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 ======================================================================-====*/
20 #include "clitkCommon.h"
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;
59 //--------------------------------------------------------------------
62 //--------------------------------------------------------------------
63 template <class InputImageType, class OutputImageType>
65 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
66 SetInput(const InputImageType * image)
68 // Process object is not const-correct so the const casting is required.
69 this->SetNthInput(0, const_cast<InputImageType *>(image));
71 //--------------------------------------------------------------------
74 //--------------------------------------------------------------------
75 template <class InputImageType, class OutputImageType>
77 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
78 GenerateInputRequestedRegion()
80 // call the superclass's implementation of this method
81 Superclass::GenerateInputRequestedRegion();
83 // get pointers to the input and output
84 InputImagePointer inputPtr =
85 const_cast< InputImageType *>( this->GetInput() );
87 // Request the entire input image
88 InputImageRegionType inputRegion;
89 inputRegion = inputPtr->GetLargestPossibleRegion();
90 inputPtr->SetRequestedRegion(inputRegion);
92 //--------------------------------------------------------------------
95 //--------------------------------------------------------------------
96 template <class InputImageType, class OutputImageType>
98 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
99 GenerateOutputInformation()
101 static const unsigned int dim = InputImageType::ImageDimension;
104 if (!std::numeric_limits<InputImagePixelType>::is_signed) {
105 if ((m_InterpolationType == BSpline) ||
106 (m_InterpolationType == B_LUT)) {
107 std::cerr << "Warning : input pixel type is not signed, use bspline interpolation at your own risk ..." << std::endl;
112 InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
114 // Perform default implementation
115 Superclass::GenerateOutputInformation();
118 InputImageSpacingType inputSpacing = input->GetSpacing();
119 InputImageSizeType inputSize = input->GetLargestPossibleRegion().GetSize();
121 if (m_OutputIsoSpacing != -1) { // apply isoSpacing
122 for(unsigned int i=0; i<dim; i++) {
123 m_OutputSpacing[i] = m_OutputIsoSpacing;
124 m_OutputSize[i] = (int)lrint(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
127 if (m_OutputSpacing[0] != -1) { // apply spacing, compute size
128 for(unsigned int i=0; i<dim; i++) {
129 m_OutputSize[i] = (int)lrint(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
132 if (m_OutputSize[0] != 0) { // apply size, compute spacing
133 for(unsigned int i=0; i<dim; i++) {
134 m_OutputSpacing[i] = (double)inputSize[i]*inputSpacing[i]/(double)m_OutputSize[i];
136 } else { // copy input size/spacing ... (no resampling)
137 m_OutputSize = inputSize;
138 m_OutputSpacing = inputSpacing;
143 // Special case for temporal image 2D+t or 3D+t
144 if (m_LastDimensionIsTime) {
146 m_OutputSize[l] = inputSize[l];
147 m_OutputSpacing[l] = inputSpacing[l];
151 OutputImagePointer outputImage = this->GetOutput(0);
152 // OutputImageRegionType region;
153 m_OutputRegion.SetSize(m_OutputSize);
154 m_OutputRegion.SetIndex(input->GetLargestPossibleRegion().GetIndex());
155 outputImage->CopyInformation(input);
156 outputImage->SetLargestPossibleRegion(m_OutputRegion);
157 outputImage->SetSpacing(m_OutputSpacing);
159 // Init Gaussian sigma
160 if (m_GaussianSigma[0] != -1) { // Gaussian filter set by user
161 m_GaussianFilteringEnabled = true;
164 if (m_GaussianFilteringEnabled) { // Automated sigma when downsample
165 for(unsigned int i=0; i<dim; i++) {
166 if (m_OutputSpacing[i] > inputSpacing[i]) { // downsample
167 m_GaussianSigma[i] = 0.5*m_OutputSpacing[i];// / inputSpacing[i]);
169 else m_GaussianSigma[i] = 0; // will be ignore after
173 if (m_GaussianFilteringEnabled && m_LastDimensionIsTime) {
174 m_GaussianSigma[dim-1] = 0;
177 //--------------------------------------------------------------------
180 //--------------------------------------------------------------------
181 template <class InputImageType, class OutputImageType>
183 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
188 InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
189 static const unsigned int dim = InputImageType::ImageDimension;
191 // Set regions and allocate
192 //this->GetOutput()->SetRegions(m_OutputRegion);
193 //this->GetOutput()->Allocate();
194 // this->GetOutput()->FillBuffer(m_DefaultPixelValue);
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()->Print(std::cout);
201 // this->GetOutput()->SetBufferedRegion(this->GetOutput()->GetLargestPossibleRegion());
202 // this->GetOutput()->Print(std::cout);
204 // Print options if needed
205 if (m_VerboseOptions) {
206 std::cout << "Output Spacing = " << m_OutputSpacing << std::endl
207 << "Output Size = " << m_OutputSize << std::endl
208 << "Gaussian = " << m_GaussianFilteringEnabled << std::endl;
209 if (m_GaussianFilteringEnabled)
210 std::cout << "Sigma = " << m_GaussianSigma << std::endl;
211 std::cout << "Interpol = ";
212 switch (m_InterpolationType) {
213 case NearestNeighbor: std::cout << "NearestNeighbor" << std::endl; break;
214 case Linear: std::cout << "Linear" << std::endl; break;
215 case BSpline: std::cout << "BSpline " << m_BSplineOrder << std::endl; break;
216 case B_LUT: std::cout << "B-LUT " << m_BSplineOrder << " " << m_BLUTSamplingFactor << std::endl; break;
217 case WSINC: std::cout << "Windowed Sinc" << std::endl; break;
219 std::cout << "Threads = " << this->GetNumberOfThreads() << std::endl;
220 std::cout << "LastDimIsTime = " << m_LastDimensionIsTime << std::endl;
223 // Instance of the transform object to be passed to the resample
224 // filter. By default, identity transform is applied
225 filter->SetTransform(m_Transform);
226 filter->SetSize(m_OutputSize);
227 filter->SetOutputSpacing(m_OutputSpacing);
228 filter->SetOutputOrigin(input->GetOrigin());
229 filter->SetDefaultPixelValue(m_DefaultPixelValue);
230 filter->SetNumberOfThreads(this->GetNumberOfThreads());
231 filter->SetOutputDirection(input->GetDirection()); // <-- NEEDED if we want to keep orientation (in case of PermutAxes for example)
233 // Select interpolator
234 switch (m_InterpolationType) {
235 case NearestNeighbor: {
236 typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, double> InterpolatorType;
237 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
238 filter->SetInterpolator(interpolator);
242 typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
243 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
244 filter->SetInterpolator(interpolator);
248 typedef itk::BSplineInterpolateImageFunction<InputImageType, double> InterpolatorType;
249 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
250 interpolator->SetSplineOrder(m_BSplineOrder);
251 filter->SetInterpolator(interpolator);
255 typedef itk::BSplineInterpolateImageFunctionWithLUT<InputImageType, double> InterpolatorType;
256 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
257 interpolator->SetSplineOrder(m_BSplineOrder);
258 interpolator->SetLUTSamplingFactor(m_BLUTSamplingFactor);
259 filter->SetInterpolator(interpolator);
263 typedef itk::WindowedSincInterpolateImageFunction<InputImageType, 4> InterpolatorType;
264 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
265 filter->SetInterpolator(interpolator);
270 // Initial Gaussian blurring if needed
271 // TODO : replace by itk::DiscreteGaussianImageFilter for small sigma
272 typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
273 std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
274 if (m_GaussianFilteringEnabled) {
275 for(unsigned int i=0; i<dim; i++) {
276 if (m_GaussianSigma[i] != 0) {
277 gaussianFilters.push_back(GaussianFilterType::New());
278 gaussianFilters[i]->SetDirection(i);
279 gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
280 gaussianFilters[i]->SetNormalizeAcrossScale(false);
281 gaussianFilters[i]->SetSigma(m_GaussianSigma[i]); // in millimeter !
282 if (gaussianFilters.size() == 1) { // first
283 gaussianFilters[0]->SetInput(input);
285 gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
289 if (gaussianFilters.size() > 0) {
290 filter->SetInput(gaussianFilters[gaussianFilters.size()-1]->GetOutput());
291 } else filter->SetInput(input);
292 } else filter->SetInput(input);
298 // DD("before Graft");
300 //this->GraftOutput(filter->GetOutput());
301 this->SetNthOutput(0, filter->GetOutput());
303 // DD("after Graft");
305 //--------------------------------------------------------------------
308 //--------------------------------------------------------------------
309 template<class InputImageType>
310 typename InputImageType::Pointer
311 clitk::ResampleImageSpacing(typename InputImageType::Pointer input,
312 typename InputImageType::SpacingType spacing,
313 int interpolationType)
315 typedef clitk::ResampleImageWithOptionsFilter<InputImageType> ResampleFilterType;
316 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
317 resampler->SetInput(input);
318 resampler->SetOutputSpacing(spacing);
319 typename ResampleFilterType::InterpolationTypeEnumeration inter=ResampleFilterType::NearestNeighbor;
320 switch(interpolationType) {
321 case 0: inter = ResampleFilterType::NearestNeighbor; break;
322 case 1: inter = ResampleFilterType::Linear; break;
323 case 2: inter = ResampleFilterType::BSpline; break;
324 case 3: inter = ResampleFilterType::B_LUT; break;
325 case 4: inter = ResampleFilterType::WSINC; break;
327 resampler->SetInterpolationType(inter);
328 resampler->SetGaussianFilteringEnabled(true);
330 return resampler->GetOutput();
332 //--------------------------------------------------------------------