template <class ImageType>
clitk::ExtractMediastinumFilter<ImageType>::
ExtractMediastinumFilter():
- clitk::FilterBase(),
- clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
- itk::ImageToImageFilter<ImageType, MaskImageType>()
+ clitk::StructuresExtractionFilter<ImageType>()
{
this->SetNumberOfRequiredInputs(1);
SetBackgroundValuePatient(0);
SetBackgroundValueBones(0);
SetForegroundValueLeftLung(1);
SetForegroundValueRightLung(2);
- SetBackgroundValue(0);
- SetForegroundValue(1);
- SetIntermediateSpacing(6);
- SetFuzzyThreshold("LR_lungs", 0.3);
- SetFuzzyThreshold("bones", 0.6);
- SetFuzzyThreshold("inf_lungs", 0.05);
SetDistanceMaxToAnteriorPartOfTheVertebralBody(10);
- SetOutputMediastinumFilename("mediastinum.mhd");
+ SetOutputMediastinumFilename("mediastinum.mha");
UseBonesOff();
}
//--------------------------------------------------------------------
// Superclass::GenerateInputRequestedRegion();
// DD("End GenerateInputRequestedRegion");
}
-
//--------------------------------------------------------------------
//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
template <class ImageType>
void
//--------------------------------------------------------------------
// Get input pointers
- LoadAFDB();
+ this->LoadAFDB();
ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
MaskImagePointer patient, lung, bones, trachea;
- patient = GetAFDB()->template GetImage <MaskImageType>("Patient");
- lung = GetAFDB()->template GetImage <MaskImageType>("Lungs");
+ patient = this->GetAFDB()->template GetImage <MaskImageType>("Patient");
+ lung = this->GetAFDB()->template GetImage <MaskImageType>("Lungs");
if (GetUseBones()) {
- bones = GetAFDB()->template GetImage <MaskImageType>("Bones");
+ bones = this->GetAFDB()->template GetImage <MaskImageType>("Bones");
}
- trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
-
+ trachea = this->GetAFDB()->template GetImage <MaskImageType>("Trachea");
+
+ //this->VerboseImageSizeFlagOn();
+
//--------------------------------------------------------------------
// Step : Crop support (patient) to lung extend in RL
- StartNewStep("Crop support like lungs along LR");
+ this->StartNewStep("[Mediastinum] Crop support like lungs along LR");
typedef clitk::CropLikeImageFilter<MaskImageType> CropFilterType;
typename CropFilterType::Pointer cropFilter = CropFilterType::New();
cropFilter->SetInput(patient);
//--------------------------------------------------------------------
// Step : Crop support (previous) to bones extend in AP
if (GetUseBones()) {
- StartNewStep("Crop support like bones along AP");
+ this->StartNewStep("[Mediastinum] 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
//--------------------------------------------------------------------
// Step : patient minus lungs, minus bones, minus trachea
- StartNewStep("Patient contours minus lungs, trachea [and bones]");
+ this->StartNewStep("[Mediastinum] Patient contours minus lungs, trachea [and bones]");
typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
boolFilter->InPlaceOn();
output = boolFilter->GetOutput();
// Auto crop to gain support area
- output = clitk::AutoCrop<MaskImageType>(output, GetBackgroundValue());
+ output = clitk::AutoCrop<MaskImageType>(output, this->GetBackgroundValue());
this->template StopCurrentStep<MaskImageType>(output);
//--------------------------------------------------------------------
// (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");
+ this->StartNewStep("[Mediastinum] Left/Right limits with lungs");
// 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->VerboseStepFlagOff();
- relPosFilter->WriteStepFlagOff();
- relPosFilter->SetInput(output);
- relPosFilter->SetInputObject(left_lung);
- relPosFilter->AddOrientationType(RelPosFilterType::AtRightTo); // warning left lung is at right ;)
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("LR_lungs"));
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
-
- relPosFilter = RelPosFilterType::New();
- relPosFilter->SetInput(output);
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->VerboseStepFlagOff();
- relPosFilter->WriteStepFlagOff();
- relPosFilter->SetInput(output);
- relPosFilter->SetInputObject(right_lung);
- relPosFilter->AddOrientationType(RelPosFilterType::AtLeftTo);
- relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
- relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("LR_lungs"));
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
- this->template StopCurrentStep<MaskImageType>(output);
-
- //--------------------------------------------------------------------
- // 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());
+ left_lung = clitk::SetBackground<MaskImageType, MaskImageType>(left_lung, left_lung, 2, 1, false);
+ right_lung = clitk::ResizeImageLike<MaskImageType>(right_lung, output, this->GetBackgroundValue());
+ left_lung = clitk::ResizeImageLike<MaskImageType>(left_lung, output, this->GetBackgroundValue());
+ this->GetAFDB()->template SetImage<MaskImageType>("RightLung", "seg/RightLung.mha",
+ right_lung, true);
+ this->GetAFDB()->template SetImage<MaskImageType>("LeftLung", "seg/LeftLung.mha",
+ left_lung, true);
+ this->GetAFDB()->Write();
this->template StopCurrentStep<MaskImageType>(output);
//--------------------------------------------------------------------
// Step : AP limits from bones
// Separate the bones in the ant-post middle
- MaskImageConstPointer bones_ant;
- MaskImageConstPointer bones_post;
- MaskImagePointType middle_AntPost__position;
+ MaskImagePointer bones_ant;
+ MaskImagePointer bones_post;
+ MaskImagePointType middle_AntPost_position;
+ middle_AntPost_position.Fill(NumericTraits<MaskImagePointType::ValueType>::Zero);
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;
+ this->StartNewStep("[Mediastinum] Ant/Post limits with bones");
+
+ // To define ant and post part of the bones with a single horizontal line
MaskImageIndexType index_bones_middle;
- bones->TransformPhysicalPointToIndex(middle_AntPost__position, index_bones_middle);
+
+ // Method1: cut in the middle (not optimal)
+ /*
+ 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;
+ DD(middle_AntPost_position);
+ bones->TransformPhysicalPointToIndex(middle_AntPost_position, index_bones_middle);
+ */
+ // Method2: Use VertebralBody, take most ant point
+ MaskImagePointer VertebralBody = this->GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
+ FindExtremaPointInAGivenDirection<MaskImageType>(VertebralBody, this->GetBackgroundValue(),
+ 1, true, middle_AntPost_position);
+ bones->TransformPhysicalPointToIndex(middle_AntPost_position, index_bones_middle);
+
// Split bone image first into two parts (ant and post), and crop
// lateraly to get vertebral
typedef itk::RegionOfInterestImageFilter<MaskImageType, MaskImageType> ROIFilterType;
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;
+ // 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);
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");
-
- // 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(GetFuzzyThreshold("bones"));
- 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(GetFuzzyThreshold("bones"));
- relPosFilter->Update();
- output = relPosFilter->GetOutput();
+ // writeImage<MaskImageType>(bones_post, "b_post.mhd");
+
+ // Now, insert this image in the AFDB ==> (needed because used in the RelativePosition config file)
+ this->GetAFDB()->template SetImage<MaskImageType>("Bones_Post", "seg/Bones_Post.mha",
+ bones_post, true);
+ this->GetAFDB()->template SetImage<MaskImageType>("Bones_Ant", "seg/Bones_Ant.mha",
+ bones_ant, true);
+ this->GetAFDB()->Write();
+
this->template StopCurrentStep<MaskImageType>(output);
}
+ //--------------------------------------------------------------------
+ // Remove VertebralBody part
+ this->StartNewStep("[Mediastinum] Remove VertebralBody");
+ MaskImagePointer VertebralBody = this->GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
+ clitk::AndNot<MaskImageType>(output, VertebralBody, this->GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+
+ //--------------------------------------------------------------------
+ // Generic RelativePosition processes
+ output = this->ApplyRelativePositionList("Mediastinum", output);
+
+
+ //--------------------------------------------------------------------
+ // FIXME --> do not put this limits here !
+ /*
+ // Step : SI limits It is better to do this limit *AFTER* the
+ // RelativePosition to avoid some issue due to superior boundaries.
+ this->StartNewStep("[Mediastinum] Keep inferior to CricoidCartilag");
+ // load Cricoid, get centroid, cut above (or below), lower bound
+ MaskImagePointType p;
+ try {
+ MaskImagePointer CricoidCartilag = this->GetAFDB()->template GetImage <MaskImageType>("CricoidCartilag");
+ p[0] = p[1] = p[2] = 0.0; // to avoid warning
+ clitk::FindExtremaPointInAGivenDirection<MaskImageType>(CricoidCartilag,
+ this->GetBackgroundValue(), 2, true, p);
+ } catch (clitk::ExceptionObject e) {
+ //DD("CricoidCartilag image not found, try CricoidCartilagZ");
+ this->GetAFDB()->GetPoint3D("CricoidCartilagPoint", p);
+ }
+ output = clitk::CropImageRemoveGreaterThan<MaskImageType>(output, 2, p[2], true, this->GetBackgroundValue());
+ this->template StopCurrentStep<MaskImageType>(output);
+ */
+
//--------------------------------------------------------------------
// Step: Get CCL
- StartNewStep("Keep main connected component");
- output = clitk::Labelize<MaskImageType>(output, GetBackgroundValue(), false, 500);
+ this->StartNewStep("[Mediastinum] Keep main connected component");
+ output = clitk::Labelize<MaskImageType>(output, this->GetBackgroundValue(), false, 500);
// output = RemoveLabels<MaskImageType>(output, BG, param->GetLabelsToRemove());
- output = clitk::KeepLabels<MaskImageType>(output, GetBackgroundValue(),
- GetForegroundValue(), 1, 1, 0);
+ output = clitk::KeepLabels<MaskImageType>(output, this->GetBackgroundValue(),
+ this->GetForegroundValue(), 1, 1, 0);
this->template StopCurrentStep<MaskImageType>(output);
//--------------------------------------------------------------------
// Step: Remove post part from VertebralBody
- StartNewStep("Remove post part according to VertebralBody");
+ this->StartNewStep("[Mediastinum] Remove post part according to VertebralBody");
RemovePostPartOfVertebralBody();
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: Slice by Slice CCL
- StartNewStep("Slice by Slice keep only one component");
+ this->StartNewStep("[Mediastinum] Slice by Slice keep only one component");
typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
// typename ExtractSliceFilterType::Pointer
ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
//--------------------------------------------------------------------
// Step 10 : AutoCrop
- StartNewStep("AutoCrop");
- output = clitk::AutoCrop<MaskImageType>(output, GetBackgroundValue());
+ this->StartNewStep("[Mediastinum] AutoCrop");
+ output = clitk::AutoCrop<MaskImageType>(output, this->GetBackgroundValue());
this->template StopCurrentStep<MaskImageType>(output);
// End, set the real size
{
this->GraftOutput(output);
// Store image filenames into AFDB
- GetAFDB()->SetImageFilename("Mediastinum", this->GetOutputMediastinumFilename());
- WriteAFDB();
+ this->GetAFDB()->SetImageFilename("Mediastinum", this->GetOutputMediastinumFilename());
+ this->WriteAFDB();
}
//--------------------------------------------------------------------
// Get VertebralBody mask image
MaskImagePointer VertebralBody =
- GetAFDB()->template GetImage <MaskImageType>("VertebralBody");
+ this->GetAFDB()->template GetImage <MaskImageType>("VertebralBody");
// Consider vertebral body slice by slice
std::vector<MaskSlicePointer> vertebralSlices;
for(uint i=0; i<vertebralSlices.size(); i++) {
MaskSlicePointType p;
bool found = clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(vertebralSlices[i],
- GetBackgroundValue(),
+ this->GetBackgroundValue(),
1, true, p);
if (found) {
vertebralAntPositionBySlice[i] = p;
itk::ImageRegionIterator<MaskImageType> it(output, region);
it.GoToBegin();
while (!it.IsAtEnd()) {
- it.Set(GetBackgroundValue());
+ it.Set(this->GetBackgroundValue());
++it;
}
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff