New ComputeOptimalThreshold

[clitk.git] / segmentation / clitkExtractLymphStationsGenericFilter.txx

diff --git a/segmentation/clitkExtractLymphStationsGenericFilter.txx b/segmentation/clitkExtractLymphStationsGenericFilter.txx
index 47dad7d904008429d12b91031934652c80fe0014..a8c3ec1dd73ce3120c85cf342c0ec78a155eadb4 100644 (file)
--- a/segmentation/clitkExtractLymphStationsGenericFilter.txx
+++ b/segmentation/clitkExtractLymphStationsGenericFilter.txx
@@ -68,6 +68,7 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
   f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
   f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
   f->SetAFDBFilename(mArgsInfo.afdb_arg);  
+  f->SetAFDBPath(mArgsInfo.afdb_path_arg);  
 
   f->SetComputeStationsSupportsFlag(!mArgsInfo.nosupport_flag);
 
@@ -114,11 +115,6 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
     f->AddComputeStation(mArgsInfo.station_arg[i]);
 
   // Station 3A
-  f->SetFuzzyThreshold("3A", "SVC", mArgsInfo.S3A_ft_SVC_arg);
-  f->SetFuzzyThreshold("3A", "Bones", mArgsInfo.S3A_ft_Bones_arg);
-  f->SetThreshold("3A", "Bones", mArgsInfo.S3A_t_Bones_arg);
-  f->SetFuzzyThreshold("3A", "Aorta", mArgsInfo.S3A_ft_Aorta_arg);
-  f->SetFuzzyThreshold("3A", "SubclavianArtery", mArgsInfo.S3A_ft_SubclavianArtery_arg);
   
   // Station 7
   f->SetFuzzyThreshold("7", "Bronchi", mArgsInfo.S7_ft_Bronchi_arg);
@@ -130,12 +126,12 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
   f->SetS7_UseMostInferiorPartOnlyFlag(mArgsInfo.S7_UseMostInferiorPartOnly_flag);
 
   // Station 2RL
-  f->SetFuzzyThreshold("2RL", "CommonCarotidArtery", mArgsInfo.S2RL_ft_CommonCarotidArtery_arg);
-  f->SetFuzzyThreshold("2RL", "BrachioCephalicTrunk", mArgsInfo.S2RL_ft_BrachioCephalicTrunk_arg);
-  f->SetFuzzyThreshold("2RL", "BrachioCephalicVein", mArgsInfo.S2RL_ft_BrachioCephalicVein_arg);
-  f->SetFuzzyThreshold("2RL", "Aorta", mArgsInfo.S2RL_ft_Aorta_arg);
-  f->SetFuzzyThreshold("2RL", "SubclavianArteryLeft", mArgsInfo.S2RL_ft_SubclavianArteryLeft_arg);
-  f->SetFuzzyThreshold("2RL", "SubclavianArteryRight", mArgsInfo.S2RL_ft_SubclavianArteryRight_arg);
+
+  // Station 1RL
+
+  // Set RelativePositionList filenames
+  for(uint i=0; i<mArgsInfo.relpos_given; i++) 
+    f->AddRelativePositionListFilename(mArgsInfo.relpos_arg[i]);
 }
 //--------------------------------------------------------------------