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_OutputOrigin.Fill(0);
58 m_OutputDirection.SetIdentity();
59 m_VerboseOptions = false;
60 SetDefaultPixelValue(0);
62 //--------------------------------------------------------------------
65 //--------------------------------------------------------------------
66 template <class InputImageType, class OutputImageType>
68 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
69 SetInput(const InputImageType * image)
71 // Process object is not const-correct so the const casting is required.
72 this->SetNthInput(0, const_cast<InputImageType *>(image));
74 //--------------------------------------------------------------------
77 //--------------------------------------------------------------------
78 template <class InputImageType, class OutputImageType>
80 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
81 GenerateInputRequestedRegion()
83 // call the superclass's implementation of this method
84 Superclass::GenerateInputRequestedRegion();
86 // get pointers to the input and output
87 InputImagePointer inputPtr =
88 const_cast< InputImageType *>( this->GetInput() );
90 // Request the entire input image
91 InputImageRegionType inputRegion;
92 inputRegion = inputPtr->GetLargestPossibleRegion();
93 inputPtr->SetRequestedRegion(inputRegion);
95 //--------------------------------------------------------------------
98 //--------------------------------------------------------------------
99 template <class InputImageType, class OutputImageType>
101 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
102 GenerateOutputInformation()
104 static const unsigned int dim = InputImageType::ImageDimension;
107 if (!std::numeric_limits<InputImagePixelType>::is_signed) {
108 if ((m_InterpolationType == BSpline) ||
109 (m_InterpolationType == B_LUT)) {
110 std::cerr << "Warning : input pixel type is not signed, use bspline interpolation at your own risk ..." << std::endl;
115 InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
117 // Perform default implementation
118 Superclass::GenerateOutputInformation();
121 InputImageSpacingType inputSpacing = input->GetSpacing();
122 InputImageSizeType inputSize = input->GetLargestPossibleRegion().GetSize();
124 if (m_OutputIsoSpacing != -1) { // apply isoSpacing
125 for(unsigned int i=0; i<dim; i++) {
126 m_OutputSpacing[i] = m_OutputIsoSpacing;
127 // floor() is used to intentionally reduce the number of slices
128 // because, from a clinical point of view, it's better to
129 // remove data than to add data that privously didn't exist.
130 if(inputSpacing[i]*m_OutputSpacing[i]<0)
131 itkExceptionMacro( << "Input and output spacings don't have the same signs, can't cope with that" );
132 m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
135 if (m_OutputSpacing[0] != -1) { // apply spacing, compute size
136 for(unsigned int i=0; i<dim; i++) {
137 if(inputSpacing[i]*m_OutputSpacing[i]<0)
138 itkExceptionMacro( << "Input and output spacings don't have the same signs, can't cope with that" );
139 // see comment above for the use of floor()
140 m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
143 if (m_OutputSize[0] != 0) { // apply size, compute spacing
144 for(unsigned int i=0; i<dim; i++) {
145 m_OutputSpacing[i] = (double)inputSize[i]*inputSpacing[i]/(double)m_OutputSize[i];
147 } else { // copy input size/spacing ... (no resampling)
148 m_OutputSize = inputSize;
149 m_OutputSpacing = inputSpacing;
154 // Special case for temporal image 2D+t or 3D+t
155 if (m_LastDimensionIsTime) {
157 m_OutputSize[l] = inputSize[l];
158 m_OutputSpacing[l] = inputSpacing[l];
162 OutputImagePointer outputImage = this->GetOutput(0);
163 // OutputImageRegionType region;
164 m_OutputRegion.SetSize(m_OutputSize);
165 m_OutputRegion.SetIndex(input->GetLargestPossibleRegion().GetIndex());
166 outputImage->CopyInformation(input);
167 outputImage->SetLargestPossibleRegion(m_OutputRegion);
168 outputImage->SetSpacing(m_OutputSpacing);
170 // Init Gaussian sigma
171 if (m_GaussianSigma[0] != -1) { // Gaussian filter set by user
172 m_GaussianFilteringEnabled = true;
175 if (m_GaussianFilteringEnabled) { // Automated sigma when downsample
176 for(unsigned int i=0; i<dim; i++) {
177 if (m_OutputSpacing[i] > inputSpacing[i]) { // downsample
178 m_GaussianSigma[i] = 0.5*m_OutputSpacing[i];// / inputSpacing[i]);
180 else m_GaussianSigma[i] = 0; // will be ignore after
184 if (m_GaussianFilteringEnabled && m_LastDimensionIsTime) {
185 m_GaussianSigma[dim-1] = 0;
188 //--------------------------------------------------------------------
191 //--------------------------------------------------------------------
192 template <class InputImageType, class OutputImageType>
194 clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
199 InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
200 static const unsigned int dim = InputImageType::ImageDimension;
202 // Create main Resample Image Filter
203 typedef itk::ResampleImageFilter<InputImageType,OutputImageType> FilterType;
204 typename FilterType::Pointer filter = FilterType::New();
205 filter->GraftOutput(this->GetOutput());
206 this->GetOutput()->SetBufferedRegion(this->GetOutput()->GetLargestPossibleRegion());
208 // Print options if needed
209 if (m_VerboseOptions) {
210 std::cout << "Output Spacing = " << m_OutputSpacing << std::endl
211 << "Output Size = " << m_OutputSize << std::endl
212 << "Gaussian = " << m_GaussianFilteringEnabled << std::endl;
213 if (m_GaussianFilteringEnabled)
214 std::cout << "Sigma = " << m_GaussianSigma << std::endl;
215 std::cout << "Interpol = ";
216 switch (m_InterpolationType) {
217 case NearestNeighbor: std::cout << "NearestNeighbor" << std::endl; break;
218 case Linear: std::cout << "Linear" << std::endl; break;
219 case BSpline: std::cout << "BSpline " << m_BSplineOrder << std::endl; break;
220 case B_LUT: std::cout << "B-LUT " << m_BSplineOrder << " " << m_BLUTSamplingFactor << std::endl; break;
221 case WSINC: std::cout << "Windowed Sinc" << std::endl; break;
223 std::cout << "Threads = " << this->GetNumberOfThreads() << std::endl;
224 std::cout << "LastDimIsTime = " << m_LastDimensionIsTime << std::endl;
227 // Compute origin based on image corner
228 typename FilterType::OriginPointType origin = input->GetOrigin();
229 for(unsigned int i=0; i<OutputImageType::ImageDimension; i++) {
230 origin[i] -= 0.5 * input->GetSpacing()[i];
231 origin[i] += 0.5 * m_OutputSpacing[i];
234 // Instance of the transform object to be passed to the resample
235 // filter. By default, identity transform is applied
236 filter->SetTransform(m_Transform);
237 filter->SetSize(m_OutputSize);
238 filter->SetOutputSpacing(m_OutputSpacing);
239 filter->SetOutputOrigin(m_OutputOrigin);
240 filter->SetDefaultPixelValue(m_DefaultPixelValue);
241 filter->SetNumberOfThreads(this->GetNumberOfThreads());
242 filter->SetOutputDirection(m_OutputDirection); // <-- NEEDED if we want to keep orientation (in case of PermutAxes for example)
244 // Select interpolator
245 switch (m_InterpolationType) {
246 case NearestNeighbor: {
247 typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, double> InterpolatorType;
248 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
249 filter->SetInterpolator(interpolator);
253 typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
254 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
255 filter->SetInterpolator(interpolator);
259 typedef itk::BSplineInterpolateImageFunction<InputImageType, double> InterpolatorType;
260 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
261 interpolator->SetSplineOrder(m_BSplineOrder);
262 filter->SetInterpolator(interpolator);
266 typedef itk::BSplineInterpolateImageFunctionWithLUT<InputImageType, double> InterpolatorType;
267 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
268 interpolator->SetSplineOrder(m_BSplineOrder);
269 interpolator->SetLUTSamplingFactor(m_BLUTSamplingFactor);
270 filter->SetInterpolator(interpolator);
274 typedef itk::WindowedSincInterpolateImageFunction<InputImageType, 4> InterpolatorType;
275 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
276 filter->SetInterpolator(interpolator);
281 // Initial Gaussian blurring if needed
282 // TODO : replace by itk::DiscreteGaussianImageFilter for small sigma
283 typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
284 std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
285 if (m_GaussianFilteringEnabled) {
286 for(unsigned int i=0; i<dim; i++) {
287 if (m_GaussianSigma[i] != 0) {
288 gaussianFilters.push_back(GaussianFilterType::New());
289 gaussianFilters[i]->SetDirection(i);
290 gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
291 gaussianFilters[i]->SetNormalizeAcrossScale(false);
292 gaussianFilters[i]->SetSigma(m_GaussianSigma[i]); // in millimeter !
293 if (gaussianFilters.size() == 1) { // first
294 gaussianFilters[0]->SetInput(input);
296 gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
300 if (gaussianFilters.size() > 0) {
301 filter->SetInput(gaussianFilters[gaussianFilters.size()-1]->GetOutput());
302 } else filter->SetInput(input);
303 } else filter->SetInput(input);
309 // DD("before Graft");
311 //this->GraftOutput(filter->GetOutput());
312 this->SetNthOutput(0, filter->GetOutput());
314 // DD("after Graft");
316 //--------------------------------------------------------------------
319 //--------------------------------------------------------------------
320 template<class InputImageType>
321 typename InputImageType::Pointer
322 clitk::ResampleImageSpacing(typename InputImageType::Pointer input,
323 typename InputImageType::SpacingType spacing,
324 int interpolationType)
326 typedef clitk::ResampleImageWithOptionsFilter<InputImageType> ResampleFilterType;
327 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
328 resampler->SetInput(input);
329 resampler->SetOutputSpacing(spacing);
330 typename ResampleFilterType::InterpolationTypeEnumeration inter=ResampleFilterType::NearestNeighbor;
331 switch(interpolationType) {
332 case 0: inter = ResampleFilterType::NearestNeighbor; break;
333 case 1: inter = ResampleFilterType::Linear; break;
334 case 2: inter = ResampleFilterType::BSpline; break;
335 case 3: inter = ResampleFilterType::B_LUT; break;
336 case 4: inter = ResampleFilterType::WSINC; break;
338 resampler->SetInterpolationType(inter);
339 resampler->SetGaussianFilteringEnabled(true);
341 return resampler->GetOutput();
343 //--------------------------------------------------------------------