X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.txx;h=58f2991d348426b184c92a37c6c7baf93848399a;hb=94cb14004ceab7bca9c892a435ace9f902e661b4;hp=aec05d782df8553d4a0bdd861f7e5d40fdf8eedb;hpb=907b0bad00cbf772fbf362879c74d673253f97bb;p=clitk.git diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx index aec05d7..58f2991 100644 --- a/segmentation/clitkExtractLymphStationsFilter.txx +++ b/segmentation/clitkExtractLymphStationsFilter.txx @@ -55,6 +55,7 @@ ExtractLymphStationsFilter(): // Default values ExtractStation_8_SetDefaultValues(); ExtractStation_3P_SetDefaultValues(); + ExtractStation_2RL_SetDefaultValues(); ExtractStation_3A_SetDefaultValues(); ExtractStation_7_SetDefaultValues(); } @@ -71,6 +72,12 @@ GenerateOutputInformation() { m_Input = dynamic_cast(itk::ProcessObject::GetInput(0)); m_Mediastinum = GetAFDB()->template GetImage ("Mediastinum"); + // Global supports for stations + StartNewStep("Supports for stations"); + StartSubStep(); + ExtractStationSupports(); + StopSubStep(); + // Extract Station8 StartNewStep("Station 8"); StartSubStep(); @@ -83,6 +90,14 @@ GenerateOutputInformation() { ExtractStation_3P(); StopSubStep(); + // Extract Station2RL + /* + StartNewStep("Station 2RL"); + StartSubStep(); + ExtractStation_2RL(); + StopSubStep(); + */ + // Extract Station3A StartNewStep("Station 3A"); StartSubStep(); @@ -102,20 +117,6 @@ GenerateOutputInformation() { //ExtractStation_4RL(); StopSubStep(); } - - - // - // typedef clitk::BooleanOperatorLabelImageFilter BFilter; - //BFilter::Pointer merge = BFilter::New(); - // writeImage(m_Output, "ouput.mhd"); - //writeImage(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(); - */ } //-------------------------------------------------------------------- @@ -196,32 +197,6 @@ AddComputeStation(std::string station) //-------------------------------------------------------------------- -//-------------------------------------------------------------------- -template -void -clitk::ExtractLymphStationsFilter:: -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(m_ListOfStations["8"], "seg/Station8.mhd"); - GetAFDB()->SetImageFilename("Station8", "seg/Station8.mhd"); - WriteAFDB(); - } -} -//-------------------------------------------------------------------- - - //-------------------------------------------------------------------- template void @@ -250,17 +225,16 @@ ExtractStation_3P() template void clitk::ExtractLymphStationsFilter:: -ExtractStation_7() { - 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(m_ListOfStations["7"], "seg/Station7.mhd"); - GetAFDB()->SetImageFilename("Station7", "seg/Station7.mhd"); - WriteAFDB(); +ExtractStation_3A() +{ + if (CheckForStation("3A")) { + ExtractStation_3A_SI_Limits(); + ExtractStation_3A_Ant_Limits(); + ExtractStation_3A_Post_Limits(); + // Store image filenames into AFDB + writeImage(m_ListOfStations["3A"], "seg/Station3A.mhd"); + GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd"); + WriteAFDB(); } } //-------------------------------------------------------------------- @@ -270,14 +244,22 @@ ExtractStation_7() { template void clitk::ExtractLymphStationsFilter:: -ExtractStation_3A() +ExtractStation_2RL() { - if (CheckForStation("3A")) { - ExtractStation_3A_SI_Limits(); - ExtractStation_3A_Ant_Limits(); + 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(m_ListOfStations["3A"], "seg/Station3A.mhd"); - GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd"); + writeImage(m_ListOfStations["2R"], "seg/Station2R.mhd"); + writeImage(m_ListOfStations["2L"], "seg/Station2L.mhd"); + GetAFDB()->SetImageFilename("Station2R", "seg/Station2R.mhd"); + GetAFDB()->SetImageFilename("Station2L", "seg/Station2L.mhd"); WriteAFDB(); } } @@ -305,10 +287,10 @@ ExtractStation_4RL() { template void clitk::ExtractLymphStationsFilter:: -Remove_Structures(std::string s) +Remove_Structures(std::string station, std::string s) { try { - StartNewStep("[Station7] Remove "+s); + StartNewStep("[Station"+station+"] Remove "+s); MaskImagePointer Structure = GetAFDB()->template GetImage(s); clitk::AndNot(m_Working_Support, Structure, GetBackgroundValue()); } @@ -319,5 +301,203 @@ Remove_Structures(std::string s) //-------------------------------------------------------------------- +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +SetFuzzyThreshold(std::string station, std::string tag, double value) +{ + m_FuzzyThreshold[station][tag] = value; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +double +clitk::ExtractLymphStationsFilter:: +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]; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B) +{ + // Create line from A to B with + // A = upper border of LLL at left + // B = lower border of bronchus intermedius (BI) or RightMiddleLobeBronchus + + try { + GetAFDB()->GetPoint3D("LineForS7S8Separation_Begin", A); + GetAFDB()->GetPoint3D("LineForS7S8Separation_End", B); + } + catch(clitk::ExceptionObject & o) { + + DD("FindLineForS7S8Separation"); + // Load LeftLowerLobeBronchus and get centroid point + MaskImagePointer LeftLowerLobeBronchus = + GetAFDB()->template GetImage ("LeftLowerLobeBronchus"); + std::vector c; + clitk::ComputeCentroids(LeftLowerLobeBronchus, GetBackgroundValue(), c); + A = c[1]; + + // Load RightMiddleLobeBronchus and get superior point (not centroid here) + MaskImagePointer RightMiddleLobeBronchus = + GetAFDB()->template GetImage ("RightMiddleLobeBronchus"); + bool b = FindExtremaPointInAGivenDirection(RightMiddleLobeBronchus, + GetBackgroundValue(), + 2, false, B); + if (!b) { + clitkExceptionMacro("Error while searching most superior point in RightMiddleLobeBronchus. Abort"); + } + + // Insert into the DB + GetAFDB()->SetPoint3D("LineForS7S8Separation_Begin", A); + GetAFDB()->SetPoint3D("LineForS7S8Separation_End", B); + } +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +double +clitk::ExtractLymphStationsFilter:: +FindCarinaSlicePosition() +{ + double z; + try { + z = GetAFDB()->GetDouble("CarinaZ"); + } + catch(clitk::ExceptionObject e) { + DD("FindCarinaSlicePosition"); + // Get Carina + MaskImagePointer Carina = GetAFDB()->template GetImage("Carina"); + + // Get Centroid and Z value + std::vector centroids; + clitk::ComputeCentroids(Carina, GetBackgroundValue(), centroids); + + // We dont need Carina structure from now + Carina->Delete(); + + // Put inside the AFDB + GetAFDB()->SetPoint3D("CarinaPoint", centroids[1]); + GetAFDB()->SetDouble("CarinaZ", centroids[1][2]); + WriteAFDB(); + z = centroids[1][2]; + } + return z; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +FindLeftAndRightBronchi() +{ + try { + m_RightBronchus = GetAFDB()->template GetImage ("RightBronchus"); + m_LeftBronchus = GetAFDB()->template GetImage ("LeftBronchus"); + } + catch(clitk::ExceptionObject & o) { + + DD("FindLeftAndRightBronchi"); + // The goal is to separate the trachea inferiorly to the carina into + // a Left and Right bronchus. + + // Get the trachea + MaskImagePointer Trachea = GetAFDB()->template GetImage("Trachea"); + + // Get the Carina position + m_CarinaZ = FindCarinaSlicePosition(); + + // Consider only inferiorly to the Carina + MaskImagePointer m_Working_Trachea = + clitk::CropImageRemoveGreaterThan(Trachea, 2, m_CarinaZ, true, // AutoCrop + GetBackgroundValue()); + + // Labelize the trachea + m_Working_Trachea = Labelize(m_Working_Trachea, 0, true, 1); + + // Carina position must at the first slice that separate the two + // main bronchus (not superiorly). We thus first check that the + // upper slice is composed of at least two labels + MaskImagePointer RightBronchus; + MaskImagePointer LeftBronchus; + typedef itk::ImageSliceIteratorWithIndex SliceIteratorType; + SliceIteratorType iter(m_Working_Trachea, m_Working_Trachea->GetLargestPossibleRegion()); + iter.SetFirstDirection(0); + iter.SetSecondDirection(1); + iter.GoToReverseBegin(); // Start from the end (because image is IS not SI) + int maxLabel=0; + while (!iter.IsAtReverseEndOfSlice()) { + while (!iter.IsAtReverseEndOfLine()) { + if (iter.Get() > maxLabel) maxLabel = iter.Get(); + --iter; + } + iter.PreviousLine(); + } + if (maxLabel < 2) { + clitkExceptionMacro("First slice from Carina does not seems to seperate the two main bronchus. Abort"); + } + + // Compute 3D centroids of both parts to identify the left from the + // right bronchus + std::vector c; + clitk::ComputeCentroids(m_Working_Trachea, GetBackgroundValue(), c); + ImagePointType C1 = c[1]; + ImagePointType C2 = c[2]; + + ImagePixelType rightLabel; + ImagePixelType leftLabel; + if (C1[0] < C2[0]) { rightLabel = 1; leftLabel = 2; } + else { rightLabel = 2; leftLabel = 1; } + + // Select LeftLabel (set one label to Backgroundvalue) + RightBronchus = + clitk::Binarize(m_Working_Trachea, rightLabel, rightLabel, + GetBackgroundValue(), GetForegroundValue()); + /* + SetBackground(m_Working_Trachea, m_Working_Trachea, + leftLabel, GetBackgroundValue(), false); + */ + LeftBronchus = clitk::Binarize(m_Working_Trachea, leftLabel, leftLabel, + GetBackgroundValue(), GetForegroundValue()); + /* + SetBackground(m_Working_Trachea, m_Working_Trachea, + rightLabel, GetBackgroundValue(), false); + */ + + // Crop images + RightBronchus = clitk::AutoCrop(RightBronchus, GetBackgroundValue()); + LeftBronchus = clitk::AutoCrop(LeftBronchus, GetBackgroundValue()); + + // Insert int AFDB if need after + GetAFDB()->template SetImage ("RightBronchus", "seg/rightBronchus.mhd", + RightBronchus, true); + GetAFDB()->template SetImage ("LeftBronchus", "seg/leftBronchus.mhd", + LeftBronchus, true); + } +} +//-------------------------------------------------------------------- #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX