clitk::ExtractLymphStationsFilter<ImageType>::
ExtractStationSupports()
{
- DD("ExtractStationSupports");
-
// Get initial Mediastinum
- m_Working_Support = m_Mediastinum = GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
-
- // Superior limits: CricoidCartilag
- // Inferior limits: lung
- // (the Mediastinum support already stop at this limit)
+ m_Working_Support = m_Mediastinum = this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
- // Consider above Carina
- m_CarinaZ = FindCarinaSlicePosition();
+ // Consider sup/inf to Carina
+ double m_CarinaZ = FindCarina();
MaskImagePointer m_Support_Superior_to_Carina =
clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2,
m_CarinaZ, true, GetBackgroundValue());
MaskImagePointer m_Support_Inferior_to_Carina =
clitk::CropImageRemoveGreaterThan<MaskImageType>(m_Working_Support, 2,
m_CarinaZ, true, GetBackgroundValue());
+ m_ListOfSupports["Support_Superior_to_Carina"] = m_Support_Superior_to_Carina;
+ m_ListOfSupports["Support_Inferior_to_Carina"] = m_Support_Inferior_to_Carina;
+ writeImage<MaskImageType>(m_Support_Inferior_to_Carina, "seg/Support_Inf_Carina.mha");
+ this->GetAFDB()->SetImageFilename("Support_Inf_Carina", "seg/Support_Inf_Carina.mha");
+ writeImage<MaskImageType>(m_Support_Superior_to_Carina, "seg/Support_Sup_Carina.mha");
+ this->GetAFDB()->SetImageFilename("Support_Sup_Carina", "seg/Support_Sup_Carina.mha");
+
+ // S1RL
+ Support_SupInf_S1RL();
+ Support_LeftRight_S1R_S1L();
+
+ // S2RL
+ Support_SupInf_S2R_S2L();
+ Support_LeftRight_S2R_S2L();
+
+ // S4RL
+ Support_SupInf_S4R_S4L();
+ Support_LeftRight_S4R_S4L();
+
+ // Post limits of S1,S2,S4
+ Support_Post_S1S2S4();
+
+ // S3AP
+ Support_S3P();
+ Support_S3A();
+
+ // S5, S6
+ Support_S5();
+ Support_S6();
+
+ // Below Carina S7,8,9,10
+ m_ListOfSupports["S7"] = clitk::Clone<MaskImageType>(m_Support_Inferior_to_Carina);
+ m_ListOfSupports["S8"] = clitk::Clone<MaskImageType>(m_Support_Inferior_to_Carina);
+ m_ListOfSupports["S9"] = clitk::Clone<MaskImageType>(m_Support_Inferior_to_Carina);
+ m_ListOfSupports["S10"] = clitk::Clone<MaskImageType>(m_Support_Inferior_to_Carina);
+ m_ListOfSupports["S11"] = clitk::Clone<MaskImageType>(m_Support_Inferior_to_Carina);
+
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfSupports["S1R"], "seg/Support_S1R.mha");
+ this->GetAFDB()->SetImageFilename("Support_S1R", "seg/Support_S1R.mha");
+ writeImage<MaskImageType>(m_ListOfSupports["S1L"], "seg/Support_S1L.mha");
+ this->GetAFDB()->SetImageFilename("Support_S1L", "seg/Support_S1L.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S2L"], "seg/Support_S2L.mha");
+ this->GetAFDB()->SetImageFilename("Support_S2L", "seg/Support_S2L.mha");
+ writeImage<MaskImageType>(m_ListOfSupports["S2R"], "seg/Support_S2R.mha");
+ this->GetAFDB()->SetImageFilename("Support_S2R", "seg/Support_S2R.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S3P"], "seg/Support_S3P.mha");
+ this->GetAFDB()->SetImageFilename("Support_S3P", "seg/Support_S3P.mha");
+ writeImage<MaskImageType>(m_ListOfSupports["S3A"], "seg/Support_S3A.mha");
+ this->GetAFDB()->SetImageFilename("Support_S3A", "seg/Support_S3A.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S4L"], "seg/Support_S4L.mha");
+ this->GetAFDB()->SetImageFilename("Support_S4L", "seg/Support_S4L.mha");
+ writeImage<MaskImageType>(m_ListOfSupports["S4R"], "seg/Support_S4R.mha");
+ this->GetAFDB()->SetImageFilename("Support_S4R", "seg/Support_S4R.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S5"], "seg/Support_S5.mha");
+ this->GetAFDB()->SetImageFilename("Support_S5", "seg/Support_S5.mha");
+ writeImage<MaskImageType>(m_ListOfSupports["S6"], "seg/Support_S6.mha");
+ this->GetAFDB()->SetImageFilename("Support_S6", "seg/Support_S6.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S7"], "seg/Support_S7.mha");
+ this->GetAFDB()->SetImageFilename("Support_S7", "seg/Support_S7.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S8"], "seg/Support_S8.mha");
+ this->GetAFDB()->SetImageFilename("Support_S8", "seg/Support_S8.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S9"], "seg/Support_S9.mha");
+ this->GetAFDB()->SetImageFilename("Support_S9", "seg/Support_S9.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S10"], "seg/Support_S10.mha");
+ this->GetAFDB()->SetImageFilename("Support_S10", "seg/Support_S10.mha");
+
+ writeImage<MaskImageType>(m_ListOfSupports["S11"], "seg/Support_S11.mha");
+ this->GetAFDB()->SetImageFilename("Support_S11", "seg/Support_S11.mha");
+ WriteAFDB();
+}
+//--------------------------------------------------------------------
- // Consider only Superior to Carina
- m_Working_Support = m_Support_Superior_to_Carina;
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_SupInf_S1RL()
+{
// Step : S1RL
- StartNewStep("[Support] sup-inf S1RL");
+ StartNewStep("[Support] Sup-Inf S1RL");
/*
- Lower border: clavicles bilaterally and, in the midline, the upper
- border of the manubrium, 1R designates right-sided nodes, 1L,
- left-sided nodes in this region
-
2R: Upper border: apex of the right lung and pleural space, and in
the midline, the upper border of the manubrium
2L: Upper border: apex of the left lung and pleural space, and in the
midline, the upper border of the manubrium
+
+ => apex / manubrium = up Sternum
+ */
+ m_Working_Support = m_ListOfSupports["Support_Superior_to_Carina"];
+ MaskImagePointer Sternum = this->GetAFDB()->template GetImage <MaskImageType>("Sternum");
+ MaskImagePointType p;
+ p[0] = p[1] = p[2] = 0.0; // to avoid warning
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Sternum, GetBackgroundValue(), 2, false, p);
+ MaskImagePointer S1RL =
+ clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2,
+ p[2], true, GetBackgroundValue());
+ m_Working_Support =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(m_Working_Support, 2,
+ p[2], true, GetBackgroundValue());
+ m_ListOfSupports["S1RL"] = S1RL;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_LeftRight_S1R_S1L()
+{
+ // Step S1RL : Left-Right
+ StartNewStep("[Support] Left-Right S1R S1L");
+ std::vector<ImagePointType> A;
+ std::vector<ImagePointType> B;
+ // Search for centroid positions of trachea
+ MaskImagePointer Trachea = this->GetAFDB()->template GetImage <MaskImageType>("Trachea");
+ MaskImagePointer S1RL = m_ListOfSupports["S1RL"];
+ Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, S1RL, GetBackgroundValue());
+ std::vector<MaskSlicePointer> slices;
+ clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices);
+ for(uint i=0; i<slices.size(); i++) {
+ slices[i] = Labelize<MaskSliceType>(slices[i], 0, false, 10);
+ std::vector<typename MaskSliceType::PointType> c;
+ clitk::ComputeCentroids<MaskSliceType>(slices[i], GetBackgroundValue(), c);
+ ImagePointType a,b;
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(c[1], Trachea, i, a);
+ A.push_back(a);
+ b = a;
+ b[1] += 50;
+ B.push_back(b);
+ }
+ clitk::WriteListOfLandmarks<MaskImageType>(A, "S1LR_A.txt");
+ clitk::WriteListOfLandmarks<MaskImageType>(B, "S1LR_B.txt");
+
+ // Clone support
+ MaskImagePointer S1R = clitk::Clone<MaskImageType>(S1RL);
+ MaskImagePointer S1L = clitk::Clone<MaskImageType>(S1RL);
+
+ // Right part
+ clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1R, A, B,
+ GetBackgroundValue(), 0, -10);
+ S1R = clitk::AutoCrop<MaskImageType>(S1R, GetBackgroundValue());
+ m_ListOfSupports["S1R"] = S1R;
+
+ // Left part
+ clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1L, A, B,
+ GetBackgroundValue(), 0, 10);
+ S1L = clitk::AutoCrop<MaskImageType>(S1L, GetBackgroundValue());
+ m_ListOfSupports["S1L"] = S1L;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_SupInf_S2R_S2L()
+{
+ // Step : S2RL Sup-Inf limits
+ /*
+ 2R Lower border: intersection of caudal margin of innominate vein with
+ the trachea
+ 2L Lower border: superior border of the aortic arch
*/
+ StartNewStep("[Support] Sup-Inf S2RL");
+ m_Working_Support = m_ListOfSupports["Support_Superior_to_Carina"];
+
+ // S2R Caudal Margin Of Left BrachiocephalicVein
+ MaskImagePointer BrachioCephalicVein = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
+ MaskImagePointType p;
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(BrachioCephalicVein, GetBackgroundValue(), 2, true, p);
+ // I add slightly more than a slice --> NO !!
+ double CaudalMarginOfLeftBrachiocephalicVeinZ=p[2];//+ 1.1*m_Working_Support->GetSpacing()[2];
+ this->GetAFDB()->SetDouble("CaudalMarginOfLeftBrachiocephalicVeinZ", CaudalMarginOfLeftBrachiocephalicVeinZ);
+ MaskImagePointer S2R =
+ clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2,
+ CaudalMarginOfLeftBrachiocephalicVeinZ, true,
+ GetBackgroundValue());
+ // S2L : Top Of Aortic Arch
+ MaskImagePointer Aorta = this->GetAFDB()->template GetImage<MaskImageType>("Aorta");
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Aorta, GetBackgroundValue(), 2, false, p);
+ // Save the TopOfAorticArchZ
+ this->GetAFDB()->SetDouble("TopOfAorticArchZ", p[2]);
+ // I substract slightly more than a slice to respect delineation
+ double TopOfAorticArchZ=p[2]- 1.1*m_Working_Support->GetSpacing()[2];
+ // this->GetAFDB()->SetDouble("TopOfAorticArchZ", TopOfAorticArchZ);
+ MaskImagePointer S2L =
+ clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2,
+ TopOfAorticArchZ, true,
+ GetBackgroundValue());
+ /*
+ // S2RL: Superior support, I use inferior part of S1RL
+ MaskImagePointer S1L = m_ListOfSupports["S1L"];
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(S1L, GetBackgroundValue(), 2, true, p);
+ DD(p);
+ S2L =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(S2L, 2,
+ p[2], true,
+ GetBackgroundValue());
+ MaskImagePointer S1R = m_ListOfSupports["S1R"];
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(S1R, GetBackgroundValue(), 2, true, p);
+ DD(p);
+ S2R =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(S2R, 2,
+ p[2], true,
+ GetBackgroundValue());
+ */
+ // Superior limits, use Sternum (but not strictly inf to S1RL
+ MaskImagePointer Sternum = this->GetAFDB()->template GetImage <MaskImageType>("Sternum");
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Sternum, GetBackgroundValue(), 2, false, p);
+ // Add one slice
+ p[2] = p[2] + m_Working_Support->GetSpacing()[2];
+ S2L =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(S2L, 2,
+ p[2], true, GetBackgroundValue());
+ S2R =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(S2R, 2,
+ p[2], true, GetBackgroundValue());
- // // LeftRight cut along trachea
- // MaskImagePointer Trachea = GetAFDB()->GetImage("Trachea");
- // // build a ant-post line for each slice
+ // The is the end
+ m_ListOfSupports["S2L"] = S2L;
+ m_ListOfSupports["S2R"] = S2R;
+}
+//--------------------------------------------------------------------
- // MaskImagePointer m_Support_SupRight =
- // clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2,
- // m_CarinaZ, true, GetBackgroundValue());
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_LeftRight_S2R_S2L()
+{
+ // ---------------------------------------------------------------------------
+ /* Step : S2RL LeftRight
+ As for lymph node station 4R, 2R includes nodes extending to the
+ left lateral border of the trachea
+ Rod says: "For station 2 there is a shift, dividing 2R from 2L, from midline
+ to the left paratracheal border."
+ */
+ StartNewStep("[Support] Separate 2R/2L according to Trachea");
+ MaskImagePointer S2R = m_ListOfSupports["S2R"];
+ MaskImagePointer S2L = m_ListOfSupports["S2L"];
+ S2R = LimitsWithTrachea(S2R, 0, 1, -10);
+ S2L = LimitsWithTrachea(S2L, 0, 1, 10);
+ m_ListOfSupports["S2R"] = S2R;
+ m_ListOfSupports["S2L"] = S2L;
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("Trachea");
+}
+//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_SupInf_S4R_S4L()
+{
+ // ---------------------------------------------------------------------------
+ /* Step : S4RL Sup-Inf
+ - start at the end of 2R and 2L
+ - stop ?
+ - 4R
+ Rod says : "The inferior border is at the lower border of the azygous vein."
+ Rod says : difficulties
+ (was : "ends at the upper lobe bronchus or where the right pulmonary artery
+ crosses the midline of the mediastinum ")
+ - 4L
+ Rod says : "The lower border is to upper margin of the left main pulmonary artery."
+ (was LLL bronchus)
+ */
+ StartNewStep("[Support] Sup-Inf limits of 4R/4L");
- // Store image filenames into AFDB
- m_ListOfSupports["S1R"] = m_Working_Support;
- writeImage<MaskImageType>(m_ListOfSupports["S1R"], "seg/Support_S1R.mhd");
- GetAFDB()->SetImageFilename("Support_S1R", "seg/Support_S1R.mhd");
- WriteAFDB();
+ // Start from the support
+ MaskImagePointer S4RL = clitk::Clone<MaskImageType>(m_Working_Support);
+ MaskImagePointer S4R = clitk::Clone<MaskImageType>(S4RL);
+ MaskImagePointer S4L = clitk::Clone<MaskImageType>(S4RL);
+
+ // Keep only what is lower than S2
+ MaskImagePointer S2R = m_ListOfSupports["S2R"];
+ MaskImagePointer S2L = m_ListOfSupports["S2L"];
+ MaskImagePointType p;
+ // Right part
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(S2R, GetBackgroundValue(),
+ 2, true, p);
+ S4R = clitk::CropImageRemoveGreaterThan<MaskImageType>(S4R, 2,
+ p[2], true, GetBackgroundValue());
+ // Left part
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(S2L, GetBackgroundValue(),
+ 2, true, p);
+ S4L = clitk::CropImageRemoveGreaterThan<MaskImageType>(S4L, 2,
+ p[2], true, GetBackgroundValue());
+
+ // Get AzygousVein and limit according to LowerBorderAzygousVein
+ MaskImagePointer LowerBorderAzygousVein
+ = this->GetAFDB()->template GetImage<MaskImageType>("LowerBorderAzygousVein");
+ std::vector<MaskImagePointType> c;
+ clitk::ComputeCentroids<MaskImageType>(LowerBorderAzygousVein, GetBackgroundValue(), c);
+ S4R = clitk::CropImageRemoveLowerThan<MaskImageType>(S4R, 2,
+ c[1][2], true, GetBackgroundValue());
+ S4R = clitk::AutoCrop<MaskImageType>(S4R, GetBackgroundValue());
+ m_ListOfSupports["S4R"] = S4R;
+
+
+ // Limit according to LeftPulmonaryArtery
+ MaskImagePointer LeftPulmonaryArtery
+ = this->GetAFDB()->template GetImage<MaskImageType>("LeftPulmonaryArtery");
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(LeftPulmonaryArtery, GetBackgroundValue(),
+ 2, false, p);
+ S4L = clitk::CropImageRemoveLowerThan<MaskImageType>(S4L, 2,
+ p[2], true, GetBackgroundValue());
+ S4L = clitk::AutoCrop<MaskImageType>(S4L, GetBackgroundValue());
+ m_ListOfSupports["S4L"] = S4L;
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_LeftRight_S4R_S4L()
+{
+ // ---------------------------------------------------------------------------
+ /* Step : S4RL LeftRight
+
+ - 4R: includes right paratracheal nodes, and pretracheal nodes
+ extending to the left lateral border of trachea
+
+ - 4L: includes nodes to the left of the left lateral border of
+ the trachea, medial to the ligamentum arteriosum
+
+ => same than 2RL
+ */
+ StartNewStep("[Support] Left Right separation of 4R/4L");
+
+ MaskImagePointer S4R = m_ListOfSupports["S4R"];
+ MaskImagePointer S4L = m_ListOfSupports["S4L"];
+ S4R = LimitsWithTrachea(S4R, 0, 1, -10);
+ S4L = LimitsWithTrachea(S4L, 0, 1, 10);
+ m_ListOfSupports["S4R"] = S4R;
+ m_ListOfSupports["S4L"] = S4L;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+typename clitk::ExtractLymphStationsFilter<ImageType>::MaskImagePointer
+clitk::ExtractLymphStationsFilter<ImageType>::
+LimitsWithTrachea(MaskImageType * input, int extremaDirection, int lineDirection,
+ double offset)
+{
+ MaskImagePointType min, max;
+ GetMinMaxBoundary<MaskImageType>(input, min, max);
+ return LimitsWithTrachea(input, extremaDirection, lineDirection, offset, max[2]);
+}
+template <class ImageType>
+typename clitk::ExtractLymphStationsFilter<ImageType>::MaskImagePointer
+clitk::ExtractLymphStationsFilter<ImageType>::
+LimitsWithTrachea(MaskImageType * input, int extremaDirection, int lineDirection,
+ double offset, double maxSupPosition)
+{
+ /*
+ Take the input mask, consider the trachea and limit according to
+ Left border of the trachea. Keep at Left or at Right according to
+ the offset
+ */
+ // Read the trachea
+ MaskImagePointer Trachea = this->GetAFDB()->template GetImage<MaskImageType>("Trachea");
+
+ // Find extrema post positions
+ std::vector<MaskImagePointType> tracheaLeftPositionsA;
+ std::vector<MaskImagePointType> tracheaLeftPositionsB;
+
+ // Crop Trachea only on the Sup-Inf axes, without autocrop
+ // Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, input, GetBackgroundValue());
+ MaskImagePointType min, max;
+ GetMinMaxBoundary<MaskImageType>(input, min, max);
+ Trachea = clitk::CropImageAlongOneAxis<MaskImageType>(Trachea, 2, min[2], max[2],
+ false, GetBackgroundValue());
+
+ // Select the main CCL (because of bronchus)
+ Trachea = SliceBySliceKeepMainCCL<MaskImageType>(Trachea, GetBackgroundValue(), GetForegroundValue());
+
+ // Slice by slice, build the separation line
+ clitk::SliceBySliceBuildLineSegmentAccordingToExtremaPosition<MaskImageType>(Trachea,
+ GetBackgroundValue(), 2,
+ extremaDirection, false, // Left
+ lineDirection, // Vertical line
+ -1, // margins
+ tracheaLeftPositionsA,
+ tracheaLeftPositionsB);
+ // Do not consider trachea above the limit
+ int indexMax=tracheaLeftPositionsA.size();
+ for(uint i=0; i<tracheaLeftPositionsA.size(); i++) {
+ if (tracheaLeftPositionsA[i][2] > maxSupPosition) {
+ indexMax = i;
+ i = tracheaLeftPositionsA.size(); // stop loop
+ }
+ }
+ tracheaLeftPositionsA.erase(tracheaLeftPositionsA.begin()+indexMax, tracheaLeftPositionsA.end());
+ tracheaLeftPositionsB.erase(tracheaLeftPositionsB.begin()+indexMax, tracheaLeftPositionsB.end());
+
+ // Cut post to this line
+ clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(input,
+ tracheaLeftPositionsA,
+ tracheaLeftPositionsB,
+ GetBackgroundValue(),
+ extremaDirection, offset);
+ MaskImagePointer output = clitk::AutoCrop<MaskImageType>(input, GetBackgroundValue());
+ return output;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_Post_S1S2S4()
+{
+ StartNewStep("[Support] Post limits of S1RL, S2RL, S4RL");
+
+ double m_ApexOfTheChest = FindApexOfTheChest();
+
+ // Post limits with Trachea
+ MaskImagePointer S1R = m_ListOfSupports["S1R"];
+ MaskImagePointer S1L = m_ListOfSupports["S1L"];
+ MaskImagePointer S2R = m_ListOfSupports["S2R"];
+ MaskImagePointer S2L = m_ListOfSupports["S2L"];
+ MaskImagePointer S4R = m_ListOfSupports["S4R"];
+ MaskImagePointer S4L = m_ListOfSupports["S4L"];
+ S1L = LimitsWithTrachea(S1L, 1, 0, -10, m_ApexOfTheChest);
+ S1R = LimitsWithTrachea(S1R, 1, 0, -10, m_ApexOfTheChest);
+ S2R = LimitsWithTrachea(S2R, 1, 0, -10, m_ApexOfTheChest);
+ S2L = LimitsWithTrachea(S2L, 1, 0, -10, m_ApexOfTheChest);
+ S4R = LimitsWithTrachea(S4R, 1, 0, -10, m_ApexOfTheChest);
+ S4L = LimitsWithTrachea(S4L, 1, 0, -10, m_ApexOfTheChest);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_S3P()
+{
+ StartNewStep("[Support] Ant limits of S3P and Post limits of S1RL, S2RL, S4RL");
+
+ // Initial S3P support
+ MaskImagePointer S3P = clitk::Clone<MaskImageType>(m_ListOfSupports["Support_Superior_to_Carina"]);
+
+ // Stop at Lung Apex
+ double m_ApexOfTheChest = FindApexOfTheChest();
+ S3P =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(S3P, 2,
+ m_ApexOfTheChest, true,
+ GetBackgroundValue());
+ // Ant limits with Trachea
+ S3P = LimitsWithTrachea(S3P, 1, 0, 10);
+ m_ListOfSupports["S3P"] = S3P;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_S3A()
+{
+ StartNewStep("[Support] Sup-Inf and Post limits for S3A");
+
+ // Initial S3A support
+ MaskImagePointer S3A = clitk::Clone<MaskImageType>(m_ListOfSupports["Support_Superior_to_Carina"]);
+
+ // Stop at Lung Apex or like S2/S1 (upper border Sternum - manubrium) ?
+
+ //double m_ApexOfTheChest = FindApexOfTheChest();
+
+ MaskImagePointer Sternum = this->GetAFDB()->template GetImage <MaskImageType>("Sternum");
+ MaskImagePointType p;
+ p[0] = p[1] = p[2] = 0.0; // to avoid warning
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Sternum, GetBackgroundValue(), 2, false, p);
+ p[2] += Sternum->GetSpacing()[2]; // we add one slice to stop 3A at the same slice than Sternum stop
+ S3A =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(S3A, 2,
+ //m_ApexOfTheChest
+ p[2], true,
+ GetBackgroundValue());
+ // Ant limits with Trachea
+ S3A = LimitsWithTrachea(S3A, 1, 0, -10);
+ m_ListOfSupports["S3A"] = S3A;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_S5()
+{
+ StartNewStep("[Support] Sup-Inf limits S5 with Aorta and MainPulmonaryArtery");
+
+ // Initial S5 support
+ MaskImagePointer S5 =
+ clitk::Clone<MaskImageType>(this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true));
+
+ // Sup limits with Aorta
+ double sup = FindInferiorBorderOfAorticArch();
+
+ // Inf limits with "upper rim of the left main pulmonary artery"
+ // For the moment only, it will change.
+ MaskImagePointer MainPulmonaryArtery = this->GetAFDB()->template GetImage<MaskImageType>("MainPulmonaryArtery");
+ MaskImagePointType p;
+ p[0] = p[1] = p[2] = 0.0; // to avoid warning
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(MainPulmonaryArtery, GetBackgroundValue(), 2, false, p);
+ p[2] += MainPulmonaryArtery->GetSpacing()[2];
+
+ // Cut Sup/Inf
+ S5 = clitk::CropImageAlongOneAxis<MaskImageType>(S5, 2, p[2], sup, true, GetBackgroundValue());
+
+ m_ListOfSupports["S5"] = S5;
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_S6()
+{
+ StartNewStep("[Support] Sup-Inf limits S6 with aorta");
+
+ // Initial S6 support like S3A
+ MaskImagePointer S6 = clitk::Clone<MaskImageType>(m_ListOfSupports["S3A"]);
+
+ // Inf Sup limits with Aorta
+ double sup = FindSuperiorBorderOfAorticArch();
+ double inf = FindInferiorBorderOfAorticArch();
+
+ // Cut Sup/Inf
+ S6 = clitk::CropImageAlongOneAxis<MaskImageType>(S6, 2, inf, sup, true, GetBackgroundValue());
+
+ m_ListOfSupports["S6"] = S6;
+}
+//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff