#include <itkBinaryDilateImageFilter.h>
#include <itkMirrorPadImageFilter.h>
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractLymphStationsFilter<ImageType>::
+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);
+}
+//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
template <class ImageType>
void
// Get Carina Z position
MaskImagePointer Carina = GetAFDB()->template GetImage<MaskImageType>("Carina");
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after read Carina");
+
+ // CHANGE TO -> OriginOfRightMiddleLobeBronchus ???
+
std::vector<MaskImagePointType> centroids;
clitk::ComputeCentroids<MaskImageType>(Carina, GetBackgroundValue(), centroids);
- DD(centroids[1]);
m_CarinaZ = centroids[1][2];
- 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
MaskImagePointer Lungs = GetAFDB()->template GetImage<MaskImageType>("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<MaskImageType>("Lungs");
+ clitk::PrintMemory(GetVerboseMemoryFlag(), "after release lungs");
/* Crop support :
Superior limit = carina
// Ant limit from carina (start) to end of S7 = originRMLB
// Get Trachea
MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after read Trachea");
MaskImagePointer m_Working_Trachea =
clitk::CropImageAbove<MaskImageType>(Trachea, 2, m_CarinaZ, true, // AutoCrop
GetBackgroundValue());
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after crop");
// Seprate into two main bronchi
MaskImagePointer LeftBronchus;
// Labelize and consider the two first (main) labels
m_Working_Trachea = Labelize<MaskImageType>(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
MaskImagePointer OriginOfRightMiddleLobeBronchus =
GetAFDB()->template GetImage<MaskImageType>("OriginOfRightMiddleLobeBronchus");
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after read OriginOfRightMiddleLobeBronchus");
std::vector<MaskImagePointType> centroids;
clitk::ComputeCentroids<MaskImageType>(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());
// We dont need Carina structure from now
OriginOfRightMiddleLobeBronchus->Delete();
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after delete OriginOfRightMiddleLobeBronchus");
LeftBronchus =
clitk::CropImageBelow<MaskImageType>(LeftBronchus, 2,
GetBackgroundValue(), 1, 10);
writeImage<MaskImageType>(m_Working_Support, "after.mhd");
-HERE
-
// Keep main 3D CCL :
m_Working_Support = Labelize<MaskImageType>(m_Working_Support, 0, false, 10);
m_Working_Support = KeepLabels<MaskImageType>(m_Working_Support,
{
//--------------------------------------------------------------------
- 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
MaskImagePointer Esophagus = GetAFDB()->template GetImage<MaskImageType>("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.
+ typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
+ typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
+ boolFilter->InPlaceOn();
+ boolFilter->SetInput1(m_Working_Support);
+ boolFilter->SetInput2(Esophagus);
+ boolFilter->SetOperationType(BoolFilterType::AndNot);
+ boolFilter->Update();
+ m_Working_Support = boolFilter->GetOutput();
+
// Crop Esophagus : keep only below the OriginOfRightMiddleLobeBronchusZ
Esophagus =
clitk::CropImageAbove<MaskImageType>(Esophagus, 2,
radiusInMM,
GetBackgroundValue(),
GetForegroundValue(), true);
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after dilate Esophagus");
writeImage<MaskImageType>(Esophagus, "enlarged-eso.mhd");
- // Remove Anterior part according to this dilatated esophagus
+ // 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<MaskImageType> RelPosFilterType;
typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
relPosFilter->VerboseStepFlagOff();
relPosFilter->SetIntermediateSpacing(3);
relPosFilter->ResampleBeforeRelativePositionFilterOn();
relPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS8());
- relPosFilter->RemoveObjectFlagOff();
+ relPosFilter->RemoveObjectFlagOff(); // Do not exclude here because it is dilated
relPosFilter->Update();
m_Working_Support = relPosFilter->GetOutput();
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after SbS Rel pos Post");
// AutoCrop (OR SbS ?)
m_Working_Support = clitk::AutoCrop<MaskImageType>(m_Working_Support, GetBackgroundValue());
- writeImage<MaskImageType>(m_Working_Support, "step1.4.1.mhd");
-
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after autocrop");
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ //--------------------------------------------------------------------
+ StartNewStep("[Station8] Left and Right limits arround esophagus (below Carina)");
// Estract slices for current support for slice by slice processing
std::vector<typename MaskSliceType::Pointer> slices;
clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices);
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after support slices");
// Estract slices of Esophagus (resize like support before to have the same set of slices)
MaskImagePointer EsophagusForSlice = clitk::ResizeImageLike<MaskImageType>(Esophagus, m_Working_Support, GetBackgroundValue());
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after Eso resize");
std::vector<typename MaskSliceType::Pointer> eso_slices;
clitk::ExtractSlices<MaskImageType>(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<MaskImageType>("VertebralBody");
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after Read VertebralBody");
VertebralBody = clitk::ResizeImageLike<MaskImageType>(VertebralBody, m_Working_Support, GetBackgroundValue());
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after VertebralBody Resize");
std::vector<typename MaskSliceType::Pointer> vert_slices;
clitk::ExtractSlices<MaskImageType>(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<MaskImageType>("Aorta");
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after Read Aorta");
Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, m_Working_Support, GetBackgroundValue());
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after Aorta Resize");
std::vector<typename MaskSliceType::Pointer> aorta_slices;
clitk::ExtractSlices<MaskImageType>(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<MaskImageType>("Mediastinum");
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after read Mediastinum");
m_Mediastinum = clitk::ResizeImageLike<MaskImageType>(m_Mediastinum, m_Working_Support, GetBackgroundValue());
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after resize Mediastinum");
std::vector<typename MaskSliceType::Pointer> mediast_slices;
clitk::ExtractSlices<MaskImageType>(m_Mediastinum, 2, mediast_slices);
- clitk::PrintMemory(GetVerboseMemoryFlag(), "after Mediastinum slices");
-
- writeImage<MaskImageType>(EsophagusForSlice, "slices_eso.mhd");
- writeImage<MaskImageType>(VertebralBody, "slices_vert.mhd");
- writeImage<MaskImageType>(Aorta, "slices_aorta.mhd");
- writeImage<MaskImageType>(m_Mediastinum, "slices_medias.mhd");
- writeImage<MaskImageType>(m_Working_Support, "slices_support.mhd");
-
// List of points
std::vector<MaskImagePointType> p_RightMostAnt;
// 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<MaskSliceType>(eso_slices[i], GetBackgroundValue(), 0, true, sp_maxRight_Eso);
- clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(aorta_slices[i], GetBackgroundValue(), 0, true, sp_maxRight_Aorta);
- clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp_maxRight_Eso, EsophagusForSlice, i, p);
- clitk::PointsUtils<MaskImageType>::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]<pp[0]) p_RightMostAnt.push_back(p); // Insert point most at right
- else p_RightMostAnt.push_back(pp);
-
// Find limit of Vertebral -> only at most Post part of current
// slice support. First found most ant point in VertebralBody
typedef MaskSliceType SliceType;
// 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) {
//clitkExceptionMacro("No foreground pixels in this VertebralBody slices ??");
j++;
}
- DD(j);
}
p_slice_ant[1] += GetDistanceMaxToAnteriorPartOfTheSpine(); // Consider offset
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<MaskImageType>::Convert2DTo3D(sp_maxRight_Vertebra, m_Mediastinum, i, p);
}
p_RightMostPost.push_back(p);
p_AllPoints.push_back(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<MaskImageType>::Convert2DTo3D(sp_maxLeft_Vertebra, m_Mediastinum, i, p);
}
p_LeftMostPost.push_back(p);
p_AllPoints.push_back(p);
+ // Find right limit of Esophagus and Aorta
+ clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(eso_slices[i], GetBackgroundValue(), 0, true, sp_maxRight_Eso);
+ bool f = clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(aorta_slices[i], GetBackgroundValue(), 0, true, sp_maxRight_Aorta);
+ clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp_maxRight_Eso, EsophagusForSlice, i, p);
+ clitk::PointsUtils<MaskImageType>::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 {
+ p_RightMostAnt.push_back(p);
+ }
+
// --------------------------------------------------------------------------
// Find the limit on the Left: most left point between Eso and
// Vertebra. (Left is left on screen, coordinate increase)
// Find left limit of Esophagus
clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(eso_slices[i], GetBackgroundValue(), 0, false, sp_maxLeft_Eso);
- clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(aorta_slices[i], GetBackgroundValue(), 0, false, sp_maxLeft_Aorta);
+ f = clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(aorta_slices[i], GetBackgroundValue(), 0, false, sp_maxLeft_Aorta);
clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp_maxLeft_Eso, EsophagusForSlice, i, p);
clitk::PointsUtils<MaskImageType>::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
+ else p_LeftMostAnt.push_back(pp);
+ }
+ else {
+ p_LeftMostAnt.push_back(p);
+ }
} // End of slice loop
clitk::WriteListOfLandmarks<MaskImageType>(p_AllPoints, "LR-Eso-Vert.txt");
clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support,
p_LeftMostAnt, p_LeftMostPost,
GetBackgroundValue(), 0, -10);
- // DEBUG
+ // END
+ StopCurrentStep<MaskImageType>(m_Working_Support);
m_ListOfStations["8"] = m_Working_Support;
return;
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff