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itkCellFeatureGenerator.h
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1 /*=========================================================================
2  Authors: The GoFigure Dev. Team.
3  at Megason Lab, Systems biology, Harvard Medical school, 2009-11
4 
5  Copyright (c) 2009-11, President and Fellows of Harvard College.
6  All rights reserved.
7 
8  Redistribution and use in source and binary forms, with or without
9  modification, are permitted provided that the following conditions are met:
10 
11  Redistributions of source code must retain the above copyright notice,
12  this list of conditions and the following disclaimer.
13  Redistributions in binary form must reproduce the above copyright notice,
14  this list of conditions and the following disclaimer in the documentation
15  and/or other materials provided with the distribution.
16  Neither the name of the President and Fellows of Harvard College
17  nor the names of its contributors may be used to endorse or promote
18  products derived from this software without specific prior written
19  permission.
20 
21  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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31  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
32 
33 =========================================================================*/
34 
35 #ifndef __itkCellFeatureGenerator_h
36 #define __itkCellFeatureGenerator_h
37 
38 #if defined( _MSC_VER )
39 #pragma warning ( disable : 4786 )
40 #endif
41 
42 #ifdef __BORLANDC__
43 #define ITK_LEAN_AND_MEAN
44 #endif
45 
46 #include "itkImageToImageFilter.h"
47 #include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
48 #include "itkSigmoidImageFilter.h"
49 #include "itkImageRegionIteratorWithIndex.h"
50 #include "itkSignedMaurerDistanceMapImageFilter.h"
51 #include "itkAbsImageFilter.h"
52 #include "itkThresholdImageFilter.h"
53 #include "itkMinimumMaximumImageCalculator.h"
54 #include "itkImageRegionIterator.h"
55 #include "itkImageRegionConstIterator.h"
56 #include "itkImageRegion.h"
57 #include "itkRegion.h"
58 #include "itkIndex.h"
59 #include "itkSize.h"
60 
61 #include "itkImageFileWriter.h"
62 
63 namespace itk
64 {
65 template< class TFeatureImage, class TInputImage, class TSegmentImage >
67  public ImageToImageFilter< TFeatureImage, TInputImage >
68 {
69 public:
71  typedef ImageToImageFilter< TFeatureImage, TInputImage > Superclass;
72  typedef SmartPointer< Self > Pointer;
73  typedef SmartPointer< const Self > ConstPointer;
74 
75  itkStaticConstMacro (ImageDimension, unsigned int,
76  TFeatureImage::ImageDimension);
77 
79  itkNewMacro (Self);
80 
82  itkTypeMacro (CellFeatureGenerator, ImageToImageFilter);
83 
85  void PrintSelf(std::ostream & os, Indent indent) const;
86 
87  typedef TFeatureImage FeatureImageType;
88  typedef typename FeatureImageType::Pointer FeatureImagePointer;
89  typedef typename FeatureImageType::ConstPointer FeatureImageConstPointer;
90  typedef typename FeatureImageType::PixelType FeatureImagePixelType;
91  typedef typename FeatureImageType::RegionType FeatureImageRegionType;
92  typedef typename FeatureImageType::SizeType FeatureImageSizeType;
93  typedef typename FeatureImageSizeType::SizeValueType FeatureImageSizeValueType;
94  typedef typename FeatureImageType::SpacingType FeatureImageSpacingType;
95  typedef typename FeatureImageType::IndexType FeatureImageIndexType;
96  typedef typename FeatureImageType::PointType FeatureImagePointType;
97 
98  typedef TInputImage ImageType;
99  typedef typename ImageType::Pointer ImagePointer;
100  typedef typename ImageType::ConstPointer ImageConstPointer;
101  typedef typename ImageType::PixelType ImagePixelType;
102  typedef typename ImageType::RegionType ImageRegionType;
103  typedef typename ImageType::SizeType ImageSizeType;
104  typedef typename ImageSizeType::SizeValueType ImageSizeValueType;
105  typedef typename ImageType::SpacingType ImageSpacingType;
106  typedef typename ImageType::IndexType ImageIndexType;
107  typedef typename ImageType::PointType ImagePointType;
108 
109  typedef TSegmentImage SegmentImageType;
110  typedef typename SegmentImageType::Pointer SegmentImagePointer;
111  typedef typename SegmentImageType::ConstPointer SegmentImageConstPointer;
112  typedef typename SegmentImageType::IndexType SegmentImageIndexType;
113  typedef typename SegmentImageType::PixelType SegmentImagePixelType;
114 
115  typedef GradientMagnitudeRecursiveGaussianImageFilter< FeatureImageType, ImageType >
117  typedef typename GradientFilterType::Pointer GradientFilterPointer;
118  typedef SigmoidImageFilter< ImageType, ImageType > SigmoidFilterType;
119  typedef typename SigmoidFilterType::Pointer SigmoidFilterPointer;
120  typedef AbsImageFilter< ImageType, ImageType > AbsFilterType;
121  typedef typename AbsFilterType::Pointer AbsFilterPointer;
122  typedef ThresholdImageFilter< ImageType > ThreshFilterType;
123  typedef typename ThreshFilterType::Pointer ThreshFilterPointer;
124  typedef ImageRegionConstIterator< FeatureImageType > ConstIteratorType;
125  typedef ImageRegionIterator< ImageType > IteratorType;
126  typedef ImageRegionIteratorWithIndex< ImageType > IndexIteratorType;
127  typedef SignedMaurerDistanceMapImageFilter< SegmentImageType, ImageType >
129  typedef typename MaurerType::Pointer MaurerPointer;
130  typedef MinimumMaximumImageCalculator< ImageType > MinMaxCalculatorType;
131  typedef typename MinMaxCalculatorType::Pointer MinMaxCalculatorPointer;
132  typedef MinimumMaximumImageCalculator< FeatureImageType > FeatureMinMaxCalculatorType;
133  typedef typename FeatureMinMaxCalculatorType::Pointer FeatureMinMaxCalculatorPointer;
134 
135  itkGetConstMacro (NucleiSigma, double);
136  itkSetMacro (NucleiSigma, double);
137  itkGetConstMacro (MembraneSigma, double);
138  itkSetMacro (MembraneSigma, double);
139  itkGetConstMacro (LargestCellRadius, double);
140  itkSetMacro (LargestCellRadius, double);
141  itkGetConstMacro (DistanceMapWeight, double);
142  itkSetMacro (DistanceMapWeight, double);
143  itkGetConstMacro (NucleiGradientWeight, double);
144  itkSetMacro (NucleiGradientWeight, double);
145  itkGetConstMacro (MembraneWeight, double);
146  itkSetMacro (MembraneWeight, double);
147 
149  {
150  m_ForegroundMap = fg;
151  }
152 
154  {
155  return m_DistanceMap;
156  }
157 
159  {
160  return m_Gradient;
161  }
162 
163 protected:
166  void DistanceMap();
167 
168  void Gradient();
169 
170  void Normalize();
171 
172  void GenerateData();
173 
180 
184 private:
185 
186  CellFeatureGenerator (Self &); // intentionally not implemented
187  void operator=(const Self &); // intentionally not implemented
188 };
189 } /* namespace itk */
190 
191 #include "itkCellFeatureGenerator.txx"
192 #endif
ImageToImageFilter< TFeatureImage, TInputImage > Superclass
SegmentImageType::PixelType SegmentImagePixelType
SigmoidImageFilter< ImageType, ImageType > SigmoidFilterType
itkStaticConstMacro(ImageDimension, unsigned int, TFeatureImage::ImageDimension)
SegmentImageType::ConstPointer SegmentImageConstPointer
GradientMagnitudeRecursiveGaussianImageFilter< FeatureImageType, ImageType > GradientFilterType
FeatureImageType::RegionType FeatureImageRegionType
ImageType::PixelType ImagePixelType
itkSetMacro(NucleiSigma, double)
FeatureImageType::SizeType FeatureImageSizeType
FeatureImageType::PixelType FeatureImagePixelType
SigmoidFilterType::Pointer SigmoidFilterPointer
ImageRegionConstIterator< FeatureImageType > ConstIteratorType
ImageType::PointType ImagePointType
ImageSizeType::SizeValueType ImageSizeValueType
ImageType::ConstPointer ImageConstPointer
ThreshFilterType::Pointer ThreshFilterPointer
itkTypeMacro(CellFeatureGenerator, ImageToImageFilter)
void SetForeground(SegmentImagePointer fg)
MinMaxCalculatorType::Pointer MinMaxCalculatorPointer
FeatureImageType::SpacingType FeatureImageSpacingType
SignedMaurerDistanceMapImageFilter< SegmentImageType, ImageType > MaurerType
GradientFilterType::Pointer GradientFilterPointer
AbsImageFilter< ImageType, ImageType > AbsFilterType
SmartPointer< const Self > ConstPointer
ImageRegionIterator< ImageType > IteratorType
void PrintSelf(std::ostream &os, Indent indent) const
MinimumMaximumImageCalculator< FeatureImageType > FeatureMinMaxCalculatorType
ImageRegionIteratorWithIndex< ImageType > IndexIteratorType
FeatureImageType::IndexType FeatureImageIndexType
itkGetConstMacro(NucleiSigma, double)
SegmentImageType::IndexType SegmentImageIndexType
ImageType::RegionType ImageRegionType
ImageType::SpacingType ImageSpacingType
FeatureImageType::PointType FeatureImagePointType
FeatureImageType::Pointer FeatureImagePointer
SegmentImageType::Pointer SegmentImagePointer
AbsFilterType::Pointer AbsFilterPointer
FeatureImageSizeType::SizeValueType FeatureImageSizeValueType
MinimumMaximumImageCalculator< ImageType > MinMaxCalculatorType
FeatureImageType::ConstPointer FeatureImageConstPointer
ImageType::IndexType ImageIndexType
ThresholdImageFilter< ImageType > ThreshFilterType
FeatureMinMaxCalculatorType::Pointer FeatureMinMaxCalculatorPointer
void operator=(const Self &)