#include "clitkExtractMediastinumFilter.h"
#include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
#include "clitkSegmentationUtils.h"
+#include "clitkExtractAirwaysTreeInfoFilter.h"
+#include "clitkCropLikeImageFilter.h"
-// itk
+// std
#include <deque>
+
+// itk
#include "itkStatisticsLabelMapFilter.h"
#include "itkLabelImageToStatisticsLabelMapFilter.h"
#include "itkRegionOfInterestImageFilter.h"
#include "RelativePositionPropImageFilter.h"
//--------------------------------------------------------------------
-template <class TImageType>
-clitk::ExtractMediastinumFilter<TImageType>::
+template <class ImageType>
+clitk::ExtractMediastinumFilter<ImageType>::
ExtractMediastinumFilter():
clitk::FilterBase(),
- itk::ImageToImageFilter<TImageType, TImageType>()
+ clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+ itk::ImageToImageFilter<ImageType, ImageType>()
{
- this->SetNumberOfRequiredInputs(3);
+ this->SetNumberOfRequiredInputs(4);
SetBackgroundValuePatient(0);
SetBackgroundValueLung(0);
SetForegroundValue(1);
SetIntermediateSpacing(6);
- SetFuzzyThreshold1(0.6);
- SetFuzzyThreshold2(0.7);
+ SetFuzzyThreshold1(0.4);
+ SetFuzzyThreshold2(0.6);
+ SetFuzzyThreshold3(0.2);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
void
-clitk::ExtractMediastinumFilter<TImageType>::
-SetInputPatientLabelImage(const TImageType * image, ImagePixelType bg) {
- this->SetNthInput(0, const_cast<TImageType *>(image));
+clitk::ExtractMediastinumFilter<ImageType>::
+SetInputPatientLabelImage(const ImageType * image, ImagePixelType bg)
+{
+ this->SetNthInput(0, const_cast<ImageType *>(image));
m_BackgroundValuePatient = bg;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
void
-clitk::ExtractMediastinumFilter<TImageType>::
-SetInputLungLabelImage(const TImageType * image, ImagePixelType bg,
- ImagePixelType fgLeft, ImagePixelType fgRight) {
- this->SetNthInput(1, const_cast<TImageType *>(image));
+clitk::ExtractMediastinumFilter<ImageType>::
+SetInputLungLabelImage(const ImageType * image, ImagePixelType bg,
+ ImagePixelType fgLeft, ImagePixelType fgRight)
+{
+ this->SetNthInput(1, const_cast<ImageType *>(image));
m_BackgroundValueLung = bg;
m_ForegroundValueLeftLung = fgLeft;
m_ForegroundValueRightLung = fgRight;
//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
void
-clitk::ExtractMediastinumFilter<TImageType>::
-SetInputBonesLabelImage(const TImageType * image, ImagePixelType bg) {
- this->SetNthInput(2, const_cast<TImageType *>(image));
+clitk::ExtractMediastinumFilter<ImageType>::
+SetInputBonesLabelImage(const ImageType * image, ImagePixelType bg)
+{
+ this->SetNthInput(2, const_cast<ImageType *>(image));
m_BackgroundValueBones = bg;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
+void
+clitk::ExtractMediastinumFilter<ImageType>::
+SetInputTracheaLabelImage(const ImageType * image, ImagePixelType bg)
+{
+ this->SetNthInput(3, const_cast<ImageType *>(image));
+ m_BackgroundValueTrachea = bg;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
template<class ArgsInfoType>
void
-clitk::ExtractMediastinumFilter<TImageType>::
+clitk::ExtractMediastinumFilter<ImageType>::
SetArgsInfo(ArgsInfoType mArgsInfo)
{
SetVerboseOption_GGO(mArgsInfo);
SetBackgroundValuePatient_GGO(mArgsInfo);
SetBackgroundValueLung_GGO(mArgsInfo);
- SetBackgroundValueBones_GGO(mArgsInfo);
+ SetBackgroundValueTrachea_GGO(mArgsInfo);
SetForegroundValueLeftLung_GGO(mArgsInfo);
SetForegroundValueRightLung_GGO(mArgsInfo);
SetIntermediateSpacing_GGO(mArgsInfo);
SetFuzzyThreshold1_GGO(mArgsInfo);
SetFuzzyThreshold2_GGO(mArgsInfo);
+ SetFuzzyThreshold3_GGO(mArgsInfo);
+
+ SetAFDBFilename_GGO(mArgsInfo);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
void
-clitk::ExtractMediastinumFilter<TImageType>::
+clitk::ExtractMediastinumFilter<ImageType>::
GenerateOutputInformation() {
- ImagePointer input = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(0));
+ ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
ImagePointer outputImage = this->GetOutput(0);
outputImage->SetRegions(outputImage->GetLargestPossibleRegion());
}
//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
void
-clitk::ExtractMediastinumFilter<TImageType>::
-GenerateInputRequestedRegion() {
+clitk::ExtractMediastinumFilter<ImageType>::
+GenerateInputRequestedRegion()
+{
// Call default
Superclass::GenerateInputRequestedRegion();
- // Get input pointers
- ImagePointer patient = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(0));
- ImagePointer lung = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(1));
- ImagePointer bones = dynamic_cast<TImageType*>(itk::ProcessObject::GetInput(2));
+
+ // Get input pointers
+ LoadAFDB();
+ ImagePointer patient = GetAFDB()->template GetImage <ImageType>("patient");
+ ImagePointer lung = GetAFDB()->template GetImage <ImageType>("lungs");
+ ImagePointer bones = GetAFDB()->template GetImage <ImageType>("bones");
+ ImagePointer trachea = GetAFDB()->template GetImage <ImageType>("trachea");
patient->SetRequestedRegion(patient->GetLargestPossibleRegion());
lung->SetRequestedRegion(lung->GetLargestPossibleRegion());
bones->SetRequestedRegion(bones->GetLargestPossibleRegion());
+ trachea->SetRequestedRegion(trachea->GetLargestPossibleRegion());
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class TImageType>
+template <class ImageType>
void
-clitk::ExtractMediastinumFilter<TImageType>::
-GenerateData() {
+clitk::ExtractMediastinumFilter<ImageType>::
+GenerateData()
+{
// Get input pointers
- ImageConstPointer patient = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(0));
- ImageConstPointer lung = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(1));
- ImageConstPointer bones = dynamic_cast<const TImageType*>(itk::ProcessObject::GetInput(2));
+ ImagePointer patient = GetAFDB()->template GetImage <ImageType>("patient");
+ ImagePointer lung = GetAFDB()->template GetImage <ImageType>("lungs");
+ ImagePointer bones = GetAFDB()->template GetImage <ImageType>("bones");
+ ImagePointer trachea = GetAFDB()->template GetImage <ImageType>("trachea");
// Get output pointer
ImagePointer output;
+ // Step 0: Crop support (patient) to lung extend in RL
+ StartNewStep("Crop support like lungs along LR");
+ typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(patient);
+ cropFilter->SetCropLikeImage(lung, 0);// Indicate that we only crop in X (Left-Right) axe
+ cropFilter->Update();
+ output = cropFilter->GetOutput();
+ this->template StopCurrentStep<ImageType>(output);
+
+ // Step 0: Crop support (previous) to bones extend in AP
+ StartNewStep("Crop support like bones along AP");
+ cropFilter = CropFilterType::New();
+ cropFilter->SetInput(output);
+ cropFilter->SetCropLikeImage(bones, 1);// Indicate that we only crop in Y (Ant-Post) axe
+ cropFilter->Update();
+ output = cropFilter->GetOutput();
+ this->template StopCurrentStep<ImageType>(output);
+
// Step 1: patient minus lungs, minus bones
StartNewStep("Patient contours minus lungs and minus bones");
typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
boolFilter->InPlaceOn();
- boolFilter->SetInput1(patient);
+ boolFilter->SetInput1(output);
boolFilter->SetInput2(lung);
boolFilter->SetOperationType(BoolFilterType::AndNot);
boolFilter->Update();
boolFilter->Update();
output = boolFilter->GetOutput();
+ // Auto crop to gain support area
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);
+ this->template StopCurrentStep<ImageType>(output);
// Step 2: LR limits from lung (need separate lung ?)
StartNewStep("Left/Right limits with lungs");
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<TImageType> RelPosFilterType;
+
+ /*
+ // WE DO NOT NEED THE FOLLOWING ?
+ // 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).
+ ImagePointer right_lung = clitk::SetBackground<ImageType, ImageType>(lung, lung, 2, 0);
+ ImagePointer left_lung = clitk::SetBackground<ImageType, ImageType>(lung, lung, 1, 0);
+ writeImage<ImageType>(right_lung, "right.mhd");
+ writeImage<ImageType>(left_lung, "left.mhd");
+ */
+
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType> RelPosFilterType;
typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
relPosFilter->VerboseStepOff();
relPosFilter->WriteStepOff();
relPosFilter->SetInput(output);
+ //relPosFilter->SetInputObject(left_lung);
relPosFilter->SetInputObject(lung);
- relPosFilter->SetOrientationType(RelPosFilterType::LeftTo);
+ relPosFilter->SetOrientationType(RelPosFilterType::LeftTo); // warning left lung is at right ;)
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
relPosFilter->Update();
output = relPosFilter->GetOutput();
+ // writeImage<ImageType>(right_lung, "step4-left.mhd");
relPosFilter->SetInput(output);
relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
relPosFilter->VerboseStepOff();
relPosFilter->WriteStepOff();
+ //relPosFilter->SetInputObject(right_lung);
relPosFilter->SetInputObject(lung);
relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
relPosFilter->Update();
output = relPosFilter->GetOutput();
- this->template StopCurrentStep<TImageType>(output);
+ this->template StopCurrentStep<ImageType>(output);
// Step 3: AP limits from bones
StartNewStep("Ant/Post limits with bones");
+ ImageConstPointer bones_ant;
+ ImageConstPointer bones_post;
+
+ // Find ant-post coordinate of trachea (assume the carena position is a
+ // good estimation of the ant-post position of the trachea)
+ ImagePointType carina;
+ LoadAFDB();
+ GetAFDB()->GetPoint3D("Carina", carina);
+ DD(carina);
+ ImageIndexType index_trachea;
+ bones->TransformPhysicalPointToIndex(carina, index_trachea);
+ DD(index_trachea);
+
+ // Split bone image first into two parts (ant and post)
+ typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> ROIFilterType;
+ // typedef itk::ExtractImageFilter<ImageType, ImageType> ROIFilterType;
+ typename ROIFilterType::Pointer roiFilter = ROIFilterType::New();
+ ImageRegionType region = bones->GetLargestPossibleRegion();
+ ImageSizeType size = region.GetSize();
+ DD(size);
+ size[1] = index_trachea[1]; //size[1]/2.0;
+ DD(size);
+ region.SetSize(size);
+ roiFilter->SetInput(bones);
+ // roiFilter->SetExtractionRegion(region);
+ roiFilter->SetRegionOfInterest(region);
+ roiFilter->ReleaseDataFlagOff();
+ roiFilter->Update();
+ bones_ant = roiFilter->GetOutput();
+ writeImage<ImageType>(bones_ant, "b_ant.mhd");
+
+ // roiFilter->ResetPipeline();// = ROIFilterType::New();
+ roiFilter = ROIFilterType::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);
+ roiFilter->SetInput(bones);
+ // roiFilter->SetExtractionRegion(region);
+ roiFilter->SetRegionOfInterest(region);
+ roiFilter->ReleaseDataFlagOff();
+ roiFilter->Update();
+ bones_post = roiFilter->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);
+ 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->SetInputObject(bones);
+ 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<TImageType>(output);
+ this->template StopCurrentStep<ImageType>(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);
+ StartNewStep("Keep main connected component");
+ output = clitk::Labelize<ImageType>(output, GetBackgroundValue(), true, 500);
+ // output = RemoveLabels<ImageType>(output, BG, param->GetLabelsToRemove());
+ output = clitk::KeepLabels<ImageType>(output, GetBackgroundValue(),
+ GetForegroundValue(), 1, 1, 0);
+ this->template StopCurrentStep<ImageType>(output);
+
+ // 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();
+ // roiFilter = ROIFilterType::New();
+ //roiFilter->SetInput(output);
+ //roiFilter->Update();
+ //output = roiFilter->GetOutput();
// Final Step -> set output
this->SetNthOutput(0, output);
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff