1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://www.centreleonberard.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ===========================================================================**/
19 #ifndef CLITKEXTRACTLUNGSFILTER_H
20 #define CLITKEXTRACTLUNGSFILTER_H
23 #include "clitkFilterBase.h"
24 #include "clitkDecomposeAndReconstructImageFilter.h"
25 #include "clitkExplosionControlledThresholdConnectedImageFilter.h"
26 #include "clitkSegmentationUtils.h"
27 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
30 #include "itkStatisticsImageFilter.h"
34 //--------------------------------------------------------------------
36 Try to extract the Lung part of a thorax CT. Inspired by
37 Rikxoort2009, Section IIA, MedPhys.
39 - First, all air besides lungs and thrachea is removed, by
40 removing the second largest label of the firstLabelImage and
41 setting the remainder to 0HU . This modified input is optimally
42 thresholded (Otsu1979).
44 - Trachea and bronchi are grown from seeds in the top of the image
45 by explosion controlled region growing, slightly dilated and
46 removed from the second label image.
48 - Left and right lung are separated (if necessary) by erosion and
49 reconstructed by conditional dilation.
51 - TRACHEA is available at the end
53 TODO ********** Remaining holes can be filled afterwards (clitkFillMask).
56 //--------------------------------------------------------------------
58 //--------------------------------------------------------------------
59 template <class TImageType>
60 class ITK_EXPORT ExtractLungFilter:
61 public virtual clitk::FilterBase,
62 public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
63 public itk::ImageToImageFilter<TImageType, itk::Image<uchar, TImageType::ImageDimension> >
67 /** Standard class typedefs. */
68 typedef itk::Image<uchar, TImageType::ImageDimension> MaskImageType;
69 typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
70 typedef ExtractLungFilter Self;
71 typedef itk::SmartPointer<Self> Pointer;
72 typedef itk::SmartPointer<const Self> ConstPointer;
74 /** Method for creation through the object factory. */
77 /** Run-time type information (and related methods). */
78 itkTypeMacro(ExtractLungFilter, ImageToImageFilter);
81 /** Some convenient typedefs */
82 typedef TImageType ImageType;
83 typedef typename ImageType::ConstPointer InputImageConstPointer;
84 typedef typename ImageType::Pointer InputImagePointer;
85 typedef typename ImageType::RegionType InputImageRegionType;
86 typedef typename ImageType::PixelType InputImagePixelType;
87 typedef typename ImageType::SizeType InputImageSizeType;
88 typedef typename ImageType::IndexType InputImageIndexType;
89 typedef typename ImageType::PointType InputImagePointType;
91 typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
92 typedef typename MaskImageType::Pointer MaskImagePointer;
93 typedef typename MaskImageType::RegionType MaskImageRegionType;
94 typedef typename MaskImageType::PixelType MaskImagePixelType;
95 typedef typename MaskImageType::SizeType MaskImageSizeType;
96 typedef typename MaskImageType::IndexType MaskImageIndexType;
97 typedef typename MaskImageType::PointType MaskImagePointType;
99 itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
100 // typedef int InternalPixelType;
101 typedef uchar InternalPixelType;
102 typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
103 typedef typename InternalImageType::Pointer InternalImagePointer;
104 typedef typename InternalImageType::IndexType InternalIndexType;
105 typedef LabelizeParameters<InternalPixelType> LabelParamType;
107 /** Connect inputs */
108 void SetInput(const ImageType * image);
109 itkSetMacro(PatientMaskBackgroundValue, MaskImagePixelType);
110 itkGetConstMacro(PatientMaskBackgroundValue, MaskImagePixelType);
112 // Output filename (for AFBD)
113 itkSetMacro(OutputLungFilename, std::string);
114 itkGetMacro(OutputLungFilename, std::string);
116 itkSetMacro(OutputTracheaFilename, std::string);
117 itkGetMacro(OutputTracheaFilename, std::string);
119 // Get output (only availabe after update !)
120 typename MaskImageType::Pointer GetTracheaImage() { return trachea; }
122 // Background / Foreground
123 itkGetConstMacro(BackgroundValue, MaskImagePixelType);
124 itkGetConstMacro(ForegroundValue, MaskImagePixelType);
126 // For common segmentation processes
127 itkSetMacro(MinimalComponentSize, int);
128 itkGetConstMacro(MinimalComponentSize, int);
130 // Step 1 options RemoveAir
131 itkSetMacro(UpperThreshold, InputImagePixelType);
132 itkGetConstMacro(UpperThreshold, InputImagePixelType);
134 itkSetMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int);
135 itkGetConstMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int);
137 itkSetMacro(LowerThreshold, InputImagePixelType);
138 itkGetConstMacro(LowerThreshold, InputImagePixelType);
139 itkSetMacro(UseLowerThreshold, bool);
140 itkGetConstMacro(UseLowerThreshold, bool);
141 itkBooleanMacro(UseLowerThreshold);
143 void SetLabelizeParameters1(LabelParamType * a) { m_LabelizeParameters1 = a; }
144 itkGetConstMacro(LabelizeParameters1, LabelParamType*);
146 // Step 2 options FindTrachea
147 itkSetMacro(UpperThresholdForTrachea, InputImagePixelType);
148 itkGetConstMacro(UpperThresholdForTrachea, InputImagePixelType);
150 itkSetMacro(MultiplierForTrachea, double);
151 itkGetConstMacro(MultiplierForTrachea, double);
153 itkSetMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
154 itkGetConstMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
156 void AddSeed(InternalIndexType s);
157 std::vector<InternalIndexType> & GetSeeds() { return m_Seeds; }
159 itkSetMacro(TracheaVolumeMustBeCheckedFlag, bool);
160 itkGetConstMacro(TracheaVolumeMustBeCheckedFlag, bool);
161 itkBooleanMacro(TracheaVolumeMustBeCheckedFlag);
163 itkSetMacro(VerboseRegionGrowingFlag, bool);
164 itkGetConstMacro(VerboseRegionGrowingFlag, bool);
165 itkBooleanMacro(VerboseRegionGrowingFlag);
167 // Step 3 options ExtractLung
168 itkSetMacro(NumberOfHistogramBins, int);
169 itkGetConstMacro(NumberOfHistogramBins, int);
171 void SetLabelizeParameters2(LabelParamType* a) { m_LabelizeParameters2 = a; }
172 itkGetConstMacro(LabelizeParameters2, LabelParamType*);
174 // Step 4 options RemoveTrachea
175 itkSetMacro(RadiusForTrachea, int);
176 itkGetConstMacro(RadiusForTrachea, int);
178 void SetLabelizeParameters3(LabelParamType * a) { m_LabelizeParameters3 = a; }
179 itkGetConstMacro(LabelizeParameters3, LabelParamType*);
181 // Step 5 final openclose
182 itkSetMacro(OpenCloseFlag, bool);
183 itkGetConstMacro(OpenCloseFlag, bool);
184 itkBooleanMacro(OpenCloseFlag);
186 itkSetMacro(OpenCloseRadius, int);
187 itkGetConstMacro(OpenCloseRadius, int);
190 itkSetMacro(FillHolesFlag, bool);
191 itkGetConstMacro(FillHolesFlag, bool);
192 itkBooleanMacro(FillHolesFlag);
196 virtual ~ExtractLungFilter() {}
199 InputImageConstPointer input;
200 MaskImagePointer patient;
201 InputImagePointer working_input;
202 std::string m_OutputLungFilename;
203 std::string m_OutputTracheaFilename;
204 MaskImagePointer working_mask;
205 MaskImagePointer trachea;
206 unsigned int m_MaxSeedNumber;
209 itkSetMacro(BackgroundValue, MaskImagePixelType);
210 itkSetMacro(ForegroundValue, MaskImagePixelType);
211 MaskImagePixelType m_PatientMaskBackgroundValue;
212 MaskImagePixelType m_BackgroundValue;
213 MaskImagePixelType m_ForegroundValue;
214 int m_MinimalComponentSize;
217 InputImagePixelType m_UpperThreshold;
218 InputImagePixelType m_LowerThreshold;
219 bool m_UseLowerThreshold;
220 LabelParamType* m_LabelizeParameters1;
223 InputImagePixelType m_UpperThresholdForTrachea;
224 InputImagePixelType m_ThresholdStepSizeForTrachea;
225 double m_MultiplierForTrachea;
226 std::vector<InternalIndexType> m_Seeds;
227 int m_NumberOfSlicesToSkipBeforeSearchingSeed;
228 bool m_TracheaVolumeMustBeCheckedFlag;
229 bool m_VerboseRegionGrowingFlag;
232 int m_NumberOfHistogramBins;
233 LabelParamType* m_LabelizeParameters2;
236 int m_RadiusForTrachea;
237 LabelParamType* m_LabelizeParameters3;
240 bool m_OpenCloseFlag;
241 int m_OpenCloseRadius;
244 bool m_FillHolesFlag;
245 InputImageSizeType m_FillHolesDirections;
248 virtual void GenerateOutputInformation();
249 virtual void GenerateInputRequestedRegion();
250 virtual void GenerateData();
252 // Functions for trachea extraction
253 bool SearchForTracheaSeed(int skip);
254 void SearchForTrachea();
255 void TracheaRegionGrowing();
256 double ComputeTracheaVolume();
259 ExtractLungFilter(const Self&); //purposely not implemented
260 void operator=(const Self&); //purposely not implemented
263 //--------------------------------------------------------------------
265 } // end namespace clitk
266 //--------------------------------------------------------------------
268 #ifndef ITK_MANUAL_INSTANTIATION
269 #include "clitkExtractLungFilter.txx"