X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.txx;h=ea9e2b678c01fe40d75fffc8d2b009f3ada6d550;hb=21799ce0c562ddbbfe00d55309809f2f5066a93b;hp=ea514a6d643924af6834d3c3a921b82b98411d05;hpb=d30d301ddbebb5f290f8d9c0104dc6448ea531e1;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx
index ea514a6..ea9e2b6 100644
--- a/segmentation/clitkExtractLymphStationsFilter.txx
+++ b/segmentation/clitkExtractLymphStationsFilter.txx
@@ -52,14 +52,9 @@ ExtractLymphStationsFilter():
   SetBackgroundValue(0);
   SetForegroundValue(1);
 
-  // Station 8
-  SetDistanceMaxToAnteriorPartOfTheSpine(10);
-  MaskImagePointType p;
-  p[0] = 15; p[1] = 2; p[2] = 1;
-  SetEsophagusDiltationForAnt(p);
-  p[0] = 5; p[1] = 10; p[2] = 1;
-  SetEsophagusDiltationForRight(p);
-  SetFuzzyThresholdForS8(0.5);
+  // Default values
+  ExtractStation_8_SetDefaultValues();
+  ExtractStation_3P_SetDefaultValues();
 
   // Station 7
   SetFuzzyThreshold(0.5);
@@ -84,14 +79,11 @@ GenerateOutputInformation() {
   ExtractStation_8();
   StopSubStep();
 
-  // Compute some interesting points in trachea
-  // ( ALTERNATIVE -> SKELETON ANALYSIS ? 
-  //    Pb : not sufficient for mostXX points ... ) 
-
-  /* ==> todo (but why ???)
-     ComputeTracheaCentroidsAboveCarina();
-     ComputeBronchusExtremaPointsBelowCarina();
-  */
+  // Extract Station3P
+  StartNewStep("Station 3P");
+  StartSubStep(); 
+  ExtractStation_3P();
+  StopSubStep();
 
   if (0) { // temporary suppress
     // Extract Station7
@@ -129,7 +121,7 @@ template <class TImageType>
 void 
 clitk::ExtractLymphStationsFilter<TImageType>::
 GenerateInputRequestedRegion() {
-  DD("GenerateInputRequestedRegion (nothing?)");
+  //DD("GenerateInputRequestedRegion (nothing?)");
 }
 //--------------------------------------------------------------------
 
@@ -149,21 +141,103 @@ GenerateData() {
 
 //--------------------------------------------------------------------
 template <class TImageType>
-void 
+bool 
 clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_8() {
+CheckForStation(std::string station) 
+{
+  // Compute Station name
+  std::string s = "Station"+station;
+  
 
-  // Check if m_ListOfStations["8"] exist. If yes -> use it as initial
-  // support instead of m_Mediastinum
-  if (m_ListOfStations["8"]) {
-    DD("Station 8 support already exist -> use it");
-    m_Working_Support = m_ListOfStations["8"];
+  // Check if station already exist in DB
+  bool found = false;
+  if (GetAFDB()->TagExist(s)) {
+    m_ListOfStations[station] = GetAFDB()->template GetImage<MaskImageType>(s);
+    found = true;
   }
-  else m_Working_Support = m_Mediastinum;
 
-  ExtractStation_8_SI_Limits();
-  ExtractStation_8_AP_Limits();
-  // ExtractStation_8_LR_Limits();
+  // Define the starting support 
+  if (found && GetComputeStation(station)) {
+    std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
+  }
+  if (!found || GetComputeStation(station)) {
+    m_Working_Support = m_Mediastinum = GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
+    return true;
+  }
+  else {
+    std::cout << "Station " << station << " found. I used it" << std::endl;
+    return false;
+  }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+bool
+clitk::ExtractLymphStationsFilter<TImageType>::
+GetComputeStation(std::string station) 
+{
+  return (m_ComputeStationMap.find(station) != m_ComputeStationMap.end());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+AddComputeStation(std::string station) 
+{
+  m_ComputeStationMap[station] = true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void 
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_8() 
+{
+  if (CheckForStation("8")) {
+    ExtractStation_8_SI_Limits();
+    ExtractStation_8_Post_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");  
+    WriteAFDB();
+  }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void 
+clitk::ExtractLymphStationsFilter<TImageType>::
+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_inf_Limits();
+    // Store image filenames into AFDB 
+    writeImage<MaskImageType>(m_ListOfStations["3P"], "seg/Station3P.mhd");
+    GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd"); 
+    WriteAFDB(); 
+  }
 }
 //--------------------------------------------------------------------
 
@@ -201,72 +275,7 @@ ExtractStation_4RL() {
 
 
 //--------------------------------------------------------------------
-template <class TImageType>
-void 
-clitk::ExtractLymphStationsFilter<TImageType>::
-FindExtremaPointsInBronchus(MaskImagePointer input, 
-			    int direction,
-			    double distance_max_from_center_point, 
-			    ListOfPointsType & LR, 
-			    ListOfPointsType & Ant, 
-			    ListOfPointsType & Post)
-{
 
-  // 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);
-    }
-  }
-} 
-//--------------------------------------------------------------------
 
 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX