--- /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://www.centreleonberard.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 clitkJacobianImageGenericFilter_h
+#define clitkJacobianImageGenericFilter_h
+
+/* =================================================
+ * @file clitkJacobianImageGenericFilter.h
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+
+// clitk include
+#include "clitkIO.h"
+#include "clitkCommon.h"
+#include "clitkJacobianImage_ggo.h"
+
+//itk include
+#include "itkLightObject.h"
+#include "itkInverseDeformationFieldImageFilter.h"
+
+namespace clitk
+{
+
+ template<class args_info_type>
+ class ITK_EXPORT JacobianImageGenericFilter : public itk::LightObject
+ {
+ public:
+ //----------------------------------------
+ // ITK
+ //----------------------------------------
+ typedef JacobianImageGenericFilter Self;
+ typedef itk::LightObject 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( JacobianImageGenericFilter, LightObject );
+
+
+ //----------------------------------------
+ // Typedefs
+ //----------------------------------------
+
+
+ //----------------------------------------
+ // Set & Get
+ //----------------------------------------
+ void SetArgsInfo(const args_info_type & a)
+ {
+ m_ArgsInfo=a;
+ m_Verbose=m_ArgsInfo.verbose_flag;
+ m_InputFileName=m_ArgsInfo.input_arg;
+ }
+
+
+ //----------------------------------------
+ // Update
+ //----------------------------------------
+ void Update();
+
+ protected:
+
+ //----------------------------------------
+ // Constructor & Destructor
+ //----------------------------------------
+ JacobianImageGenericFilter();
+ ~JacobianImageGenericFilter() {};
+
+
+ //----------------------------------------
+ // Templated members
+ //----------------------------------------
+ template <unsigned int Dimension> void UpdateWithDim(std::string PixelType);
+ template <unsigned int Dimension, class PixelType> void UpdateWithDimAndPixelType();
+
+
+ //----------------------------------------
+ // Data members
+ //----------------------------------------
+ args_info_type m_ArgsInfo;
+ bool m_Verbose;
+ std::string m_InputFileName;
+
+ };
+
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkJacobianImageGenericFilter.txx"
+#endif
+
+#endif // #define clitkJacobianImageGenericFilter_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://www.centreleonberard.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 clitkJacobianImageGenericFilter_txx
+#define clitkJacobianImageGenericFilter_txx
+
+/* =================================================
+ * @file clitkJacobianImageGenericFilter.txx
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include "clitkImageCommon.h"
+#include "itkDeformationFieldJacobianDeterminantFilter.h"
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkVector.h"
+#include "itkNormalizeImageFilter.h"
+
+namespace clitk
+{
+
+//-----------------------------------------------------------
+// Constructor
+//-----------------------------------------------------------
+template<class args_info_type>
+JacobianImageGenericFilter<args_info_type>::JacobianImageGenericFilter()
+{
+ m_Verbose=false;
+ m_InputFileName="";
+}
+
+
+//-----------------------------------------------------------
+// Update
+//-----------------------------------------------------------
+template<class args_info_type>
+void JacobianImageGenericFilter<args_info_type>::Update()
+{
+ // Read the Dimension and PixelType
+ int Dimension;
+ std::string PixelType;
+ ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
+
+
+ // Call UpdateWithDim
+ if(Dimension==2) UpdateWithDim<2>(PixelType);
+ else if(Dimension==3) UpdateWithDim<3>(PixelType);
+ // else if (Dimension==4)UpdateWithDim<4>(PixelType);
+ else {
+ std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
+ return;
+ }
+}
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions
+//-------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dimension>
+void
+JacobianImageGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
+{
+ if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
+
+ // if(PixelType == "short"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, signed short>();
+ // }
+ // else if(PixelType == "unsigned_short"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, unsigned short>();
+ // }
+
+ // else if (PixelType == "unsigned_char"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, unsigned char>();
+ // }
+
+ // else if (PixelType == "char"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, signed char>();
+ // }
+ // else {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, itk::Vector<float, Dimension> >();
+ // }
+}
+
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//-------------------------------------------------------------------
+template<class args_info_type>
+template <unsigned int Dimension, class PixelType>
+void
+JacobianImageGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
+{
+ std::string vfield_file = m_ArgsInfo.input_arg;
+
+ const unsigned int dim = Dimension;
+ typedef itk::Vector<double, dim> VectorType;
+ typedef itk::Image<VectorType, dim> VectorFieldType;
+ typedef itk::ImageFileReader<VectorFieldType> VectorFieldReaderType;
+
+ typename VectorFieldReaderType::Pointer vfield_reader = VectorFieldReaderType::New();
+ vfield_reader->SetFileName(vfield_file.c_str());
+
+ typedef double OutputPixelType;
+ typedef itk::Image<OutputPixelType, dim> ImageType;
+ //typedef itk::DeformationFieldJacobianDeterminantFilter<VectorFieldType, PixelType, ImageType> JacobianFilterType;
+ typedef itk::DisplacementFieldJacobianDeterminantFilter<VectorFieldType, OutputPixelType, ImageType> JacobianFilterType;
+
+ typename VectorFieldType::Pointer vfield = vfield_reader->GetOutput();
+ typename JacobianFilterType::Pointer jac = JacobianFilterType::New();
+ jac->SetInput(vfield);
+ jac->Update();
+
+ typedef itk::NormalizeImageFilter<ImageType, ImageType> NormalizeFilterType;
+ typename NormalizeFilterType::Pointer normalize = NormalizeFilterType::New();
+ normalize->SetInput(jac->GetOutput());
+ normalize->Update();
+
+ typedef itk::ImageFileWriter<ImageType> ImageFileWriterType;
+ typename ImageFileWriterType::Pointer image_writer = ImageFileWriterType::New();
+
+ std::string image_file = m_ArgsInfo.output_arg;
+ image_writer->SetFileName(image_file.c_str());
+ image_writer->SetInput(jac->GetOutput());
+ image_writer->Update();
+
+}
+
+
+}//end clitk
+
+#endif //#define clitkJacobianImageGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff