clitk::ExtractLymphStationsFilter<TImageType>::
ExtractStation_4RL_SI_Limits()
{
+
+ /*
+ 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
+ - 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_RightPulmoArteyrCrossesMidMediastinumZPositionInMM;
// Get Inputs
- m_TopOfAorticArchInMM = GetAFDB()->GetPoint3D("topOfAorticArch", 2);
+ m_TopOfAorticArchInMM = GetAFDB()->GetPoint3D("TopOfAorticArch", 2);
DD(m_TopOfAorticArchInMM);
- m_UpperLobeBronchusZPositionInMM = GetAFDB()->GetPoint3D("rightUpperLobeBronchus", 2);
+ m_UpperLobeBronchusZPositionInMM = GetAFDB()->GetPoint3D("RightUpperLobeBronchus", 2);
DD(m_UpperLobeBronchusZPositionInMM);
- m_RightPulmoArteyrCrossesMidMediastinumZPositionInMM = GetAFDB()->GetPoint3D("rightPulmoArteryCrossesMidMediastinum", 2);
+ 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,
+ clitk::CropImageAlongOneAxis<MaskImageType>(m_Mediastinum, 2,
inf,
m_TopOfAorticArchInMM, true,
GetBackgroundValue());
StopCurrentStep<MaskImageType>(m_Working_Support);
-
- m_Station4RL = m_Working_Support;
}
//--------------------------------------------------------------------
// - 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
+
+
+ // ----------------------------------------------------------
+ StartNewStep("[Station 4R] Left limits with midline of trachea ");
- // skeleton ? -> need path description ? follow from slice to slice
- // OR CENTROID at each slice ?
-
- // Crop trachea
- // Extract list of slice from trachea
- // Loop slice -> Get centroid crop along line (BB limit) -> two supports
+ /*
+ 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>(m_Trachea, m_Working_Support, GetBackgroundValue());
+ clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
writeImage<MaskImageType>(crop_trachea, "croptrachea.mhd");
// 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);
+ 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());
}
//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_4RL_AP_Limits()
+{
+
+ /*
+ 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);
+
+ // POST -> horizontal lines bronchus --> points dectection in S7 to store.
+}
+//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff