Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
- ======================================================================-====*/
+ ===========================================================================**/
#ifndef CLITKEXTRACTMEDIASTINUMFILTER_TXX
#define CLITKEXTRACTMEDIASTINUMFILTER_TXX
#include "clitkCommon.h"
#include "clitkExtractMediastinumFilter.h"
#include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
+#include "clitkSliceBySliceRelativePositionFilter.h"
#include "clitkSegmentationUtils.h"
#include "clitkExtractAirwaysTreeInfoFilter.h"
#include "clitkCropLikeImageFilter.h"
#include "itkLabelImageToStatisticsLabelMapFilter.h"
#include "itkRegionOfInterestImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
+#include "itkScalarImageKmeansImageFilter.h"
// itk ENST
#include "RelativePositionPropImageFilter.h"
ExtractMediastinumFilter():
clitk::FilterBase(),
clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
- itk::ImageToImageFilter<ImageType, ImageType>()
+ itk::ImageToImageFilter<ImageType, MaskImageType>()
{
- this->SetNumberOfRequiredInputs(4);
+ this->SetNumberOfRequiredInputs(1);
SetBackgroundValuePatient(0);
SetBackgroundValueLung(0);
SetForegroundValue(1);
SetIntermediateSpacing(6);
- SetFuzzyThreshold1(0.4);
+ SetFuzzyThreshold1(0.5);
SetFuzzyThreshold2(0.6);
- SetFuzzyThreshold3(0.2);
+ SetFuzzyThreshold3(0.05);
+
+ SetOutputMediastinumFilename("mediastinum.mhd");
+
+ UseBonesOff();
}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractMediastinumFilter<ImageType>::
-SetInputPatientLabelImage(const ImageType * image, ImagePixelType bg)
+SetInputPatientLabelImage(const MaskImageType * image, MaskImagePixelType bg)
{
- this->SetNthInput(0, const_cast<ImageType *>(image));
+ this->SetNthInput(0, const_cast<MaskImageType *>(image));
m_BackgroundValuePatient = bg;
}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractMediastinumFilter<ImageType>::
-SetInputLungLabelImage(const ImageType * image, ImagePixelType bg,
- ImagePixelType fgLeft, ImagePixelType fgRight)
+SetInputLungLabelImage(const MaskImageType * image, MaskImagePixelType bg,
+ MaskImagePixelType fgLeft, MaskImagePixelType fgRight)
{
- this->SetNthInput(1, const_cast<ImageType *>(image));
+ this->SetNthInput(1, const_cast<MaskImageType *>(image));
m_BackgroundValueLung = bg;
m_ForegroundValueLeftLung = fgLeft;
m_ForegroundValueRightLung = fgRight;
template <class ImageType>
void
clitk::ExtractMediastinumFilter<ImageType>::
-SetInputBonesLabelImage(const ImageType * image, ImagePixelType bg)
+SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg)
{
- this->SetNthInput(2, const_cast<ImageType *>(image));
+ this->SetNthInput(2, const_cast<MaskImageType *>(image));
m_BackgroundValueBones = bg;
}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractMediastinumFilter<ImageType>::
-SetInputTracheaLabelImage(const ImageType * image, ImagePixelType bg)
+SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg)
{
- this->SetNthInput(3, const_cast<ImageType *>(image));
+ this->SetNthInput(3, const_cast<MaskImageType *>(image));
m_BackgroundValueTrachea = bg;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template <class ImageType>
-template<class ArgsInfoType>
void
clitk::ExtractMediastinumFilter<ImageType>::
-SetArgsInfo(ArgsInfoType mArgsInfo)
+GenerateInputRequestedRegion()
{
- SetVerboseOption_GGO(mArgsInfo);
- SetVerboseStep_GGO(mArgsInfo);
- SetWriteStep_GGO(mArgsInfo);
- SetVerboseWarningOff_GGO(mArgsInfo);
-
- SetBackgroundValuePatient_GGO(mArgsInfo);
- SetBackgroundValueLung_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);
+ // DD("GenerateInputRequestedRegion");
+ // Do not call default
+ // Superclass::GenerateInputRequestedRegion();
+ // DD("End GenerateInputRequestedRegion");
}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::ExtractMediastinumFilter<ImageType>::
-GenerateOutputInformation() {
- ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
- ImagePointer outputImage = this->GetOutput(0);
- outputImage->SetRegions(outputImage->GetLargestPossibleRegion());
-}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractMediastinumFilter<ImageType>::
-GenerateInputRequestedRegion()
+SetInput(const ImageType * image)
{
- // Call default
- Superclass::GenerateInputRequestedRegion();
-
- // 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());
+ this->SetNthInput(0, const_cast<ImageType *>(image));
}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractMediastinumFilter<ImageType>::
-GenerateData()
-{
+GenerateOutputInformation() {
+ // Do not call default
+ // Superclass::GenerateOutputInformation();
+
+ //--------------------------------------------------------------------
// Get input pointers
- 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");
+ clitk::PrintMemory(GetVerboseMemoryFlag(), "Initial memory"); // OK
+ LoadAFDB();
+ ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
+ MaskImagePointer patient = GetAFDB()->template GetImage <MaskImageType>("Patient");
+ MaskImagePointer lung = GetAFDB()->template GetImage <MaskImageType>("Lungs");
+ MaskImagePointer bones;
+ if (GetUseBones()) {
+ bones = GetAFDB()->template GetImage <MaskImageType>("Bones");
+ }
+ MaskImagePointer trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
- // Get output pointer
- ImagePointer output;
-
- // Step 0: Crop support (patient) to lung extend in RL
+ clitk::PrintMemory(GetVerboseMemoryFlag(), "After read patient, lung");
+
+ //--------------------------------------------------------------------
+ // Step 1: Crop support (patient) to lung extend in RL
StartNewStep("Crop support like lungs along LR");
- typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
+ typedef clitk::CropLikeImageFilter<MaskImageType> 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;
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step 2: Crop support (previous) to bones extend in AP
+ if (GetUseBones()) {
+ 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<MaskImageType>(output);
+ }
+
+ //--------------------------------------------------------------------
+ // Step 3: patient minus lungs, minus bones, minus trachea
+ StartNewStep("Patient contours minus lungs, trachea [and bones]");
+ typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
boolFilter->InPlaceOn();
boolFilter->SetInput1(output);
boolFilter->SetInput2(lung);
boolFilter->SetOperationType(BoolFilterType::AndNot);
boolFilter->Update();
+ if (GetUseBones()) {
+ boolFilter->SetInput1(boolFilter->GetOutput());
+ boolFilter->SetInput2(bones);
+ boolFilter->SetOperationType(BoolFilterType::AndNot);
+ boolFilter->Update();
+ }
boolFilter->SetInput1(boolFilter->GetOutput());
- boolFilter->SetInput2(bones);
+ boolFilter->SetInput2(trachea);
boolFilter->SetOperationType(BoolFilterType::AndNot);
boolFilter->Update();
output = boolFilter->GetOutput();
// Auto crop to gain support area
- output = clitk::AutoCrop<ImageType>(output, GetBackgroundValue());
- this->template StopCurrentStep<ImageType>(output);
-
- // Step 2: LR limits from lung (need separate lung ?)
+ output = clitk::AutoCrop<MaskImageType>(output, GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step 4: 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 ? )
StartNewStep("Left/Right limits with lungs");
-
- /*
- // 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;
+
+ // 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);
+ right_lung = clitk::ResizeImageLike<MaskImageType>(right_lung, output, GetBackgroundValue());
+ left_lung = clitk::ResizeImageLike<MaskImageType>(left_lung, output, GetBackgroundValue());
+ // writeImage<MaskImageType>(right_lung, "right.mhd");
+ // writeImage<MaskImageType>(left_lung, "left.mhd");
+
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
relPosFilter->SetInput(output);
- //relPosFilter->SetInputObject(left_lung);
- relPosFilter->SetInputObject(lung);
- relPosFilter->SetOrientationType(RelPosFilterType::LeftTo); // warning left lung is at right ;)
+ relPosFilter->SetInputObject(left_lung);
+ // relPosFilter->SetInputObject(lung);
+ relPosFilter->AddOrientationType(RelPosFilterType::AtRightTo); // warning left lung is at right ;)
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
relPosFilter->Update();
output = relPosFilter->GetOutput();
- // writeImage<ImageType>(right_lung, "step4-left.mhd");
+ //writeImage<MaskImageType>(right_lung, "step4-left.mhd");
+ relPosFilter = RelPosFilterType::New();
relPosFilter->SetInput(output);
relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- //relPosFilter->SetInputObject(right_lung);
- relPosFilter->SetInputObject(lung);
- relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetInput(output);
+ relPosFilter->SetInputObject(right_lung);
+ //relPosFilter->SetInputObject(lung);
+ relPosFilter->AddOrientationType(RelPosFilterType::AtLeftTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
relPosFilter->Update();
output = relPosFilter->GetOutput();
- 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");
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Step 5: 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);
- // 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_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
+ // 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(GetFuzzyThreshold2());
+ 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(GetFuzzyThreshold2());
+ relPosFilter->Update();
+ output = relPosFilter->GetOutput();
+ this->template StopCurrentStep<MaskImageType>(output);
+ }
+
+ //--------------------------------------------------------------------
+ // Step 6: Get CCL
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::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 8: Trial segmentation KMeans
+ if (0) {
+ StartNewStep("K means");
+ // Take input, crop like current mask
+ typedef CropLikeImageFilter<ImageType> CropLikeFilterType;
+ typename CropLikeFilterType::Pointer cropLikeFilter = CropLikeFilterType::New();
+ cropLikeFilter->SetInput(input);
+ cropLikeFilter->SetCropLikeImage(output);
+ cropLikeFilter->Update();
+ ImagePointer working_input = cropLikeFilter->GetOutput();
+ writeImage<ImageType>(working_input, "crop-input.mhd");
+ // Set bG at -1000
+ working_input = clitk::SetBackground<ImageType, MaskImageType>(working_input, output, GetBackgroundValue(), -1000, true);
+ writeImage<ImageType>(working_input, "crop-input2.mhd");
+ // Kmeans
+ typedef itk::ScalarImageKmeansImageFilter<ImageType> KMeansFilterType;
+ typename KMeansFilterType::Pointer kmeansFilter = KMeansFilterType::New();
+ kmeansFilter->SetInput(working_input);
+ // const unsigned int numberOfInitialClasses = 3;
+ // const unsigned int useNonContiguousLabels = 0;
+ kmeansFilter->AddClassWithInitialMean(-1000);
+ kmeansFilter->AddClassWithInitialMean(30);
+ kmeansFilter->AddClassWithInitialMean(-40); // ==> I want this one
+ DD("Go!");
+ kmeansFilter->Update();
+ DD("End");
+ typename KMeansFilterType::ParametersType estimatedMeans = kmeansFilter->GetFinalMeans();
+ const unsigned int numberOfClasses = estimatedMeans.Size();
+ for ( unsigned int i = 0 ; i < numberOfClasses ; ++i ) {
+ std::cout << "cluster[" << i << "] ";
+ std::cout << " estimated mean : " << estimatedMeans[i] << std::endl;
+ }
+ MaskImageType::Pointer kmeans = kmeansFilter->GetOutput();
+ kmeans = clitk::SetBackground<MaskImageType, MaskImageType>(kmeans, kmeans,
+ 1, GetBackgroundValue(), true);
+ writeImage<MaskImageType>(kmeans, "kmeans.mhd");
+ // Get final results, and remove from current mask
+ boolFilter = BoolFilterType::New();
+ boolFilter->InPlaceOn();
+ boolFilter->SetInput1(output);
+ boolFilter->SetInput2(kmeans);
+ boolFilter->SetOperationType(BoolFilterType::And);
+ boolFilter->Update();
+ output = boolFilter->GetOutput();
+ writeImage<MaskImageType>(output, "out-kmean.mhd");
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ // TODO -> FillMASK ?
+ // comment speed ? mask ? 2 class ?
+
+
+ //TODO
+ // Confidence connected ?
+
+ }
+
+ //--------------------------------------------------------------------
+ // Step 8: Lower limits from lung (need separate lung ?)
+ if (0) {
+ // StartNewStep("Trial : minus segmented struct");
+ // MaskImagePointer heart = GetAFDB()->template GetImage <MaskImageType>("heart");
+ // boolFilter = BoolFilterType::New();
+ // boolFilter->InPlaceOn();
+ // boolFilter->SetInput1(output);
+ // boolFilter->SetInput2(heart);
+ // boolFilter->SetOperationType(BoolFilterType::AndNot);
+ // boolFilter->Update();
+ // output = boolFilter->GetOutput(); // not needed because InPlace
+
+ // Not below the heart
+ // relPosFilter = RelPosFilterType::New();
+ // relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ // relPosFilter->VerboseStepFlagOff();
+ // relPosFilter->WriteStepFlagOff();
+ // relPosFilter->SetInput(output);
+ // relPosFilter->SetInputObject(heart);
+ // relPosFilter->SetOrientationType(RelPosFilterType::SupTo);
+ // relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+ // relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold3());
+ // relPosFilter->Update();
+ // output = relPosFilter->GetOutput();
+ }
+
+ //--------------------------------------------------------------------
+ // Step 8: Lower limits from lung (need separate lung ?)
+ if (0) {
+ StartNewStep("Lower limits with lungs");
+ // TODO BOFFF ????
+ relPosFilter = RelPosFilterType::New();
+ relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetInput(output);
+ // relPosFilter->SetInputObject(left_lung);
+ relPosFilter->SetInputObject(lung);
+ relPosFilter->AddOrientationType(RelPosFilterType::SupTo);
+ relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold3());
+ relPosFilter->Update();
+ output = relPosFilter->GetOutput();
+ this->template StopCurrentStep<MaskImageType>(output);
+ }
+
+ //--------------------------------------------------------------------
+ // Step 10: 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 9: Binarize to remove too high HU
+ // --> warning CCL slice by slice must be done before
+ if (0) {
+ StartNewStep("Remove hypersignal (bones and injected part");
+ // Crop initial ct like current support
+ typedef CropLikeImageFilter<ImageType> CropLikeFilterType;
+ typename CropLikeFilterType::Pointer cropLikeFilter = CropLikeFilterType::New();
+ cropLikeFilter->SetInput(input);
+ cropLikeFilter->SetCropLikeImage(output);
+ cropLikeFilter->Update();
+ ImagePointer working_input = cropLikeFilter->GetOutput();
+ // writeImage<ImageType>(working_input, "crop-ct.mhd");
+ // Binarize
+ typedef itk::BinaryThresholdImageFilter<ImageType, MaskImageType> InputBinarizeFilterType;
+ typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
+ binarizeFilter->SetInput(working_input);
+ binarizeFilter->SetLowerThreshold(GetLowerThreshold());
+ binarizeFilter->SetUpperThreshold(GetUpperThreshold());
+ binarizeFilter->SetInsideValue(this->GetBackgroundValue()); // opposite
+ binarizeFilter->SetOutsideValue(this->GetForegroundValue()); // opposite
+ binarizeFilter->Update();
+ MaskImagePointer working_bin = binarizeFilter->GetOutput();
+ // writeImage<MaskImageType>(working_bin, "bin.mhd");
+ // Remove from support
+ boolFilter = BoolFilterType::New();
+ boolFilter->InPlaceOn();
+ boolFilter->SetInput1(output);
+ boolFilter->SetInput2(working_bin);
+ boolFilter->SetOperationType(BoolFilterType::AndNot);
+ boolFilter->Update();
+ output = boolFilter->GetOutput();
+ StopCurrentStep<MaskImageType>(output);
+ }
+
+ //--------------------------------------------------------------------
+ // Step 10 : AutoCrop
+ StartNewStep("AutoCrop");
+ output = clitk::AutoCrop<MaskImageType>(output, GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ // Bones ? pb with RAM ? FillHoles ?
+
+ // how to do with post part ? spine /lung ?
+ // POST the spine (should be separated from the rest)
+ /// DO THAT ---->>
+ // histo Y on the whole bones_post (3D) -> result is the Y center on the spine (?)
+ // by slice on bones_post
+ // find the most ant point in the center
+ // from this point go to post until out of bones.
+ //
+
+
+ // 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());
+}
+//--------------------------------------------------------------------
- output = clitk::AutoCrop<ImageType>(output, GetBackgroundValue());
- // roiFilter = ROIFilterType::New();
- //roiFilter->SetInput(output);
- //roiFilter->Update();
- //output = roiFilter->GetOutput();
- // Final Step -> set output
- this->SetNthOutput(0, output);
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractMediastinumFilter<ImageType>::
+GenerateData()
+{
+ this->GraftOutput(output);
+ // Store image filenames into AFDB
+ GetAFDB()->SetImageFilename("Mediastinum", this->GetOutputMediastinumFilename());
+ WriteAFDB();
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff