// itk
#include <itkImageDuplicator.h>
-//--------------------------------------------------------------------
-template<class PointType>
-class comparePointsX {
-public:
- bool operator() (PointType i, PointType j) { return (i[0]<j[0]); }
-};
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class PairType>
-class comparePointsWithAngle {
-public:
- bool operator() (PairType i, PairType j) { return (i.second < j.second); }
-};
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<int Dim>
-void HypercubeCorners(std::vector<itk::Point<double, Dim> > & out) {
- std::vector<itk::Point<double, Dim-1> > previous;
- HypercubeCorners<Dim-1>(previous);
- out.resize(previous.size()*2);
- for(uint i=0; i<out.size(); i++) {
- itk::Point<double, Dim> p;
- if (i<previous.size()) p[0] = 0;
- else p[0] = 1;
- for(int j=0; j<Dim-1; j++)
- {
- p[j+1] = previous[i%previous.size()][j];
- }
- out[i] = p;
- }
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<>
-void HypercubeCorners<1>(std::vector<itk::Point<double, 1> > & out) {
- out.resize(2);
- out[0][0] = 0;
- out[1][0] = 1;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-void ComputeImageBoundariesCoordinates(typename ImageType::Pointer image,
- std::vector<typename ImageType::PointType> & bounds)
-{
- // Get image max/min coordinates
- const uint dim=ImageType::ImageDimension;
- typedef typename ImageType::PointType PointType;
- typedef typename ImageType::IndexType IndexType;
- PointType min_c, max_c;
- IndexType min_i, max_i;
- min_i = image->GetLargestPossibleRegion().GetIndex();
- for(uint i=0; i<dim; i++) max_i[i] = image->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
- image->TransformIndexToPhysicalPoint(min_i, min_c);
- image->TransformIndexToPhysicalPoint(max_i, max_c);
-
- // Get corners coordinates
- HypercubeCorners<ImageType::ImageDimension>(bounds);
- for(uint i=0; i<bounds.size(); i++) {
- for(uint j=0; j<dim; j++) {
- if (bounds[i][j] == 0) bounds[i][j] = min_c[j];
- if (bounds[i][j] == 1) bounds[i][j] = max_c[j];
- }
- }
-}
-//--------------------------------------------------------------------
-
-
//--------------------------------------------------------------------
template <class ImageType>
void
ExtractStation_2RL_SetDefaultValues()
{
SetFuzzyThreshold("2RL", "CommonCarotidArtery", 0.7);
- SetFuzzyThreshold("2RL", "BrachioCephalicTrunk", 0.7);
+ SetFuzzyThreshold("2RL", "BrachioCephalicArtery", 0.7);
SetFuzzyThreshold("2RL", "BrachioCephalicVein", 0.3);
SetFuzzyThreshold("2RL", "Aorta", 0.7);
SetFuzzyThreshold("2RL", "SubclavianArteryRight", 0.5);
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_2RL()
+{
+ if ((!CheckForStation("2R")) && (!CheckForStation("2L"))) return;
+
+ 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<MaskImageType>(m_ListOfStations["2R"], "seg/Station2R.mhd");
+ writeImage<MaskImageType>(m_ListOfStations["2L"], "seg/Station2L.mhd");
+ GetAFDB()->SetImageFilename("Station2R", "seg/Station2R.mhd");
+ GetAFDB()->SetImageFilename("Station2L", "seg/Station2L.mhd");
+ WriteAFDB();
+
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
template <class ImageType>
void
// -----------------------------------------------------
// Remove Ant to H line from the Ant most part of the
// CommonCarotidArtery until we reach the first slice of
- // BrachioCephalicTrunk
+ // BrachioCephalicArtery
StartNewStep("[Station 2RL] Ant limits with CommonCarotidArtery, H line");
- // First, find the first slice of BrachioCephalicTrunk
- MaskImagePointer BrachioCephalicTrunk = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicTrunk");
- MaskImagePointType p = BrachioCephalicTrunk->GetOrigin(); // initialise to avoid warning
- clitk::FindExtremaPointInAGivenDirection<MaskImageType>(BrachioCephalicTrunk, GetBackgroundValue(), 2, false, p);
- double TopOfBrachioCephalicTrunkZ=p[2] + BrachioCephalicTrunk->GetSpacing()[2]; // Add one slice
+ // First, find the first slice of BrachioCephalicArtery
+ MaskImagePointer BrachioCephalicArtery = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
+ MaskImagePointType p = BrachioCephalicArtery->GetOrigin(); // initialise to avoid warning
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(BrachioCephalicArtery, GetBackgroundValue(), 2, false, p);
+ double TopOfBrachioCephalicArteryZ=p[2] + BrachioCephalicArtery->GetSpacing()[2]; // Add one slice
// Remove CommonCarotidArtery below this point
- CommonCarotidArtery = clitk::CropImageRemoveLowerThan<MaskImageType>(CommonCarotidArtery, 2, TopOfBrachioCephalicTrunkZ, true, GetBackgroundValue());
+ CommonCarotidArtery = clitk::CropImageRemoveLowerThan<MaskImageType>(CommonCarotidArtery, 2, TopOfBrachioCephalicArteryZ, true, GetBackgroundValue());
// Find most Ant points
std::vector<MaskImagePointType> ccaAntPositionA;
m_ListOfStations["2L"] = m_Working_Support;
// -----------------------------------------------------
- // Ant limit with the BrachioCephalicTrunk
- StartNewStep("[Station 2RL] Ant limits with BrachioCephalicTrunk line");
+ // Ant limit with the BrachioCephalicArtery
+ StartNewStep("[Station 2RL] Ant limits with BrachioCephalicArtery line");
- // Remove Ant to BrachioCephalicTrunk
+ // Remove Ant to BrachioCephalicArtery
m_Working_Support =
- clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, BrachioCephalicTrunk, 2,
- GetFuzzyThreshold("2RL", "BrachioCephalicTrunk"), "NotAntTo", false, 2, true, false);
+ clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, BrachioCephalicArtery, 2,
+ GetFuzzyThreshold("2RL", "BrachioCephalicArtery"), "NotAntTo", false, 2, true, false);
// End
StopCurrentStep<MaskImageType>(m_Working_Support);
m_ListOfStations["2R"] = m_Working_Support;
m_ListOfStations["2L"] = m_Working_Support;
// -----------------------------------------------------
- // Ant limit with the BrachioCephalicTrunk H line
- StartNewStep("[Station 2RL] Ant limits with BrachioCephalicTrunk, Horizontal line");
+ // Ant limit with the BrachioCephalicArtery H line
+ StartNewStep("[Station 2RL] Ant limits with BrachioCephalicArtery, Horizontal line");
// Find most Ant points
std::vector<MaskImagePointType> bctAntPositionA;
std::vector<MaskImagePointType> bctAntPositionB;
- clitk::SliceBySliceBuildLineSegmentAccordingToExtremaPosition<MaskImageType>(BrachioCephalicTrunk,
+ clitk::SliceBySliceBuildLineSegmentAccordingToExtremaPosition<MaskImageType>(BrachioCephalicArtery,
GetBackgroundValue(), 2,
1, true, // Ant
0, // Horizontal line
template <class ImageType>
void
clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_2RL_Ant_Limits2()
+ExtractStation_2RL_Ant_Limits2()
{
- // -----------------------------------------------------
- /* Rod says: "The anterior border, as with the Atlas – UM, is
- posterior to the vessels (right subclavian vein, left
- brachiocephalic vein, right brachiocephalic vein, left subclavian
- artery, left common carotid artery and brachiocephalic trunk).
- These vessels are not included in the nodal station. The anterior
- border is drawn to the midpoint of the vessel and an imaginary
- line joins the middle of these vessels. Between the vessels,
- station 2 is in contact with station 3a." */
-
// -----------------------------------------------------
StartNewStep("[Station 2RL] Ant limits with vessels centroids");
-
- /* Here, we consider the vessels form a kind of anterior barrier. We
- link all vessels centroids and remove what is post to it.
- - select the list of structure
- vessel1 = BrachioCephalicTrunk
- vessel2 = BrachioCephalicVein (warning several CCL, keep most at Right)
- vessel3 = CommonCarotidArtery
- vessel4 = SubclavianArtery
- other = Thyroid
- other = Aorta
- - crop images as needed
- - slice by slice, choose the CCL and extract centroids
- - slice by slice, sort according to polar angle wrt Trachea centroid.
- - slice by slice, link centroids and close contour
- - remove outside this contour
- - merge with support
- */
-
- // Read structures
- MaskImagePointer BrachioCephalicTrunk = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicTrunk");
- MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
- MaskImagePointer CommonCarotidArtery = GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArtery");
- MaskImagePointer SubclavianArtery = GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
- MaskImagePointer Thyroid = GetAFDB()->template GetImage<MaskImageType>("Thyroid");
- MaskImagePointer Aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
- MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
-
- // Resize all structures like support
- BrachioCephalicTrunk =
- clitk::ResizeImageLike<MaskImageType>(BrachioCephalicTrunk, m_Working_Support, GetBackgroundValue());
- CommonCarotidArtery =
- clitk::ResizeImageLike<MaskImageType>(CommonCarotidArtery, m_Working_Support, GetBackgroundValue());
- SubclavianArtery =
- clitk::ResizeImageLike<MaskImageType>(SubclavianArtery, m_Working_Support, GetBackgroundValue());
- Thyroid =
- clitk::ResizeImageLike<MaskImageType>(Thyroid, m_Working_Support, GetBackgroundValue());
- Aorta =
- clitk::ResizeImageLike<MaskImageType>(Aorta, m_Working_Support, GetBackgroundValue());
- BrachioCephalicVein =
- clitk::ResizeImageLike<MaskImageType>(BrachioCephalicVein, m_Working_Support, GetBackgroundValue());
- Trachea =
- clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
-
- // Extract slices
- std::vector<MaskSlicePointer> slices_BrachioCephalicTrunk;
- clitk::ExtractSlices<MaskImageType>(BrachioCephalicTrunk, 2, slices_BrachioCephalicTrunk);
- std::vector<MaskSlicePointer> slices_BrachioCephalicVein;
- clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, slices_BrachioCephalicVein);
- std::vector<MaskSlicePointer> slices_CommonCarotidArtery;
- clitk::ExtractSlices<MaskImageType>(CommonCarotidArtery, 2, slices_CommonCarotidArtery);
- std::vector<MaskSlicePointer> slices_SubclavianArtery;
- clitk::ExtractSlices<MaskImageType>(SubclavianArtery, 2, slices_SubclavianArtery);
- std::vector<MaskSlicePointer> slices_Thyroid;
- clitk::ExtractSlices<MaskImageType>(Thyroid, 2, slices_Thyroid);
- std::vector<MaskSlicePointer> slices_Aorta;
- clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices_Aorta);
- std::vector<MaskSlicePointer> slices_Trachea;
- clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices_Trachea);
- uint n= slices_BrachioCephalicTrunk.size();
- // Get the boundaries of one slice
- std::vector<MaskSlicePointType> bounds;
- ComputeImageBoundariesCoordinates<MaskSliceType>(slices_BrachioCephalicTrunk[0], bounds);
-
- // For all slices, for all structures, find the centroid and build the contour
- // List of 3D points (for debug)
- std::vector<MaskImagePointType> p3D;
-
- vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
- for(uint i=0; i<n; i++) {
- // Labelize the slices
- slices_CommonCarotidArtery[i] = Labelize<MaskSliceType>(slices_CommonCarotidArtery[i],
- GetBackgroundValue(), true, 1);
- slices_SubclavianArtery[i] = Labelize<MaskSliceType>(slices_SubclavianArtery[i],
- GetBackgroundValue(), true, 1);
- slices_BrachioCephalicTrunk[i] = Labelize<MaskSliceType>(slices_BrachioCephalicTrunk[i],
- GetBackgroundValue(), true, 1);
- slices_BrachioCephalicVein[i] = Labelize<MaskSliceType>(slices_BrachioCephalicVein[i],
- GetBackgroundValue(), true, 1);
- slices_Thyroid[i] = Labelize<MaskSliceType>(slices_Thyroid[i],
- GetBackgroundValue(), true, 1);
- slices_Aorta[i] = Labelize<MaskSliceType>(slices_Aorta[i],
- GetBackgroundValue(), true, 1);
-
- // Search centroids
- std::vector<MaskSlicePointType> points2D;
- std::vector<MaskSlicePointType> centroids1;
- std::vector<MaskSlicePointType> centroids2;
- std::vector<MaskSlicePointType> centroids3;
- std::vector<MaskSlicePointType> centroids4;
- std::vector<MaskSlicePointType> centroids5;
- std::vector<MaskSlicePointType> centroids6;
- ComputeCentroids<MaskSliceType>(slices_CommonCarotidArtery[i], GetBackgroundValue(), centroids1);
- ComputeCentroids<MaskSliceType>(slices_SubclavianArtery[i], GetBackgroundValue(), centroids2);
- ComputeCentroids<MaskSliceType>(slices_BrachioCephalicTrunk[i], GetBackgroundValue(), centroids3);
- ComputeCentroids<MaskSliceType>(slices_Thyroid[i], GetBackgroundValue(), centroids4);
- ComputeCentroids<MaskSliceType>(slices_Aorta[i], GetBackgroundValue(), centroids5);
- ComputeCentroids<MaskSliceType>(slices_BrachioCephalicVein[i], GetBackgroundValue(), centroids6);
-
- // BrachioCephalicVein -> when it is separated into two CCL, we
- // only consider the most at Right one
- if (centroids6.size() > 2) {
- if (centroids6[1][0] < centroids6[2][0]) centroids6.erase(centroids6.begin()+2);
- else centroids6.erase(centroids6.begin()+1);
- }
-
- // BrachioCephalicVein -> when SubclavianArtery has 2 CCL
- // (BrachioCephalicTrunk is divided) -> forget BrachioCephalicVein
- if ((centroids3.size() ==1) && (centroids2.size() > 2)) {
- centroids6.clear();
- }
-
- for(uint j=1; j<centroids1.size(); j++) points2D.push_back(centroids1[j]);
- for(uint j=1; j<centroids2.size(); j++) points2D.push_back(centroids2[j]);
- for(uint j=1; j<centroids3.size(); j++) points2D.push_back(centroids3[j]);
- for(uint j=1; j<centroids4.size(); j++) points2D.push_back(centroids4[j]);
- for(uint j=1; j<centroids5.size(); j++) points2D.push_back(centroids5[j]);
- for(uint j=1; j<centroids6.size(); j++) points2D.push_back(centroids6[j]);
-
- // Sort by angle according to trachea centroid and vertical line,
- // in polar coordinates :
- // http://en.wikipedia.org/wiki/Polar_coordinate_system
- std::vector<MaskSlicePointType> centroids_trachea;
- ComputeCentroids<MaskSliceType>(slices_Trachea[i], GetBackgroundValue(), centroids_trachea);
- typedef std::pair<MaskSlicePointType, double> PointAngleType;
- std::vector<PointAngleType> angles;
- for(uint j=0; j<points2D.size(); j++) {
- //double r = centroids_trachea[1].EuclideanDistanceTo(points2D[j]);
- double x = (points2D[j][0]-centroids_trachea[1][0]); // X : Right to Left
- double y = (centroids_trachea[1][1]-points2D[j][1]); // Y : Post to Ant
- double angle = 0;
- if (x>0) angle = atan(y/x);
- if ((x<0) && (y>=0)) angle = atan(y/x)+M_PI;
- if ((x<0) && (y<0)) angle = atan(y/x)-M_PI;
- if (x==0) {
- if (y>0) angle = M_PI/2.0;
- if (y<0) angle = -M_PI/2.0;
- if (y==0) angle = 0;
- }
- angle = clitk::rad2deg(angle);
- // Angle is [-180;180] wrt the X axis. We change the X axis to
- // be the vertical line, because we want to sort from Right to
- // Left from Post to Ant.
- if (angle>0)
- angle = (270-angle);
- if (angle<0) {
- angle = -angle-90;
- if (angle<0) angle = 360-angle;
- }
- PointAngleType a;
- a.first = points2D[j];
- a.second = angle;
- angles.push_back(a);
- }
-
- // Do nothing if less than 2 points --> n
- if (points2D.size() < 3) { //continue;
- continue;
- }
-
- // Sort points2D according to polar angles
- std::sort(angles.begin(), angles.end(), comparePointsWithAngle<PointAngleType>());
- for(uint j=0; j<angles.size(); j++) {
- points2D[j] = angles[j].first;
- }
- // DDV(points2D, points2D.size());
-
- /* When vessels are far away, we try to replace the line segment
- with a curved line that join the two vessels but stay
- approximately at the same distance from the trachea centroids
- than the vessels.
-
- For that:
- - let a and c be two successive vessels centroids
- - id distance(a,c) < threshold, next point
-
- TODO HERE
-
- - compute mid position between two successive points -
- compute dist to trachea centroid for the 3 pts - if middle too
- low, add one point
- */
- std::vector<MaskSlicePointType> toadd;
- uint index = 0;
- double dmax = 5;
- while (index<points2D.size()-1) {
- MaskSlicePointType a = points2D[index];
- MaskSlicePointType c = points2D[index+1];
-
- double dac = a.EuclideanDistanceTo(c);
- if (dac>dmax) {
-
- MaskSlicePointType b;
- b[0] = a[0]+(c[0]-a[0])/2.0;
- b[1] = a[1]+(c[1]-a[1])/2.0;
-
- // Compute distance to trachea centroid
- MaskSlicePointType m = centroids_trachea[1];
- double da = m.EuclideanDistanceTo(a);
- double db = m.EuclideanDistanceTo(b);
- //double dc = m.EuclideanDistanceTo(c);
-
- // Mean distance, find point on the line from trachea centroid
- // to b
- double alpha = (da+db)/2.0;
- MaskSlicePointType v;
- double n = sqrt( pow(b[0]-m[0], 2) + pow(b[1]-m[1], 2));
- v[0] = (b[0]-m[0])/n;
- v[1] = (b[1]-m[1])/n;
- MaskSlicePointType r;
- r[0] = m[0]+alpha*v[0];
- r[1] = m[1]+alpha*v[1];
- points2D.insert(points2D.begin()+index+1, r);
- }
- else {
- index++;
- }
- }
- // DDV(points2D, points2D.size());
-
- // Add some points to close the contour
- // - H line towards Right
- MaskSlicePointType p = points2D[0];
- p[0] = bounds[0][0];
- points2D.insert(points2D.begin(), p);
- // - corner Right/Post
- p = bounds[0];
- points2D.insert(points2D.begin(), p);
- // - H line towards Left
- p = points2D.back();
- p[0] = bounds[2][0];
- points2D.push_back(p);
- // - corner Right/Post
- p = bounds[2];
- points2D.push_back(p);
- // Close contour with the first point
- points2D.push_back(points2D[0]);
- // DDV(points2D, points2D.size());
-
- // Build 3D points from the 2D points
- std::vector<ImagePointType> points3D;
- clitk::PointsUtils<MaskImageType>::Convert2DListTo3DList(points2D, i, m_Working_Support, points3D);
- for(uint x=0; x<points3D.size(); x++) p3D.push_back(points3D[x]);
-
- // Build the mesh from the contour's points
- vtkSmartPointer<vtkPolyData> mesh = Build3DMeshFrom2DContour(points3D);
- append->AddInput(mesh);
- }
-
- // DEBUG: write points3D
- clitk::WriteListOfLandmarks<MaskImageType>(p3D, "vessels-centroids.txt");
-
- // Build the final 3D mesh form the list 2D mesh
- append->Update();
- vtkSmartPointer<vtkPolyData> mesh = append->GetOutput();
-
- // Debug, write the mesh
- /*
- vtkSmartPointer<vtkPolyDataWriter> w = vtkSmartPointer<vtkPolyDataWriter>::New();
- w->SetInput(mesh);
- w->SetFileName("bidon.vtk");
- w->Write();
- */
+ // WARNING, as I used "And" after, empty slice in binarizedContour
+ // lead to remove part of the support, although we want to keep
+ // unchanged. So we decide to ResizeImageLike but pad with
+ // ForegroundValue instead of BG
+
+ // Get or compute the binary mask that separate Ant/Post part
+ // according to vessels
+ MaskImagePointer binarizedContour = FindAntPostVessels2();
+ binarizedContour = clitk::ResizeImageLike<MaskImageType>(binarizedContour,
+ m_Working_Support,
+ GetForegroundValue());
- // Compute a single binary 3D image from the list of contours
- clitk::MeshToBinaryImageFilter<MaskImageType>::Pointer filter =
- clitk::MeshToBinaryImageFilter<MaskImageType>::New();
- filter->SetMesh(mesh);
- filter->SetLikeImage(m_Working_Support);
- filter->Update();
- MaskImagePointer binarizedContour = filter->GetOutput();
-
- // Inverse binary mask if needed. We test a point that we know must be in FG. If it is not, inverse
- ImagePointType p = p3D[2]; // This is the first centroid of the first slice
- p[1] += 50; // 50 mm Post from this point must be kept
- ImageIndexType index;
- binarizedContour->TransformPhysicalPointToIndex(p, index);
- bool isInside = (binarizedContour->GetPixel(index) != GetBackgroundValue());
-
// remove from support
typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
boolFilter->SetInput2(binarizedContour);
boolFilter->SetBackgroundValue1(GetBackgroundValue());
boolFilter->SetBackgroundValue2(GetBackgroundValue());
- if (isInside)
- boolFilter->SetOperationType(BoolFilterType::And);
- else
- boolFilter->SetOperationType(BoolFilterType::AndNot);
+ boolFilter->SetOperationType(BoolFilterType::And);
boolFilter->Update();
m_Working_Support = boolFilter->GetOutput();
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff