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)
-
- // Consider above Carina
- m_CarinaZ = FindCarinaSlicePosition();
- 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());
-
- // Consider only Superior to Carina
- m_Working_Support = m_Support_Superior_to_Carina;
-
- // Step : 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
- */
+ m_Working_Support = m_Mediastinum = this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
+
+ // Remove some computed structures
+ this->GetAFDB()->RemoveTag("CarinaZ");
+ this->GetAFDB()->RemoveTag("ApexOfTheChestZ");
+
+ // Superior and inferior limits.
+ Support_SI_Limit("inferior", "Sup_to_Carina", "inferior", "Carina", 0);
+ Support_SI_Limit("superior", "Inf_to_Carina", "inferior", "Carina", m_Working_Support->GetSpacing()[2]);
+ // Initialise all others supports
+ // m_ListOfSupports["S1R"] = m_ListOfSupports["Sup_to_Carina"];
+ // m_ListOfSupports["S1L"] = m_ListOfSupports["Sup_to_Carina"];
+ // m_ListOfSupports["S2R"] = m_ListOfSupports["Sup_to_Carina"];
+ // m_ListOfSupports["S2L"] = m_ListOfSupports["Sup_to_Carina"];
+ // m_ListOfSupports["S3A"] = m_ListOfSupports["Sup_to_Carina"];
+ // m_ListOfSupports["S3P"] = m_ListOfSupports["Sup_to_Carina"];
+ // m_ListOfSupports["S4R"] = m_ListOfSupports["Sup_to_Carina"];
+ // m_ListOfSupports["S4L"] = m_ListOfSupports["Sup_to_Carina"];
+ // m_ListOfSupports["S5"] = m_Mediastinum; // Not above Carina
+ // m_ListOfSupports["S6"] = m_Mediastinum; // Not above Carina
+
+ // Read all support limits in a file and apply them
+ ReadSupportLimits(GetSupportLimitsFilename());
+ for(unsigned int i=0; i<m_ListOfSupportLimits.size(); i++) {
+ SupportLimitsType s = m_ListOfSupportLimits[i];
+ Support_SI_Limit(s.station_limit, s.station, s.structure_limit,
+ s.structure, s.offset*m_Working_Support->GetSpacing()[2]);
+ }
+ // S1RL
+ Support_LeftRight_S1R_S1L();
+ // S2RL
+ Support_LeftRight_S2R_S2L();
+ // S4RL
+ Support_LeftRight_S4R_S4L();
+
+ // Post limits of S1,S2,S4
+ Support_Post_S1S2S4();
+ // S3P
+ StartNewStep("[Support] Ant limits of S3P with trachea");
+ m_ListOfSupports["S3P"] = LimitsWithTrachea(m_ListOfSupports["S3P"], 1, 0, 10);
+
+ // S3A
+ StartNewStep("[Support] Ant limits of S3A with trachea");
+ m_ListOfSupports["S3A"] = LimitsWithTrachea(m_ListOfSupports["S3A"], 1, 0, -10);
+
+ // I will do it later
+ // Below Carina S7,8,9,10
+ m_ListOfSupports["S7"] = clitk::Clone<MaskImageType>(m_ListOfSupports["Inf_to_Carina"]);
+ m_ListOfSupports["S8"] = clitk::Clone<MaskImageType>(m_ListOfSupports["Inf_to_Carina"]);
+ m_ListOfSupports["S9"] = clitk::Clone<MaskImageType>(m_ListOfSupports["Inf_to_Carina"]);
+ m_ListOfSupports["S10"] = clitk::Clone<MaskImageType>(m_ListOfSupports["Inf_to_Carina"]);
+ m_ListOfSupports["S11"] = clitk::Clone<MaskImageType>(m_ListOfSupports["Inf_to_Carina"]);
+
+ // Store image filenames into AFDB
+ WriteImageSupport("S1R"); WriteImageSupport("S1L");
+ WriteImageSupport("S2R"); WriteImageSupport("S2L");
+ WriteImageSupport("S3A"); WriteImageSupport("S3P");
+ WriteImageSupport("S4R"); WriteImageSupport("S4L");
+ WriteImageSupport("S5");
+ WriteImageSupport("S6");
+ WriteImageSupport("S7");
+ WriteImageSupport("S8");
+ WriteImageSupport("S9");
+ WriteImageSupport("S10");
+ WriteImageSupport("S11");
+ WriteAFDB();
+}
+//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+Support_SI_Limit(const std::string station_limit, const std::string station,
+ const std::string structure_limit, const std::string structure,
+ const double offset)
+{
+ if (!GetCheckSupportFlag())
+ StartNewStep("[Support] "+station_limit+" limit of "+station+" is "+structure_limit+" limit of "+structure);
+ // Check
+ if ((station_limit != "superior") && (station_limit != "inferior")) {
+ clitkExceptionMacro("Error station_limit must be 'inferior' or 'superior', not '"<< station_limit);
+ }
+ if ((structure_limit != "superior") && (structure_limit != "inferior")) {
+ clitkExceptionMacro("Error structure_limit must be 'inferior' or 'superior', not '"<< structure_limit);
+ }
- // // LeftRight cut along trachea
- // MaskImagePointer Trachea = GetAFDB()->GetImage("Trachea");
- // // build a ant-post line for each slice
+ // Get current support
+ if (m_ListOfSupports.find(station) == m_ListOfSupports.end()) {
+ // std::cerr << "Warning: support " << station << " not initialized" << std::endl;
+ m_ListOfSupports[station] = m_Mediastinum;
+ }
+ m_Working_Support = m_ListOfSupports[station];
+
+ // Get structure or structureZ
+ double z;
+ int found=0;
+ std::string file;
- // MaskImagePointer m_Support_SupRight =
- // clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2,
- // m_CarinaZ, true, GetBackgroundValue());
+ // Try to load structure and compute extrema point
+ if (this->GetAFDB()->TagExist(structure)) {
+ MaskImagePointer Structure = this->GetAFDB()->template GetImage <MaskImageType>(structure);
+ file = this->GetAFDB()->GetTagValue(structure);
+ MaskImagePointType p;
+ p[0] = p[1] = p[2] = 0.0; // to avoid warning
+ if (structure_limit == "superior")
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Structure, GetBackgroundValue(), 2, false, p);
+ else
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Structure, GetBackgroundValue(), 2, true, p);
+ z = p[2];
+ found=1;
+ }
+ // Try to load structureZ
+ if ((found==0) && (this->GetAFDB()->TagExist(structure+"Z"))) {
+ z = this->GetAFDB()->GetDouble(structure+"Z");
+ found=2;
+ }
+
+ // Try to load structurePoint
+ if ((found==0) && (this->GetAFDB()->TagExist(structure+"Point"))) {
+ MaskImagePointType p;
+ this->GetAFDB()->GetPoint3D(structure+"Point", p);
+ z = p[2];
+ found=3;
+ }
+ // Try to see if it is an already computed support
+ if (found==0) {
+ if (m_ListOfSupports.find(structure) != m_ListOfSupports.end()) {
+ MaskImagePointer Structure = m_ListOfSupports[structure];
+ MaskImagePointType p;
+ if (structure_limit == "superior")
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Structure, GetBackgroundValue(), 2, false, p);
+ else
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Structure, GetBackgroundValue(), 2, true, p);
+ z = p[2];
+ found=4;
+ }
+ }
+
+ // Try special case : "FindApexOfTheChest"
+ if (structure == "FindApexOfTheChest") {
+ z = FindApexOfTheChest();
+ found=5;
+ }
+ if (structure == "FindInferiorBorderOfAorticArch") {
+ z = FindInferiorBorderOfAorticArch();
+ found=6;
+ }
+ if (structure == "FindSuperiorBorderOfAorticArch") {
+ z = FindSuperiorBorderOfAorticArch();
+ found=6;
+ }
+ // If we find anything
+ if (found == 0) {
+ std::cerr << "ERROR : I could not find " << structure << " nor " << structure << "Z nor "
+ << structure << "Point" << std::endl;
+ exit(EXIT_FAILURE);
+ }
+ // Apply offset
+ z += offset;
- // 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();
+ // Remove Lower or greater
+ if (station_limit == "inferior") {
+ m_Working_Support =
+ clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2, z, true, GetBackgroundValue());
+ }
+ else {
+ m_Working_Support =
+ clitk::CropImageRemoveGreaterThan<MaskImageType>(m_Working_Support, 2, z, true, GetBackgroundValue());
+ }
+
+ // Check: if reference station is given, display information
+ if (GetCheckSupportFlag()) {
+ try {
+ MaskImagePointer Ref = this->GetAFDB()->template GetImage <MaskImageType>(station+"_Ref");
+ MaskImagePointType p_support;
+ MaskImagePointType p_ref;
+ if (station_limit == "superior") {
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Ref, GetBackgroundValue(), 2, false, p_ref);
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(m_Working_Support, GetBackgroundValue(), 2, false, p_support);
+ }
+ else {
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Ref, GetBackgroundValue(), 2, true, p_ref);
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(m_Working_Support, GetBackgroundValue(), 2, true, p_support);
+ }
+ std::ostringstream os;
+ os << "[Support] \t" << station << "\t" << station_limit << " "
+ << "Z = " << z << std::setprecision(2) << std::fixed
+ << "\tSupport = " << p_support[2]
+ << "\tRef = " << p_ref[2]
+ << "\tdiff = " << p_support[2]-p_ref[2] << "\t"
+ << structure << " " << structure_limit;
+ if (found==1) os << " (S "+file+")";
+ if (found==2) os << " (Z)";
+ if (found==3) os << " (P)";
+ if (found==4) os << " (p)";
+ if (found==5) os << " (Apex)";
+ if (found==6) os << " (AorticArch)";
+ StartNewStep(os.str());
+ } catch(clitk::ExceptionObject e) { }
+ }
+
+ // Set support
+ m_ListOfSupports[station] = m_Working_Support;
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+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["S1R"];
+ 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;
+ StopCurrentStep<MaskImageType>(m_ListOfSupports["S1L"]);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+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);
+ S2R = clitk::AutoCrop<MaskImageType>(S2R, GetBackgroundValue());
+ S2L = clitk::AutoCrop<MaskImageType>(S2L, GetBackgroundValue());
+ m_ListOfSupports["S2R"] = S2R;
+ m_ListOfSupports["S2L"] = S2L;
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("Trachea");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+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"];
+ m_ListOfSupports["S1R"] = LimitsWithTrachea(S1L, 1, 0, -10, m_ApexOfTheChest);
+ m_ListOfSupports["S1L"] = LimitsWithTrachea(S1R, 1, 0, -10, m_ApexOfTheChest);
+ m_ListOfSupports["S2R"] = LimitsWithTrachea(S2R, 1, 0, -10, m_ApexOfTheChest);
+ m_ListOfSupports["S2L"] = LimitsWithTrachea(S2L, 1, 0, -10, m_ApexOfTheChest);
+ m_ListOfSupports["S4R"] = LimitsWithTrachea(S4R, 1, 0, -10, m_ApexOfTheChest);
+ m_ListOfSupports["S4L"] = LimitsWithTrachea(S4L, 1, 0, -10, m_ApexOfTheChest);
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff