#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 4860 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 4889 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 4865 of file processor.h.
References NAME.
04866 { 04867 return NAME; 04868 }
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 4875 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
04876 { 04877 TypeDict d; 04878 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 04879 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 04880 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 04881 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 04882 d.put("nshells", EMObject::INT, "The number of dilation operations"); 04883 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 04884 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 04885 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 04886 return d; 04887 }
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 5295 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().
05296 { 05297 if (!image) { 05298 LOGWARN("NULL Image"); 05299 return; 05300 } 05301 05302 if (image->get_ndim() != 2) { 05303 throw ImageDimensionException("This processor only supports 2D images."); 05304 } 05305 05306 /* 05307 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 05308 To get around this just use the return_mask parameter. 05309 string mask_output = params.set_default("write_mask", ""); 05310 if ( mask_output != "") { 05311 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."); 05312 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 05313 } 05314 */ 05315 05316 int radius=0; 05317 if (params.has_key("radius")) { 05318 radius = params["radius"]; 05319 } 05320 int nmaxseed=0; 05321 if (params.has_key("nmaxseed")) { 05322 nmaxseed = params["nmaxseed"]; 05323 } 05324 05325 float threshold=0.0; 05326 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 05327 else threshold=params["threshold"]; 05328 05329 05330 int nshells = params["nshells"]; 05331 int nshellsgauss = params["nshellsgauss"]; 05332 int verbose=params.set_default("verbose",0); 05333 05334 int nx = image->get_xsize(); 05335 int ny = image->get_ysize(); 05336 05337 EMData *amask = new EMData(); 05338 amask->set_size(nx, ny); 05339 05340 float *dat = image->get_data(); 05341 float *dat2 = amask->get_data(); 05342 int i,j; 05343 size_t l = 0; 05344 05345 if (verbose) printf("%f\t%f\t%f\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold); 05346 05347 // Seeds with the highest valued pixels 05348 if (nmaxseed>0) { 05349 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 05350 05351 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 05352 amask->set_value_at((*i).x,(*i).y,0,1.0); 05353 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 05354 } 05355 } 05356 05357 // Seeds with a circle 05358 if (radius>0) { 05359 // start with an initial circle 05360 l=0; 05361 for (j = -ny / 2; j < ny / 2; ++j) { 05362 for (i = -nx / 2; i < nx / 2; ++i,++l) { 05363 if ( abs(j) > radius || abs(i) > radius) continue; 05364 // 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 05365 if ( (j * j + i * i) > (radius*radius) ) continue; 05366 dat2[l] = 1.0f; 05367 } 05368 } 05369 } 05370 05371 // iteratively 'flood fills' the map... recursion would be better 05372 int done=0; 05373 int iter=0; 05374 while (!done) { 05375 iter++; 05376 done=1; 05377 if (verbose && iter%10==0) printf("%d iterations\n",iter); 05378 for (j=1; j<ny-1; ++j) { 05379 for (i=1; i<nx-1; ++i) { 05380 l=i+j*nx; 05381 if (dat2[l]) continue; 05382 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) { 05383 dat2[l]=1.0; 05384 done=0; 05385 } 05386 } 05387 } 05388 } 05389 05390 amask->update(); 05391 05392 if (verbose) printf("extending mask\n"); 05393 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 05394 05395 bool return_mask = params.set_default("return_mask",false); 05396 if (return_mask) { 05397 // 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. 05398 memcpy(dat,dat2,image->get_size()*sizeof(float)); 05399 } else { 05400 image->mult(*amask); 05401 } 05402 05403 // EMAN2 policy is not to allow file io from with a processor 05404 //if (mask_output != "") { 05405 // amask->write_image(mask_output); 05406 //} 05407 05408 05409 delete amask; 05410 }
const string AutoMask2DProcessor::NAME = "mask.auto2d" [static] |