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++) {
+ for(unsigned int i=0; i<out.size(); i++) {
itk::Point<double, Dim> p;
if (i<previous.size()) p[0] = 0;
else p[0] = 1;
std::vector<typename ImageType::PointType> & bounds)
{
// Get image max/min coordinates
- const uint dim=ImageType::ImageDimension;
+ const unsigned int 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];
+ for(unsigned int 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++) {
+ for(unsigned int i=0; i<bounds.size(); i++) {
+ for(unsigned int 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];
}
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);
// -----------------------------------------------------
// 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
/* 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
+ vessel1 = BrachioCephalicArtery
vessel2 = BrachioCephalicVein (warning several CCL, keep most at Right)
vessel3 = CommonCarotidArtery
vessel4 = SubclavianArtery
*/
// Read structures
- MaskImagePointer BrachioCephalicTrunk = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicTrunk");
+ MaskImagePointer BrachioCephalicArtery = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicArtery");
MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
MaskImagePointer CommonCarotidArtery = GetAFDB()->template GetImage<MaskImageType>("CommonCarotidArtery");
MaskImagePointer SubclavianArtery = GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
// Resize all structures like support
- BrachioCephalicTrunk =
- clitk::ResizeImageLike<MaskImageType>(BrachioCephalicTrunk, m_Working_Support, GetBackgroundValue());
+ BrachioCephalicArtery =
+ clitk::ResizeImageLike<MaskImageType>(BrachioCephalicArtery, m_Working_Support, GetBackgroundValue());
CommonCarotidArtery =
clitk::ResizeImageLike<MaskImageType>(CommonCarotidArtery, m_Working_Support, GetBackgroundValue());
SubclavianArtery =
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_BrachioCephalicArtery;
+ clitk::ExtractSlices<MaskImageType>(BrachioCephalicArtery, 2, slices_BrachioCephalicArtery);
std::vector<MaskSlicePointer> slices_BrachioCephalicVein;
clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, slices_BrachioCephalicVein);
std::vector<MaskSlicePointer> slices_CommonCarotidArtery;
clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices_Aorta);
std::vector<MaskSlicePointer> slices_Trachea;
clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices_Trachea);
- uint n= slices_BrachioCephalicTrunk.size();
+ unsigned int n= slices_BrachioCephalicArtery.size();
// Get the boundaries of one slice
std::vector<MaskSlicePointType> bounds;
- ComputeImageBoundariesCoordinates<MaskSliceType>(slices_BrachioCephalicTrunk[0], bounds);
+ ComputeImageBoundariesCoordinates<MaskSliceType>(slices_BrachioCephalicArtery[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++) {
+ for(unsigned int 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],
+ slices_BrachioCephalicArtery[i] = Labelize<MaskSliceType>(slices_BrachioCephalicArtery[i],
GetBackgroundValue(), true, 1);
slices_BrachioCephalicVein[i] = Labelize<MaskSliceType>(slices_BrachioCephalicVein[i],
GetBackgroundValue(), true, 1);
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_BrachioCephalicArtery[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 SubclavianArtery has 2 CCL
- // (BrachioCephalicTrunk is divided) -> forget BrachioCephalicVein
+ // (BrachioCephalicArtery 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]);
+ for(unsigned int j=1; j<centroids1.size(); j++) points2D.push_back(centroids1[j]);
+ for(unsigned int j=1; j<centroids2.size(); j++) points2D.push_back(centroids2[j]);
+ for(unsigned int j=1; j<centroids3.size(); j++) points2D.push_back(centroids3[j]);
+ for(unsigned int j=1; j<centroids4.size(); j++) points2D.push_back(centroids4[j]);
+ for(unsigned int j=1; j<centroids5.size(); j++) points2D.push_back(centroids5[j]);
+ for(unsigned int j=1; j<centroids6.size(); j++) points2D.push_back(centroids6[j]);
// Sort by angle according to trachea centroid and vertical line,
// in polar coordinates :
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++) {
+ for(u
nsigned int 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
// Sort points2D according to polar angles
std::sort(angles.begin(), angles.end(), comparePointsWithAngle<PointAngleType>());
- for(uint j=0; j<angles.size(); j++) {
+ for(u
nsigned int j=0; j<angles.size(); j++) {
points2D[j] = angles[j].first;
}
// DDV(points2D, points2D.size());
low, add one point
*/
std::vector<MaskSlicePointType> toadd;
- uint index = 0;
+ unsigned int index = 0;
double dmax = 5;
while (index<points2D.size()-1) {
MaskSlicePointType a = points2D[index];
// 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]);
+ for(u
nsigned int x=0; x<points3D.size(); x++) p3D.push_back(points3D[x]);
// Build the mesh from the contour's points
vtkSmartPointer<vtkPolyData> mesh = Build3DMeshFrom2DContour(points3D);
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff