itk::ImageToImageFilter<ImageType, MaskImageType>()
{
this->SetNumberOfRequiredInputs(1);
-
SetBackgroundValuePatient(0);
SetBackgroundValueLung(0);
SetBackgroundValueBones(0);
SetForegroundValueRightLung(2);
SetBackgroundValue(0);
SetForegroundValue(1);
-
SetIntermediateSpacing(6);
- SetFuzzyThreshold1(0.5);
- SetFuzzyThreshold2(0.6);
- SetFuzzyThreshold3(0.05);
-
- SetOutputMediastinumFilename("mediastinum.mhd");
-
+ SetFuzzyThreshold("LR_lungs", 0.3);
+ SetFuzzyThreshold("bones", 0.6);
+ SetFuzzyThreshold("inf_lungs", 0.05);
+ SetDistanceMaxToAnteriorPartOfTheVertebralBody(10);
+ SetOutputMediastinumFilename("mediastinum.mhd");
UseBonesOff();
}
//--------------------------------------------------------------------
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractMediastinumFilter<ImageType>::
+SetFuzzyThreshold(std::string tag, double value)
+{
+ m_FuzzyThreshold[tag] = value;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+double
+clitk::ExtractMediastinumFilter<ImageType>::
+GetFuzzyThreshold(std::string tag)
+{
+ if (m_FuzzyThreshold.find(tag) == m_FuzzyThreshold.end()) {
+ clitkExceptionMacro("Could not find options "+tag+" in the list of FuzzyThresholds.");
+ return 0.0;
+ }
+
+ return m_FuzzyThreshold[tag];
+}
+//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
template <class ImageType>
//--------------------------------------------------------------------
// 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;
+ MaskImagePointer patient, lung, bones, trachea;
+ patient = GetAFDB()->template GetImage <MaskImageType>("Patient");
+ lung = GetAFDB()->template GetImage <MaskImageType>("Lungs");
if (GetUseBones()) {
bones = GetAFDB()->template GetImage <MaskImageType>("Bones");
}
- MaskImagePointer trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
-
- clitk::PrintMemory(GetVerboseMemoryFlag(), "After read patient, lung");
+ trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
//--------------------------------------------------------------------
- // Step 1: Crop support (patient) to lung extend in RL
+ // Step : Crop support (patient) to lung extend in RL
StartNewStep("Crop support like lungs along LR");
typedef clitk::CropLikeImageFilter<MaskImageType> CropFilterType;
typename CropFilterType::Pointer cropFilter = CropFilterType::New();
cropFilter->Update();
output = cropFilter->GetOutput();
this->template StopCurrentStep<MaskImageType>(output);
-
+
//--------------------------------------------------------------------
- // Step 2: Crop support (previous) to bones extend in AP
+ // Step : Crop support (previous) to bones extend in AP
if (GetUseBones()) {
StartNewStep("Crop support like bones along AP");
cropFilter = CropFilterType::New();
}
//--------------------------------------------------------------------
- // Step 3: patient minus lungs, minus bones, minus trachea
+ // Step : 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();
this->template StopCurrentStep<MaskImageType>(output);
//--------------------------------------------------------------------
- // Step 4: LR limits from lung (need separate lung ?)
+ // Step : 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
relPosFilter->WriteStepFlagOff();
relPosFilter->SetInput(output);
relPosFilter->SetInputObject(left_lung);
- // relPosFilter->SetInputObject(lung);
relPosFilter->AddOrientationType(RelPosFilterType::AtRightTo); // warning left lung is at right ;)
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("LR_lungs"));
relPosFilter->Update();
output = relPosFilter->GetOutput();
- //writeImage<MaskImageType>(right_lung, "step4-left.mhd");
relPosFilter = RelPosFilterType::New();
relPosFilter->SetInput(output);
relPosFilter->WriteStepFlagOff();
relPosFilter->SetInput(output);
relPosFilter->SetInputObject(right_lung);
- //relPosFilter->SetInputObject(lung);
relPosFilter->AddOrientationType(RelPosFilterType::AtLeftTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("LR_lungs"));
relPosFilter->Update();
output = relPosFilter->GetOutput();
this->template StopCurrentStep<MaskImageType>(output);
//--------------------------------------------------------------------
- // Step 5: AP limits from bones
+ // 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;
relPosFilter->SetInputObject(bones_post);
relPosFilter->AddOrientationType(RelPosFilterType::AntTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("bones"));
relPosFilter->Update();
output = relPosFilter->GetOutput();
// writeImage<MaskImageType>(output, "post.mhd");
relPosFilter->SetInputObject(bones_ant);
relPosFilter->AddOrientationType(RelPosFilterType::PostTo);
relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
+ relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("bones"));
relPosFilter->Update();
output = relPosFilter->GetOutput();
this->template StopCurrentStep<MaskImageType>(output);
}
//--------------------------------------------------------------------
- // Step 6: Get CCL
+ // Step: Get CCL
StartNewStep("Keep main connected component");
output = clitk::Labelize<MaskImageType>(output, GetBackgroundValue(), false, 500);
// output = RemoveLabels<MaskImageType>(output, BG, param->GetLabelsToRemove());
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: Remove post part from VertebralBody
+ StartNewStep("Remove post part according to VertebralBody");
+ RemovePostPartOfVertebralBody();
+ this->template StopCurrentStep<MaskImageType>(output);
//--------------------------------------------------------------------
- // 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: 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 10: Slice by Slice CCL
+ // Step: Slice by Slice CCL
StartNewStep("Slice by Slice keep only one component");
typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
// typename ExtractSliceFilterType::Pointer
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());
WriteAFDB();
}
//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::ExtractMediastinumFilter<ImageType>::
+RemovePostPartOfVertebralBody()
+{
+
+ /*
+ Posteriorly, Station 8 abuts the descending aorta and the anterior
+ aspect of the vertebral body until an imaginary horizontal line
+ running 1 cm posterior to the anterior border of the vertebral
+ body (Fig. 3C).
+
+ => We use this definition for all the mediastinum
+
+ Find most Ant point in VertebralBody. Consider the horizontal line
+ which is 'DistanceMaxToAnteriorPartOfTheVertebralBody' away from
+ the most ant point.
+ */
+
+ // Get VertebralBody mask image
+ MaskImagePointer VertebralBody =
+ GetAFDB()->template GetImage <MaskImageType>("VertebralBody");
+
+ // Consider vertebral body slice by slice
+ std::vector<MaskSlicePointer> vertebralSlices;
+ clitk::ExtractSlices<MaskImageType>(VertebralBody, 2, vertebralSlices);
+
+ // For each slice, compute the most anterior point
+ std::map<int, MaskSlicePointType> vertebralAntPositionBySlice;
+ for(uint i=0; i<vertebralSlices.size(); i++) {
+ MaskSlicePointType p;
+ bool found = clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(vertebralSlices[i],
+ GetBackgroundValue(),
+ 1, true, p);
+ if (found) {
+ vertebralAntPositionBySlice[i] = p;
+ }
+ else {
+ // It should not happen ! But sometimes, a contour is missing or
+ // the VertebralBody is not delineated enough inferiorly ... in
+ // those cases, we consider the first found slice.
+ // std::cerr << "No foreground pixels in this VertebralBody slices !?? I try with the previous/next slice" << std::endl;
+ // [ Possible alternative -> consider previous limit ]
+ }
+ }
+
+ // Convert 2D points in slice into 3D points
+ std::vector<MaskImagePointType> vertebralAntPositions;
+ clitk::PointsUtils<MaskImageType>::Convert2DMapTo3DList(vertebralAntPositionBySlice,
+ VertebralBody,
+ vertebralAntPositions);
+
+ // DEBUG : write list of points
+ clitk::WriteListOfLandmarks<MaskImageType>(vertebralAntPositions,
+ "VertebralBodyMostAnteriorPoints.txt");
+
+ // Cut support posteriorly 1cm the most anterior point of the
+ // VertebralBody. Do nothing below and above the VertebralBody. To
+ // do that compute several region, slice by slice and fill.
+ MaskImageRegionType region;
+ MaskImageSizeType size;
+ MaskImageIndexType start;
+ size[2] = 1; // a single slice
+ start[0] = output->GetLargestPossibleRegion().GetIndex()[0];
+ size[0] = output->GetLargestPossibleRegion().GetSize()[0];
+ for(uint i=0; i<vertebralAntPositions.size(); i++) {
+ typedef typename itk::ImageRegionIterator<MaskImageType> IteratorType;
+ IteratorType iter =
+ IteratorType(output, output->GetLargestPossibleRegion());
+ MaskImageIndexType index;
+ // Consider some cm posterior to most anterior positions (usually
+ // 1 cm).
+ vertebralAntPositions[i][1] += GetDistanceMaxToAnteriorPartOfTheVertebralBody();
+ // Get index of this point
+ output->TransformPhysicalPointToIndex(vertebralAntPositions[i], index);
+ // Compute region (a single slice)
+ start[2] = index[2];
+ start[1] = output->GetLargestPossibleRegion().GetIndex()[1]+index[1];
+ size[1] = output->GetLargestPossibleRegion().GetSize()[1]-start[1];
+ region.SetSize(size);
+ region.SetIndex(start);
+ // Fill region
+ if (output->GetLargestPossibleRegion().IsInside(start)) {
+ itk::ImageRegionIterator<MaskImageType> it(output, region);
+ it.GoToBegin();
+ while (!it.IsAtEnd()) {
+ it.Set(GetBackgroundValue());
+ ++it;
+ }
+ }
+ }
+}
+//--------------------------------------------------------------------
+
#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff