SetForegroundValueLeftLung(1);
SetForegroundValueRightLung(2);
SetDistanceMaxToAnteriorPartOfTheVertebralBody(10);
- SetOutputMediastinumFilename("mediastinum.mhd");
+ SetOutputMediastinumFilename("mediastinum.mha");
UseBonesOff();
}
//--------------------------------------------------------------------
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.mhd",
+ this->GetAFDB()->template SetImage<MaskImageType>("RightLung", "seg/RightLung.mha",
right_lung, true);
- this->GetAFDB()->template SetImage<MaskImageType>("LeftLung", "seg/LeftLung.mhd",
+ this->GetAFDB()->template SetImage<MaskImageType>("LeftLung", "seg/LeftLung.mha",
left_lung, true);
this->GetAFDB()->Write();
this->template StopCurrentStep<MaskImageType>(output);
bones_post = roiFilter->GetOutput();
// writeImage<MaskImageType>(bones_post, "b_post.mhd");
- // Now, insert this image in the AFDB
- this->GetAFDB()->template SetImage<MaskImageType>("Bones_Post", "seg/Bones_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.mhd",
+ this->GetAFDB()->template SetImage<MaskImageType>("Bones_Ant", "seg/Bones_Ant.mha",
bones_ant, true);
- this->GetAFDB()->Write();
+ this->GetAFDB()->Write();
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
- MaskImagePointer CricoidCartilag = this->GetAFDB()->template GetImage <MaskImageType>("CricoidCartilag");
MaskImagePointType p;
- p[0] = p[1] = p[2] = 0.0; // to avoid warning
- clitk::FindExtremaPointInAGivenDirection<MaskImageType>(CricoidCartilag,
- this->GetBackgroundValue(), 2, true, 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