1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
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
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.
13 It is distributed under dual licence
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
21 -------------------------------------------------------------------
22 * @file clitkImageResampleGenericFilter.cxx
23 * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
24 * @date 23 Feb 2008 08:37:53
28 -------------------------------------------------------------------*/
30 #include "clitkImageResampleGenericFilter.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"
46 //--------------------------------------------------------------------
47 clitk::ImageResampleGenericFilter::ImageResampleGenericFilter():
48 ImageToImageGenericFilter<Self>("ImageResample") {
49 mApplyGaussianFilterBefore = false;
50 mDefaultPixelValue = 0.0;
51 mInterpolatorName = "NN";
53 InitializeImageTypeWithDim<2>();
54 InitializeImageTypeWithDim<3>();
55 InitializeImageTypeWithDim<4>();
57 //--------------------------------------------------------------------
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);
71 //--------------------------------------------------------------------
74 //--------------------------------------------------------------------
75 template<class InputImageType>
76 void clitk::ImageResampleGenericFilter::UpdateWithInputImageType() {
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;
86 typename InputImageType::Pointer input = this->GetInput<InputImageType>(0);
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;
96 if (mOutputSize.size() != dim) {
97 std::cerr << "Please set size with " << dim << " dimensions." << std::endl;
100 if (mOutputSpacing.size() != dim) {
101 std::cerr << "Please set spacing with " << dim << " dimensions." << std::endl;
104 mOutputOrigin.resize(dim);
106 if (mApplyGaussianFilterBefore && mSigma.size() != dim) {
107 std::cerr << "Please set sigma with " << dim << " dimensions." << std::endl;
111 // Create Image Filter
112 typedef itk::ResampleImageFilter<InputImageType,InputImageType> FilterType;
113 typename FilterType::Pointer filter = FilterType::New();
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);
121 // Set filter's parameters
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];
131 filter->SetSize(outputSize);
132 filter->SetOutputSpacing(outputSpacing);
133 filter->SetOutputOrigin(outputOrigin);
134 filter->SetDefaultPixelValue(static_cast<PixelType>(mDefaultPixelValue));//DS TODO//JV comme ça?
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);
143 if (mInterpolatorName == "linear") {
144 typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
145 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
146 filter->SetInterpolator(interpolator);
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);
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);
164 std::cerr << "Sorry, I do not know the interpolator '" << mInterpolatorName
165 << "'. Known interpolators are : nn, linear, bspline, blut" << std::endl;
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++) {
178 gaussianFilters.push_back(GaussianFilterType::New());
180 gaussianFilters[i]->SetDirection(i);
181 gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
182 gaussianFilters[i]->SetNormalizeAcrossScale(false);
183 gaussianFilters[i]->SetSigma(mSigma[i]); // in millimeter !
185 if (i==0) gaussianFilters[i]->SetInput(input);
186 else gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
188 filter->SetInput(gaussianFilters[InputImageType::ImageDimension-1]->GetOutput());
191 filter->SetInput(input);
198 catch( itk::ExceptionObject & err ) {
199 std::cerr << "Error while filtering " << mInputFilenames[0].c_str()
200 << " " << err << std::endl;
205 typename InputImageType::Pointer outputImage = filter->GetOutput();
207 // Write/save results
208 this->SetNextOutput<InputImageType>(outputImage);
211 //--------------------------------------------------------------------
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());
219 //--------------------------------------------------------------------
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());
226 //--------------------------------------------------------------------
228 //--------------------------------------------------------------------
229 void clitk::ImageResampleGenericFilter::SetInterpolationName(const std::string & inter) {
230 mInterpolatorName = inter;
232 //--------------------------------------------------------------------
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());
240 //--------------------------------------------------------------------