X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStation_8.txx;h=d4bbfc389217188c9ba4470d63a56dec39b33a65;hb=b2fd61648c05339dd302e102361c22c4b11d48ff;hp=75c012998366232a6be82df8c307cf87d1e7e372;hpb=573d80d0f7a17607d2ee883c21c940c0ba020282;p=clitk.git diff --git a/segmentation/clitkExtractLymphStation_8.txx b/segmentation/clitkExtractLymphStation_8.txx index 75c0129..d4bbfc3 100644 --- a/segmentation/clitkExtractLymphStation_8.txx +++ b/segmentation/clitkExtractLymphStation_8.txx @@ -1,20 +1,3 @@ -/*========================================================================= - Program: vv http://www.creatis.insa-lyon.fr/rio/vv - - Authors belong to: - - University of LYON http://www.universite-lyon.fr/ - - Léon Bérard cancer center http://www.centreleonberard.fr - - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr - - This software is distributed WITHOUT ANY WARRANTY; without even - the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR - PURPOSE. See the copyright notices for more information. - - It is distributed under dual licence - - - BSD See included LICENSE.txt file - - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html -===========================================================================*/ #include #include @@ -25,17 +8,42 @@ 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); - SetFuzzyThresholdForS8(0.5); + SetFuzzyThreshold("8", "Esophagus", 0.5); SetInjectedThresholdForS8(150); } //-------------------------------------------------------------------- +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +ExtractStation_8() +{ + if (!CheckForStation("8")) return; + + StartNewStep("Station 8"); + StartSubStep(); + ExtractStation_8_SI_Limits(); // OK, validated + ExtractStation_8_Ant_Limits(); // OK, validated + ExtractStation_8_Left_Sup_Limits(); // OK, validated + ExtractStation_8_Left_Inf_Limits(); // OK, validated + ExtractStation_8_Single_CCL_Limits(); // OK, validated + ExtractStation_8_Remove_Structures(); // OK, validated + + // Store image filenames into AFDB + writeImage(m_ListOfStations["8"], "seg/Station8.mhd"); + GetAFDB()->SetImageFilename("Station8", "seg/Station8.mhd"); + WriteAFDB(); + StopSubStep(); +} +//-------------------------------------------------------------------- + + //-------------------------------------------------------------------- template void @@ -59,63 +67,42 @@ ExtractStation_8_SI_Limits() left; the lower border of the bronchus intermedius on the right" */ - StartNewStep("[Station8] Inf/Sup mediastinum limits with carina/diaphragm junction"); + StartNewStep("[Station8] Sup/Inf limits with LeftLower/RightMiddle Lobe and diaphragm"); - // Get Carina Z position - MaskImagePointer Carina = GetAFDB()->template GetImage("Carina"); - - std::vector centroids; - clitk::ComputeCentroids(Carina, GetBackgroundValue(), centroids); - m_CarinaZ = centroids[1][2]; - // DD(m_CarinaZ); - // add one slice to include carina ? - m_CarinaZ += m_Mediastinum->GetSpacing()[2]; - // We dont need Carina structure from now - Carina->Delete(); - GetAFDB()->SetDouble("CarinaZ", m_CarinaZ); + /* ----------------------------------------------- + NEW SUPERIOR LIMIT = LeftLowerLobeBronchus / + RightMiddleLobeBronchus See FindLineForS7S8Separation + ----------------------------------------------- + */ + ImagePointType A; + ImagePointType B; + FindLineForS7S8Separation(A, B); + + // add one slice to be adjacent to Station7 + B[2] += m_Working_Support->GetSpacing()[2]; + A[2] += m_Working_Support->GetSpacing()[2]; + + // Use the line to remove the inferior part + m_Working_Support = + SliceBySliceSetBackgroundFromSingleLine(m_Working_Support, + GetBackgroundValue(), A, B, 2, 0, true); + /* ----------------------------------------------- + INFERIOR LIMIT = Diaphragm + ----------------------------------------------- + */ + // 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; - // 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 - Inferior limit = DiaphragmInferiorLimit (old=Gastroesphogeal junction) */ m_Working_Support = clitk::CropImageAlongOneAxis(m_Working_Support, 2, - m_DiaphragmInferiorLimit, //GOjunctionZ, - m_CarinaZ, true, + m_DiaphragmInferiorLimit, + B[2], true, GetBackgroundValue()); - - // Remove some structures that we know are excluded - MaskImagePointer VertebralBody = - GetAFDB()->template GetImage ("VertebralBody"); - MaskImagePointer Aorta = - GetAFDB()->template GetImage ("Aorta"); - - typedef clitk::BooleanOperatorLabelImageFilter BoolFilterType; - typename BoolFilterType::Pointer boolFilter = BoolFilterType::New(); - boolFilter->InPlaceOn(); - boolFilter->SetInput1(m_Working_Support); - boolFilter->SetInput2(VertebralBody); - boolFilter->SetOperationType(BoolFilterType::AndNot); - 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. StopCurrentStep(m_Working_Support); m_ListOfStations["8"] = m_Working_Support; @@ -127,290 +114,8 @@ ExtractStation_8_SI_Limits() template void clitk::ExtractLymphStationsFilter:: -ExtractStation_8_Post_Limits() -{ - /* - Station 8: paraeosphageal nodes - - Anteriorly, it is in contact with Station 7 and the - left main stem bronchus in its superior aspect (Fig. 3C–H) and - with the heart more inferiorly. Posteriorly, Station 8 abuts the - descending aorta and the anterior aspect of the vertebral body - until an imaginary horizontal line running 1 cm posterior to the - anterior border of the vertebral body (Fig. 3C). - - New classification IASCL 2009 : - - "Nodes lying adjacent to the wall of the esophagus and to the - right or left of the midline, excluding subcarinal nodes (S7) - Upper" - - */ - - StartNewStep("[Station8] Post limits with vertebral body"); - MaskImagePointer VertebralBody = - GetAFDB()->template GetImage ("VertebralBody"); - - // Consider vertebral body slice by slice - typedef clitk::ExtractSliceFilter ExtractSliceFilterType; - typename ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New(); - typedef typename ExtractSliceFilterType::SliceType SliceType; - std::vector vertebralSlices; - extractSliceFilter->SetInput(VertebralBody); - extractSliceFilter->SetDirection(2); - extractSliceFilter->Update(); - extractSliceFilter->GetOutputSlices(vertebralSlices); - - // For each slice, compute the most anterior point - std::map vertebralAntPositionBySlice; - for(uint i=0; i(vertebralSlices[i], - GetBackgroundValue(), - 1, true, p); - if (found) { - vertebralAntPositionBySlice[i] = p; - } - else { - // no Foreground in this slice (it appends generally at the - // beginning and the end of the volume). Do nothing in this - // case. - } - } - - // Convert 2D points in slice into 3D points - std::vector vertebralAntPositions; - clitk::PointsUtils::Convert2DTo3DList(vertebralAntPositionBySlice, - VertebralBody, - vertebralAntPositions); - - // DEBUG : write list of points - clitk::WriteListOfLandmarks(vertebralAntPositions, - "S8-vertebralMostAntPositions-points.txt"); - - // Cut support posteriorly 1cm the most anterior point of the - // VertebralBody. Do nothing below and above the VertebralBody. To - // do that compute several region, slice by slice and fill. - MaskImageRegionType region; - MaskImageSizeType size; - MaskImageIndexType start; - size[2] = 1; // a single slice - start[0] = m_Working_Support->GetLargestPossibleRegion().GetIndex()[0]; - size[0] = m_Working_Support->GetLargestPossibleRegion().GetSize()[0]; - for(uint i=0; i IteratorType; - IteratorType iter = - IteratorType(m_Working_Support, m_Working_Support->GetLargestPossibleRegion()); - MaskImageIndexType index; - // Consider some cm posterior to most anterior positions (usually - // 1 cm). - vertebralAntPositions[i][1] += GetDistanceMaxToAnteriorPartOfTheSpine(); - // Get index of this point - m_Working_Support->TransformPhysicalPointToIndex(vertebralAntPositions[i], index); - // Compute region (a single slice) - start[2] = index[2]; - start[1] = m_Working_Support->GetLargestPossibleRegion().GetIndex()[1]+index[1]; - size[1] = m_Working_Support->GetLargestPossibleRegion().GetSize()[1]-start[1]; - region.SetSize(size); - region.SetIndex(start); - // Fill region - if (m_Working_Support->GetLargestPossibleRegion().IsInside(start)) { - itk::ImageRegionIterator it(m_Working_Support, region); - it.GoToBegin(); - while (!it.IsAtEnd()) { - it.Set(GetBackgroundValue()); - ++it; - } - } - } - - StopCurrentStep(m_Working_Support); - m_ListOfStations["8"] = m_Working_Support; -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -void -clitk::ExtractLymphStationsFilter:: -ExtractStation_8_Ant_Sup_Limits() +ExtractStation_8_Ant_Limits() { - //-------------------------------------------------------------------- - StartNewStep("[Station8] Ant limits with S7 above Carina"); - /* - Anteriorly, it is in contact with Station 7 and the - left main stem bronchus in its superior aspect (Fig. 3C–H) and - with the heart more inferiorly. - - 1) line post wall bronchi (S7), till originRMLB - - LUL bronchus : to detect in trachea. But not needed here ?? - 2) heart ! -> not delineated. - ==> below S7, crop CT not to far away (ant), then try with threshold - - 1) ==> how to share with S7 ? Prepare both support at the same time ! - NEED vector of initial support for each station ? No -> map if it exist before, take it !! - - */ - - // Ant limit from carina (start) to end of S7 = originRMLB - // Get Trachea - MaskImagePointer Trachea = GetAFDB()->template GetImage("Trachea"); - - MaskImagePointer m_Working_Trachea = - clitk::CropImageAbove(Trachea, 2, m_CarinaZ, true, // AutoCrop - GetBackgroundValue()); - - // Seprate into two main bronchi - MaskImagePointer RightBronchus; - MaskImagePointer LeftBronchus; - - // Labelize and consider the two first (main) labels - m_Working_Trachea = Labelize(m_Working_Trachea, 0, true, 1); - - // Carina position must at the first slice that separate the two - // main bronchus (not superiorly). We thus first check that the - // upper slice is composed of at least two labels - typedef itk::ImageSliceIteratorWithIndex SliceIteratorType; - SliceIteratorType iter(m_Working_Trachea, m_Working_Trachea->GetLargestPossibleRegion()); - iter.SetFirstDirection(0); - iter.SetSecondDirection(1); - iter.GoToReverseBegin(); // Start from the end (because image is IS not SI) - int maxLabel=0; - while (!iter.IsAtReverseEndOfSlice()) { - while (!iter.IsAtReverseEndOfLine()) { - if (iter.Get() > maxLabel) maxLabel = iter.Get(); - --iter; - } - iter.PreviousLine(); - } - if (maxLabel < 2) { - clitkExceptionMacro("First slice form Carina does not seems to seperate the two main bronchus. Abort"); - } - - // Compute 3D centroids of both parts to identify the left from the - // right bronchus - std::vector c; - clitk::ComputeCentroids(m_Working_Trachea, GetBackgroundValue(), c); - ImagePointType C1 = c[1]; - ImagePointType C2 = c[2]; - - 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) - RightBronchus = - clitk::Binarize(m_Working_Trachea, rightLabel, rightLabel, - GetBackgroundValue(), GetForegroundValue()); - /* - SetBackground(m_Working_Trachea, m_Working_Trachea, - leftLabel, GetBackgroundValue(), false); - */ - LeftBronchus = clitk::Binarize(m_Working_Trachea, leftLabel, leftLabel, - GetBackgroundValue(), GetForegroundValue()); - /* - SetBackground(m_Working_Trachea, m_Working_Trachea, - rightLabel, GetBackgroundValue(), false); - */ - - // Crop images - RightBronchus = clitk::AutoCrop(RightBronchus, GetBackgroundValue()); - LeftBronchus = clitk::AutoCrop(LeftBronchus, GetBackgroundValue()); - - // Insert int AFDB if need after - 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"); - std::vector centroids; - clitk::ComputeCentroids(OriginOfRightMiddleLobeBronchus, GetBackgroundValue(), centroids); - m_OriginOfRightMiddleLobeBronchusZ = centroids[1][2]; - // add one slice to include carina ? - m_OriginOfRightMiddleLobeBronchusZ += RightBronchus->GetSpacing()[2]; - // We dont need Carina structure from now - OriginOfRightMiddleLobeBronchus->Delete(); - - RightBronchus = - clitk::CropImageBelow(RightBronchus, 2, - m_OriginOfRightMiddleLobeBronchusZ, - true, // AutoCrop - GetBackgroundValue()); - LeftBronchus = - clitk::CropImageBelow(LeftBronchus, 2, - m_OriginOfRightMiddleLobeBronchusZ, - true, // AutoCrop - GetBackgroundValue()); - - // 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(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, "S8-LeftBronchus-points.txt"); - - v.clear(); - 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, "S8-RightLeftBronchus-points.txt"); - - - // Now uses these points to limit, slice by slice - // line is mainly horizontal, so mainDirection=1 - clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, - m_PostMostInRightBronchus, - m_PostMostInLeftBronchus, - GetBackgroundValue(), 1, 10); - - // Keep main 3D CCL : - m_Working_Support = Labelize(m_Working_Support, 0, false, 10); - m_Working_Support = KeepLabels(m_Working_Support, - GetBackgroundValue(), - GetForegroundValue(), 1, 1, true); - - // Autocrop - m_Working_Support = clitk::AutoCrop(m_Working_Support, GetBackgroundValue()); - - // End of step - StopCurrentStep(m_Working_Support); - // m_ListOfStations["8"] = m_Working_Support; - -} - -//-------------------------------------------------------------------- -template -void -clitk::ExtractLymphStationsFilter:: -ExtractStation_8_Ant_Inf_Limits() -{ - //-------------------------------------------------------------------- StartNewStep("[Station8] Ant part: not post to Esophagus"); /* @@ -421,7 +126,6 @@ ExtractStation_8_Ant_Inf_Limits() // Get 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 @@ -433,46 +137,17 @@ ExtractStation_8_Ant_Inf_Limits() //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 + // Resize Esophagus like current support m_Esophagus = - clitk::CropImageAbove(m_Esophagus, 2, - m_OriginOfRightMiddleLobeBronchusZ, - true, // AutoCrop - GetBackgroundValue()); + clitk::ResizeImageLike(m_Esophagus, m_Working_Support, GetBackgroundValue()); // Needed ? // Dilate to keep only not Anterior positions MaskImagePointType radiusInMM = GetEsophagusDiltationForAnt(); - - // 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”) - + // Keep what is Posterior to Esophagus typedef clitk::SliceBySliceRelativePositionFilter RelPosFilterType; typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New(); relPosFilter->VerboseStepFlagOff(); @@ -482,10 +157,10 @@ ExtractStation_8_Ant_Inf_Limits() relPosFilter->AddOrientationTypeString("PostTo"); // relPosFilter->InverseOrientationFlagOff(); relPosFilter->SetDirection(2); // Z axis - relPosFilter->UniqueConnectedComponentBySliceOff(); + relPosFilter->UniqueConnectedComponentBySliceFlagOff(); relPosFilter->SetIntermediateSpacing(3); relPosFilter->IntermediateSpacingFlagOn(); - relPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS8()); + relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("8", "Esophagus")); relPosFilter->RemoveObjectFlagOff(); // Do not exclude here because it is dilated relPosFilter->CombineWithOrFlagOff(); // NO ! relPosFilter->IgnoreEmptySliceObjectFlagOn(); @@ -505,88 +180,10 @@ ExtractStation_8_Ant_Inf_Limits() 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() +ExtractStation_8_Left_Sup_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"); + StartNewStep("[Station8] Left limits: remove Left to line from Aorta to PulmonaryTrunk"); /* We consider a line from Left part of Aorta to left part of @@ -699,280 +296,14 @@ ExtractStation_8_Single_CCL_Limits() 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); - - // 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(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_RightMostAnt; - std::vector p_RightMostPost; - 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 - 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). - */ - - // Loop slices - MaskImagePointType p; - MaskImagePointType pp; - for(uint i=0; i only at most Post part of current - // slice support. First found most ant point in VertebralBody - typedef MaskSliceType SliceType; - typename SliceType::PointType p_slice_ant; - bool found = clitk::FindExtremaPointInAGivenDirection(vert_slices[i], GetBackgroundValue(), 1, true, p_slice_ant); - 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; - int j=i++; - bool found = false; - while (!found) { - found = clitk::FindExtremaPointInAGivenDirection(vert_slices[j], GetBackgroundValue(), 1, true, p_slice_ant); - //clitkExceptionMacro("No foreground pixels in this VertebralBody slices ??"); - j++; - } - } - p_slice_ant[1] += GetDistanceMaxToAnteriorPartOfTheSpine(); // Consider offset - - // The, find most Right and Left points on that AP position - typename SliceType::IndexType indexR; - typename SliceType::IndexType indexL; - vert_slices[i]->TransformPhysicalPointToIndex(p_slice_ant, indexR); - indexL = indexR; - // Check that is inside the mask - indexR[1] = std::min(indexR[1], (long)vert_slices[i]->GetLargestPossibleRegion().GetSize()[1]-1); - indexL[1] = indexR[1]; - while (vert_slices[i]->GetPixel(indexR) != GetBackgroundValue()) { - indexR[0] --; // Go to the right - } - while (vert_slices[i]->GetPixel(indexL) != GetBackgroundValue()) { - indexL[0] ++; // Go to the left - } - vert_slices[i]->TransformIndexToPhysicalPoint(indexR, sp_maxRight_Vertebra); - clitk::PointsUtils::Convert2DTo3D(sp_maxRight_Vertebra, VertebralBody, i, p); - p_AllPoints.push_back(p); - vert_slices[i]->TransformIndexToPhysicalPoint(indexL, sp_maxLeft_Vertebra); - clitk::PointsUtils::Convert2DTo3D(sp_maxLeft_Vertebra, VertebralBody, i, p); - p_AllPoints.push_back(p); - - // Find last point out of the mediastinum on this line, Right : - mediast_slices[i]->TransformPhysicalPointToIndex(sp_maxRight_Vertebra, indexR); - double distance = 0.0; - while (mediast_slices[i]->GetPixel(indexR) != GetBackgroundValue()) { - indexR[0] --; - distance += mediast_slices[i]->GetSpacing()[0]; - } - if (distance < 30) { // Ok in this case, we found limit with lung - mediast_slices[i]->TransformIndexToPhysicalPoint(indexR, sp_maxRight_Vertebra); - clitk::PointsUtils::Convert2DTo3D(sp_maxRight_Vertebra, m_Mediastinum, i, p); - } - 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); - - // Find last point out of the mediastinum on this line, Left : - mediast_slices[i]->TransformPhysicalPointToIndex(sp_maxLeft_Vertebra, indexL); - distance = 0.0; - while (mediast_slices[i]->GetPixel(indexL) != GetBackgroundValue()) { - indexL[0] ++; - distance += mediast_slices[i]->GetSpacing()[0]; - } - if (distance < 30) { // Ok in this case, we found limit with lung - mediast_slices[i]->TransformIndexToPhysicalPoint(indexL, sp_maxLeft_Vertebra); - clitk::PointsUtils::Convert2DTo3D(sp_maxLeft_Vertebra, m_Mediastinum, i, p); - } - 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::CropImageAbove(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 - // Eso. (Left is left on screen, coordinate increase) - - // Find left limit of Esophagus - clitk::FindExtremaPointInAGivenDirection(eso_slices[i], GetBackgroundValue(), 0, false, sp_maxLeft_Eso); - 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' - 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, "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 - clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, - p_RightMostAnt, p_RightMostPost, - GetBackgroundValue(), 0, 10); - clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, - p_LeftMostAnt, p_LeftMostPost, - GetBackgroundValue(), 0, -10); - 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() +ExtractStation_8_Left_Inf_Limits() { - //-------------------------------------------------------------------- - StartNewStep("[Station8] Left and Right limits arround esophagus with lines from VertebralBody-Aorta-Esophagus"); + StartNewStep("[Station8] Left limits around 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). @@ -981,13 +312,18 @@ ExtractStation_8_LR_Limits() 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()); + 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()); + // Remove what is outside the support to not consider what is to + // posterior in the VertebralBody (post the horizontal line) + clitk::And(VertebralBody, m_Working_Support, GetBackgroundValue()); + // writeImage(VertebralBody, "vb.mhd"); std::vector vert_slices; clitk::ExtractSlices(VertebralBody, 2, vert_slices); @@ -1023,80 +359,67 @@ ExtractStation_8_LR_Limits() // Temporary 3D point MaskImagePointType p; + typename MaskSliceType::PointType minSlicePoint; + typename MaskSliceType::PointType maxSlicePoint; + clitk::GetMinMaxPointPosition(vert_slices[0], minSlicePoint, maxSlicePoint); + // 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 + Find first point not in mediastinum at LEFT + */ + clitk::FindExtremaPointInAGivenDirection(vert_slices[i], GetBackgroundValue(), + 0, false, sp_MostLeftVertebralBody); + // clitk::PointsUtils::Convert2DTo3D(sp_MostLeftVertebralBody, VertebralBody, i, p); + // DD(p); - // Crop the vertebralbody below this most post line - vert_slices[j] = - clitk::CropImageAbove(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"); + sp_MostLeftVertebralBody = + clitk::FindExtremaPointInAGivenLine(mediast_slices[i], 0, false, + sp_MostLeftVertebralBody, GetBackgroundValue(), 30); + // clitk::PointsUtils::Convert2DTo3D(sp_MostLeftVertebralBody, VertebralBody, i, p); + // DD(p); - // 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 + // clitk::PointsUtils::Convert2DTo3D(sp_MostLeftVertebralBody, VertebralBody, i, p); + // DD(p); // 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 first point not in mediastinum at RIGHT. Not used yet. + clitk::FindExtremaPointInAGivenDirection(vert_slices[i], 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); + */ + + /* ------------------------------------------------------------------------------------- Find most Left point in Esophagus */ - found = clitk::FindExtremaPointInAGivenDirection(eso_slices[i], GetBackgroundValue(), 0, false, sp_MostLeftEsophagus); + bool 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; - // } + //DD("no eso pop back"); + p_MostLeftVertebralBody.pop_back(); } else { clitk::PointsUtils::Convert2DTo3D(sp_MostLeftEsophagus, EsophagusForSlice, i, p); p_MostLeftEsophagus.push_back(p); - // sp_temp = sp_MostLeftEsophagus; // Store previous 2D position } /* ------------------------------------------------------------------------------------- @@ -1118,7 +441,7 @@ ExtractStation_8_LR_Limits() } // 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_MostRightVertebralBody, "S8-MostRight-VB-points.txt"); clitk::WriteListOfLandmarks(p_MostLeftAorta, "S8-MostLeft-Aorta-points.txt"); clitk::WriteListOfLandmarks(p_MostLeftEsophagus, "S8-MostLeft-eso-points.txt"); @@ -1129,7 +452,6 @@ ExtractStation_8_LR_Limits() clitk::SliceBySliceSetBackgroundFromLineSeparation(m_Working_Support, p_MostLeftAorta, p_MostLeftEsophagus, GetBackgroundValue(), 0, -10); - // END StopCurrentStep(m_Working_Support); m_ListOfStations["8"] = m_Working_Support; @@ -1144,12 +466,10 @@ void clitk::ExtractLymphStationsFilter:: ExtractStation_8_Remove_Structures() { - //-------------------------------------------------------------------- - StartNewStep("[Station8] remove some structures"); - - Remove_Structures("Aorta"); - Remove_Structures("Esophagus"); + Remove_Structures("8", "Aorta"); + Remove_Structures("8", "Esophagus"); + Remove_Structures("8", "VertebralBody"); // END StopCurrentStep(m_Working_Support); @@ -1159,143 +479,6 @@ ExtractStation_8_Remove_Structures() //-------------------------------------------------------------------- -//-------------------------------------------------------------------- -template -typename clitk::ExtractLymphStationsFilter::MaskImagePointer -clitk::ExtractLymphStationsFilter:: -EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & Esophagus) -{ - // Check if Esophagus is delineated at least until Diaphragm. Now, - // because we use AutoCrop, Origin[2] gives this max inferior - // position. - - 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::CropImageBelow(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; - - // Pad