X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.txx;h=aec05d782df8553d4a0bdd861f7e5d40fdf8eedb;hb=119a42cb1444930c78314e862e590f54c2f7678d;hp=70d540bf636e2b3ba94a110a9a3a7791c1569d1d;hpb=bf4928c59a1d39f53fe03deb4b73ecb7e1cf214b;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx
index 70d540b..aec05d7 100644
--- a/segmentation/clitkExtractLymphStationsFilter.txx
+++ b/segmentation/clitkExtractLymphStationsFilter.txx
@@ -55,10 +55,8 @@ ExtractLymphStationsFilter():
   // Default values
   ExtractStation_8_SetDefaultValues();
   ExtractStation_3P_SetDefaultValues();
-
-  // Station 7
-  SetFuzzyThreshold(0.5);
-  SetStation7Filename("station7.mhd");
+  ExtractStation_3A_SetDefaultValues();
+  ExtractStation_7_SetDefaultValues();
 }
 //--------------------------------------------------------------------
 
@@ -79,21 +77,25 @@ GenerateOutputInformation() {
   ExtractStation_8();
   StopSubStep();
 
-  DD(GetCurrentStepNumber());
-
   // Extract Station3P
   StartNewStep("Station 3P");
   StartSubStep(); 
   ExtractStation_3P();
   StopSubStep();
 
-  if (0) { // temporary suppress
-    // Extract Station7
-    StartNewStep("Station 7");
-    StartSubStep();
-    ExtractStation_7();
-    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();
@@ -123,7 +125,7 @@ template <class TImageType>
 void 
 clitk::ExtractLymphStationsFilter<TImageType>::
 GenerateInputRequestedRegion() {
-  DD("GenerateInputRequestedRegion (nothing?)");
+  //DD("GenerateInputRequestedRegion (nothing?)");
 }
 //--------------------------------------------------------------------
 
@@ -133,8 +135,6 @@ template <class TImageType>
 void 
 clitk::ExtractLymphStationsFilter<TImageType>::
 GenerateData() {
-  DD("GenerateData, graft output");
-
   // Final Step -> graft output (if SetNthOutput => redo)
   this->GraftOutput(m_ListOfStations["8"]);
 }
@@ -159,10 +159,10 @@ CheckForStation(std::string station)
   }
 
   // Define the starting support 
-  if (found && GetComputeStation("8")) {
+  if (found && GetComputeStation(station)) {
     std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
   }
-  if (!found || GetComputeStation("8")) {
+  if (!found || GetComputeStation(station)) {
     m_Working_Support = m_Mediastinum = GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
     return true;
   }
@@ -205,8 +205,14 @@ ExtractStation_8()
   if (CheckForStation("8")) {
     ExtractStation_8_SI_Limits();
     ExtractStation_8_Post_Limits();
-    ExtractStation_8_Ant_Limits();
+    ExtractStation_8_Ant_Sup_Limits();
+    ExtractStation_8_Ant_Inf_Limits();
+    ExtractStation_8_LR_1_Limits();
+    ExtractStation_8_LR_2_Limits();
     ExtractStation_8_LR_Limits();
+    ExtractStation_8_Ant_Injected_Limits();
+    ExtractStation_8_Single_CCL_Limits();
+    ExtractStation_8_Remove_Structures();
     // Store image filenames into AFDB 
     writeImage<MaskImageType>(m_ListOfStations["8"], "seg/Station8.mhd");
     GetAFDB()->SetImageFilename("Station8", "seg/Station8.mhd");  
@@ -224,9 +230,17 @@ ExtractStation_3P()
 {
   if (CheckForStation("3P")) {
     ExtractStation_3P_SI_Limits();
+    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");  
+    GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd"); 
+    WriteAFDB(); 
   }
 }
 //--------------------------------------------------------------------
@@ -237,14 +251,35 @@ 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();
+    // Store image filenames into AFDB 
+    writeImage<MaskImageType>(m_ListOfStations["3A"], "seg/Station3A.mhd");
+    GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd"); 
+    WriteAFDB(); 
+  }
 }
 //--------------------------------------------------------------------
 
@@ -254,6 +289,8 @@ template <class TImageType>
 void 
 clitk::ExtractLymphStationsFilter<TImageType>::
 ExtractStation_4RL() {
+  DD("TODO");
+  exit(0);
   /*
     WARNING ONLY 4R FIRST !!! (not same inf limits)
   */    
@@ -265,75 +302,22 @@ ExtractStation_4RL() {
 
 
 //--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
 void 
-clitk::ExtractLymphStationsFilter<TImageType>::
-FindExtremaPointsInBronchus(MaskImagePointer input, 
-			    int direction,
-			    double distance_max_from_center_point, 
-			    ListOfPointsType & LR, 
-			    ListOfPointsType & Ant, 
-			    ListOfPointsType & Post)
+clitk::ExtractLymphStationsFilter<ImageType>::
+Remove_Structures(std::string s)
 {
-
-  // Other solution ==> with auto bounding box ! (but pb to prevent to
-  // be too distant from the center point
-
-  // Extract slices
-  std::vector<typename MaskSliceType::Pointer> slices;
-  clitk::ExtractSlices<MaskImageType>(input, 2, slices);
-  
-  // Loop on slices
-  bool found;
-  for(uint i=0; i<slices.size(); i++) {
-    /*
-    // Keep main CCL
-    slices[i] = Labelize<MaskSliceType>(slices[i], 0, true, 10);
-    slices[i] = KeepLabels<MaskSliceType>(slices[i], 
-					  GetBackgroundValue(), 
-					  GetForegroundValue(), 1, 1, true);
-    */
-
-    // ------- Find rightmost or leftmost point  ------- 
-    MaskSliceType::PointType LRMost;
-    found = 
-      clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], 
-                                                              GetBackgroundValue(), 
-                                                              0, // axis XY
-                                                              (direction==0?false:true),  // right or left according to direction
-                                                              LRMost);
-    // ------- Find postmost point  ------- 
-    MaskSliceType::PointType postMost;
-    found = 
-      clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], 
-                                                              GetBackgroundValue(), 
-                                                              1, false, LRMost, 
-                                                              distance_max_from_center_point, 
-                                                              postMost);
-    // ------- Find antmost point  ------- 
-    MaskSliceType::PointType antMost;
-    found = 
-      clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], 
-                                                              GetBackgroundValue(), 
-                                                              1, true, LRMost, 
-                                                              distance_max_from_center_point, 
-                                                              antMost);
-    // Only add point if found
-    if (found)  {
-      // ------- Convert 2D to 3D points --------
-      MaskImageType::PointType p;
-      clitk::PointsUtils<MaskImageType>::Convert2DTo3D(LRMost, input, i, p);
-      LR.push_back(p); 
-      clitk::PointsUtils<MaskImageType>::Convert2DTo3D(antMost, input, i, p);
-      Ant.push_back(p);
-      clitk::PointsUtils<MaskImageType>::Convert2DTo3D(postMost, input, i, p);
-      Post.push_back(p);
-    }
+  try {
+    StartNewStep("[Station7] 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;
+  }
+}
 //--------------------------------------------------------------------
 
+
+
 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX