SimpleITK  
sitkElastixImageFilter.h
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18 #ifndef sitkElastixImageFilter_h
19 #define sitkElastixImageFilter_h
20 
21 #include "sitkElastixTransformixWrappers.h"
22 #include "sitkCommon.h"
23 #include "sitkImage.h"
24 
25 #include <map>
26 #include <memory> // For unique_ptr.
27 #include <string>
28 #include <vector>
29 
30 namespace itk {
31  namespace simple {
32 
36 class SITKElastix_EXPORT ElastixImageFilter
37 {
38 public:
39 
40  ElastixImageFilter();
41  ~ElastixImageFilter();
42 
43  typedef ElastixImageFilter Self;
44 
45  typedef std::vector< Image > VectorOfImage;
46 
47  typedef std::string ParameterKeyType;
48  typedef std::string ParameterValueType;
49  typedef std::vector< ParameterValueType > ParameterValueVectorType;
50  typedef ParameterValueVectorType::iterator ParameterValueVectorIterator;
51  typedef std::map< ParameterKeyType, ParameterValueVectorType > ParameterMapType;
52  typedef std::vector< ParameterMapType > ParameterMapVectorType;
53  typedef ParameterMapType::iterator ParameterMapIterator;
54  typedef ParameterMapType::const_iterator ParameterMapConstIterator;
55 
56  std::string GetName() const;
57 
62  SITK_RETURN_SELF_TYPE_HEADER SetFixedImage( const Image& fixedImage );
69  SITK_RETURN_SELF_TYPE_HEADER SetFixedImage( const VectorOfImage& fixedImages );
72  // TODO: Add Doxygen documentation for all methods.
73  SITK_RETURN_SELF_TYPE_HEADER AddFixedImage( const Image& fixedImage );
74 
75 
76  Image& GetFixedImage( const unsigned long index );
77  VectorOfImage& GetFixedImage();
78  SITK_RETURN_SELF_TYPE_HEADER RemoveFixedImage( const unsigned long index );
79  SITK_RETURN_SELF_TYPE_HEADER RemoveFixedImage();
80  unsigned int GetNumberOfFixedImages();
81 
82  SITK_RETURN_SELF_TYPE_HEADER SetMovingImage( const Image& movingImages );
83  SITK_RETURN_SELF_TYPE_HEADER SetMovingImage( const VectorOfImage& movingImage );
84  SITK_RETURN_SELF_TYPE_HEADER AddMovingImage( const Image& movingImage );
85  Image& GetMovingImage( const unsigned long index );
86  VectorOfImage& GetMovingImage();
87  SITK_RETURN_SELF_TYPE_HEADER RemoveMovingImage( const unsigned long index );
88  SITK_RETURN_SELF_TYPE_HEADER RemoveMovingImage();
89  unsigned int GetNumberOfMovingImages();
90 
91  SITK_RETURN_SELF_TYPE_HEADER SetFixedMask( const Image& fixedMask );
92  SITK_RETURN_SELF_TYPE_HEADER SetFixedMask( const VectorOfImage& fixedMasks );
93  SITK_RETURN_SELF_TYPE_HEADER AddFixedMask( const Image& fixedMask );
94  Image& GetFixedMask( const unsigned long index );
95  VectorOfImage& GetFixedMask();
96  SITK_RETURN_SELF_TYPE_HEADER RemoveFixedMask( const unsigned long index );
97  SITK_RETURN_SELF_TYPE_HEADER RemoveFixedMask();
98  unsigned int GetNumberOfFixedMasks();
99 
100  SITK_RETURN_SELF_TYPE_HEADER SetMovingMask( const Image& movingMask );
101  SITK_RETURN_SELF_TYPE_HEADER SetMovingMask( const VectorOfImage& movingMasks );
102  SITK_RETURN_SELF_TYPE_HEADER AddMovingMask( const Image& movingMask );
103  Image& GetMovingMask( const unsigned long index );
104  VectorOfImage& GetMovingMask();
105  SITK_RETURN_SELF_TYPE_HEADER RemoveMovingMask( const unsigned long index );
106  SITK_RETURN_SELF_TYPE_HEADER RemoveMovingMask();
107  unsigned int GetNumberOfMovingMasks();
108 
109  SITK_RETURN_SELF_TYPE_HEADER SetFixedPointSetFileName( const std::string movingPointSetFileName );
110  std::string GetFixedPointSetFileName();
111  SITK_RETURN_SELF_TYPE_HEADER RemoveFixedPointSetFileName();
112 
113  SITK_RETURN_SELF_TYPE_HEADER SetMovingPointSetFileName( const std::string movingPointSetFileName );
114  std::string GetMovingPointSetFileName();
115  SITK_RETURN_SELF_TYPE_HEADER RemoveMovingPointSetFileName();
116 
117  SITK_RETURN_SELF_TYPE_HEADER SetOutputDirectory( const std::string outputDirectory );
118  std::string GetOutputDirectory();
119  SITK_RETURN_SELF_TYPE_HEADER RemoveOutputDirectory();
120 
121  SITK_RETURN_SELF_TYPE_HEADER SetLogFileName( const std::string logFileName );
122  std::string GetLogFileName();
123  SITK_RETURN_SELF_TYPE_HEADER RemoveLogFileName();
124 
125  SITK_RETURN_SELF_TYPE_HEADER SetLogToFile( const bool logToFile );
126  bool GetLogToFile();
127  SITK_RETURN_SELF_TYPE_HEADER LogToFileOn();
128  SITK_RETURN_SELF_TYPE_HEADER LogToFileOff();
129 
130  SITK_RETURN_SELF_TYPE_HEADER SetLogToConsole( bool );
131  bool GetLogToConsole();
132  SITK_RETURN_SELF_TYPE_HEADER LogToConsoleOn();
133  SITK_RETURN_SELF_TYPE_HEADER LogToConsoleOff();
134 
135  SITK_RETURN_SELF_TYPE_HEADER SetNumberOfThreads( int n );
136  int GetNumberOfThreads();
137 
138  SITK_RETURN_SELF_TYPE_HEADER SetParameterMap( const std::string transformName, const unsigned int numberOfResolutions = 4u, const double finalGridSpacingInPhysicalUnits = 10.0 );
139  SITK_RETURN_SELF_TYPE_HEADER SetParameterMap( const std::vector< std::map< std::string, std::vector< std::string > > > parameterMapVector );
140  SITK_RETURN_SELF_TYPE_HEADER SetParameterMap( const std::map< std::string, std::vector< std::string > > parameterMap );
141  SITK_RETURN_SELF_TYPE_HEADER AddParameterMap( const std::map< std::string, std::vector< std::string > > parameterMap );
142  std::vector< std::map< std::string, std::vector< std::string > > > GetParameterMap();
143  std::map< std::string, std::vector< std::string > > GetDefaultParameterMap( const std::string transformName, const unsigned int numberOfResolutions = 4, const double finalGridSpacingInPhysicalUnits = 10.0 );
144  unsigned int GetNumberOfParameterMaps();
145 
146  SITK_RETURN_SELF_TYPE_HEADER SetParameter( const std::string key, const std::string value );
147  SITK_RETURN_SELF_TYPE_HEADER SetParameter( const std::string key, const std::vector< std::string > value );
148  SITK_RETURN_SELF_TYPE_HEADER SetParameter( const unsigned int index, const std::string key, const std::string value );
149  SITK_RETURN_SELF_TYPE_HEADER SetParameter( const unsigned int index, const std::string key, const std::vector< std::string > value );
150  SITK_RETURN_SELF_TYPE_HEADER AddParameter( const std::string key, const std::string value );
151  SITK_RETURN_SELF_TYPE_HEADER AddParameter( const unsigned int index, const std::string key, const std::string value );
152  SITK_RETURN_SELF_TYPE_HEADER AddParameter( const std::string key, const std::vector< std::string > value );
153  SITK_RETURN_SELF_TYPE_HEADER AddParameter( const unsigned int index, const std::string key, const std::vector< std::string > value );
154  std::vector< std::string > GetParameter( const std::string key );
155  std::vector< std::string > GetParameter( const unsigned int index, const std::string key );
156  SITK_RETURN_SELF_TYPE_HEADER RemoveParameter( const std::string key );
157  SITK_RETURN_SELF_TYPE_HEADER RemoveParameter( const unsigned int index, const std::string key );
158 
159  SITK_RETURN_SELF_TYPE_HEADER SetInitialTransformParameterFileName( const std::string initialTransformParmaterFileName );
160  std::string GetInitialTransformParameterFileName();
161  SITK_RETURN_SELF_TYPE_HEADER RemoveInitialTransformParameterFileName();
162 
163  std::map< std::string, std::vector< std::string > > ReadParameterFile( const std::string filename );
164  SITK_RETURN_SELF_TYPE_HEADER WriteParameterFile( const std::map< std::string, std::vector< std::string > > parameterMap, const std::string filename );
165 
166  Image Execute();
167  std::vector< std::map< std::string, std::vector< std::string > > > GetTransformParameterMap();
168  std::map< std::string, std::vector< std::string > > GetTransformParameterMap( const unsigned int index );
169  Image GetResultImage();
170 
171  SITK_RETURN_SELF_TYPE_HEADER PrintParameterMap();
172  SITK_RETURN_SELF_TYPE_HEADER PrintParameterMap( const ParameterMapType parameterMapVector );
173  SITK_RETURN_SELF_TYPE_HEADER PrintParameterMap( const ParameterMapVectorType parameterMapVector );
174 
175 private:
176 
177  class ElastixImageFilterImpl;
178  const std::unique_ptr<ElastixImageFilterImpl> m_Pimple;
179 
180 };
181 
182 // Procedural Interface
183 SITKElastix_EXPORT std::map< std::string, std::vector< std::string > > GetDefaultParameterMap( const std::string transform, const unsigned int numberOfResolutions = 4, const double finalGridSpacingInPhysicalUnits = 8.0 );
184 SITKElastix_EXPORT std::map< std::string, std::vector< std::string > > ReadParameterFile( const std::string filename );
185 SITKElastix_EXPORT void WriteParameterFile( const std::map< std::string, std::vector< std::string > > parameterMap, const std::string filename );
186 SITKElastix_EXPORT void PrintParameterMap( const std::map< std::string, std::vector< std::string > > parameterMap );
187 SITKElastix_EXPORT void PrintParameterMap( const std::vector< std::map< std::string, std::vector< std::string > > > parameterMapVector );
188 SITKElastix_EXPORT Image Elastix( const Image& fixedImage, const Image& movingImage, const bool logToConsole = false, const bool logToFile = false, const std::string outputDirectory = "." );
189 SITKElastix_EXPORT Image Elastix( const Image& fixedImage, const Image& movingImage, const Image& fixedMask, const Image& movingMask, const bool logToConsole = false, const bool logToFile = false, const std::string outputDirectory = "." );
190 SITKElastix_EXPORT Image Elastix( const Image& fixedImage, const Image& movingImage, const std::string defaultParameterMapName, const bool logToConsole = false, const bool logToFile = false, const std::string outputDirectory = "." );
191 SITKElastix_EXPORT Image Elastix( const Image& fixedImage, const Image& movingImage, const std::map< std::string, std::vector< std::string > > parameterMap, const bool logToConsole = false, const bool logToFile = false, const std::string outputDirectory = "." );
192 SITKElastix_EXPORT Image Elastix( const Image& fixedImage, const Image& movingImage, const std::vector< std::map< std::string, std::vector< std::string > > > parameterMapVector, const bool logToConsole = false, const bool logToFile = false, const std::string outputDirectory = "." );
193 SITKElastix_EXPORT Image Elastix( const Image& fixedImage, const Image& movingImage, const std::string defaultParameterMapName, const Image& fixedMask, const Image& movingMask, const bool logToConsole = false, const bool logToFile = false, const std::string outputDirectory = "." );
194 SITKElastix_EXPORT Image Elastix( const Image& fixedImage, const Image& movingImage, const std::map< std::string, std::vector< std::string > >, const Image& fixedMask, const Image& movingMask, const bool logToConsole = false, const bool logToFile = false, const std::string outputDirectory = "." );
195 SITKElastix_EXPORT Image Elastix( const Image& fixedImage, const Image& movingImage, std::vector< std::map< std::string, std::vector< std::string > > > parameterMapVector, const Image& fixedMask, const Image& movingMask, const bool logToConsole = false, const bool logToFile = false, const std::string outputDirectory = "." );
196 
197 } // end namespace simple
198 } // end namespace itk
199 
200 #endif // sitkElastixImageFilter_h
itk::simple::Image
The Image class for SimpleITK.
Definition: sitkImage.h:76
itk::simple::ElastixImageFilter::ParameterValueVectorType
std::vector< ParameterValueType > ParameterValueVectorType
Definition: sitkElastixImageFilter.h:49
itk::simple::ReadParameterFile
SITKElastix_EXPORT std::map< std::string, std::vector< std::string > > ReadParameterFile(const std::string filename)
itk::simple::ElastixImageFilter::ParameterMapIterator
ParameterMapType::iterator ParameterMapIterator
Definition: sitkElastixImageFilter.h:53
sitkCommon.h
sitkImage.h
itk::simple::ElastixImageFilter::ParameterValueType
std::string ParameterValueType
Definition: sitkElastixImageFilter.h:48
itk::simple::ElastixImageFilter::ParameterKeyType
std::string ParameterKeyType
Definition: sitkElastixImageFilter.h:47
SITKElastix_EXPORT
#define SITKElastix_EXPORT
Definition: sitkElastixTransformixWrappers.h:32
itk::simple::ElastixImageFilter::VectorOfImage
std::vector< Image > VectorOfImage
Definition: sitkElastixImageFilter.h:45
itk::simple::ElastixImageFilter
The class that wraps the elastix registration library.
Definition: sitkElastixImageFilter.h:36
sitkElastixTransformixWrappers.h
itk::simple::GetDefaultParameterMap
SITKElastix_EXPORT std::map< std::string, std::vector< std::string > > GetDefaultParameterMap(const std::string transform, const unsigned int numberOfResolutions=4, const double finalGridSpacingInPhysicalUnits=8.0)
itk::simple::ElastixImageFilter::ParameterMapConstIterator
ParameterMapType::const_iterator ParameterMapConstIterator
Definition: sitkElastixImageFilter.h:54
itk::simple::ElastixImageFilter::Self
ElastixImageFilter Self
Definition: sitkElastixImageFilter.h:43
itk::simple::ElastixImageFilter::ParameterMapType
std::map< ParameterKeyType, ParameterValueVectorType > ParameterMapType
Definition: sitkElastixImageFilter.h:51
itk::simple::WriteParameterFile
SITKElastix_EXPORT void WriteParameterFile(const std::map< std::string, std::vector< std::string > > parameterMap, const std::string filename)
itk::simple::ElastixImageFilter::m_Pimple
const std::unique_ptr< ElastixImageFilterImpl > m_Pimple
Definition: sitkElastixImageFilter.h:177
itk
itk::simple::Elastix
SITKElastix_EXPORT Image Elastix(const Image &fixedImage, const Image &movingImage, const bool logToConsole=false, const bool logToFile=false, const std::string outputDirectory=".")
itk::simple::ElastixImageFilter::ParameterMapVectorType
std::vector< ParameterMapType > ParameterMapVectorType
Definition: sitkElastixImageFilter.h:52
itk::simple::ElastixImageFilter::ParameterValueVectorIterator
ParameterValueVectorType::iterator ParameterValueVectorIterator
Definition: sitkElastixImageFilter.h:50
itk::simple::PrintParameterMap
SITKElastix_EXPORT void PrintParameterMap(const std::map< std::string, std::vector< std::string > > parameterMap)
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