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);
146 transformParameters.Fill(0.0);
147 if (m_ArgsInfo.rotate_given)
150 transformParameters[0] = m_ArgsInfo.rotate_arg[0];
152 for (unsigned int i = 0; i < 3; i++)
153 transformParameters[i] = m_ArgsInfo.rotate_arg[i];
155 if (m_ArgsInfo.translate_given)
160 for (unsigned int i = 0; i < Dimension && i < 3; i++)
161 transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
165 matrix.SetIdentity();
166 itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
167 for (unsigned int i = 0; i < 3; ++i)
168 for (unsigned int j = 0; j < 3; ++j)
169 matrix[i][j] = tmp[i][j];
170 for (unsigned int i = 0; i < 3; ++i)
171 matrix[i][4] = tmp[i][3];
174 matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
178 if (m_ArgsInfo.matrix_given)
180 matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
181 if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
184 matrix.SetIdentity();
187 std::cout << "Using the following matrix:" << std::endl
188 << matrix << std::endl;
189 typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
190 typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
193 typedef itk::AffineTransform<double, Dimension> AffineTransformType;
194 typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
195 affineTransform->SetMatrix(rotationMatrix);
196 affineTransform->SetTranslation(translationPart);
199 typedef clitk::GenericInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
200 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
201 genericInterpolator->SetArgsInfo(m_ArgsInfo);
204 if (m_ArgsInfo.like_given) {
205 typename InputReaderType::Pointer likeReader=InputReaderType::New();
206 likeReader->SetFileName(m_ArgsInfo.like_arg);
207 likeReader->Update();
208 resampler->SetOutputParametersFromImage(likeReader->GetOutput());
209 } else if(m_ArgsInfo.transform_grid_flag) {
210 typename itk::Matrix<double, Dimension+1, Dimension+1> invMatrix( matrix.GetInverse() );
211 typename itk::Matrix<double, Dimension, Dimension> invRotMatrix( clitk::GetRotationalPartMatrix(invMatrix) );
212 typename itk::Vector<double,Dimension> invTrans = clitk::GetTranslationPartMatrix(invMatrix);
214 // Spacing is influenced by affine transform matrix and input direction
215 typename InputImageType::SpacingType outputSpacing;
216 outputSpacing = invRotMatrix *
217 input->GetDirection() *
220 // Origin is influenced by translation but not by input direction
221 typename InputImageType::PointType outputOrigin;
222 outputOrigin = invRotMatrix *
226 // Size is influenced by affine transform matrix and input direction
227 // Size is converted to double, transformed and converted back to size type.
228 vnl_vector<double> vnlOutputSize(Dimension);
229 for(unsigned int i=0; i< Dimension; i++) {
230 vnlOutputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
232 vnlOutputSize = invRotMatrix *
233 input->GetDirection().GetVnlMatrix() *
235 typename OutputImageType::SizeType outputSize;
236 for(unsigned int i=0; i< Dimension; i++) {
237 // If the size is negative, we have a flip and we must modify
238 // the origin and the spacing accordingly.
239 if(vnlOutputSize[i]<0.) {
240 vnlOutputSize[i] *= -1.;
241 outputOrigin[i] = outputOrigin[i] + outputSpacing[i] * (vnlOutputSize[i]-1);
242 outputSpacing[i] *= -1.;
244 outputSize[i] = lrint(vnlOutputSize[i]);
246 resampler->SetSize( outputSize );
247 resampler->SetOutputSpacing( outputSpacing );
248 resampler->SetOutputOrigin( outputOrigin );
251 typename OutputImageType::SizeType outputSize;
252 if (m_ArgsInfo.size_given) {
253 for(unsigned int i=0; i< Dimension; i++)
254 outputSize[i]=m_ArgsInfo.size_arg[i];
255 } else outputSize=input->GetLargestPossibleRegion().GetSize();
258 typename OutputImageType::SpacingType outputSpacing;
259 if (m_ArgsInfo.spacing_given) {
260 for(unsigned int i=0; i< Dimension; i++)
261 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
262 } else outputSpacing=input->GetSpacing();
265 typename OutputImageType::PointType outputOrigin;
266 if (m_ArgsInfo.origin_given) {
267 for(unsigned int i=0; i< Dimension; i++)
268 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
269 } else outputOrigin=input->GetOrigin();
272 resampler->SetSize( outputSize );
273 resampler->SetOutputSpacing( outputSpacing );
274 resampler->SetOutputOrigin( outputOrigin );
278 if (m_ArgsInfo.verbose_flag) {
279 std::cout << "Setting the output size to " << resampler->GetSize() << "..." << std::endl;
280 std::cout << "Setting the output spacing to " << resampler->GetOutputSpacing() << "..." << std::endl;
281 std::cout << "Setting the output origin to " << resampler->GetOutputOrigin() << "..." << std::endl;
284 resampler->SetInput( input );
285 resampler->SetTransform( affineTransform );
286 resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
287 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
291 } catch(itk::ExceptionObject) {
292 std::cerr<<"Error resampling the image"<<std::endl;
295 typename OutputImageType::Pointer output = resampler->GetOutput();
298 typedef itk::ImageFileWriter<OutputImageType> WriterType;
299 typename WriterType::Pointer writer = WriterType::New();
300 writer->SetFileName(m_ArgsInfo.output_arg);
301 writer->SetInput(output);
306 //-------------------------------------------------------------------
307 // Update with the number of dimensions and the pixeltype (components)
308 //-------------------------------------------------------------------
309 template<class args_info_type>
310 template<unsigned int Dimension, class PixelType>
311 void AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndVectorType()
314 typedef itk::Image<PixelType, Dimension> InputImageType;
315 typedef itk::Image<PixelType, Dimension> OutputImageType;
318 typedef itk::ImageFileReader<InputImageType> InputReaderType;
319 typename InputReaderType::Pointer reader = InputReaderType::New();
320 reader->SetFileName( m_InputFileName);
322 typename InputImageType::Pointer input= reader->GetOutput();
325 typedef itk::VectorResampleImageFilter< InputImageType,OutputImageType, double > ResampleFilterType;
326 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
329 typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
330 if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
332 if (m_ArgsInfo.matrix_given)
334 std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
337 itk::Array<double> transformParameters(2 * Dimension);
338 transformParameters.Fill(0.0);
339 if (m_ArgsInfo.rotate_given)
342 transformParameters[0] = m_ArgsInfo.rotate_arg[0];
344 for (unsigned int i = 0; i < 3; i++)
345 transformParameters[i] = m_ArgsInfo.rotate_arg[i];
347 if (m_ArgsInfo.translate_given)
352 for (unsigned int i = 0; i < Dimension && i < 3; i++)
353 transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
357 matrix.SetIdentity();
358 itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
359 for (unsigned int i = 0; i < 3; ++i)
360 for (unsigned int j = 0; j < 3; ++j)
361 matrix[i][j] = tmp[i][j];
362 for (unsigned int i = 0; i < 3; ++i)
363 matrix[i][4] = tmp[i][3];
366 matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
370 if (m_ArgsInfo.matrix_given)
372 matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
373 if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
376 matrix.SetIdentity();
379 std::cout << "Using the following matrix:" << std::endl
380 << matrix << std::endl;
381 typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
382 typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
385 typedef itk::AffineTransform<double, Dimension> AffineTransformType;
386 typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
387 affineTransform->SetMatrix(rotationMatrix);
388 affineTransform->SetTranslation(translationPart);
391 typedef clitk::GenericVectorInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
392 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
393 genericInterpolator->SetArgsInfo(m_ArgsInfo);
396 if (m_ArgsInfo.like_given) {
397 typename InputReaderType::Pointer likeReader=InputReaderType::New();
398 likeReader->SetFileName(m_ArgsInfo.like_arg);
399 likeReader->Update();
400 resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
401 resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
402 resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
405 typename OutputImageType::SizeType outputSize;
406 if (m_ArgsInfo.size_given) {
407 for(unsigned int i=0; i< Dimension; i++)
408 outputSize[i]=m_ArgsInfo.size_arg[i];
409 } else outputSize=input->GetLargestPossibleRegion().GetSize();
410 std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
413 typename OutputImageType::SpacingType outputSpacing;
414 if (m_ArgsInfo.spacing_given) {
415 for(unsigned int i=0; i< Dimension; i++)
416 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
417 } else outputSpacing=input->GetSpacing();
418 std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
421 typename OutputImageType::PointType outputOrigin;
422 if (m_ArgsInfo.origin_given) {
423 for(unsigned int i=0; i< Dimension; i++)
424 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
425 } else outputOrigin=input->GetOrigin();
426 std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
429 resampler->SetSize( outputSize );
430 resampler->SetOutputSpacing( outputSpacing );
431 resampler->SetOutputOrigin( outputOrigin );
435 resampler->SetInput( input );
436 resampler->SetTransform( affineTransform );
437 resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
438 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
442 } catch(itk::ExceptionObject) {
443 std::cerr<<"Error resampling the image"<<std::endl;
446 typename OutputImageType::Pointer output = resampler->GetOutput();
449 typedef itk::ImageFileWriter<OutputImageType> WriterType;
450 typename WriterType::Pointer writer = WriterType::New();
451 writer->SetFileName(m_ArgsInfo.output_arg);
452 writer->SetInput(output);
460 #endif //#define clitkAffineTransformGenericFilter_txx