#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 4681 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 4710 of file processor.h. 04711 { 04712 return "2D version of mask.auto3d"; 04713 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 4686 of file processor.h. 04687 {
04688 return NAME;
04689 }
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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 4696 of file processor.h. References EMAN::TypeDict::put(). 04697 { 04698 TypeDict d; 04699 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 04700 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 04701 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 04702 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 04703 d.put("nshells", EMObject::INT, "The number of dilation operations"); 04704 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 04705 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 04706 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 04707 return d; 04708 }
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Definition at line 4691 of file processor.h. 04692 { 04693 return new AutoMask2DProcessor(); 04694 }
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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 5205 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(). 05206 { 05207 if (!image) { 05208 LOGWARN("NULL Image"); 05209 return; 05210 } 05211 05212 if (image->get_ndim() != 2) { 05213 throw ImageDimensionException("This processor only supports 2D images."); 05214 } 05215 05216 /* 05217 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 05218 To get around this just use the return_mask parameter. 05219 string mask_output = params.set_default("write_mask", ""); 05220 if ( mask_output != "") { 05221 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."); 05222 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 05223 } 05224 */ 05225 05226 int radius=0; 05227 if (params.has_key("radius")) { 05228 radius = params["radius"]; 05229 } 05230 int nmaxseed=0; 05231 if (params.has_key("nmaxseed")) { 05232 nmaxseed = params["nmaxseed"]; 05233 } 05234 05235 float threshold=0.0; 05236 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 05237 else threshold=params["threshold"]; 05238 05239 05240 int nshells = params["nshells"]; 05241 int nshellsgauss = params["nshellsgauss"]; 05242 int verbose=params.set_default("verbose",0); 05243 05244 int nx = image->get_xsize(); 05245 int ny = image->get_ysize(); 05246 05247 EMData *amask = new EMData(); 05248 amask->set_size(nx, ny); 05249 05250 float *dat = image->get_data(); 05251 float *dat2 = amask->get_data(); 05252 int i,j; 05253 size_t l = 0; 05254 05255 if (verbose) printf("%f\t%f\t%f\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold); 05256 05257 // Seeds with the highest valued pixels 05258 if (nmaxseed>0) { 05259 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 05260 05261 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 05262 amask->set_value_at((*i).x,(*i).y,0,1.0); 05263 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 05264 } 05265 } 05266 05267 // Seeds with a circle 05268 if (radius>0) { 05269 // start with an initial circle 05270 l=0; 05271 for (j = -ny / 2; j < ny / 2; ++j) { 05272 for (i = -nx / 2; i < nx / 2; ++i,++l) { 05273 if ( abs(j) > radius || abs(i) > radius) continue; 05274 // 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 05275 if ( (j * j + i * i) > (radius*radius) ) continue; 05276 dat2[l] = 1.0f; 05277 } 05278 } 05279 } 05280 05281 // iteratively 'flood fills' the map... recursion would be better 05282 int done=0; 05283 int iter=0; 05284 while (!done) { 05285 iter++; 05286 done=1; 05287 if (verbose && iter%10==0) printf("%d iterations\n",iter); 05288 for (j=1; j<ny-1; ++j) { 05289 for (i=1; i<nx-1; ++i) { 05290 l=i+j*nx; 05291 if (dat2[l]) continue; 05292 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) { 05293 dat2[l]=1.0; 05294 done=0; 05295 } 05296 } 05297 } 05298 } 05299 05300 amask->update(); 05301 05302 if (verbose) printf("extending mask\n"); 05303 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 05304 05305 bool return_mask = params.set_default("return_mask",false); 05306 if (return_mask) { 05307 // 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. 05308 memcpy(dat,dat2,image->get_size()*sizeof(float)); 05309 } else { 05310 image->mult(*amask); 05311 } 05312 05313 // EMAN2 policy is not to allow file io from with a processor 05314 //if (mask_output != "") { 05315 // amask->write_image(mask_output); 05316 //} 05317 05318 05319 delete amask; 05320 }
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Definition at line 160 of file processor.cpp. |