}
//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
template <class ImageType>
void
{
/*
Apex of the chest & Carina.
- */
+ */
StartNewStep("[Station 3P] Inf/Sup limits with apex of the chest and carina");
- writeImage<MaskImageType>(m_Working_Support, "support.mhd");
-
// Get Carina position (has been determined in Station8)
m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
- DD(m_CarinaZ);
- // Get Apex of the Chest
+ // Get Apex of the Chest. The "lungs" structure is autocroped so we
+ // consider the most superior point.
MaskImagePointer Lungs = GetAFDB()->template GetImage<MaskImageType>("Lungs");
- DD("lung ok");
+ MaskImageIndexType index = Lungs->GetLargestPossibleRegion().GetIndex();
+ index += Lungs->GetLargestPossibleRegion().GetSize();
MaskImagePointType p;
- bool found = clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Lungs,
- GetBackgroundValue(),
- 1, true, p);
- DD(found);
- DD(p);
+ Lungs->TransformIndexToPhysicalPoint(index, p);
+ p[2] -= 5; // 5 mm below because the autocrop is slightly above the apex
double m_ApexOfTheChest = p[2];
- DD(m_ApexOfTheChest);
/* Crop support :
Superior limit = carina
Inferior limit = Apex of the chest */
m_Working_Support =
clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2,
- m_ApexOfTheChest,
- m_CarinaZ, true,
+ m_CarinaZ,
+ m_ApexOfTheChest, true,
GetBackgroundValue());
StopCurrentStep<MaskImageType>(m_Working_Support);
m_ListOfStations["3P"] = m_Working_Support;
}
//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_Remove_Structures()
+{
+ /*
+ 3 - (sup) remove Aorta, VB, subcl
+ not LR subcl ! -> a séparer LR ?
+ (inf) remove Eso, Aorta, Azygousvein
+ */
+
+ StartNewStep("[Station 3P] Remove some structures.");
+
+ MaskImagePointer Aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
+ clitk::AndNot<MaskImageType>(m_Working_Support, Aorta, GetBackgroundValue());
+
+ MaskImagePointer VertebralBody = GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
+ clitk::AndNot<MaskImageType>(m_Working_Support, VertebralBody);
+
+ MaskImagePointer SubclavianArtery = GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
+ clitk::AndNot<MaskImageType>(m_Working_Support, SubclavianArtery);
+
+ MaskImagePointer Esophagus = GetAFDB()->template GetImage<MaskImageType>("Esophagus");
+ clitk::AndNot<MaskImageType>(m_Working_Support, Esophagus);
+
+ MaskImagePointer AzygousVein = GetAFDB()->template GetImage<MaskImageType>("AzygousVein");
+ clitk::AndNot<MaskImageType>(m_Working_Support, AzygousVein);
+
+ MaskImagePointer Thyroid = GetAFDB()->template GetImage<MaskImageType>("Thyroid");
+ clitk::AndNot<MaskImageType>(m_Working_Support, Thyroid);
+
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_Ant_Limits()
+{
+ /*
+ Ant Post limit :
+
+ Anteriorly, it is in contact with the posterior aspect of Stations
+ 1–2 superiorly (Fig. 2A–C) and with Stations 4R and 4L inferiorly
+ (Fig. 2D–I and 3A–C). The anterior limit of Station 3P is kept
+ posterior to the trachea, which is defined by an imaginary
+ horizontal line running along the posterior wall of the trachea
+ (Fig. 2B,E, red line). Posteriorly, it is delineated along the
+ anterior and lateral borders of the vertebral body until an
+ imaginary horizontal line running 1 cm posteriorly to the
+ anterior border of the vertebral body (Fig. 2D).
+
+ 1 - post to the trachea : define an imaginary line just post the
+ Trachea and remove what is anterior.
+
+ */
+ StartNewStep("[Station 3P] Ant limits with Trachea ");
+
+ // Load Trachea
+ MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+
+ // Crop like current support (need by SliceBySliceSetBackgroundFromLineSeparation after)
+ Trachea =
+ clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
+
+ // Slice by slice, determine the most post point of the trachea (A)
+ // and consider a second point on the same horizontal line (B)
+ std::vector<MaskImagePointType> p_A;
+ std::vector<MaskImagePointType> p_B;
+ std::vector<typename MaskSliceType::Pointer> slices;
+ clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices);
+ MaskImagePointType p;
+ typename MaskSliceType::PointType sp;
+ for(uint i=0; i<slices.size(); i++) {
+ // First only consider the main CCL (trachea, not bronchus)
+ slices[i] = Labelize<MaskSliceType>(slices[i], 0, true, 100);
+ slices[i] = KeepLabels<MaskSliceType>(slices[i], GetBackgroundValue(),
+ GetForegroundValue(), 1, 1, true);
+ // Find most posterior point
+ clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(),
+ 1, false, sp);
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp, Trachea, i, p);
+ p_A.push_back(p);
+ p[0] -= 20;
+ p_B.push_back(p);
+ }
+ clitk::WriteListOfLandmarks<MaskImageType>(p_A, "trachea-post.txt");
+
+ // Remove Ant part above those lines
+ clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support,
+ p_A, p_B,
+ GetBackgroundValue(),
+ 1, 10);
+ // End, release memory
+ GetAFDB()->template ReleaseImage<MaskImageType>("Trachea");
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_Post_Limits()
+{
+ /*
+ Ant Post limit :
+
+ Anteriorly, it is in contact with the posterior aspect of Stations
+ 1–2 superiorly (Fig. 2A–C) and with Stations 4R and 4L inferiorly
+ (Fig. 2D–I and 3A–C). The anterior limit of Station 3P is kept
+ posterior to the trachea, which is defined by an imaginary
+ horizontal line running along the posterior wall of the trachea
+ (Fig. 2B,E, red line). Posteriorly, it is delineated along the
+ anterior and lateral borders of the vertebral body until an
+ imaginary horizontal line running 1 cm posteriorly to the
+ anterior border of the vertebral body (Fig. 2D).
+
+ 2 - post to the trachea : define an imaginary line just post the
+ Trachea and remove what is anterior.
+
+ */
+ StartNewStep("[Station 3P] Post limits with VertebralBody ");
+
+ // Load VertebralBody
+ MaskImagePointer VertebralBody = GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
+
+ // Crop like current support (need by SliceBySliceSetBackgroundFromLineSeparation after)
+ VertebralBody = clitk::ResizeImageLike<MaskImageType>(VertebralBody, m_Working_Support, GetBackgroundValue());
+
+ writeImage<MaskImageType>(VertebralBody, "vb.mhd");
+
+ // Compute VertebralBody most Ant position (again because slices
+ // changes). Slice by slice, determine the most post point of the
+ // trachea (A) and consider a second point on the same horizontal
+ // line (B)
+ std::vector<MaskImagePointType> p_A;
+ std::vector<MaskImagePointType> p_B;
+ std::vector<typename MaskSliceType::Pointer> slices;
+ clitk::ExtractSlices<MaskImageType>(VertebralBody, 2, slices);
+ MaskImagePointType p;
+ typename MaskSliceType::PointType sp;
+ for(uint i=0; i<slices.size(); i++) {
+ // Find most anterior point
+ bool found = clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(),
+ 1, true, sp);
+
+ // If the VertebralBody stop superiorly before the end of
+ // m_Working_Support, we consider the same previous point.
+ if (!found) {
+ p = p_A.back();
+ p[2] += VertebralBody->GetSpacing()[2];
+ p_A.push_back(p);
+ p = p_B.back();
+ p[2] += VertebralBody->GetSpacing()[2];
+ p_B.push_back(p);
+ }
+ else {
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp, VertebralBody, i, p);
+ p[1] += 10; // Consider 10 mm more post
+ p_A.push_back(p);
+ p[0] -= 20;
+ p_B.push_back(p);
+ }
+ }
+ clitk::WriteListOfLandmarks<MaskImageType>(p_A, "vb-ant.txt");
+
+
+ // Remove Ant part above those lines
+ clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support,
+ p_A, p_B,
+ GetBackgroundValue(),
+ 1, -10);
+ writeImage<MaskImageType>(m_Working_Support, "a.mhd");
+
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_LR_sup_Limits()
+{
+ /*
+ "On the right side, the limit is defined by the air–soft-tissue
+ interface. On the left side, it is defined by the air–tissue
+ interface superiorly (Fig. 2A–C) and the aorta inferiorly
+ (Figs. 2D–I and 3A–C)."
+
+ sup :
+ Resizelike support : Trachea, SubclavianArtery
+ Trachea, slice by slice, get centroid trachea
+ SubclavianArtery, slice by slice, CCL
+ prendre la 1ère à L et R, not at Left
+
+ */
+ StartNewStep("[Station 3P] Left/Right limits (superior part) ");
+
+ // Load structures
+ MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+ MaskImagePointer SubclavianArtery = GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
+
+ // Crop like current support
+ Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
+ SubclavianArtery = clitk::ResizeImageLike<MaskImageType>(SubclavianArtery, m_Working_Support, GetBackgroundValue());
+
+ writeImage<MaskImageType>(Trachea, "tr.mhd");
+ writeImage<MaskImageType>(SubclavianArtery, "sca.mhd");
+
+ // Get list of slices
+ std::vector<MaskSlicePointer> slices_support;
+ std::vector<MaskSlicePointer> slices_trachea;
+ std::vector<MaskSlicePointer> slices_subclavianartery;
+ clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices_support);
+ clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices_trachea);
+ clitk::ExtractSlices<MaskImageType>(SubclavianArtery, 2, slices_subclavianartery);
+
+ // Loop on slices
+ std::vector<MaskImagePointType> points;
+ MaskImagePointType p;
+ for(uint i=0; i<slices_support.size(); i++) {
+ // Get Trachea centroid
+ std::vector<typename MaskSliceType::PointType> centroids;
+ typename MaskSliceType::PointType c;
+ ComputeCentroids<MaskSliceType>(slices_trachea[i], GetBackgroundValue(), centroids);
+ c = centroids[1];
+
+ // [debug] Store point
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[1], Trachea, i, p);
+ points.push_back(p);
+
+ // Get Right and Left CCL in SubclavianArtery
+ slices_subclavianartery[i] = Labelize<MaskSliceType>(slices_subclavianartery[i], 0, true, 10);
+ ComputeCentroids<MaskSliceType>(slices_subclavianartery[i], GetBackgroundValue(), centroids);
+
+ if (centroids.size() > 1) {
+ // Determine the one at Right/Left -> first after Trachea
+ // centroid
+ typename MaskSliceType::PointType right;
+ typename MaskSliceType::PointType left;
+ int label_right=-1;
+ int label_left=-1;
+ right[0] = c[0]-100;
+ left[0] = c[0]+100;
+ for(uint j=1; j<centroids.size(); j++) {
+ if (centroids[j][0] < c[0]) { // At Right of Trachea centroid
+ if (centroids[j][0] >= right[0]) {
+ right = centroids[j];
+ label_right = j;
+ }
+ }
+ if (centroids[j][0] > c[0]) { // At Left of Trachea centroid
+ if (centroids[j][0] <= left[0]) {
+ left = centroids[j];
+ label_left = j;
+ }
+ }
+ }
+
+ if (label_right != -1) {
+
+ // Debug points
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[label_right], SubclavianArtery, i, p);
+ points.push_back(p);
+
+ // Set Background and ForegroundValue according to label_right
+ MaskSlicePointer object =
+ clitk::Binarize<MaskSliceType>(slices_subclavianartery[i], label_right, label_right,
+ GetBackgroundValue(), GetForegroundValue());
+
+ // Relative Position : not at Right
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskSliceType> RelPosFilterType;
+ typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(slices_support[i]);
+ relPosFilter->SetInputObject(object);
+ relPosFilter->AddOrientationTypeString("R");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->Update();
+ slices_support[i] = relPosFilter->GetOutput();
+
+ // Relative Position : not Anterior
+ relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(slices_support[i]);
+ relPosFilter->SetInputObject(object);
+ relPosFilter->AddOrientationTypeString("A");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->Update();
+ slices_support[i] = relPosFilter->GetOutput();
+
+ } // End RelativePosition for Right
+
+
+ if (label_left != -1) {
+
+ // Debug points
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[label_left], SubclavianArtery, i, p);
+ points.push_back(p);
+
+ // Set Background and ForegroundValue according to label_right
+ MaskSlicePointer object =
+ clitk::Binarize<MaskSliceType>(slices_subclavianartery[i], label_left, label_left,
+ GetBackgroundValue(), GetForegroundValue());
+
+ // Relative Position : not at Right
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskSliceType> RelPosFilterType;
+ typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(slices_support[i]);
+ relPosFilter->SetInputObject(object);
+ relPosFilter->AddOrientationTypeString("L");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->Update();
+ slices_support[i] = relPosFilter->GetOutput();
+
+ // Relative Position : not Anterior
+ relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(slices_support[i]);
+ relPosFilter->SetInputObject(object);
+ relPosFilter->AddOrientationTypeString("A");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->Update();
+ slices_support[i] = relPosFilter->GetOutput();
+
+ }
+
+
+ } // if centroids.size > 1
+ } // End loop slices
+
+ // Joint slices
+ m_Working_Support = clitk::JoinSlices<MaskImageType>(slices_support, m_Working_Support, 2);
+
+ // Save list points
+ clitk::WriteListOfLandmarks<MaskImageType>(points, "subcl-lr.txt");
+
+
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_LR_inf_Limits()
+{
+ /*
+ "On the right side, the limit is defined by the air–soft-tissue
+ interface. On the left side, it is defined by the air–tissue
+ interface superiorly (Fig. 2A–C) and the aorta inferiorly
+ (Figs. 2D–I and 3A–C)."
+
+ inf : not Right to Azygousvein
+ */
+ StartNewStep("[Station 3P] Left/Right limits (inferior part) ");
+
+ // Load structures
+ MaskImagePointer AzygousVein = GetAFDB()->template GetImage<MaskImageType>("AzygousVein");
+
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
+ typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(m_Working_Support);
+ relPosFilter->SetInputObject(AzygousVein);
+ relPosFilter->AddOrientationTypeString("R");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOn();
+ relPosFilter->Update();
+ m_Working_Support = relPosFilter->GetOutput();
+
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff