05417 int nshells = params["nshells"]; 05418 int nshellsgauss = params["nshellsgauss"]; 05419 int verbose=params.set_default("verbose",0); 05420 05421 int nx = image->get_xsize(); 05422 int ny = image->get_ysize(); 05423 05424 EMData *amask = new EMData(); 05425 amask->set_size(nx, ny); 05426 05427 float *dat = image->get_data(); 05428 float *dat2 = amask->get_data(); 05429 int i,j; 05430 size_t l = 0; 05431 05432 if (verbose) printf("%f\t%f\t%f\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold); 05433 05434 // Seeds with the highest valued pixels 05435 if (nmaxseed>0) { 05436 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 05437 05438 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 05439 amask->set_value_at((*i).x,(*i).y,0,1.0); 05440 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 05441 } 05442 } 05443 05444 // Seeds with a circle 05445 if (radius>0) { 05446 // start with an initial circle 05447 l=0; 05448 for (j = -ny / 2; j < ny / 2; ++j) { 05449 for (i = -nx / 2; i < nx / 2; ++i,++l) { 05450 if ( abs(j) > radius || abs(i) > radius) continue; 05451 // 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 05452 if ( (j * j + i * i) > (radius*radius) ) continue; 05453 dat2[l] = 1.0f; 05454 } 05455 } 05456 } 05457 05458 // iteratively 'flood fills' the map... recursion would be better 05459 int done=0; 05460 int iter=0; 05461 while (!done) { 05462 iter++; 05463 done=1; 05464 if (verbose && iter%10==0) printf("%d iterations\n",iter); 05465 for (j=1; j<ny-1; ++j) { 05466 for (i=1; i<nx-1; ++i) { 05467 l=i+j*nx; 05468 if (dat2[l]) continue; 05469 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) { 05470 dat2[l]=1.0; 05471 done=0; 05472 } 05473 } 05474 } 05475 } 05476 05477 amask->update(); 05478 05479 if (verbose) printf("extending mask\n"); 05480 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 05481 05482 bool return_mask = params.set_default("return_mask",false); 05483 if (return_mask) { 05484 // 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. 05485 memcpy(dat,dat2,image->get_size()*sizeof(float)); 05486 } else { 05487 image->mult(*amask); 05488 } 05489 05490 // EMAN2 policy is not to allow file io from with a processor 05491 //if (mask_output != "") { 05492 // amask->write_image(mask_output); 05493 //} 05494 05495 05496 delete amask; 05497 }
const string AutoMask2DProcessor::NAME = "mask.auto2d" [static] |