registration/clitkBSplinePyramidGenericFilter.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://www.centreleonberard.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 clitkBSplinePyramidGenericFilter_txx
  19 #define clitkBSplinePyramidGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkBSplinePyramidGenericFilter.txx
  23  * @author
  24  * @date
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30
  31 namespace clitk
  32 {
  33
  34   //-------------------------------------------------------------------
  35   // Update with the number of dimensions
  36   //-------------------------------------------------------------------
  37   template<unsigned int Dimension>
  38   void
  39   BSplinePyramidGenericFilter::UpdateWithDim(std::string PixelType, unsigned int Components)
  40   {
  41     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<<  PixelType<<"..."<<std::endl;
  42
  43     if (Components==1)
  44       {
  45         if(PixelType == "short"){
  46           if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  47           UpdateWithDimAndPixelType<Dimension, signed short>();
  48         }
  49         //    else if(PixelType == "unsigned_short"){
  50         //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  51         //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  52         //     }
  53
  54         else if (PixelType == "unsigned_char"){
  55           if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  56           UpdateWithDimAndPixelType<Dimension, unsigned char>();
  57         }
  58
  59         //     else if (PixelType == "char"){
  60         //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  61         //       UpdateWithDimAndPixelType<Dimension, signed char>();
  62         //     }
  63         else {
  64           if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  65           UpdateWithDimAndPixelType<Dimension, float>();
  66         }
  67       }
  68     else if (Components==3)
  69       {
  70         if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
  71         UpdateWithDimAndVectorType<Dimension, itk::Vector<float, 3> >();
  72       }
  73     else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
  74
  75   }
  76
  77
  78
  79   //-------------------------------------------------------------------
  80   // Update with the number of dimensions and the pixeltype
  81   //-------------------------------------------------------------------
  82   template <unsigned int Dimension, class  PixelType>
  83   void
  84   BSplinePyramidGenericFilter::UpdateWithDimAndPixelType()
  85   {
  86
  87     // ImageTypes
  88     typedef itk::Image<PixelType, Dimension> InputImageType;
  89     typedef itk::Image<PixelType, Dimension> OutputImageType;
  90
  91     // Read the input
  92     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  93     typename InputReaderType::Pointer reader = InputReaderType::New();
  94     reader->SetFileName( m_InputFileName);
  95     reader->Update();
  96     typename InputImageType::Pointer input= reader->GetOutput();
  97
  98     // Resampler Types
  99     typedef itk::BSplineResampleImageFilterBase<InputImageType, InputImageType> ResamplerType;
 100     typedef itk::BSplineCenteredResampleImageFilterBase<InputImageType, InputImageType> CenteredResamplerType;
 101     typedef itk::BSplineL2ResampleImageFilterBase<InputImageType, InputImageType> L2ResamplerType;
 102     typedef itk::BSplineCenteredL2ResampleImageFilterBase<InputImageType, InputImageType> CenteredL2ResamplerType;
 103
 104     // Filter
 105     typedef itk::ImageToImageFilter< InputImageType, InputImageType > ImageToImageFilterType;
 106     typename  ImageToImageFilterType::Pointer filter;
 107
 108     if (!m_ArgsInfo.up_flag)
 109       {
 110         switch (m_ArgsInfo.resamplerType_arg)
 111           {
 112
 113             // Resampler
 114           case 0: {
 115             typename itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, ResamplerType >::Pointer df
 116               = itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, ResamplerType >::New();
 117             df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 118             filter=df;
 119             if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with standard Resampler"<<std::endl;
 120             break;
 121           }
 122
 123             //CenteredResamplerType
 124           case 1: {
 125             typename itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, CenteredResamplerType >::Pointer df
 126               = itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, CenteredResamplerType >::New();
 127             df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 128             filter=df;
 129             if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with centered Resampler"<<std::endl;
 130             break;
 131           }
 132
 133             //L2ResamplerType
 134           case 2:
 135             {
 136               typename itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, L2ResamplerType >::Pointer df
 137                 = itk::BSplineDownsampleImageFilter< InputImageType,InputImageType,L2ResamplerType >::New();
 138               df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 139               filter=df;
 140               if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with L2 Resampler"<<std::endl;
 141               break;
 142             }
 143
 144             //Centered L2ResamplerType
 145           case 3:
 146             {
 147               typename itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, CenteredL2ResamplerType >::Pointer df
 148                 = itk::BSplineDownsampleImageFilter< InputImageType,InputImageType,CenteredL2ResamplerType >::New();
 149               df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 150               filter=df;
 151               if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with L2 centered Resampler"<<std::endl;
 152               break;
 153             }
 154
 155           }
 156       }
 157     else
 158       {
 159         switch (m_ArgsInfo.resamplerType_arg)
 160           {
 161
 162             // Resampler
 163           case 0: {
 164             typename itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, ResamplerType >::Pointer df
 165               = itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, ResamplerType >::New();
 166             df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 167             filter=df;
 168             if (m_Verbose) std::cout<<"Using the BSpline upsample image filter with standard Resampler"<<std::endl;
 169             break;
 170           }
 171
 172             //CenteredResamplerType
 173           case 1: {
 174             typename itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, CenteredResamplerType >::Pointer df
 175               = itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, CenteredResamplerType >::New();
 176             df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 177             filter=df;
 178             if (m_Verbose) std::cout<<"Using the BSpline upsample image filter with centered Resampler"<<std::endl;
 179             break;
 180           }
 181
 182             //L2ResamplerType
 183           case 2:
 184             {
 185               typename itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, L2ResamplerType >::Pointer df
 186                 = itk::BSplineUpsampleImageFilter< InputImageType,InputImageType,L2ResamplerType >::New();
 187               df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 188               filter=df;
 189               if (m_Verbose) std::cout<<"Using the BSpline upsample image filter with L2 Resampler"<<std::endl;
 190               break;
 191             }
 192
 193             //Centered L2ResamplerType
 194           case 3:
 195             {
 196               typename itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, CenteredL2ResamplerType >::Pointer df
 197                 = itk::BSplineUpsampleImageFilter< InputImageType,InputImageType,CenteredL2ResamplerType >::New();
 198               df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 199               filter=df;
 200               if (m_Verbose) std::cout<<"Using the BSpline upsample image filter with L2 centered Resampler"<<std::endl;
 201               break;
 202             }
 203
 204           }
 205       }
 206
 207
 208     // Update
 209     filter->SetInput(input);
 210     filter->Update();
 211     typename OutputImageType::Pointer output=filter->GetOutput();
 212
 213     // Output
 214     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 215     typename WriterType::Pointer writer = WriterType::New();
 216     writer->SetFileName(m_ArgsInfo.output_arg);
 217     writer->SetInput(output);
 218     writer->Update();
 219
 220   }
 221
 222
 223   //-------------------------------------------------------------------
 224   // Update with the number of dimensions and the pixeltype
 225   //-------------------------------------------------------------------
 226   template <unsigned int Dimension, class  VectorType>
 227   void
 228   BSplinePyramidGenericFilter::UpdateWithDimAndVectorType()
 229   {
 230
 231     // ImageTypes
 232     typedef typename VectorType::ValueType PixelType;
 233     typedef itk::Image<VectorType, Dimension> VectorInputImageType;
 234     typedef itk::Image<PixelType, Dimension> InputImageType;
 235     typedef itk::Image<PixelType, Dimension> OutputImageType;
 236     typedef itk::Image<VectorType, Dimension> VectorOutputImageType;
 237
 238     // Read the input
 239     typedef itk::ImageFileReader<VectorInputImageType> InputReaderType;
 240     typename InputReaderType::Pointer reader = InputReaderType::New();
 241     reader->SetFileName( m_InputFileName);
 242     reader->Update();
 243     typename VectorInputImageType::Pointer vectorInput= reader->GetOutput();
 244
 245     // Process components separetely and gather afterwards
 246     std::vector<typename OutputImageType::Pointer> components;
 247
 248     for (unsigned int i=0; i<3;i++)
 249       {
 250         // Extract component
 251         typedef clitk::VectorImageToImageFilter<VectorInputImageType, OutputImageType> FilterType;
 252         typename FilterType::Pointer dfilter=FilterType::New();
 253         dfilter->SetInput(vectorInput);
 254         dfilter->SetComponentIndex(i);
 255         dfilter->Update();
 256         typename InputImageType::Pointer input=dfilter->GetOutput();
 257
 258         //============================================================================================
 259         // Resampler Types
 260         typedef itk::BSplineResampleImageFilterBase<InputImageType, InputImageType> ResamplerType;
 261         typedef itk::BSplineCenteredResampleImageFilterBase<InputImageType, InputImageType> CenteredResamplerType;
 262         typedef itk::BSplineL2ResampleImageFilterBase<InputImageType, InputImageType> L2ResamplerType;
 263         typedef itk::BSplineCenteredL2ResampleImageFilterBase<InputImageType, InputImageType> CenteredL2ResamplerType;
 264
 265         // Filter
 266         typedef itk::ImageToImageFilter< InputImageType, InputImageType > ImageToImageFilterType;
 267         typename  ImageToImageFilterType::Pointer filter;
 268
 269         if (!m_ArgsInfo.up_flag)
 270           {
 271             switch (m_ArgsInfo.resamplerType_arg)
 272               {
 273
 274                 // Resampler
 275               case 0: {
 276                 typename itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, ResamplerType >::Pointer df
 277                   = itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, ResamplerType >::New();
 278                 df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 279                 filter=df;
 280                 if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with standard Resampler"<<std::endl;
 281                 break;
 282               }
 283
 284                 //CenteredResamplerType
 285               case 1: {
 286                 typename itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, CenteredResamplerType >::Pointer df
 287                   = itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, CenteredResamplerType >::New();
 288                 df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 289                 filter=df;
 290                 if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with centered Resampler"<<std::endl;
 291                 break;
 292               }
 293
 294                 //L2ResamplerType
 295               case 2:
 296                 {
 297                   typename itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, L2ResamplerType >::Pointer df
 298                     = itk::BSplineDownsampleImageFilter< InputImageType,InputImageType,L2ResamplerType >::New();
 299                   df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 300                   filter=df;
 301                   if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with L2 Resampler"<<std::endl;
 302                   break;
 303                 }
 304
 305                 //Centered L2ResamplerType
 306               case 3:
 307                 {
 308                   typename itk::BSplineDownsampleImageFilter< InputImageType,InputImageType, CenteredL2ResamplerType >::Pointer df
 309                     = itk::BSplineDownsampleImageFilter< InputImageType,InputImageType,CenteredL2ResamplerType >::New();
 310                   df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 311                   filter=df;
 312                   if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with L2 centered Resampler"<<std::endl;
 313                   break;
 314                 }
 315
 316               }
 317           }
 318         else
 319           {
 320             switch (m_ArgsInfo.resamplerType_arg)
 321               {
 322
 323                 // Resampler
 324               case 0: {
 325                 typename itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, ResamplerType >::Pointer df
 326                   = itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, ResamplerType >::New();
 327                 df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 328                 filter=df;
 329                 if (m_Verbose) std::cout<<"Using the BSpline upsample image filter with standard Resampler"<<std::endl;
 330                 break;
 331               }
 332
 333                 //CenteredResamplerType
 334               case 1: {
 335                 typename itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, CenteredResamplerType >::Pointer df
 336                   = itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, CenteredResamplerType >::New();
 337                 df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 338                 filter=df;
 339                 if (m_Verbose) std::cout<<"Using the BSpline upsample image filter with centered Resampler"<<std::endl;
 340                 break;
 341               }
 342
 343                 //L2ResamplerType
 344               case 2:
 345                 {
 346                   typename itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, L2ResamplerType >::Pointer df
 347                     = itk::BSplineUpsampleImageFilter< InputImageType,InputImageType,L2ResamplerType >::New();
 348                   df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 349                   filter=df;
 350                   if (m_Verbose) std::cout<<"Using the BSpline upsample image filter with L2 Resampler"<<std::endl;
 351                   break;
 352                 }
 353
 354                 //Centered L2ResamplerType
 355               case 3:
 356                 {
 357                   typename itk::BSplineUpsampleImageFilter< InputImageType,InputImageType, CenteredL2ResamplerType >::Pointer df
 358                     = itk::BSplineUpsampleImageFilter< InputImageType,InputImageType,CenteredL2ResamplerType >::New();
 359                   df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 360                   filter=df;
 361                   if (m_Verbose) std::cout<<"Using the BSpline upsample image filter with L2 centered Resampler"<<std::endl;
 362                   break;
 363                 }
 364
 365               }
 366           }
 367
 368         // Update
 369         filter->SetInput(input);
 370         filter->Update();
 371         typename OutputImageType::Pointer output=filter->GetOutput();
 372
 373         //===============================================================================
 374         // keep component
 375         components.push_back(output);
 376       }
 377
 378     // Join
 379     typedef itk::Compose3DVectorImageFilter<InputImageType,VectorOutputImageType> ComposeFilterType;
 380     typename ComposeFilterType::Pointer composeFilter=ComposeFilterType::New();
 381     for (unsigned int i=0; i<3;i++)
 382       composeFilter->SetInput(i,components[i]);
 383     composeFilter->Update();
 384     typename VectorOutputImageType::Pointer vectorOutput = composeFilter->GetOutput();
 385
 386
 387     // Output
 388     typedef itk::ImageFileWriter<VectorOutputImageType> WriterType;
 389     typename WriterType::Pointer writer = WriterType::New();
 390     writer->SetFileName(m_ArgsInfo.output_arg);
 391     writer->SetInput(vectorOutput);
 392     writer->Update();
 393
 394   }
 395
 396 }//end clitk
 397
 398 #endif //#define clitkBSplinePyramidGenericFilter_txx