DGtal 1.4.2
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DicomReader.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 DicomReader.ih
19 * @author Adrien Krähenbühl (\c adrien.krahenbuhl@loria.fr )
20 * LORIA (CNRS, UMR 7503), Université de Lorraine, France
21 *
22 * @date 2013/10/10
23 *
24 * Implementation of inline methods defined in DicomReader.h
25 *
26 * This file is part of the DGtal library.
27 */
28
29///////////////////////////////////////////////////////////////////////////////
30// IMPLEMENTATION of inline methods.
31///////////////////////////////////////////////////////////////////////////////
32
33//////////////////////////////////////////////////////////////////////////////
34#include <cstdlib>
35#include <iostream>
36#include <fstream>
37#include <sstream>
38
39#include "DGtal/io/Color.h"
40#include "DGtal/images/ConstImageAdapter.h"
41
42// Required ITK files to read serie DICOM files
43// DGtal must be compiled with "-DWITH_ITK=true" option
44#if defined(__GNUG__)
45#pragma GCC diagnostic push
46#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
47#pragma GCC diagnostic ignored "-Wpedantic"
48#if __GNUC__ >= 9
49#pragma GCC diagnostic ignored "-Wdeprecated-copy"
50#endif
51#endif
52#if defined(__clang__)
53#pragma clang diagnostic push
54#pragma clang diagnostic ignored "-Wdocumentation"
55#endif
56#include <itkImage.h>
57#include <itkImageSeriesReader.h>
58#include <itkGDCMImageIO.h>
59#include <itkGDCMSeriesFileNames.h>
60#if defined(__clang__)
61#pragma clang diagnostic pop
62#endif
63#if defined(__GNUG__)
64#pragma GCC diagnostic pop
65#endif
66//////////////////////////////////////////////////////////////////////////////
67
68
69
70///////////////////////////////////////////////////////////////////////////////
71// Implementation of inline methods //
72
73
74///////////////////////////////////////////////////////////////////////////////
75// Implementation of inline functions and external operators //
76
77
78namespace DGtal {
79
80template <typename TImageContainer, typename TFunctor>
81template <typename Domain, typename PixelType>
82inline
83ImageContainerByITKImage<Domain, PixelType>
84DicomReader<TImageContainer, TFunctor>::
85importDicomFiles_( const std::vector<std::string> & filenames )
86{
87 // Definition of image type
88 const unsigned int dimension = Domain::dimension;
89 typedef itk::Image<PixelType, dimension> ItkImage;
90 typedef itk::ImageSeriesReader<ItkImage> ItkReader;
91 typename ItkReader::Pointer reader = ItkReader::New();
92
93 // Definition of ITK Dicom reader
94 //typedef itk::GDCMImageIO ItkImageIO;
95 //ItkImageIO::Pointer dicomIO = ItkImageIO::New();
96 //reader->SetImageIO( dicomIO );
97
98 // Series reader
99 reader->SetFileNames( filenames );
100
101 typedef ImageContainerByITKImage<Domain, PixelType> TypeDGtalImage;
102 typedef typename TypeDGtalImage::ITKImagePointer ITKImagePointer;
103 ITKImagePointer itkImage = nullptr;
104
105 // Image reading
106 try
107 {
108 reader->Update();
109 }
110 catch( ... )
111 {
112 trace.error() << "DicomReader: can't read " << filenames.size()
113 << " files"<<std::endl;
114 throw IOException();
115 }
116
117 itkImage = reader->GetOutput();
118
119 const typename ItkImage::SizeType& inputSize =
120 itkImage->GetLargestPossibleRegion().GetSize();
121 const auto width = inputSize[0];
122 const auto height = inputSize[1];
123 const auto depth = inputSize[2];
124 if ( !height || !width || !depth )
125 {
126 trace.error() << "DicomReader: one dimension is null (w=" << width
127 << ", h=" << height << ", d=" << depth << ")"
128 << std::endl;
129 throw IOException();
130 }
131
132 const TypeDGtalImage dgtalItkImage( itkImage );
133
134 return dgtalItkImage;
135}
136
137template <typename TImageContainer, typename TFunctor>
138template <typename Image, typename Domain, typename OutPixelType,
139 typename PixelType>
140Image
141DicomReader<TImageContainer, TFunctor>::Aux<Image, Domain, OutPixelType,
142 PixelType>::
143importDicomFiles( const std::vector<std::string> & filenames,
144 const TFunctor & aFunctor )
145{
146 typedef OutPixelType Value;
147
148 typedef ImageContainerByITKImage<Domain, PixelType> TypeDGtalImage;
149 const TypeDGtalImage dgtalItkImage =
150 importDicomFiles_<Domain, PixelType>( filenames );
151
152 const Domain& domain = dgtalItkImage.domain();
153
154 typedef ConstImageAdapter<TypeDGtalImage, Domain, functors::Identity,
155 Value, TFunctor> AdaptedImage;
156 const functors::Identity identityFunctor{};
157 const AdaptedImage adapted( dgtalItkImage, domain, identityFunctor,
158 aFunctor );
159
160 TImageContainer image( domain );
161 std::copy( adapted.constRange().begin(), adapted.constRange().end(),
162 image.range().outputIterator() );
163 return image;
164}
165
166
167//specialization
168template <typename TImageContainer, typename TFunctor>
169template <typename Domain, typename OutPixelType, typename PixelType>
170ImageContainerByITKImage<Domain, OutPixelType>
171DicomReader<TImageContainer, TFunctor>::
172Aux<ImageContainerByITKImage<Domain, OutPixelType>, Domain, OutPixelType,
173 PixelType>::
174importDicomFiles( const std::vector<std::string> & filenames,
175 const TFunctor & aFunctor )
176{
177 typedef OutPixelType Value;
178
179 typedef ImageContainerByITKImage<Domain, PixelType> TypeDGtalImage;
180 const TypeDGtalImage dgtalItkImage =
181 importDicomFiles_<Domain, PixelType>( filenames );
182
183 const Domain& domain = dgtalItkImage.domain();
184
185 typedef ConstImageAdapter<TypeDGtalImage, Domain, functors::Identity, Value,
186 TFunctor> AdaptedImage;
187 const functors::Identity identityFunctor{};
188 const AdaptedImage adapted( dgtalItkImage, domain, identityFunctor, aFunctor );
189
190 TImageContainer image( domain );
191 std::copy( adapted.constRange().begin(), adapted.constRange().end(),
192 image.range().outputIterator() );
193
194 //copy ITKImage parameters
195 image.getITKImagePointer()->SetOrigin(
196 dgtalItkImage.getITKImagePointer()->GetOrigin() );
197 image.getITKImagePointer()->SetSpacing(
198 dgtalItkImage.getITKImagePointer()->GetSpacing() );
199 image.getITKImagePointer()->SetDirection(
200 dgtalItkImage.getITKImagePointer()->GetDirection() );
201
202 return image;
203}
204
205
206template <typename TImageContainer, typename TFunctor>
207template <typename PixelType>
208inline TImageContainer
209DicomReader<TImageContainer, TFunctor>::
210importDicomFiles( const std::vector<std::string> & filenames,
211 const TFunctor & aFunctor )
212{
213 typedef typename TImageContainer::Domain Domain;
214 return Aux<TImageContainer, Domain, Value, PixelType>::
215 importDicomFiles( filenames, aFunctor );
216}
217
218
219template <typename TImageContainer, typename TFunctor>
220inline
221TImageContainer
222DicomReader<TImageContainer, TFunctor>::
223importDicom( const std::string & aFilename,
224 const TFunctor & aFunctor )
225{
226 std::string directory = aFilename.substr( 0, aFilename.find_last_of("/") );
227
228 typedef itk::GDCMSeriesFileNames ItkNamesGenerator;
229 ItkNamesGenerator::Pointer nameGenerator = ItkNamesGenerator::New();
230 nameGenerator->SetDirectory( directory );
231 const std::vector<std::string> &filenames =
232 nameGenerator->GetInputFileNames();
233
234 return importDicomFiles<PixelType>( filenames, aFunctor );
235}
236
237template <typename TImageContainer, typename TFunctor>
238inline
239TImageContainer
240DicomReader<TImageContainer, TFunctor>::
241importDicomSeries( const std::vector<std::string> & filenames,
242 const Functor & aFunctor )
243{
244 return importDicomFiles<PixelType>( filenames, aFunctor );
245}
246
247}
248
249// //
250///////////////////////////////////////////////////////////////////////////////
251
252