filters/clitkImageResampleGenericFilter.cxx

   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 CLITKIMAGERESAMPLEGENERICFILTER2_CXX
  19 #define CLITKIMAGERESAMPLEGENERICFILTER2_CXX
  20 /**
  21  -------------------------------------------------------------------
  22  * @file   clitkImageResampleGenericFilter.cxx
  23  * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
  24  * @date   23 Feb 2008 08:37:53
  25
  26  * @brief
  27
  28  -------------------------------------------------------------------*/
  29
  30 #include "clitkImageResampleGenericFilter.h"
  31
  32 // itk include
  33 #include "itkImage.h"
  34 #include "itkImageFileReader.h"
  35 #include "itkImageSeriesReader.h"
  36 #include "itkImageFileWriter.h"
  37 #include "itkRecursiveGaussianImageFilter.h"
  38 #include "itkResampleImageFilter.h"
  39 #include "itkAffineTransform.h"
  40 #include "itkNearestNeighborInterpolateImageFunction.h"
  41 #include "itkLinearInterpolateImageFunction.h"
  42 #include "itkBSplineInterpolateImageFunction.h"
  43 #include "itkBSplineInterpolateImageFunctionWithLUT.h"
  44 #include "itkCommand.h"
  45
  46 //--------------------------------------------------------------------
  47 clitk::ImageResampleGenericFilter::ImageResampleGenericFilter():
  48   ImageToImageGenericFilter<Self>("ImageResample")
  49 {
  50   mApplyGaussianFilterBefore = false;
  51   mDefaultPixelValue = 0.0;
  52   mInterpolatorName = "NN";
  53   mBSplineOrder=3;
  54   InitializeImageTypeWithDim<2>();
  55   InitializeImageTypeWithDim<3>();
  56   InitializeImageTypeWithDim<4>();
  57 }
  58 //--------------------------------------------------------------------
  59
  60
  61 //--------------------------------------------------------------------
  62 template<unsigned int Dim>
  63 void clitk::ImageResampleGenericFilter::InitializeImageTypeWithDim()
  64 {
  65   ADD_DEFAULT_IMAGE_TYPES(Dim);
  66 }
  67 //--------------------------------------------------------------------
  68
  69
  70 //--------------------------------------------------------------------
  71 template<class InputImageType>
  72 void clitk::ImageResampleGenericFilter::UpdateWithInputImageType()
  73 {
  74
  75   // Some typedefs
  76   typedef typename InputImageType::SizeType    SizeType;
  77   typedef typename InputImageType::SpacingType SpacingType;
  78   typedef typename InputImageType::PointType   PointType;
  79   typedef typename InputImageType::PixelType   PixelType;
  80   static unsigned int dim = InputImageType::ImageDimension;
  81
  82   // Reading input
  83   typename InputImageType::Pointer input = this->GetInput<InputImageType>(0);
  84
  85   // Warning
  86   if (!std::numeric_limits<PixelType>::is_signed) {
  87     if ((mInterpolatorName == "bspline") || (mInterpolatorName == "blut")) {
  88       std::cerr << "Warning : input pixel type is not signed, use bspline interpolation at your own risk ..." << std::endl;
  89     }
  90   }
  91
  92   // Check options
  93   if (mOutputSize.size() != dim) {
  94     std::cerr << "Please set size with " << dim << " dimensions." << std::endl;
  95     return;
  96   }
  97   if (mOutputSpacing.size() != dim) {
  98     std::cerr << "Please set spacing with " << dim << " dimensions." << std::endl;
  99     return;
 100   }
 101   mOutputOrigin.resize(dim);
 102
 103   if (mApplyGaussianFilterBefore && mSigma.size() != dim) {
 104     std::cerr << "Please set sigma with " << dim << " dimensions." << std::endl;
 105     return;
 106   }
 107
 108   // Create Image Filter
 109   typedef itk::ResampleImageFilter<InputImageType,InputImageType> FilterType;
 110   typename FilterType::Pointer filter = FilterType::New();
 111
 112   // Instance of the transform object to be passed to the resample
 113   // filter. By default, identity transform is applied
 114   typedef itk::AffineTransform<double, InputImageType::ImageDimension> TransformType;
 115   typename TransformType::Pointer transform =  TransformType::New();
 116   filter->SetTransform(transform);
 117
 118   // Set filter's parameters
 119   SizeType outputSize;
 120   SpacingType outputSpacing;
 121   PointType outputOrigin;
 122   for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
 123     outputSize[i] = mOutputSize[i];
 124     outputSpacing[i] = mOutputSpacing[i];
 125     outputOrigin[i] = input->GetOrigin()[i];
 126   }
 127
 128   filter->SetSize(outputSize);
 129   filter->SetOutputSpacing(outputSpacing);
 130   filter->SetOutputOrigin(outputOrigin);
 131   filter->SetDefaultPixelValue(static_cast<PixelType>(mDefaultPixelValue));//DS TODO//JV comme ça?
 132
 133   // Select interpolator
 134   if (mInterpolatorName == "nn") {
 135     typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, double> InterpolatorType;
 136     typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 137     filter->SetInterpolator(interpolator);
 138   } else {
 139     if (mInterpolatorName == "linear") {
 140       typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
 141       typename InterpolatorType::Pointer interpolator =  InterpolatorType::New();
 142       filter->SetInterpolator(interpolator);
 143     } else {
 144       if (mInterpolatorName == "bspline") {
 145         typedef itk::BSplineInterpolateImageFunction<InputImageType, double> InterpolatorType;
 146         typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 147         interpolator->SetSplineOrder(mBSplineOrder);
 148         filter->SetInterpolator(interpolator);
 149       } else {
 150         if (mInterpolatorName == "blut") {
 151           typedef itk::BSplineInterpolateImageFunctionWithLUT<InputImageType, double> InterpolatorType;
 152           typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 153           interpolator->SetSplineOrder(mBSplineOrder);
 154           interpolator->SetLUTSamplingFactor(mSamplingFactors[0]);
 155           filter->SetInterpolator(interpolator);
 156         } else {
 157           std::cerr << "Sorry, I do not know the interpolator '" << mInterpolatorName
 158                     << "'. Known interpolators are :  nn, linear, bspline, blut" << std::endl;
 159           exit(0);
 160         }
 161       }
 162     }
 163   }
 164
 165   // Build initial Gaussian bluring (if needed)
 166   typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
 167   std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
 168   if (mApplyGaussianFilterBefore) {
 169     for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
 170       // Create filter
 171       gaussianFilters.push_back(GaussianFilterType::New());
 172       // Set options
 173       gaussianFilters[i]->SetDirection(i);
 174       gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
 175       gaussianFilters[i]->SetNormalizeAcrossScale(false);
 176       gaussianFilters[i]->SetSigma(mSigma[i]); // in millimeter !
 177       // Set input
 178       if (i==0) gaussianFilters[i]->SetInput(input);
 179       else gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
 180     }
 181     filter->SetInput(gaussianFilters[InputImageType::ImageDimension-1]->GetOutput());
 182   } else {
 183     filter->SetInput(input);
 184   }
 185
 186   // Go !
 187   try {
 188     filter->Update();
 189   } catch( itk::ExceptionObject & err ) {
 190     std::cerr << "Error while filtering " << mInputFilenames[0].c_str()
 191               << " " << err << std::endl;
 192     exit(0);
 193   }
 194
 195   // Get result
 196   typename InputImageType::Pointer outputImage = filter->GetOutput();
 197
 198   // Write/save results
 199   this->SetNextOutput<InputImageType>(outputImage);
 200
 201 }
 202 //--------------------------------------------------------------------
 203
 204
 205 //--------------------------------------------------------------------
 206 void clitk::ImageResampleGenericFilter::SetOutputSize(const std::vector<int> & size)
 207 {
 208   mOutputSize.resize(size.size());
 209   std::copy(size.begin(), size.end(), mOutputSize.begin());
 210 }
 211 //--------------------------------------------------------------------
 212
 213 //--------------------------------------------------------------------
 214 void clitk::ImageResampleGenericFilter::SetOutputSpacing(const std::vector<double> & spacing)
 215 {
 216   mOutputSpacing.resize(spacing.size());
 217   std::copy(spacing.begin(), spacing.end(), mOutputSpacing.begin());
 218 }
 219 //--------------------------------------------------------------------
 220
 221 //--------------------------------------------------------------------
 222 void clitk::ImageResampleGenericFilter::SetInterpolationName(const std::string & inter)
 223 {
 224   mInterpolatorName = inter;
 225 }
 226 //--------------------------------------------------------------------
 227
 228 //--------------------------------------------------------------------
 229 void clitk::ImageResampleGenericFilter::SetGaussianSigma(const std::vector<double> & sigma)
 230 {
 231   mApplyGaussianFilterBefore = true;
 232   mSigma.resize(sigma.size());
 233   std::copy(sigma.begin(), sigma.end(), mSigma.begin());
 234 }
 235 //--------------------------------------------------------------------
 236
 237 #endif
 238