+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step : superior limits
+ StartNewStep("Keep inferior to CricoidCartilag");
+ // load Cricoid, get centroid, cut above (or below), lower bound
+ MaskImagePointer CricoidCartilag = GetAFDB()->template GetImage <MaskImageType>("CricoidCartilag");
+ MaskImagePointType p;
+ p[0] = p[1] = p[2] = 0.0; // to avoid warning
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(CricoidCartilag, GetBackgroundValue(), 2, true, p);
+ output = clitk::CropImageRemoveGreaterThan<MaskImageType>(output, 2, p[2], true, GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step : AP limits from bones
+ // Separate the bones in the ant-post middle
+ MaskImageConstPointer bones_ant;
+ MaskImageConstPointer bones_post;
+ MaskImagePointType middle_AntPost__position;
+ if (GetUseBones()) {
+ StartNewStep("Ant/Post limits with bones");
+ 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;
+ MaskImageIndexType index_bones_middle;
+ 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");
+
+ // Go !
+ relPosFilter->SetCurrentStepNumber(0);
+ relPosFilter->ResetPipeline();// = RelPosFilterType::New();
+ relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetInput(output);
+ relPosFilter->SetInputObject(bones_post);
+ relPosFilter->AddOrientationType(RelPosFilterType::AntTo);
+ relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("bones"));
+ relPosFilter->Update();
+ output = relPosFilter->GetOutput();
+ // writeImage<MaskImageType>(output, "post.mhd");
+
+ relPosFilter->SetInput(relPosFilter->GetOutput());
+ relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetInput(output);
+ relPosFilter->SetInputObject(bones_ant);
+ relPosFilter->AddOrientationType(RelPosFilterType::PostTo);
+ relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("bones"));
+ relPosFilter->Update();
+ output = relPosFilter->GetOutput();
+ this->template StopCurrentStep<MaskImageType>(output);
+ }
+
+ //--------------------------------------------------------------------
+ // Step: Get CCL
+ StartNewStep("Keep main connected component");
+ output = clitk::Labelize<MaskImageType>(output, GetBackgroundValue(), false, 500);
+ // output = RemoveLabels<MaskImageType>(output, BG, param->GetLabelsToRemove());
+ output = clitk::KeepLabels<MaskImageType>(output, GetBackgroundValue(),
+ GetForegroundValue(), 1, 1, 0);
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step: Remove post part from VertebralBody
+ StartNewStep("Remove post part according to VertebralBody");
+ RemovePostPartOfVertebralBody();
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step: Remove ant part according to Sternum
+ StartNewStep("Remove ant part according to Sternum");
+ MaskImagePointer Sternum = GetAFDB()->template GetImage <MaskImageType>("Sternum");
+ output = clitk::SliceBySliceRelativePosition<MaskImageType>(output, Sternum, 2,
+ GetFuzzyThreshold("ant_sternum"),
+ "PostTo", false, 3, true, false);
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step: Slice by Slice CCL
+ StartNewStep("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
+ StartNewStep("AutoCrop");
+ output = clitk::AutoCrop<MaskImageType>(output, 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());
+}
+//--------------------------------------------------------------------