--- /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
+======================================================================-====*/
+
+/* =================================================
+ * @file clitkMedianTemporalDimension.cxx
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+
+// clitk
+#include "clitkMedianTemporalDimension_ggo.h"
+#include "clitkIO.h"
+#include "clitkCommon.h"
+#include "clitkMedianTemporalDimensionGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkMedianTemporalDimension, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::MedianTemporalDimensionGenericFilter<args_info_clitkMedianTemporalDimension> FilterType;
+ FilterType::Pointer genericFilter = FilterType::New();
+
+ genericFilter->SetArgsInfo(args_info);
+ genericFilter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /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 clitkMedianTemporalDimensionGenericFilter_h
+#define clitkMedianTemporalDimensionGenericFilter_h
+
+/* =================================================
+ * @file clitkMedianTemporalDimensionGenericFilter.h
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+
+// clitk include
+#include "clitkIO.h"
+#include "clitkImageCommon.h"
+#include "clitkMedianTemporalDimension_ggo.h"
+
+//itk include
+#include "itkLightObject.h"
+
+namespace clitk
+{
+
+ template<class args_info_type>
+ class ITK_EXPORT MedianTemporalDimensionGenericFilter : public itk::LightObject
+ {
+ public:
+ //----------------------------------------
+ // ITK
+ //----------------------------------------
+ typedef MedianTemporalDimensionGenericFilter 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( MedianTemporalDimensionGenericFilter, 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[0];
+ }
+
+
+ //----------------------------------------
+ // Update
+ //----------------------------------------
+ void Update();
+
+ protected:
+
+ //----------------------------------------
+ // Constructor & Destructor
+ //----------------------------------------
+ MedianTemporalDimensionGenericFilter();
+ ~MedianTemporalDimensionGenericFilter() {};
+
+
+ //----------------------------------------
+ // Templated members
+ //----------------------------------------
+ template <unsigned int Dimension> void UpdateWithDim(const std::string PixelType, const int Components);
+ 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 "clitkMedianTemporalDimensionGenericFilter.txx"
+#endif
+
+#endif // #define clitkMedianTemporalDimensionGenericFilter_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 clitkMedianTemporalDimensionGenericFilter_txx
+#define clitkMedianTemporalDimensionGenericFilter_txx
+
+/* =================================================
+ * @file clitkMedianTemporalDimensionGenericFilter.txx
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include <algorithm>
+
+namespace clitk
+{
+
+ //-----------------------------------------------------------
+ // Constructor
+ //-----------------------------------------------------------
+ template<class args_info_type>
+ MedianTemporalDimensionGenericFilter<args_info_type>::MedianTemporalDimensionGenericFilter()
+ {
+ m_Verbose=false;
+ m_InputFileName="";
+ }
+
+
+ //-----------------------------------------------------------
+ // Update
+ //-----------------------------------------------------------
+ template<class args_info_type>
+ void MedianTemporalDimensionGenericFilter<args_info_type>::Update()
+ {
+ // Read the Dimension and PixelType
+ int Dimension, Components;
+ std::string PixelType;
+ ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
+
+
+ // Call UpdateWithDim
+ if (m_ArgsInfo.input_given>1) Dimension+=1;
+ if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
+ else if(Dimension==3)UpdateWithDim<3>(PixelType, Components);
+ else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
+ else {
+ std::cout<<"Error, Only for 2, 3 or 4D!!!"<<std::endl ;
+ return;
+ }
+ }
+
+ //-------------------------------------------------------------------
+ // Update with the number of dimensions
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dimension>
+ void
+ MedianTemporalDimensionGenericFilter<args_info_type>::UpdateWithDim(const std::string PixelType, const int Components)
+ {
+ if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D with "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
+
+ if (Components==1) {
+ 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_char") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, unsigned char>();
+ }
+ else if (PixelType == "float") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, float>();
+ }
+ else if (PixelType == "double") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, double>();
+ }
+ else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
+ }
+ }
+
+
+ //-------------------------------------------------------------------
+ // Update with the number of dimensions and the pixeltype
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ template <unsigned int Dimension, class PixelType>
+ void
+ MedianTemporalDimensionGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
+ {
+
+ // ImageTypes
+ typedef itk::Image<PixelType, Dimension> InputImageType;
+ typedef itk::Image<PixelType, Dimension-1> OutputImageType;
+ typename InputImageType::Pointer input;
+
+ if (m_ArgsInfo.input_given ==1 ) {
+ // Read the input
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ typename InputReaderType::Pointer reader = InputReaderType::New();
+ reader->SetFileName( m_InputFileName);
+ reader->Update();
+ input= reader->GetOutput();
+ }
+
+ else {
+ // Read and join multiple inputs
+ if (m_Verbose) std::cout<<m_ArgsInfo.input_given<<" inputs given..."<<std::endl;
+ std::vector<std::string> filenames;
+ for(unsigned int i=0; i<m_ArgsInfo.input_given; i++) {
+ if (m_Verbose) std::cout<<m_ArgsInfo.input_arg[i]<<std::endl;
+ filenames.push_back(m_ArgsInfo.input_arg[i]);
+ }
+
+ typedef itk::ImageSeriesReader<InputImageType> ImageReaderType;
+ typename ImageReaderType::Pointer reader= ImageReaderType::New();
+ reader->SetFileNames(filenames);
+ reader->Update();
+ input =reader->GetOutput();
+ }
+
+
+ // Output properties
+ typename OutputImageType::RegionType region;
+ typename OutputImageType::RegionType::SizeType size;
+ typename OutputImageType::IndexType index;
+ typename OutputImageType::SpacingType spacing;
+ typename OutputImageType::PointType origin;
+ typename InputImageType::RegionType region4D=input->GetLargestPossibleRegion();
+ typename InputImageType::RegionType::SizeType size4D=region4D.GetSize();
+ typename InputImageType::IndexType index4D=region4D.GetIndex();
+ typename InputImageType::SpacingType spacing4D=input->GetSpacing();
+ typename InputImageType::PointType origin4D=input->GetOrigin();
+
+ for (unsigned int i=0; i< Dimension-1; i++) {
+ size[i]=size4D[i];
+ index[i]=index4D[i];
+ spacing[i]=spacing4D[i];
+ origin[i]=origin4D[i];
+ }
+ region.SetSize(size);
+ region.SetIndex(index);
+ typename OutputImageType::Pointer output= OutputImageType::New();
+ output->SetRegions(region);
+ output->SetSpacing(spacing);
+ output->SetOrigin(origin);
+ output->Allocate();
+
+
+ // Region iterators
+ typedef itk::ImageRegionIterator<InputImageType> IteratorType;
+ std::vector<IteratorType> iterators(size4D[Dimension-1]);
+ for (unsigned int i=0; i< size4D[Dimension-1]; i++) {
+ typename InputImageType::RegionType regionIt=region4D;
+ typename InputImageType::RegionType::SizeType sizeIt=regionIt.GetSize();
+ sizeIt[Dimension-1]=1;
+ regionIt.SetSize(sizeIt);
+ typename InputImageType::IndexType indexIt=regionIt.GetIndex();
+ indexIt[Dimension-1]=i;
+ regionIt.SetIndex(indexIt);
+ iterators[i]=IteratorType(input, regionIt);
+ }
+
+ typedef itk::ImageRegionIterator<OutputImageType> OutputIteratorType;
+ OutputIteratorType avIt(output, output->GetLargestPossibleRegion());
+
+ // Take the median
+ double value;
+ while (!(iterators[0]).IsAtEnd()) {
+ value=0.;
+ std::vector<PixelType> temp;
+ for (unsigned int i=0; i<size4D[Dimension-1]; i++) {
+ temp.push_back(iterators[i].Get());
+ ++(iterators[i]);
+ }
+ if (temp.size() % 2) {
+ nth_element(temp.begin(),temp.begin()+((temp.size()-1)/2+1),temp.end());
+ value=temp[(temp.size()-1)/2];
+ } else {
+ nth_element(temp.begin(),temp.begin()+(temp.size())/2,temp.end());
+ value=temp[temp.size()/2];
+ nth_element(temp.begin(),temp.begin()+ (temp.size()/2+1),temp.end());
+ value+=temp[temp.size()/2+1];
+ value/=2;
+ }
+ value/=size4D[Dimension-1];
+ avIt.Set(value);
+ ++avIt;
+ }
+
+ // Output
+ typedef itk::ImageFileWriter<OutputImageType> WriterType;
+ typename WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(m_ArgsInfo.output_arg);
+ writer->SetInput(output);
+ writer->Update();
+
+}
+
+
+}//end clitk
+
+#endif //#define clitkMedianTemporalDimensionGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff