Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
- ======================================================================-====*/
+ ===========================================================================**/
#ifndef CLITKEXTRACTMEDIASTINUMFILTER_H
#define CLITKEXTRACTMEDIASTINUMFILTER_H
-#include "clitkFilterBase.h"
+#include "clitkStructuresExtractionFilter.h"
namespace clitk {
//--------------------------------------------------------------------
/*
Try to extract the mediastinum part of a thorax CT.
- Inputs :
- - Patient label image
- - Lungs label image
- - Bones label image
- - Trachea label image
+ Input masks needed :
+ - Patient
+ - Lungs
+ - Bones [Optional]
+ - Trachea
+ - VertebralBody
*/
//--------------------------------------------------------------------
template <class TImageType>
class ITK_EXPORT ExtractMediastinumFilter:
- public clitk::FilterBase,
- public itk::ImageToImageFilter<TImageType, TImageType>
+ public clitk::StructuresExtractionFilter<TImageType>
{
public:
+ /** Some convenient typedefs. */
+ typedef TImageType ImageType;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::RegionType ImageRegionType;
+ typedef typename ImageType::PixelType ImagePixelType;
+ typedef typename ImageType::SizeType ImageSizeType;
+ typedef typename ImageType::IndexType ImageIndexType;
+ typedef typename ImageType::PointType ImagePointType;
+
+ /** Some convenient typedefs. */
+ typedef uchar MaskImagePixelType;
+ typedef itk::Image<MaskImagePixelType, 3> MaskImageType;
+ typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
+ typedef typename MaskImageType::Pointer MaskImagePointer;
+ typedef typename MaskImageType::RegionType MaskImageRegionType;
+ typedef typename MaskImageType::SizeType MaskImageSizeType;
+ typedef typename MaskImageType::IndexType MaskImageIndexType;
+ typedef typename MaskImageType::PointType MaskImagePointType;
+
+ typedef itk::Image<MaskImagePixelType, 2> MaskSliceType;
+ typedef typename MaskSliceType::Pointer MaskSlicePointer;
+ typedef typename MaskSliceType::PointType MaskSlicePointType;
+
/** Standard class typedefs. */
- typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
+ // typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
+ typedef clitk::StructuresExtractionFilter<TImageType> Superclass;
typedef ExtractMediastinumFilter Self;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
itkTypeMacro(ExtractMediastinumFilter, InPlaceImageFilter);
FILTERBASE_INIT;
- /** Some convenient typedefs. */
- typedef TImageType ImageType;
- typedef typename ImageType::ConstPointer ImageConstPointer;
- typedef typename ImageType::Pointer ImagePointer;
- typedef typename ImageType::RegionType ImageRegionType;
- typedef typename ImageType::PixelType ImagePixelType;
- typedef typename ImageType::SizeType ImageSizeType;
- typedef typename ImageType::IndexType ImageIndexType;
- typedef typename ImageType::PointType ImagePointType;
-
/** Connect inputs */
- void SetInputPatientLabelImage(const TImageType * image, ImagePixelType bg=0);
- void SetInputLungLabelImage(const TImageType * image, ImagePixelType bg=0,
- ImagePixelType fgLeftLung=1, ImagePixelType fgRightLung=2);
- void SetInputBonesLabelImage(const TImageType * image, ImagePixelType bg=0);
- void SetInputTracheaLabelImage(const TImageType * image, ImagePixelType bg=0);
-
+ void SetInput(const ImageType * image);
+ void SetInputPatientLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
+ void SetInputLungLabelImage(const MaskImageType * image, MaskImagePixelType bg=0,
+ MaskImagePixelType fgLeftLung=1, MaskImagePixelType fgRightLung=2);
+ void SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
+ void SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
+
+ // Output filename (for AFBD)
+ itkSetMacro(OutputMediastinumFilename, std::string);
+ itkGetConstMacro(OutputMediastinumFilename, std::string);
+
/** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int, TImageType::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
- // Set all options at a time
- template<class ArgsInfoType>
- void SetArgsInfo(ArgsInfoType arg);
-
// Background / Foreground
- itkSetMacro(BackgroundValuePatient, ImagePixelType);
- itkGetConstMacro(BackgroundValuePatient, ImagePixelType);
- GGO_DefineOption(patientBG, SetBackgroundValuePatient, ImagePixelType);
+ itkSetMacro(BackgroundValuePatient, MaskImagePixelType);
+ itkGetConstMacro(BackgroundValuePatient, MaskImagePixelType);
- itkSetMacro(BackgroundValueLung, ImagePixelType);
- itkGetConstMacro(BackgroundValueLung, ImagePixelType);
- GGO_DefineOption(lungBG, SetBackgroundValueLung, ImagePixelType);
+ itkSetMacro(BackgroundValueLung, MaskImagePixelType);
+ itkGetConstMacro(BackgroundValueLung, MaskImagePixelType);
- itkSetMacro(BackgroundValueBones, ImagePixelType);
- itkGetConstMacro(BackgroundValueBones, ImagePixelType);
- GGO_DefineOption(bonesBG, SetBackgroundValueBones, ImagePixelType);
+ itkSetMacro(BackgroundValueBones, MaskImagePixelType);
+ itkGetConstMacro(BackgroundValueBones, MaskImagePixelType);
- itkGetConstMacro(BackgroundValue, ImagePixelType);
- itkGetConstMacro(ForegroundValue, ImagePixelType);
-
- itkSetMacro(ForegroundValueLeftLung, ImagePixelType);
- itkGetConstMacro(ForegroundValueLeftLung, ImagePixelType);
- GGO_DefineOption(lungLeft, SetForegroundValueLeftLung, ImagePixelType);
+ itkSetMacro(ForegroundValueLeftLung, MaskImagePixelType);
+ itkGetConstMacro(ForegroundValueLeftLung, MaskImagePixelType);
- itkSetMacro(ForegroundValueRightLung, ImagePixelType);
- itkGetConstMacro(ForegroundValueRightLung, ImagePixelType);
- GGO_DefineOption(lungRight, SetForegroundValueRightLung, ImagePixelType);
+ itkSetMacro(ForegroundValueRightLung, MaskImagePixelType);
+ itkGetConstMacro(ForegroundValueRightLung, MaskImagePixelType);
- itkSetMacro(BackgroundValueTrachea, ImagePixelType);
- itkGetConstMacro(BackgroundValueTrachea, ImagePixelType);
- GGO_DefineOption(lungBG, SetBackgroundValueTrachea, ImagePixelType);
+ itkSetMacro(BackgroundValueTrachea, MaskImagePixelType);
+ itkGetConstMacro(BackgroundValueTrachea, MaskImagePixelType);
itkSetMacro(IntermediateSpacing, double);
itkGetConstMacro(IntermediateSpacing, double);
- GGO_DefineOption(spacing, SetIntermediateSpacing, double);
- itkSetMacro(FuzzyThreshold1, double);
- itkGetConstMacro(FuzzyThreshold1, double);
- GGO_DefineOption(fuzzy1, SetFuzzyThreshold1, double);
+ itkBooleanMacro(UseBones);
+ itkSetMacro(UseBones, bool);
+ itkGetConstMacro(UseBones, bool);
- itkSetMacro(FuzzyThreshold2, double);
- itkGetConstMacro(FuzzyThreshold2, double);
- GGO_DefineOption(fuzzy2, SetFuzzyThreshold2, double);
+ itkSetMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
+ itkGetConstMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
- itkSetMacro(FuzzyThreshold3, double);
- itkGetConstMacro(FuzzyThreshold3, double);
- GGO_DefineOption(fuzzy3, SetFuzzyThreshold3, double);
+ void SetFuzzyThreshold(std::string tag, double value);
+ double GetFuzzyThreshold(std::string tag);
protected:
ExtractMediastinumFilter();
virtual void GenerateOutputInformation();
virtual void GenerateInputRequestedRegion();
virtual void GenerateData();
-
- itkSetMacro(BackgroundValue, ImagePixelType);
- itkSetMacro(ForegroundValue, ImagePixelType);
-
- ImagePixelType m_BackgroundValuePatient;
- ImagePixelType m_BackgroundValueLung;
- ImagePixelType m_BackgroundValueBones;
- ImagePixelType m_BackgroundValueTrachea;
- ImagePixelType m_ForegroundValueLeftLung;
- ImagePixelType m_ForegroundValueRightLung;
-
- ImagePixelType m_BackgroundValue;
- ImagePixelType m_ForegroundValue;
-
+
+ MaskImagePixelType m_BackgroundValuePatient;
+ MaskImagePixelType m_BackgroundValueLung;
+ MaskImagePixelType m_BackgroundValueBones;
+ MaskImagePixelType m_BackgroundValueTrachea;
+ MaskImagePixelType m_ForegroundValueLeftLung;
+ MaskImagePixelType m_ForegroundValueRightLung;
+
+ MaskImagePointer output;
+ MaskImagePointer patient;
+ MaskImagePointer lung;
+ MaskImagePointer bones;
+ MaskImagePointer trachea;
+
+ std::map<std::string, double> m_FuzzyThreshold;
double m_IntermediateSpacing;
- double m_FuzzyThreshold1;
- double m_FuzzyThreshold2;
- double m_FuzzyThreshold3;
+ bool m_UseBones;
+ double m_DistanceMaxToAnteriorPartOfTheVertebralBody;
+
+ void RemovePostPartOfVertebralBody();
+
+ std::string m_OutputMediastinumFilename;
private:
ExtractMediastinumFilter(const Self&); //purposely not implemented
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff