X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.txx;h=98768b278bfdaf105662efb118684db4d5c2713d;hb=7f7c290c75d4917446f8751856ae7d450f58a6f0;hp=9051ec154df9cf5c8a8cc94cb640556a27f73819;hpb=42e050104aebe7830f2111d096f0dd6673987d1e;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx
index 9051ec1..98768b2 100644
--- a/segmentation/clitkExtractLymphStationsFilter.txx
+++ b/segmentation/clitkExtractLymphStationsFilter.txx
@@ -55,7 +55,9 @@ ExtractLymphStationsFilter():
   this->SetNumberOfRequiredInputs(1);
   SetBackgroundValue(0);
   SetForegroundValue(1);
-  ComputeStationsSupportsFlagOn();
+  ForceSupportsFlagOn();
+  SetSupportLimitsFilename("none");
+  CheckSupportFlagOff();
 
   // Default values
   ExtractStation_3P_SetDefaultValues();
@@ -84,34 +86,39 @@ GenerateOutputInformation() {
   m_Mediastinum = this->GetAFDB()->template GetImage <MaskImageType>("Mediastinum");
 
   // Clean some computer landmarks to force the recomputation
+  // FIXME -> to put elsewhere ?
   this->GetAFDB()->RemoveTag("AntPostVesselsSeparation");
 
-  // Global supports for stations
+  // Must I compute the supports ?
   bool supportsExist = true;
-  try {
-    m_ListOfSupports["S1R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1R");
-    m_ListOfSupports["S1L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1L");
-    m_ListOfSupports["S2R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2R");
-    m_ListOfSupports["S2L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2L");
-    m_ListOfSupports["S4R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4R");
-    m_ListOfSupports["S4L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4L");
-    
-    m_ListOfSupports["S3A"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3A");
-    m_ListOfSupports["S3P"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3P");
-    m_ListOfSupports["S5"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S5");
-    m_ListOfSupports["S6"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S6");
-    m_ListOfSupports["S7"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S7");
-    m_ListOfSupports["S8"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S8");
-    m_ListOfSupports["S9"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S9");
-    m_ListOfSupports["S10"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S10");
-    m_ListOfSupports["S11"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S11");
-  } catch(clitk::ExceptionObject o) {
-    supportsExist = false;
+  if (!GetForceSupportsFlag()) {
+    try {
+      m_ListOfSupports["S1R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1R");
+      m_ListOfSupports["S1L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1L");
+      m_ListOfSupports["S2R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2R");
+      m_ListOfSupports["S2L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2L");
+      m_ListOfSupports["S4R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4R");
+      m_ListOfSupports["S4L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4L");
+      
+      m_ListOfSupports["S3A"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3A");
+      m_ListOfSupports["S3P"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3P");
+      m_ListOfSupports["S5"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S5");
+      m_ListOfSupports["S6"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S6");
+      m_ListOfSupports["S7"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S7");
+      m_ListOfSupports["S8"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S8");
+      m_ListOfSupports["S9"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S9");
+      m_ListOfSupports["S10"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S10");
+      m_ListOfSupports["S11"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S11");
+    } catch(clitk::ExceptionObject o) {
+      supportsExist = false;
+    }
   }
 
-  if (!supportsExist || GetComputeStationsSupportsFlag()) {
+  if (!supportsExist || GetForceSupportsFlag()) {
     this->StartNewStep("Supports for stations");
     this->StartSubStep(); 
+    
+    // FIXME : why should I remove theses tags ???
     this->GetAFDB()->RemoveTag("CarinaZ");
     this->GetAFDB()->RemoveTag("ApexOfTheChestZ");
     this->GetAFDB()->RemoveTag("ApexOfTheChest");
@@ -126,24 +133,25 @@ GenerateOutputInformation() {
   }
 
   // Extract Stations
+  ExtractStation_1RL();
+  ExtractStation_2RL();
   ExtractStation_3P();
   ExtractStation_3A();
-  ExtractStation_2RL();
-  ExtractStation_1RL();
-  ExtractStation_4RL();
+  ExtractStation_4R();
+  ExtractStation_4L();
   ExtractStation_5();
   ExtractStation_6();
 
-  // ---------- TODO -----------------------
+  // ---------- todo -----------------------
 
   // Extract Station8
-  ExtractStation_8();
+  //  ExtractStation_8();
 
   // Extract Station7
-  this->StartNewStep("Station 7");
-  this->StartSubStep();
-  ExtractStation_7();
-  this->StopSubStep();
+  //this->StartNewStep("Station 7");
+  //this->StartSubStep();
+  //ExtractStation_7();
+  //this->StopSubStep();
   
