X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsGenericFilter.txx;h=a27b4a629e41e2893b95513646ef599f5a790485;hb=dd3badf7621c63f24a8dcfb831af3dcaf41fbe6c;hp=ffa6c3c87e6a668373182b87b629a3a47040fd75;hpb=a360b70353c02d20482d950c96ba7b289deca184;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsGenericFilter.txx b/segmentation/clitkExtractLymphStationsGenericFilter.txx
index ffa6c3c..a27b4a6 100644
--- a/segmentation/clitkExtractLymphStationsGenericFilter.txx
+++ b/segmentation/clitkExtractLymphStationsGenericFilter.txx
@@ -68,11 +68,15 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
   f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
   f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
   f->SetAFDBFilename(mArgsInfo.afdb_arg);  
+  if (mArgsInfo.afdb_path_given) f->SetAFDBPath(mArgsInfo.afdb_path_arg);  
+  f->SetForceSupportsFlag(mArgsInfo.force_support_flag);
+  f->SetSupportLimitsFilename(mArgsInfo.support_limits_arg);
+  f->SetCheckSupportFlag(mArgsInfo.check_support_limits_flag);
 
   // Station 8
-  f->SetDistanceMaxToAnteriorPartOfTheSpine(mArgsInfo.maxAntSpine_arg);
-  f->SetFuzzyThreshold("8", "Esophagus", mArgsInfo.tS8_Esophagus_arg);
-  f->SetInjectedThresholdForS8(mArgsInfo.injectedThresholdForS8_arg);
+  //f->SetDistanceMaxToAnteriorPartOfTheSpine(mArgsInfo.S8_maxAntSpine_arg);
+  f->SetFuzzyThreshold("8", "Esophagus", mArgsInfo.S8_ft_Esophagus_arg);
+  //  f->SetInjectedThresholdForS8(mArgsInfo.tS8_injectedThreshold_arg);
 
   // Check multiple options for radius dilatation
   /*
@@ -83,27 +87,27 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
    */
   typename FilterType::MaskImagePointType p;
   p[0] = 7; p[1] = 5; p[2] = 0; // default value
-  if (mArgsInfo.esophagusDilatationForAnt_given == 3) {
+  if (mArgsInfo.S8_esophagusDilatationForAnt_given == 3) {
     for(uint i=0; i<3; i++)
-      p[i] = mArgsInfo.esophagusDilatationForAnt_arg[i];
+      p[i] = mArgsInfo.S8_esophagusDilatationForAnt_arg[i];
   }
   else {
-    if (mArgsInfo.esophagusDilatationForAnt_given == 1) {
+    if (mArgsInfo.S8_esophagusDilatationForAnt_given == 1) {
       for(uint i=0; i<3; i++)
-        p[i] = mArgsInfo.esophagusDilatationForAnt_arg[0];
+        p[i] = mArgsInfo.S8_esophagusDilatationForAnt_arg[0];
     }
   }
   f->SetEsophagusDiltationForAnt(p);
   
   p[0] = 5; p[1] = 10; p[2] = 1; // default value
-  if (mArgsInfo.esophagusDilatationForRight_given == 3) {
+  if (mArgsInfo.S8_esophagusDilatationForRight_given == 3) {
     for(uint i=0; i<3; i++)
-      p[i] = mArgsInfo.esophagusDilatationForRight_arg[i];
+      p[i] = mArgsInfo.S8_esophagusDilatationForRight_arg[i];
   }
   else {
-    if (mArgsInfo.esophagusDilatationForRight_given == 1) {
+    if (mArgsInfo.S8_esophagusDilatationForRight_given == 1) {
       for(uint i=0; i<3; i++)
-        p[i] = mArgsInfo.esophagusDilatationForRight_arg[0];
+        p[i] = mArgsInfo.S8_esophagusDilatationForRight_arg[0];
     }
   }
   f->SetEsophagusDiltationForRight(p);  
@@ -111,25 +115,24 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
   for(uint i=0; i<mArgsInfo.station_given; i++)
     f->AddComputeStation(mArgsInfo.station_arg[i]);
 
-  // Station 7
-  f->SetFuzzyThreshold("7", "Bronchi", mArgsInfo.tS7_Bronchi_arg);
-  f->SetFuzzyThreshold("7", "LeftSuperiorPulmonaryVein", mArgsInfo.tS7_LeftSuperiorPulmonaryVein_arg);
-  f->SetFuzzyThreshold("7", "RightSuperiorPulmonaryVein", mArgsInfo.tS7_RightSuperiorPulmonaryVein_arg);
-  f->SetFuzzyThreshold("7", "RightPulmonaryArtery", mArgsInfo.tS7_RightPulmonaryArtery_arg);
-  f->SetFuzzyThreshold("7", "LeftPulmonaryArtery", mArgsInfo.tS7_LeftPulmonaryArtery_arg);
-  f->SetFuzzyThreshold("7", "SVC", mArgsInfo.tS7_SVC_arg);
-
   // Station 3A
-  f->SetFuzzyThreshold("3A", "Sternum", mArgsInfo.tS3A_Sternum_arg);
-  f->SetFuzzyThreshold("3A", "SubclavianArtery", mArgsInfo.tS3A_SubclavianArtery_arg);
   
+  // Station 7
+  f->SetFuzzyThreshold("7", "Bronchi", mArgsInfo.S7_ft_Bronchi_arg);
+  f->SetFuzzyThreshold("7", "LeftSuperiorPulmonaryVein", mArgsInfo.S7_ft_LeftSuperiorPulmonaryVein_arg);
+  f->SetFuzzyThreshold("7", "RightSuperiorPulmonaryVein", mArgsInfo.S7_ft_RightSuperiorPulmonaryVein_arg);
+  f->SetFuzzyThreshold("7", "RightPulmonaryArtery", mArgsInfo.S7_ft_RightPulmonaryArtery_arg);
+  f->SetFuzzyThreshold("7", "LeftPulmonaryArtery", mArgsInfo.S7_ft_LeftPulmonaryArtery_arg);
+  f->SetFuzzyThreshold("7", "SVC", mArgsInfo.S7_ft_SVC_arg);
+  f->SetS7_UseMostInferiorPartOnlyFlag(mArgsInfo.S7_UseMostInferiorPartOnly_flag);
+
   // Station 2RL
-  f->SetFuzzyThreshold("2RL", "CommonCarotidArtery", mArgsInfo.tS2RL_CommonCarotidArtery_arg);
-  f->SetFuzzyThreshold("2RL", "BrachioCephalicTrunk", mArgsInfo.tS2RL_BrachioCephalicTrunk_arg);
-  f->SetFuzzyThreshold("2RL", "BrachioCephalicVein", mArgsInfo.tS2RL_BrachioCephalicVein_arg);
-  f->SetFuzzyThreshold("2RL", "Aorta", mArgsInfo.tS2RL_Aorta_arg);
-  f->SetFuzzyThreshold("2RL", "SubclavianArteryLeft", mArgsInfo.tS2RL_SubclavianArteryLeft_arg);
-  f->SetFuzzyThreshold("2RL", "SubclavianArteryRight", mArgsInfo.tS2RL_SubclavianArteryRight_arg);
+
+  // Station 1RL
+
+  // Set RelativePositionList filenames
+  for(uint i=0; i<mArgsInfo.relpos_given; i++) 
+    f->AddRelativePositionListFilename(mArgsInfo.relpos_arg[i]);
 }
 //--------------------------------------------------------------------