-#include <itkBinaryDilateImageFilter.h>
-#include <itkMirrorPadImageFilter.h>
-
//--------------------------------------------------------------------
template <class ImageType>
void
}
//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_3P()
+{
+ if (!CheckForStation("3P")) return;
+
+ StartNewStep("Station 3P");
+ StartSubStep();
+
+ // Get the current support
+ StartNewStep("[Station 3P] Get the current 3P suppport");
+ m_Working_Support = m_ListOfSupports["S3P"];
+ m_ListOfStations["3P"] = m_Working_Support;
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+
+ // Generic RelativePosition processes
+ m_ListOfStations["3P"] = this->ApplyRelativePositionList("Station_3P", m_ListOfStations["3P"]);
+ m_Working_Support = m_ListOfStations["3P"];
+ ExtractStation_8_Single_CCL_Limits(); // YES 8 !
+ ExtractStation_3P_Remove_Structures(); // after CCL
+ m_ListOfStations["3P"] = m_Working_Support;
+
+ // Old stuff
+ // LR limits superiorly => not here for the moment because not clear in the def
+ // ExtractStation_3P_LR_sup_Limits_2(); //TODO
+ // ExtractStation_3P_LR_sup_Limits(); // old version to change
+ // ExtractStation_3P_LR_inf_Limits(); // <-- done in RelPosList
+
+ // Store image filenames into AFDB
+ writeImage<MaskImageType>(m_ListOfStations["3P"], "seg/Station3P.mhd");
+ GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd");
+ WriteAFDB();
+ StopSubStep();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_Remove_Structures()
+{
+ StartNewStep("[Station 3P] Remove some structures.");
+ Remove_Structures("3P", "Esophagus");
+ Remove_Structures("3P", "Thyroid");
+ Remove_Structures("3P", "VertebralArtery"); // (inside the station)
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3P_SI_Limits()
+ExtractStation_3P_LR_sup_Limits()
{
/*
- Apex of the chest & Carina.
- */
- StartNewStep("[Station 3P] Inf/Sup limits with apex of the chest and carina");
+ "On the right side, the limit is defined by the air–soft-tissue
+ interface. On the left side, it is defined by the air–tissue
+ interface superiorly (Fig. 2A–C) and the aorta inferiorly
+ (Figs. 2D–I and 3A–C)."
- writeImage<MaskImageType>(m_Working_Support, "support.mhd");
+ sup :
+ Resizelike support : Trachea, SubclavianArtery
+ Trachea, slice by slice, get centroid trachea
+ SubclavianArtery, slice by slice, CCL
+ prendre la 1ère à L et R, not at Left
+
+ */
+ StartNewStep("[Station 3P] Left/Right limits (superior part) ");
- // Get Carina position (has been determined in Station8)
- m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
- DD(m_CarinaZ);
+ // Load structures
+ MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+ MaskImagePointer SubclavianArtery = GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
+
+ // Crop like current support
+ Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
+ SubclavianArtery = clitk::ResizeImageLike<MaskImageType>(SubclavianArtery, m_Working_Support, GetBackgroundValue());
+
+ // writeImage<MaskImageType>(Trachea, "tr.mhd");
+ // writeImage<MaskImageType>(SubclavianArtery, "sca.mhd");
- // Get Apex of the Chest
- MaskImagePointer Lungs = GetAFDB()->template GetImage<MaskImageType>("Lungs");
- DD("lung ok");
+ // Get list of slices
+ std::vector<MaskSlicePointer> slices_support;
+ std::vector<MaskSlicePointer> slices_trachea;
+ std::vector<MaskSlicePointer> slices_subclavianartery;
+ clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices_support);
+ clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices_trachea);
+ clitk::ExtractSlices<MaskImageType>(SubclavianArtery, 2, slices_subclavianartery);
+
+ // Loop on slices
+ std::vector<MaskImagePointType> points;
MaskImagePointType p;
- bool found = clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Lungs,
- GetBackgroundValue(),
- 1, true, p);
- DD(found);
- DD(p);
- double m_ApexOfTheChest = p[2];
- DD(m_ApexOfTheChest);
-
- /* Crop support :
- Superior limit = carina
- Inferior limit = Apex of the chest */
- m_Working_Support =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2,
- m_ApexOfTheChest,
- m_CarinaZ, true,
- GetBackgroundValue());
+ for(uint i=0; i<slices_support.size(); i++) {
+ // Get Trachea centroid
+ std::vector<typename MaskSliceType::PointType> centroids;
+ typename MaskSliceType::PointType c;
+ ComputeCentroids<MaskSliceType>(slices_trachea[i], GetBackgroundValue(), centroids);
+ c = centroids[1];
+
+ // [debug] Store point
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[1], Trachea, i, p);
+ points.push_back(p);
+
+ // Get Right and Left CCL in SubclavianArtery
+ slices_subclavianartery[i] = Labelize<MaskSliceType>(slices_subclavianartery[i], 0, true, 10);
+ ComputeCentroids<MaskSliceType>(slices_subclavianartery[i], GetBackgroundValue(), centroids);
+
+ if (centroids.size() > 1) {
+ // Determine the one at Right/Left -> first after Trachea
+ // centroid
+ typename MaskSliceType::PointType right;
+ typename MaskSliceType::PointType left;
+ int label_right=-1;
+ int label_left=-1;
+ right[0] = c[0]-100;
+ left[0] = c[0]+100;
+ for(uint j=1; j<centroids.size(); j++) {
+ if (centroids[j][0] < c[0]) { // At Right of Trachea centroid
+ if (centroids[j][0] >= right[0]) {
+ right = centroids[j];
+ label_right = j;
+ }
+ }
+ if (centroids[j][0] > c[0]) { // At Left of Trachea centroid
+ if (centroids[j][0] <= left[0]) {
+ left = centroids[j];
+ label_left = j;
+ }
+ }
+ }
+
+ if (label_right != -1) {
+
+ // Debug points
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[label_right], SubclavianArtery, i, p);
+ points.push_back(p);
+
+ // Set Background and ForegroundValue according to label_right
+ MaskSlicePointer object =
+ clitk::Binarize<MaskSliceType>(slices_subclavianartery[i], label_right, label_right,
+ GetBackgroundValue(), GetForegroundValue());
+
+ // Relative Position : not at Right
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskSliceType> RelPosFilterType;
+ typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(slices_support[i]);
+ relPosFilter->SetInputObject(object);
+ relPosFilter->AddOrientationTypeString("RightTo");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->Update();
+ slices_support[i] = relPosFilter->GetOutput();
+
+ // Relative Position : not Anterior
+ relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(slices_support[i]);
+ relPosFilter->SetInputObject(object);
+ relPosFilter->AddOrientationTypeString("AntTo");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->Update();
+ slices_support[i] = relPosFilter->GetOutput();
+
+ } // End RelativePosition for Right
+
+
+ if (label_left != -1) {
+
+ // Debug points
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[label_left], SubclavianArtery, i, p);
+ points.push_back(p);
+
+ // Set Background and ForegroundValue according to label_right
+ MaskSlicePointer object =
+ clitk::Binarize<MaskSliceType>(slices_subclavianartery[i], label_left, label_left,
+ GetBackgroundValue(), GetForegroundValue());
+
+ // Relative Position : not at Right
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskSliceType> RelPosFilterType;
+ typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(slices_support[i]);
+ relPosFilter->SetInputObject(object);
+ relPosFilter->AddOrientationTypeString("L");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->Update();
+ slices_support[i] = relPosFilter->GetOutput();
+
+ // Relative Position : not Anterior
+ relPosFilter = RelPosFilterType::New();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(GetBackgroundValue());
+ relPosFilter->SetInput(slices_support[i]);
+ relPosFilter->SetInputObject(object);
+ relPosFilter->AddOrientationTypeString("A");
+ relPosFilter->SetInverseOrientationFlag(true);
+ // relPosFilter->SetIntermediateSpacing(3);
+ relPosFilter->SetIntermediateSpacingFlag(false);
+ relPosFilter->SetFuzzyThreshold(0.7);
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->Update();
+ slices_support[i] = relPosFilter->GetOutput();
+
+ }
+
+
+ } // if centroids.size > 1
+ } // End loop slices
+
+ // Joint slices
+ m_Working_Support = clitk::JoinSlices<MaskImageType>(slices_support, m_Working_Support, 2);
+
+ // Save list points
+ clitk::WriteListOfLandmarks<MaskImageType>(points, "subcl-lr.txt");
+
StopCurrentStep<MaskImageType>(m_Working_Support);
m_ListOfStations["3P"] = m_Working_Support;
}
//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_LR_sup_Limits_2()
+{
+ /*
+ "On the right side, the limit is defined by the air–soft-tissue
+ interface. On the left side, it is defined by the air–tissue
+ interface superiorly (Fig. 2A–C) and the aorta inferiorly
+ (Figs. 2D–I and 3A–C)."
+
+ sup :
+ Resizelike support : Trachea, SubclavianArtery
+ Trachea, slice by slice, get centroid trachea
+ SubclavianArtery, slice by slice, CCL
+ prendre la 1ère à L et R, not at Left
+
+ */
+ // StartNewStep("[Station 3P] Left/Right limits (superior part) ");
+
+
+}
+//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff