SetFuzzyThreshold2(0.6);
SetFuzzyThreshold3(0.05);
- SetDistanceMaxToAnteriorPartOfTheSpine(10);
SetOutputMediastinumFilename("mediastinum.mhd");
UseBonesOff();
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-template <class ImageType>
-template<class ArgsInfoType>
-void
-clitk::ExtractMediastinumFilter<ImageType>::
-SetArgsInfo(ArgsInfoType mArgsInfo)
-{
- SetVerboseOption_GGO(mArgsInfo);
- SetVerboseStep_GGO(mArgsInfo);
- SetWriteStep_GGO(mArgsInfo);
- SetVerboseWarningOff_GGO(mArgsInfo);
-
- SetIntermediateSpacing_GGO(mArgsInfo);
- SetFuzzyThreshold1_GGO(mArgsInfo);
- SetFuzzyThreshold2_GGO(mArgsInfo);
- SetFuzzyThreshold3_GGO(mArgsInfo);
-
- SetAFDBFilename_GGO(mArgsInfo);
- SetDistanceMaxToAnteriorPartOfTheSpine_GGO(mArgsInfo);
- SetUseBones_GGO(mArgsInfo);
-
- SetLowerThreshold_GGO(mArgsInfo);
- SetUpperThreshold_GGO(mArgsInfo);
-}
-//--------------------------------------------------------------------
-
-
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractMediastinumFilter<ImageType>::
GenerateInputRequestedRegion()
{
- //DD("GenerateInputRequestedRegion");
+ // DD("GenerateInputRequestedRegion");
// Do not call default
- // Superclass::GenerateInputRequestedRegion();
- // DD("End GenerateInputRequestedRegion");
+ // Superclass::GenerateInputRequestedRegion();
+ // DD("End GenerateInputRequestedRegion");
}
//--------------------------------------------------------------------
void
clitk::ExtractMediastinumFilter<ImageType>::
GenerateOutputInformation() {
- // DD("GenerateOutputInformation");
// Do not call default
- // Superclass::GenerateOutputInformation();
+ // Superclass::GenerateOutputInformation();
//--------------------------------------------------------------------
// Get input pointers
+ 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 = GetAFDB()->template GetImage <MaskImageType>("bones");
- MaskImagePointer trachea = GetAFDB()->template GetImage <MaskImageType>("trachea");
+ 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");
+ clitk::PrintMemory(GetVerboseMemoryFlag(), "After read patient, lung");
+
//--------------------------------------------------------------------
// Step 1: Crop support (patient) to lung extend in RL
StartNewStep("Crop support like lungs along LR");
cropFilter->Update();
output = cropFilter->GetOutput();
this->template StopCurrentStep<MaskImageType>(output);
-
+
//--------------------------------------------------------------------
// Step 2: Crop support (previous) to bones extend in AP
if (GetUseBones()) {
//--------------------------------------------------------------------
// Step 3: patient minus lungs, minus bones, minus trachea
- StartNewStep("Patient contours minus lungs, bones, trachea");
+ StartNewStep("Patient contours minus lungs, trachea [and bones]");
typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
boolFilter->InPlaceOn();
// (label must be '1' because right is greater than left). (WE DO
// NOT NEED TO SEPARATE ? )
StartNewStep("Left/Right limits with lungs");
- /*
- ImagePointer right_lung = clitk::SetBackground<MaskImageType, MaskImageType>(lung, lung, 2, 0);
- ImagePointer left_lung = clitk::SetBackground<MaskImageType, MaskImageType>(lung, lung, 1, 0);
- writeImage<MaskImageType>(right_lung, "right.mhd");
- writeImage<MaskImageType>(left_lung, "left.mhd");
- */
+
+ // 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::LeftTo); // warning left lung is at right ;)
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
relPosFilter->Update();
output = relPosFilter->GetOutput();
//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::RightTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
relPosFilter->Update();
roiFilter->ReleaseDataFlagOff();
roiFilter->Update();
bones_ant = roiFilter->GetOutput();
- writeImage<MaskImageType>(bones_ant, "b_ant.mhd");
+ // writeImage<MaskImageType>(bones_ant, "b_ant.mhd");
// POST part
roiFilter = ROIFilterType::New();
index[1] = bones->GetLargestPossibleRegion().GetIndex()[1] + size[1]-1;
roiFilter->ReleaseDataFlagOff();
roiFilter->Update();
bones_post = roiFilter->GetOutput();
- writeImage<MaskImageType>(bones_post, "b_post.mhd");
+ // writeImage<MaskImageType>(bones_post, "b_post.mhd");
// Go !
