- output = clitk::AutoCrop<ImageType>(output, GetBackgroundValue());
- ////autoCropFilter->GetOutput(); typedef clitk::AutoCropFilter<ImageType> CropFilterType;
- //typename CropFilterType::Pointer cropFilter = CropFilterType::New();
- //cropFilter->SetInput(output);
- //cropFilter->Update();
- //output = cropFilter->GetOutput();
-
- this->template StopCurrentStep<TImageType>(output);
-
- // Step 2: LR limits from lung (need separate lung ?)
- StartNewStep("Left/Right limits with lungs");
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<TImageType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInput(output);
- relPosFilter->SetInputObject(lung);
- relPosFilter->SetOrientationType(RelPosFilterType::LeftTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
-
- relPosFilter->SetInput(output);
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInputObject(lung);
- relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
- this->template StopCurrentStep<TImageType>(output);
-
- // Step 3: AP limits from bones
- StartNewStep("Ant/Post limits with bones");
- relPosFilter->SetCurrentStepNumber(0);
- relPosFilter->ResetPipeline();// = RelPosFilterType::New();
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInput(output);
- relPosFilter->SetInputObject(bones);
- relPosFilter->SetOrientationType(RelPosFilterType::AntTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
- relPosFilter->Update();
-
- relPosFilter->SetInput(relPosFilter->GetOutput());
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInputObject(bones);
- relPosFilter->SetOrientationType(RelPosFilterType::PostTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
- this->template StopCurrentStep<TImageType>(output);
-
- // Get CCL
- output = clitk::Labelize<TImageType>(output, GetBackgroundValue(), true, 100);
- // output = RemoveLabels<TImageType>(output, BG, param->GetLabelsToRemove());
- output = clitk::KeepLabels<TImageType>(output, GetBackgroundValue(),
- GetForegroundValue(), 1, 1, 0);
-
- output = clitk::AutoCrop<ImageType>(output, GetBackgroundValue());
- // cropFilter = CropFilterType::New();
- //cropFilter->SetInput(output);
- //cropFilter->Update();
- //output = cropFilter->GetOutput();
-
- // Final Step -> set output
- this->SetNthOutput(0, output);
+ // Auto crop to gain support area
+ output = clitk::AutoCrop<MaskImageType>(output, this->GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step : LR limits from lung (need separate lung ?)
+ // Get separate lung images to get only the right and left lung
+ // (because RelativePositionPropImageFilter only consider fg=1);
+ // (label must be '1' because right is greater than left). (WE DO
+ // NOT NEED TO SEPARATE ? )
+ this->StartNewStep("[Mediastinum] Left/Right limits with lungs");
+
+ // The following cannot be "inplace" because mask is the same than input ...
+ MaskImagePointer right_lung =
+ clitk::SetBackground<MaskImageType, MaskImageType>(lung, lung, 2, 0, false);
+ MaskImagePointer left_lung =
+ clitk::SetBackground<MaskImageType, MaskImageType>(lung, lung, 1, 0, false);
+ left_lung = clitk::SetBackground<MaskImageType, MaskImageType>(left_lung, left_lung, 2, 1, false);
+ right_lung = clitk::ResizeImageLike<MaskImageType>(right_lung, output, this->GetBackgroundValue());
+ left_lung = clitk::ResizeImageLike<MaskImageType>(left_lung, output, this->GetBackgroundValue());
+ this->GetAFDB()->template SetImage<MaskImageType>("RightLung", "seg/RightLung.mha",
+ right_lung, true);
+ this->GetAFDB()->template SetImage<MaskImageType>("LeftLung", "seg/LeftLung.mha",
+ left_lung, true);
+ this->GetAFDB()->Write();
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step : AP limits from bones
+ // Separate the bones in the ant-post middle
+ MaskImagePointer bones_ant;
+ MaskImagePointer bones_post;
+ MaskImagePointType middle_AntPost_position;
+ if (GetUseBones()) {
+ this->StartNewStep("[Mediastinum] Ant/Post limits with bones");
+
+ // To define ant and post part of the bones with a single horizontal line
+ MaskImageIndexType index_bones_middle;
+
+ // Method1: cut in the middle (not optimal)
+ /*
+ middle_AntPost_position[0] = middle_AntPost_position[2] = 0;
+ middle_AntPost_position[1] = bones->GetOrigin()[1]+
+ (bones->GetLargestPossibleRegion().GetSize()[1]*bones->GetSpacing()[1])/2.0;
+ DD(middle_AntPost_position);
+ bones->TransformPhysicalPointToIndex(middle_AntPost_position, index_bones_middle);
+ */
+
+ // Method2: Use VertebralBody, take most ant point
+ MaskImagePointer VertebralBody = this->GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
+ FindExtremaPointInAGivenDirection<MaskImageType>(VertebralBody, this->GetBackgroundValue(),
+ 1, true, middle_AntPost_position);
+ bones->TransformPhysicalPointToIndex(middle_AntPost_position, index_bones_middle);
+
+ // Split bone image first into two parts (ant and post), and crop
+ // lateraly to get vertebral
+ typedef itk::RegionOfInterestImageFilter<MaskImageType, MaskImageType> ROIFilterType;
+ // typedef itk::ExtractImageFilter<MaskImageType, MaskImageType> ROIFilterType;
+ typename ROIFilterType::Pointer roiFilter = ROIFilterType::New();
+ MaskImageRegionType region = bones->GetLargestPossibleRegion();
+ MaskImageSizeType size = region.GetSize();
+ MaskImageIndexType index = region.GetIndex();
+ // ANT part
+ // crop LR to keep 1/4 center part
+ // index[0] = size[0]/4+size[0]/8;
+ //size[0] = size[0]/4;
+ // crop AP to keep first (ant) part
+ size[1] = index_bones_middle[1]; //size[1]/2.0;
+ region.SetSize(size);
+ region.SetIndex(index);
+ roiFilter->SetInput(bones);
+ roiFilter->SetRegionOfInterest(region);
+ roiFilter->ReleaseDataFlagOff();
+ roiFilter->Update();
+ bones_ant = roiFilter->GetOutput();
+ // writeImage<MaskImageType>(bones_ant, "b_ant.mhd");
+ // POST part
+ roiFilter = ROIFilterType::New();
+ index[1] = bones->GetLargestPossibleRegion().GetIndex()[1] + size[1]-1;
+ size[1] = bones->GetLargestPossibleRegion().GetSize()[1] - size[1];
+ region.SetIndex(index);
+ region.SetSize(size);
+ roiFilter->SetInput(bones);
+ roiFilter->SetRegionOfInterest(region);
+ roiFilter->ReleaseDataFlagOff();
+ roiFilter->Update();
+ bones_post = roiFilter->GetOutput();
+ // writeImage<MaskImageType>(bones_post, "b_post.mhd");
+
+ // Now, insert this image in the AFDB ==> (needed because used in the RelativePosition config file)
+ this->GetAFDB()->template SetImage<MaskImageType>("Bones_Post", "seg/Bones_Post.mha",
+ bones_post, true);
+ this->GetAFDB()->template SetImage<MaskImageType>("Bones_Ant", "seg/Bones_Ant.mha",
+ bones_ant, true);
+ this->GetAFDB()->Write();
+
+ this->template StopCurrentStep<MaskImageType>(output);
+ }
+
+ //--------------------------------------------------------------------
+ // Remove VertebralBody part
+ this->StartNewStep("[Mediastinum] Remove VertebralBody");
+ MaskImagePointer VertebralBody = this->GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
+ clitk::AndNot<MaskImageType>(output, VertebralBody, this->GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Generic RelativePosition processes
+ output = this->ApplyRelativePositionList("Mediastinum", output);
+
+ //--------------------------------------------------------------------
+ // Step : SI limits It is better to do this limit *AFTER* the
+ // RelativePosition to avoid some issue due to superior boundaries.
+ this->StartNewStep("[Mediastinum] Keep inferior to CricoidCartilag");
+ // load Cricoid, get centroid, cut above (or below), lower bound
+ MaskImagePointer CricoidCartilag = this->GetAFDB()->template GetImage <MaskImageType>("CricoidCartilag");
+ MaskImagePointType p;
+ p[0] = p[1] = p[2] = 0.0; // to avoid warning
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(CricoidCartilag,
+ this->GetBackgroundValue(), 2, true, p);
+ output = clitk::CropImageRemoveGreaterThan<MaskImageType>(output, 2, p[2], true, this->GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step: Get CCL
+ this->StartNewStep("[Mediastinum] Keep main connected component");
+ output = clitk::Labelize<MaskImageType>(output, this->GetBackgroundValue(), false, 500);
+ // output = RemoveLabels<MaskImageType>(output, BG, param->GetLabelsToRemove());
+ output = clitk::KeepLabels<MaskImageType>(output, this->GetBackgroundValue(),
+ this->GetForegroundValue(), 1, 1, 0);
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step: Remove post part from VertebralBody
+ this->StartNewStep("[Mediastinum] Remove post part according to VertebralBody");
+ RemovePostPartOfVertebralBody();
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step: Slice by Slice CCL
+ this->StartNewStep("[Mediastinum] Slice by Slice keep only one component");
+ typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
+ // typename ExtractSliceFilterType::Pointer
+ ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
+ extractSliceFilter->SetInput(output);
+ extractSliceFilter->SetDirection(2);
+ extractSliceFilter->Update();
+ typedef typename ExtractSliceFilterType::SliceType SliceType;
+ std::vector<typename SliceType::Pointer> mSlices;
+ extractSliceFilter->GetOutputSlices(mSlices);
+ for(unsigned int i=0; i<mSlices.size(); i++) {
+ mSlices[i] = Labelize<SliceType>(mSlices[i], 0, true, 100);
+ mSlices[i] = KeepLabels<SliceType>(mSlices[i], 0, 1, 1, 1, true);
+ }
+ typedef itk::JoinSeriesImageFilter<SliceType, MaskImageType> JoinSeriesFilterType;
+ typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
+ joinFilter->SetOrigin(output->GetOrigin()[2]);
+ joinFilter->SetSpacing(output->GetSpacing()[2]);
+ for(unsigned int i=0; i<mSlices.size(); i++) {
+ joinFilter->PushBackInput(mSlices[i]);
+ }
+ joinFilter->Update();
+ output = joinFilter->GetOutput();
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step 10 : AutoCrop
+ this->StartNewStep("[Mediastinum] AutoCrop");
+ output = clitk::AutoCrop<MaskImageType>(output, this->GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ // End, set the real size
+ this->GetOutput(0)->SetRegions(output->GetLargestPossibleRegion());
+ this->GetOutput(0)->SetLargestPossibleRegion(output->GetLargestPossibleRegion());
+ this->GetOutput(0)->SetRequestedRegion(output->GetLargestPossibleRegion());
+ this->GetOutput(0)->SetBufferedRegion(output->GetLargestPossibleRegion());