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
24 #include <itkCenteredEuler3DTransform.h>
29 //-----------------------------------------------------------
31 //-----------------------------------------------------------
32 template<class args_info_type>
33 AffineTransformGenericFilter<args_info_type>::AffineTransformGenericFilter()
38 //-------------------------------------------------------------------
41 //-----------------------------------------------------------
43 //-----------------------------------------------------------
44 template<class args_info_type>
45 void AffineTransformGenericFilter<args_info_type>::Update()
47 // Read the Dimension and PixelType
48 int Dimension, Components;
49 std::string PixelType;
50 ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
53 if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
55 if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
56 else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
58 std::cout<<"Error, Only for 2, 3 or 4 Dimensions!!!"<<std::endl ;
62 //-------------------------------------------------------------------
65 //-------------------------------------------------------------------
66 // Update with the number of dimensions
67 //-------------------------------------------------------------------
68 template<class args_info_type>
69 template<unsigned int Dimension>
71 AffineTransformGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType, int Components)
73 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
76 if(PixelType == "short") {
77 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
78 UpdateWithDimAndPixelType<Dimension, signed short>();
80 else if(PixelType == "unsigned_short"){
81 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
82 UpdateWithDimAndPixelType<Dimension, unsigned short>();
85 else if (PixelType == "unsigned_char") {
86 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
87 UpdateWithDimAndPixelType<Dimension, unsigned char>();
90 // else if (PixelType == "char"){
91 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
92 // UpdateWithDimAndPixelType<Dimension, signed char>();
95 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
96 UpdateWithDimAndPixelType<Dimension, float>();
100 else if (Components==3) {
101 if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
102 UpdateWithDimAndVectorType<Dimension, itk::Vector<float, Dimension> >();
105 else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
108 //-------------------------------------------------------------------
111 //-------------------------------------------------------------------
112 // Update with the number of dimensions and the pixeltype
113 //-------------------------------------------------------------------
114 template<class args_info_type>
115 template <unsigned int Dimension, class PixelType>
117 AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
121 typedef itk::Image<PixelType, Dimension> InputImageType;
122 typedef itk::Image<PixelType, Dimension> OutputImageType;
125 typedef itk::ImageFileReader<InputImageType> InputReaderType;
126 typename InputReaderType::Pointer reader = InputReaderType::New();
127 reader->SetFileName( m_InputFileName);
129 typename InputImageType::Pointer input= reader->GetOutput();
132 typedef itk::ResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
133 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
136 typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
137 if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
139 if (m_ArgsInfo.matrix_given)
141 std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
144 itk::Array<double> transformParameters(2 * Dimension);
145 transformParameters.Fill(0.0);
146 if (m_ArgsInfo.rotate_given)
149 transformParameters[0] = m_ArgsInfo.rotate_arg[0];
151 for (unsigned int i = 0; i < 3; i++)
152 transformParameters[i] = m_ArgsInfo.rotate_arg[i];
154 if (m_ArgsInfo.translate_given)
159 for (unsigned int i = 0; i < Dimension && i < 3; i++)
160 transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
164 matrix.SetIdentity();
165 itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
166 for (unsigned int i = 0; i < 3; ++i)
167 for (unsigned int j = 0; j < 3; ++j)
168 matrix[i][j] = tmp[i][j];
169 for (unsigned int i = 0; i < 3; ++i)
170 matrix[i][4] = tmp[i][3];
173 matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
177 if (m_ArgsInfo.matrix_given)
179 matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
180 if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
183 if (m_ArgsInfo.elastix_given) {
184 std::vector<std::string> s;
185 for(uint i=0; i<m_ArgsInfo.elastix_given; i++) s.push_back(m_ArgsInfo.elastix_arg[i]);
186 matrix = createMatrixFromElastixFile<Dimension,PixelType>(s);
189 matrix.SetIdentity();
193 std::cout << "Using the following matrix:" << std::endl
194 << matrix << std::endl;
195 typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
196 typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
199 typedef itk::AffineTransform<double, Dimension> AffineTransformType;
200 typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
201 affineTransform->SetMatrix(rotationMatrix);
202 affineTransform->SetTranslation(translationPart);
205 typedef clitk::GenericInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
206 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
207 genericInterpolator->SetArgsInfo(m_ArgsInfo);
210 if (m_ArgsInfo.like_given) {
211 typename InputReaderType::Pointer likeReader=InputReaderType::New();
212 likeReader->SetFileName(m_ArgsInfo.like_arg);
213 likeReader->Update();
214 resampler->SetOutputParametersFromImage(likeReader->GetOutput());
215 } else if(m_ArgsInfo.transform_grid_flag) {
216 typename itk::Matrix<double, Dimension+1, Dimension+1> invMatrix( matrix.GetInverse() );
217 typename itk::Matrix<double, Dimension, Dimension> invRotMatrix( clitk::GetRotationalPartMatrix(invMatrix) );
218 typename itk::Vector<double,Dimension> invTrans = clitk::GetTranslationPartMatrix(invMatrix);
221 if (m_ArgsInfo.spacing_given)
222 std::cout << "Warning --spacing ignored (because --transform_grid_flag)" << std::endl;
223 if (m_ArgsInfo.origin_given)
224 std::cout << "Warning --origin ignored (because --transform_grid_flag)" << std::endl;
226 // Spacing is influenced by affine transform matrix and input direction
227 typename InputImageType::SpacingType outputSpacing;
228 outputSpacing = invRotMatrix *
229 input->GetDirection() *
232 // Origin is influenced by translation but not by input direction
233 typename InputImageType::PointType outputOrigin;
234 outputOrigin = invRotMatrix *
238 // Size is influenced by affine transform matrix and input direction
239 // Size is converted to double, transformed and converted back to size type.
240 vnl_vector<double> vnlOutputSize(Dimension);
241 for(unsigned int i=0; i< Dimension; i++) {
242 vnlOutputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
244 vnlOutputSize = invRotMatrix *
245 input->GetDirection().GetVnlMatrix() *
247 typename OutputImageType::SizeType outputSize;
248 for(unsigned int i=0; i< Dimension; i++) {
249 // If the size is negative, we have a flip and we must modify
250 // the origin and the spacing accordingly.
251 if(vnlOutputSize[i]<0.) {
252 vnlOutputSize[i] *= -1.;
253 outputOrigin[i] = outputOrigin[i] + outputSpacing[i] * (vnlOutputSize[i]-1);
254 outputSpacing[i] *= -1.;
256 outputSize[i] = lrint(vnlOutputSize[i]);
258 resampler->SetSize( outputSize );
259 resampler->SetOutputSpacing( outputSpacing );
260 resampler->SetOutputOrigin( outputOrigin );
263 typename OutputImageType::SizeType outputSize;
264 if (m_ArgsInfo.size_given) {
265 for(unsigned int i=0; i< Dimension; i++)
266 outputSize[i]=m_ArgsInfo.size_arg[i];
267 } else outputSize=input->GetLargestPossibleRegion().GetSize();
270 typename OutputImageType::SpacingType outputSpacing;
271 if (m_ArgsInfo.spacing_given) {
272 for(unsigned int i=0; i< Dimension; i++)
273 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
274 } else outputSpacing=input->GetSpacing();
277 typename OutputImageType::PointType outputOrigin;
278 if (m_ArgsInfo.origin_given) {
279 for(unsigned int i=0; i< Dimension; i++)
280 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
281 } else outputOrigin=input->GetOrigin();
284 resampler->SetSize( outputSize );
285 resampler->SetOutputSpacing( outputSpacing );
286 resampler->SetOutputOrigin( outputOrigin );
290 if (m_ArgsInfo.spacinglike_given) {
291 typename InputReaderType::Pointer likeReader=InputReaderType::New();
292 likeReader->SetFileName(m_ArgsInfo.spacinglike_arg);
293 likeReader->Update();
295 // set the support like the image
296 if (m_ArgsInfo.like_given) {
297 typename OutputImageType::SizeType outputSize;
298 outputSize[0] = ceil(resampler->GetSize()[0]*resampler->GetOutputSpacing()[0]
299 /likeReader->GetOutput()->GetSpacing()[0]);
300 outputSize[1] = ceil(resampler->GetSize()[1]*resampler->GetOutputSpacing()[1]
301 /likeReader->GetOutput()->GetSpacing()[1]);
302 outputSize[2] = ceil(resampler->GetSize()[2]*resampler->GetOutputSpacing()[2]
303 /likeReader->GetOutput()->GetSpacing()[2]);
304 if (m_ArgsInfo.verbose_flag) {
305 std::cout << "Compute the number of pixels such as the support is like " << m_ArgsInfo.like_arg << std::endl;
307 resampler->SetSize( outputSize );
310 resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
313 if (m_ArgsInfo.verbose_flag) {
314 std::cout << "Setting the output size to " << resampler->GetSize() << "..." << std::endl;
315 std::cout << "Setting the output spacing to " << resampler->GetOutputSpacing() << "..." << std::endl;
316 std::cout << "Setting the output origin to " << resampler->GetOutputOrigin() << "..." << std::endl;
319 resampler->SetInput( input );
320 resampler->SetTransform( affineTransform );
321 resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
322 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
326 } catch(itk::ExceptionObject) {
327 std::cerr<<"Error resampling the image"<<std::endl;
330 typename OutputImageType::Pointer output = resampler->GetOutput();
333 typedef itk::ImageFileWriter<OutputImageType> WriterType;
334 typename WriterType::Pointer writer = WriterType::New();
335 writer->SetFileName(m_ArgsInfo.output_arg);
336 writer->SetInput(output);
340 //-------------------------------------------------------------------
343 //-------------------------------------------------------------------
344 // Update with the number of dimensions and the pixeltype (components)
345 //-------------------------------------------------------------------
346 template<class args_info_type>
347 template<unsigned int Dimension, class PixelType>
348 void AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndVectorType()
351 typedef itk::Image<PixelType, Dimension> InputImageType;
352 typedef itk::Image<PixelType, Dimension> OutputImageType;
355 typedef itk::ImageFileReader<InputImageType> InputReaderType;
356 typename InputReaderType::Pointer reader = InputReaderType::New();
357 reader->SetFileName( m_InputFileName);
359 typename InputImageType::Pointer input= reader->GetOutput();
362 typedef itk::VectorResampleImageFilter< InputImageType,OutputImageType, double > ResampleFilterType;
363 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
366 typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
367 if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
369 if (m_ArgsInfo.matrix_given)
371 std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
374 itk::Array<double> transformParameters(2 * Dimension);
375 transformParameters.Fill(0.0);
376 if (m_ArgsInfo.rotate_given)
379 transformParameters[0] = m_ArgsInfo.rotate_arg[0];
381 for (unsigned int i = 0; i < 3; i++)
382 transformParameters[i] = m_ArgsInfo.rotate_arg[i];
384 if (m_ArgsInfo.translate_given)
389 for (unsigned int i = 0; i < Dimension && i < 3; i++)
390 transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
394 matrix.SetIdentity();
395 itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
396 for (unsigned int i = 0; i < 3; ++i)
397 for (unsigned int j = 0; j < 3; ++j)
398 matrix[i][j] = tmp[i][j];
399 for (unsigned int i = 0; i < 3; ++i)
400 matrix[i][4] = tmp[i][3];
403 matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
407 if (m_ArgsInfo.matrix_given)
409 matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
410 if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
413 matrix.SetIdentity();
416 std::cout << "Using the following matrix:" << std::endl
417 << matrix << std::endl;
418 typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
419 typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
422 typedef itk::AffineTransform<double, Dimension> AffineTransformType;
423 typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
424 affineTransform->SetMatrix(rotationMatrix);
425 affineTransform->SetTranslation(translationPart);
428 typedef clitk::GenericVectorInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
429 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
430 genericInterpolator->SetArgsInfo(m_ArgsInfo);
433 if (m_ArgsInfo.like_given) {
434 typename InputReaderType::Pointer likeReader=InputReaderType::New();
435 likeReader->SetFileName(m_ArgsInfo.like_arg);
436 likeReader->Update();
437 resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
438 resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
439 resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
442 typename OutputImageType::SizeType outputSize;
443 if (m_ArgsInfo.size_given) {
444 for(unsigned int i=0; i< Dimension; i++)
445 outputSize[i]=m_ArgsInfo.size_arg[i];
446 } else outputSize=input->GetLargestPossibleRegion().GetSize();
447 std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
450 typename OutputImageType::SpacingType outputSpacing;
451 if (m_ArgsInfo.spacing_given) {
452 for(unsigned int i=0; i< Dimension; i++)
453 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
454 } else outputSpacing=input->GetSpacing();
455 std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
458 typename OutputImageType::PointType outputOrigin;
459 if (m_ArgsInfo.origin_given) {
460 for(unsigned int i=0; i< Dimension; i++)
461 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
462 } else outputOrigin=input->GetOrigin();
463 std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
466 resampler->SetSize( outputSize );
467 resampler->SetOutputSpacing( outputSpacing );
468 resampler->SetOutputOrigin( outputOrigin );
472 resampler->SetInput( input );
473 resampler->SetTransform( affineTransform );
474 resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
475 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
479 } catch(itk::ExceptionObject) {
480 std::cerr<<"Error resampling the image"<<std::endl;
483 typename OutputImageType::Pointer output = resampler->GetOutput();
486 typedef itk::ImageFileWriter<OutputImageType> WriterType;
487 typename WriterType::Pointer writer = WriterType::New();
488 writer->SetFileName(m_ArgsInfo.output_arg);
489 writer->SetInput(output);
493 //-------------------------------------------------------------------
496 //-------------------------------------------------------------------
497 template<class args_info_type>
498 template<unsigned int Dimension, class PixelType>
499 typename itk::Matrix<double, Dimension+1, Dimension+1>
500 AffineTransformGenericFilter<args_info_type>::createMatrixFromElastixFile(std::vector<std::string> & filename)
502 if (Dimension != 3) {
503 FATAL("Only 3D yet" << std::endl);
505 typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
507 itk::CenteredEuler3DTransform<double>::Pointer mat = itk::CenteredEuler3DTransform<double>::New();
508 itk::CenteredEuler3DTransform<double>::Pointer previous;
509 for(uint j=0; j<filename.size(); j++) {
512 if (m_Verbose) std::cout << "Read elastix parameters in " << filename[j] << std::endl;
514 clitk::openFileForReading(is, filename[j]);
518 bool b = GetElastixValueFromTag(is, "Transform ", s);
520 FATAL("Error must read 'Transform' in " << filename[j] << std::endl);
522 if (s != "EulerTransform") {
523 FATAL("Sorry only 'EulerTransform'" << std::endl);
527 // (InitialTransformParametersFilename[j] "NoInitialTransform")
529 // Get CenterOfRotationPoint
530 GetElastixValueFromTag(is, "CenterOfRotationPoint ", s); // space is needed
532 FATAL("Error must read 'CenterOfRotationPoint' in " << filename[j] << std::endl);
534 std::vector<std::string> cor;
535 GetValuesFromValue(s, cor);
537 // Get Transformparameters
538 GetElastixValueFromTag(is, "TransformParameters ", s); // space is needed
540 FATAL("Error must read 'TransformParameters' in " << filename[j] << std::endl);
542 std::vector<std::string> results;
543 GetValuesFromValue(s, results);
545 // construct a stream from the string
546 itk::CenteredEuler3DTransform<double>::ParametersType p;
548 for(uint i=0; i<3; i++)
549 p[i] = atof(results[i].c_str()); // Rotation
550 for(uint i=0; i<3; i++)
551 p[i+3] = atof(cor[i].c_str()); // Centre of rotation
552 for(uint i=0; i<3; i++)
553 p[i+6] = atof(results[i+3].c_str()); // Translation
554 mat->SetParameters(p);
557 std::cout << "Rotation (deg) : " << rad2deg(p[0]) << " " << rad2deg(p[1]) << " " << rad2deg(p[2]) << std::endl;
558 std::cout << "Center of rot (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
559 std::cout << "Translation (phy) : " << p[6] << " " << p[7] << " " << p[8] << std::endl;
562 // Compose with previous if needed
564 mat->Compose(previous);
566 std::cout << "Composed rotation (deg) : " << rad2deg(mat->GetAngleX()) << " " << rad2deg(mat->GetAngleY()) << " " << rad2deg(mat->GetAngleZ()) << std::endl;
567 std::cout << "Composed center of rot (phy) : " << mat->GetCenter() << std::endl;
568 std::cout << "Compsoed translation (phy) : " << mat->GetTranslation() << std::endl;
571 // previous = mat->Clone(); // ITK4
572 previous = itk::CenteredEuler3DTransform<double>::New();
573 previous->SetParameters(mat->GetParameters());
577 for(uint i=0; i<3; i++)
578 for(uint j=0; j<3; j++)
579 matrix[i][j] = mat->GetMatrix()[i][j];
580 // Offset is -Rc + t + c
581 matrix[0][3] = mat->GetOffset()[0];
582 matrix[1][3] = mat->GetOffset()[1];
583 matrix[2][3] = mat->GetOffset()[2];
589 //-------------------------------------------------------------------
590 template<class args_info_type>
592 AffineTransformGenericFilter<args_info_type>::GetElastixValueFromTag(std::ifstream & is,
597 is.seekg (0, is.beg);
598 while(std::getline(is, line)) {
599 unsigned pos = line.find(tag);
600 if (pos<line.size()) {
601 value=line.substr(pos+tag.size(),line.size()-2);// remove last ')'
602 value.erase (std::remove (value.begin(), value.end(), '"'), value.end());
603 value.erase (std::remove (value.begin(), value.end(), ')'), value.end());
609 //-------------------------------------------------------------------
612 //-------------------------------------------------------------------
613 template<class args_info_type>
615 AffineTransformGenericFilter<args_info_type>::GetValuesFromValue(const std::string & s,
616 std::vector<std::string> & values)
618 std::stringstream strstr(s);
619 std::istream_iterator<std::string> it(strstr);
620 std::istream_iterator<std::string> end;
621 std::vector<std::string> results(it, end);
623 values.resize(results.size());
624 for(uint i=0; i<results.size(); i++) values[i] = results[i];
626 //-------------------------------------------------------------------
631 #endif //#define clitkAffineTransformGenericFilter_txx