 }
 //--------------------------------------------------------------------
@@ -165,7 +173,7 @@ void
 clitk::ExtractLymphStationsFilter<TImageType>::
 GenerateData() {
   // Final Step -> graft output (if SetNthOutput => redo)
-  this->GraftOutput(m_ListOfStations["8"]);
+  // this->GraftOutput(m_ListOfStations["8"]);
 }
 //--------------------------------------------------------------------
   
@@ -180,25 +188,29 @@ CheckForStation(std::string station)
   std::string s = "Station"+station;
   
 
-  // Check if station already exist in DB
-  bool found = false;
-  if (this->GetAFDB()->TagExist(s)) {
-    m_ListOfStations[station] = this->GetAFDB()->template GetImage<MaskImageType>(s);
-    found = true;
-  }
-
   // Define the starting support 
-  if (found && GetComputeStation(station)) {
-    std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
-  }
-  if (!found || GetComputeStation(station)) {
+  // if (GetComputeStation(station)) {
+  //   std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
+  // }
+  if (GetComputeStation(station)) {
     m_Working_Support = m_Mediastinum = this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
     return true;
   }
-  else {
-    std::cout << "Station " << station << " found. I used it" << std::endl;
-    return false;
+  else return false;
+  // else {
+  //   std::cout << "Station " << station << " found. I used it" << std::endl;
+  //   return false;
+  // }
+
+  // Check if station already exist in DB
+  
+  // FIXME -> do nothing if not on the command line. Is it what I want ?
+  //bool found = false;
+  if (this->GetAFDB()->TagExist(s)) {
+    m_ListOfStations[station] = this->GetAFDB()->template GetImage<MaskImageType>(s);
+    //found = true;
   }
+
 }
 //--------------------------------------------------------------------
 
@@ -438,7 +450,7 @@ FindCarina()
     z = this->GetAFDB()->GetDouble("CarinaZ");
   }
   catch(clitk::ExceptionObject e) {
-    DD("FindCarinaSlicePosition");
+    //DD("FindCarinaSlicePosition");
     // Get Carina
     MaskImagePointer Carina = this->GetAFDB()->template GetImage<MaskImageType>("Carina");
     
@@ -471,7 +483,9 @@ FindApexOfTheChest()
     z = this->GetAFDB()->GetDouble("ApexOfTheChestZ");
   }
   catch(clitk::ExceptionObject e) {
-    DD("FindApexOfTheChestPosition");
+
+    /*
+    //DD("FindApexOfTheChestPosition");
     MaskImagePointer Lungs = this->GetAFDB()->template GetImage<MaskImageType>("Lungs");
     MaskImagePointType p;
     p[0] = p[1] = p[2] =  0.0; // to avoid warning
@@ -486,6 +500,23 @@ FindApexOfTheChest()
     this->GetAFDB()->SetDouble("ApexOfTheChestZ", p[2]);
     this->WriteAFDB();
     z = p[2];
+    */
+    
+    // the superior border becomes the more inferior of the two apices
+    MaskImagePointer RightLung = this->GetAFDB()->template GetImage<MaskImageType>("RightLung");
+    MaskImagePointer LeftLung = this->GetAFDB()->template GetImage<MaskImageType>("LeftLung");
+    MaskImagePointType pr;
+    MaskImagePointType pl;
+    clitk::FindExtremaPointInAGivenDirection<MaskImageType>(RightLung, GetBackgroundValue(), 2, false, pr);
+    clitk::FindExtremaPointInAGivenDirection<MaskImageType>(LeftLung, GetBackgroundValue(), 2, false, pl);
+    // We dont need Lungs structure from now
+    this->GetAFDB()->template ReleaseImage<MaskImageType>("RightLung");
+    this->GetAFDB()->template ReleaseImage<MaskImageType>("LeftLung");
+    // Put inside the AFDB
+    if (pr[2] < pl[2]) z = pr[2];
+    else z = pl[2];
+    this->GetAFDB()->SetDouble("ApexOfTheChestZ", z);
+    this->WriteAFDB();
   }
   return z;
 }
@@ -596,7 +627,7 @@ FindSuperiorBorderOfAorticArch()
     z = this->GetAFDB()->GetDouble("SuperiorBorderOfAorticArchZ");
   }
   catch(clitk::ExceptionObject e) {
-    DD("FindSuperiorBorderOfAorticArch");
+    //    DD("FindSuperiorBorderOfAorticArch");
     MaskImagePointer Aorta = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
     MaskImagePointType p;
     p[0] = p[1] = p[2] =  0.0; // to avoid warning
@@ -628,7 +659,7 @@ FindInferiorBorderOfAorticArch()
     z = this->GetAFDB()->GetDouble("InferiorBorderOfAorticArchZ");
   }
   catch(clitk::ExceptionObject e) {
-    DD("FindInferiorBorderOfAorticArch");
+    //DD("FindInferiorBorderOfAorticArch");
     MaskImagePointer Aorta = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
     std::vector<MaskSlicePointer> slices;
     clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
@@ -988,8 +1019,8 @@ FindAntPostVesselsOLD()
   binarizedContour = clitk::CropImageAlongOneAxis<MaskImageType>(binarizedContour, 2, inf, sup, 
                                                         false, GetBackgroundValue());
   // Update the AFDB
-  writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mhd");
-  this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mhd");  
+  writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mha");
+  this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mha");
   this->WriteAFDB();
   return binarizedContour;
 
@@ -1076,10 +1107,10 @@ FindAntPostVessels2()
   typedef std::map<std::string, MaskImagePointer>::iterator MapIter;
   MapOfStructures["BrachioCephalicArtery"] = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
   MapOfStructures["BrachioCephalicVein"] = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
-  MapOfStructures["CommonCarotidArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArteryLeft");
-  MapOfStructures["CommonCarotidArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArteryRight");
-  MapOfStructures["SubclavianArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryLeft");
-  MapOfStructures["SubclavianArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryRight");
+  MapOfStructures["CommonCarotidArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("LeftCommonCarotidArtery");
+  MapOfStructures["CommonCarotidArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("RightCommonCarotidArtery");
+  MapOfStructures["SubclavianArteryLeft"] = this->GetAFDB()->template GetImage<MaskImageType>("LeftSubclavianArtery");
+  MapOfStructures["SubclavianArteryRight"] = this->GetAFDB()->template GetImage<MaskImageType>("RightSubclavianArtery");
   MapOfStructures["Thyroid"] = this->GetAFDB()->template GetImage<MaskImageType>("Thyroid");
   MapOfStructures["Aorta"] = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
   MapOfStructures["Trachea"] = this->GetAFDB()->template GetImage<MaskImageType>("Trachea");
@@ -1347,8 +1378,8 @@ FindAntPostVessels2()
                                                         false, GetBackgroundValue());
 
   // Update the AFDB
-  writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mhd");
-  this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mhd");  
+  writeImage<MaskImageType>(binarizedContour, "seg/AntPostVesselsSeparation.mha");
+  this->GetAFDB()->SetImageFilename("AntPostVesselsSeparation", "seg/AntPostVesselsSeparation.mha");
   this->WriteAFDB();
   return binarizedContour;
 
@@ -1383,6 +1414,65 @@ FindAntPostVessels2()
 }
 //--------------------------------------------------------------------
 
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+WriteImageSupport(std::string support)
+{
+  writeImage<MaskImageType>(m_ListOfSupports[support], this->GetAFDBPath()+"/"+"seg/Support_"+support+".mha");
+  this->GetAFDB()->SetImageFilename("Support_"+support, "seg/Support_"+support+".mha");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+WriteImageStation(std::string station)
+{
+  writeImage<MaskImageType>(m_ListOfStations[station], GetAFDB()->GetPath()+"/seg/Station"+station+".mha");
+  GetAFDB()->SetImageFilename("Station"+station, "seg/Station"+station+".mha"); 
+  WriteAFDB();
+}
+//--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ComputeOverlapWithRef(std::string station)
+{
+  if (GetComputeStation(station)) {
+    MaskImagePointer ref = this->GetAFDB()->template GetImage <MaskImageType>("Station"+station+"_Ref");
+    typedef clitk::LabelImageOverlapMeasureFilter<MaskImageType> FilterType;
+    typename FilterType::Pointer filter = FilterType::New();
+    filter->SetInput(0, m_ListOfStations[station]);
+    filter->SetInput(1, ref);
+    filter->Update();
+  }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ReadSupportLimits(std::string filename)
+{
+  m_ListOfSupportLimits.clear();
+  ifstream is;
+  openFileForReading(is, filename);
+  while (is) {
+    skipComment(is);
+    SupportLimitsType s;
+    s.Read(is);
+    if (is) m_ListOfSupportLimits.push_back(s);
+  }
+}
+//--------------------------------------------------------------------
+
 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
+