- // cropFilter->ResetPipeline();// = CropFilterType::New();
- cropFilter = CropFilterType::New();
- ImageIndexType index = region.GetIndex();
- index[1] = bones->GetLargestPossibleRegion().GetIndex()[1] + size[1]-1;
- size[1] = bones->GetLargestPossibleRegion().GetSize()[1] - size[1];
- DD(size);
- region.SetIndex(index);
- region.SetSize(size);
- cropFilter->SetInput(bones);
- // cropFilter->SetExtractionRegion(region);
- cropFilter->SetRegionOfInterest(region);
- cropFilter->ReleaseDataFlagOff();
- cropFilter->Update();
- bones_post = cropFilter->GetOutput();
- writeImage<ImageType>(bones_post, "b_post.mhd");
-
- // Go !
- relPosFilter->SetCurrentStepNumber(0);
- relPosFilter->ResetPipeline();// = RelPosFilterType::New();
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInput(output);
- relPosFilter->SetInputObject(bones_post);
- relPosFilter->SetOrientationType(RelPosFilterType::AntTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
- writeImage<ImageType>(output, "post.mhd");
-
- relPosFilter->SetInput(relPosFilter->GetOutput());
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInput(output);
- relPosFilter->SetInputObject(bones_ant);
- relPosFilter->SetOrientationType(RelPosFilterType::PostTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
- this->template StopCurrentStep<ImageType>(output);
- // Get CCL
- output = clitk::Labelize<ImageType>(output, GetBackgroundValue(), true, 100);
- // output = RemoveLabels<ImageType>(output, BG, param->GetLabelsToRemove());
- output = clitk::KeepLabels<ImageType>(output, GetBackgroundValue(),
- GetForegroundValue(), 1, 1, 0);
-
-
- // Step : Lower limits from lung (need separate lung ?)
- StartNewStep("Lower limits with lungs");
- relPosFilter = RelPosFilterType::New();
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetInput(output);
- DD(output->GetLargestPossibleRegion().GetIndex());
- // relPosFilter->SetInputObject(left_lung);
- relPosFilter->SetInputObject(lung);
- relPosFilter->SetOrientationType(RelPosFilterType::SupTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold3());
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
- DD(output->GetLargestPossibleRegion());
-
- 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);
+ // 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
+ this->GetAFDB()->template SetImage<MaskImageType>("Bones_Post", "seg/Bones_Post.mhd",
+ bones_post, true);
+ this->GetAFDB()->template SetImage<MaskImageType>("Bones_Ant", "seg/Bones_Ant.mhd",
+ 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());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractMediastinumFilter<ImageType>::
+GenerateData()
+{
+ this->GraftOutput(output);
+ // Store image filenames into AFDB
+ this->GetAFDB()->SetImageFilename("Mediastinum", this->GetOutputMediastinumFilename());
+ this->WriteAFDB();