X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStation_8.txx;h=fc39203ebf7ee646fbc2b169adfad864d9aabd92;hb=d64e6b39ec8d4bb7b99f9d1a531e9dba3121e2bc;hp=69e24c92053b5c59d9d772865b0cdc29f3ef02a5;hpb=726fc21726f96f8f32015dda4c3b1efeb7d81851;p=clitk.git diff --git a/segmentation/clitkExtractLymphStation_8.txx b/segmentation/clitkExtractLymphStation_8.txx index 69e24c9..fc39203 100644 --- a/segmentation/clitkExtractLymphStation_8.txx +++ b/segmentation/clitkExtractLymphStation_8.txx @@ -2,6 +2,23 @@ #include #include +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8_SetDefaultValues() +{ + SetDistanceMaxToAnteriorPartOfTheSpine(10); + MaskImagePointType p; + p[0] = 15; p[1] = 2; p[2] = 1; + SetEsophagusDiltationForAnt(p); + p[0] = 5; p[1] = 10; p[2] = 1; + SetEsophagusDiltationForRight(p); + SetFuzzyThreshold("8", "Esophagus", 0.5); + SetInjectedThresholdForS8(150); +} +//-------------------------------------------------------------------- + //-------------------------------------------------------------------- template void @@ -29,36 +46,25 @@ ExtractStation_8_SI_Limits() // Get Carina Z position MaskImagePointer Carina = GetAFDB()->template GetImage("Carina"); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after read Carina"); + std::vector centroids; clitk::ComputeCentroids(Carina, GetBackgroundValue(), centroids); - DD(centroids[1]); m_CarinaZ = centroids[1][2]; - DD(m_CarinaZ); + // DD(m_CarinaZ); // add one slice to include carina ? m_CarinaZ += m_Mediastinum->GetSpacing()[2]; - DD(m_CarinaZ); // We dont need Carina structure from now Carina->Delete(); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after delete Carina"); + GetAFDB()->SetDouble("CarinaZ", m_CarinaZ); - // Get left lower lobe bronchus (L), take the upper border - // Get right bronchus intermedius (RML), take the lower border - - /* - double m_CarinaZ = GetAFDB()->GetPoint3D("Carina", 2) + - m_Mediastinum->GetSpacing()[2]; // add one slice to include carina - // double GOjunctionZ = GetAFDB()->GetPoint3D("GOjunction", 2); - */ - // Found most inferior part of the lung MaskImagePointer Lungs = GetAFDB()->template GetImage("Lungs"); // It should be already croped, so I took the origin and add 10mm above m_DiaphragmInferiorLimit = Lungs->GetOrigin()[2]+10; - DD(m_DiaphragmInferiorLimit); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after read Lung"); - Lungs->Delete(); // we don't need it, release memory - clitk::PrintMemory(GetVerboseMemoryFlag(), "after release Lung"); + // Lungs->Delete(); // we don't need it, release memory -> it we want to release, also free in AFDB + clitk::PrintMemory(GetVerboseMemoryFlag(), "after reading lungs"); + GetAFDB()->template ReleaseImage("Lungs"); + clitk::PrintMemory(GetVerboseMemoryFlag(), "after release lungs"); /* Crop support : Superior limit = carina @@ -81,11 +87,16 @@ ExtractStation_8_SI_Limits() boolFilter->SetInput1(m_Working_Support); boolFilter->SetInput2(VertebralBody); boolFilter->SetOperationType(BoolFilterType::AndNot); - boolFilter->Update(); - boolFilter->SetInput1(boolFilter->GetOutput()); - boolFilter->SetInput2(Aorta); - boolFilter->SetOperationType(BoolFilterType::AndNot); - boolFilter->Update(); + boolFilter->Update(); + /* + + DO NOT REMOVE AORTA YET (LATER) + + boolFilter->SetInput1(boolFilter->GetOutput()); + boolFilter->SetInput2(Aorta); + boolFilter->SetOperationType(BoolFilterType::AndNot); + boolFilter->Update(); + */ m_Working_Support = boolFilter->GetOutput(); // Done. @@ -152,13 +163,13 @@ ExtractStation_8_Post_Limits() // Convert 2D points in slice into 3D points std::vector vertebralAntPositions; - clitk::PointsUtils::Convert2DTo3DList(vertebralAntPositionBySlice, - VertebralBody, - vertebralAntPositions); + clitk::PointsUtils::Convert2DMapTo3DList(vertebralAntPositionBySlice, + VertebralBody, + vertebralAntPositions); // DEBUG : write list of points clitk::WriteListOfLandmarks(vertebralAntPositions, - "vertebralMostAntPositions.txt"); + "S8-vertebralMostAntPositions-points.txt"); // Cut support posteriorly 1cm the most anterior point of the // VertebralBody. Do nothing below and above the VertebralBody. To @@ -206,7 +217,7 @@ ExtractStation_8_Post_Limits() template void clitk::ExtractLymphStationsFilter:: -ExtractStation_8_Ant_Limits() +ExtractStation_8_Ant_Sup_Limits() { //-------------------------------------------------------------------- StartNewStep("[Station8] Ant limits with S7 above Carina"); @@ -228,20 +239,17 @@ ExtractStation_8_Ant_Limits() // Ant limit from carina (start) to end of S7 = originRMLB // Get Trachea MaskImagePointer Trachea = GetAFDB()->template GetImage("Trachea"); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after read Trachea"); MaskImagePointer m_Working_Trachea = - clitk::CropImageAbove(Trachea, 2, m_CarinaZ, true, // AutoCrop + clitk::CropImageRemoveGreaterThan(Trachea, 2, m_CarinaZ, true, // AutoCrop GetBackgroundValue()); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after crop"); // Seprate into two main bronchi - MaskImagePointer LeftBronchus; MaskImagePointer RightBronchus; + MaskImagePointer LeftBronchus; // Labelize and consider the two first (main) labels m_Working_Trachea = Labelize(m_Working_Trachea, 0, true, 1); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after labelize"); // Carina position must at the first slice that separate the two // main bronchus (not superiorly). We thus first check that the @@ -270,56 +278,56 @@ ExtractStation_8_Ant_Limits() ImagePointType C1 = c[1]; ImagePointType C2 = c[2]; - ImagePixelType leftLabel; - ImagePixelType rightLabel; - if (C1[0] < C2[0]) { leftLabel = 1; rightLabel = 2; } - else { leftLabel = 2; rightLabel = 1; } + ImagePixelType rightLabel; + ImagePixelType leftLabel; + if (C1[0] < C2[0]) { rightLabel = 1; leftLabel = 2; } + else { rightLabel = 2; leftLabel = 1; } // Select LeftLabel (set one label to Backgroundvalue) - LeftBronchus = + RightBronchus = + clitk::Binarize(m_Working_Trachea, rightLabel, rightLabel, + GetBackgroundValue(), GetForegroundValue()); + /* SetBackground(m_Working_Trachea, m_Working_Trachea, - rightLabel, GetBackgroundValue(), false); - RightBronchus = + leftLabel, GetBackgroundValue(), false); + */ + LeftBronchus = clitk::Binarize(m_Working_Trachea, leftLabel, leftLabel, + GetBackgroundValue(), GetForegroundValue()); + /* SetBackground(m_Working_Trachea, m_Working_Trachea, - leftLabel, GetBackgroundValue(), false); + rightLabel, GetBackgroundValue(), false); + */ + // Crop images - LeftBronchus = clitk::AutoCrop(LeftBronchus, GetBackgroundValue()); RightBronchus = clitk::AutoCrop(RightBronchus, GetBackgroundValue()); + LeftBronchus = clitk::AutoCrop(LeftBronchus, GetBackgroundValue()); // Insert int AFDB if need after - GetAFDB()->template SetImage ("LeftBronchus", "seg/leftBronchus.mhd", - LeftBronchus, true); GetAFDB()->template SetImage ("RightBronchus", "seg/rightBronchus.mhd", RightBronchus, true); + GetAFDB()->template SetImage ("LeftBronchus", "seg/leftBronchus.mhd", + LeftBronchus, true); // Now crop below OriginOfRightMiddleLobeBronchusZ // It is not done before to keep entire bronchi. MaskImagePointer OriginOfRightMiddleLobeBronchus = GetAFDB()->template GetImage("OriginOfRightMiddleLobeBronchus"); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after read OriginOfRightMiddleLobeBronchus"); std::vector centroids; clitk::ComputeCentroids(OriginOfRightMiddleLobeBronchus, GetBackgroundValue(), centroids); - DD(centroids.size()); - DD(centroids[0]); // BG - DD(centroids[1]); m_OriginOfRightMiddleLobeBronchusZ = centroids[1][2]; - DD(m_OriginOfRightMiddleLobeBronchusZ); // add one slice to include carina ? - m_OriginOfRightMiddleLobeBronchusZ += LeftBronchus->GetSpacing()[2]; - DD(m_OriginOfRightMiddleLobeBronchusZ); - DD(OriginOfRightMiddleLobeBronchus->GetReferenceCount()); + m_OriginOfRightMiddleLobeBronchusZ += RightBronchus->GetSpacing()[2]; // We dont need Carina structure from now OriginOfRightMiddleLobeBronchus->Delete(); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after delete OriginOfRightMiddleLobeBronchus"); - LeftBronchus = - clitk::CropImageBelow(LeftBronchus, 2, + RightBronchus = + clitk::CropImageRemoveLowerThan(RightBronchus, 2, m_OriginOfRightMiddleLobeBronchusZ, true, // AutoCrop GetBackgroundValue()); - RightBronchus = - clitk::CropImageBelow(RightBronchus, 2, + LeftBronchus = + clitk::CropImageRemoveLowerThan(LeftBronchus, 2, m_OriginOfRightMiddleLobeBronchusZ, true, // AutoCrop GetBackgroundValue()); @@ -327,39 +335,42 @@ ExtractStation_8_Ant_Limits() // Search for points that are the most left/post/ant and most // right/post/ant of the left and right bronchus // 15 = not 15 mm more distance than the middle point. - FindExtremaPointsInBronchus(LeftBronchus, 0, 10, m_RightMostInLeftBronchus, - m_AntMostInLeftBronchus, m_PostMostInLeftBronchus); - FindExtremaPointsInBronchus(RightBronchus, 1, 10, m_LeftMostInRightBronchus, + FindExtremaPointsInBronchus(RightBronchus, 0, 10, m_LeftMostInRightBronchus, m_AntMostInRightBronchus, m_PostMostInRightBronchus); + FindExtremaPointsInBronchus(LeftBronchus, 1, 10, m_RightMostInLeftBronchus, + m_AntMostInLeftBronchus, m_PostMostInLeftBronchus); + // DEBUG : write the list of points ListOfPointsType v; + v.reserve(m_LeftMostInRightBronchus.size()+m_AntMostInRightBronchus.size()+ + m_PostMostInRightBronchus.size()); + v.insert(v.end(), m_LeftMostInRightBronchus.begin(), m_LeftMostInRightBronchus.end() ); + v.insert(v.end(), m_AntMostInRightBronchus.begin(), m_AntMostInRightBronchus.end() ); + v.insert(v.end(), m_PostMostInRightBronchus.begin(), m_PostMostInRightBronchus.end() ); + clitk::WriteListOfLandmarks(v, "S8-RightBronchus-points.txt"); + + v.clear(); v.reserve(m_RightMostInLeftBronchus.size()+m_AntMostInLeftBronchus.size()+ m_PostMostInLeftBronchus.size()); v.insert(v.end(), m_RightMostInLeftBronchus.begin(), m_RightMostInLeftBronchus.end() ); v.insert(v.end(), m_AntMostInLeftBronchus.begin(), m_AntMostInLeftBronchus.end() ); v.insert(v.end(), m_PostMostInLeftBronchus.begin(), m_PostMostInLeftBronchus.end() ); - clitk::WriteListOfLandmarks(v, "LeftBronchusPoints.txt"); + clitk::WriteListOfLandmarks(v, "S8-LeftBronchus-points.txt"); v.clear(); - v.reserve(m_LeftMostInRightBronchus.size()+m_AntMostInRightBronchus.size()+ - m_PostMostInRightBronchus.size()); - v.insert(v.end(), m_LeftMostInRightBronchus.begin(), m_LeftMostInRightBronchus.end() ); - v.insert(v.end(), m_AntMostInRightBronchus.begin(), m_AntMostInRightBronchus.end() ); + v.reserve(m_PostMostInLeftBronchus.size()+m_PostMostInRightBronchus.size()); + v.insert(v.end(), m_PostMostInLeftBronchus.begin(), m_PostMostInLeftBronchus.end() ); v.insert(v.end(), m_PostMostInRightBronchus.begin(), m_PostMostInRightBronchus.end() ); - clitk::WriteListOfLandmarks(v, "RightBronchusPoints.txt"); + clitk::WriteListOfLandmarks(v, "S8-RightLeftBronchus-points.txt"); // Now uses these points to limit, slice by slice // line is mainly horizontal, so mainDirection=1 - writeImage(m_Working_Support, "before.mhd"); clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, - m_PostMostInLeftBronchus, m_PostMostInRightBronchus, + m_PostMostInLeftBronchus, GetBackgroundValue(), 1, 10); - writeImage(m_Working_Support, "after.mhd"); - -HERE // Keep main 3D CCL : m_Working_Support = Labelize(m_Working_Support, 0, false, 10); @@ -380,11 +391,11 @@ HERE template void clitk::ExtractLymphStationsFilter:: -ExtractStation_8_LR_Limits() +ExtractStation_8_Ant_Inf_Limits() { //-------------------------------------------------------------------- - StartNewStep("[Station8] Left and Right limits arround esophagus (below Carina)"); + StartNewStep("[Station8] Ant part: not post to Esophagus"); /* Consider Esophagus, dilate it and remove ant part. It remains part on L & R, than can be partly removed by cutting what remains at @@ -392,96 +403,331 @@ ExtractStation_8_LR_Limits() */ // Get Esophagus - MaskImagePointer Esophagus = GetAFDB()->template GetImage("Esophagus"); + m_Esophagus = GetAFDB()->template GetImage("Esophagus"); clitk::PrintMemory(GetVerboseMemoryFlag(), "after read Esophagus"); + // In images from the original article, Atlas – UM, the oesophagus + //was included in nodal stations 3p and 8. Having said that, in the + //description for station 8, it indicates that “the delineation of + //station 8 is limited to the soft tissues surrounding the + //oesophagus”. In the recent article, The IASLC Lung Cancer Staging + //Project (J Thorac Oncol 4:5, 568-77), the images drawn by + //Dr. Aletta Frasier exclude this structure. From an oncological + //prospective, the oesophagus should be excluded from these nodal + //stations. + + /* NOT YET !! DO IT LATER + + typedef clitk::BooleanOperatorLabelImageFilter BoolFilterType; + typename BoolFilterType::Pointer boolFilter = BoolFilterType::New(); + boolFilter->InPlaceOn(); + boolFilter->SetInput1(m_Working_Support); + boolFilter->SetInput2(m_Esophagus); + boolFilter->SetOperationType(BoolFilterType::AndNot); + boolFilter->Update(); + m_Working_Support = boolFilter->GetOutput(); + + */ + // Crop Esophagus : keep only below the OriginOfRightMiddleLobeBronchusZ - Esophagus = - clitk::CropImageAbove(Esophagus, 2, + m_Esophagus = + clitk::CropImageRemoveGreaterThan(m_Esophagus, 2, m_OriginOfRightMiddleLobeBronchusZ, true, // AutoCrop GetBackgroundValue()); // Dilate to keep only not Anterior positions MaskImagePointType radiusInMM = GetEsophagusDiltationForAnt(); - Esophagus = EnlargeEsophagusDilatationRadiusInferiorly(Esophagus); - Esophagus = clitk::Dilate(Esophagus, - radiusInMM, - GetBackgroundValue(), - GetForegroundValue(), true); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after dilate Esophagus"); - writeImage(Esophagus, "enlarged-eso.mhd"); - // Remove Anterior part according to this dilatated esophagus + // m_Esophagus = EnlargeEsophagusDilatationRadiusInferiorly(m_Esophagus); + + m_Esophagus = clitk::Dilate(m_Esophagus, + radiusInMM, + GetBackgroundValue(), + GetForegroundValue(), true); + + // Remove Anterior part according to this dilatated esophagus. Note: + // because we crop Esophagus with ORML, the support will also be + // croped in the same way. Here it is a desired feature. If we dont + // want, use SetIgnoreEmptySliceObject(true) + + // In the new IASCL definition, it is not clear if sup limits is + // around carina or On the right, it is “the lower border of the + // bronchus intermedius”, indicated on the image set as a point + // (“lower border of the bronchus intermedius”) + typedef clitk::SliceBySliceRelativePositionFilter RelPosFilterType; typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New(); relPosFilter->VerboseStepFlagOff(); + relPosFilter->WriteStepFlagOff(); relPosFilter->SetInput(m_Working_Support); - relPosFilter->SetInputObject(Esophagus); - relPosFilter->AddOrientationTypeString("P"); - relPosFilter->InverseOrientationFlagOff(); + relPosFilter->SetInputObject(m_Esophagus); + relPosFilter->AddOrientationTypeString("PostTo"); + // relPosFilter->InverseOrientationFlagOff(); relPosFilter->SetDirection(2); // Z axis relPosFilter->UniqueConnectedComponentBySliceOff(); relPosFilter->SetIntermediateSpacing(3); - relPosFilter->ResampleBeforeRelativePositionFilterOn(); - relPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS8()); - relPosFilter->RemoveObjectFlagOff(); + relPosFilter->IntermediateSpacingFlagOn(); + relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("8", "Esophagus")); + relPosFilter->RemoveObjectFlagOff(); // Do not exclude here because it is dilated + relPosFilter->CombineWithOrFlagOff(); // NO ! + relPosFilter->IgnoreEmptySliceObjectFlagOn(); relPosFilter->Update(); m_Working_Support = relPosFilter->GetOutput(); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after SbS Rel pos Post"); // AutoCrop (OR SbS ?) m_Working_Support = clitk::AutoCrop(m_Working_Support, GetBackgroundValue()); - writeImage(m_Working_Support, "step1.4.1.mhd"); + StopCurrentStep(m_Working_Support); + m_ListOfStations["8"] = m_Working_Support; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8_Ant_Injected_Limits() +{ + + //-------------------------------------------------------------------- + StartNewStep("[Station8] Ant part (remove high density, injected part)"); + + // Consider initial image, crop to current support + ImagePointer working_input = + clitk::ResizeImageLike(m_Input, + m_Working_Support, + (short)GetBackgroundValue()); + + // Threshold + typedef itk::BinaryThresholdImageFilter BinarizeFilterType; + typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New(); + binarizeFilter->SetInput(working_input); + binarizeFilter->SetLowerThreshold(GetInjectedThresholdForS8()); + binarizeFilter->SetInsideValue(GetForegroundValue()); + binarizeFilter->SetOutsideValue(GetBackgroundValue()); + binarizeFilter->Update(); + MaskImagePointer injected = binarizeFilter->GetOutput(); + + // Combine with current support + clitk::AndNot(m_Working_Support, injected, GetBackgroundValue()); + + StopCurrentStep(m_Working_Support); + m_ListOfStations["8"] = m_Working_Support; +} +//-------------------------------------------------------------------- + + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8_LR_1_Limits() +{ + //-------------------------------------------------------------------- + StartNewStep("[Station8] Left and Right (from Carina to PulmonaryTrunk): Right to LeftPulmonaryArtery"); + + /* + We remove LeftPulmonaryArtery structure and what is at Left to + this structure. + */ + MaskImagePointer LeftPulmonaryArtery = GetAFDB()->template GetImage("LeftPulmonaryArtery"); + + // Relative Position : not at Left + typedef clitk::AddRelativePositionConstraintToLabelImageFilter RelPosFilterType; + typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New(); + relPosFilter->VerboseStepFlagOff(); + relPosFilter->WriteStepFlagOff(); + relPosFilter->SetBackgroundValue(GetBackgroundValue()); + relPosFilter->SetInput(m_Working_Support); + relPosFilter->SetInputObject(LeftPulmonaryArtery); + relPosFilter->RemoveObjectFlagOn(); // remove the object too + relPosFilter->AddOrientationTypeString("L"); + relPosFilter->InverseOrientationFlagOn(); // Not at Left + relPosFilter->SetIntermediateSpacing(3); + relPosFilter->IntermediateSpacingFlagOn(); + relPosFilter->SetFuzzyThreshold(0.7); + relPosFilter->AutoCropFlagOn(); + relPosFilter->Update(); + m_Working_Support = relPosFilter->GetOutput(); + + // Release LeftPulmonaryArtery + GetAFDB()->template ReleaseImage("LeftPulmonaryArtery"); + + StopCurrentStep(m_Working_Support); + m_ListOfStations["8"] = m_Working_Support; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8_LR_2_Limits() +{ + //-------------------------------------------------------------------- + StartNewStep("[Station8] Left and Right (from PulmTrunk to OriginMiddleLobeBronchus) Right to line from Aorta to PulmonaryTrunk"); + + /* + We consider a line from Left part of Aorta to left part of + PulmonaryTrunk and remove what is at Left. + */ + + // Load the structures + MaskImagePointer Aorta = GetAFDB()->template GetImage("Aorta"); + MaskImagePointer PulmonaryTrunk = GetAFDB()->template GetImage("PulmonaryTrunk"); + + // Resize like the PT and define the slices + MaskImagePointType min, max; + clitk::GetMinMaxPointPosition(PulmonaryTrunk, min, max); + Aorta = clitk::CropImageAlongOneAxis(Aorta, 2, min[2], max[2], false, GetBackgroundValue()); + std::vector slices_aorta; + clitk::ExtractSlices(Aorta, 2, slices_aorta); + std::vector slices_PT; + clitk::ExtractSlices(PulmonaryTrunk, 2, slices_PT); + + // Find the points at left + std::vector p_A; + std::vector p_B; + MaskImagePointType pA; + MaskImagePointType pB; + for(uint i=0; i(slices_aorta[i], GetBackgroundValue(), 0, false, ps); + clitk::PointsUtils::Convert2DTo3D(ps, Aorta, i, pA); + + if (found) { + // In PT : generally 2 CCL, we keep the most at left + found = + clitk::FindExtremaPointInAGivenDirection(slices_PT[i], GetBackgroundValue(), 0, false, ps); + clitk::PointsUtils::Convert2DTo3D(ps, PulmonaryTrunk, i, pB); + } + + if (found) { + p_A.push_back(pA); + p_B.push_back(pB); + } + } + clitk::WriteListOfLandmarks(p_A, "S8-Aorta-Left-points.txt"); + clitk::WriteListOfLandmarks(p_B, "S8-PT-Left-points.txt"); + + // Remove part at Left + clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, + p_A, p_B, + GetBackgroundValue(), + 0, -10); + + StopCurrentStep(m_Working_Support); + m_ListOfStations["8"] = m_Working_Support; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8_Single_CCL_Limits() +{ + //-------------------------------------------------------------------- + StartNewStep("[Station8 or 3P] Slice by slice, keep a single CCL (the closest to VertebralBody)"); + + // Consider slices + std::vector slices; + std::vector slices_vb; + clitk::ExtractSlices(m_Working_Support, 2, slices); + MaskImagePointer VertebralBody = + GetAFDB()->template GetImage ("VertebralBody"); + VertebralBody = clitk::ResizeImageLike(VertebralBody, m_Working_Support, GetBackgroundValue()); + clitk::ExtractSlices(VertebralBody, 2, slices_vb); + + for(uint i=0; i(slices[i], 0, true, 100); + // Compute centroids coordinate + std::vector centroids; + std::vector c; + clitk::ComputeCentroids(slices[i], GetBackgroundValue(), centroids); + clitk::ComputeCentroids(slices_vb[i], GetBackgroundValue(), c); + if ((c.size() > 1) && (centroids.size() > 1)) { + // keep the one which is the closer to vertebralbody centroid + double distance=1000000; + int index=0; + for(uint j=1; j(slices[i], GetBackgroundValue(), + GetForegroundValue(), index, index, true); + } + } + m_Working_Support = clitk::JoinSlices(slices, m_Working_Support, 2); + + StopCurrentStep(m_Working_Support); + m_ListOfStations["8"] = m_Working_Support; +} +//-------------------------------------------------------------------- + - clitk::PrintMemory(GetVerboseMemoryFlag(), "after autocrop"); +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8_LR_Limits_old2() +{ + + //-------------------------------------------------------------------- + StartNewStep("[Station8] Left and Right limits arround esophagus (below Carina)"); // Estract slices for current support for slice by slice processing std::vector slices; clitk::ExtractSlices(m_Working_Support, 2, slices); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after support slices"); + // Dilate the Esophagus to consider a margins around + MaskImagePointType radiusInMM = GetEsophagusDiltationForAnt(); + m_Esophagus = clitk::Dilate(m_Esophagus, + radiusInMM, + GetBackgroundValue(), + GetForegroundValue(), true); + + // Remove what is outside the mediastinum in this enlarged Esophagus -> it allows to select + // 'better' extrema points (not too post). + MaskImagePointer Lungs = GetAFDB()->template GetImage("Lungs"); + clitk::AndNot(m_Esophagus, Lungs, GetBackgroundValue()); + GetAFDB()->template ReleaseImage("Lungs"); + // Estract slices of Esophagus (resize like support before to have the same set of slices) - MaskImagePointer EsophagusForSlice = clitk::ResizeImageLike(Esophagus, m_Working_Support, GetBackgroundValue()); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after Eso resize"); + MaskImagePointer EsophagusForSlice = clitk::ResizeImageLike(m_Esophagus, m_Working_Support, GetBackgroundValue()); + std::vector eso_slices; clitk::ExtractSlices(EsophagusForSlice, 2, eso_slices); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after Eso slices"); // Estract slices of Vertebral (resize like support before to have the same set of slices) MaskImagePointer VertebralBody = GetAFDB()->template GetImage("VertebralBody"); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after Read VertebralBody"); VertebralBody = clitk::ResizeImageLike(VertebralBody, m_Working_Support, GetBackgroundValue()); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after VertebralBody Resize"); std::vector vert_slices; clitk::ExtractSlices(VertebralBody, 2, vert_slices); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after VertebralBody slices"); // Estract slices of Aorta (resize like support before to have the same set of slices) MaskImagePointer Aorta = GetAFDB()->template GetImage("Aorta"); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after Read Aorta"); Aorta = clitk::ResizeImageLike(Aorta, m_Working_Support, GetBackgroundValue()); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after Aorta Resize"); std::vector aorta_slices; clitk::ExtractSlices(Aorta, 2, aorta_slices); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after Aorta slices"); // Extract slices of Mediastinum (resize like support before to have the same set of slices) m_Mediastinum = GetAFDB()->template GetImage("Mediastinum"); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after read Mediastinum"); m_Mediastinum = clitk::ResizeImageLike(m_Mediastinum, m_Working_Support, GetBackgroundValue()); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after resize Mediastinum"); std::vector mediast_slices; clitk::ExtractSlices(m_Mediastinum, 2, mediast_slices); - clitk::PrintMemory(GetVerboseMemoryFlag(), "after Mediastinum slices"); - - writeImage(EsophagusForSlice, "slices_eso.mhd"); - writeImage(VertebralBody, "slices_vert.mhd"); - writeImage(Aorta, "slices_aorta.mhd"); - writeImage(m_Mediastinum, "slices_medias.mhd"); - writeImage(m_Working_Support, "slices_support.mhd"); - // List of points std::vector p_RightMostAnt; @@ -489,6 +735,8 @@ ExtractStation_8_LR_Limits() std::vector p_LeftMostAnt; std::vector p_LeftMostPost; std::vector p_AllPoints; + std::vector p_LeftAorta; + std::vector p_LeftEso; /* In the following, we search for the LeftRight limits. We search @@ -499,7 +747,7 @@ ExtractStation_8_LR_Limits() is concave between Eso/VertebralBody. Esophagus is a bit dilatated. On VertebralBody we go right (or left) until we reach the lung (but no more 20 mm). - */ + */ // Loop slices MaskImagePointType p; @@ -516,17 +764,6 @@ ExtractStation_8_LR_Limits() // Right is at left on screen, coordinate decrease // Left is at right on screen, coordinate increase - // Find right limit of Esophagus and Aorta - clitk::FindExtremaPointInAGivenDirection(eso_slices[i], GetBackgroundValue(), 0, true, sp_maxRight_Eso); - clitk::FindExtremaPointInAGivenDirection(aorta_slices[i], GetBackgroundValue(), 0, true, sp_maxRight_Aorta); - clitk::PointsUtils::Convert2DTo3D(sp_maxRight_Eso, EsophagusForSlice, i, p); - clitk::PointsUtils::Convert2DTo3D(sp_maxRight_Aorta, Aorta, i, pp); - pp[0] -= 2; // Add a margin of 2 mm to include the 'wall' - p_AllPoints.push_back(p); - p_AllPoints.push_back(pp); - if (p[0] only at most Post part of current // slice support. First found most ant point in VertebralBody typedef MaskSliceType SliceType; @@ -537,7 +774,6 @@ ExtractStation_8_LR_Limits() // the VertebralBody is not delineated enough inferiorly ... in // those cases, we consider the first found slice. std::cerr << "No foreground pixels in this VertebralBody slices !?? I try with the previous/next slice" << std::endl; - DD(i); int j=i++; bool found = false; while (!found) { @@ -545,7 +781,6 @@ ExtractStation_8_LR_Limits() //clitkExceptionMacro("No foreground pixels in this VertebralBody slices ??"); j++; } - DD(j); } p_slice_ant[1] += GetDistanceMaxToAnteriorPartOfTheSpine(); // Consider offset @@ -584,6 +819,7 @@ ExtractStation_8_LR_Limits() else { // in that case, we are probably below the diaphragm, so we // add aribtrarly few mm sp_maxRight_Vertebra[0] -= 2; // Leave 2 mm around the VertebralBody + clitk::PointsUtils::Convert2DTo3D(sp_maxRight_Vertebra, m_Mediastinum, i, p); } p_RightMostPost.push_back(p); p_AllPoints.push_back(p); @@ -602,27 +838,85 @@ ExtractStation_8_LR_Limits() else { // in that case, we are probably below the diaphragm, so we // add aribtrarly few mm sp_maxLeft_Vertebra[0] += 2; // Leave 2 mm around the VertebralBody + clitk::PointsUtils::Convert2DTo3D(sp_maxLeft_Vertebra, m_Mediastinum, i, p); } p_LeftMostPost.push_back(p); p_AllPoints.push_back(p); + // Find Eso slice centroid and do not consider what is post to + // this centroid. + std::vector c; + clitk::ComputeCentroids(eso_slices[i], GetBackgroundValue(), c); + if (c.size() >1) { + eso_slices[i] = + clitk::CropImageRemoveGreaterThan(eso_slices[i], 1, c[1][1], false, GetBackgroundValue()); + eso_slices[i] = + clitk::ResizeImageLike(eso_slices[i], aorta_slices[i], GetBackgroundValue()); + // writeImage(eso_slices[i], "eso-slice-"+toString(i)+".mhd"); + } + + // Find right limit of Esophagus and Aorta + bool f = + clitk::FindExtremaPointInAGivenDirection(eso_slices[i], GetBackgroundValue(), + 0, true, sp_maxRight_Eso); + f = f && + clitk::FindExtremaPointInAGivenDirection(aorta_slices[i], GetBackgroundValue(), + 0, true, sp_maxRight_Aorta); + clitk::PointsUtils::Convert2DTo3D(sp_maxRight_Eso, EsophagusForSlice, i, p); + clitk::PointsUtils::Convert2DTo3D(sp_maxRight_Aorta, Aorta, i, pp); + pp[0] -= 2; // Add a margin of 2 mm to include the Aorta 'wall' + p_AllPoints.push_back(p); + if (f) { + p_AllPoints.push_back(pp); + MaskImagePointType A = p_RightMostPost.back(); + MaskImagePointType B = p; + MaskImagePointType C = pp; + double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]); + if (s>0) p_RightMostAnt.push_back(p); + else p_RightMostAnt.push_back(pp); + } + else { // No more Esophagus in this slice : do nothing + // p_RightMostAnt.push_back(p); + p_RightMostPost.pop_back(); + } + // -------------------------------------------------------------------------- // Find the limit on the Left: most left point between Eso and - // Vertebra. (Left is left on screen, coordinate increase) + // Eso. (Left is left on screen, coordinate increase) // Find left limit of Esophagus clitk::FindExtremaPointInAGivenDirection(eso_slices[i], GetBackgroundValue(), 0, false, sp_maxLeft_Eso); - clitk::FindExtremaPointInAGivenDirection(aorta_slices[i], GetBackgroundValue(), 0, false, sp_maxLeft_Aorta); + f = clitk::FindExtremaPointInAGivenDirection(aorta_slices[i], GetBackgroundValue(), 0, false, sp_maxLeft_Aorta); clitk::PointsUtils::Convert2DTo3D(sp_maxLeft_Eso, EsophagusForSlice, i, p); clitk::PointsUtils::Convert2DTo3D(sp_maxLeft_Aorta, Aorta, i, pp); p_AllPoints.push_back(p); pp[0] += 2; // Add a margin of 2 mm to include the 'wall' - p_AllPoints.push_back(pp); - if (p[0]>pp[0]) p_LeftMostAnt.push_back(p); // Insert point most at right - else p_LeftMostAnt.push_back(pp); + if (f) { // not below Aorta + p_AllPoints.push_back(pp); + MaskImagePointType A = p_LeftMostPost.back(); + MaskImagePointType B = p; + MaskImagePointType C = pp; + double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]); + if (s<0) { + p_LeftMostAnt.push_back(p); // Insert point most at Left, Eso + } + else { + // in this case -> two lines ! + p_LeftMostAnt.push_back(pp); // Insert point most at Left, Aorta (Vert to Aorta) + // but also consider Aorta to Eso + p_LeftAorta.push_back(pp); + p_LeftEso.push_back(p); + } + } + else { // No more Esophagus in this slice : do nothing + p_LeftMostPost.pop_back(); + //p_LeftMostAnt.push_back(p); + } } // End of slice loop - clitk::WriteListOfLandmarks(p_AllPoints, "LR-Eso-Vert.txt"); + clitk::WriteListOfLandmarks(p_AllPoints, "S8-LR-Eso-Vert.txt"); + clitk::WriteListOfLandmarks(p_LeftEso, "S8-Left-Eso.txt"); + clitk::WriteListOfLandmarks(p_LeftAorta, "S8-Left-Aorta.txt"); // Now uses these points to limit, slice by slice // Line is mainly vertical, so mainDirection=0 @@ -632,7 +926,216 @@ ExtractStation_8_LR_Limits() clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, p_LeftMostAnt, p_LeftMostPost, GetBackgroundValue(), 0, -10); - // DEBUG + clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, + p_LeftEso,p_LeftAorta, + GetBackgroundValue(), 0, -10); + // END + StopCurrentStep(m_Working_Support); + m_ListOfStations["8"] = m_Working_Support; + return; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8_LR_Limits() +{ + + //-------------------------------------------------------------------- + StartNewStep("[Station8] Left and Right limits arround esophagus with lines from VertebralBody-Aorta-Esophagus"); + + // Estract slices for current support for slice by slice processing + std::vector slices; + clitk::ExtractSlices(m_Working_Support, 2, slices); + + // Dilate the Esophagus to consider a margins around + MaskImagePointType radiusInMM = GetEsophagusDiltationForAnt(); + m_Esophagus = clitk::Dilate(m_Esophagus, radiusInMM, + GetBackgroundValue(), GetForegroundValue(), true); + // m_Esophagus = EnlargeEsophagusDilatationRadiusInferiorly(m_Esophagus); + + // Remove what is outside the mediastinum in this enlarged Esophagus -> it allows to select + // 'better' extrema points (not too post). + MaskImagePointer Lungs = GetAFDB()->template GetImage("Lungs"); + clitk::AndNot(m_Esophagus, Lungs, GetBackgroundValue()); + GetAFDB()->template ReleaseImage("Lungs"); + + // Estract slices of Esophagus (resize like support before to have the same set of slices) + MaskImagePointer EsophagusForSlice = clitk::ResizeImageLike(m_Esophagus, m_Working_Support, GetBackgroundValue()); + std::vector eso_slices; + clitk::ExtractSlices(EsophagusForSlice, 2, eso_slices); + + // Estract slices of Vertebral (resize like support before to have the same set of slices) + MaskImagePointer VertebralBody = GetAFDB()->template GetImage("VertebralBody"); + VertebralBody = clitk::ResizeImageLike(VertebralBody, m_Working_Support, GetBackgroundValue()); + std::vector vert_slices; + clitk::ExtractSlices(VertebralBody, 2, vert_slices); + + // Estract slices of Aorta (resize like support before to have the same set of slices) + MaskImagePointer Aorta = GetAFDB()->template GetImage("Aorta"); + Aorta = clitk::ResizeImageLike(Aorta, m_Working_Support, GetBackgroundValue()); + std::vector aorta_slices; + clitk::ExtractSlices(Aorta, 2, aorta_slices); + + // Extract slices of Mediastinum (resize like support before to have the same set of slices) + m_Mediastinum = GetAFDB()->template GetImage("Mediastinum"); + m_Mediastinum = clitk::ResizeImageLike(m_Mediastinum, m_Working_Support, GetBackgroundValue()); + std::vector mediast_slices; + clitk::ExtractSlices(m_Mediastinum, 2, mediast_slices); + + // List of points + std::vector p_MostLeftVertebralBody; + std::vector p_MostRightVertebralBody; + std::vector p_MostLeftAorta; + std::vector p_MostLeftEsophagus; + + /* + In the following, we search for the LeftRight limits. We search + for the most Right points in Esophagus and in VertebralBody and + consider a line between those to most right points. All points in + the support which are most right to this line are discarded. Same + for the left part. The underlying assumption is that the support + is concave between Eso/VertebralBody. Esophagus is a bit + dilatated. On VertebralBody we go right (or left) until we reach + the lung (but no more 20 mm). + */ + + // Temporary 3D point + MaskImagePointType p; + + // Loop slices + for(uint i=0; i(vert_slices[j], GetBackgroundValue(), 1, true, sp_MostAntVertebralBody); + if (!found) { + // It should not happen ! But sometimes, a contour is missing or + // the VertebralBody is not delineated enough inferiorly ... in + // those cases, we consider the first found slice. + std::cerr << "No foreground pixels in this VertebralBody slices !?? I try with the previous/next slice" << std::endl; + j++; + } + } + sp_MostAntVertebralBody[1] += GetDistanceMaxToAnteriorPartOfTheSpine(); // Consider offset + + // Crop the vertebralbody below this most post line + vert_slices[j] = + clitk::CropImageRemoveGreaterThan(vert_slices[j], 1, sp_MostAntVertebralBody[1], false, GetBackgroundValue()); + vert_slices[j] = + clitk::ResizeImageLike(vert_slices[j], aorta_slices[i], GetBackgroundValue()); + // writeImage(vert_slices[i], "vert-slice-"+toString(i)+".mhd"); + + // Find first point not in mediastinum + clitk::FindExtremaPointInAGivenDirection(vert_slices[j], GetBackgroundValue(), 0, false, sp_MostLeftVertebralBody); + sp_MostLeftVertebralBody = clitk::FindExtremaPointInAGivenLine(mediast_slices[i], 0, false, sp_MostLeftVertebralBody, GetBackgroundValue(), 30); + sp_MostLeftVertebralBody[0] += 2; // 2mm margin + clitk::FindExtremaPointInAGivenDirection(vert_slices[j], GetBackgroundValue(), 0, true, sp_MostRightVertebralBody); + sp_MostRightVertebralBody = clitk::FindExtremaPointInAGivenLine(mediast_slices[i], 0, true, sp_MostRightVertebralBody, GetBackgroundValue(),30); + sp_MostRightVertebralBody[0] -= 2; // 2 mm margin + + // Convert 2D points into 3D + clitk::PointsUtils::Convert2DTo3D(sp_MostRightVertebralBody, VertebralBody, i, p); + p_MostRightVertebralBody.push_back(p); + clitk::PointsUtils::Convert2DTo3D(sp_MostLeftVertebralBody, VertebralBody, i, p); + p_MostLeftVertebralBody.push_back(p); + + /* ------------------------------------------------------------------------------------- + Find most Left point in Esophagus + */ + found = clitk::FindExtremaPointInAGivenDirection(eso_slices[i], GetBackgroundValue(), 0, false, sp_MostLeftEsophagus); + if (!found) { // No more Esophagus, I remove the previous point + + // if (p_MostLeftEsophagus.size() < 1) { + p_MostLeftVertebralBody.pop_back(); + // } + // else { + // // Consider the previous point + // p = p_MostLeftEsophagus.back(); + // p_MostLeftEsophagus.push_back(p); + // sp_MostLeftEsophagus = sp_temp; // Retrieve previous 2D position + // found = true; + // } + } + else { + clitk::PointsUtils::Convert2DTo3D(sp_MostLeftEsophagus, EsophagusForSlice, i, p); + p_MostLeftEsophagus.push_back(p); + // sp_temp = sp_MostLeftEsophagus; // Store previous 2D position + } + + /* ------------------------------------------------------------------------------------- + Find most Left point in Aorta + */ + if (found) { + clitk::FindExtremaPointInAGivenDirection(aorta_slices[i], GetBackgroundValue(), 0, false, sp_MostLeftAorta); + sp_MostLeftAorta = clitk::FindExtremaPointInAGivenLine(mediast_slices[i], 0, false, sp_MostLeftAorta, GetBackgroundValue(), 10); + typename MaskSliceType::PointType temp=sp_MostLeftEsophagus; + temp[0] -= 10; + if (clitk::IsOnTheSameLineSide(sp_MostLeftAorta, sp_MostLeftVertebralBody, sp_MostLeftEsophagus, temp)) { + // sp_MostLeftAorta is on the same side than temp (at Right) -> ignore Aorta + sp_MostLeftAorta = sp_MostLeftEsophagus; + } + clitk::PointsUtils::Convert2DTo3D(sp_MostLeftAorta, Aorta, i, p); + p_MostLeftAorta.push_back(p); + } + + } // End of slice loop + + clitk::WriteListOfLandmarks(p_MostLeftVertebralBody, "S8-MostLeft-VB-points.txt"); + clitk::WriteListOfLandmarks(p_MostRightVertebralBody, "S8-MostRight-VB-points.txt"); + clitk::WriteListOfLandmarks(p_MostLeftAorta, "S8-MostLeft-Aorta-points.txt"); + clitk::WriteListOfLandmarks(p_MostLeftEsophagus, "S8-MostLeft-eso-points.txt"); + + clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, + p_MostLeftVertebralBody, p_MostLeftAorta, + GetBackgroundValue(), 0, -10); + + clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, + p_MostLeftAorta, p_MostLeftEsophagus, + GetBackgroundValue(), 0, -10); + + // END + StopCurrentStep(m_Working_Support); + m_ListOfStations["8"] = m_Working_Support; + return; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8_Remove_Structures() +{ + + //-------------------------------------------------------------------- + StartNewStep("[Station8] remove some structures"); + + Remove_Structures("8", "Aorta"); + Remove_Structures("8", "Esophagus"); + + // END + StopCurrentStep(m_Working_Support); m_ListOfStations["8"] = m_Working_Support; return; } @@ -645,12 +1148,25 @@ typename clitk::ExtractLymphStationsFilter::MaskImagePointer clitk::ExtractLymphStationsFilter:: EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & Esophagus) { - // Check if Esophagus is delineated at least until GOjunction. Now, + // Check if Esophagus is delineated at least until Diaphragm. Now, // because we use AutoCrop, Origin[2] gives this max inferior // position. - // double GOjunctionZ = GetAFDB()->GetPoint3D("GOjunction", 2); + + DD("BUGGY DONT USE"); + exit(0); if (Esophagus->GetOrigin()[2] > m_DiaphragmInferiorLimit) { + // crop first slice without mask + MaskImagePointType pt; + clitk::FindExtremaPointInAGivenDirection(Esophagus, GetBackgroundValue(), 2, true, pt); + DD(pt); + Esophagus = + clitk::CropImageRemoveLowerThan(Esophagus, 2, + pt[2], + false, // AutoCrop + GetBackgroundValue()); + writeImage(Esophagus, "crop-eso.mhd"); + std::cout << "Warning Esophagus is not delineated until Diaphragm. I mirror-pad it." << std::endl; double extraSize = Esophagus->GetOrigin()[2]-m_DiaphragmInferiorLimit; @@ -714,12 +1230,12 @@ ExtractStation_8_LR_Limits_old() relPosFilter->WriteStepFlagOff(); relPosFilter->SetInput(m_Working_Support); relPosFilter->SetInputObject(Esophagus); - relPosFilter->AddOrientationTypeString("L"); - relPosFilter->InverseOrientationFlagOn(); // Not Left to + relPosFilter->AddOrientationTypeString("NotLeftTo"); + // relPosFilter->InverseOrientationFlagOn(); // Not Left to relPosFilter->SetDirection(2); // Z axis relPosFilter->UniqueConnectedComponentBySliceOff(); // important relPosFilter->SetIntermediateSpacing(4); - relPosFilter->ResampleBeforeRelativePositionFilterOn(); + relPosFilter->IntermediateSpacingFlagOn(); relPosFilter->SetFuzzyThreshold(0.9); // remove few part only relPosFilter->RemoveObjectFlagOff(); relPosFilter->Update(); @@ -749,7 +1265,7 @@ ExtractStation_8_LR_Limits_old() relPosFilter->SetDirection(2); // Z axis relPosFilter->UniqueConnectedComponentBySliceOff(); // important relPosFilter->SetIntermediateSpacing(4); - relPosFilter->ResampleBeforeRelativePositionFilterOn(); + relPosFilter->IntermediateSpacingFlagOn(); relPosFilter->CombineWithOrFlagOn(); relPosFilter->SetFuzzyThreshold(0.9); // remove few part only relPosFilter->RemoveObjectFlagOff(); @@ -761,3 +1277,73 @@ ExtractStation_8_LR_Limits_old() m_ListOfStations["8"] = m_Working_Support; } //-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +FindExtremaPointsInBronchus(MaskImagePointer input, + int direction, + double distance_max_from_center_point, + ListOfPointsType & LR, + ListOfPointsType & Ant, + ListOfPointsType & Post) +{ + + // Other solution ==> with auto bounding box ! (but pb to prevent to + // be too distant from the center point + + // Extract slices + std::vector slices; + clitk::ExtractSlices(input, 2, slices); + + // Loop on slices + bool found; + for(uint i=0; i(slices[i], 0, true, 10); + slices[i] = KeepLabels(slices[i], + GetBackgroundValue(), + GetForegroundValue(), 1, 1, true); + */ + + // ------- Find rightmost or leftmost point ------- + MaskSliceType::PointType LRMost; + found = + clitk::FindExtremaPointInAGivenDirection(slices[i], + GetBackgroundValue(), + 0, // axis XY + (direction==0?false:true), // right or left according to direction + LRMost); + // ------- Find postmost point ------- + MaskSliceType::PointType postMost; + found = + clitk::FindExtremaPointInAGivenDirection(slices[i], + GetBackgroundValue(), + 1, false, LRMost, + distance_max_from_center_point, + postMost); + // ------- Find antmost point ------- + MaskSliceType::PointType antMost; + found = + clitk::FindExtremaPointInAGivenDirection(slices[i], + GetBackgroundValue(), + 1, true, LRMost, + distance_max_from_center_point, + antMost); + // Only add point if found + if (found) { + // ------- Convert 2D to 3D points -------- + MaskImageType::PointType p; + clitk::PointsUtils::Convert2DTo3D(LRMost, input, i, p); + LR.push_back(p); + clitk::PointsUtils::Convert2DTo3D(antMost, input, i, p); + Ant.push_back(p); + clitk::PointsUtils::Convert2DTo3D(postMost, input, i, p); + Post.push_back(p); + } + } +} +//--------------------------------------------------------------------