+
+
//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
void
-clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_4RL_SI_Limits()
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_4RL_SetDefaultValues()
{
-
- /*
- Station 4R: right lower paratracheal nodes From superior to
- inferior, the delineation of Station 4R starts at the top of the
- aortic arch (Fig. 2D) and ends at the upper lobe bronchus or where the
- right pulmonary artery crosses the midline of the mediastinum
- (Fig. 3E,F). On the left side, Station 4R is defined by the midline of
- the trachea (Fig. 2D). On the right side, it is contained within the
- pleural envelope in the upper part, medial to the superior vena cava
- and the arch of the azygos vein in the intermediate section (Fig. 2I
- and 3A,B) and the right upper lobe pulmonary vein in its very caudal
- part. Anteriorly, it is limited most supe- riorly by the right
- brachiocephalic vein (Fig. 2D–H), fol- lowed by the superior vena cava
- and the arch or ascending section of the aorta (Figs. 2I and 3A–E). In
- between the superior vena cava and the aorta, we recommend delineating
- Station 4R so that it extends halfway between the two vessels where it
- will contact Station 3A or 6 (Figs. 2H,I and 3A–D). Posteriorly,
- Station 4R is defined at its superior extent by an imaginary horizontal
- line running along the posterior wall of the trachea
- (Fig. 2E). Inferiorly, it remains anterior to the right main stem
- bronchus, filling the soft- tissue space between the vessels.
- */
-
- StartNewStep("[Station 4R]Inf/Sup mediastinum limits with aortic arch/upperLBronchus");
- /* 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 */
- double inf = std::max(m_UpperLobeBronchusZPositionInMM, m_RightPulmoArteyrCrossesMidMediastinumZPositionInMM);
- m_Working_Support =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_Mediastinum, 2,
- inf,
- m_TopOfAorticArchInMM, true,
- GetBackgroundValue());
- StopCurrentStep<MaskImageType>(m_Working_Support);
}
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_4RL_LR_Limits()
-{
- // 4R first
-
- // 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 ??
-
- // 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
-
-
- // ----------------------------------------------------------
- StartNewStep("[Station 4R] Left limits with midline of trachea ");
+ExtractStation_4RL() {
+ if ((!CheckForStation("4R")) && (!CheckForStation("4L"))) return;
+
+ StartNewStep("Stations 4RL");
+ StartSubStep();
+
+ // Get the current support
+ StartNewStep("[Station 4RL] Get the current 4RL suppport");
+ m_ListOfStations["4R"] = m_ListOfSupports["S4R"];
+ m_ListOfStations["4L"] = m_ListOfSupports["S4L"];
+ StopCurrentStep<MaskImageType>(m_ListOfStations["4R"]);
+
+ // Generic RelativePosition processes
+ m_ListOfStations["4R"] = this->ApplyRelativePositionList("Station_4R", m_ListOfStations["4R"]);
+ 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;
- /*
- Two possible approaches
- 1) use trachea skeleton (clitkExtractAirwaysTreeInfo)
- -> but need to analyse the tree to remove "false" bifurcation
- -> need to track from top to bottom, with each bronchus
- -> how to stay on the main path ?
-
- 2) analyse slice by slice the trachea, labelize and take the first
- or two first connected components -> find centroids.
- -> not really "smooth" when bronchus slicing lead to "splated" region
-
- ==> we choose 2
- */
-
- // Crop the trachea like the current support
- MaskImagePointer Trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
- MaskImagePointer crop_trachea =
- clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
- writeImage<MaskImageType>(crop_trachea, "croptrachea.mhd");
-
- // Extract all the slices
- std::vector<typename MaskSliceType::Pointer> bronchi_slices;
- clitk::ExtractSlices<MaskImageType>(crop_trachea, 2, bronchi_slices);
-
- // List of midpoints
- std::vector<MaskImagePointType> midpoints;
-
- // Add mid points below carina, from foot to head
- for(uint i=0; i<m_LeftMostInRightBronchus.size(); i++) {
- MaskImagePointType p;
- p[0] = (m_LeftMostInRightBronchus[i][0]+m_RightMostInLeftBronchus[i][0])/2.0;
- p[1] = (m_LeftMostInRightBronchus[i][1]+m_RightMostInLeftBronchus[i][1])/2.0;
- p[2] = m_LeftMostInRightBronchus[i][2];
- midpoints.push_back(p);
- }
-
- // Crop the trachea above the carina. Find largest Z position
- MaskImageIndexType p = Trachea->GetLargestPossibleRegion().GetIndex();
- for(uint i=0; i<3; i++) {
- p[i] += Trachea->GetLargestPossibleRegion().GetSize()[i];
- }
- MaskImagePointType q;
- Trachea->TransformIndexToPhysicalPoint(p, q);
- double maxZ = q[2];
- double m_CarinaZ = GetAFDB()->GetPoint3D("Carina", 2);
- MaskImagePointer m_above_carina =
- clitk::CropImageAlongOneAxis<MaskImageType>(Trachea, 2,
- m_CarinaZ,
- maxZ, true,
- GetBackgroundValue());
- writeImage<MaskImageType>(m_above_carina, "above.mhd");
-
- // Extract all the slices
- std::vector<typename MaskSliceType::Pointer> trachea_slices;
- clitk::ExtractSlices<MaskImageType>(m_above_carina, 2, trachea_slices);
-
- // Find centroid of the trachea in each slice
- std::vector<MaskImagePointType> points;
- typedef typename MaskSliceType::PointType SlicePointType;
- SlicePointType previous;
- // Start from patient top (head)
- for(uint i=0; i<trachea_slices.size(); i++) {
- // Labelize
- trachea_slices[i] = Labelize<MaskSliceType>(trachea_slices[i], GetBackgroundValue(), true, 10);
- // Get centroid
- std::vector<SlicePointType> c;
- clitk::ComputeCentroids<MaskSliceType>(trachea_slices[i], GetBackgroundValue(), c);
- // Keep first one (first connected component label) and convert to 3D
- MaskImagePointType p;
- p[2] = m_above_carina->GetOrigin()[2] + i*m_above_carina->GetSpacing()[2];
- p[0] = c[1][0];
- p[1] = c[1][1];
- midpoints.push_back(p);
- }
-
- // DEBUG POINTS
- std::ofstream osp;
- openFileForWriting(osp, "mp.txt");
- osp << "LANDMARKS1" << std::endl;
- for(uint i=0; i<midpoints.size(); i++) {
- osp << i << " " << midpoints[i][0] << " "
- << midpoints[i][1] << " " << midpoints[i][2] << " 0 0 " << std::endl;
- }
- osp.close();
-
- // Create and allocate left and right part of the support (we create
- // images because we will then crop them)
- m_LeftSupport = clitk::NewImageLike<MaskImageType>(m_Working_Support);
- m_RightSupport = clitk::NewImageLike<MaskImageType>(m_Working_Support);
-
- // Loop on current support, slice by slice
- typedef itk::ImageSliceIteratorWithIndex<MaskImageType> SliceIteratorType;
- SliceIteratorType iter = SliceIteratorType(m_Working_Support,
- m_Working_Support->GetLargestPossibleRegion());
- SliceIteratorType iterL = SliceIteratorType(m_LeftSupport,
- m_LeftSupport->GetLargestPossibleRegion());
- SliceIteratorType iterR = SliceIteratorType(m_RightSupport,
- m_RightSupport->GetLargestPossibleRegion());
- iter.SetFirstDirection(0);
- iter.SetSecondDirection(1);
- iter.GoToBegin();
- iterL.SetFirstDirection(0);
- iterL.SetSecondDirection(1);
- iterL.GoToBegin();
- iterR.SetFirstDirection(0);
- iterR.SetSecondDirection(1);
- iterR.GoToBegin();
-
- int slice=0;
- // Assert starting of image has the same Z than first midpoints
- while (midpoints[slice][2] != m_Working_Support->GetOrigin()[2]) {
- slice++;
- if ((uint)slice >= midpoints.size()) {
- clitkExceptionMacro("Bug while searching for first midpoint to use");
- }
- }
-
- // Start loop
- while (!iter.IsAtEnd()) {
- ImageIndexType index;
- m_Working_Support->TransformPhysicalPointToIndex(midpoints[slice], index);
- while (!iter.IsAtEndOfSlice()) {
- // convert into index
- while (!iter.IsAtEndOfLine()) {
- // if indexcourant <index this is Right part. Left otherwise
- if (iter.GetIndex()[0]<index[0]) {
- iterR.Set(iter.Get());
- iterL.Set(GetBackgroundValue());
- }
- else {
- iterL.Set(iter.Get());
- iterR.Set(GetBackgroundValue());
- }
- ++iter;
- ++iterL;
- ++iterR;
- }
- iter.NextLine();
- iterL.NextLine();
- iterR.NextLine();
-
- }
- iter.NextSlice();
- iterL.NextSlice();
- iterR.NextSlice();
- ++slice;
- }
-
- // Auto crop !
