GGO(clitkResampleImage, args_info);
// Filter
- typedef clitk::ResampleImageGenericFilter<args_info_clitkResampleImage> FilterType;
+ typedef clitk::ResampleImageGenericFilter FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetArgsInfo(args_info);
--- /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 "like" l "Resample like this image" string no
+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
+ ======================================================================-====*/
+
+// clitk
+#include "clitkResampleImageGenericFilter.h"
+#include "clitkResampleImageWithOptionsFilter.h"
+
+//--------------------------------------------------------------------
+clitk::ResampleImageGenericFilter::ResampleImageGenericFilter():
+ ImageToImageGenericFilter<Self>("Resample")
+{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<unsigned int Dim>
+void clitk::ResampleImageGenericFilter::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+ ADD_IMAGE_TYPE(Dim, short);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::ResampleImageGenericFilter::SetArgsInfo(const ArgsInfoType & 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);
+ }
+}
+//--------------------------------------------------------------------
+
--- /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 "clitkResampleImage_ggo.h"
+#include "clitkImageToImageGenericFilter.h"
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ class ITK_EXPORT ResampleImageGenericFilter:
+ public ImageToImageGenericFilter<ResampleImageGenericFilter> {
+
+ public:
+ // Constructor
+ ResampleImageGenericFilter();
+
+ // Types
+ typedef ResampleImageGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef args_info_clitkResampleImage ArgsInfoType;
+
+ // New
+ itkNewMacro(Self);
+
+ // Args
+ void SetArgsInfo(const ArgsInfoType & a);
+
+ // Main function
+ template<class InputImageType> void UpdateWithInputImageType();
+
+ protected:
+ ArgsInfoType 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"
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class InputImageType>
+void
+clitk::ResampleImageGenericFilter::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.like_given) {
+ DD("like");
+
+ }
+ else {
+ if (mArgsInfo.spacing_given == 1) {
+ filter->SetOutputIsoSpacing(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 {
+ if (interp == "windowed sinc") {
+ filter->SetInterpolationType(ResampleImageFilterType::WSINC);
+ } else {
+ std::cerr << "Error. I do not know interpolation '" << mArgsInfo.interp_arg
+ << "'. Choose among: nn, linear, bspline, blut, windowed sinc" << 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 */
+
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