From: David Sarrut Date: Mon, 5 Dec 2011 09:13:44 +0000 (+0100) Subject: Correct LR or S1. Add Post S1 S3P. Add Post S1 and Ant S2RL X-Git-Tag: v1.3.0~104^2~24 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=31ae3f744e457adcd92677eaddd4c54d2702a392;p=clitk.git Correct LR or S1. Add Post S1 S3P. Add Post S1 and Ant S2RL --- diff --git a/segmentation/clitkExtractLymphStation_Supports.txx b/segmentation/clitkExtractLymphStation_Supports.txx index fa640a2..952c08e 100644 --- a/segmentation/clitkExtractLymphStation_Supports.txx +++ b/segmentation/clitkExtractLymphStation_Supports.txx @@ -19,18 +19,6 @@ ExtractStationSupports() Support_SI_Limit("inferior", "Sup_to_Carina", "inferior", "Carina", 0); Support_SI_Limit("superior", "Inf_to_Carina", "inferior", "Carina", m_Working_Support->GetSpacing()[2]); - // Initialise all others supports - // m_ListOfSupports["S1R"] = m_ListOfSupports["Sup_to_Carina"]; - // m_ListOfSupports["S1L"] = m_ListOfSupports["Sup_to_Carina"]; - // m_ListOfSupports["S2R"] = m_ListOfSupports["Sup_to_Carina"]; - // m_ListOfSupports["S2L"] = m_ListOfSupports["Sup_to_Carina"]; - // m_ListOfSupports["S3A"] = m_ListOfSupports["Sup_to_Carina"]; - // m_ListOfSupports["S3P"] = m_ListOfSupports["Sup_to_Carina"]; - // m_ListOfSupports["S4R"] = m_ListOfSupports["Sup_to_Carina"]; - // m_ListOfSupports["S4L"] = m_ListOfSupports["Sup_to_Carina"]; - // m_ListOfSupports["S5"] = m_Mediastinum; // Not above Carina - // m_ListOfSupports["S6"] = m_Mediastinum; // Not above Carina - // Read all support limits in a file and apply them ReadSupportLimits(GetSupportLimitsFilename()); for(int i=0; i here limit with + // trachea only StartNewStep("[Support] Ant limits of S3A with trachea"); m_ListOfSupports["S3A"] = LimitsWithTrachea(m_ListOfSupports["S3A"], 1, 0, -10); + + // S1RL - posterior limits when SI overlap with S3P + Support_Post_S1_S3P(); + + // S1RL - posterior limits with S2RL above sternal notch + Support_Post_S1_Ant_S2RL(); // I will do it later // Below Carina S7,8,9,10 @@ -235,6 +234,11 @@ void clitk::ExtractLymphStationsFilter:: Support_LeftRight_S1R_S1L() { + /* + Medially, station 1R and 1L are separated by the midline of the + trachea, whilst excluding the thyroid gland. + */ + // Step S1RL : Left-Right StartNewStep("[Support] Left-Right S1R S1L"); std::vector A; @@ -265,13 +269,13 @@ Support_LeftRight_S1R_S1L() // Right part clitk::SliceBySliceSetBackgroundFromLineSeparation(S1R, A, B, - GetBackgroundValue(), 0, 10); + GetBackgroundValue(), 0, -10); S1R = clitk::AutoCrop(S1R, GetBackgroundValue()); m_ListOfSupports["S1R"] = S1R; // Left part clitk::SliceBySliceSetBackgroundFromLineSeparation(S1L, A, B, - GetBackgroundValue(), 0, -10); + GetBackgroundValue(), 0, 10); S1L = clitk::AutoCrop(S1L, GetBackgroundValue()); m_ListOfSupports["S1L"] = S1L; StopCurrentStep(m_ListOfSupports["S1L"]); @@ -286,11 +290,14 @@ clitk::ExtractLymphStationsFilter:: Support_LeftRight_S2R_S2L() { // --------------------------------------------------------------------------- - /* Step : S2RL LeftRight - As for lymph node station 4R, 2R includes nodes extending to the - left lateral border of the trachea - Rod says: "For station 2 there is a shift, dividing 2R from 2L, from midline - to the left paratracheal border." + /* Step : S2RL LeftRight As for lymph node station 4R, 2R includes + nodes extending to the left lateral border of the trachea. + + Rod says: "For station 2 there is a shift in the IASLC definition + dividing 2R from 2L, from the midline to the left lateral + tracheal border. This is represented in the atlas as a vertical + line passing tangentially along the left lateral tracheal border + " */ StartNewStep("[Support] Separate 2R/2L according to Trachea"); MaskImagePointer S2R = m_ListOfSupports["S2R"]; @@ -313,15 +320,10 @@ clitk::ExtractLymphStationsFilter:: Support_LeftRight_S4R_S4L() { // --------------------------------------------------------------------------- - /* Step : S4RL LeftRight - - - 4R: includes right paratracheal nodes, and pretracheal nodes - extending to the left lateral border of trachea - - - 4L: includes nodes to the left of the left lateral border of - the trachea, medial to the ligamentum arteriosum - - => same than 2RL + /* + The medial border of station 4R is defined as an imaginary line + running vertically from the left lateral tracheal border. This is + the same medial border as was described for station 2R. */ StartNewStep("[Support] Left Right separation of 4R/4L"); @@ -409,21 +411,21 @@ LimitsWithTrachea(MaskImageType * input, int extremaDirection, int lineDirection template void clitk::ExtractLymphStationsFilter:: -Support_Post_S1S2S4() +Support_Post_S2S4() { - StartNewStep("[Support] Post limits of S1RL, S2RL, S4RL"); + StartNewStep("[Support] Post limits of S2RL, S4RL"); double m_ApexOfTheChest = FindApexOfTheChest(); // Post limits with Trachea - MaskImagePointer S1R = m_ListOfSupports["S1R"]; - MaskImagePointer S1L = m_ListOfSupports["S1L"]; + // MaskImagePointer S1R = m_ListOfSupports["S1R"]; + // MaskImagePointer S1L = m_ListOfSupports["S1L"]; MaskImagePointer S2R = m_ListOfSupports["S2R"]; MaskImagePointer S2L = m_ListOfSupports["S2L"]; MaskImagePointer S4R = m_ListOfSupports["S4R"]; MaskImagePointer S4L = m_ListOfSupports["S4L"]; - m_ListOfSupports["S1R"] = LimitsWithTrachea(S1L, 1, 0, -10, m_ApexOfTheChest); - m_ListOfSupports["S1L"] = LimitsWithTrachea(S1R, 1, 0, -10, m_ApexOfTheChest); + // m_ListOfSupports["S1R"] = LimitsWithTrachea(S1L, 1, 0, -10, m_ApexOfTheChest); + // m_ListOfSupports["S1L"] = LimitsWithTrachea(S1R, 1, 0, -10, m_ApexOfTheChest); m_ListOfSupports["S2R"] = LimitsWithTrachea(S2R, 1, 0, -10, m_ApexOfTheChest); m_ListOfSupports["S2L"] = LimitsWithTrachea(S2L, 1, 0, -10, m_ApexOfTheChest); m_ListOfSupports["S4R"] = LimitsWithTrachea(S4R, 1, 0, -10, m_ApexOfTheChest); @@ -432,3 +434,161 @@ Support_Post_S1S2S4() //-------------------------------------------------------------------- +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +Support_Post_S1_S3P() +{ + StartNewStep("[Support] If S1RL and S3P have Sup-Inf overlap, define S1RL posterior limits with S3P anterior limits (post wall trachea)"); + + // Get current supports + MaskImagePointer S1R = m_ListOfSupports["S1R"]; + MaskImagePointer S1L = m_ListOfSupports["S1L"]; + + // Find extrema ant positions for 3P + std::vector A; + std::vector B; + + // Crop S3P like S1R + MaskImagePointer S3P = clitk::Clone(m_ListOfSupports["S3P"]); + S3P = clitk::ResizeImageLike(S3P, S1R, GetBackgroundValue()); + + // Slice by slice, build the separation line + clitk::SliceBySliceBuildLineSegmentAccordingToExtremaPosition(S3P, + GetBackgroundValue(), 2, + 1, true, // Ant-Post + 0, // Horizontal line + 0, // margins + A, B); + + // clitk::WriteListOfLandmarks(A, "A-S1S3P.txt"); + // clitk::WriteListOfLandmarks(B, "B-S1S3P.txt"); + + // Cut post to this line + clitk::SliceBySliceSetBackgroundFromLineSeparation(S1R, A, B, + GetBackgroundValue(), + 1, -10); + + // Crop S3P like S1L (Redo for S1L) + S3P = clitk::Clone(m_ListOfSupports["S3P"]); + S3P = clitk::ResizeImageLike(S3P, S1L, GetBackgroundValue()); + + // Slice by slice, build the separation line + A.clear(); + B.clear(); + clitk::SliceBySliceBuildLineSegmentAccordingToExtremaPosition(S3P, + GetBackgroundValue(), 2, + 1, true, // Ant-Post + 0, // Horizontal line + 0, // margins + A, B); + // Cut post to this line + clitk::SliceBySliceSetBackgroundFromLineSeparation(S1L, A, B, + GetBackgroundValue(), + 1, -10); + + // Crop both images + S1R = clitk::AutoCrop(S1R, GetBackgroundValue()); + S1L = clitk::AutoCrop(S1L, GetBackgroundValue()); + + StopCurrentStep(S1R); + + m_ListOfSupports["S1R"] = S1R; + m_ListOfSupports["S1L"] = S1L; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +Support_Post_S1_Ant_S2RL() +{ + StartNewStep("[Support] Define S1RL posterior limits with S2RL anterior limits when overlap"); + + // Get RightLung + MaskImagePointer RightLung = this->GetAFDB()->template GetImage("RightLung"); + + // Find common area between S1 and S2 + MaskImagePointType p_min; + MaskImagePointType p_max; + clitk::FindExtremaPointInAGivenDirection(m_ListOfSupports["S2R"], + GetBackgroundValue(), 2, false, p_max); + clitk::FindExtremaPointInAGivenDirection(m_ListOfSupports["S1R"], + GetBackgroundValue(), 2, true, p_min); + p_min[2] -= RightLung->GetSpacing()[2]; // consider the slice below (remove lower or equal) + p_max[2] += RightLung->GetSpacing()[2]; // consider the slice abov (remove greater or equal) + + if (p_min[2] > p_max[2]) { + + // Crop RightLung + RightLung = clitk::Clone(RightLung); + RightLung = clitk::ResizeImageLike(RightLung, m_ListOfSupports["S1R"], GetBackgroundValue()); + RightLung = clitk::CropImageRemoveLowerThan(RightLung, 2, p_min[2], true, GetBackgroundValue()); + RightLung = clitk::CropImageRemoveGreaterThan(RightLung, 2, p_max[2], true, GetBackgroundValue()); + + // Find extrema ant positions for RightLung + std::vector A; + std::vector B; + clitk::SliceBySliceBuildLineSegmentAccordingToExtremaPosition(RightLung, + GetBackgroundValue(), 2, + 1, true, // Ant-Post + 0, // Horizontal line + 0, // margins + A, B); + clitk::SliceBySliceSetBackgroundFromLineSeparation(m_ListOfSupports["S1R"], + A, B, + GetBackgroundValue(), + 1, -10); + // I add one pixel to abupt S2R to S1R + for(int i=0; iGetSpacing()[1]; + B[i][1] -= RightLung->GetSpacing()[1]; + } + clitk::SliceBySliceSetBackgroundFromLineSeparation(m_ListOfSupports["S2R"], + A, B, + GetBackgroundValue(), + 1, 10); + } + + // Get LeftLung, crop + MaskImagePointer LeftLung = this->GetAFDB()->template GetImage("LeftLung"); + clitk::FindExtremaPointInAGivenDirection(m_ListOfSupports["S2L"], + GetBackgroundValue(), 2, false, p_max); + clitk::FindExtremaPointInAGivenDirection(m_ListOfSupports["S1L"], + GetBackgroundValue(), 2, true, p_min); + p_min[2] -= LeftLung->GetSpacing()[2]; // consider the slice below (remove lower or equal) + p_max[2] += LeftLung->GetSpacing()[2]; // consider the slice abov (remove greater or equal) + + if (p_min[2] > p_max[2]) { + LeftLung = clitk::ResizeImageLike(LeftLung, m_ListOfSupports["S1L"], GetBackgroundValue()); + LeftLung = clitk::CropImageRemoveLowerThan(LeftLung, 2, p_min[2], true, GetBackgroundValue()); + LeftLung = clitk::CropImageRemoveGreaterThan(LeftLung, 2, p_max[2], true, GetBackgroundValue()); + + // Find extrema ant positions for LeftLung + std::vector A; + std::vector B; + clitk::SliceBySliceBuildLineSegmentAccordingToExtremaPosition(LeftLung, + GetBackgroundValue(), 2, + 1, true, // Ant-Post + 0, // Horizontal line + 0, // margins + A, B); + clitk::SliceBySliceSetBackgroundFromLineSeparation(m_ListOfSupports["S1L"], + A, B, + GetBackgroundValue(), + 1, -10); + // I add one pixel to abupt S2R to S1R + for(int i=0; iGetSpacing()[1]; + B[i][1] -= LeftLung->GetSpacing()[1]; + } + clitk::SliceBySliceSetBackgroundFromLineSeparation(m_ListOfSupports["S2L"], + A, B, + GetBackgroundValue(), + 1, 10); + } +} +//--------------------------------------------------------------------