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