tools/clitkAffineTransformGenericFilter.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   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.
  12
  13   It is distributed under dual licence
  14
  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
  20
  21 /* =================================================
  22  * @file   clitkAffineTransformGenericFilter.txx
  23  * @author
  24  * @date
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30
  31 namespace clitk
  32 {
  33
  34 //-----------------------------------------------------------
  35 // Constructor
  36 //-----------------------------------------------------------
  37 template<class args_info_type>
  38 AffineTransformGenericFilter<args_info_type>::AffineTransformGenericFilter()
  39 {
  40   m_Verbose=false;
  41   m_InputFileName="";
  42 }
  43
  44
  45 //-----------------------------------------------------------
  46 // Update
  47 //-----------------------------------------------------------
  48 template<class args_info_type>
  49 void AffineTransformGenericFilter<args_info_type>::Update()
  50 {
  51   // Read the Dimension and PixelType
  52   int Dimension, Components;
  53   std::string PixelType;
  54   ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
  55
  56
  57   // Call UpdateWithDim
  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);
  61   else {
  62     std::cout<<"Error, Only for 2, 3 or 4  Dimensions!!!"<<std::endl ;
  63     return;
  64   }
  65 }
  66
  67 //-------------------------------------------------------------------
  68 // Update with the number of dimensions
  69 //-------------------------------------------------------------------
  70 template<class args_info_type>
  71 template<unsigned int Dimension>
  72 void
  73 AffineTransformGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType, int Components)
  74 {
  75   if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<<  PixelType<<"..."<<std::endl;
  76
  77   if (Components==1) {
  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>();
  81     }
  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>();
  85     //     }
  86
  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>();
  90     }
  91
  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>();
  95     //     }
  96     else {
  97       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  98       UpdateWithDimAndPixelType<Dimension, float>();
  99     }
 100   }
 101
 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> >();
 105   }
 106
 107   else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
 108
 109 }
 110
 111
 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>
 117 void
 118 AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
 119 {
 120
 121   // ImageTypes
 122   typedef itk::Image<PixelType, Dimension> InputImageType;
 123   typedef itk::Image<PixelType, Dimension> OutputImageType;
 124
 125   // Read the input
 126   typedef itk::ImageFileReader<InputImageType> InputReaderType;
 127   typename InputReaderType::Pointer reader = InputReaderType::New();
 128   reader->SetFileName( m_InputFileName);
 129   reader->Update();
 130   typename InputImageType::Pointer input= reader->GetOutput();
 131
 132   //Filter
 133   typedef  itk::ResampleImageFilter< InputImageType,OutputImageType >  ResampleFilterType;
 134   typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
 135
 136   // Matrix
 137   typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
 138   if (m_ArgsInfo.matrix_given) {
 139     matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
 140     if (m_Verbose) std::cout<<"Reading the matrix..."<<std::endl;
 141   } else {
 142     matrix.SetIdentity();
 143   }
 144   if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
 145   if (m_Verbose) std::cout<<matrix<<std::endl;
 146   typename itk::Matrix<double, Dimension, Dimension> rotationMatrix=clitk::GetRotationalPartMatrix(matrix);
 147   typename itk::Vector<double,Dimension> translationPart= clitk::GetTranslationPartMatrix(matrix);
 148
 149   // Transform
 150   typedef itk::AffineTransform<double, Dimension> AffineTransformType;
 151   typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
 152   affineTransform->SetMatrix(rotationMatrix);
 153   affineTransform->SetTranslation(translationPart);
 154
 155   // Interp
 156   typedef clitk::GenericInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
 157   typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
 158   genericInterpolator->SetArgsInfo(m_ArgsInfo);
 159
 160   // Properties
 161   if (m_ArgsInfo.like_given) {
 162     typename InputReaderType::Pointer likeReader=InputReaderType::New();
 163     likeReader->SetFileName(m_ArgsInfo.like_arg);
 164     likeReader->Update();
 165     resampler->SetOutputParametersFromImage(likeReader->GetOutput());
 166   } else {
 167     //Size
 168     typename OutputImageType::SizeType outputSize;
 169     if (m_ArgsInfo.size_given) {
 170       for(unsigned int i=0; i< Dimension; i++)
 171         outputSize[i]=m_ArgsInfo.size_arg[i];
 172     } else outputSize=input->GetLargestPossibleRegion().GetSize();
 173     std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
 174
 175     //Spacing
 176     typename OutputImageType::SpacingType outputSpacing;
 177     if (m_ArgsInfo.spacing_given) {
 178       for(unsigned int i=0; i< Dimension; i++)
 179         outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
 180     } else outputSpacing=input->GetSpacing();
 181     std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
 182
 183     //Origin
 184     typename OutputImageType::PointType outputOrigin;
 185     if (m_ArgsInfo.origin_given) {
 186       for(unsigned int i=0; i< Dimension; i++)
 187         outputOrigin[i]=m_ArgsInfo.origin_arg[i];
 188     } else outputOrigin=input->GetOrigin();
 189     std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
 190
 191     // Set
 192     resampler->SetSize( outputSize );
 193     resampler->SetOutputSpacing( outputSpacing );
 194     resampler->SetOutputOrigin(  outputOrigin );
 195
 196   }
 197
 198   resampler->SetInput( input );
 199   resampler->SetTransform( affineTransform );
 200   resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
 201   resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
 202
 203   try {
 204     resampler->Update();
 205   } catch(itk::ExceptionObject) {
 206     std::cerr<<"Error resampling the image"<<std::endl;
 207   }
 208
 209   typename OutputImageType::Pointer output = resampler->GetOutput();
 210
 211   // Output
 212   typedef itk::ImageFileWriter<OutputImageType> WriterType;
 213   typename WriterType::Pointer writer = WriterType::New();
 214   writer->SetFileName(m_ArgsInfo.output_arg);
 215   writer->SetInput(output);
 216   writer->Update();
 217
 218 }
 219
 220 //-------------------------------------------------------------------
 221 // Update with the number of dimensions and the pixeltype (components)
 222 //-------------------------------------------------------------------
 223 template<class args_info_type>
 224 template<unsigned int Dimension, class PixelType>
 225 void AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndVectorType()
 226 {
 227   // ImageTypes
 228   typedef itk::Image<PixelType, Dimension> InputImageType;
 229   typedef itk::Image<PixelType, Dimension> OutputImageType;
 230
 231   // Read the input
 232   typedef itk::ImageFileReader<InputImageType> InputReaderType;
 233   typename InputReaderType::Pointer reader = InputReaderType::New();
 234   reader->SetFileName( m_InputFileName);
 235   reader->Update();
 236   typename InputImageType::Pointer input= reader->GetOutput();
 237
 238   //Filter
 239   typedef  itk::VectorResampleImageFilter< InputImageType,OutputImageType, double >  ResampleFilterType;
 240   typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
 241
 242   // Matrix
 243   typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
 244   if (m_ArgsInfo.matrix_given)
 245     matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
 246   else
 247     matrix.SetIdentity();
 248   if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
 249   if (m_Verbose) std::cout<<matrix<<std::endl;
 250   typename itk::Matrix<double, Dimension, Dimension> rotationMatrix=clitk::GetRotationalPartMatrix(matrix);
 251   typename itk::Vector<double, Dimension> translationPart= clitk::GetTranslationPartMatrix(matrix);
 252
 253   // Transform
 254   typedef itk::AffineTransform<double, Dimension> AffineTransformType;
 255   typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
 256   affineTransform->SetMatrix(rotationMatrix);
 257   affineTransform->SetTranslation(translationPart);
 258
 259   // Interp
 260   typedef clitk::GenericVectorInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
 261   typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
 262   genericInterpolator->SetArgsInfo(m_ArgsInfo);
 263
 264   // Properties
 265   if (m_ArgsInfo.like_given) {
 266     typename InputReaderType::Pointer likeReader=InputReaderType::New();
 267     likeReader->SetFileName(m_ArgsInfo.like_arg);
 268     likeReader->Update();
 269     resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
 270     resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
 271     resampler->SetOutputOrigin(  likeReader->GetOutput()->GetOrigin() );
 272   } else {
 273     //Size
 274     typename OutputImageType::SizeType outputSize;
 275     if (m_ArgsInfo.size_given) {
 276       for(unsigned int i=0; i< Dimension; i++)
 277         outputSize[i]=m_ArgsInfo.size_arg[i];
 278     } else outputSize=input->GetLargestPossibleRegion().GetSize();
 279     std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
 280
 281     //Spacing
 282     typename OutputImageType::SpacingType outputSpacing;
 283     if (m_ArgsInfo.spacing_given) {
 284       for(unsigned int i=0; i< Dimension; i++)
 285         outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
 286     } else outputSpacing=input->GetSpacing();
 287     std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
 288
 289     //Origin
 290     typename OutputImageType::PointType outputOrigin;
 291     if (m_ArgsInfo.origin_given) {
 292       for(unsigned int i=0; i< Dimension; i++)
 293         outputOrigin[i]=m_ArgsInfo.origin_arg[i];
 294     } else outputOrigin=input->GetOrigin();
 295     std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
 296
 297     // Set
 298     resampler->SetSize( outputSize );
 299     resampler->SetOutputSpacing( outputSpacing );
 300     resampler->SetOutputOrigin(  outputOrigin );
 301
 302   }
 303
 304   resampler->SetInput( input );
 305   resampler->SetTransform( affineTransform );
 306   resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
 307   resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
 308
 309   try {
 310     resampler->Update();
 311   } catch(itk::ExceptionObject) {
 312     std::cerr<<"Error resampling the image"<<std::endl;
 313   }
 314
 315   typename OutputImageType::Pointer output = resampler->GetOutput();
 316
 317   // Output
 318   typedef itk::ImageFileWriter<OutputImageType> WriterType;
 319   typename WriterType::Pointer writer = WriterType::New();
 320   writer->SetFileName(m_ArgsInfo.output_arg);
 321   writer->SetInput(output);
 322   writer->Update();
 323
 324 }
 325
 326
 327 } //end clitk
 328
 329 #endif //#define clitkAffineTransformGenericFilter_txx