with few more slices - typedef itk::MirrorPadImageFilter PadFilterType; - typename PadFilterType::Pointer padFilter = PadFilterType::New(); - padFilter->SetInput(Esophagus); - MaskImageSizeType b; - b[0] = 0; b[1] = 0; b[2] = (uint)ceil(extraSize/Esophagus->GetSpacing()[2])+1; - padFilter->SetPadLowerBound(b); - padFilter->Update(); - Esophagus = padFilter->GetOutput(); - } - return Esophagus; -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -void -clitk::ExtractLymphStationsFilter:: -ExtractStation_8_LR_Limits_old() -{ - /* - Station 8: paraeosphageal nodes - - Laterally, it is within the pleural envelope and again abuts the - descending aorta on the left. Reasonably, the delineation of - Station 8 is limited to the soft tissue surrounding the esophagus - (Fig. 3C–H). - */ - - StartNewStep("[Station8] Right limits (around esophagus)"); - // Get Esophagus - MaskImagePointer Esophagus = GetAFDB()->template GetImage("Esophagus"); - - // Autocrop to get first slice with starting Esophagus - Esophagus = clitk::AutoCrop(Esophagus, GetBackgroundValue()); - - // Dilate - // LR dilatation -> large to keep point inside - // AP dilatation -> few mm - // SI dilatation -> enough to cover Diaphragm (old=GOjunctionZ) - MaskImagePointType radiusInMM = GetEsophagusDiltationForRight(); - Esophagus = EnlargeEsophagusDilatationRadiusInferiorly(Esophagus); - Esophagus = clitk::Dilate(Esophagus, - radiusInMM, - GetBackgroundValue(), - GetForegroundValue(), true); - writeImage(Esophagus, "dilateEso2.mhd"); - - writeImage(m_Working_Support, "before-relpos2.mhd"); - - // Remove Right (Left on the screen) part according to this - // dilatated esophagus - typedef clitk::SliceBySliceRelativePositionFilter RelPosFilterType; - typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New(); - relPosFilter->VerboseStepFlagOff(); - relPosFilter->WriteStepFlagOff(); - relPosFilter->SetInput(m_Working_Support); - relPosFilter->SetInputObject(Esophagus); - relPosFilter->AddOrientationTypeString("NotLeftTo"); - // relPosFilter->InverseOrientationFlagOn(); // Not Left to - relPosFilter->SetDirection(2); // Z axis - relPosFilter->UniqueConnectedComponentBySliceOff(); // important - relPosFilter->SetIntermediateSpacing(4); - relPosFilter->IntermediateSpacingFlagOn(); - relPosFilter->SetFuzzyThreshold(0.9); // remove few part only - relPosFilter->RemoveObjectFlagOff(); - relPosFilter->Update(); - m_Working_Support = relPosFilter->GetOutput(); - - // Get a single 3D CCL - m_Working_Support = Labelize(m_Working_Support, 0, false, 10); - m_Working_Support = KeepLabels(m_Working_Support, - GetBackgroundValue(), - GetForegroundValue(), 1, 1, true); - - - /* - // Re-Add post to Esophagus -> sometimes previous relpos remove some - // correct part below esophagus. - MaskImagePointer Esophagus = GetAFDB()->template GetImage("Esophagus"); - EnlargeEsophagusDilatationRadiusInferiorly(Esophagus); - writeImage(Esophagus, "e-again.mhd"); - typedef clitk::SliceBySliceRelativePositionFilter RelPosFilterType; - typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New(); - relPosFilter->VerboseStepOff(); - relPosFilter->WriteStepOff(); - relPosFilter->SetInput(m_Working_Support); - relPosFilter->SetInputObject(Esophagus); - relPosFilter->SetOrientationTypeString("P"); - relPosFilter->InverseOrientationFlagOff(); - relPosFilter->SetDirection(2); // Z axis - relPosFilter->UniqueConnectedComponentBySliceOff(); // important - relPosFilter->SetIntermediateSpacing(4); - relPosFilter->IntermediateSpacingFlagOn(); - relPosFilter->CombineWithOrFlagOn(); - relPosFilter->SetFuzzyThreshold(0.9); // remove few part only - relPosFilter->RemoveObjectFlagOff(); - relPosFilter->Update(); - m_Working_Support = relPosFilter->GetOutput(); - */ - - StopCurrentStep(m_Working_Support); - m_ListOfStations["8"] = m_Working_Support; -} -//-------------------------------------------------------------------- - - //-------------------------------------------------------------------- template void