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://oncora1.lyon.fnclcc.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 itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
102 typedef typename InternalImageType::Pointer InternalImagePointer;
103 typedef typename InternalImageType::IndexType InternalIndexType;
104 typedef LabelizeParameters<InternalPixelType> LabelParamType;
106 /** Connect inputs */
107 void SetInput(const ImageType * image);
108 itkSetMacro(PatientMaskBackgroundValue, MaskImagePixelType);
109 itkGetConstMacro(PatientMaskBackgroundValue, MaskImagePixelType);
110 GGO_DefineOption(patientBG, SetPatientMaskBackgroundValue, MaskImagePixelType);
112 // Output filename (for AFBD)
113 itkSetMacro(OutputLungFilename, std::string);
114 itkGetMacro(OutputLungFilename, std::string);
115 GGO_DefineOption(output, SetOutputLungFilename, std::string);
117 itkSetMacro(OutputTracheaFilename, std::string);
118 itkGetMacro(OutputTracheaFilename, std::string);
119 GGO_DefineOption(outputTrachea, SetOutputTracheaFilename, std::string);
121 // Set all options at a time
122 template<class ArgsInfoType>
123 void SetArgsInfo(ArgsInfoType arg);
125 // Get output (only availabe after update !)
126 typename MaskImageType::Pointer GetTracheaImage() { return trachea; }
128 // Background / Foreground
129 itkGetConstMacro(BackgroundValue, MaskImagePixelType);
130 itkGetConstMacro(ForegroundValue, MaskImagePixelType);
132 // For common segmentation processes
133 itkSetMacro(MinimalComponentSize, int);
134 itkGetConstMacro(MinimalComponentSize, int);
135 GGO_DefineOption(minSize, SetMinimalComponentSize, int);
137 // Step 1 options RemoveAir
138 itkSetMacro(UpperThreshold, InputImagePixelType);
139 itkGetConstMacro(UpperThreshold, InputImagePixelType);
140 GGO_DefineOption(upper, SetUpperThreshold, InputImagePixelType);
142 itkSetMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int);
143 itkGetConstMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int);
144 GGO_DefineOption(skipslices, SetNumberOfSlicesToSkipBeforeSearchingSeed, int);
146 itkSetMacro(LowerThreshold, InputImagePixelType);
147 itkGetConstMacro(LowerThreshold, InputImagePixelType);
148 itkSetMacro(UseLowerThreshold, bool);
149 itkGetConstMacro(UseLowerThreshold, bool);
150 itkBooleanMacro(UseLowerThreshold);
151 GGO_DefineOption_WithTest(lower, SetLowerThreshold, InputImagePixelType, UseLowerThreshold);
153 void SetLabelizeParameters1(LabelParamType * a) { m_LabelizeParameters1 = a; }
154 itkGetConstMacro(LabelizeParameters1, LabelParamType*);
155 GGO_DefineOption_LabelParam(1, SetLabelizeParameters1, LabelParamType);
157 // Step 2 options FindTrachea
158 itkSetMacro(UpperThresholdForTrachea, InputImagePixelType);
159 itkGetConstMacro(UpperThresholdForTrachea, InputImagePixelType);
160 GGO_DefineOption(upperThresholdForTrachea, SetUpperThresholdForTrachea, InputImagePixelType);
162 itkSetMacro(MultiplierForTrachea, double);
163 itkGetConstMacro(MultiplierForTrachea, double);
164 GGO_DefineOption(multiplierForTrachea, SetMultiplierForTrachea, double);
166 itkSetMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
167 itkGetConstMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
168 GGO_DefineOption(thresholdStepSizeForTrachea, SetThresholdStepSizeForTrachea, InputImagePixelType);
170 void AddSeed(InternalIndexType s);
171 std::vector<InternalIndexType> & GetSeeds() { return m_Seeds; }
172 GGO_DefineOption_Vector(seed, AddSeed, InternalIndexType, ImageType::ImageDimension, true);
174 // Step 3 options ExtractLung
175 itkSetMacro(NumberOfHistogramBins, int);
176 itkGetConstMacro(NumberOfHistogramBins, int);
177 GGO_DefineOption(bins, SetNumberOfHistogramBins, int);
179 void SetLabelizeParameters2(LabelParamType* a) { m_LabelizeParameters2 = a; }
180 itkGetConstMacro(LabelizeParameters2, LabelParamType*);
181 GGO_DefineOption_LabelParam(2, SetLabelizeParameters2, LabelParamType);
183 // Step 4 options RemoveTrachea
184 itkSetMacro(RadiusForTrachea, int);
185 itkGetConstMacro(RadiusForTrachea, int);
186 GGO_DefineOption(radius, SetRadiusForTrachea, int);
188 void SetLabelizeParameters3(LabelParamType * a) { m_LabelizeParameters3 = a; }
189 itkGetConstMacro(LabelizeParameters3, LabelParamType*);
190 GGO_DefineOption_LabelParam(3, SetLabelizeParameters3, LabelParamType);
192 // Step 5 final openclose
193 itkSetMacro(OpenClose, bool);
194 itkGetConstMacro(OpenClose, bool);
195 itkBooleanMacro(OpenClose);
196 GGO_DefineOption_Flag(openclose, SetOpenClose);
198 itkSetMacro(OpenCloseRadius, int);
199 itkGetConstMacro(OpenCloseRadius, int);
200 GGO_DefineOption(opencloseRadius, SetOpenCloseRadius, int);
203 itkSetMacro(FillHoles, bool);
204 itkGetConstMacro(FillHoles, bool);
205 itkBooleanMacro(FillHoles);
206 GGO_DefineOption_Flag(doNotFillHoles, SetFillHoles);
210 virtual ~ExtractLungFilter() {}
213 InputImageConstPointer input;
214 MaskImageConstPointer patient;
215 InputImagePointer working_input;
216 std::string m_OutputLungFilename;
217 std::string m_OutputTracheaFilename;
218 typename InternalImageType::Pointer working_image;
219 typename InternalImageType::Pointer trachea_tmp;
220 MaskImagePointer trachea;
221 MaskImagePointer output;
222 unsigned int m_MaxSeedNumber;
225 itkSetMacro(BackgroundValue, MaskImagePixelType);
226 itkSetMacro(ForegroundValue, MaskImagePixelType);
227 MaskImagePixelType m_PatientMaskBackgroundValue;
228 MaskImagePixelType m_BackgroundValue;
229 MaskImagePixelType m_ForegroundValue;
230 int m_MinimalComponentSize;
233 InputImagePixelType m_UpperThreshold;
234 InputImagePixelType m_LowerThreshold;
235 bool m_UseLowerThreshold;
236 LabelParamType* m_LabelizeParameters1;
239 InputImagePixelType m_UpperThresholdForTrachea;
240 InputImagePixelType m_ThresholdStepSizeForTrachea;
241 double m_MultiplierForTrachea;
242 std::vector<InternalIndexType> m_Seeds;
243 int m_NumberOfSlicesToSkipBeforeSearchingSeed;
246 int m_NumberOfHistogramBins;
247 LabelParamType* m_LabelizeParameters2;
250 int m_RadiusForTrachea;
251 LabelParamType* m_LabelizeParameters3;
255 int m_OpenCloseRadius;
259 InputImageSizeType m_FillHolesDirections;
262 virtual void GenerateOutputInformation();
263 virtual void GenerateData();
265 // Functions for trachea extraction
266 bool SearchForTracheaSeed(int skip);
267 void SearchForTrachea();
268 void TracheaRegionGrowing();
269 double ComputeTracheaVolume();
272 ExtractLungFilter(const Self&); //purposely not implemented
273 void operator=(const Self&); //purposely not implemented
276 //--------------------------------------------------------------------
278 } // end namespace clitk
279 //--------------------------------------------------------------------
281 #ifndef ITK_MANUAL_INSTANTIATION
282 #include "clitkExtractLungFilter.txx"