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itkGradientWeightedDistanceImageFilter.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:
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12  this list of conditions and the following disclaimer.
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14  this list of conditions and the following disclaimer in the documentation
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17  nor the names of its contributors may be used to endorse or promote
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21  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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32 
33 =========================================================================*/
34 
35 #ifndef __itkGradientWeightedDistanceImageFilter_h
36 #define __itkGradientWeightedDistanceImageFilter_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"
52 #include "itkRescaleIntensityImageFilter.h"
53 #include "itkAbsImageFilter.h"
54 #include "itkThresholdImageFilter.h"
55 #include "itkMinimumMaximumImageCalculator.h"
56 #include "itkImageRegionIterator.h"
57 #include "itkImageRegionConstIterator.h"
58 #include "itkImageRegion.h"
59 #include "itkRegion.h"
60 #include "itkIndex.h"
61 #include "itkSize.h"
62 
63 #include "itkImageFileWriter.h"
64 
65 namespace itk
66 {
67 template< class TFeatureImage, class TInputImage, class TSegmentImage >
69  public ImageToImageFilter< TFeatureImage, TInputImage >
70 {
71 public:
73  typedef ImageToImageFilter< TFeatureImage, TInputImage > Superclass;
74  typedef SmartPointer< Self > Pointer;
75  typedef SmartPointer< const Self > ConstPointer;
76 
77  itkStaticConstMacro (ImageDimension, unsigned int,
78  TFeatureImage::ImageDimension);
79 
81  itkNewMacro (Self);
82 
85 
87  void PrintSelf(std::ostream & os, Indent indent) const;
88 
89  typedef TFeatureImage FeatureImageType;
90  typedef typename FeatureImageType::Pointer FeatureImagePointer;
91  typedef typename FeatureImageType::ConstPointer FeatureImageConstPointer;
92  typedef typename FeatureImageType::PixelType FeatureImagePixelType;
93  typedef typename FeatureImageType::RegionType FeatureImageRegionType;
94  typedef typename FeatureImageType::SizeType FeatureImageSizeType;
95  typedef typename FeatureImageSizeType::SizeValueType FeatureImageSizeValueType;
96  typedef typename FeatureImageType::SpacingType FeatureImageSpacingType;
97  typedef typename FeatureImageType::IndexType FeatureImageIndexType;
98  typedef typename FeatureImageType::PointType FeatureImagePointType;
99 
100  typedef TInputImage ImageType;
101  typedef typename ImageType::Pointer ImagePointer;
102  typedef typename ImageType::ConstPointer ImageConstPointer;
103  typedef typename ImageType::PixelType ImagePixelType;
104  typedef typename ImageType::RegionType ImageRegionType;
105  typedef typename ImageType::SizeType ImageSizeType;
106  typedef typename ImageSizeType::SizeValueType ImageSizeValueType;
107  typedef typename ImageType::SpacingType ImageSpacingType;
108  typedef typename ImageType::IndexType ImageIndexType;
109  typedef typename ImageType::PointType ImagePointType;
110 
111  typedef TSegmentImage SegmentImageType;
112  typedef typename SegmentImageType::Pointer SegmentImagePointer;
113  typedef typename SegmentImageType::ConstPointer SegmentImageConstPointer;
114  typedef typename SegmentImageType::IndexType SegmentImageIndexType;
115  typedef typename SegmentImageType::PixelType SegmentImagePixelType;
116 
120  typedef RescaleIntensityImageFilter< ImageType, ImageType >
122  typedef typename RescaleFilterType::Pointer RescaleFilterPointer;
123 
124  typedef GradientMagnitudeRecursiveGaussianImageFilter< FeatureImageType, ImageType >
126  typedef typename GradientFilterType::Pointer GradientFilterPointer;
127  typedef SigmoidImageFilter< ImageType, ImageType > SigmoidFilterType;
128  typedef typename SigmoidFilterType::Pointer SigmoidFilterPointer;
129  typedef AbsImageFilter< ImageType, ImageType > AbsFilterType;
130  typedef typename AbsFilterType::Pointer AbsFilterPointer;
131  typedef ThresholdImageFilter< ImageType > ThreshFilterType;
132  typedef typename ThreshFilterType::Pointer ThreshFilterPointer;
133  typedef ImageRegionConstIterator< FeatureImageType > ConstIteratorType;
134  typedef ImageRegionIterator< ImageType > IteratorType;
135  typedef ImageRegionIteratorWithIndex< ImageType > IndexIteratorType;
136  typedef SignedMaurerDistanceMapImageFilter< SegmentImageType, ImageType >
138  typedef typename MaurerType::Pointer MaurerPointer;
139  typedef MinimumMaximumImageCalculator< ImageType > MinMaxCalculatorType;
140  typedef typename MinMaxCalculatorType::Pointer MinMaxCalculatorPointer;
141  typedef MinimumMaximumImageCalculator< FeatureImageType > FeatureMinMaxCalculatorType;
142  typedef typename FeatureMinMaxCalculatorType::Pointer FeatureMinMaxCalculatorPointer;
143 
144  itkGetConstMacro (UseLevelSet, bool);
145  itkSetMacro (UseLevelSet, bool);
146  itkGetConstMacro (LargestCellRadius, double);
147  itkSetMacro (LargestCellRadius, double);
148  itkGetConstMacro (NucleiSigma, double);
149  itkSetMacro (NucleiSigma, double);
150  itkGetConstMacro (Alpha, double);
151  itkSetMacro (Alpha, double);
152  itkGetConstMacro (Beta, double);
153  itkSetMacro (Beta, double);
154 
156  {
157  m_ForegroundMap = fg;
158  }
159 
161  {
162  return m_DistanceMap;
163  }
164 
166  {
167  return m_Gradient;
168  }
169 
170 protected:
173  void DistanceMap();
174 
175  void Normalize();
176 
177  void GenerateData();
178 
182  double m_Alpha;
183  double m_Beta;
184 
188 private:
189 
190  GradientWeightedDistanceImageFilter (Self &); // intentionally not implemented
191  void operator=(const Self &); // intentionally not implemented
192 };
193 } /* namespace itk */
194 
195 #include "itkGradientWeightedDistanceImageFilter.txx"
196 #endif
FeatureMinMaxCalculatorType::Pointer FeatureMinMaxCalculatorPointer
ImageRegionIteratorWithIndex< ImageType > IndexIteratorType
ImageRegionConstIterator< FeatureImageType > ConstIteratorType
SigmoidImageFilter< ImageType, ImageType > SigmoidFilterType
GradientMagnitudeRecursiveGaussianImageFilter< FeatureImageType, ImageType > GradientFilterType
MinimumMaximumImageCalculator< FeatureImageType > FeatureMinMaxCalculatorType
void PrintSelf(std::ostream &os, Indent indent) const
ImageToImageFilter< TFeatureImage, TInputImage > Superclass
MultiScaleLoGImageFilter< FeatureImageType, ImageType > MultiScaleLoGFilterType
SignedMaurerDistanceMapImageFilter< SegmentImageType, ImageType > MaurerType
itkStaticConstMacro(ImageDimension, unsigned int, TFeatureImage::ImageDimension)
A filter to enhance 3D blob structures using LoG filter.
MinimumMaximumImageCalculator< ImageType > MinMaxCalculatorType
itkTypeMacro(GradientWeightedDistanceImageFilter, ImageToImageFilter)
RescaleIntensityImageFilter< ImageType, ImageType > RescaleFilterType