#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 | |
Processor * | NEW () |
Static Public Attributes | |
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.
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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. 04966 { 04967 return "2D version of mask.auto3d"; 04968 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 4941 of file processor.h. 04942 {
04943 return NAME;
04944 }
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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::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 }
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Definition at line 4946 of file processor.h. 04947 { 04948 return new AutoMask2DProcessor(); 04949 }
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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.
Implements EMAN::Processor. Definition at line 5386 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(), nx, ny, EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), EMAN::EMData::set_size(), EMAN::EMData::set_value_at(), and EMAN::EMData::update(). 05387 { 05388 if (!image) { 05389 LOGWARN("NULL Image"); 05390 return; 05391 } 05392 05393 if (image->get_ndim() != 2) { 05394 throw ImageDimensionException("This processor only supports 2D images."); 05395 } 05396 05397 /* 05398 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 05399 To get around this just use the return_mask parameter. 05400 string mask_output = params.set_default("write_mask", ""); 05401 if ( mask_output != "") { 05402 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."); 05403 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 05404 } 05405 */ 05406 05407 int radius=0; 05408 if (params.has_key("radius")) { 05409 radius = params["radius"]; 05410 } 05411 int nmaxseed=0; 05412 if (params.has_key("nmaxseed")) { 05413 nmaxseed = params["nmaxseed"]; 05414 } 05415 05416 float threshold=0.0; 05417 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 05418 else threshold=params["threshold"]; 05419 05420 05421 int nshells = params["nshells"]; 05422 int nshellsgauss = params["nshellsgauss"]; 05423 int verbose=params.set_default("verbose",0); 05424 05425 int nx = image->get_xsize(); 05426 int ny = image->get_ysize(); 05427 05428 EMData *amask = new EMData(); 05429 amask->set_size(nx, ny); 05430 05431 float *dat = image->get_data(); 05432 float *dat2 = amask->get_data(); 05433 int i,j; 05434 size_t l = 0; 05435 05436 if (verbose) printf("%f\t%f\t%f\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold); 05437 05438 // Seeds with the highest valued pixels 05439 if (nmaxseed>0) { 05440 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 05441 05442 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 05443 amask->set_value_at((*i).x,(*i).y,0,1.0); 05444 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 05445 } 05446 } 05447 05448 // Seeds with a circle 05449 if (radius>0) { 05450 // start with an initial circle 05451 l=0; 05452 for (j = -ny / 2; j < ny / 2; ++j) { 05453 for (i = -nx / 2; i < nx / 2; ++i,++l) { 05454 if ( abs(j) > radius || abs(i) > radius) continue; 05455 // 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 05456 if ( (j * j + i * i) > (radius*radius) ) continue; 05457 dat2[l] = 1.0f; 05458 } 05459 } 05460 } 05461 05462 // iteratively 'flood fills' the map... recursion would be better 05463 int done=0; 05464 int iter=0; 05465 while (!done) { 05466 iter++; 05467 done=1; 05468 if (verbose && iter%10==0) printf("%d iterations\n",iter); 05469 for (j=1; j<ny-1; ++j) { 05470 for (i=1; i<nx-1; ++i) { 05471 l=i+j*nx; 05472 if (dat2[l]) continue; 05473 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) { 05474 dat2[l]=1.0; 05475 done=0; 05476 } 05477 } 05478 } 05479 } 05480 05481 amask->update(); 05482 05483 if (verbose) printf("extending mask\n"); 05484 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 05485 05486 bool return_mask = params.set_default("return_mask",false); 05487 if (return_mask) { 05488 // 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. 05489 memcpy(dat,dat2,image->get_size()*sizeof(float)); 05490 } else { 05491 image->mult(*amask); 05492 } 05493 05494 // EMAN2 policy is not to allow file io from with a processor 05495 //if (mask_output != "") { 05496 // amask->write_image(mask_output); 05497 //} 05498 05499 05500 delete amask; 05501 }
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Definition at line 166 of file processor.cpp. |