X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.txx;h=ea514a6d643924af6834d3c3a921b82b98411d05;hb=d30d301ddbebb5f290f8d9c0104dc6448ea531e1;hp=aab78d85c01730c9778c4be1cf81d99c28726728;hpb=6e16222234a90c6079a8f4696c92de7349a496bb;p=clitk.git diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx index aab78d8..ea514a6 100644 --- a/segmentation/clitkExtractLymphStationsFilter.txx +++ b/segmentation/clitkExtractLymphStationsFilter.txx @@ -34,6 +34,7 @@ #include #include #include +#include #include // itk ENST @@ -44,16 +45,25 @@ template clitk::ExtractLymphStationsFilter:: ExtractLymphStationsFilter(): clitk::FilterBase(), - itk::ImageToImageFilter() + clitk::FilterWithAnatomicalFeatureDatabaseManagement(), + itk::ImageToImageFilter() { this->SetNumberOfRequiredInputs(1); - SetBackgroundValueMediastinum(0); - SetBackgroundValueTrachea(0); SetBackgroundValue(0); SetForegroundValue(1); - SetIntermediateSpacing(6); - SetFuzzyThreshold1(0.6); + // Station 8 + 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); + + // Station 7 + SetFuzzyThreshold(0.5); + SetStation7Filename("station7.mhd"); } //-------------------------------------------------------------------- @@ -62,13 +72,54 @@ ExtractLymphStationsFilter(): template void clitk::ExtractLymphStationsFilter:: -SetInputMediastinumLabelImage(const TImageType * image, ImagePixelType bg) { - this->SetNthInput(0, const_cast(image)); - m_BackgroundValueMediastinum = bg; - SetCarenaZPositionInMM(image->GetOrigin()[2]+image->GetLargestPossibleRegion().GetSize()[2]*image->GetSpacing()[2]); - SetMiddleLobeBronchusZPositionInMM(image->GetOrigin()[2]); - // DD(m_CarenaZPositionInMM); -// DD(m_MiddleLobeBronchusZPositionInMM); +GenerateOutputInformation() { + // Get inputs + LoadAFDB(); + m_Input = dynamic_cast(itk::ProcessObject::GetInput(0)); + m_Mediastinum = GetAFDB()->template GetImage ("Mediastinum"); + + // Extract Station8 + StartNewStep("Station 8"); + StartSubStep(); + ExtractStation_8(); + StopSubStep(); + + // Compute some interesting points in trachea + // ( ALTERNATIVE -> SKELETON ANALYSIS ? + // Pb : not sufficient for mostXX points ... ) + + /* ==> todo (but why ???) + ComputeTracheaCentroidsAboveCarina(); + ComputeBronchusExtremaPointsBelowCarina(); + */ + + if (0) { // temporary suppress + // Extract Station7 + StartNewStep("Station 7"); + StartSubStep(); + ExtractStation_7(); + StopSubStep(); + + // Extract Station4RL + StartNewStep("Station 4RL"); + StartSubStep(); + //ExtractStation_4RL(); + StopSubStep(); + } + + + // + // typedef clitk::BooleanOperatorLabelImageFilter BFilter; + //BFilter::Pointer merge = BFilter::New(); + // writeImage(m_Output, "ouput.mhd"); + //writeImage(m_Working_Support, "ws.mhd"); + /*merge->SetInput1(m_Station7); + merge->SetInput2(m_Station4RL); // support + merge->SetOperationType(BFilter::AndNot); CHANGE OPERATOR + merge->SetForegroundValue(4); + merge->Update(); + m_Output = merge->GetOutput(); + */ } //-------------------------------------------------------------------- @@ -77,193 +128,42 @@ SetInputMediastinumLabelImage(const TImageType * image, ImagePixelType bg) { template void clitk::ExtractLymphStationsFilter:: -SetInputTracheaLabelImage(const TImageType * image, ImagePixelType bg) { - this->SetNthInput(1, const_cast(image)); - m_BackgroundValueTrachea = bg; +GenerateInputRequestedRegion() { + DD("GenerateInputRequestedRegion (nothing?)"); } //-------------------------------------------------------------------- //-------------------------------------------------------------------- template -template void clitk::ExtractLymphStationsFilter:: -SetArgsInfo(ArgsInfoType mArgsInfo) -{ - SetVerboseOption_GGO(mArgsInfo); - SetVerboseStep_GGO(mArgsInfo); - SetWriteStep_GGO(mArgsInfo); - SetVerboseWarningOff_GGO(mArgsInfo); - SetCarenaZPositionInMM_GGO(mArgsInfo); - SetMiddleLobeBronchusZPositionInMM_GGO(mArgsInfo); - SetIntermediateSpacing_GGO(mArgsInfo); - SetFuzzyThreshold1_GGO(mArgsInfo); - //SetBackgroundValueMediastinum_GGO(mArgsInfo); +GenerateData() { + DD("GenerateData, graft output"); + + // Final Step -> graft output (if SetNthOutput => redo) + this->GraftOutput(m_ListOfStations["8"]); } //-------------------------------------------------------------------- - + //-------------------------------------------------------------------- template void clitk::ExtractLymphStationsFilter:: -GenerateOutputInformation() { - // Superclass::GenerateOutputInformation(); - - // Get input - m_mediastinum = dynamic_cast(itk::ProcessObject::GetInput(0)); - m_trachea = dynamic_cast(itk::ProcessObject::GetInput(1)); - - // ---------------------------------------------------------------- - // ---------------------------------------------------------------- - // Superior limit = carena - // Inferior limit = origine middle lobe bronchus - StartNewStep("Inf/Sup mediastinum limits with carena/bronchus"); - ImageRegionType region = m_mediastinum->GetLargestPossibleRegion(); DD(region); - ImageSizeType size = region.GetSize(); - ImageIndexType index = region.GetIndex(); - DD(m_CarenaZPositionInMM); - DD(m_MiddleLobeBronchusZPositionInMM); - index[2] = floor((m_MiddleLobeBronchusZPositionInMM - m_mediastinum->GetOrigin()[2]) / m_mediastinum->GetSpacing()[2]); - size[2] = ceil((m_CarenaZPositionInMM-m_MiddleLobeBronchusZPositionInMM) / m_mediastinum->GetSpacing()[2]); - region.SetSize(size); - region.SetIndex(index); - DD(region); - typedef itk::RegionOfInterestImageFilter CropFilterType; - typename CropFilterType::Pointer cropFilter = CropFilterType::New(); - cropFilter->SetInput(m_mediastinum); - cropFilter->SetRegionOfInterest(region); - cropFilter->Update(); - m_working_image = cropFilter->GetOutput(); - // Auto Crop (because following rel pos is faster) - m_working_image = clitk::AutoCrop(m_working_image, 0); - StopCurrentStep(m_working_image); - m_output = m_working_image; - - // ---------------------------------------------------------------- - // ---------------------------------------------------------------- - // Separate trachea in two CCL - StartNewStep("Separate trachea under carena"); - // DD(region); - ImageRegionType trachea_region = m_trachea->GetLargestPossibleRegion(); - for(int i=0; i<3; i++) { - index[i] = floor(((index[i]*m_mediastinum->GetSpacing()[i])+m_mediastinum->GetOrigin()[i] - -m_trachea->GetOrigin()[i])/m_trachea->GetSpacing()[i]); - // DD(index[i]); - size[i] = ceil((size[i]*m_mediastinum->GetSpacing()[i])/m_trachea->GetSpacing()[i]); - // DD(size[i]); - if (index[i] < 0) { - size[i] += index[i]; - index[i] = 0; - } - if (size[i]+index[i] > (trachea_region.GetSize()[i] + trachea_region.GetIndex()[i])) { - size[i] = trachea_region.GetSize()[i] + trachea_region.GetIndex()[i] - index[i]; - } - } - // DD(index); - // DD(size); - region.SetIndex(index); - region.SetSize(size); - // typedef itk::RegionOfInterestImageFilter CropFilterType; - // typename CropFilterType::Pointer - cropFilter = CropFilterType::New(); - // m_trachea.Print(std::cout); - cropFilter->SetInput(m_trachea); - cropFilter->SetRegionOfInterest(region); - cropFilter->Update(); - m_working_trachea = cropFilter->GetOutput(); - - // Labelize and consider two main labels - m_working_trachea = Labelize(m_working_trachea, 0, true, 1); - - // Detect wich label is at Left - typedef itk::ImageSliceConstIteratorWithIndex SliceIteratorType; - SliceIteratorType iter(m_working_trachea, m_working_trachea->GetLargestPossibleRegion()); - iter.SetFirstDirection(0); - iter.SetSecondDirection(1); - iter.GoToBegin(); - bool stop = false; - ImagePixelType leftLabel; - ImagePixelType rightLabel; - while (!stop) { - if (iter.Get() != m_BackgroundValueTrachea) { - // DD(iter.GetIndex()); - // DD((int)iter.Get()); - leftLabel = iter.Get(); - stop = true; - } - ++iter; - } - if (leftLabel == 1) rightLabel = 2; - else rightLabel = 1; - DD((int)leftLabel); - DD((int)rightLabel); +ExtractStation_8() { - // End step - StopCurrentStep(m_working_trachea); - - //----------------------------------------------------- - /* DD("TEST Skeleton"); - typedef itk::BinaryThinningImageFilter SkeletonFilterType; - typename SkeletonFilterType::Pointer skeletonFilter = SkeletonFilterType::New(); - skeletonFilter->SetInput(m_working_trachea); - skeletonFilter->Update(); - writeImage(skeletonFilter->GetOutput(), "skel.mhd"); - writeImage(skeletonFilter->GetThinning(), "skel2.mhd"); - */ + // Check if m_ListOfStations["8"] exist. If yes -> use it as initial + // support instead of m_Mediastinum + if (m_ListOfStations["8"]) { + DD("Station 8 support already exist -> use it"); + m_Working_Support = m_ListOfStations["8"]; + } + else m_Working_Support = m_Mediastinum; - //----------------------------------------------------- - StartNewStep("Left limits with bronchus (slice by slice)"); - // Select LeftLabel (set right label to 0) - ImagePointer temp = SetBackground(m_working_trachea, m_working_trachea, rightLabel, 0); - writeImage(temp, "temp1.mhd"); - - typedef clitk::SliceBySliceRelativePositionFilter SliceRelPosFilterType; - typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New(); - sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId()); - sliceRelPosFilter->VerboseStepOn(); - sliceRelPosFilter->WriteStepOn(); - sliceRelPosFilter->SetInput(m_working_image); - sliceRelPosFilter->SetInputObject(temp); - sliceRelPosFilter->SetDirection(2); - sliceRelPosFilter->SetFuzzyThreshold(0.5); - sliceRelPosFilter->SetOrientationType(SliceRelPosFilterType::RelPosFilterType::RightTo); - sliceRelPosFilter->Update(); - m_working_image = sliceRelPosFilter->GetOutput(); - writeImage(m_working_image, "afterslicebyslice.mhd"); - - - //----------------------------------------------------- - StartNewStep("Right limits with bronchus (slice by slice)"); - // Select LeftLabel (set right label to 0) - temp = SetBackground(m_working_trachea, m_working_trachea, leftLabel, 0); - writeImage(temp, "temp2.mhd"); - - sliceRelPosFilter = SliceRelPosFilterType::New(); - sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId()); - sliceRelPosFilter->VerboseStepOn(); - sliceRelPosFilter->WriteStepOn(); - sliceRelPosFilter->SetInput(m_working_image); - sliceRelPosFilter->SetInputObject(temp); - sliceRelPosFilter->SetDirection(2); - sliceRelPosFilter->SetFuzzyThreshold(0.5); - sliceRelPosFilter->SetOrientationType(SliceRelPosFilterType::RelPosFilterType::LeftTo); - sliceRelPosFilter->Update(); - m_working_image = sliceRelPosFilter->GetOutput(); - writeImage(m_working_image, "afterslicebyslice.mhd"); - - - DD("end"); - m_output = m_working_image; - StopCurrentStep(m_output); - - // Set output image information (required) - ImagePointer outputImage = this->GetOutput(0); - outputImage->SetRegions(m_working_image->GetLargestPossibleRegion()); - outputImage->SetOrigin(m_working_image->GetOrigin()); - outputImage->SetRequestedRegion(m_working_image->GetLargestPossibleRegion()); - DD("end2"); + ExtractStation_8_SI_Limits(); + ExtractStation_8_AP_Limits(); + // ExtractStation_8_LR_Limits(); } //-------------------------------------------------------------------- @@ -272,15 +172,15 @@ GenerateOutputInformation() { template void clitk::ExtractLymphStationsFilter:: -GenerateInputRequestedRegion() { - DD("GenerateInputRequestedRegion"); - // Call default - Superclass::GenerateInputRequestedRegion(); - // Following needed because output region can be greater than input (trachea) - ImagePointer mediastinum = dynamic_cast(itk::ProcessObject::GetInput(0)); - ImagePointer trachea = dynamic_cast(itk::ProcessObject::GetInput(1)); - mediastinum->SetRequestedRegion(mediastinum->GetLargestPossibleRegion()); - trachea->SetRequestedRegion(trachea->GetLargestPossibleRegion()); +ExtractStation_7() { + if (m_ListOfStations["7"]) { + DD("Station 7 support already exist -> use it"); + m_Working_Support = m_ListOfStations["7"]; + } + else m_Working_Support = m_Mediastinum; + ExtractStation_7_SI_Limits(); + ExtractStation_7_RL_Limits(); + ExtractStation_7_Posterior_Limits(); } //-------------------------------------------------------------------- @@ -289,12 +189,84 @@ GenerateInputRequestedRegion() { template void clitk::ExtractLymphStationsFilter:: -GenerateData() { - DD("GenerateData"); - // Final Step -> graft output (if SetNthOutput => redo) - this->GraftOutput(m_output); +ExtractStation_4RL() { + /* + WARNING ONLY 4R FIRST !!! (not same inf limits) + */ + ExtractStation_4RL_SI_Limits(); + ExtractStation_4RL_LR_Limits(); + ExtractStation_4RL_AP_Limits(); } //-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLymphStationsFilter:: +FindExtremaPointsInBronchus(MaskImagePointer input, + int direction, + double distance_max_from_center_point, + ListOfPointsType & LR, + ListOfPointsType & Ant, + ListOfPointsType & Post) +{ + + // Other solution ==> with auto bounding box ! (but pb to prevent to + // be too distant from the center point + + // Extract slices + std::vector slices; + clitk::ExtractSlices(input, 2, slices); + // Loop on slices + bool found; + for(uint i=0; i(slices[i], 0, true, 10); + slices[i] = KeepLabels(slices[i], + GetBackgroundValue(), + GetForegroundValue(), 1, 1, true); + */ + + // ------- Find rightmost or leftmost point ------- + MaskSliceType::PointType LRMost; + found = + clitk::FindExtremaPointInAGivenDirection(slices[i], + GetBackgroundValue(), + 0, // axis XY + (direction==0?false:true), // right or left according to direction + LRMost); + // ------- Find postmost point ------- + MaskSliceType::PointType postMost; + found = + clitk::FindExtremaPointInAGivenDirection(slices[i], + GetBackgroundValue(), + 1, false, LRMost, + distance_max_from_center_point, + postMost); + // ------- Find antmost point ------- + MaskSliceType::PointType antMost; + found = + clitk::FindExtremaPointInAGivenDirection(slices[i], + GetBackgroundValue(), + 1, true, LRMost, + distance_max_from_center_point, + antMost); + // Only add point if found + if (found) { + // ------- Convert 2D to 3D points -------- + MaskImageType::PointType p; + clitk::PointsUtils::Convert2DTo3D(LRMost, input, i, p); + LR.push_back(p); + clitk::PointsUtils::Convert2DTo3D(antMost, input, i, p); + Ant.push_back(p); + clitk::PointsUtils::Convert2DTo3D(postMost, input, i, p); + Post.push_back(p); + } + } +} +//-------------------------------------------------------------------- #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX