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