#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 4856 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 4885 of file processor.h. 04886 { 04887 return "2D version of mask.auto3d"; 04888 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 4861 of file processor.h. 04862 {
04863 return NAME;
04864 }
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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 4871 of file processor.h. References EMAN::TypeDict::put(). 04872 { 04873 TypeDict d; 04874 d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. "); 04875 d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses."); 04876 d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass."); 04877 d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma"); 04878 d.put("nshells", EMObject::INT, "The number of dilation operations"); 04879 d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations"); 04880 d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume."); 04881 d.put("verbose", EMObject::INT, "How verbose to be (stdout)"); 04882 return d; 04883 }
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Definition at line 4866 of file processor.h. 04867 { 04868 return new AutoMask2DProcessor(); 04869 }
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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 5206 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(). 05207 { 05208 if (!image) { 05209 LOGWARN("NULL Image"); 05210 return; 05211 } 05212 05213 if (image->get_ndim() != 2) { 05214 throw ImageDimensionException("This processor only supports 2D images."); 05215 } 05216 05217 /* 05218 The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor 05219 To get around this just use the return_mask parameter. 05220 string mask_output = params.set_default("write_mask", ""); 05221 if ( mask_output != "") { 05222 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."); 05223 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized"); 05224 } 05225 */ 05226 05227 int radius=0; 05228 if (params.has_key("radius")) { 05229 radius = params["radius"]; 05230 } 05231 int nmaxseed=0; 05232 if (params.has_key("nmaxseed")) { 05233 nmaxseed = params["nmaxseed"]; 05234 } 05235 05236 float threshold=0.0; 05237 if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"]; 05238 else threshold=params["threshold"]; 05239 05240 05241 int nshells = params["nshells"]; 05242 int nshellsgauss = params["nshellsgauss"]; 05243 int verbose=params.set_default("verbose",0); 05244 05245 int nx = image->get_xsize(); 05246 int ny = image->get_ysize(); 05247 05248 EMData *amask = new EMData(); 05249 amask->set_size(nx, ny); 05250 05251 float *dat = image->get_data(); 05252 float *dat2 = amask->get_data(); 05253 int i,j,k; 05254 size_t l = 0; 05255 05256 if (verbose) printf("%f\t%f\t%f\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold); 05257 05258 // Seeds with the highest valued pixels 05259 if (nmaxseed>0) { 05260 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed); 05261 05262 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) { 05263 amask->set_value_at((*i).x,(*i).y,0,1.0); 05264 if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value); 05265 } 05266 } 05267 05268 // Seeds with a circle 05269 if (radius>0) { 05270 // start with an initial circle 05271 l=0; 05272 for (j = -ny / 2; j < ny / 2; ++j) { 05273 for (i = -nx / 2; i < nx / 2; ++i,++l) { 05274 if ( abs(j) > radius || abs(i) > radius) continue; 05275 // 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 05276 if ( (j * j + i * i) > (radius*radius) ) continue; 05277 dat2[l] = 1.0f; 05278 } 05279 } 05280 } 05281 05282 // iteratively 'flood fills' the map... recursion would be better 05283 int done=0; 05284 int iter=0; 05285 while (!done) { 05286 iter++; 05287 done=1; 05288 if (verbose && iter%10==0) printf("%d iterations\n",iter); 05289 for (j=1; j<ny-1; ++j) { 05290 for (i=1; i<nx-1; ++i) { 05291 l=i+j*nx; 05292 if (dat2[l]) continue; 05293 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) { 05294 dat2[l]=1.0; 05295 done=0; 05296 } 05297 } 05298 } 05299 } 05300 05301 amask->update(); 05302 05303 if (verbose) printf("extending mask\n"); 05304 amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss)); 05305 05306 bool return_mask = params.set_default("return_mask",false); 05307 if (return_mask) { 05308 // 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. 05309 memcpy(dat,dat2,image->get_size()*sizeof(float)); 05310 } else { 05311 image->mult(*amask); 05312 } 05313 05314 // EMAN2 policy is not to allow file io from with a processor 05315 //if (mask_output != "") { 05316 // amask->write_image(mask_output); 05317 //} 05318 05319 05320 delete amask; 05321 }
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Definition at line 165 of file processor.cpp. |