1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://www.centreleonberard.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ===========================================================================**/
18 #ifndef clitkAffineTransformGenericFilter_txx
19 #define clitkAffineTransformGenericFilter_txx
21 /* =================================================
22 * @file clitkAffineTransformGenericFilter.txx
28 ===================================================*/
34 //-----------------------------------------------------------
36 //-----------------------------------------------------------
37 template<class args_info_type>
38 AffineTransformGenericFilter<args_info_type>::AffineTransformGenericFilter()
45 //-----------------------------------------------------------
47 //-----------------------------------------------------------
48 template<class args_info_type>
49 void AffineTransformGenericFilter<args_info_type>::Update()
51 // Read the Dimension and PixelType
52 int Dimension, Components;
53 std::string PixelType;
54 ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
58 if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
59 else if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
60 else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
62 std::cout<<"Error, Only for 2, 3 or 4 Dimensions!!!"<<std::endl ;
67 //-------------------------------------------------------------------
68 // Update with the number of dimensions
69 //-------------------------------------------------------------------
70 template<class args_info_type>
71 template<unsigned int Dimension>
73 AffineTransformGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType, int Components)
75 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
78 if(PixelType == "short") {
79 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
80 UpdateWithDimAndPixelType<Dimension, signed short>();
82 // else if(PixelType == "unsigned_short"){
83 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
84 // UpdateWithDimAndPixelType<Dimension, unsigned short>();
87 else if (PixelType == "unsigned_char") {
88 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
89 UpdateWithDimAndPixelType<Dimension, unsigned char>();
92 // else if (PixelType == "char"){
93 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
94 // UpdateWithDimAndPixelType<Dimension, signed char>();
97 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
98 UpdateWithDimAndPixelType<Dimension, float>();
102 else if (Components==3) {
103 if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
104 UpdateWithDimAndVectorType<Dimension, itk::Vector<float, Dimension> >();
107 else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
112 //-------------------------------------------------------------------
113 // Update with the number of dimensions and the pixeltype
114 //-------------------------------------------------------------------
115 template<class args_info_type>
116 template <unsigned int Dimension, class PixelType>
118 AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
122 typedef itk::Image<PixelType, Dimension> InputImageType;
123 typedef itk::Image<PixelType, Dimension> OutputImageType;
126 typedef itk::ImageFileReader<InputImageType> InputReaderType;
127 typename InputReaderType::Pointer reader = InputReaderType::New();
128 reader->SetFileName( m_InputFileName);
130 typename InputImageType::Pointer input= reader->GetOutput();
133 typedef itk::ResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
134 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
137 typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
138 if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
140 if (m_ArgsInfo.matrix_given)
142 std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
145 itk::Array<double> transformParameters(2 * Dimension);
148 transformParameters[pos++] = m_ArgsInfo.rotate_arg[0];
150 for (unsigned int i = 0; i < 3; i++)
151 transformParameters[pos++] = m_ArgsInfo.rotate_arg[i];
152 for (unsigned int i = 0; i < Dimension && i < 3; i++)
153 transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
156 matrix.SetIdentity();
157 itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
158 for (unsigned int i = 0; i < 3; ++i)
159 for (unsigned int j = 0; j < 3; ++j)
160 matrix[i][j] = tmp[i][j];
161 for (unsigned int i = 0; i < 3; ++i)
162 matrix[i][4] = tmp[i][3];
165 matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
169 if (m_ArgsInfo.matrix_given)
171 matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
172 if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
175 matrix.SetIdentity();
178 std::cout << "Using the following matrix:" << std::endl
179 << matrix << std::endl;
180 typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
181 typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
184 typedef itk::AffineTransform<double, Dimension> AffineTransformType;
185 typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
186 affineTransform->SetMatrix(rotationMatrix);
187 affineTransform->SetTranslation(translationPart);
190 typedef clitk::GenericInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
191 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
192 genericInterpolator->SetArgsInfo(m_ArgsInfo);
195 if (m_ArgsInfo.like_given) {
196 typename InputReaderType::Pointer likeReader=InputReaderType::New();
197 likeReader->SetFileName(m_ArgsInfo.like_arg);
198 likeReader->Update();
199 resampler->SetOutputParametersFromImage(likeReader->GetOutput());
200 } else if(m_ArgsInfo.transform_grid_flag) {
201 typename itk::Matrix<double, Dimension+1, Dimension+1> invMatrix( matrix.GetInverse() );
202 typename itk::Matrix<double, Dimension, Dimension> invRotMatrix( clitk::GetRotationalPartMatrix(invMatrix) );
203 typename itk::Vector<double,Dimension> invTrans = clitk::GetTranslationPartMatrix(invMatrix);
205 // Spacing is influenced by affine transform matrix and input direction
206 typename InputImageType::SpacingType outputSpacing;
207 outputSpacing = invRotMatrix *
208 input->GetDirection() *
211 // Origin is influenced by translation but not by input direction
212 typename InputImageType::PointType outputOrigin;
213 outputOrigin = invRotMatrix *
217 // Size is influenced by affine transform matrix and input direction
218 // Size is converted to double, transformed and converted back to size type.
219 vnl_vector<double> vnlOutputSize(Dimension);
220 for(unsigned int i=0; i< Dimension; i++) {
221 vnlOutputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
223 vnlOutputSize = invRotMatrix *
224 input->GetDirection().GetVnlMatrix() *
226 typename OutputImageType::SizeType outputSize;
227 for(unsigned int i=0; i< Dimension; i++) {
228 // If the size is negative, we have a flip and we must modify
229 // the origin and the spacing accordingly.
230 if(vnlOutputSize[i]<0.) {
231 vnlOutputSize[i] *= -1.;
232 outputOrigin[i] = outputOrigin[i] + outputSpacing[i] * (vnlOutputSize[i]-1);
233 outputSpacing[i] *= -1.;
235 outputSize[i] = lrint(vnlOutputSize[i]);
237 resampler->SetSize( outputSize );
238 resampler->SetOutputSpacing( outputSpacing );
239 resampler->SetOutputOrigin( outputOrigin );
242 typename OutputImageType::SizeType outputSize;
243 if (m_ArgsInfo.size_given) {
244 for(unsigned int i=0; i< Dimension; i++)
245 outputSize[i]=m_ArgsInfo.size_arg[i];
246 } else outputSize=input->GetLargestPossibleRegion().GetSize();
249 typename OutputImageType::SpacingType outputSpacing;
250 if (m_ArgsInfo.spacing_given) {
251 for(unsigned int i=0; i< Dimension; i++)
252 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
253 } else outputSpacing=input->GetSpacing();
256 typename OutputImageType::PointType outputOrigin;
257 if (m_ArgsInfo.origin_given) {
258 for(unsigned int i=0; i< Dimension; i++)
259 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
260 } else outputOrigin=input->GetOrigin();
263 resampler->SetSize( outputSize );
264 resampler->SetOutputSpacing( outputSpacing );
265 resampler->SetOutputOrigin( outputOrigin );
269 if (m_ArgsInfo.verbose_flag) {
270 std::cout << "Setting the output size to " << resampler->GetSize() << "..." << std::endl;
271 std::cout << "Setting the output spacing to " << resampler->GetOutputSpacing() << "..." << std::endl;
272 std::cout << "Setting the output origin to " << resampler->GetOutputOrigin() << "..." << std::endl;
275 resampler->SetInput( input );
276 resampler->SetTransform( affineTransform );
277 resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
278 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
282 } catch(itk::ExceptionObject) {
283 std::cerr<<"Error resampling the image"<<std::endl;
286 typename OutputImageType::Pointer output = resampler->GetOutput();
289 typedef itk::ImageFileWriter<OutputImageType> WriterType;
290 typename WriterType::Pointer writer = WriterType::New();
291 writer->SetFileName(m_ArgsInfo.output_arg);
292 writer->SetInput(output);
297 //-------------------------------------------------------------------
298 // Update with the number of dimensions and the pixeltype (components)
299 //-------------------------------------------------------------------
300 template<class args_info_type>
301 template<unsigned int Dimension, class PixelType>
302 void AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndVectorType()
305 typedef itk::Image<PixelType, Dimension> InputImageType;
306 typedef itk::Image<PixelType, Dimension> OutputImageType;
309 typedef itk::ImageFileReader<InputImageType> InputReaderType;
310 typename InputReaderType::Pointer reader = InputReaderType::New();
311 reader->SetFileName( m_InputFileName);
313 typename InputImageType::Pointer input= reader->GetOutput();
316 typedef itk::VectorResampleImageFilter< InputImageType,OutputImageType, double > ResampleFilterType;
317 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
320 typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
321 if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
323 if (m_ArgsInfo.matrix_given)
325 std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
328 itk::Array<double> transformParameters(2 * Dimension);
331 transformParameters[pos++] = m_ArgsInfo.rotate_arg[0];
333 for (unsigned int i = 0; i < 3; i++)
334 transformParameters[pos++] = m_ArgsInfo.rotate_arg[i];
335 for (unsigned int i = 0; i < Dimension && i < 3; i++)
336 transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
339 matrix.SetIdentity();
340 itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
341 for (unsigned int i = 0; i < 3; ++i)
342 for (unsigned int j = 0; j < 3; ++j)
343 matrix[i][j] = tmp[i][j];
344 for (unsigned int i = 0; i < 3; ++i)
345 matrix[i][4] = tmp[i][3];
348 matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
352 if (m_ArgsInfo.matrix_given)
354 matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
355 if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
358 matrix.SetIdentity();
361 std::cout << "Using the following matrix:" << std::endl
362 << matrix << std::endl;
363 typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
364 typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
367 typedef itk::AffineTransform<double, Dimension> AffineTransformType;
368 typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
369 affineTransform->SetMatrix(rotationMatrix);
370 affineTransform->SetTranslation(translationPart);
373 typedef clitk::GenericVectorInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
374 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
375 genericInterpolator->SetArgsInfo(m_ArgsInfo);
378 if (m_ArgsInfo.like_given) {
379 typename InputReaderType::Pointer likeReader=InputReaderType::New();
380 likeReader->SetFileName(m_ArgsInfo.like_arg);
381 likeReader->Update();
382 resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
383 resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
384 resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
387 typename OutputImageType::SizeType outputSize;
388 if (m_ArgsInfo.size_given) {
389 for(unsigned int i=0; i< Dimension; i++)
390 outputSize[i]=m_ArgsInfo.size_arg[i];
391 } else outputSize=input->GetLargestPossibleRegion().GetSize();
392 std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
395 typename OutputImageType::SpacingType outputSpacing;
396 if (m_ArgsInfo.spacing_given) {
397 for(unsigned int i=0; i< Dimension; i++)
398 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
399 } else outputSpacing=input->GetSpacing();
400 std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
403 typename OutputImageType::PointType outputOrigin;
404 if (m_ArgsInfo.origin_given) {
405 for(unsigned int i=0; i< Dimension; i++)
406 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
407 } else outputOrigin=input->GetOrigin();
408 std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
411 resampler->SetSize( outputSize );
412 resampler->SetOutputSpacing( outputSpacing );
413 resampler->SetOutputOrigin( outputOrigin );
417 resampler->SetInput( input );
418 resampler->SetTransform( affineTransform );
419 resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
420 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
424 } catch(itk::ExceptionObject) {
425 std::cerr<<"Error resampling the image"<<std::endl;
428 typename OutputImageType::Pointer output = resampler->GetOutput();
431 typedef itk::ImageFileWriter<OutputImageType> WriterType;
432 typename WriterType::Pointer writer = WriterType::New();
433 writer->SetFileName(m_ArgsInfo.output_arg);
434 writer->SetInput(output);
442 #endif //#define clitkAffineTransformGenericFilter_txx