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://www.centreleonberard.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 ===========================================================================**/
24 #include "itkImageFileReader.h"
25 #include "itkImageSeriesReader.h"
26 #include "itkImageFileWriter.h"
27 #include "itkRecursiveGaussianImageFilter.h"
28 #include "itkResampleImageFilter.h"
29 #include "itkAffineTransform.h"
30 #include "itkNearestNeighborInterpolateImageFunction.h"
31 #include "itkWindowedSincInterpolateImageFunction.h"
32 #include "itkLinearInterpolateImageFunction.h"
33 #include "itkBSplineInterpolateImageFunction.h"
34 #include "itkBSplineInterpolateImageFunctionWithLUT.h"
35 #include "itkCommand.h"
37 //--------------------------------------------------------------------
38 template <class InputImageType, class OutputImageType>
39 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
40 ResampleImageWithOptionsFilter():itk::ImageToImageFilter<InputImageType, OutputImageType>()
42 static const unsigned int dim = InputImageType::ImageDimension;
43 this->SetNumberOfRequiredInputs(1);
44 m_OutputIsoSpacing = -1;
45 m_InterpolationType = NearestNeighbor;
46 m_GaussianFilteringEnabled = true;
48 m_BLUTSamplingFactor = 20;
49 m_LastDimensionIsTime = false;
50 m_Transform = TransformType::New();
51 if (dim == 4) m_LastDimensionIsTime = true; // by default 4D is 3D+t
52 for(unsigned int i=0; i<dim; i++) {
54 m_OutputSpacing[i] = -1;
55 m_GaussianSigma[i] = -1;
57 m_VerboseOptions = false;
58 SetDefaultPixelValue(0);
60 //--------------------------------------------------------------------
63 //--------------------------------------------------------------------
64 template <class InputImageType, class OutputImageType>
66 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
67 SetInput(const InputImageType * image)
69 // Process object is not const-correct so the const casting is required.
70 this->SetNthInput(0, const_cast<InputImageType *>(image));
72 //--------------------------------------------------------------------
75 //--------------------------------------------------------------------
76 template <class InputImageType, class OutputImageType>
78 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
79 GenerateInputRequestedRegion()
81 // call the superclass's implementation of this method
82 Superclass::GenerateInputRequestedRegion();
84 // get pointers to the input and output
85 InputImagePointer inputPtr =
86 const_cast< InputImageType *>( this->GetInput() );
88 // Request the entire input image
89 InputImageRegionType inputRegion;
90 inputRegion = inputPtr->GetLargestPossibleRegion();
91 inputPtr->SetRequestedRegion(inputRegion);
93 //--------------------------------------------------------------------
96 //--------------------------------------------------------------------
97 template <class InputImageType, class OutputImageType>
99 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
100 GenerateOutputInformation()
102 static const unsigned int dim = InputImageType::ImageDimension;
105 if (!std::numeric_limits<InputImagePixelType>::is_signed) {
106 if ((m_InterpolationType == BSpline) ||
107 (m_InterpolationType == B_LUT)) {
108 std::cerr << "Warning : input pixel type is not signed, use bspline interpolation at your own risk ..." << std::endl;
113 InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
115 // Perform default implementation
116 Superclass::GenerateOutputInformation();
119 InputImageSpacingType inputSpacing = input->GetSpacing();
120 InputImageSizeType inputSize = input->GetLargestPossibleRegion().GetSize();
122 if (m_OutputIsoSpacing != -1) { // apply isoSpacing
123 for(unsigned int i=0; i<dim; i++) {
124 m_OutputSpacing[i] = m_OutputIsoSpacing;
125 // floor() is used to intentionally reduce the number of slices
126 // because, from a clinical point of view, it's better to
127 // remove data than to add data that privously didn't exist.
128 m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
131 if (m_OutputSpacing[0] != -1) { // apply spacing, compute size
132 for(unsigned int i=0; i<dim; i++) {
133 // see comment above for the use of floor()
134 m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
137 if (m_OutputSize[0] != 0) { // apply size, compute spacing
138 for(unsigned int i=0; i<dim; i++) {
139 m_OutputSpacing[i] = (double)inputSize[i]*inputSpacing[i]/(double)m_OutputSize[i];
141 } else { // copy input size/spacing ... (no resampling)
142 m_OutputSize = inputSize;
143 m_OutputSpacing = inputSpacing;
148 // Special case for temporal image 2D+t or 3D+t
149 if (m_LastDimensionIsTime) {
151 m_OutputSize[l] = inputSize[l];
152 m_OutputSpacing[l] = inputSpacing[l];
156 OutputImagePointer outputImage = this->GetOutput(0);
157 // OutputImageRegionType region;
158 m_OutputRegion.SetSize(m_OutputSize);
159 m_OutputRegion.SetIndex(input->GetLargestPossibleRegion().GetIndex());
160 outputImage->CopyInformation(input);
161 outputImage->SetLargestPossibleRegion(m_OutputRegion);
162 outputImage->SetSpacing(m_OutputSpacing);
164 // Init Gaussian sigma
165 if (m_GaussianSigma[0] != -1) { // Gaussian filter set by user
166 m_GaussianFilteringEnabled = true;
169 if (m_GaussianFilteringEnabled) { // Automated sigma when downsample
170 for(unsigned int i=0; i<dim; i++) {
171 if (m_OutputSpacing[i] > inputSpacing[i]) { // downsample
172 m_GaussianSigma[i] = 0.5*m_OutputSpacing[i];// / inputSpacing[i]);
174 else m_GaussianSigma[i] = 0; // will be ignore after
178 if (m_GaussianFilteringEnabled && m_LastDimensionIsTime) {
179 m_GaussianSigma[dim-1] = 0;
182 //--------------------------------------------------------------------
185 //--------------------------------------------------------------------
186 template <class InputImageType, class OutputImageType>
188 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
193 InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
194 static const unsigned int dim = InputImageType::ImageDimension;
196 // Create main Resample Image Filter
197 typedef itk::ResampleImageFilter<InputImageType,OutputImageType> FilterType;
198 typename FilterType::Pointer filter = FilterType::New();
199 filter->GraftOutput(this->GetOutput());
200 this->GetOutput()->SetBufferedRegion(this->GetOutput()->GetLargestPossibleRegion());
202 // Print options if needed
203 if (m_VerboseOptions) {
204 std::cout << "Output Spacing = " << m_OutputSpacing << std::endl
205 << "Output Size = " << m_OutputSize << std::endl
206 << "Gaussian = " << m_GaussianFilteringEnabled << std::endl;
207 if (m_GaussianFilteringEnabled)
208 std::cout << "Sigma = " << m_GaussianSigma << std::endl;
209 std::cout << "Interpol = ";
210 switch (m_InterpolationType) {
211 case NearestNeighbor: std::cout << "NearestNeighbor" << std::endl; break;
212 case Linear: std::cout << "Linear" << std::endl; break;
213 case BSpline: std::cout << "BSpline " << m_BSplineOrder << std::endl; break;
214 case B_LUT: std::cout << "B-LUT " << m_BSplineOrder << " " << m_BLUTSamplingFactor << std::endl; break;
215 case WSINC: std::cout << "Windowed Sinc" << std::endl; break;
217 std::cout << "Threads = " << this->GetNumberOfThreads() << std::endl;
218 std::cout << "LastDimIsTime = " << m_LastDimensionIsTime << std::endl;
221 // Instance of the transform object to be passed to the resample
222 // filter. By default, identity transform is applied
223 filter->SetTransform(m_Transform);
224 filter->SetSize(m_OutputSize);
225 filter->SetOutputSpacing(m_OutputSpacing);
226 filter->SetOutputOrigin(input->GetOrigin());
227 filter->SetDefaultPixelValue(m_DefaultPixelValue);
228 filter->SetNumberOfThreads(this->GetNumberOfThreads());
229 filter->SetOutputDirection(input->GetDirection()); // <-- NEEDED if we want to keep orientation (in case of PermutAxes for example)
231 // Select interpolator
232 switch (m_InterpolationType) {
233 case NearestNeighbor: {
234 typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, double> InterpolatorType;
235 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
236 filter->SetInterpolator(interpolator);
240 typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
241 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
242 filter->SetInterpolator(interpolator);
246 typedef itk::BSplineInterpolateImageFunction<InputImageType, double> InterpolatorType;
247 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
248 interpolator->SetSplineOrder(m_BSplineOrder);
249 filter->SetInterpolator(interpolator);
253 typedef itk::BSplineInterpolateImageFunctionWithLUT<InputImageType, double> InterpolatorType;
254 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
255 interpolator->SetSplineOrder(m_BSplineOrder);
256 interpolator->SetLUTSamplingFactor(m_BLUTSamplingFactor);
257 filter->SetInterpolator(interpolator);
261 typedef itk::WindowedSincInterpolateImageFunction<InputImageType, 4> InterpolatorType;
262 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
263 filter->SetInterpolator(interpolator);
268 // Initial Gaussian blurring if needed
269 // TODO : replace by itk::DiscreteGaussianImageFilter for small sigma
270 typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
271 std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
272 if (m_GaussianFilteringEnabled) {
273 for(unsigned int i=0; i<dim; i++) {
274 if (m_GaussianSigma[i] != 0) {
275 gaussianFilters.push_back(GaussianFilterType::New());
276 gaussianFilters[i]->SetDirection(i);
277 gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
278 gaussianFilters[i]->SetNormalizeAcrossScale(false);
279 gaussianFilters[i]->SetSigma(m_GaussianSigma[i]); // in millimeter !
280 if (gaussianFilters.size() == 1) { // first
281 gaussianFilters[0]->SetInput(input);
283 gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
287 if (gaussianFilters.size() > 0) {
288 filter->SetInput(gaussianFilters[gaussianFilters.size()-1]->GetOutput());
289 } else filter->SetInput(input);
290 } else filter->SetInput(input);
296 // DD("before Graft");
298 //this->GraftOutput(filter->GetOutput());
299 this->SetNthOutput(0, filter->GetOutput());
301 // DD("after Graft");
303 //--------------------------------------------------------------------
306 //--------------------------------------------------------------------
307 template<class InputImageType>
308 typename InputImageType::Pointer
309 clitk::ResampleImageSpacing(typename InputImageType::Pointer input,
310 typename InputImageType::SpacingType spacing,
311 int interpolationType)
313 typedef clitk::ResampleImageWithOptionsFilter<InputImageType> ResampleFilterType;
314 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
315 resampler->SetInput(input);
316 resampler->SetOutputSpacing(spacing);
317 typename ResampleFilterType::InterpolationTypeEnumeration inter=ResampleFilterType::NearestNeighbor;
318 switch(interpolationType) {
319 case 0: inter = ResampleFilterType::NearestNeighbor; break;
320 case 1: inter = ResampleFilterType::Linear; break;
321 case 2: inter = ResampleFilterType::BSpline; break;
322 case 3: inter = ResampleFilterType::B_LUT; break;
323 case 4: inter = ResampleFilterType::WSINC; break;
325 resampler->SetInterpolationType(inter);
326 resampler->SetGaussianFilteringEnabled(true);
328 return resampler->GetOutput();
330 //--------------------------------------------------------------------