+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ======================================================================-====*/
+
+// clitk
+#include "clitkCommon.h"
+
+// itk include
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageSeriesReader.h"
+#include "itkImageFileWriter.h"
+#include "itkRecursiveGaussianImageFilter.h"
+#include "itkResampleImageFilter.h"
+#include "itkAffineTransform.h"
+#include "itkNearestNeighborInterpolateImageFunction.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkBSplineInterpolateImageFunction.h"
+#include "itkBSplineInterpolateImageFunctionWithLUT.h"
+#include "itkCommand.h"
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template <class TInputImage, class TOutputImage>
+ ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+ ResampleImageWithOptionsFilter():itk::ImageToImageFilter<TInputImage, TOutputImage>() {
+ static const unsigned int dim = InputImageType::ImageDimension;
+ this->SetNumberOfRequiredInputs(1);
+ m_IsoSpacing = -1;
+ m_InterpolationType = NearestNeighbor;
+ m_GaussianFilteringEnabled = true;
+ m_BSplineOrder = 3;
+ m_BLUTSamplingFactor = 20;
+ m_LastDimensionIsTime = false;
+ m_Transform = TransformType::New();
+ if (dim == 4) m_LastDimensionIsTime = true; // by default 4D is 3D+t
+ for(unsigned int i=0; i<dim; i++) {
+ m_OutputSize[i] = 0;
+ m_OutputSpacing[i] = -1;
+ m_GaussianSigma[i] = -1;
+ }
+ m_VerboseOptions = false;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template <class TInputImage, class TOutputImage>
+ void
+ ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+ SetInput(const InputImageType * image) {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput(0, const_cast<InputImageType *>(image));
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template <class TInputImage, class TOutputImage>
+ void
+ ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+ GenerateInputRequestedRegion() {
+ // call the superclass's implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // get pointers to the input and output
+ InputImagePointer inputPtr =
+ const_cast< TInputImage *>( this->GetInput() );
+
+ // Request the entire input image
+ InputImageRegionType inputRegion;
+ inputRegion = inputPtr->GetLargestPossibleRegion();
+ inputPtr->SetRequestedRegion(inputRegion);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template <class TInputImage, class TOutputImage>
+ void
+ ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+ GenerateOutputInformation() {
+ static const unsigned int dim = InputImageType::ImageDimension;
+
+ // Warning
+ if (!std::numeric_limits<InputImagePixelType>::is_signed) {
+ if ((m_InterpolationType == BSpline) ||
+ (m_InterpolationType == B_LUT)) {
+ std::cerr << "Warning : input pixel type is not signed, use bspline interpolation at your own risk ..." << std::endl;
+ }
+ }
+
+ // Get input pointer
+ InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
+
+ // Perform default implementation
+ Superclass::GenerateOutputInformation();
+
+ // Compute sizes
+ InputImageSpacingType inputSpacing = input->GetSpacing();
+ InputImageSizeType inputSize = input->GetLargestPossibleRegion().GetSize();
+
+ if (m_IsoSpacing != -1) { // apply isoSpacing
+ for(unsigned int i=0; i<dim; i++) {
+ m_OutputSpacing[i] = m_IsoSpacing;
+ m_OutputSize[i] = (int)lrint(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
+ }
+ }
+ else {
+ if (m_OutputSpacing[0] != -1) { // apply spacing, compute size
+ for(unsigned int i=0; i<dim; i++) {
+ m_OutputSize[i] = (int)lrint(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
+ }
+ }
+ else {
+ if (m_OutputSize[0] != 0) { // apply size, compute spacing
+ for(unsigned int i=0; i<dim; i++) {
+ m_OutputSpacing[i] = (double)inputSize[i]*inputSpacing[i]/(double)m_OutputSize[i];
+ }
+ }
+ else { // copy input size/spacing ... (no resampling)
+ m_OutputSize = inputSize;
+ m_OutputSpacing = inputSpacing;
+ }
+ }
+ }
+
+ // Special case for temporal image 2D+t or 3D+t
+ if (m_LastDimensionIsTime) {
+ int l = dim-1;
+ m_OutputSize[l] = inputSize[l];
+ m_OutputSpacing[l] = inputSpacing[l];
+ }
+
+ // Set Size/Spacing
+ OutputImagePointer outputImage = this->GetOutput(0);
+ OutputImageRegionType region;
+ region.SetSize(m_OutputSize);
+ region.SetIndex(input->GetLargestPossibleRegion().GetIndex());
+ outputImage->SetLargestPossibleRegion(region);
+
+ // Init Gaussian sigma
+ if (m_GaussianSigma[0] != -1) { // Gaussian filter set by user
+ m_GaussianFilteringEnabled = true;
+ }
+ else {
+ if (m_GaussianFilteringEnabled) { // Automated sigma when downsample
+ for(unsigned int i=0; i<dim; i++) {
+ if (m_OutputSpacing[i] > inputSpacing[i]) { // downsample
+ m_GaussianSigma[i] = 0.5*m_OutputSpacing[i];// / inputSpacing[i]);
+ }
+ else m_GaussianSigma[i] = 0; // will be ignore after
+ }
+ }
+ }
+ if (m_GaussianFilteringEnabled && m_LastDimensionIsTime) {
+ m_GaussianSigma[dim-1] = 0;
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template <class TInputImage, class TOutputImage>
+ void
+ ResampleImageWithOptionsFilter<TInputImage, TOutputImage>::
+ GenerateData() {
+
+ // Get input pointer
+ InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
+ static const unsigned int dim = InputImageType::ImageDimension;
+
+ // Create main Resample Image Filter
+ typedef itk::ResampleImageFilter<InputImageType,OutputImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->GraftOutput(this->GetOutput());
+
+ // Print options if needed
+ if (m_VerboseOptions) {
+ std::cout << "Output Spacing = " << m_OutputSpacing << std::endl
+ << "Output Size = " << m_OutputSize << std::endl
+ << "Gaussian = " << m_GaussianFilteringEnabled << std::endl;
+ if (m_GaussianFilteringEnabled)
+ std::cout << "Sigma = " << m_GaussianSigma << std::endl;
+ std::cout << "Interpol = ";
+ switch (m_InterpolationType) {
+ case NearestNeighbor: std::cout << "NearestNeighbor" << std::endl; break;
+ case Linear: std::cout << "Linear" << std::endl; break;
+ case BSpline: std::cout << "BSpline " << m_BSplineOrder << std::endl; break;
+ case B_LUT: std::cout << "B-LUT " << m_BSplineOrder << " " << m_BLUTSamplingFactor << std::endl; break;
+ }
+ std::cout << "Threads = " << this->GetNumberOfThreads() << std::endl;
+ std::cout << "LastDimIsTime = " << m_LastDimensionIsTime << std::endl;
+ }
+
+ // Instance of the transform object to be passed to the resample
+ // filter. By default, identity transform is applied
+ filter->SetTransform(m_Transform);
+ filter->SetSize(m_OutputSize);
+ filter->SetOutputSpacing(m_OutputSpacing);
+ filter->SetOutputOrigin(input->GetOrigin());
+ filter->SetDefaultPixelValue(m_DefaultPixelValue);
+ filter->SetNumberOfThreads(this->GetNumberOfThreads());
+
+ // Select interpolator
+ switch (m_InterpolationType) {
+ case NearestNeighbor:
+ {
+ typedef itk::NearestNeighborInterpolateImageFunction<InputImageType, double> InterpolatorType;
+ typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
+ filter->SetInterpolator(interpolator);
+ break;
+ }
+ case Linear:
+ {
+ typedef itk::LinearInterpolateImageFunction<InputImageType, double> InterpolatorType;
+ typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
+ filter->SetInterpolator(interpolator);
+ break;
+ }
+ case BSpline:
+ {
+ typedef itk::BSplineInterpolateImageFunction<InputImageType, double> InterpolatorType;
+ typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
+ interpolator->SetSplineOrder(m_BSplineOrder);
+ filter->SetInterpolator(interpolator);
+ break;
+ }
+ case B_LUT:
+ {
+ typedef itk::BSplineInterpolateImageFunctionWithLUT<InputImageType, double> InterpolatorType;
+ typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
+ interpolator->SetSplineOrder(m_BSplineOrder);
+ interpolator->SetLUTSamplingFactor(m_BLUTSamplingFactor);
+ filter->SetInterpolator(interpolator);
+ break;
+ }
+ }
+
+ // Initial Gaussian blurring if needed
+ typedef itk::RecursiveGaussianImageFilter<InputImageType, InputImageType> GaussianFilterType;
+ std::vector<typename GaussianFilterType::Pointer> gaussianFilters;
+ if (m_GaussianFilteringEnabled) {
+ for(unsigned int i=0; i<dim; i++) {
+ if (m_GaussianSigma[i] != 0) {
+ gaussianFilters.push_back(GaussianFilterType::New());
+ gaussianFilters[i]->SetDirection(i);
+ gaussianFilters[i]->SetOrder(GaussianFilterType::ZeroOrder);
+ gaussianFilters[i]->SetNormalizeAcrossScale(false);
+ gaussianFilters[i]->SetSigma(m_GaussianSigma[i]); // in millimeter !
+ if (gaussianFilters.size() == 1) { // first
+ gaussianFilters[0]->SetInput(input);
+ }
+ else {
+ gaussianFilters[i]->SetInput(gaussianFilters[i-1]->GetOutput());
+ }
+ }
+ }
+ if (gaussianFilters.size() > 0) {
+ filter->SetInput(gaussianFilters[gaussianFilters.size()-1]->GetOutput());
+ }
+ else filter->SetInput(input);
+ }
+ else filter->SetInput(input);
+
+ // Go !
+ filter->Update();
+
+ // Set output
+ this->GraftOutput(filter->GetOutput());
+ }
+ //--------------------------------------------------------------------
+
+}//end clitk
+