relPosFilter->SetCurrentStepNumber(0);
relPosFilter->ResetPipeline();// = RelPosFilterType::New();
relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
relPosFilter->SetInput(output);
relPosFilter->SetInputObject(bones_post);
- relPosFilter->SetOrientationType(RelPosFilterType::AntTo);
+ relPosFilter->AddOrientationType(RelPosFilterType::AntTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
relPosFilter->Update();
output = relPosFilter->GetOutput();
- writeImage<MaskImageType>(output, "post.mhd");
+ // writeImage<MaskImageType>(output, "post.mhd");
relPosFilter->SetInput(relPosFilter->GetOutput());
relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
relPosFilter->SetInput(output);
relPosFilter->SetInputObject(bones_ant);
- relPosFilter->SetOrientationType(RelPosFilterType::PostTo);
+ relPosFilter->AddOrientationType(RelPosFilterType::PostTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
relPosFilter->Update();
GetForegroundValue(), 1, 1, 0);
this->template StopCurrentStep<MaskImageType>(output);
- //--------------------------------------------------------------------
- // Step 7 : Slice by Slice to optimize posterior part
- // Warning slice does not necesseraly correspond between 'output' and 'bones'
- typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
- typename ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
- typedef typename ExtractSliceFilterType::SliceType SliceType;
- std::vector<typename SliceType::Pointer> mSlices;
- if (GetUseBones()) {
- StartNewStep("Rafine posterior part according to vertebral body");
- extractSliceFilter->SetInput(bones_post);
- extractSliceFilter->SetDirection(2);
- extractSliceFilter->Update();
- std::vector<double> mVertebralAntPositionBySlice;
- extractSliceFilter->GetOutputSlices(mSlices);
- for(unsigned int i=0; i<mSlices.size(); i++) {
- mSlices[i] = Labelize<SliceType>(mSlices[i], 0, true, 10);
- mSlices[i] = KeepLabels<SliceType>(mSlices[i],
- GetBackgroundValue(),
- GetForegroundValue(), 1, 2, true); // keep two first
- // Find most anterior point (start of the vertebral)
- typename itk::ImageRegionIteratorWithIndex<SliceType>
- iter(mSlices[i], mSlices[i]->GetLargestPossibleRegion());
- iter.GoToBegin();
- bool stop = false;
- while (!stop) {
- if (iter.Get() != GetBackgroundValue())
- stop = true; // not foreground because we keep two main label
- ++iter;
- if (iter.IsAtEnd()) stop = true;
- }
- if (!iter.IsAtEnd()) {
- typename SliceType::PointType p;
- mSlices[i]->TransformIndexToPhysicalPoint(iter.GetIndex(),p);
- mVertebralAntPositionBySlice.push_back(p[1]);
- }
- else {
- mVertebralAntPositionBySlice.push_back(bones_post->GetOrigin()[1]+(bones->GetLargestPossibleRegion().GetSize()[1]*bones->GetSpacing()[1]));
- DD(mVertebralAntPositionBySlice.back());
- DD("ERROR ?? NO FG in bones here ?");
- }
- }
-
- // Cut Post position slice by slice
- {
- MaskImageRegionType region;
- MaskImageSizeType size;
- MaskImageIndexType start;
- size[2] = 1;
- start[0] = output->GetLargestPossibleRegion().GetIndex()[0];
- for(unsigned int i=0; i<mSlices.size(); i++) {
- // Compute index
- MaskImagePointType point;
- point[0] = 0;
-
- //TODO 10 mm OPTION
-
- point[1] = mVertebralAntPositionBySlice[i]+GetDistanceMaxToAnteriorPartOfTheSpine();// ADD ONE CM
- point[2] = bones_post->GetOrigin()[2]+(bones_post->GetLargestPossibleRegion().GetIndex()[2]+i)*bones_post->GetSpacing()[2];
- MaskImageIndexType index;
- output->TransformPhysicalPointToIndex(point, index);
- // Compute region
- start[2] = index[2];
- start[1] = output->GetLargestPossibleRegion().GetIndex()[1]+index[1];
- size[0] = output->GetLargestPossibleRegion().GetSize()[0];
- size[1] = output->GetLargestPossibleRegion().GetSize()[1]-start[1];
- region.SetSize(size);
- region.SetIndex(start);
- // Fill Region
- if (output->GetLargestPossibleRegion().IsInside(start)) {
- itk::ImageRegionIteratorWithIndex<MaskImageType> it(output, region);
- it.GoToBegin();
- while (!it.IsAtEnd()) {
- it.Set(GetBackgroundValue());
- ++it;
- }
- }
- }
- }
- this->template StopCurrentStep<MaskImageType>(output);
- }
//--------------------------------------------------------------------
// Step 8: Trial segmentation KMeans
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);
+ 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;
}
MaskImageType::Pointer kmeans = kmeansFilter->GetOutput();
kmeans = clitk::SetBackground<MaskImageType, MaskImageType>(kmeans, kmeans,
- 1, GetBackgroundValue());
+ 1, GetBackgroundValue(), true);
writeImage<MaskImageType>(kmeans, "kmeans.mhd");
// Get final results, and remove from current mask
boolFilter = BoolFilterType::New();
// Not below the heart
// relPosFilter = RelPosFilterType::New();
// relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- // relPosFilter->VerboseStepOff();
- // relPosFilter->WriteStepOff();
+ // relPosFilter->VerboseStepFlagOff();
+ // relPosFilter->WriteStepFlagOff();
// relPosFilter->SetInput(output);
// relPosFilter->SetInputObject(heart);
// relPosFilter->SetOrientationType(RelPosFilterType::SupTo);
// TODO BOFFF ????
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::SupTo);
+ relPosFilter->AddOrientationType(RelPosFilterType::SupTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold3());
relPosFilter->Update();
StartNewStep("Slice by Slice keep only one component");
typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
// typename ExtractSliceFilterType::Pointer
- extractSliceFilter = ExtractSliceFilterType::New();
+ ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
extractSliceFilter->SetInput(output);
extractSliceFilter->SetDirection(2);
extractSliceFilter->Update();
typedef typename ExtractSliceFilterType::SliceType SliceType;
- // std::vector<typename SliceType::Pointer>
- mSlices.clear();
+ 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);
//--------------------------------------------------------------------
// Step 9: Binarize to remove too high HU
// --> warning CCL slice by slice must be done before
- 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);
+ 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
clitk::ExtractMediastinumFilter<ImageType>::
GenerateData()
{
- DD("GenerateData");
this->GraftOutput(output);
// Store image filenames into AFDB
- GetAFDB()->SetImageFilename("mediastinum", this->GetOutputMediastinumFilename());
+ GetAFDB()->SetImageFilename("Mediastinum", this->GetOutputMediastinumFilename());
WriteAFDB();
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff