X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=filters%2FclitkImageResampleGenericFilter.cxx;h=ab8e1131dad78ff1bd86f13ea6a3609c55286f3f;hb=0bbf0c26e4e2b917143315bec9ce1c52a357a500;hp=0187e493f9c76a2a83912a332a780e4d30994057;hpb=931a42358442f4ee4f314613c991c838d4b4e3b7;p=clitk.git

diff --git a/filters/clitkImageResampleGenericFilter.cxx b/filters/clitkImageResampleGenericFilter.cxx
index 0187e49..ab8e113 100644
--- a/filters/clitkImageResampleGenericFilter.cxx
+++ b/filters/clitkImageResampleGenericFilter.cxx
@@ -1,65 +1,240 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to:
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+======================================================================-====*/
 #ifndef CLITKIMAGERESAMPLEGENERICFILTER2_CXX
 #define CLITKIMAGERESAMPLEGENERICFILTER2_CXX
-
 /**
  -------------------------------------------------------------------
  * @file   clitkImageResampleGenericFilter.cxx
  * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
  * @date   23 Feb 2008 08:37:53
 
- * @brief  
+ * @brief
 
  -------------------------------------------------------------------*/
 
 #include "clitkImageResampleGenericFilter.h"
 
+// itk include
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageSeriesReader.h"
+#include "itkImageFileWriter.h"
+#include "itkRecursiveGaussianImageFilter.h"
+#include "itkResampleImageFilter.h"
+#include "itkAffineTransform.h"
+#include "itkNearestNeighborInterpolateImageFunction.h"
+#include "itkWindowedSincInterpolateImageFunction.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkBSplineInterpolateImageFunction.h"
+#include "itkBSplineInterpolateImageFunctionWithLUT.h"
+#include "itkCommand.h"
+
 //--------------------------------------------------------------------
-clitk::ImageResampleGenericFilter::ImageResampleGenericFilter() {
+clitk::ImageResampleGenericFilter::ImageResampleGenericFilter():
+  ImageToImageGenericFilter<Self>("ImageResample")
+{
   mApplyGaussianFilterBefore = false;
   mDefaultPixelValue = 0.0;
   mInterpolatorName = "NN";
   mBSplineOrder=3;
+  InitializeImageTypeWithDim<2>();
+  InitializeImageTypeWithDim<3>();
+  InitializeImageTypeWithDim<4>();
 }
 //--------------------------------------------------------------------
 
+
 //--------------------------------------------------------------------
-void clitk::ImageResampleGenericFilter::Update() {
+template<unsigned int Dim>
+void clitk::ImageResampleGenericFilter::InitializeImageTypeWithDim()
+{
+  ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class InputImageType>
+void clitk::ImageResampleGenericFilter::UpdateWithInputImageType()
+{
+
+  // Some typedefs
+  typedef typename InputImageType::SizeType    SizeType;
+  typedef typename InputImageType::SpacingType SpacingType;
+  typedef typename InputImageType::PointType   PointType;
+  typedef typename InputImageType::PixelType   PixelType;
+  static unsigned int dim = InputImageType::ImageDimension;
 
-  // Determine dim, pixel type, number of components
-  this->GetInputImageDimensionAndPixelType(mDim,mPixelTypeName,mNbOfComponents);
+  // Reading input
+  typename InputImageType::Pointer input = this->GetInput<InputImageType>(0);
 
-  // Switch by dimension
-  if (mDim == 2) { Update_WithDim<2>(); return; }
-  if (mDim == 3) { Update_WithDim<3>(); return; }
-  if (mDim == 4) { Update_WithDim<4>(); return; }
+  // Warning
+  if (!std::numeric_limits<PixelType>::is_signed) {
+    if ((mInterpolatorName == "bspline") || (mInterpolatorName == "blut")) {
+      std::cerr << "Warning : input pixel type is not signed, use bspline interpolation at your own risk ..." << std::endl;
+    }
+  }
+
+  // Check options
+  if (mOutputSize.size() != dim) {
+    std::cerr << "Please set size with " << dim << " dimensions." << std::endl;
+    return;
+  }
+  if (mOutputSpacing.size() != dim) {
+    std::cerr << "Please set spacing with " << dim << " dimensions." << std::endl;
+    return;
+  }
+  mOutputOrigin.resize(dim);
+
+  if (mApplyGaussianFilterBefore && mSigma.size() != dim) {
+    std::cerr << "Please set sigma with " << dim << " dimensions." << std::endl;
+    return;
+  }
+
+  // Create Image Filter
+  typedef itk::ResampleImageFilter<InputImageType,InputImageType> FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+
+  // Instance of the transform object to be passed to the resample
+  // filter. By default, identity transform is applied
+  typedef itk::AffineTransform<double, InputImageType::ImageDimension> TransformType;
+  typename TransformType::Pointer transform =  TransformType::New();
+  filter->SetTransform(transform);
+
+  // Set filter's parameters
+  SizeType outputSize;
+  SpacingType outputSpacing;
+  PointType outputOrigin;
+  for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
+    outputSize[i] = mOutputSize[i];
+    outputSpacing[i] = mOutputSpacing[i];
+    outputOrigin[i] = input->GetOrigin()[i];
+  }
+
+  filter->SetSize(outputSize);
+  filter->SetOutputSpacing(outputSpacing);
+  filter->SetOutputOrigin(outputOrigin);
+  filter->SetDefaultPixelValue(static_cast<PixelType>(mDefaultPixelValue));//DS TODO//JV comme ça?
+
+  // Select interpolator
+  if (mInterpolatorName == "nn") {
+    typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, double> InterpolatorType;
+    typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
+    filter->SetInterpolator(interpolator);
+  } else {
+    if (mInterpolatorName == "linear") {
+      typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
+      typename InterpolatorType::Pointer interpolator =  InterpolatorType::New();
+      filter->SetInterpolator(interpolator);
+    } else {
+      if (mInterpolatorName == "windowed sinc") {
+        typedef itk::WindowedSincInterpolateImageFunction<InputImageType, 4> InterpolatorType;
+        typename InterpolatorType::Pointer interpolator =  InterpolatorType::New();
+        filter->SetInterpolator(interpolator);
+      } else {
+        if (mInterpolatorName == "bspline") {
+          typedef itk::BSplineInterpolateImageFunction<InputImageType, double> InterpolatorType;
+          typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
+          interpolator->SetSplineOrder(mBSplineOrder);
+          filter->SetInterpolator(interpolator); 
+        } else {
+          if (mInterpolatorName == "blut") {
+            typedef itk::BSplineInterpolateImageFunctionWithLUT<InputImageType, double> InterpolatorType;
+            typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
+            interpolator->SetSplineOrder(mBSplineOrder);
+            interpolator->SetLUTSamplingFactor(mSamplingFactors[0]);
+            filter->SetInterpolator(interpolator);
+          } else {
+            std::cerr << "Sorry, I do not know the interpolator '" << mInterpolatorName
+              << "'. Known interpolators are :  nn, linear, bspline, blut" << std::endl;
+            exit(0);
+          }
+        }
+      }
+    }
+  }
+
+  // Build initial Gaussian bluring (if needed)
+  typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
+  std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
+  if (mApplyGaussianFilterBefore) {
+    for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
+      // Create filter
+      gaussianFilters.push_back(GaussianFilterType::New());
+      // Set options
+      gaussianFilters[i]->SetDirection(i);
+      gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
+      gaussianFilters[i]->SetNormalizeAcrossScale(false);
+      gaussianFilters[i]->SetSigma(mSigma[i]); // in millimeter !
+      // Set input
+      if (i==0) gaussianFilters[i]->SetInput(input);
+      else gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
+    }
+    filter->SetInput(gaussianFilters[InputImageType::ImageDimension-1]->GetOutput());
+  } else {
+    filter->SetInput(input);
+  }
+
+  // Go !
+  try {
+    filter->Update();
+  } catch( itk::ExceptionObject & err ) {
+    std::cerr << "Error while filtering " << m_InputFilenames[0].c_str()
+              << " " << err << std::endl;
+    exit(0);
+  }
+
+  // Get result
+  typename InputImageType::Pointer outputImage = filter->GetOutput();
+
+  // Write/save results
+  this->SetNextOutput<InputImageType>(outputImage);
 
-  std::cerr << "Error, dimension of input image is " << mDim << ", but I only work with 2,3,4." << std::endl;
-  exit(0);
 }
 //--------------------------------------------------------------------
 
+
 //--------------------------------------------------------------------
-void clitk::ImageResampleGenericFilter::SetOutputSize(const std::vector<int> & size) {
+void clitk::ImageResampleGenericFilter::SetOutputSize(const std::vector<int> & size)
+{
   mOutputSize.resize(size.size());
   std::copy(size.begin(), size.end(), mOutputSize.begin());
 }
 //--------------------------------------------------------------------
 
 //--------------------------------------------------------------------
-void clitk::ImageResampleGenericFilter::SetOutputSpacing(const std::vector<double> & spacing) {
+void clitk::ImageResampleGenericFilter::SetOutputSpacing(const std::vector<double> & spacing)
+{
   mOutputSpacing.resize(spacing.size());
   std::copy(spacing.begin(), spacing.end(), mOutputSpacing.begin());
 }
 //--------------------------------------------------------------------
 
 //--------------------------------------------------------------------
-void clitk::ImageResampleGenericFilter::SetInterpolationName(const std::string & inter) {
+void clitk::ImageResampleGenericFilter::SetInterpolationName(const std::string & inter)
+{
   mInterpolatorName = inter;
 }
 //--------------------------------------------------------------------
 
 //--------------------------------------------------------------------
-void clitk::ImageResampleGenericFilter::SetGaussianSigma(const std::vector<double> & sigma) {
+void clitk::ImageResampleGenericFilter::SetGaussianSigma(const std::vector<double> & sigma)
+{
   mApplyGaussianFilterBefore = true;
   mSigma.resize(sigma.size());
   std::copy(sigma.begin(), sigma.end(), mSigma.begin());