+++ /dev/null
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3P_SetDefaultValues()
-{
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-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_LR_sup_Limits()
-{
- /*
- "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) ");
-
- // 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 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;
- 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