#include "clitkSetBackgroundImageFilter.h"
#include "clitkSegmentationUtils.h"
#include "clitkAutoCropFilter.h"
+#include "clitkFillMaskFilter.h"
// itk
#include "itkBinaryThresholdImageFilter.h"
SetRadius2(s);
SetSampleRate2(0);
AutoCropOn();
+ FillHolesOn();
}
//--------------------------------------------------------------------
SetWriteStep_GGO(mArgsInfo);
SetVerboseWarningOff_GGO(mArgsInfo);
+ SetAFDBFilename_GGO(mArgsInfo);
SetOutputBonesFilename_GGO(mArgsInfo);
SetInitialSmoothing_GGO(mArgsInfo);
SetRadius2_GGO(mArgsInfo);
SetSampleRate2_GGO(mArgsInfo);
SetAutoCrop_GGO(mArgsInfo);
-
- SetAFDBFilename_GGO(mArgsInfo);
+ SetFillHoles_GGO(mArgsInfo);
}
//--------------------------------------------------------------------
output = setBackgroundFilter->GetOutput();
+ //--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ // Fill Bones
+ if (GetFillHoles()) {
+ StartNewStep("Fill Holes");
+ typedef clitk::FillMaskFilter<InternalImageType> FillMaskFilterType;
+ typename FillMaskFilterType::Pointer fillMaskFilter = FillMaskFilterType::New();
+ fillMaskFilter->SetInput(output);
+ fillMaskFilter->AddDirection(2);
+ fillMaskFilter->Update();
+ output = fillMaskFilter->GetOutput();
+ StopCurrentStep<InternalImageType>(output);
+ }
+
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// [Optional]