filters/clitkImageResampleGenericFilter.cxx

   1 #ifndef CLITKIMAGERESAMPLEGENERICFILTER2_CXX
   2 #define CLITKIMAGERESAMPLEGENERICFILTER2_CXX
   3
   4 /**
   5  -------------------------------------------------------------------
   6  * @file   clitkImageResampleGenericFilter.cxx
   7  * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
   8  * @date   23 Feb 2008 08:37:53
   9
  10  * @brief
  11
  12  -------------------------------------------------------------------*/
  13
  14 #include "clitkImageResampleGenericFilter.h"
  15
  16 // itk include
  17 #include "itkImage.h"
  18 #include "itkImageFileReader.h"
  19 #include "itkImageSeriesReader.h"
  20 #include "itkImageFileWriter.h"
  21 #include "itkRecursiveGaussianImageFilter.h"
  22 #include "itkResampleImageFilter.h"
  23 #include "itkAffineTransform.h"
  24 #include "itkNearestNeighborInterpolateImageFunction.h"
  25 #include "itkLinearInterpolateImageFunction.h"
  26 #include "itkBSplineInterpolateImageFunction.h"
  27 #include "itkBSplineInterpolateImageFunctionWithLUT.h"
  28 #include "itkCommand.h"
  29
  30 //--------------------------------------------------------------------
  31 clitk::ImageResampleGenericFilter::ImageResampleGenericFilter():
  32   ImageToImageGenericFilter<Self>("ImageResample") {
  33   mApplyGaussianFilterBefore = false;
  34   mDefaultPixelValue = 0.0;
  35   mInterpolatorName = "NN";
  36   mBSplineOrder=3;
  37   InitializeImageTypeWithDim<2>();
  38   InitializeImageTypeWithDim<3>();
  39   InitializeImageTypeWithDim<4>();
  40 }
  41 //--------------------------------------------------------------------
  42
  43
  44 //--------------------------------------------------------------------
  45 template<unsigned int Dim>
  46 void clitk::ImageResampleGenericFilter::InitializeImageTypeWithDim() {
  47   ADD_IMAGE_TYPE(Dim, char);
  48   ADD_IMAGE_TYPE(Dim, short);
  49   ADD_IMAGE_TYPE(Dim, int);
  50   ADD_IMAGE_TYPE(Dim, float);
  51 }
  52 //--------------------------------------------------------------------
  53
  54
  55 //--------------------------------------------------------------------
  56 template<class InputImageType>
  57 void clitk::ImageResampleGenericFilter::UpdateWithInputImageType() {
  58
  59   // Some typedefs
  60   typedef typename InputImageType::SizeType    SizeType;
  61   typedef typename InputImageType::SpacingType SpacingType;
  62   typedef typename InputImageType::PointType   PointType;
  63   typedef typename InputImageType::PixelType   PixelType;
  64   static unsigned int dim = InputImageType::ImageDimension;
  65
  66   // Reading input
  67   typename InputImageType::Pointer input = this->GetInput<InputImageType>(0);
  68
  69   // Warning
  70   if (!std::numeric_limits<PixelType>::is_signed) {
  71     if ((mInterpolatorName == "bspline") || (mInterpolatorName == "blut")) {
  72       std::cerr << "Warning : input pixel type is not signed, use bspline interpolation at your own risk ..." << std::endl;
  73     }
  74   }
  75
  76   // Check options
  77   if (mOutputSize.size() != dim) {
  78     std::cerr << "Please set size with " << dim << " dimensions." << std::endl;
  79     return;
  80   }
  81   if (mOutputSpacing.size() != dim) {
  82     std::cerr << "Please set spacing with " << dim << " dimensions." << std::endl;
  83     return;
  84   }
  85   mOutputOrigin.resize(dim);
  86
  87   if (mApplyGaussianFilterBefore && mSigma.size() != dim) {
  88     std::cerr << "Please set sigma with " << dim << " dimensions." << std::endl;
  89     return;
  90   }
  91
  92   // Create Image Filter
  93   typedef itk::ResampleImageFilter<InputImageType,InputImageType> FilterType;
  94   typename FilterType::Pointer filter = FilterType::New();
  95
  96   // Instance of the transform object to be passed to the resample
  97   // filter. By default, identity transform is applied
  98   typedef itk::AffineTransform<double, InputImageType::ImageDimension> TransformType;
  99   typename TransformType::Pointer transform =  TransformType::New();
 100   filter->SetTransform(transform);
 101
 102   // Set filter's parameters
 103   SizeType outputSize;
 104   SpacingType outputSpacing;
 105   PointType outputOrigin;
 106   for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
 107     outputSize[i] = mOutputSize[i];
 108     outputSpacing[i] = mOutputSpacing[i];
 109     outputOrigin[i] = input->GetOrigin()[i];
 110   }
 111
 112   filter->SetSize(outputSize);
 113   filter->SetOutputSpacing(outputSpacing);
 114   filter->SetOutputOrigin(outputOrigin);
 115   filter->SetDefaultPixelValue(static_cast<PixelType>(mDefaultPixelValue));//DS TODO//JV comme ça?
 116
 117   // Select interpolator
 118   if (mInterpolatorName == "nn") {
 119     typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, double> InterpolatorType;
 120     typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 121     filter->SetInterpolator(interpolator);
 122   }
 123   else {
 124     if (mInterpolatorName == "linear") {
 125       typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
 126       typename InterpolatorType::Pointer interpolator =  InterpolatorType::New();
 127       filter->SetInterpolator(interpolator);
 128     }
 129     else {
 130       if (mInterpolatorName == "bspline") {
 131         typedef itk::BSplineInterpolateImageFunction<InputImageType, double> InterpolatorType;
 132         typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 133         interpolator->SetSplineOrder(mBSplineOrder);
 134         filter->SetInterpolator(interpolator);
 135       }
 136       else {
 137         if (mInterpolatorName == "blut") {
 138           typedef itk::BSplineInterpolateImageFunctionWithLUT<InputImageType, double> InterpolatorType;
 139           typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 140           interpolator->SetSplineOrder(mBSplineOrder);
 141           interpolator->SetLUTSamplingFactor(mSamplingFactors[0]);
 142           filter->SetInterpolator(interpolator);
 143         }
 144         else {
 145           std::cerr << "Sorry, I do not know the interpolator '" << mInterpolatorName
 146                     << "'. Known interpolators are :  nn, linear, bspline, blut" << std::endl;
 147           exit(0);
 148         }
 149       }
 150     }
 151   }
 152
 153   // Build initial Gaussian bluring (if needed)
 154   typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
 155   std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
 156   if (mApplyGaussianFilterBefore) {
 157     for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
 158       // Create filter
 159       gaussianFilters.push_back(GaussianFilterType::New());
 160       // Set options
 161       gaussianFilters[i]->SetDirection(i);
 162       gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
 163       gaussianFilters[i]->SetNormalizeAcrossScale(false);
 164       gaussianFilters[i]->SetSigma(mSigma[i]); // in millimeter !
 165       // Set input
 166       if (i==0) gaussianFilters[i]->SetInput(input);
 167       else gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
 168     }
 169     filter->SetInput(gaussianFilters[InputImageType::ImageDimension-1]->GetOutput());
 170   }
 171   else {
 172     filter->SetInput(input);
 173   }
 174
 175   // Go !
 176   try {
 177     filter->Update();
 178   }
 179   catch( itk::ExceptionObject & err ) {
 180     std::cerr << "Error while filtering " << mInputFilenames[0].c_str()
 181               << " " << err << std::endl;
 182     exit(0);
 183   }
 184
 185   // Get result
 186    typename InputImageType::Pointer outputImage = filter->GetOutput();
 187
 188   // Write/save results
 189   this->SetNextOutput<InputImageType>(outputImage);
 190
 191 }
 192 //--------------------------------------------------------------------
 193
 194
 195 //--------------------------------------------------------------------
 196 void clitk::ImageResampleGenericFilter::SetOutputSize(const std::vector<int> & size) {
 197   mOutputSize.resize(size.size());
 198   std::copy(size.begin(), size.end(), mOutputSize.begin());
 199 }
 200 //--------------------------------------------------------------------
 201
 202 //--------------------------------------------------------------------
 203 void clitk::ImageResampleGenericFilter::SetOutputSpacing(const std::vector<double> & spacing) {
 204   mOutputSpacing.resize(spacing.size());
 205   std::copy(spacing.begin(), spacing.end(), mOutputSpacing.begin());
 206 }
 207 //--------------------------------------------------------------------
 208
 209 //--------------------------------------------------------------------
 210 void clitk::ImageResampleGenericFilter::SetInterpolationName(const std::string & inter) {
 211   mInterpolatorName = inter;
 212 }
 213 //--------------------------------------------------------------------
 214
 215 //--------------------------------------------------------------------
 216 void clitk::ImageResampleGenericFilter::SetGaussianSigma(const std::vector<double> & sigma) {
 217   mApplyGaussianFilterBefore = true;
 218   mSigma.resize(sigma.size());
 219   std::copy(sigma.begin(), sigma.end(), mSigma.begin());
 220 }
 221 //--------------------------------------------------------------------
 222
 223 #endif
 224