X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.txx;h=1823e998c40cf228444cb29439c5adc760d5cd0e;hb=431fea9a7c825943b07fc4b4f3423355a5fee501;hp=ea9e2b678c01fe40d75fffc8d2b009f3ada6d550;hpb=a339bdc482ea9752ec53195bc9a47e8b05dba582;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx
index ea9e2b6..1823e99 100644
--- a/segmentation/clitkExtractLymphStationsFilter.txx
+++ b/segmentation/clitkExtractLymphStationsFilter.txx
@@ -55,10 +55,9 @@ ExtractLymphStationsFilter():
   // Default values
   ExtractStation_8_SetDefaultValues();
   ExtractStation_3P_SetDefaultValues();
-
-  // Station 7
-  SetFuzzyThreshold(0.5);
-  SetStation7Filename("station7.mhd");
+  ExtractStation_2RL_SetDefaultValues();
+  ExtractStation_3A_SetDefaultValues();
+  ExtractStation_7_SetDefaultValues();
 }
 //--------------------------------------------------------------------
 
@@ -85,33 +84,31 @@ GenerateOutputInformation() {
   ExtractStation_3P();
   StopSubStep();
 
-  if (0) { // temporary suppress
-    // Extract Station7
-    StartNewStep("Station 7");
-    StartSubStep();
-    ExtractStation_7();
-    StopSubStep();
+  // Extract Station2RL
+  StartNewStep("Station 2RL");
+  StartSubStep(); 
+  ExtractStation_2RL();
+  StopSubStep();
+
+  // Extract Station3A
+  StartNewStep("Station 3A");
+  StartSubStep(); 
+  ExtractStation_3A();
+  StopSubStep();
 
+  // Extract Station7
+  StartNewStep("Station 7");
+  StartSubStep();
+  ExtractStation_7();
+  StopSubStep();
+
+  if (0) { // temporary suppress
     // Extract Station4RL
     StartNewStep("Station 4RL");
     StartSubStep();
     //ExtractStation_4RL();
     StopSubStep();
   }
-
-
-  //
-  //  typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BFilter;
-  //BFilter::Pointer merge = BFilter::New();  
-  // writeImage<MaskImageType>(m_Output, "ouput.mhd");
-  //writeImage<MaskImageType>(m_Working_Support, "ws.mhd");
-  /*merge->SetInput1(m_Station7);
-    merge->SetInput2(m_Station4RL); // support
-    merge->SetOperationType(BFilter::AndNot); CHANGE OPERATOR
-    merge->SetForegroundValue(4);
-    merge->Update();
-    m_Output = merge->GetOutput();
-  */
 }
 //--------------------------------------------------------------------
 
@@ -131,8 +128,6 @@ template <class TImageType>
 void 
 clitk::ExtractLymphStationsFilter<TImageType>::
 GenerateData() {
-  DD("GenerateData, graft output");
-
   // Final Step -> graft output (if SetNthOutput => redo)
   this->GraftOutput(m_ListOfStations["8"]);
 }
@@ -228,11 +223,13 @@ ExtractStation_3P()
 {
   if (CheckForStation("3P")) {
     ExtractStation_3P_SI_Limits();
-    ExtractStation_3P_Remove_Structures();
     ExtractStation_3P_Ant_Limits();
     ExtractStation_3P_Post_Limits();
     ExtractStation_3P_LR_sup_Limits();
+    //    ExtractStation_3P_LR_sup_Limits_2();
     ExtractStation_3P_LR_inf_Limits();
+    ExtractStation_8_Single_CCL_Limits(); // YES 8 !
+    ExtractStation_3P_Remove_Structures(); // after CCL
     // Store image filenames into AFDB 
     writeImage<MaskImageType>(m_ListOfStations["3P"], "seg/Station3P.mhd");
     GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd"); 
@@ -247,14 +244,62 @@ template <class TImageType>
 void 
 clitk::ExtractLymphStationsFilter<TImageType>::
 ExtractStation_7() {
-  if (m_ListOfStations["7"]) {
-    DD("Station 7 support already exist -> use it");
-    m_Working_Support = m_ListOfStations["7"];
-  }
-  else m_Working_Support = m_Mediastinum;
+  if (CheckForStation("7")) {
   ExtractStation_7_SI_Limits();
   ExtractStation_7_RL_Limits();
   ExtractStation_7_Posterior_Limits();
+  //  ExtractStation_8_Single_CCL_Limits(); // Yes the same than 8
+  ExtractStation_7_Remove_Structures();
+  // Store image filenames into AFDB 
+  writeImage<MaskImageType>(m_ListOfStations["7"], "seg/Station7.mhd");
+  GetAFDB()->SetImageFilename("Station7", "seg/Station7.mhd");  
+  WriteAFDB();
+  }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void 
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_3A()
+{
+  if (CheckForStation("3A")) {
+    ExtractStation_3A_SI_Limits();
+    ExtractStation_3A_Ant_Limits();
+    ExtractStation_3A_Post_Limits();
+    // Store image filenames into AFDB 
+    writeImage<MaskImageType>(m_ListOfStations["3A"], "seg/Station3A.mhd");
+    GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd"); 
+    WriteAFDB(); 
+  }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void 
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_2RL()
+{
+  if (CheckForStation("2RL")) {
+    ExtractStation_2RL_SI_Limits();
+    ExtractStation_2RL_Post_Limits();
+    ExtractStation_2RL_Ant_Limits2();
+    ExtractStation_2RL_Ant_Limits(); 
+    ExtractStation_2RL_LR_Limits(); 
+    ExtractStation_2RL_Remove_Structures(); 
+    ExtractStation_2RL_SeparateRL(); 
+    
+    // Store image filenames into AFDB 
+    writeImage<MaskImageType>(m_ListOfStations["2R"], "seg/Station2R.mhd");
+    writeImage<MaskImageType>(m_ListOfStations["2L"], "seg/Station2L.mhd");
+    GetAFDB()->SetImageFilename("Station2R", "seg/Station2R.mhd"); 
+    GetAFDB()->SetImageFilename("Station2L", "seg/Station2L.mhd"); 
+    WriteAFDB(); 
+  }
 }
 //--------------------------------------------------------------------
 
@@ -264,6 +309,8 @@ template <class TImageType>
 void 
 clitk::ExtractLymphStationsFilter<TImageType>::
 ExtractStation_4RL() {
+  DD("TODO");
+  exit(0);
   /*
     WARNING ONLY 4R FIRST !!! (not same inf limits)
   */    
@@ -275,6 +322,54 @@ ExtractStation_4RL() {
 
 
 //--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+Remove_Structures(std::string station, std::string s)
+{
+  try {
+    StartNewStep("[Station"+station+"] Remove "+s);  
+    MaskImagePointer Structure = GetAFDB()->template GetImage<MaskImageType>(s);
+    clitk::AndNot<MaskImageType>(m_Working_Support, Structure, GetBackgroundValue());
+  }
+  catch(clitk::ExceptionObject e) {
+    std::cout << s << " not found, skip." << std::endl;
+  }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void 
+clitk::ExtractLymphStationsFilter<TImageType>::
+SetFuzzyThreshold(std::string station, std::string tag, double value)
+{
+  m_FuzzyThreshold[station][tag] = value;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+double 
+clitk::ExtractLymphStationsFilter<TImageType>::
+GetFuzzyThreshold(std::string station, std::string tag)
+{
+  if (m_FuzzyThreshold.find(station) == m_FuzzyThreshold.end()) {
+    clitkExceptionMacro("Could not find options for station "+station+" in the list (while searching for tag "+tag+").");
+    return 0.0;
+  }
+
+  if (m_FuzzyThreshold[station].find(tag) == m_FuzzyThreshold[station].end()) {
+    clitkExceptionMacro("Could not find options "+tag+" in the list of FuzzyThreshold for station "+station+".");
+    return 0.0;
+  }
+  
+  return m_FuzzyThreshold[station][tag]; 
+}
+//--------------------------------------------------------------------
+