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_IMAGE_TYPE(Dim, char);
  64     ADD_IMAGE_TYPE(Dim, uchar);
  65     ADD_IMAGE_TYPE(Dim, short);
  66     ADD_IMAGE_TYPE(Dim, ushort);
  67     ADD_IMAGE_TYPE(Dim, int);
  68     ADD_IMAGE_TYPE(Dim, float);
  69     ADD_IMAGE_TYPE(Dim, double);
  70 }
  71 //--------------------------------------------------------------------
  72
  73
  74 //--------------------------------------------------------------------
  75 template<class InputImageType>
  76 void clitk::ImageResampleGenericFilter::UpdateWithInputImageType() {
  77
  78   // Some typedefs
  79   typedef typename InputImageType::SizeType    SizeType;
  80   typedef typename InputImageType::SpacingType SpacingType;
  81   typedef typename InputImageType::PointType   PointType;
  82   typedef typename InputImageType::PixelType   PixelType;
  83   static unsigned int dim = InputImageType::ImageDimension;
  84
  85   // Reading input
  86   typename InputImageType::Pointer input = this->GetInput<InputImageType>(0);
  87
  88   // Warning
  89   if (!std::numeric_limits<PixelType>::is_signed) {
  90     if ((mInterpolatorName == "bspline") || (mInterpolatorName == "blut")) {
  91       std::cerr << "Warning : input pixel type is not signed, use bspline interpolation at your own risk ..." << std::endl;
  92     }
  93   }
  94
  95   // Check options
  96   if (mOutputSize.size() != dim) {
  97     std::cerr << "Please set size with " << dim << " dimensions." << std::endl;
  98     return;
  99   }
 100   if (mOutputSpacing.size() != dim) {
 101     std::cerr << "Please set spacing with " << dim << " dimensions." << std::endl;
 102     return;
 103   }
 104   mOutputOrigin.resize(dim);
 105
 106   if (mApplyGaussianFilterBefore && mSigma.size() != dim) {
 107     std::cerr << "Please set sigma with " << dim << " dimensions." << std::endl;
 108     return;
 109   }
 110
 111   // Create Image Filter
 112   typedef itk::ResampleImageFilter<InputImageType,InputImageType> FilterType;
 113   typename FilterType::Pointer filter = FilterType::New();
 114
 115   // Instance of the transform object to be passed to the resample
 116   // filter. By default, identity transform is applied
 117   typedef itk::AffineTransform<double, InputImageType::ImageDimension> TransformType;
 118   typename TransformType::Pointer transform =  TransformType::New();
 119   filter->SetTransform(transform);
 120
 121   // Set filter's parameters
 122   SizeType outputSize;
 123   SpacingType outputSpacing;
 124   PointType outputOrigin;
 125   for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
 126     outputSize[i] = mOutputSize[i];
 127     outputSpacing[i] = mOutputSpacing[i];
 128     outputOrigin[i] = input->GetOrigin()[i];
 129   }
 130
 131   filter->SetSize(outputSize);
 132   filter->SetOutputSpacing(outputSpacing);
 133   filter->SetOutputOrigin(outputOrigin);
 134   filter->SetDefaultPixelValue(static_cast<PixelType>(mDefaultPixelValue));//DS TODO//JV comme ça?
 135
 136   // Select interpolator
 137   if (mInterpolatorName == "nn") {
 138     typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, double> InterpolatorType;
 139     typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 140     filter->SetInterpolator(interpolator);
 141   }
 142   else {
 143     if (mInterpolatorName == "linear") {
 144       typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
 145       typename InterpolatorType::Pointer interpolator =  InterpolatorType::New();
 146       filter->SetInterpolator(interpolator);
 147     }
 148     else {
 149       if (mInterpolatorName == "bspline") {
 150         typedef itk::BSplineInterpolateImageFunction<InputImageType, double> InterpolatorType;
 151         typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 152         interpolator->SetSplineOrder(mBSplineOrder);
 153         filter->SetInterpolator(interpolator);
 154       }
 155       else {
 156         if (mInterpolatorName == "blut") {
 157           typedef itk::BSplineInterpolateImageFunctionWithLUT<InputImageType, double> InterpolatorType;
 158           typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
 159           interpolator->SetSplineOrder(mBSplineOrder);
 160           interpolator->SetLUTSamplingFactor(mSamplingFactors[0]);
 161           filter->SetInterpolator(interpolator);
 162         }
 163         else {
 164           std::cerr << "Sorry, I do not know the interpolator '" << mInterpolatorName
 165                     << "'. Known interpolators are :  nn, linear, bspline, blut" << std::endl;
 166           exit(0);
 167         }
 168       }
 169     }
 170   }
 171
 172   // Build initial Gaussian bluring (if needed)
 173   typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
 174   std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
 175   if (mApplyGaussianFilterBefore) {
 176     for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
 177       // Create filter
 178       gaussianFilters.push_back(GaussianFilterType::New());
 179       // Set options
 180       gaussianFilters[i]->SetDirection(i);
 181       gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
 182       gaussianFilters[i]->SetNormalizeAcrossScale(false);
 183       gaussianFilters[i]->SetSigma(mSigma[i]); // in millimeter !
 184       // Set input
 185       if (i==0) gaussianFilters[i]->SetInput(input);
 186       else gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
 187     }
 188     filter->SetInput(gaussianFilters[InputImageType::ImageDimension-1]->GetOutput());
 189   }
 190   else {
 191     filter->SetInput(input);
 192   }
 193
 194   // Go !
 195   try {
 196     filter->Update();
 197   }
 198   catch( itk::ExceptionObject & err ) {
 199     std::cerr << "Error while filtering " << mInputFilenames[0].c_str()
 200               << " " << err << std::endl;
 201     exit(0);
 202   }
 203
 204   // Get result
 205    typename InputImageType::Pointer outputImage = filter->GetOutput();
 206
 207   // Write/save results
 208   this->SetNextOutput<InputImageType>(outputImage);
 209
 210 }
 211 //--------------------------------------------------------------------
 212
 213
 214 //--------------------------------------------------------------------
 215 void clitk::ImageResampleGenericFilter::SetOutputSize(const std::vector<int> & size) {
 216   mOutputSize.resize(size.size());
 217   std::copy(size.begin(), size.end(), mOutputSize.begin());
 218 }
 219 //--------------------------------------------------------------------
 220
 221 //--------------------------------------------------------------------
 222 void clitk::ImageResampleGenericFilter::SetOutputSpacing(const std::vector<double> & spacing) {
 223   mOutputSpacing.resize(spacing.size());
 224   std::copy(spacing.begin(), spacing.end(), mOutputSpacing.begin());
 225 }
 226 //--------------------------------------------------------------------
 227
 228 //--------------------------------------------------------------------
 229 void clitk::ImageResampleGenericFilter::SetInterpolationName(const std::string & inter) {
 230   mInterpolatorName = inter;
 231 }
 232 //--------------------------------------------------------------------
 233
 234 //--------------------------------------------------------------------
 235 void clitk::ImageResampleGenericFilter::SetGaussianSigma(const std::vector<double> & sigma) {
 236   mApplyGaussianFilterBefore = true;
 237   mSigma.resize(sigma.size());
 238   std::copy(sigma.begin(), sigma.end(), mSigma.begin());
 239 }
 240 //--------------------------------------------------------------------
 241
 242 #endif
 243