clitkFooImage.ggo
clitkImageArithm.ggo
clitkMedianImageFilter.ggo
+ clitkResampleImage.ggo
)
SET(clitkFilters_SRC
--- /dev/null
+#File clitkImageResample.ggo
+package "clitkImageResample"
+version "2.0"
+purpose "Resample an image. You can specify the interpolation, you can apply a Gaussian filter before (automated if downsample)."
+
+section "Common"
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
+option "imagetypes" - "Verbose: allowed image types" flag off
+option "thread" - "Nb of thread to use (default=max)" int no
+
+section "Input & Output options"
+option "input" i "Input image filename" string yes
+option "output" o "Output image filename" string yes
+option "size" - "Number of pixels of each coordonate" int no multiple default="0"
+option "spacing" - "Spacing in mm between pixels" float no multiple default="-1.0"
+option "default" d "Default pixel value" float no default = "0.0"
+option "time" t "Last Dimension Is Time -> do not resample it (auto on for 4D)" flag off
+
+section "Interpolation"
+option "interp" - "Interpolation type: {nn, linear, bspline, blut}" string no default="nn"
+option "order" b "BSpline ordre (range 0-5)" int no default="3"
+option "sampling" s "BLUT sampling value" int no default="30"
+
+section "Gaussian filtering"
+option "gauss" g "Apply Gaussian before (sigma in mm)" float no multiple default="0.0"
+option "autogauss" a "Apply Gaussian with auto sigma when downsample" flag off
--- /dev/null
+/*=========================================================================
+ 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
+======================================================================-====*/
+
+#ifndef CLITKIRESAMPLEIMAGEGENERICFILTER_H
+#define CLITKIRESAMPLEIMAGEGENERICFILTER_H
+
+// clitk include
+#include "clitkImageToImageGenericFilter.h"
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ class ITK_EXPORT ResampleImageGenericFilter:
+ public ImageToImageGenericFilter<ResampleImageGenericFilter<args_info_type> > {
+
+ public:
+ // Constructor
+ ResampleImageGenericFilter();
+
+ // Types
+ typedef ResampleImageGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ // New
+ itkNewMacro(Self);
+
+ // Args
+ void SetArgsInfo(const args_info_type & a);
+
+ // Main function
+ template<class InputImageType> void UpdateWithInputImageType();
+
+ protected:
+ args_info_type mArgsInfo;
+ template<unsigned int Dim> void InitializeImageType();
+
+ }; // end class ResampleImageGenericFilter
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkResampleImageGenericFilter.txx"
+#endif
+//--------------------------------------------------------------------
+
+#endif /* end #define CLITKIRESAMPLEIMAGEGENERICFILTER_H */
+
--- /dev/null
+/*=========================================================================
+ 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
+======================================================================-====*/
+
+#ifndef CLITKRESAMPLEIMAGEGENERICFILTER_TXX
+#define CLITKRESAMPLEIMAGEGENERICFILTER_TXX
+
+// clitk
+#include "clitkResampleImageWithOptionsFilter.h"
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ ResampleImageGenericFilter<args_info_type>::ResampleImageGenericFilter():
+ ImageToImageGenericFilter<Self>("Resample") {
+ // InitializeImageType<2>();
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dim>
+ void ResampleImageGenericFilter<args_info_type>::InitializeImageType() {
+ // ADD_DEFAULT_IMAGE_TYPES(Dim);
+ ADD_IMAGE_TYPE(Dim, short);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ void ResampleImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
+ mArgsInfo=a;
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.input_given) {
+ SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ SetOutputFilename(mArgsInfo.output_arg);
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ // Update with the number of dimensions and the pixeltype
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<class InputImageType>
+ void
+ ResampleImageGenericFilter<args_info_type>::UpdateWithInputImageType() {
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ // Main filter
+ typedef typename InputImageType::PixelType PixelType;
+ typedef InputImageType OutputImageType; // to change to float is user ask it (?)
+
+ // Filter
+ typedef clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType> ResampleImageFilterType;
+ typename ResampleImageFilterType::Pointer filter = ResampleImageFilterType::New();
+ filter->SetInput(input);
+
+ // Set Verbose
+ filter->SetVerboseOptions(mArgsInfo.verbose_flag);
+
+ // Set size / spacing
+ static const unsigned int dim = OutputImageType::ImageDimension;
+ typename OutputImageType::SpacingType spacing;
+ typename OutputImageType::SizeType size;
+ if (mArgsInfo.spacing_given == 1) {
+ filter->SetIsoSpacing(mArgsInfo.spacing_arg[0]);
+ }
+ else {
+ if ((mArgsInfo.spacing_given != 0) && (mArgsInfo.size_given != 0)) {
+ std::cerr << "Error: use spacing or size, not both." << std::endl;
+ exit(0);
+ }
+
+ if (!((mArgsInfo.spacing_given == 0) && (mArgsInfo.size_given == 0))) {
+
+ if ((mArgsInfo.spacing_given != 0) && (mArgsInfo.spacing_given != dim)) {
+ std::cerr << "Error: spacing should have one or " << dim << " values." << std::endl;
+ exit(0);
+ }
+ if ((mArgsInfo.size_given != 0) && (mArgsInfo.size_given != dim)) {
+ std::cerr << "Error: size should have " << dim << " values." << std::endl;
+ exit(0);
+ }
+ if (mArgsInfo.spacing_given)
+ for(unsigned int i=0; i<dim; i++)
+ spacing[i] = mArgsInfo.spacing_arg[i];
+ if (mArgsInfo.size_given)
+ for(unsigned int i=0; i<dim; i++)
+ size[i] = mArgsInfo.size_arg[i];
+ filter->SetOutputSpacing(spacing);
+ filter->SetOutputSize(size);
+ }
+ }
+
+ // Set temporal dimension
+ filter->SetLastDimensionIsTime(mArgsInfo.time_flag);
+
+ // Set Gauss
+ filter->SetGaussianFilteringEnabled(mArgsInfo.autogauss_flag);
+ if (mArgsInfo.gauss_given != 0) {
+ typename ResampleImageFilterType::GaussianSigmaType g;
+ for(unsigned int i=0; i<dim; i++) {
+ g[i] = mArgsInfo.gauss_arg[i];
+ }
+ filter->SetGaussianSigma(g);
+ }
+
+ // Set Interpolation
+ std::string interp = std::string(mArgsInfo.interp_arg);
+ if (interp == "nn") {
+ filter->SetInterpolationType(ResampleImageFilterType::NearestNeighbor);
+ }
+ else {
+ if (interp == "linear") {
+ filter->SetInterpolationType(ResampleImageFilterType::Linear);
+ }
+ else {
+ if (interp == "bspline") {
+ filter->SetInterpolationType(ResampleImageFilterType::BSpline);
+ }
+ else {
+ if (interp == "blut") {
+ filter->SetInterpolationType(ResampleImageFilterType::B_LUT);
+ }
+ else {
+ std::cerr << "Error. I do not know interpolation '" << mArgsInfo.interp_arg
+ << "'. Choose among: nn, linear, bspline, blut" << std::endl;
+ exit(0);
+ }
+ }
+ }
+ }
+
+ // Set default pixel value
+ filter->SetDefaultPixelValue(mArgsInfo.default_arg);
+
+ // Set thread
+ if (mArgsInfo.thread_given) {
+ filter->SetNumberOfThreads(mArgsInfo.thread_arg);
+ }
+
+ // Go !
+ filter->Update();
+ typename OutputImageType::Pointer outputImage = filter->GetOutput();
+ this->template SetNextOutput<OutputImageType>(outputImage);
+ }
+ //--------------------------------------------------------------------
+
+}
+
+#endif /* end #define CLITKRESAMPLEIMAGEGENERICFILTER_TXX */
+
--- /dev/null
+/*=========================================================================
+ 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
+ ======================================================================-====*/
+
+#ifndef CLITKRESAMPLEIMAGEWITHOPTIONSFILTER_H
+#define CLITKRESAMPLEIMAGEWITHOPTIONSFILTER_H
+
+#include "itkImageToImageFilter.h"
+#include "itkAffineTransform.h"
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ /*
+ Image resampling with several interpolations and Gaussian filtering included.
+ */
+ //--------------------------------------------------------------------
+
+ template <class TInputImage, class TOutputImage=TInputImage>
+ class ITK_EXPORT ResampleImageWithOptionsFilter:
+ public itk::ImageToImageFilter<TInputImage, TOutputImage> {
+
+ public:
+ /** Standard class typedefs. */
+ typedef ResampleImageWithOptionsFilter Self;
+ typedef itk::ImageToImageFilter<TInputImage, TOutputImage> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(ResampleImageWithOptionsFilter, ImageToImageFilter);
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename InputImageType::SpacingType InputImageSpacingType;
+ typedef typename InputImageType::SizeType InputImageSizeType;
+
+ typedef TOutputImage OutputImageType;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+ typedef typename OutputImageType::SpacingType OutputImageSpacingType;
+ typedef typename OutputImageType::SizeType OutputImageSizeType;
+
+ typedef itk::AffineTransform<double, InputImageType::ImageDimension> TransformType;
+ typedef typename InputImageType::SpacingType GaussianSigmaType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TOutputImage::ImageDimension);
+ itkConceptMacro(SameDimensionCheck,
+ (itk::Concept::SameDimension<InputImageDimension, OutputImageDimension>));
+
+ /** Interpolation types */
+ typedef enum {
+ NearestNeighbor = 0,
+ Linear = 1,
+ BSpline = 2,
+ B_LUT = 3
+ } InterpolationTypeEnumeration;
+
+ /** Input : image to resample */
+ void SetInput(const InputImageType * image);
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension);
+
+ // Options
+ itkGetMacro(LastDimensionIsTime, bool);
+ itkSetMacro(LastDimensionIsTime, bool);
+ itkSetMacro(IsoSpacing, double);
+ itkGetMacro(IsoSpacing, double);
+ itkSetMacro(OutputSpacing, OutputImageSpacingType);
+ itkGetMacro(OutputSpacing, OutputImageSpacingType);
+ itkSetMacro(OutputSize, OutputImageSizeType);
+ itkGetMacro(OutputSize, OutputImageSizeType);
+ itkGetMacro(InterpolationType, InterpolationTypeEnumeration);
+ itkSetMacro(InterpolationType, InterpolationTypeEnumeration);
+ itkGetMacro(GaussianFilteringEnabled, bool);
+ itkSetMacro(GaussianFilteringEnabled, bool);
+ itkGetMacro(BSplineOrder, int);
+ itkSetMacro(BSplineOrder, int);
+ itkGetMacro(BLUTSamplingFactor, int);
+ itkSetMacro(BLUTSamplingFactor, int);
+ itkGetMacro(Transform, typename TransformType::Pointer);
+ itkSetMacro(Transform, typename TransformType::Pointer);
+ itkGetMacro(GaussianSigma, GaussianSigmaType);
+ itkSetMacro(GaussianSigma, GaussianSigmaType);
+ itkGetMacro(DefaultPixelValue, OutputImagePixelType);
+ itkSetMacro(DefaultPixelValue, OutputImagePixelType);
+ itkGetMacro(VerboseOptions, bool);
+ itkSetMacro(VerboseOptions, bool);
+
+ protected:
+ ResampleImageWithOptionsFilter();
+ virtual ~ResampleImageWithOptionsFilter() {}
+
+ bool m_LastDimensionIsTime;
+ double m_IsoSpacing;
+ InterpolationTypeEnumeration m_InterpolationType;
+ bool m_GaussianFilteringEnabled;
+ int m_BSplineOrder;
+ int m_BLUTSamplingFactor;
+ OutputImageSizeType m_OutputSize;
+ OutputImageSpacingType m_OutputSpacing;
+ typename TransformType::Pointer m_Transform;
+ GaussianSigmaType m_GaussianSigma;
+ OutputImagePixelType m_DefaultPixelValue;
+ bool m_VerboseOptions;
+
+ virtual void GenerateInputRequestedRegion();
+ virtual void GenerateOutputInformation();
+ virtual void GenerateData();
+
+ private:
+ ResampleImageWithOptionsFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkResampleImageWithOptionsFilter.txx"
+#endif
+
+#endif
--- /dev/null
+/*=========================================================================
+ 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
+
WRAP_GGO(clitkMedianImageFilter_GGO_C clitkMedianImageFilter.ggo)
ADD_EXECUTABLE(clitkMedianImageFilter clitkMedianImageFilter.cxx)
TARGET_LINK_LIBRARIES(clitkMedianImageFilter clitkCommon ITKIO clitkFilters ITKBasicFilters)
+
+ADD_EXECUTABLE(clitkResampleImage clitkResampleImage.cxx ${clitkResampleImage_GGO_C})
+TARGET_LINK_LIBRARIES(clitkResampleImage clitkCommon ITKIO clitkFilters)
+
--- /dev/null
+/*=========================================================================
+ 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 "clitkResampleImage_ggo.h"
+#include "clitkIO.h"
+#include "clitkResampleImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkResampleImage, args_info);
+
+ // Filter
+ typedef clitk::ResampleImageGenericFilter<args_info_clitkResampleImage> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ // this is the end my friend
+ return EXIT_SUCCESS;
+
+}// end main
+//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff