#include "clitkExtractMediastinumFilter.h"
#include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
#include "clitkSegmentationUtils.h"
-#include "clitkExtractAirwayTreeInfoFilter.h"
+#include "clitkExtractAirwaysTreeInfoFilter.h"
+#include "clitkCropLikeImageFilter.h"
-// itk
+// std
#include <deque>
+
+// itk
#include "itkStatisticsLabelMapFilter.h"
#include "itkLabelImageToStatisticsLabelMapFilter.h"
#include "itkRegionOfInterestImageFilter.h"
clitk::ExtractMediastinumFilter<ImageType>::
ExtractMediastinumFilter():
clitk::FilterBase(),
+ clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
itk::ImageToImageFilter<ImageType, ImageType>()
{
this->SetNumberOfRequiredInputs(4);
SetFuzzyThreshold1_GGO(mArgsInfo);
SetFuzzyThreshold2_GGO(mArgsInfo);
SetFuzzyThreshold3_GGO(mArgsInfo);
+
+ SetAFDBFilename_GGO(mArgsInfo);
}
//--------------------------------------------------------------------
{
// Call default
Superclass::GenerateInputRequestedRegion();
- // Get input pointers
- ImagePointer patient = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
- ImagePointer lung = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
- ImagePointer bones = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(2));
- ImagePointer trachea = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(3));
+
+ // 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());
GenerateData()
{
// Get input pointers
- ImageConstPointer patient = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
- ImageConstPointer lung = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(1));
- ImageConstPointer bones = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(2));
- ImageConstPointer trachea = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(3));
+ 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();
// Step 2: LR limits from lung (need separate lung ?)
StartNewStep("Left/Right limits with lungs");
- /* // WE DO NOT NEED THE FOLLOWING
- // Get separate lung images to get only the right and left lung
- // (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");
+ /*
+ // 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;
relPosFilter->VerboseStepOff();
relPosFilter->WriteStepOff();
relPosFilter->SetInput(output);
- DD(output->GetLargestPossibleRegion().GetIndex());
- // relPosFilter->SetInputObject(left_lung);
+ //relPosFilter->SetInputObject(left_lung);
relPosFilter->SetInputObject(lung);
relPosFilter->SetOrientationType(RelPosFilterType::LeftTo); // warning left lung is at right ;)
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
relPosFilter->Update();
output = relPosFilter->GetOutput();
- DD(output->GetLargestPossibleRegion());
+ // writeImage<ImageType>(right_lung, "step4-left.mhd");
relPosFilter->SetInput(output);
relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
relPosFilter->VerboseStepOff();
relPosFilter->WriteStepOff();
- // relPosFilter->SetInputObject(right_lung);
+ //relPosFilter->SetInputObject(right_lung);
relPosFilter->SetInputObject(lung);
relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
relPosFilter->Update();
output = relPosFilter->GetOutput();
- DD(output->GetLargestPossibleRegion());
this->template StopCurrentStep<ImageType>(output);
// Step 3: AP limits from bones
// Find ant-post coordinate of trachea (assume the carena position is a
// good estimation of the ant-post position of the trachea)
- typedef clitk::ExtractAirwayTreeInfoFilter<ImageType> AirwayFilter;
- typename AirwayFilter::Pointer airwayfilter = AirwayFilter::New();
- airwayfilter->SetVerboseStep(false);
- airwayfilter->SetWriteStep(false);
- airwayfilter->SetInput(trachea);
- airwayfilter->Update();
- DD(airwayfilter->GetFirstTracheaPoint());
- ImagePointType point_trachea = airwayfilter->GetCarinaPoint();
+ ImagePointType carina;
+ LoadAFDB();
+ GetAFDB()->GetPoint3D("Carina", carina);
+ DD(carina);
ImageIndexType index_trachea;
- bones->TransformPhysicalPointToIndex(point_trachea, index_trachea);
- DD(point_trachea);
+ bones->TransformPhysicalPointToIndex(carina, index_trachea);
DD(index_trachea);
// Split bone image first into two parts (ant and post)
- typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
- // typedef itk::ExtractImageFilter<ImageType, ImageType> CropFilterType;
- typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ 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);
- cropFilter->SetInput(bones);
- // cropFilter->SetExtractionRegion(region);
- cropFilter->SetRegionOfInterest(region);
- cropFilter->ReleaseDataFlagOff();
- cropFilter->Update();
- bones_ant = cropFilter->GetOutput();
+ roiFilter->SetInput(bones);
+ // roiFilter->SetExtractionRegion(region);
+ roiFilter->SetRegionOfInterest(region);
+ roiFilter->ReleaseDataFlagOff();
+ roiFilter->Update();
+ bones_ant = roiFilter->GetOutput();
writeImage<ImageType>(bones_ant, "b_ant.mhd");
- // cropFilter->ResetPipeline();// = CropFilterType::New();
- cropFilter = CropFilterType::New();
+ // 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);
- cropFilter->SetInput(bones);
- // cropFilter->SetExtractionRegion(region);
- cropFilter->SetRegionOfInterest(region);
- cropFilter->ReleaseDataFlagOff();
- cropFilter->Update();
- bones_post = cropFilter->GetOutput();
+ 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->Update();
output = relPosFilter->GetOutput();
this->template StopCurrentStep<ImageType>(output);
+
// Get CCL
- output = clitk::Labelize<ImageType>(output, GetBackgroundValue(), true, 100);
+ 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");
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