+
//--------------------------------------------------------------------
template <class TImageType>
void
clitk::ExtractLymphStationsFilter<TImageType>::
ExtractStation_7_SI_Limits()
{
- // Local variables
- double m_CarinaZPositionInMM;
- double m_MiddleLobeBronchusZPositionInMM;
-
// Get Inputs
- m_Trachea = GetAFDB()->template GetImage <MaskImageType>("trachea");
- m_CarinaZPositionInMM = GetAFDB()->GetPoint3D("carina", 2);
- DD(m_CarinaZPositionInMM);
- m_MiddleLobeBronchusZPositionInMM = GetAFDB()->GetPoint3D("rightMiddleLobeBronchus", 2);
- DD(m_MiddleLobeBronchusZPositionInMM);
+ MaskImagePointer Trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
+ double m_CarinaZ = GetAFDB()->GetPoint3D("Carina", 2);
+ DD(m_CarinaZ);
+ double m_OriginOfRightMiddleLobeBronchusZ = GetAFDB()->GetPoint3D("OriginOfRightMiddleLobeBronchus", 2);
+ DD(m_OriginOfRightMiddleLobeBronchusZ);
/* Crop support :
- Superior limit = carina
- Inferior limit = origin right middle lobe bronchus */
- StartNewStep("Inf/Sup mediastinum limits with carina/bronchus");
+ Superior limit = carina
+ Inferior limit = origin right middle lobe bronchus */
+ StartNewStep("[Station7] Inf/Sup mediastinum limits with carina/bronchus");
m_Working_Support =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_Support, 2,
- m_MiddleLobeBronchusZPositionInMM,
- m_CarinaZPositionInMM, true,
+ clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2,
+ m_OriginOfRightMiddleLobeBronchusZ,
+ m_CarinaZ, true,
GetBackgroundValue());
- StopCurrentStep<MaskImageType>(m_Working_Support);
-
/* Crop trachea
- Superior limit = carina
- Inferior limit = origin right middle lobe bronchus*/
- StartNewStep("Inf/Sup trachea limits with carina/bronchus");
+ Superior limit = carina
+ Inferior limit = origin right middle lobe bronchus*/
m_working_trachea =
- clitk::CropImageAlongOneAxis<MaskImageType>(m_Trachea, 2,
- m_MiddleLobeBronchusZPositionInMM,
- m_CarinaZPositionInMM, true,
+ clitk::CropImageAlongOneAxis<MaskImageType>(Trachea, 2,
+ m_OriginOfRightMiddleLobeBronchusZ,
+ m_CarinaZ, true,
GetBackgroundValue());
- StopCurrentStep<MaskImageType>(m_working_trachea);
- m_Station7 = m_Working_Support;
+ StopCurrentStep<MaskImageType>(m_Working_Support);
+ m_ListOfStations["7"] = m_Working_Support;
}
//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
template <class TImageType>
void
{
// ----------------------------------------------------------------
// Separate trachea in two CCL
- StartNewStep("Separate trachea under carina");
+ StartNewStep("[Station7] Separate trachea under carina");
// Labelize and consider two main labels
m_working_trachea = Labelize<MaskImageType>(m_working_trachea, 0, true, 1);
- // Carina position must at the first slice that separate the two main bronchus (not superiorly)
- // Check that upper slice is composed of at least two labels
+ // Carina position must at the first slice that separate the two
+ // main bronchus (not superiorly) Check that upper slice is composed
+ // of at least two labels
typedef itk::ImageSliceIteratorWithIndex<MaskImageType> SliceIteratorType;
SliceIteratorType iter(m_working_trachea, m_working_trachea->GetLargestPossibleRegion());
iter.SetFirstDirection(0);
int maxLabel=0;
while (!iter.IsAtReverseEndOfSlice()) {
while (!iter.IsAtReverseEndOfLine()) {
- // DD(iter.GetIndex());
if (iter.Get() > maxLabel) maxLabel = iter.Get();
--iter;
}
clitkExceptionMacro("First slice form Carina does not seems to seperate the two main bronchus. Abort");
}
- // Compute centroid of both parts to identify the left from the right bronchus
- typedef long LabelType;
- static const unsigned int Dim = ImageType::ImageDimension;
- typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
- typedef itk::LabelMap< LabelObjectType > LabelMapType;
- typedef itk::LabelImageToLabelMapFilter<MaskImageType, LabelMapType> ImageToMapFilterType;
- typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
- typedef itk::ShapeLabelMapFilter<LabelMapType, MaskImageType> ShapeFilterType;
- typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
- imageToLabelFilter->SetBackgroundValue(GetBackgroundValue());
- imageToLabelFilter->SetInput(m_working_trachea);
- statFilter->SetInput(imageToLabelFilter->GetOutput());
- statFilter->Update();
- typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
-
- ImagePointType C1 = labelMap->GetLabelObject(1)->GetCentroid();
- ImagePointType C2 = labelMap->GetLabelObject(2)->GetCentroid();
+ // Compute 3D centroids of both parts to identify the left from the
+ // right bronchus
+ std::vector<ImagePointType> c;
+ clitk::ComputeCentroids<MaskImageType>(m_working_trachea, GetBackgroundValue(), c);
+ 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; }
- DD(leftLabel);
- DD(rightLabel);
StopCurrentStep<MaskImageType>(m_working_trachea);
//-----------------------------------------------------
- StartNewStep("Left limits with bronchus (slice by slice)");
// Select LeftLabel (set one label to Backgroundvalue)
m_LeftBronchus =
SetBackground<MaskImageType, MaskImageType>(m_working_trachea, m_working_trachea,
- rightLabel, GetBackgroundValue());
+ rightLabel, GetBackgroundValue(), false);
m_RightBronchus =
SetBackground<MaskImageType, MaskImageType>(m_working_trachea, m_working_trachea,
- leftLabel, GetBackgroundValue());
- writeImage<MaskImageType>(m_LeftBronchus, "left.mhd");
- writeImage<MaskImageType>(m_RightBronchus, "right.mhd");
+ leftLabel, GetBackgroundValue(), false);
+ StartNewStep("[Station7] Limits with bronchus (slice by slice) : RightTo left bronchus");
m_Working_Support =
clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support,
m_LeftBronchus, 2,
GetFuzzyThreshold(), "RightTo",
true, 4);
+
+ StartNewStep("[Station7] Limits with bronchus (slice by slice) : LeftTo right bronchus");
m_Working_Support =
clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support,
m_RightBronchus,
2, GetFuzzyThreshold(), "LeftTo",
true, 4);
+
+ StartNewStep("[Station7] Limits with bronchus (slice by slice) : not AntTo left bronchus");
m_Working_Support =
clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support,
m_LeftBronchus,
2, GetFuzzyThreshold(), "AntTo",
true, 4, true); // NOT
+
+ StartNewStep("[Station7] Limits with bronchus (slice by slice) : not AntTo right bronchus");
m_Working_Support =
clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support,
m_RightBronchus,
2, GetFuzzyThreshold(), "AntTo",
true, 4, true);
+
+ StartNewStep("[Station7] Limits with bronchus (slice by slice) : not PostTo left bronchus");
m_Working_Support =
clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support,
m_LeftBronchus,
2, GetFuzzyThreshold(), "PostTo",
true, 4, true);
+
+ StartNewStep("[Station7] Limits with bronchus (slice by slice) : not PostTo right bronchus");
m_Working_Support =
clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support,
m_RightBronchus,
clitk::ExtractLymphStationsFilter<TImageType>::
ExtractStation_7_Posterior_Limits()
{
- StartNewStep("Posterior limits");
-
- // Left Bronchus slices
- typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
- typedef typename ExtractSliceFilterType::SliceType SliceType;
- typename ExtractSliceFilterType::Pointer
- extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(m_LeftBronchus);
- extractSliceFilter->SetDirection(2);
- extractSliceFilter->Update();
- std::vector<typename SliceType::Pointer> leftBronchusSlices;
- extractSliceFilter->GetOutputSlices(leftBronchusSlices);
-
- // Right Bronchus slices
- extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(m_RightBronchus);
- extractSliceFilter->SetDirection(2);
- extractSliceFilter->Update();
- std::vector<typename SliceType::Pointer> rightBronchusSlices ;
- extractSliceFilter->GetOutputSlices(rightBronchusSlices);
-
- assert(leftBronchusSlices.size() == rightBronchusSlices.size());
-
- std::vector<MaskImageType::PointType> leftPoints;
- std::vector<MaskImageType::PointType> rightPoints;
- for(uint i=0; i<leftBronchusSlices.size(); i++) {
- // Keep main CCL
- leftBronchusSlices[i] = Labelize<SliceType>(leftBronchusSlices[i], 0, true, 10);
- leftBronchusSlices[i] = KeepLabels<SliceType>(leftBronchusSlices[i],
- GetBackgroundValue(),
- GetForegroundValue(), 1, 1, true);
- rightBronchusSlices[i] = Labelize<SliceType>(rightBronchusSlices[i], 0, true, 10);
- rightBronchusSlices[i] = KeepLabels<SliceType>(rightBronchusSlices[i],
- GetBackgroundValue(),
- GetForegroundValue(), 1, 1, true);
- double distance_max_from_center_point = 15;
-
- // ------- Find point in left Bronchus -------
- // find right most point in left = rightMost
- SliceType::PointType a;
- SliceType::PointType rightMost =
- clitk::FindExtremaPointInAGivenDirection<SliceType>(leftBronchusSlices[i],
- GetBackgroundValue(),
- 0, false, a, 0);
- // find post most point in left, not far away from rightMost
- SliceType::PointType p =
- clitk::FindExtremaPointInAGivenDirection<SliceType>(leftBronchusSlices[i],
- GetBackgroundValue(),
- 1, false, rightMost,
- distance_max_from_center_point);
- MaskImageType::PointType pp;
- pp[0] = p[0]; pp[1] = p[1];
- pp[2] = i*m_LeftBronchus->GetSpacing()[2] + m_LeftBronchus->GetOrigin()[2];
- leftPoints.push_back(pp);
-
- // ------- Find point in right Bronchus -------
- // find left most point in right = leftMost
- SliceType::PointType leftMost =
- clitk::FindExtremaPointInAGivenDirection<SliceType>(rightBronchusSlices[i],
- GetBackgroundValue(),
- 0, true, a, 0);
- // find post most point in left, not far away from leftMost
- p = clitk::FindExtremaPointInAGivenDirection<SliceType>(rightBronchusSlices[i],
- GetBackgroundValue(),
- 1, false, leftMost,
- distance_max_from_center_point);
- pp[0] = p[0]; pp[1] = p[1];
- pp[2] = i*m_RightBronchus->GetSpacing()[2] + m_RightBronchus->GetOrigin()[2];
- rightPoints.push_back(pp);
- }
+ StartNewStep("[Station7] Posterior limits -> must be AntTo post wall of the bronchi");
+ // Search for points that are the most left/post/ant and most
+ // right/post/ant of the left and right bronchus
+
+ // extract, loop slices, label/keep, find extrema x 3
+ FindExtremaPointsInBronchus(m_LeftBronchus, 0, 15,
+ m_RightMostInLeftBronchus,
+ m_AntMostInLeftBronchus,
+ m_PostMostInLeftBronchus);
+ FindExtremaPointsInBronchus(m_RightBronchus, 1, 15,
+ m_LeftMostInRightBronchus,
+ m_AntMostInRightBronchus,
+ m_PostMostInRightBronchus);
// DEBUG
- std::ofstream osl;
- openFileForWriting(osl, "left.txt");
- osl << "LANDMARKS1" << std::endl;
- std::ofstream osr;
- openFileForWriting(osr, "right.txt");
- osr << "LANDMARKS1" << std::endl;
- for(uint i=0; i<leftBronchusSlices.size(); i++) {
- osl << i << " " << leftPoints[i][0] << " " << leftPoints[i][1]
- << " " << leftPoints[i][2] << " 0 0 " << std::endl;
- osr << i << " " << rightPoints[i][0] << " " << rightPoints[i][1]
- << " " << rightPoints[i][2] << " 0 0 " << std::endl;
+ std::ofstream osrl; openFileForWriting(osrl, "osrl.txt"); osrl << "LANDMARKS1" << std::endl;
+ std::ofstream osal; openFileForWriting(osal, "osal.txt"); osal << "LANDMARKS1" << std::endl;
+ std::ofstream ospl; openFileForWriting(ospl, "ospl.txt"); ospl << "LANDMARKS1" << std::endl;
+ std::ofstream osrr; openFileForWriting(osrr, "osrr.txt"); osrr << "LANDMARKS1" << std::endl;
+ std::ofstream osar; openFileForWriting(osar, "osar.txt"); osar << "LANDMARKS1" << std::endl;
+ std::ofstream ospr; openFileForWriting(ospr, "ospr.txt"); ospr << "LANDMARKS1" << std::endl;
+
+ for(uint i=0; i<m_RightMostInLeftBronchus.size(); i++) {
+ osrl << i << " " << m_RightMostInLeftBronchus[i][0] << " " << m_RightMostInLeftBronchus[i][1]
+ << " " << m_RightMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
+ osal << i << " " << m_AntMostInLeftBronchus[i][0] << " " << m_AntMostInLeftBronchus[i][1]
+ << " " << m_AntMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
+ ospl << i << " " << m_PostMostInLeftBronchus[i][0] << " " << m_PostMostInLeftBronchus[i][1]
+ << " " << m_PostMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
+
+ osrr << i << " " << m_LeftMostInRightBronchus[i][0] << " " << m_LeftMostInRightBronchus[i][1]
+ << " " << m_LeftMostInRightBronchus[i][2] << " 0 0 " << std::endl;
+ osar << i << " " << m_AntMostInRightBronchus[i][0] << " " << m_AntMostInRightBronchus[i][1]
+ << " " << m_AntMostInRightBronchus[i][2] << " 0 0 " << std::endl;
+ ospr << i << " " << m_PostMostInRightBronchus[i][0] << " " << m_PostMostInRightBronchus[i][1]
+ << " " << m_PostMostInRightBronchus[i][2] << " 0 0 " << std::endl;
}
- osl.close();
- osr.close();
+ osrl.close();
+ osal.close();
+ ospl.close();
// Now uses these points to limit, slice by slice
// http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
MaskImageType::PointType B;
MaskImageType::PointType C;
while (!iter.IsAtEnd()) {
- A = leftPoints[i];
- B = rightPoints[i];
+ A = m_PostMostInLeftBronchus[i];
+ B = m_PostMostInRightBronchus[i];
C = A;
C[1] -= 10; // I know I must keep this point
double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
}
//-----------------------------------------------------
- // StartNewStep("Anterior limits");
+ // StartNewStep("[Station7] Anterior limits");
// MISSING FROM NOW
m_Station7 = m_Working_Support;
}
//--------------------------------------------------------------------
+
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff