X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStation_3A.txx;h=50e394852123e6fec950275934f2de39978a84ec;hb=82029e7928db0cb8c17273c6da1c95314b1593c6;hp=4b1d3c2906b13dac04cd915b881f66673f2f446b;hpb=8f785a7646e65eb73b28e274871b2aafcb34d85c;p=clitk.git diff --git a/segmentation/clitkExtractLymphStation_3A.txx b/segmentation/clitkExtractLymphStation_3A.txx index 4b1d3c2..50e3948 100644 --- a/segmentation/clitkExtractLymphStation_3A.txx +++ b/segmentation/clitkExtractLymphStation_3A.txx @@ -5,8 +5,6 @@ void clitk::ExtractLymphStationsFilter:: ExtractStation_3A_SetDefaultValues() { - SetFuzzyThreshold("3A", "Sternum", 0.5); - SetFuzzyThreshold("3A", "SubclavianArtery", 0.5); } //-------------------------------------------------------------------- @@ -28,25 +26,19 @@ ExtractStation_3A() m_ListOfStations["3A"] = m_Working_Support; StopCurrentStep(m_Working_Support); - ExtractStation_3A_AntPost_S5(); - ExtractStation_3A_AntPost_S6(); + ExtractStation_3A_Post_Left_Limits_With_Aorta_S5_Support(); + ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support(); ExtractStation_3A_AntPost_Superiorly(); ExtractStation_3A_Remove_Structures(); - - Remove_Structures("3A", "Aorta"); - Remove_Structures("3A", "SubclavianArteryLeft"); - Remove_Structures("3A", "SubclavianArteryRight"); - Remove_Structures("3A", "Thyroid"); - Remove_Structures("3A", "CommonCarotidArteryLeft"); - Remove_Structures("3A", "CommonCarotidArteryRight"); - Remove_Structures("3A", "BrachioCephalicArtery"); - - ExtractStation_3A_PostToBones(); - + // Generic RelativePosition processes + m_ListOfStations["3A"] = this->ApplyRelativePositionList("Station_3A", m_ListOfStations["3A"]); - // ExtractStation_3A_Ant_Limits(); --> No, already in support; to remove - // ExtractStation_3A_Post_Limits(); --> No, more complex, see Vessels etc + // Keep a single CCL + m_ListOfStations["3A"] = + clitk::SliceBySliceKeepMainCCL(m_ListOfStations["3A"], + GetBackgroundValue(), + GetForegroundValue()); // Store image filenames into AFDB writeImage(m_ListOfStations["3A"], "seg/Station3A.mhd"); @@ -57,74 +49,16 @@ ExtractStation_3A() //-------------------------------------------------------------------- -//-------------------------------------------------------------------- -template -void -clitk::ExtractLymphStationsFilter:: -ExtractStation_3A_Ant_Limits() -{ - StartNewStep("[Station 3A] Ant limits with Sternum"); - - // Get Sternum, keep posterior part. - MaskImagePointer Sternum = GetAFDB()->template GetImage("Sternum"); - m_Working_Support = - clitk::SliceBySliceRelativePosition(m_Working_Support, Sternum, 2, - GetFuzzyThreshold("3A", "Sternum"), "PostTo", - false, 3, true, false); - StopCurrentStep(m_Working_Support); - m_ListOfStations["3A"] = m_Working_Support; -} -//-------------------------------------------------------------------- - //-------------------------------------------------------------------- template void clitk::ExtractLymphStationsFilter:: -ExtractStation_3A_Post_Limits() +ExtractStation_3A_Post_Left_Limits_With_Aorta_S5_Support() { - StartNewStep("[Station 3A] Post limits with SubclavianArtery"); - - // Get Sternum, keep posterior part. - MaskImagePointer SubclavianArteryLeft = - GetAFDB()->template GetImage("SubclavianArteryLeft"); - MaskImagePointer SubclavianArteryRight = - GetAFDB()->template GetImage("SubclavianArteryRight"); - - m_Working_Support = - clitk::SliceBySliceRelativePosition(m_Working_Support, SubclavianArteryLeft, 2, - GetFuzzyThreshold("3A", "SubclavianArtery"), "AntTo", - false, 3, true, false); - m_Working_Support = - clitk::SliceBySliceRelativePosition(m_Working_Support, SubclavianArteryRight, 2, - GetFuzzyThreshold("3A", "SubclavianArtery"), "AntTo", - false, 3, true, false); - StopCurrentStep(m_Working_Support); - m_ListOfStations["3A"] = m_Working_Support; -} -//-------------------------------------------------------------------- + StartNewStep("[Station 3A] Post limits in S5 support according to Aorta"); - -//-------------------------------------------------------------------- -template -void -clitk::ExtractLymphStationsFilter:: -ExtractStation_3A_AntPost_S5() -{ - StartNewStep("[Station 3A] Post limits around S5"); - - // First remove post to SVC - MaskImagePointer SVC = GetAFDB()->template GetImage ("SVC"); - - // Trial in 3D -> difficulties superiorly. Stay slice by slice. - // Slice by slice not post to SVC. Use initial spacing - m_Working_Support = - clitk::SliceBySliceRelativePosition(m_Working_Support, SVC, 2, - GetFuzzyThreshold("3A", "SVC"), - "NotPostTo", true, - SVC->GetSpacing()[0], false, false); - - // Consider Aorta, remove Left/Post part ; only around S5 + // Consider Aorta, remove Left/Post part ; only around S5 // Get S5 support and Aorta MaskImagePointer S5 = m_ListOfSupports["S5"]; MaskImagePointer Aorta = GetAFDB()->template GetImage ("Aorta"); @@ -133,6 +67,13 @@ ExtractStation_3A_AntPost_S5() // Inferiorly, Aorta has two CCL that merge into a single one when // S6 appears. Loop on Aorta slices, select the most ant one, detect // the most ant point. + + + + // ====> TO BE CHANGED USING AscendingAorta and DescendingAorta + + + std::vector slices; clitk::ExtractSlices(Aorta, 2, slices); std::vector points; @@ -188,9 +129,9 @@ ExtractStation_3A_AntPost_S5() template void clitk::ExtractLymphStationsFilter:: -ExtractStation_3A_AntPost_S6() +ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support() { - StartNewStep("[Station 3A] Post limits around S6"); + StartNewStep("[Station 3A] Post limits with dilated Aorta"); // Consider Aorta MaskImagePointer Aorta = GetAFDB()->template GetImage ("Aorta"); @@ -206,13 +147,11 @@ ExtractStation_3A_AntPost_S6() radius[2] = 0; // required Aorta = clitk::Dilate(Aorta, radius, GetBackgroundValue(), GetForegroundValue(), false); - // Not Post to - m_Working_Support = - clitk::SliceBySliceRelativePosition(m_Working_Support, Aorta, 2, - GetFuzzyThreshold("3A", "Aorta"), - "NotPostTo", true, - Aorta->GetSpacing()[0], false, false); - + // Now, insert this image in the AFDB (but do not store on disk) + GetAFDB()->template SetImage("Aorta_Dilated_Anteriorly", "seg/Aorta_Dilated_Anteriorly.mha", Aorta, false); + writeImage(Aorta, "seg/Aorta_Dilated_Anteriorly.mha"); + GetAFDB()->Write(); + StopCurrentStep(m_Working_Support); m_ListOfStations["3A"] = m_Working_Support; } @@ -226,30 +165,6 @@ clitk::ExtractLymphStationsFilter:: ExtractStation_3A_AntPost_Superiorly() { StartNewStep("[Station 3A] Post limits superiorly"); - - /* - MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage ("BrachioCephalicVein"); - MaskImagePointer BrachioCephalicArtery = GetAFDB()->template GetImage ("BrachioCephalicArtery"); - MaskImagePointer CommonCarotidArteryLeft = GetAFDB()->template GetImage ("CommonCarotidArteryLeft"); - MaskImagePointer CommonCarotidArteryRight = GetAFDB()->template GetImage ("CommonCarotidArteryRight"); - MaskImagePointer SubclavianArteryLeft = GetAFDB()->template GetImage ("SubclavianArteryLeft"); - MaskImagePointer SubclavianArteryRight = GetAFDB()->template GetImage ("SubclavianArteryRight"); - - // Not Post to -#define RP(STRUCTURE) \ - m_Working_Support = \ - clitk::SliceBySliceRelativePosition(m_Working_Support, STRUCTURE, 2, \ - 0.5, \ - "NotPostTo", true, \ - STRUCTURE->GetSpacing()[0], false, false); - - // RP(BrachioCephalicVein); - RP(BrachioCephalicArtery); - RP(CommonCarotidArteryRight); - RP(CommonCarotidArteryLeft); - RP(SubclavianArteryRight); - RP(SubclavianArteryLeft); - */ // Get or compute the binary mask that separate Ant/Post part // according to vessels @@ -282,13 +197,14 @@ void clitk::ExtractLymphStationsFilter:: ExtractStation_3A_Remove_Structures() { - Remove_Structures("3A", "Aorta"); - Remove_Structures("3A", "SubclavianArteryLeft"); - Remove_Structures("3A", "SubclavianArteryRight"); - Remove_Structures("3A", "Thyroid"); - Remove_Structures("3A", "CommonCarotidArteryLeft"); - Remove_Structures("3A", "CommonCarotidArteryRight"); - Remove_Structures("3A", "BrachioCephalicArtery"); + Remove_Structures(" 3A", "Aorta"); + Remove_Structures(" 3A", "LeftSubclavianArtery"); + Remove_Structures(" 3A", "RightSubclavianArtery"); + Remove_Structures(" 3A", "Thyroid"); + Remove_Structures(" 3A", "LeftCommonCarotidArtery"); + Remove_Structures(" 3A", "RightCommonCarotidArtery"); + Remove_Structures(" 3A", "BrachioCephalicArtery"); + // Remove_Structures("3A", "Bones"); --> should be in extractmediastinum // Remove_Structures("3A", "BrachioCephalicVein"); ? StartNewStep("[Station 3A] Remove part of BrachioCephalicVein"); @@ -341,3 +257,5 @@ ExtractStation_3A_Remove_Structures() m_ListOfStations["3A"] = m_Working_Support; } //-------------------------------------------------------------------- + +