segmentation / netmets

Commit c0c0ea3928e0d5ca02ce7ee3d4c836cca6aa7ca4

Authored by pranathivemuri
1 parent 19809858

writes 7 features to csv file 1st row - feature name, 2nd row-Gt Features, 3rd row- T features

Showing 1 changed file with 44 additions and 11 deletions   Show diff stats
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@@ -8,6 +8,7 @@ @@ -8,6 +8,7 @@
8 8
9 //STIM includes 9 //STIM includes
10 #include <stim/visualization/gl_network.h> 10 #include <stim/visualization/gl_network.h>
  11 +#include <stim/biomodels/network.h>
11 #include <stim/visualization/gl_aaboundingbox.h> 12 #include <stim/visualization/gl_aaboundingbox.h>
12 #include <stim/parser/arguments.h> 13 #include <stim/parser/arguments.h>
13 #include <stim/visualization/camera.h> 14 #include <stim/visualization/camera.h>
@@ -207,6 +208,46 @@ void compare(float sigma){ @@ -207,6 +208,46 @@ void compare(float sigma){
207 std::cout << "FPR: " << FNR << std::endl; 208 std::cout << "FPR: " << FNR << std::endl;
208 } 209 }
209 210
  211 +// writes features of the networks i.e average segment length, tortuosity, branching index, contraction, fractal dimension, number of end and branch points to a csv file
  212 +void features(){
  213 + double avgL_t, avgL_gt, avgT_t, avgT_gt, avgB_t, avgB_gt, avgC_t, avgC_gt, avgFD_t, avgFD_gt;
  214 + unsigned int e_t, e_gt, b_gt, b_t;
  215 + avgL_gt = GT.Lengths();
  216 + avgT_gt = GT.Tortuosities();
  217 + //std::cout<<avgL_gt<<"---average segment length in the ground truth network"<<std::endl;
  218 + //std::cout<<avgT_gt<<"---average segment tortuosity in the ground truth network"<<std::endl;
  219 + avgL_t = T.Lengths();
  220 + avgT_t = T.Tortuosities();
  221 + //std::cout<<avgL_t<<"---average segment length in the truth network"<<std::endl;
  222 + //std::cout<<avgT_t<<"---average segment tortuosity in the truth network"<<std::endl;
  223 + avgB_gt = GT.BranchingIndex();
  224 + //std::cout<<avgB_gt<<"---average branching index in the ground truth"<<std::endl;
  225 + avgB_t = T.BranchingIndex();
  226 + //std::cout<<avgB_t<<"---average branching index in the truth case"<<std::endl;
  227 + avgC_gt = GT.Contractions();
  228 + avgFD_gt = GT.FractalDimensions();
  229 + //std::cout<<avgC_gt<<"---average segment contraction in the ground truth network"<<std::endl;
  230 + //std::cout<<avgFD_gt<<"---average segment fractal dimension in the ground truth network"<<std::endl;
  231 + avgC_t = T.Contractions();
  232 + avgFD_t = T.FractalDimensions();
  233 + //std::cout<<avgC_t<<"---average segment contraction in the truth network"<<std::endl;
  234 + //std::cout<<avgFD_t<<"---average segment fractal dimension in the truth network"<<std::endl;
  235 + e_gt = GT.EndP();
  236 + //std::cout<<e_gt<<"---Number of tips in the ground truth"<<std::endl;
  237 + e_t = T.EndP();
  238 + //std::cout<<e_t<<"---Number of tips in the truth case"<<std::endl;
  239 + b_gt = GT.BranchP();
  240 + //std::cout<<b_gt<<"---Number of branch points in the ground truth"<<std::endl;
  241 + b_t = T.BranchP();
  242 + //std::cout<<b_t<<"---Number of branch points in the truth case"<<std::endl;
  243 + std::ofstream myfile;
  244 + myfile.open ("features.csv");
  245 + myfile << "Length, Tortuosity, Contraction, Fractal Dimension, Branch Points, End points, Branching Index, \n";
  246 + myfile << avgL_gt << "," << avgT_gt << "," << avgC_gt << "," << avgFD_gt << "," << b_gt << "," << e_gt << "," << avgB_gt <<std::endl;
  247 + myfile << avgL_t << "," << avgT_t << "," << avgC_t << "," << avgFD_t << "," << b_t << "," << e_t << "," << avgB_t <<std::endl;
  248 + myfile.close();
  249 +}
  250 +
210 // Output an advertisement for the lab, authors, and usage information 251 // Output an advertisement for the lab, authors, and usage information
211 void advertise(){ 252 void advertise(){
212 std::cout<<std::endl<<std::endl; 253 std::cout<<std::endl<<std::endl;
@@ -243,24 +284,16 @@ int main(int argc, char* argv[]) @@ -243,24 +284,16 @@ int main(int argc, char* argv[])
243 if(args.nargs() >= 1){ //if at least one network file is specified 284 if(args.nargs() >= 1){ //if at least one network file is specified
244 num_nets = 1; //set the number of networks to one 285 num_nets = 1; //set the number of networks to one
245 GT.load_obj(args.arg(0)); //load the specified file as the ground truth 286 GT.load_obj(args.arg(0)); //load the specified file as the ground truth
  287 + /*GT.to_txt("Graph.txt");*/
246 } 288 }
247 289
248 if(args.nargs() == 2){ //if two files are specified, they will be displayed in neighboring viewports and compared 290 if(args.nargs() == 2){ //if two files are specified, they will be displayed in neighboring viewports and compared
249 num_nets = 2; //set the number of networks to two 291 num_nets = 2; //set the number of networks to two
250 float sigma = args["sigma"].as_float(); //get the sigma value from the user 292 float sigma = args["sigma"].as_float(); //get the sigma value from the user
251 - T.load_obj(args.arg(1)); //load the second (test) network  
252 - double avgL, avgT;  
253 - avgL = GT.Lengths();  
254 - avgT = GT.Tortuosities();  
255 - std::cout<<avgL<<"---average segment length in the ground truth network"<<std::endl;  
256 - std::cout<<avgT<<"---average segment tortuosity in the ground truth network"<<std::endl;  
257 - avgL = T.Lengths();  
258 - avgT = T.Tortuosities();  
259 - std::cout<<avgL<<"---average segment length in the truth network"<<std::endl;  
260 - std::cout<<avgT<<"---average segment tortuosity in the truth network"<<std::endl; 293 + T.load_obj(args.arg(1)); //load the second (test) network
  294 + features();
261 GT = GT.resample(resample_rate * sigma); //resample both networks based on the sigma value 295 GT = GT.resample(resample_rate * sigma); //resample both networks based on the sigma value
262 T = T.resample(resample_rate * sigma); 296 T = T.resample(resample_rate * sigma);
263 -  
264 compare(sigma); //run the comparison algorithm 297 compare(sigma); //run the comparison algorithm
265 } 298 }
266 299