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 itkSetMacro(TracheaSeedAlgorithm, int);
147 itkGetConstMacro(TracheaSeedAlgorithm, int);
149 // Step 2 options FindTrachea
150 itkSetMacro(UpperThresholdForTrachea, InputImagePixelType);
151 itkGetConstMacro(UpperThresholdForTrachea, InputImagePixelType);
153 itkSetMacro(MultiplierForTrachea, double);
154 itkGetConstMacro(MultiplierForTrachea, double);
156 itkSetMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
157 itkGetConstMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
159 // options FindTrachea2
160 itkSetMacro(NumSlices, int);
161 itkGetConstMacro(NumSlices, int);
162 itkSetMacro(MaxElongation, double);
163 itkGetConstMacro(MaxElongation, double);
164 itkSetMacro(SeedPreProcessingThreshold, int);
165 itkGetConstMacro(SeedPreProcessingThreshold, int);
167 void AddSeed(InternalIndexType s);
168 std::vector<InternalIndexType> & GetSeeds() { return m_Seeds; }
170 itkSetMacro(TracheaVolumeMustBeCheckedFlag, bool);
171 itkGetConstMacro(TracheaVolumeMustBeCheckedFlag, bool);
172 itkBooleanMacro(TracheaVolumeMustBeCheckedFlag);
174 itkSetMacro(VerboseRegionGrowingFlag, bool);
175 itkGetConstMacro(VerboseRegionGrowingFlag, bool);
176 itkBooleanMacro(VerboseRegionGrowingFlag);
178 itkSetMacro(RemoveSmallLabelBeforeSeparationFlag, bool);
179 itkGetConstMacro(RemoveSmallLabelBeforeSeparationFlag, bool);
180 itkBooleanMacro(RemoveSmallLabelBeforeSeparationFlag);
182 // Step 3 options ExtractLung
183 itkSetMacro(NumberOfHistogramBins, int);
184 itkGetConstMacro(NumberOfHistogramBins, int);
186 void SetLabelizeParameters2(LabelParamType* a) { m_LabelizeParameters2 = a; }
187 itkGetConstMacro(LabelizeParameters2, LabelParamType*);
189 // Step 4 options RemoveTrachea
190 itkSetMacro(RadiusForTrachea, int);
191 itkGetConstMacro(RadiusForTrachea, int);
193 void SetLabelizeParameters3(LabelParamType * a) { m_LabelizeParameters3 = a; }
194 itkGetConstMacro(LabelizeParameters3, LabelParamType*);
196 // Step 5 final openclose
197 itkSetMacro(OpenCloseFlag, bool);
198 itkGetConstMacro(OpenCloseFlag, bool);
199 itkBooleanMacro(OpenCloseFlag);
201 itkSetMacro(OpenCloseRadius, int);
202 itkGetConstMacro(OpenCloseRadius, int);
205 itkSetMacro(FillHolesFlag, bool);
206 itkGetConstMacro(FillHolesFlag, bool);
207 itkBooleanMacro(FillHolesFlag);
210 itkSetMacro(SeparateLungsFlag, bool);
211 itkGetConstMacro(SeparateLungsFlag, bool);
212 itkBooleanMacro(SeparateLungsFlag);
215 itkSetMacro(AutoCrop, bool);
216 itkGetConstMacro(AutoCrop, bool);
217 itkBooleanMacro(AutoCrop);
221 virtual ~ExtractLungFilter() {}
224 InputImageConstPointer input;
225 MaskImagePointer patient;
226 InputImagePointer working_input;
227 std::string m_OutputLungFilename;
228 std::string m_OutputTracheaFilename;
229 MaskImagePointer working_mask;
230 MaskImagePointer trachea;
231 unsigned int m_MaxSeedNumber;
234 itkSetMacro(BackgroundValue, MaskImagePixelType);
235 itkSetMacro(ForegroundValue, MaskImagePixelType);
236 MaskImagePixelType m_PatientMaskBackgroundValue;
237 MaskImagePixelType m_BackgroundValue;
238 MaskImagePixelType m_ForegroundValue;
239 int m_MinimalComponentSize;
241 bool m_RemoveSmallLabelBeforeSeparationFlag;
244 InputImagePixelType m_UpperThreshold;
245 InputImagePixelType m_LowerThreshold;
246 bool m_UseLowerThreshold;
247 LabelParamType* m_LabelizeParameters1;
250 int m_TracheaSeedAlgorithm;
251 InputImagePixelType m_UpperThresholdForTrachea;
252 InputImagePixelType m_ThresholdStepSizeForTrachea;
253 double m_MultiplierForTrachea;
254 std::vector<InternalIndexType> m_Seeds;
255 int m_NumberOfSlicesToSkipBeforeSearchingSeed;
256 bool m_TracheaVolumeMustBeCheckedFlag;
257 bool m_VerboseRegionGrowingFlag;
259 double m_MaxElongation;
260 int m_SeedPreProcessingThreshold;
263 int m_NumberOfHistogramBins;
264 LabelParamType* m_LabelizeParameters2;
267 int m_RadiusForTrachea;
268 LabelParamType* m_LabelizeParameters3;
271 bool m_OpenCloseFlag;
272 int m_OpenCloseRadius;
275 bool m_FillHolesFlag;
276 InputImageSizeType m_FillHolesDirections;
278 bool m_SeparateLungsFlag;
281 virtual void GenerateOutputInformation();
282 virtual void GenerateInputRequestedRegion();
283 virtual void GenerateData();
285 // Functions for trachea extraction
286 bool SearchForTracheaSeed(int skip);
287 bool SearchForTracheaSeed2(int numberOfSlices);
288 void SearchForTrachea();
289 void TracheaRegionGrowing();
290 double ComputeTracheaVolume();
293 ExtractLungFilter(const Self&); //purposely not implemented
294 void operator=(const Self&); //purposely not implemented
297 //--------------------------------------------------------------------
299 } // end namespace clitk
300 //--------------------------------------------------------------------
302 #ifndef ITK_MANUAL_INSTANTIATION
303 #include "clitkExtractLungFilter.txx"