X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsGenericFilter.txx;h=317c78ab588b1e0d36f53fe0c4d76241de15c1b7;hb=8d4aeabfafe155775a520eeb1aabf330e3a9d886;hp=977cf93444e3a442139a3e0daaa2c0f63e8b63be;hpb=765020625fbc092d283e221e36c83e60a1844cb7;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsGenericFilter.txx b/segmentation/clitkExtractLymphStationsGenericFilter.txx
index 977cf93..317c78a 100644
--- a/segmentation/clitkExtractLymphStationsGenericFilter.txx
+++ b/segmentation/clitkExtractLymphStationsGenericFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ===========================================================================**/
+  ======================================================================-====*/
 
 #ifndef CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
 #define CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
@@ -68,9 +68,13 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
   f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
   f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
   f->SetAFDBFilename(mArgsInfo.afdb_arg);  
-  f->SetDistanceMaxToAnteriorPartOfTheSpine(mArgsInfo.maxAntSpine_arg);
-  f->SetFuzzyThresholdForS8(mArgsInfo.fuzzyThresholdForS8_arg);
-  f->SetInjectedThresholdForS8(mArgsInfo.injectedThresholdForS8_arg);
+
+  f->SetComputeStationsSupportsFlag(!mArgsInfo.nosupport_flag);
+
+  // Station 8
+  //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
   /*
@@ -81,27 +85,27 @@ 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);  
@@ -109,13 +113,24 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
   for(uint i=0; i<mArgsInfo.station_given; i++)
     f->AddComputeStation(mArgsInfo.station_arg[i]);
 
+  // Station 3A
+  
   // Station 7
-  f->SetFuzzyThresholdForS7("Bronchi", mArgsInfo.tS7_Bronchi_arg);
-  f->SetFuzzyThresholdForS7("LeftSuperiorPulmonaryVein", mArgsInfo.tS7_LeftSuperiorPulmonaryVein_arg);
-  f->SetFuzzyThresholdForS7("RightSuperiorPulmonaryVein", mArgsInfo.tS7_RightSuperiorPulmonaryVein_arg);
-  f->SetFuzzyThresholdForS7("RightPulmonaryArtery", mArgsInfo.tS7_RightPulmonaryArtery_arg);
-  f->SetFuzzyThresholdForS7("LeftPulmonaryArtery", mArgsInfo.tS7_LeftPulmonaryArtery_arg);
-  f->SetFuzzyThresholdForS7("SVC", mArgsInfo.tS7_SVC_arg);
+  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
+
+  // Station 1RL
+
+  // Set RelativePositionList filenames
+  for(uint i=0; i<mArgsInfo.relpos_given; i++) 
+    f->AddRelativePositionListFilename(mArgsInfo.relpos_arg[i]);
 }
 //--------------------------------------------------------------------