+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_4RL_SetDefaultValues()
+{
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_4RL_SI_Limits()
-{
- /* SupInf limits :
- - top of aortic arch
- - ends at the upper lobe bronchus or where the right pulmonary artery crosses the midline of the mediastinum
- */
-
- // Local variables
- double m_TopOfAorticArchInMM;
- double m_UpperLobeBronchusZPositionInMM;
- double m_RightPulmoArteyrCrossesMidMediastinumZPositionInMM;
-
- // Get Inputs
- m_TopOfAorticArchInMM = GetAFDB()->GetPoint3D("topOfAorticArch", 2);
- DD(m_TopOfAorticArchInMM);
- m_UpperLobeBronchusZPositionInMM = GetAFDB()->GetPoint3D("rightUpperLobeBronchus", 2);
- DD(m_UpperLobeBronchusZPositionInMM);
- m_RightPulmoArteyrCrossesMidMediastinumZPositionInMM = GetAFDB()->GetPoint3D("rightPulmoArteryCrossesMidMediastinum", 2);
- DD(m_RightPulmoArteyrCrossesMidMediastinumZPositionInMM);
-
- /* Crop support */
- StartNewStep("Inf/Sup mediastinum limits with aortic arch/upperLBronchus");
- double inf = std::max(m_UpperLobeBronchusZPositionInMM, m_RightPulmoArteyrCrossesMidMediastinumZPositionInMM);
- m_Working_Support =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_Support, 2,
- inf,
- m_TopOfAorticArchInMM, true,
- GetBackgroundValue());
- StopCurrentStep<MaskImageType>(m_Working_Support);
+ExtractStation_4R() {
+ if (!CheckForStation("4R")) return;
+ StartNewStep("Stations 4R");
+ StartSubStep();
- m_Station4RL = m_Working_Support;
+ // Get the current support
+ StartNewStep("[Station 4R] Get the current 4RL suppport");
+ m_ListOfStations["4R"] = m_ListOfSupports["S4R"];
+ StopCurrentStep<MaskImageType>(m_ListOfStations["4R"]);
+
+ // Generic RelativePosition processes
+ m_ListOfStations["4R"] = this->ApplyRelativePositionList("Station_4R", m_ListOfStations["4R"]);
+
+ // Store image filenames into AFDB
+ WriteImageStation("4R");
+ StopSubStep();
+ ComputeOverlapWithRef("4R");
}
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_4RL_LR_Limits()
-{
- // 4R first
+ExtractStation_4L() {
+ if (!CheckForStation("4L")) return;
+ StartNewStep("Stations 4L");
+ StartSubStep();
- // Left : midline of the trachea
- // Right : "- upper part : contained within the pleural envelope
- //- intermediate section : medial to the superior vena cava and the arch of the azygos vein
- // - very caudal part : right upper lobe pulmonary vein"
- // AAV ??
-
- // Constraint at right from the SVC
- MaskImagePointer svc = GetAFDB()->template GetImage<MaskImageType>("SVC");
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInput(m_Working_Support);
- relPosFilter->SetInputObject(svc);
- relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
- relPosFilter->SetIntermediateSpacing(2);
- relPosFilter->SetFuzzyThreshold(0.3);
- relPosFilter->Update();
- m_Working_Support = relPosFilter->GetOutput();
- m_Station4RL = m_Working_Support;
-
- // Left -> midline of the trachea
- // slice by slice, find X coord of 2D centroid (?)
- // check with previous line in order to not move too fast
-
- // skeleton ? -> need path description ? follow from slice to slice
- // OR CENTROID at each slice ?
+ // Get the current support
+ StartNewStep("[Station 4L] Get the current 4RL suppport");
+ m_ListOfStations["4L"] = m_ListOfSupports["S4L"];
+ StopCurrentStep<MaskImageType>(m_ListOfStations["4L"]);
+
+ // Generic RelativePosition processes
+ m_ListOfStations["4L"] = this->ApplyRelativePositionList("Station_4L", m_ListOfStations["4L"]);
+
+ // Separation Ant/Post
+ m_Working_Support = m_ListOfStations["4L"];
+ ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(10);
+ m_ListOfStations["4L"] = m_Working_Support;
- // Crop trachea
- // Extract list of slice from trachea
- // Loop slice -> Get centroid crop along line (BB limit) -> two supports
+ // Keep only one single CCL by slice
+ StartNewStep("[Station 4L] Keep only one CCL by slice");
+ m_ListOfStations["4L"] = SliceBySliceKeepMainCCL<MaskImageType>(m_ListOfStations["4L"],
+ GetBackgroundValue(),
+ GetForegroundValue());
+ StopCurrentStep<MaskImageType>(m_ListOfStations["4L"]);
- // Crop the trachea like the current support
- MaskImagePointer crop_trachea =
- clitk::ResizeImageLike<MaskImageType>(m_Trachea, m_Working_Support, GetBackgroundValue());
- writeImage<MaskImageType>(crop_trachea, "croptrachea.mhd");
+ // Store image filenames into AFDB
+ WriteImageStation("4L");
+ StopSubStep();
+ ComputeOverlapWithRef("4L");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(int KeepPoint)
+{
+ // ----------------------------------------------------------
+ StartNewStep("[Station 4L] Limits between Asc and Desc Aorta, and with LeftPulmonaryArtery ");
+
+ // Separate Aorta into DescendingAorta AscendingAorta
+ MaskImagePointer AscendingAorta = GetAFDB()->template GetImage<MaskImageType>("AscendingAorta");
+ MaskImagePointer DescendingAorta = GetAFDB()->template GetImage<MaskImageType>("DescendingAorta");
+
+ // Crop like support (inferiorly)
+ m_Working_Support = clitk::AutoCrop<MaskImageType>(m_Working_Support, GetBackgroundValue());
+ AscendingAorta =
+ clitk::ResizeImageLike<MaskImageType>(AscendingAorta, m_Working_Support, GetBackgroundValue());
+ DescendingAorta =
+ clitk::ResizeImageLike<MaskImageType>(DescendingAorta, m_Working_Support, GetBackgroundValue());
+
+ // Crop superior part (when AscendingAorta and DescendingAorta join)
+ MaskImagePointType p;
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(AscendingAorta,
+ GetBackgroundValue(), 2, false, p);
+ double max = p[2]+AscendingAorta->GetSpacing()[2];
+ AscendingAorta =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
+ DescendingAorta =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(DescendingAorta, 2, max, false, GetBackgroundValue());
- // Extract all the slices
- typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
- typedef typename ExtractSliceFilterType::SliceType SliceType;
- typename ExtractSliceFilterType::Pointer
- extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(crop_trachea);
- extractSliceFilter->SetDirection(2);
- extractSliceFilter->Update();
- std::vector<typename SliceType::Pointer> trachea_slices;
- extractSliceFilter->GetOutputSlices(trachea_slices);
+ // Crop inferior part, where LeftPulmonaryArtery start
+ MaskImagePointer AscendingAortaCopy = clitk::Clone<MaskImageType>(AscendingAorta);
+ MaskImagePointer LeftPulmonaryArtery = GetAFDB()->template GetImage<MaskImageType>("LeftPulmonaryArtery");
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(LeftPulmonaryArtery,
+ GetBackgroundValue(), 2, false, p);
+ max = p[2]+LeftPulmonaryArtery->GetSpacing()[2];
+ AscendingAorta =
+ clitk::CropImageRemoveLowerThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
+ DescendingAorta =
+ clitk::CropImageRemoveLowerThan<MaskImageType>(DescendingAorta, 2, max, false, GetBackgroundValue());
+ // Find closest points
+ std::vector<MaskImagePointType> A;
+ std::vector<MaskImagePointType> B;
+ clitk::SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures<MaskImageType>(AscendingAorta,
+ DescendingAorta,
+ GetBackgroundValue(),
+ 2, A, B);
+ // Separate according to AB lines
+ // clitk::WriteListOfLandmarks<MaskImageType>(A, "A.txt");
+ // clitk::WriteListOfLandmarks<MaskImageType>(B, "B.txt");
+ clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, A, B,
+ GetBackgroundValue(),
+ 1, KeepPoint); // Keep point along axis 1
+ // Now, same principle between AscendingAorta and LeftPulmonaryArtery
+ AscendingAorta =
+ clitk::ResizeImageLike<MaskImageType>(AscendingAortaCopy, m_Working_Support, GetBackgroundValue());
+ LeftPulmonaryArtery =
+ clitk::ResizeImageLike<MaskImageType>(LeftPulmonaryArtery, m_Working_Support, GetBackgroundValue());
+ AscendingAorta =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
+ LeftPulmonaryArtery =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(LeftPulmonaryArtery, 2, max, false, GetBackgroundValue());
+ A.clear();
+ B.clear();
+ clitk::SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures<MaskImageType>(AscendingAorta,
+ LeftPulmonaryArtery,
+ GetBackgroundValue(),
+ 2, A, B);
+ clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, A, B,
+ GetBackgroundValue(),
+ 1, KeepPoint); // Keep point along axis 1
+ // AutoCrop
+ m_Working_Support = clitk::AutoCrop<MaskImageType>(m_Working_Support, GetBackgroundValue());
+
+ // End
+ StopCurrentStep<MaskImageType>(m_Working_Support);
}
//--------------------------------------------------------------------
+
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff