tools/clitkFilterGenericFilter.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 clitkFilterGenericFilter_txx
  19 #define clitkFilterGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkFilterGenericFilter.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   FilterGenericFilter::UpdateWithDim(std::string PixelType)
  40   {
  41     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  42
  43 //     if(PixelType == "short"){
  44 //       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  45 //       UpdateWithDimAndPixelType<Dimension, signed short>();
  46 //     }
  47     //    else if(PixelType == "unsigned_short"){
  48     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  49     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  50     //     }
  51
  52 //     else if (PixelType == "unsigned_char"){
  53 //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  54 //       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  55 //     }
  56
  57     //     else if (PixelType == "char"){
  58     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  59     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  60     //     }
  61  //    else {
  62       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  63       UpdateWithDimAndPixelType<Dimension, float>();
  64 //     }
  65   }
  66
  67
  68   //-------------------------------------------------------------------
  69   // Update with the number of dimensions and the pixeltype
  70   //-------------------------------------------------------------------
  71   template <unsigned int Dimension, class  InternalPixelType>
  72   void
  73   FilterGenericFilter::UpdateWithDimAndPixelType()
  74   {
  75
  76     // ImageTypes
  77     typedef itk::Image<InternalPixelType, Dimension> InputImageType;
  78     typedef itk::Image<InternalPixelType, Dimension> InternalImageType;
  79     typedef itk::Image<InternalPixelType, Dimension> OutputImageType;
  80
  81     // Read the input
  82     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  83     typename InputReaderType::Pointer reader = InputReaderType::New();
  84     reader->SetFileName( m_InputFileName);
  85     reader->Update();
  86     typename InputImageType::Pointer input= reader->GetOutput();
  87
  88
  89     // Filter
  90     typedef itk::ImageToImageFilter< InternalImageType, InternalImageType > ImageToImageFilterType;
  91     typename  ImageToImageFilterType::Pointer filter;
  92
  93     switch ( m_ArgsInfo.type_arg ){
  94
  95     case 0:{
  96       typename itk::DerivativeImageFilter< InternalImageType,InternalImageType >::Pointer df = itk::DerivativeImageFilter<InternalImageType,InternalImageType >::New();
  97
  98       //Set parameters
  99       df->SetDirection(m_ArgsInfo.direction_arg);
 100       df->SetOrder(m_ArgsInfo.order_arg);
 101       filter=df;
 102       if (m_Verbose) std::cout<<"Using the derivative image filter with order "<<m_ArgsInfo.order_arg <<" on direction "<< m_ArgsInfo.direction_arg << "..." << std::endl;
 103       break;
 104     }
 105     case 1:{
 106       typename itk::GradientMagnitudeImageFilter< InternalImageType,InternalImageType >::Pointer gf = itk::GradientMagnitudeImageFilter<InternalImageType,InternalImageType >::New();
 107
 108       //Set parameters
 109       gf->SetUseImageSpacingOn();
 110
 111       filter=gf;
 112       if (m_Verbose) std::cout<<"Using the gradient magnitude image filter... "<< std::endl;
 113       break;
 114     }
 115     case 2:{
 116
 117       switch ( m_ArgsInfo.projection_arg ){
 118
 119       case 0:{
 120         //Sum
 121         typename itk::SumProjectionImageFilter< InternalImageType,InternalImageType >::Pointer pf = itk::SumProjectionImageFilter<InternalImageType,InternalImageType>::New();
 122         //Set parameters
 123         pf->SetProjectionDimension(m_ArgsInfo.direction_arg);
 124
 125         filter=pf;
 126         if (m_Verbose) std::cout<<"Using the Sum projection image filter on the dimension "<<  m_ArgsInfo.direction_arg << "..."<<std::endl;
 127         break;
 128       }
 129       case 1:{
 130         //Max
 131         typename itk::MaximumProjectionImageFilter< InternalImageType,InternalImageType >::Pointer pf = itk::MaximumProjectionImageFilter<InternalImageType,InternalImageType>::New();
 132         //Set parameters
 133         pf->SetProjectionDimension(m_ArgsInfo.direction_arg);
 134
 135         filter=pf;
 136         if (m_Verbose) std::cout<<"Using the maximum intensity projection image filter on the dimension "<<  m_ArgsInfo.direction_arg << "..."<<std::endl;
 137         break;
 138       }
 139       case 2:{
 140         //Sum
 141         typename itk::MinimumProjectionImageFilter< InternalImageType,InternalImageType >::Pointer pf = itk::MinimumProjectionImageFilter<InternalImageType,InternalImageType>::New();
 142         //Set parameters
 143         pf->SetProjectionDimension(m_ArgsInfo.direction_arg);
 144
 145         filter=pf;
 146         if (m_Verbose) std::cout<<"Using the minimum intensity projection image filter on the dimension "<<  m_ArgsInfo.direction_arg << "..."<<std::endl;
 147         break;
 148       }
 149       }
 150       break;
 151     }//end case projection filter
 152
 153     case 3: {
 154       typename itk::IntensityWindowingImageFilter< InternalImageType,InternalImageType >::Pointer pf
 155         = itk::IntensityWindowingImageFilter<InternalImageType,InternalImageType>::New();
 156       //Set parameters
 157       pf->SetWindowMinimum((InternalPixelType) m_ArgsInfo.inputMin_arg);
 158       pf->SetWindowMaximum((InternalPixelType) m_ArgsInfo.inputMax_arg);
 159       pf->SetOutputMinimum((InternalPixelType) m_ArgsInfo.outputMin_arg);
 160       pf->SetOutputMaximum((InternalPixelType) m_ArgsInfo.outputMax_arg);
 161
 162       filter=pf;
 163       if (m_Verbose) std::cout<<"Using the window intensity image filter with the window min and max being  "
 164                               <<  m_ArgsInfo.inputMin_arg << " and "<< m_ArgsInfo.inputMax_arg
 165                               <<" and the output min and max being "<<m_ArgsInfo.outputMin_arg<<" and "
 166                               << m_ArgsInfo.outputMax_arg << std::endl;
 167       break;
 168     }
 169     case 4: {
 170
 171       //Downsample using bsplines: four types of resamplers
 172       typedef itk::BSplineResampleImageFilterBase<InternalImageType, InternalImageType> ResamplerType;
 173       typedef itk::BSplineCenteredResampleImageFilterBase<InternalImageType, InternalImageType> CenteredResamplerType;
 174       typedef itk::BSplineL2ResampleImageFilterBase<InternalImageType, InternalImageType> L2ResamplerType;
 175       typedef itk::BSplineCenteredL2ResampleImageFilterBase<InternalImageType, InternalImageType> CenteredL2ResamplerType;
 176
 177       //ResamplerType
 178       if(m_ArgsInfo.resamplerType_arg==0)
 179         {
 180           typename itk::BSplineDownsampleImageFilter< InternalImageType,InternalImageType, ResamplerType >::Pointer df
 181             = itk::BSplineDownsampleImageFilter< InternalImageType,InternalImageType, ResamplerType >::New();
 182           df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 183           filter=df;
 184           if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with Standard Resampler"<<std::endl;
 185         }
 186       //CenteredResamplerType
 187       else if(m_ArgsInfo.resamplerType_arg==1)
 188         {
 189           typename itk::BSplineDownsampleImageFilter< InternalImageType,InternalImageType, CenteredResamplerType >::Pointer df
 190             = itk::BSplineDownsampleImageFilter< InternalImageType,InternalImageType, CenteredResamplerType >::New();
 191           df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 192           filter=df;
 193           if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with  Centered Resampler"<<std::endl;
 194         }
 195       //L2ResamplerType
 196       else if(m_ArgsInfo.resamplerType_arg==2)
 197         {
 198           typename itk::BSplineDownsampleImageFilter< InternalImageType,InternalImageType, L2ResamplerType >::Pointer df
 199             = itk::BSplineDownsampleImageFilter< InternalImageType,InternalImageType,L2ResamplerType >::New();
 200           df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 201           filter=df;
 202           if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with L2 Resampler"<<std::endl;
 203         }
 204       else if(m_ArgsInfo.resamplerType_arg==3)
 205         {
 206           typename itk::BSplineDownsampleImageFilter< InternalImageType,InternalImageType, CenteredL2ResamplerType >::Pointer df
 207             = itk::BSplineDownsampleImageFilter< InternalImageType,InternalImageType,CenteredL2ResamplerType >::New();
 208           df->SetSplineOrder(m_ArgsInfo.splineOrder_arg);
 209           filter=df;
 210           if (m_Verbose) std::cout<<"Using the BSpline downsample image filter with L2 Centered Resampler"<<std::endl;
 211         }
 212       break;
 213     }
 214     case 5: {
 215       typedef itk::NormalizeImageFilter<InternalImageType, InternalImageType> NormalizeFilterType;
 216       typename  NormalizeFilterType::Pointer  df = NormalizeFilterType::New();
 217       filter=df;
 218       if (m_Verbose) std::cout <<  "Normalizing image intensities to a zero mean and 1 SD (float!)..." << std::endl;
 219       break;
 220     }
 221 //     case 6: {
 222 //       typedef itk::AnisotropicDiffusionImageFilter<InternalImageType, InternalImageType> FilterType;
 223 //       typename FilterType::Pointer  df = FilterType::New();
 224 //       df->SetConductanceParameter(m_ArgsInfo.cond_arg);
 225 //       df->SetNumberOfIterations(m_ArgsInfo.iter_arg);
 226 //       df->SetTimeStep(m_ArgsInfo.time_arg);
 227 //       df->SetUseImageSpacing(true);
 228
 229 //       filter=df;
 230 //       if (m_Verbose) std::cout <<  "Using the anisotropic diffusion image filter..." << std::endl;
 231 //       break;
 232 //     }
 233
 234     case 7: {
 235       typedef itk::GradientAnisotropicDiffusionImageFilter<InternalImageType, InternalImageType> FilterType;
 236       typename FilterType::Pointer  df = FilterType::New();
 237       df->SetConductanceParameter(m_ArgsInfo.cond_arg);
 238       df->SetNumberOfIterations(m_ArgsInfo.iter_arg);
 239       df->SetTimeStep(m_ArgsInfo.time_arg);
 240       df->SetUseImageSpacing(true);
 241
 242       filter=df;
 243       if (m_Verbose) std::cout <<  "Using the gradient anisotropic diffusion image filter..." << std::endl;
 244       break;
 245     }
 246
 247     case 8: {
 248       typedef itk::CurvatureAnisotropicDiffusionImageFilter<InternalImageType, InternalImageType> FilterType;
 249       typename  FilterType::Pointer  df = FilterType::New();
 250       df->SetConductanceParameter(m_ArgsInfo.cond_arg);
 251       df->SetNumberOfIterations(m_ArgsInfo.iter_arg);
 252       df->SetTimeStep(m_ArgsInfo.time_arg);
 253       df->SetUseImageSpacing(true);
 254
 255       filter=df;
 256       if (m_Verbose) std::cout <<  "Using the Curvature anisotropic diffusion image filter..." << std::endl;
 257       break;
 258     }
 259
 260     case 9: {
 261       typedef itk::CurvatureFlowImageFilter<InternalImageType, InternalImageType> FilterType;
 262       typename  FilterType::Pointer  df = FilterType::New();
 263       df->SetTimeStep(m_ArgsInfo.time_arg);
 264       df->SetUseImageSpacing(true);
 265       df->SetNumberOfIterations(m_ArgsInfo.iter_arg);
 266       filter=df;
 267       if (m_Verbose) std::cout <<  "Using the curvature flow image filter......" << std::endl;
 268       break;
 269     }
 270
 271
 272     }//end switch filterType
 273
 274
 275     //==================================================================
 276     //execute the filter
 277     filter->SetInput(input);
 278
 279
 280     if (m_Verbose)std::cout<<"Starting filter..."<<std::endl;
 281
 282     try {
 283       filter->Update();
 284     }
 285     catch( itk::ExceptionObject & err )
 286       {
 287         std::cerr << "ExceptionObject caught! Filter failed!" << std::endl;
 288         std::cerr << err << std::endl;
 289         return;
 290       }
 291
 292     // Output
 293     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 294     typename WriterType::Pointer writer = WriterType::New();
 295     writer->SetFileName(m_ArgsInfo.output_arg);
 296     writer->SetInput(filter->GetOutput());
 297     writer->Update();
 298
 299   }
 300
 301
 302 }//end clitk
 303
 304 #endif //#define clitkFilterGenericFilter_txx