clitk::ExtractLymphStationsFilter<ImageType>::
ExtractStationSupports()
{
- DD("ExtractStationSupports");
-
// Get initial Mediastinum
m_Working_Support = m_Mediastinum = this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
- // 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.mhd");
- this->GetAFDB()->SetImageFilename("Support_Inf_Carina", "seg/Support_Inf_Carina.mhd");
- writeImage<MaskImageType>(m_Support_Superior_to_Carina, "seg/Support_Sup_Carina.mhd");
- this->GetAFDB()->SetImageFilename("Support_Sup_Carina", "seg/Support_Sup_Carina.mhd");
+ // 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_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();
+ // 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_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);
+ 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
- writeImage<MaskImageType>(m_ListOfSupports["S1R"], "seg/Support_S1R.mhd");
- this->GetAFDB()->SetImageFilename("Support_S1R", "seg/Support_S1R.mhd");
- writeImage<MaskImageType>(m_ListOfSupports["S1L"], "seg/Support_S1L.mhd");
- this->GetAFDB()->SetImageFilename("Support_S1L", "seg/Support_S1L.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S2L"], "seg/Support_S2L.mhd");
- this->GetAFDB()->SetImageFilename("Support_S2L", "seg/Support_S2L.mhd");
- writeImage<MaskImageType>(m_ListOfSupports["S2R"], "seg/Support_S2R.mhd");
- this->GetAFDB()->SetImageFilename("Support_S2R", "seg/Support_S2R.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S3P"], "seg/Support_S3P.mhd");
- this->GetAFDB()->SetImageFilename("Support_S3P", "seg/Support_S3P.mhd");
- writeImage<MaskImageType>(m_ListOfSupports["S3A"], "seg/Support_S3A.mhd");
- this->GetAFDB()->SetImageFilename("Support_S3A", "seg/Support_S3A.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S4L"], "seg/Support_S4L.mhd");
- this->GetAFDB()->SetImageFilename("Support_S4L", "seg/Support_S4L.mhd");
- writeImage<MaskImageType>(m_ListOfSupports["S4R"], "seg/Support_S4R.mhd");
- this->GetAFDB()->SetImageFilename("Support_S4R", "seg/Support_S4R.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S5"], "seg/Support_S5.mhd");
- this->GetAFDB()->SetImageFilename("Support_S5", "seg/Support_S5.mhd");
- writeImage<MaskImageType>(m_ListOfSupports["S6"], "seg/Support_S6.mhd");
- this->GetAFDB()->SetImageFilename("Support_S6", "seg/Support_S6.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S7"], "seg/Support_S7.mhd");
- this->GetAFDB()->SetImageFilename("Support_S7", "seg/Support_S7.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S8"], "seg/Support_S8.mhd");
- this->GetAFDB()->SetImageFilename("Support_S8", "seg/Support_S8.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S9"], "seg/Support_S9.mhd");
- this->GetAFDB()->SetImageFilename("Support_S9", "seg/Support_S9.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S10"], "seg/Support_S10.mhd");
- this->GetAFDB()->SetImageFilename("Support_S10", "seg/Support_S10.mhd");
-
- writeImage<MaskImageType>(m_ListOfSupports["S11"], "seg/Support_S11.mhd");
- this->GetAFDB()->SetImageFilename("Support_S11", "seg/Support_S11.mhd");
+ 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_SupInf_S1RL()
+Support_SI_Limit(const std::string station_limit, const std::string station,
+ const std::string structure_limit, const std::string structure,
+ const double offset)
{
- // Step : S1RL
- StartNewStep("[Support] Sup-Inf S1RL");
- /*
- 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
+ if (!GetCheckSupportFlag())
+ StartNewStep("[Support] "+station_limit+" limit of "+station+" is "+structure_limit+" limit of "+structure);
- => 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;
+ // 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);
+ }
+
+ // 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;
+
+ // 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;
+
+ // 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);
}
//--------------------------------------------------------------------
std::vector<ImagePointType> B;
// Search for centroid positions of trachea
MaskImagePointer Trachea = this->GetAFDB()->template GetImage <MaskImageType>("Trachea");
- MaskImagePointer S1RL = m_ListOfSupports["S1RL"];
+ MaskImagePointer S1RL = m_ListOfSupports["S1R"];
Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, S1RL, GetBackgroundValue());
std::vector<MaskSlicePointer> slices;
clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices);
// Right part
clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1R, A, B,
- GetBackgroundValue(), 0, -10);
+ GetBackgroundValue(), 0, 10);
S1R = clitk::AutoCrop<MaskImageType>(S1R, GetBackgroundValue());
m_ListOfSupports["S1R"] = S1R;
// Left part
clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1L, A, B,
- GetBackgroundValue(), 0, 10);
+ 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_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
- 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());
-
- // The is the end
- m_ListOfSupports["S2L"] = S2L;
- m_ListOfSupports["S2R"] = S2R;
-}
-//--------------------------------------------------------------------
-
-
-
//--------------------------------------------------------------------
template <class ImageType>
void
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_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");
-
- // 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);
- DD(p);
- writeImage<MaskImageType>(S4R, "before.mha");
- S4R = clitk::CropImageRemoveGreaterThan<MaskImageType>(S4R, 2,
- p[2], true, GetBackgroundValue());
- writeImage<MaskImageType>(S4R, "after.mha");
-
- // Left part
- clitk::FindExtremaPointInAGivenDirection<MaskImageType>(S2L, GetBackgroundValue(),
- 2, true, p);
- DD(p);
- S4L = clitk::CropImageRemoveGreaterThan<MaskImageType>(S4L, 2,
- p[2], true, GetBackgroundValue());
- // S4R = clitk::AutoCrop<MaskImageType>(S4R, GetBackgroundValue());
- // S4L = clitk::AutoCrop<MaskImageType>(S4L, 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
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);
-
- 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;
+ 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);
}
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-Support_S5()
-{
- StartNewStep("[Support] Sup-Inf limits S5 with aorta");
-
- // 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 PulmonaryTrunk = this->GetAFDB()->template GetImage<MaskImageType>("PulmonaryTrunk");
- MaskImagePointType p;
- p[0] = p[1] = p[2] = 0.0; // to avoid warning
- clitk::FindExtremaPointInAGivenDirection<MaskImageType>(PulmonaryTrunk, GetBackgroundValue(), 2, false, p);
- p[2] += PulmonaryTrunk->GetSpacing()[2];
- DD(p);
-
- // 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