DGtal  1.1.0
ITKReader.ih
1 /**
2  * This program is free software: you can redistribute it and/or modify
3  * it under the terms of the GNU Lesser General Public License as
4  * published by the Free Software Foundation, either version 3 of the
5  * License, or (at your option) any later version.
6  *
7  * This program is distributed in the hope that it will be useful,
8  * but WITHOUT ANY WARRANTY; without even the implied warranty of
9  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10  * GNU General Public License for more details.
11  *
12  * You should have received a copy of the GNU General Public License
13  * along with this program. If not, see <http://www.gnu.org/licenses/>.
14  *
15  **/
16 
17 /**
18  * @file
19  * @author Pierre Gueth (\c pierre.gueth@gmail.com )
20  * Laboratoire d'InfoRmatique en Image et Systèmes d'information - LIRIS (CNRS,
21  * UMR 5205), CNRS, France
22  *
23  *
24  * @author Bertrand Kerautret (\c bertrand.kerautret@loria.fr )
25  * LORIA (CNRS, UMR 7503), University of Lorraine, France
26  *
27  * @date 2013/10/28
28  *
29  * Header file for module ITKReader.cpp
30  *
31  * This file is part of the DGtal library.
32  */
33 
34 #include "DGtal/images/ConstImageAdapter.h"
35 #if defined(__GNUG__)
36 #pragma GCC diagnostic push
37 #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
38 #endif
39 #if defined(__clang__)
40 #pragma clang diagnostic push
41 #pragma clang diagnostic ignored "-Wdocumentation"
42 #endif
43 #include <itkImageFileReader.h>
44 #if defined(__clang__)
45 #pragma clang diagnostic pop
46 #endif
47 #if defined(__GNUG__)
48 #pragma GCC diagnostic pop
49 #endif
50 
51 namespace DGtal {
52 
53  template <typename I>
54  I ITKReader<I>::importITK(
55  const std::string & filename, bool shiftDomainUsingOrigin )
56  {
57  typename DGtal::ITKIOTrait<typename I::Value>::DefaultReadFunctor def;
58  return DGtal::ITKReader<I>::importITK(filename,def , shiftDomainUsingOrigin);
59  }
60 
61  template <typename I>
62  template <typename TFunctor>
63  I ITKReader<I>::importITK(
64  const std::string & filename,
65  const TFunctor & aFunctor, bool shiftDomainUsingOrigin )
66  {
67  typedef typename Image::Domain Domain;
68  typedef itk::ImageIOBase::IOComponentType IOComponentType;
69  BOOST_CONCEPT_ASSERT( (concepts::CUnaryFunctor<TFunctor, ValueOut, Value>));
70  const IOComponentType componentType = getITKComponentType( filename );
71  switch ( componentType )
72  {
73 
74  default:
75  case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
76  trace.warning() << "[ITKReader] Unknown and unsupported component type! "
77  "File will be loaded with UCHAR component type" << std::endl;
78  //fallthrough
79  case itk::ImageIOBase::UCHAR:
80  {
81  typedef ImageContainerByITKImage<Domain, unsigned char> DGtalITKImage;
82  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
83  }
84  case itk::ImageIOBase::CHAR:
85  {
86  typedef ImageContainerByITKImage<Domain, char> DGtalITKImage;
87  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
88  }
89  case itk::ImageIOBase::USHORT:
90  {
91  typedef ImageContainerByITKImage<Domain, unsigned short> DGtalITKImage;
92  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
93  }
94  case itk::ImageIOBase::SHORT:
95  {
96  typedef ImageContainerByITKImage<Domain, short> DGtalITKImage;
97  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
98  }
99  case itk::ImageIOBase::UINT:
100  {
101  typedef ImageContainerByITKImage<Domain, unsigned int> DGtalITKImage;
102  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
103  }
104  case itk::ImageIOBase::INT:
105  {
106  typedef ImageContainerByITKImage<Domain, int> DGtalITKImage;
107  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
108  }
109  case itk::ImageIOBase::ULONG:
110  {
111  typedef ImageContainerByITKImage<Domain, unsigned long> DGtalITKImage;
112  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
113  }
114  case itk::ImageIOBase::LONG:
115  {
116  typedef ImageContainerByITKImage<Domain, long> DGtalITKImage;
117  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
118  }
119 #if (ITK_VERSION_MAJOR > 4)\
120  || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR >= 13)
121  case itk::ImageIOBase::ULONGLONG:
122  {
123  typedef ImageContainerByITKImage<Domain, unsigned long long>
124  DGtalITKImage;
125  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
126  }
127  case itk::ImageIOBase::LONGLONG:
128  {
129  typedef ImageContainerByITKImage<Domain, long long> DGtalITKImage;
130  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
131  }
132 #endif
133  case itk::ImageIOBase::FLOAT:
134  {
135  typedef ImageContainerByITKImage<Domain, float> DGtalITKImage;
136  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
137  }
138  case itk::ImageIOBase::DOUBLE:
139  {
140  typedef ImageContainerByITKImage<Domain, double> DGtalITKImage;
141  return readDGtalImageFromITKtypes<DGtalITKImage>( filename, aFunctor, shiftDomainUsingOrigin );
142  }
143  }
144  }
145 
146  template <typename I>
147  itk::ImageIOBase::IOComponentType
148  ITKReader<I>::getITKComponentType( const std::string & filename )
149  {
150  typedef itk::ImageIOBase::IOComponentType IOComponentType;
151  IOComponentType componentType;
152  try
153  {
154  itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(
155  filename.c_str(), itk::ImageIOFactory::ReadMode );
156  if (imageIO)
157  {
158  imageIO->SetFileName( filename.c_str() );
159  imageIO->ReadImageInformation();
160  componentType = imageIO->GetComponentType();
161  }
162  }
163  catch ( itk::ExceptionObject & e )
164  {
165  trace.error() << e;
166  throw IOException();
167  }
168  return componentType;
169  }
170 
171  template <typename I>
172  template <typename Domain, typename PixelType>
173  inline
174  ImageContainerByITKImage<Domain, PixelType>
175  ITKReader<I>::readDGtalITKImage(const std::string & filename, bool shiftDomainUsingOrigin)
176  {
177  typedef ImageContainerByITKImage<Domain, PixelType> TypeDGtalImage;
178  const unsigned int dimension = Domain::dimension;
179  typedef itk::Image<PixelType, dimension> ItkImage;
180  typedef itk::ImageFileReader<ItkImage> ITKImageReader;
181  typedef typename TypeDGtalImage::ITKImagePointer ITKImagePointer;
182  ITKImagePointer itk_image = nullptr;
183 
184  try
185  {
186  typename ITKImageReader::Pointer reader = ITKImageReader::New();
187  reader->SetFileName( filename );
188  reader->Update();
189  reader->GetOutput();
190 
191  itk_image = reader->GetOutput();
192  }
193  catch ( itk::ExceptionObject &e )
194  {
195  trace.error() << e;
196  throw IOException();
197  }
198 
199  TypeDGtalImage image( itk_image );
200  if (shiftDomainUsingOrigin)
201  {
202  const auto c = itk_image->GetOrigin();
203  typename Domain::Point p;
204  for (unsigned int k = 0; k < dimension; k++)
205  {
206  p[k] = static_cast<typename Domain::Integer>(c[k]);
207  }
208  image.updateDomain(p);
209  }
210  return image;
211  }
212 
213  template <typename I>
214  template <typename Image, typename Domain, typename OrigValue,
215  typename TFunctor, typename Value>
216  Image
217  ITKReader<I>::Aux<Image, Domain, OrigValue, TFunctor, Value>::
218  readDGtalImageFromITKtypes(const std::string & filename,
219  const TFunctor & aFunctor, bool shiftDomainUsingOrigin)
220  {
221  typedef ImageContainerByITKImage<Domain, OrigValue> TypeDGtalImage;
222  TypeDGtalImage dgtal_itk_image =
223  ITKReader<I>::readDGtalITKImage<Domain, OrigValue>( filename , shiftDomainUsingOrigin);
224 
225  const Domain& domain = dgtal_itk_image.domain();
226 
227  typedef ConstImageAdapter<TypeDGtalImage, Domain, functors::Identity,
228  Value, TFunctor> AdaptedImage;
229  const functors::Identity identityFunctor{};
230  const AdaptedImage adapted( dgtal_itk_image, domain, identityFunctor,
231  aFunctor );
232 
233  Image image( domain );
234  std::copy( adapted.constRange().begin(), adapted.constRange().end(),
235  image.range().outputIterator() );
236 
237  return image;
238  }
239 
240 
241  //specialization
242  template <typename I>
243  template <typename Domain, typename OrigValue, typename TFunctor,
244  typename Value>
245  ImageContainerByITKImage<Domain, Value>
246  ITKReader<I>::Aux<ImageContainerByITKImage<Domain, Value>, Domain, OrigValue,
247  TFunctor, Value>::
248  readDGtalImageFromITKtypes( const std::string & filename,
249  const TFunctor & aFunctor, bool shiftDomainUsingOrigin )
250  {
251  typedef ImageContainerByITKImage<Domain, Value> Image;
252 
253  typedef ImageContainerByITKImage<Domain, OrigValue> TypeDGtalImage;
254  TypeDGtalImage dgtal_itk_image =
255  ITKReader<I>::readDGtalITKImage<Domain, OrigValue>( filename, shiftDomainUsingOrigin );
256 
257  const Domain& domain = dgtal_itk_image.domain();
258 
259  typedef ConstImageAdapter<TypeDGtalImage, Domain, functors::Identity,
260  Value, TFunctor>
261  AdaptedImage;
262  const functors::Identity identityFunctor{};
263  const AdaptedImage adapted( dgtal_itk_image, domain, identityFunctor,
264  aFunctor );
265 
266  Image image( domain );
267  std::copy( adapted.constRange().begin(), adapted.constRange().end(),
268  image.range().outputIterator() );
269 
270  //copy ITKImage spatial parameters
271  image.getITKImagePointer()->SetOrigin(
272  dgtal_itk_image.getITKImagePointer()->GetOrigin() );
273  image.getITKImagePointer()->SetSpacing(
274  dgtal_itk_image.getITKImagePointer()->GetSpacing() );
275  image.getITKImagePointer()->SetDirection(
276  dgtal_itk_image.getITKImagePointer()->GetDirection() );
277 
278  return image;
279  }
280 
281 
282 
283  template <typename I>
284  template <typename TypeDGtalImage, typename TFunctor>
285  typename ITKReader<I>::Image ITKReader<I>::
286  readDGtalImageFromITKtypes( const std::string & filename,
287  const TFunctor & aFunctor, bool shiftDomainUsingOrigin )
288  {
289  typedef typename Image::Domain Domain;
290  typedef typename TypeDGtalImage::Value OrigValue;
291 
292  return Aux<Image, Domain, OrigValue, TFunctor,
293  Value>::readDGtalImageFromITKtypes( filename, aFunctor, shiftDomainUsingOrigin );
294  }
295 
296 }//namespace