- m_LeftSupport = clitk::AutoCrop<MaskImageType>(m_LeftSupport, GetBackgroundValue());
- m_RightSupport = clitk::AutoCrop<MaskImageType>(m_RightSupport, GetBackgroundValue());
- writeImage<MaskImageType>(m_LeftSupport, "lsac.mhd");
- writeImage<MaskImageType>(m_RightSupport, "rsac.mhd");
-
- StopCurrentStep<MaskImageType>(m_RightSupport);
-
- // -------------------------------------------------------------------------
- // Constraint at right from the SVC. Must be after MidTrachea limits
- // (if not, bronchus can be split, midposition is false)
- StartNewStep("[Station 4R] R limits with SVC ");
- MaskImagePointer svc = GetAFDB()->template GetImage<MaskImageType>("SVC");
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- /* relPosFilter->SetVerboseStep(false);
- relPosFilter->SetInput(m_RightSupport); // only right here ...
- relPosFilter->SetInputObject(svc);
- relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
- relPosFilter->SetIntermediateSpacing(2);
- relPosFilter->SetFuzzyThreshold(0.3);
- relPosFilter->Update();
- m_RightSupport = relPosFilter->GetOutput();
- */
-
- /*
- ==> TODO RIGHT TO MEDIAL TO SVC :
- get centroid, cut in X direction to get medial
-
- ==> REDO OPERATOR to find extrma points ?
- centroid or skeleton ?
-
- */
-
- relPosFilter = RelPosFilterType::New();
- relPosFilter->VerboseStepFlagOff();
- relPosFilter->SetInput(m_RightSupport); // only right here ...
- relPosFilter->SetInputObject(svc);
- relPosFilter->AddOrientationType(RelPosFilterType::AntTo);
- relPosFilter->InverseOrientationFlagOn();
- relPosFilter->SetIntermediateSpacing(2); // this is important to put it low
- relPosFilter->SetFuzzyThreshold(0.6);
- relPosFilter->Update();
- m_RightSupport = relPosFilter->GetOutput();
-
- // AutoCrop
- m_RightSupport = clitk::AutoCrop<MaskImageType>(m_RightSupport, GetBackgroundValue());
+ // 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"]);
+
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["4R"], "seg/Station4R.mhd");
+ writeImage<MaskImageType>(m_ListOfStations["4L"], "seg/Station4L.mhd");
+ GetAFDB()->SetImageFilename("Station4R", "seg/Station4R.mhd");
+ GetAFDB()->SetImageFilename("Station4L", "seg/Station4L.mhd");
+ WriteAFDB();
+ StopSubStep();
}
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_4RL_AP_Limits()
+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());
+
+ // 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
- /*
- post of S4R
- - sup part -> cut line post wall trachea
- - inf part (where ???) -> remains anterior to the right main stem bronchus
- ==> bo
- */
-
- // Post (not Ant) to Aorta
- MaskImagePointer aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
- // Crop according to current support
- aorta = clitk::ResizeImageLike<MaskImageType>(aorta, m_RightSupport, GetBackgroundValue());
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- relPosFilter = RelPosFilterType::New();
- relPosFilter->VerboseStepFlagOff();
- relPosFilter->SetInput(m_RightSupport); // only right here ...
- relPosFilter->SetInputObject(aorta);
- relPosFilter->AddOrientationType(RelPosFilterType::PostTo);
- // relPosFilter->NotFlagOn();
- relPosFilter->SetIntermediateSpacing(2); // this is important to put it low
- relPosFilter->SetFuzzyThreshold(0.6);
- relPosFilter->Update();
- m_RightSupport = relPosFilter->GetOutput();
-
- m_ListOfStations["4R"] = m_RightSupport;
- StopCurrentStep<MaskImageType>(m_RightSupport);
+ // AutoCrop
+ m_Working_Support = clitk::AutoCrop<MaskImageType>(m_Working_Support, GetBackgroundValue());
- // POST -> horizontal lines bronchus --> points dectection in S7 to store.
+ // End
+ StopCurrentStep<MaskImageType>(m_Working_Support);
}
//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff