// 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.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");
+ // 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(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.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");
+ 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);
- // DD(p);
- p[2] += Sternum->GetSpacing()[2]; // add one slice: start just superiorly
- 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 --> 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());
-
- // The is the end
- m_ListOfSupports["S2L"] = S2L;
- m_ListOfSupports["S2R"] = S2R;
-}
-//--------------------------------------------------------------------
-
-
-
//--------------------------------------------------------------------
template <class ImageType>
void
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-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);
- 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
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-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;
-}
-//--------------------------------------------------------------------
-
this->SetNumberOfRequiredInputs(1);
SetBackgroundValue(0);
SetForegroundValue(1);
- ComputeStationsSupportsFlagOn();
+ ForceSupportsFlagOn();
+ SetSupportLimitsFilename("none");
+ CheckSupportFlagOff();
// Default values
ExtractStation_3P_SetDefaultValues();
m_Mediastinum = this->GetAFDB()->template GetImage <MaskImageType>("Mediastinum");
// Clean some computer landmarks to force the recomputation
+ // FIXME -> to put elsewhere ?
this->GetAFDB()->RemoveTag("AntPostVesselsSeparation");
- // Global supports for stations
+ // Must I compute the supports ?
bool supportsExist = true;
- try {
- m_ListOfSupports["S1R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1R");
- m_ListOfSupports["S1L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1L");
- m_ListOfSupports["S2R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2R");
- m_ListOfSupports["S2L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2L");
- m_ListOfSupports["S4R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4R");
- m_ListOfSupports["S4L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4L");
-
- m_ListOfSupports["S3A"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3A");
- m_ListOfSupports["S3P"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3P");
- m_ListOfSupports["S5"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S5");
- m_ListOfSupports["S6"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S6");
- m_ListOfSupports["S7"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S7");
- m_ListOfSupports["S8"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S8");
- m_ListOfSupports["S9"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S9");
- m_ListOfSupports["S10"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S10");
- m_ListOfSupports["S11"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S11");
- } catch(clitk::ExceptionObject o) {
- supportsExist = false;
+ if (!GetForceSupportsFlag()) {
+ try {
+ m_ListOfSupports["S1R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1R");
+ m_ListOfSupports["S1L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S1L");
+ m_ListOfSupports["S2R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2R");
+ m_ListOfSupports["S2L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S2L");
+ m_ListOfSupports["S4R"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4R");
+ m_ListOfSupports["S4L"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S4L");
+
+ m_ListOfSupports["S3A"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3A");
+ m_ListOfSupports["S3P"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S3P");
+ m_ListOfSupports["S5"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S5");
+ m_ListOfSupports["S6"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S6");
+ m_ListOfSupports["S7"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S7");
+ m_ListOfSupports["S8"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S8");
+ m_ListOfSupports["S9"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S9");
+ m_ListOfSupports["S10"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S10");
+ m_ListOfSupports["S11"] = this->GetAFDB()->template GetImage<MaskImageType>("Support_S11");
+ } catch(clitk::ExceptionObject o) {
+ supportsExist = false;
+ }
}
- if (!supportsExist || GetComputeStationsSupportsFlag()) {
+ if (!supportsExist || GetForceSupportsFlag()) {
this->StartNewStep("Supports for stations");
this->StartSubStep();
+
+ // FIXME : why should I remove theses tags ???
this->GetAFDB()->RemoveTag("CarinaZ");
this->GetAFDB()->RemoveTag("ApexOfTheChestZ");
this->GetAFDB()->RemoveTag("ApexOfTheChest");
ExtractStation_2RL();
ExtractStation_3P();
ExtractStation_3A();
- ExtractStation_4RL();
+ ExtractStation_4R();
+ ExtractStation_4L();
ExtractStation_5();
ExtractStation_6();
- // ---------- TODO -----------------------
+ // ---------- todo -----------------------
// Extract Station8
// ExtractStation_8();
clitk::ExtractLymphStationsFilter<TImageType>::
GenerateData() {
// Final Step -> graft output (if SetNthOutput => redo)
- this->GraftOutput(m_ListOfStations["8"]);
+ // this->GraftOutput(m_ListOfStations["8"]);
}
//--------------------------------------------------------------------
std::string s = "Station"+station;
+ // Define the starting support
+ // if (GetComputeStation(station)) {
+ // std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
+ // }
+ if (GetComputeStation(station)) {
+ m_Working_Support = m_Mediastinum = this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
+ return true;
+ }
+ else return false;
+ // else {
+ // std::cout << "Station " << station << " found. I used it" << std::endl;
+ // return false;
+ // }
+
// Check if station already exist in DB
+
+ // FIXME -> do nothing if not on the command line. Is it what I want ?
bool found = false;
if (this->GetAFDB()->TagExist(s)) {
m_ListOfStations[station] = this->GetAFDB()->template GetImage<MaskImageType>(s);
found = true;
}
- // Define the starting support
- if (found && GetComputeStation(station)) {
- std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
- }
- if (!found || GetComputeStation(station)) {
- m_Working_Support = m_Mediastinum = this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
- return true;
- }
- else {
- std::cout << "Station " << station << " found. I used it" << std::endl;
- return false;
- }
}
//--------------------------------------------------------------------
z = this->GetAFDB()->GetDouble("ApexOfTheChestZ");
}
catch(clitk::ExceptionObject e) {
+
+ /*
//DD("FindApexOfTheChestPosition");
MaskImagePointer Lungs = this->GetAFDB()->template GetImage<MaskImageType>("Lungs");
MaskImagePointType p;
this->GetAFDB()->SetDouble("ApexOfTheChestZ", p[2]);
this->WriteAFDB();
z = p[2];
+ */
+
+ // the superior border becomes the more inferior of the two apices
+ MaskImagePointer RightLung = this->GetAFDB()->template GetImage<MaskImageType>("RightLung");
+ MaskImagePointer LeftLung = this->GetAFDB()->template GetImage<MaskImageType>("LeftLung");
+ MaskImagePointType pr;
+ MaskImagePointType pl;
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(RightLung, GetBackgroundValue(), 2, false, pr);
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(LeftLung, GetBackgroundValue(), 2, false, pl);
+ // We dont need Lungs structure from now
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("RightLung");
+ this->GetAFDB()->template ReleaseImage<MaskImageType>("LeftLung");
+ // Put inside the AFDB
+ if (pr[2] < pl[2]) z = pr[2];
+ else z = pl[2];
+ this->GetAFDB()->SetDouble("ApexOfTheChestZ", z);
+ this->WriteAFDB();
}
return z;
}
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+WriteImageSupport(std::string support)
+{
+ writeImage<MaskImageType>(m_ListOfSupports[support], this->GetAFDBPath()+"/"+"seg/Support_"+support+".mha");
+ this->GetAFDB()->SetImageFilename("Support_"+support, "seg/Support_"+support+".mha");
+}
+//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+WriteImageStation(std::string station)
+{
+ writeImage<MaskImageType>(m_ListOfStations[station], GetAFDB()->GetPath()+"/seg/Station"+station+".mha");
+ GetAFDB()->SetImageFilename("Station"+station, "seg/Station"+station+".mha");
+ WriteAFDB();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ComputeOverlapWithRef(std::string station)
+{
+ if (GetComputeStation(station)) {
+ MaskImagePointer ref = this->GetAFDB()->template GetImage <MaskImageType>("Station"+station+"_Ref");
+ typedef clitk::LabelImageOverlapMeasureFilter<MaskImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetInput(0, m_ListOfStations[station]);
+ filter->SetInput(1, ref);
+ filter->Update();
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ReadSupportLimits(std::string filename)
+{
+ m_ListOfSupportLimits.clear();
+ ifstream is;
+ openFileForReading(is, filename);
+ while (is) {
+ skipComment(is);
+ SupportLimitsType s;
+ s.Read(is);
+ if (is) m_ListOfSupportLimits.push_back(s);
+ }
+}
+//--------------------------------------------------------------------
+
#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff