1 #ifndef CLITKVFRESAMPLEGENERICFILTER_CXX
2 #define CLITKVFRESAMPLEGENERICFILTER_CXX
5 -------------------------------------------------------------------
6 * @file clitkVFResampleGenericFilter.cxx
7 * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
8 * @date 23 Feb 2008 08:37:53
12 -------------------------------------------------------------------*/
14 #include "clitkVFResampleGenericFilter.h"
16 //--------------------------------------------------------------------
17 clitk::VFResampleGenericFilter::VFResampleGenericFilter():
18 clitk::ImageToImageGenericFilter<Self>("VFResample") {
19 InitializeImageType<2>();
20 InitializeImageType<3>();
21 InitializeImageType<4>();
22 mApplyGaussianFilterBefore = false;
23 mDefaultPixelValue = 0.0;
24 mInterpolatorName = "NN";
27 //--------------------------------------------------------------------
30 //--------------------------------------------------------------------
31 template<unsigned int Dim>
32 void clitk::VFResampleGenericFilter::InitializeImageType() {
33 ADD_IMAGE_TYPE(Dim, float);
35 //--------------------------------------------------------------------
38 //--------------------------------------------------------------------
39 template<class ImageType>
40 void clitk::VFResampleGenericFilter::UpdateWithInputImageType() {
42 if (mNbOfComponents == 1) {
43 std::cerr << "Error, only one components ? Use clitkImageResample instead." << std::endl;
46 typedef typename ImageType::PixelType PixelType;
47 if (mNbOfComponents == 2) Update_WithDimAndPixelTypeAndComponent<ImageType::ImageDimension,PixelType,2>();
48 if (mNbOfComponents == 3) Update_WithDimAndPixelTypeAndComponent<ImageType::ImageDimension,PixelType,3>();
49 if (mNbOfComponents == 4) Update_WithDimAndPixelTypeAndComponent<ImageType::ImageDimension,PixelType,4>();
51 //--------------------------------------------------------------------
54 //--------------------------------------------------------------------
55 template<unsigned int Dim, class PixelType, unsigned int DimCompo>
56 void clitk::VFResampleGenericFilter::Update_WithDimAndPixelTypeAndComponent() {
58 typedef itk::Vector<PixelType, DimCompo> DisplacementType;
59 typedef itk::Image< DisplacementType, Dim > ImageType;
61 typename ImageType::Pointer input = clitk::readImage<ImageType>(mInputFilenames, mIOVerbose);
64 typename ImageType::Pointer outputImage = ComputeImage<ImageType>(input);
67 SetNextOutput<ImageType>(outputImage);
69 //--------------------------------------------------------------------
71 //--------------------------------------------------------------------
72 template<class ImageType>
73 typename ImageType::Pointer
74 clitk::VFResampleGenericFilter::ComputeImage(typename ImageType::Pointer inputImage) {
77 static unsigned int dim = ImageType::ImageDimension;
78 if (mOutputSize.size() != dim) {
79 std::cerr << "Please set size with " << dim << " dimensions." << std::endl;
82 if (mOutputSpacing.size() != dim) {
83 std::cerr << "Please set spacing with " << dim << " dimensions." << std::endl;
86 mOutputOrigin.resize(dim);
88 if (mApplyGaussianFilterBefore && mSigma.size() != dim) {
89 std::cerr << "Please set sigma with " << dim << " dimensions." << std::endl;
94 typedef typename ImageType::SizeType SizeType;
95 typedef typename ImageType::SpacingType SpacingType;
96 typedef typename ImageType::PointType PointType;
98 // Create Image Filter
99 typedef itk::VectorResampleImageFilter<ImageType,ImageType> FilterType;
100 typename FilterType::Pointer filter = FilterType::New();
102 // Instance of the transform object to be passed to the resample
103 // filter. By default, identity transform is applied
104 typedef itk::AffineTransform<double, ImageType::ImageDimension> TransformType;
105 typename TransformType::Pointer transform = TransformType::New();
106 filter->SetTransform(transform);
108 // Set filter's parameters
110 SpacingType outputSpacing;
111 PointType outputOrigin;
112 for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
113 outputSize[i] = mOutputSize[i];
114 outputSpacing[i] = mOutputSpacing[i];
115 outputOrigin[i] = inputImage->GetOrigin()[i];
118 filter->SetSize(outputSize);
119 filter->SetOutputSpacing(outputSpacing);
120 filter->SetOutputOrigin(outputOrigin);
121 filter->SetDefaultPixelValue(static_cast<typename ImageType::PixelType>(mDefaultPixelValue));
123 // Select interpolator
124 if (mInterpolatorName == "nn") {
125 typedef itk::VectorNearestNeighborInterpolateImageFunction<ImageType, double> InterpolatorType;
126 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
127 filter->SetInterpolator(interpolator);
130 if (mInterpolatorName == "linear") {
131 typedef itk::VectorLinearInterpolateImageFunction<ImageType, double> InterpolatorType;
132 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
133 filter->SetInterpolator(interpolator);
136 std::cerr << "Sorry, I do not know the interpolator (for vector field) '" << mInterpolatorName
137 << "'. Known interpolators are : nn, linear" << std::endl;
142 // Build initial Gaussian bluring (if needed)
143 typedef itk::RecursiveGaussianImageFilter<ImageType, ImageType> GaussianFilterType;
144 std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
145 if (mApplyGaussianFilterBefore) {
146 for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
148 gaussianFilters.push_back(GaussianFilterType::New());
150 gaussianFilters[i]->SetDirection(i);
151 gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
152 gaussianFilters[i]->SetNormalizeAcrossScale(false);
153 gaussianFilters[i]->SetSigma(mSigma[i]); // in millimeter !
155 if (i==0) gaussianFilters[i]->SetInput(inputImage);
156 else gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
158 filter->SetInput(gaussianFilters[ImageType::ImageDimension-1]->GetOutput());
161 filter->SetInput(inputImage);
168 catch( itk::ExceptionObject & err ) {
169 std::cerr << "Error while filtering " << mInputFilenames[0].c_str()
170 << " " << err << std::endl;
175 return filter->GetOutput();
178 //--------------------------------------------------------------------
181 //--------------------------------------------------------------------
182 void clitk::VFResampleGenericFilter::SetOutputSize(const std::vector<int> & size) {
183 mOutputSize.resize(size.size());
184 std::copy(size.begin(), size.end(), mOutputSize.begin());
186 //--------------------------------------------------------------------
188 //--------------------------------------------------------------------
189 void clitk::VFResampleGenericFilter::SetOutputSpacing(const std::vector<double> & spacing) {
190 mOutputSpacing.resize(spacing.size());
191 std::copy(spacing.begin(), spacing.end(), mOutputSpacing.begin());
193 //--------------------------------------------------------------------
195 //--------------------------------------------------------------------
196 void clitk::VFResampleGenericFilter::SetInterpolationName(const std::string & inter) {
197 mInterpolatorName = inter;
199 //--------------------------------------------------------------------
201 //--------------------------------------------------------------------
202 void clitk::VFResampleGenericFilter::SetGaussianSigma(const std::vector<double> & sigma) {
203 mApplyGaussianFilterBefore = true;
204 mSigma.resize(sigma.size());
205 std::copy(sigma.begin(), sigma.end(), mSigma.begin());
207 //--------------------------------------------------------------------