DGtal  1.1.0
ITKDicomReader.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 ITKDicomReader.ih
19  * @author Boris Mansencal (\c boris.mansencal@labri.fr )
20  * LaBRI (CNRS, UMR 5800, University of Bordeaux, Bordeaux-INP, France
21  *
22  * @date 2019/02/05
23  *
24  * Header file for module ITKDicomReader.cpp
25  *
26  * This file is part of the DGtal library.
27  */
28 
29 #include "DGtal/images/ConstImageAdapter.h"
30 #include "DGtal/io/readers/ITKReader.h"
31 #if defined(__GNUG__)
32 #pragma GCC diagnostic push
33 #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
34 #endif
35 #if defined(__clang__)
36 #pragma clang diagnostic push
37 #pragma clang diagnostic ignored "-Wdocumentation"
38 #endif
39 #include <itkImageSeriesReader.h>
40 #include <itkGDCMImageIO.h>
41 #if defined(__clang__)
42 #pragma clang diagnostic pop
43 #endif
44 #if defined(__GNUG__)
45 #pragma GCC diagnostic pop
46 #endif
47 
48 namespace DGtal {
49 
50  template <typename I>
51  template <typename TFunctor>
52  I ITKDicomReader<I>::importDICOM( const std::vector<std::string> & filenames,
53  const TFunctor & aFunctor )
54  {
55  if ( filenames.empty() )
56  {
57  trace.error() << "[ITKDicomReader] empty filenames vector passed.";
58  throw IOException();
59  }
60 
61  typedef typename Image::Domain Domain;
62  typedef itk::ImageIOBase::IOComponentType IOComponentType;
63  BOOST_CONCEPT_ASSERT( (concepts::CUnaryFunctor<TFunctor, ValueOut, Value>));
64  const IOComponentType componentType =
65  ITKReader<I>::getITKComponentType( filenames[0] );
66  // We suppose all file have the same 'componentType'.
67 
68  switch ( componentType )
69  {
70 
71  default:
72  case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
73  {
74  trace.error()
75  << "[ITKDicomReader] Unknown and unsupported component type!";
76  throw IOException();
77  }
78  case itk::ImageIOBase::UCHAR:
79  {
80  typedef ImageContainerByITKImage<Domain, unsigned char> DGtalITKImage;
81  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
82  }
83  case itk::ImageIOBase::CHAR:
84  {
85  typedef ImageContainerByITKImage<Domain, char> DGtalITKImage;
86  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
87  }
88  case itk::ImageIOBase::USHORT:
89  {
90  typedef ImageContainerByITKImage<Domain, unsigned short> DGtalITKImage;
91  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
92  }
93  case itk::ImageIOBase::SHORT:
94  {
95  typedef ImageContainerByITKImage<Domain, short> DGtalITKImage;
96  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
97  }
98  case itk::ImageIOBase::UINT:
99  {
100  typedef ImageContainerByITKImage<Domain, unsigned int> DGtalITKImage;
101  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
102  }
103  case itk::ImageIOBase::INT:
104  {
105  typedef ImageContainerByITKImage<Domain, int> DGtalITKImage;
106  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
107  }
108  case itk::ImageIOBase::ULONG:
109  {
110  typedef ImageContainerByITKImage<Domain, unsigned long> DGtalITKImage;
111  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
112  }
113  case itk::ImageIOBase::LONG:
114  {
115  typedef ImageContainerByITKImage<Domain, long> DGtalITKImage;
116  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
117  }
118 #if (ITK_VERSION_MAJOR > 4)\
119  || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR >= 13)
120  case itk::ImageIOBase::ULONGLONG:
121  {
122  typedef ImageContainerByITKImage<Domain, unsigned long long>
123  DGtalITKImage;
124  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
125  }
126  case itk::ImageIOBase::LONGLONG:
127  {
128  typedef ImageContainerByITKImage<Domain, long long> DGtalITKImage;
129  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
130  }
131 #endif
132  case itk::ImageIOBase::FLOAT:
133  {
134  typedef ImageContainerByITKImage<Domain, float> DGtalITKImage;
135  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
136  }
137  case itk::ImageIOBase::DOUBLE:
138  {
139  typedef ImageContainerByITKImage<Domain, double> DGtalITKImage;
140  return readDGtalImageFromITKtypes<DGtalITKImage>( filenames, aFunctor );
141  }
142  }
143  }
144 
145 
146  template <typename I>
147  template <typename Domain, typename PixelType>
148  inline
149  ImageContainerByITKImage<Domain, PixelType>
150  ITKDicomReader<I>::
151  importDicomFiles(const std::vector<std::string> & filenames)
152  {
153  typedef ImageContainerByITKImage<Domain, PixelType> ImageContainer;
154 
155  const unsigned int dimension = Domain::dimension;
156  typedef itk::Image<PixelType, dimension> ItkImage;
157  typedef itk::ImageSeriesReader<ItkImage> ItkReader;
158 
159  //typedef itk::GDCMImageIO ItkImageIO;
160 
161  typedef typename ImageContainer::ITKImagePointer ITKImagePointer;
162  ITKImagePointer itkImage = nullptr;
163 
164  try
165  {
166  typename ItkReader::Pointer reader = ItkReader::New();
167  //ItkImageIO::Pointer dicomIO = ItkImageIO::New();
168  //reader->SetImageIO( dicomIO );
169 
170  reader->SetFileNames( filenames );
171  reader->Update();
172 
173  itkImage = reader->GetOutput();
174  }
175  catch ( itk::ExceptionObject & e )
176  {
177  trace.error() << e;
178  throw IOException();
179  }
180  catch( ... )
181  {
182  trace.error() << "ITKDicomReader: can't read " << filenames.size()
183  << " files"<<std::endl;
184  throw IOException();
185  }
186 
187  const typename ItkImage::SizeType& inputSize =
188  itkImage->GetLargestPossibleRegion().GetSize();
189  const unsigned int width = inputSize[0];
190  const unsigned int height = inputSize[1];
191  const unsigned int depth = inputSize[2];
192  if ( !height || !width || !depth )
193  {
194  trace.error() << "ITKDicomReader: one dimension is null (w=" << width
195  << ", h=" << height << ", d=" << depth << ")" << std::endl;
196  throw IOException();
197  }
198 
199  const ImageContainer image( itkImage );
200 
201  return image;
202  }
203 
204 
205  template <typename I>
206  template <typename Image, typename Domain, typename OrigValue,
207  typename TFunctor, typename Value>
208  Image
209  ITKDicomReader<I>::Aux<Image, Domain, OrigValue, TFunctor, Value>::
210  readDGtalImageFromITKtypes( const std::vector<std::string> & filenames,
211  const TFunctor & aFunctor )
212  {
213  typedef ImageContainerByITKImage<Domain, OrigValue> TypeDGtalImage;
214  TypeDGtalImage dgtalItkImage =
215  importDicomFiles<Domain, OrigValue>( filenames );
216 
217  const Domain& domain = dgtalItkImage.domain();
218 
219  typedef ConstImageAdapter<TypeDGtalImage, Domain, functors::Identity,
220  Value, TFunctor>
221  AdaptedImage;
222  const functors::Identity identityFunctor{};
223  const AdaptedImage adapted( dgtalItkImage, domain, identityFunctor,
224  aFunctor);
225 
226  Image image( domain );
227  std::copy( adapted.constRange().begin(), adapted.constRange().end(),
228  image.range().outputIterator() );
229 
230  return image;
231  }
232 
233 
234 
235  //specialization
236  template <typename I>
237  template <typename Domain, typename OrigValue, typename TFunctor,
238  typename Value>
239  ImageContainerByITKImage<Domain, Value>
240  ITKDicomReader<I>::Aux<ImageContainerByITKImage<Domain, Value>, Domain,
241  OrigValue, TFunctor, Value>::
242  readDGtalImageFromITKtypes( const std::vector<std::string> & filenames,
243  const TFunctor & aFunctor )
244  {
245  typedef ImageContainerByITKImage<Domain, Value> Image;
246 
247  typedef ImageContainerByITKImage<Domain, OrigValue> TypeDGtalImage;
248  TypeDGtalImage dgtalItkImage =
249  importDicomFiles<Domain, OrigValue>( filenames );
250 
251  const Domain& domain = dgtalItkImage.domain();
252 
253  typedef ConstImageAdapter<TypeDGtalImage, Domain, functors::Identity,
254  Value, TFunctor>
255  AdaptedImage;
256  const functors::Identity identityFunctor{};
257  const AdaptedImage adapted( dgtalItkImage, domain, identityFunctor,
258  aFunctor);
259 
260  Image image( domain );
261  std::copy( adapted.constRange().begin(), adapted.constRange().end(),
262  image.range().outputIterator() );
263 
264  //copy ITKImage spatial parameters
265  image.getITKImagePointer()->SetOrigin(
266  dgtalItkImage.getITKImagePointer()->GetOrigin() );
267  image.getITKImagePointer()->SetSpacing(
268  dgtalItkImage.getITKImagePointer()->GetSpacing() );
269  image.getITKImagePointer()->SetDirection(
270  dgtalItkImage.getITKImagePointer()->GetDirection() );
271 
272  return image;
273  }
274 
275 
276  template <typename I>
277  template <typename TypeDGtalImage, typename TFunctor>
278  typename ITKDicomReader<I>::Image ITKDicomReader<I>::
279  readDGtalImageFromITKtypes( const std::vector<std::string> & filenames,
280  const TFunctor & aFunctor )
281  {
282  typedef typename Image::Domain Domain;
283  typedef typename TypeDGtalImage::Value OrigValue;
284 
285  return Aux<Image, Domain, OrigValue, TFunctor, Value>::
286  readDGtalImageFromITKtypes( filenames, aFunctor );
287  }
288 
289 }//namespace