From: David Sarrut Date: Fri, 3 Feb 2012 06:57:12 +0000 (+0100) Subject: Moved from repository clitk to clitk.private/tests_dav X-Git-Tag: v1.4.0~310 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=d0696e373aa90e6c42264e20383f798f14f1f299;p=clitk.git Moved from repository clitk to clitk.private/tests_dav --- diff --git a/tests_dav/clitkRegionGrowing.cxx b/tests_dav/clitkRegionGrowing.cxx new file mode 100644 index 0000000..83aa816 --- /dev/null +++ b/tests_dav/clitkRegionGrowing.cxx @@ -0,0 +1,51 @@ +/*========================================================================= + 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 +===========================================================================**/ + +/* ================================================= + * @file clitkRegionGrowing.cxx + * @author + * @date + * + * @brief + * + ===================================================*/ + + +// clitk +#include "clitkRegionGrowing_ggo.h" +#include "clitkIO.h" +#include "clitkRegionGrowingGenericFilter.h" + + +//-------------------------------------------------------------------- +int main(int argc, char * argv[]) { + + // Init command line + GGO(clitkRegionGrowing, args_info); + CLITK_INIT; + + // Filter + clitk::RegionGrowingGenericFilter::Pointer genericFilter=clitk::RegionGrowingGenericFilter::New(); + + genericFilter->SetArgsInfo(args_info); + genericFilter->Update(); + + return EXIT_SUCCESS; +}// end main + +//-------------------------------------------------------------------- diff --git a/tests_dav/clitkRegionGrowing.ggo b/tests_dav/clitkRegionGrowing.ggo new file mode 100644 index 0000000..60bcae2 --- /dev/null +++ b/tests_dav/clitkRegionGrowing.ggo @@ -0,0 +1,34 @@ +#File clitkRegionGrowing.ggo +package "clitkRegionGrowing" +version "1.0" +purpose "Region growing from a seed point using various types of conditions to control the growing" + +option "config" - "Config file" string no +option "verbose" v "Verbose" flag off + +section "I/O" + +option "input" i "Input image filename" string yes +option "output" o "Output image filename" string yes + + +section "Parameters" + +option "type" t "Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3= locally-adaptive-threshold, 4= explosion-controlled-threshold" int no default="0" +option "lower" l "1,2,3,4: Lower threshold value" double no default="0" +option "upper" u "1,2,3,4: Upper threshold value" double no default="1" +option "maxUpper" - "4: Maximum upper threshold value" double no default="2000" +option "minLower" - "4: Minimum lower threshold value" double no default="-1000" +option "step" - "4: Threshold step size" double no default="64.0" +option "minStep" - "4: Minimum threshold step size" double no default="1" +option "adaptLower" - "3,4: (locally) adapt lower thresholding" flag off +option "adaptUpper" - "3,4: (locally) adapt upper thresholding" flag off +option "multiplier" m "2-4: (2-3) accept if within mean+-mutiplier*SD, (4) explosion if size increases multiplier times" double no default="2.0" +option "seed" s "Seed index postion (in voxels)" int multiple no default="0" +option "seedRadius" - "Radius used for seed dilatation(in voxel)" int multiple no default="0" +option "pad" p "The replace padding value" double no default="1.0" +option "radius" r "1-3: The radius of the neighborhood" int no multiple default="1" +option "maxSD" - "3: Limit to SD" double no +option "full" - "4: use full connectivity (not implemented yet)" flag off +option "iter" - "2: Iterations" int no default="5" + diff --git a/tests_dav/clitkRegionGrowingGenericFilter.cxx b/tests_dav/clitkRegionGrowingGenericFilter.cxx new file mode 100644 index 0000000..f5092ba --- /dev/null +++ b/tests_dav/clitkRegionGrowingGenericFilter.cxx @@ -0,0 +1,72 @@ +/*========================================================================= + 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 clitkRegionGrowingGenericFilter_cxx +#define clitkRegionGrowingGenericFilter_cxx + +/* ================================================= + * @file clitkRegionGrowingGenericFilter.cxx + * @author + * @date + * + * @brief + * + ===================================================*/ + +#include "clitkRegionGrowingGenericFilter.h" + + +namespace clitk +{ + + + //----------------------------------------------------------- + // Constructor + //----------------------------------------------------------- + RegionGrowingGenericFilter::RegionGrowingGenericFilter() + { + m_Verbose=false; + m_InputFileName=""; + } + + + //----------------------------------------------------------- + // Update + //----------------------------------------------------------- + void RegionGrowingGenericFilter::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!!!"< Pointer; + typedef itk::SmartPointer ConstPointer; + + // Method for creation through the object factory + itkNewMacro(Self); + + // Run-time type information (and related methods) + itkTypeMacro( RegionGrowingGenericFilter, LightObject ); + + + //---------------------------------------- + // Typedefs + //---------------------------------------- + + + //---------------------------------------- + // Set & Get + //---------------------------------------- + void SetArgsInfo(const args_info_clitkRegionGrowing & a) + { + m_ArgsInfo=a; + m_Verbose=m_ArgsInfo.verbose_flag; + m_InputFileName=m_ArgsInfo.input_arg; + } + + + //---------------------------------------- + // Update + //---------------------------------------- + void Update(); + + protected: + + //---------------------------------------- + // Constructor & Destructor + //---------------------------------------- + RegionGrowingGenericFilter(); + ~RegionGrowingGenericFilter() {}; + + + //---------------------------------------- + // Templated members + //---------------------------------------- + template void UpdateWithDim(std::string PixelType); + template void UpdateWithDimAndPixelType(); + + + //---------------------------------------- + // Data members + //---------------------------------------- + args_info_clitkRegionGrowing m_ArgsInfo; + bool m_Verbose; + std::string m_InputFileName; + + }; + + +} // end namespace clitk + +#ifndef ITK_MANUAL_INSTANTIATION +#include "clitkRegionGrowingGenericFilter.txx" +#endif + +#endif // #define clitkRegionGrowingGenericFilter_h diff --git a/tests_dav/clitkRegionGrowingGenericFilter.txx b/tests_dav/clitkRegionGrowingGenericFilter.txx new file mode 100644 index 0000000..eead0d5 --- /dev/null +++ b/tests_dav/clitkRegionGrowingGenericFilter.txx @@ -0,0 +1,302 @@ +/*========================================================================= + 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 clitkRegionGrowingGenericFilter_txx +#define clitkRegionGrowingGenericFilter_txx +#include +#include + +namespace clitk +{ + + //------------------------------------------------------------------- + // Update with the number of dimensions + //------------------------------------------------------------------- + template + void + RegionGrowingGenericFilter::UpdateWithDim(std::string PixelType) + { + if (m_Verbose) std::cout << "Image was detected to be "<(); + } + // else if(PixelType == "unsigned_short"){ + // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl; + // UpdateWithDimAndPixelType(); + // } + + else if (PixelType == "unsigned_char"){ + if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl; + UpdateWithDimAndPixelType(); + } + + // else if (PixelType == "char"){ + // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl; + // UpdateWithDimAndPixelType(); + // } + else { + if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl; + UpdateWithDimAndPixelType(); + } + } + + + //------------------------------------------------------------------- + // Update with the number of dimensions and the pixeltype + //------------------------------------------------------------------- + template + void + RegionGrowingGenericFilter::UpdateWithDimAndPixelType() + { + + // ImageTypes + typedef itk::Image InputImageType; + typedef itk::Image OutputImageType; + + // Read the input + typedef itk::ImageFileReader InputReaderType; + typename InputReaderType::Pointer reader = InputReaderType::New(); + reader->SetFileName( m_InputFileName); + reader->Update(); + typename InputImageType::Pointer input= reader->GetOutput(); + + // Seed + typedef typename std::vector SeedsType; + SeedsType seeds(1); + if(m_ArgsInfo.seed_given==Dimension) + for (unsigned int i=0; i BallType; + typename BallType::RadiusType r; + + if (m_ArgsInfo.seedRadius_given == Dimension) + for (unsigned i = 0; i < Dimension; i++) + r[i] = m_ArgsInfo.seedRadius_arg[i]; + else + r.Fill(m_ArgsInfo.seedRadius_arg[0]); + + BallType ball; + ball.SetRadius(r); + ball.CreateStructuringElement(); + + typedef itk::ConstShapedNeighborhoodIterator IteratorType; + IteratorType it(ball.GetRadius(), + input, + input->GetLargestPossibleRegion()); +#if ITK_VERSION_MAJOR < 4 + typename BallType::ConstIterator nit; + unsigned idx = 0; + for (nit = ball.Begin(); nit != ball.End(); ++nit, ++idx) + { + if (*nit) + { + it.ActivateOffset(it.GetOffset(idx)); + } + else + { + it.DeactivateOffset(it.GetOffset(idx)); + } + } +#else + it.CreateActiveListFromNeighborhood(ball); + it.NeedToUseBoundaryConditionOff(); +#endif + + it.SetLocation(seeds[0]); + for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i) + { + typename InputImageType::IndexType id = seeds[0] + i.GetNeighborhoodOffset(); + if (id != seeds[0] && input->GetLargestPossibleRegion().IsInside(id)) + seeds.push_back(id); + } + } + + // Filter + typedef itk::ImageToImageFilter ImageToImageFilterType; + typename ImageToImageFilterType::Pointer filter; + + switch (m_ArgsInfo.type_arg) + { + case 0: { + + typedef itk::ConnectedThresholdImageFilter ImageFilterType; + typename ImageFilterType::Pointer f= ImageFilterType::New(); + + f->SetLower(m_ArgsInfo.lower_arg); + f->SetUpper(m_ArgsInfo.upper_arg); + f->SetReplaceValue(static_cast(m_ArgsInfo.pad_arg)); + for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it) + f->AddSeed(*it); + filter=f; + if(m_Verbose)std::cout<<"Using the connected threshold image filter..."< ImageFilterType; + typename ImageFilterType::Pointer f= ImageFilterType::New(); + + // Radius + typename InputImageType::SizeType size; + if(m_ArgsInfo.radius_given==Dimension) + for (unsigned int i=0; iSetLower(m_ArgsInfo.lower_arg); + f->SetUpper(m_ArgsInfo.upper_arg); + f->SetReplaceValue(static_cast(m_ArgsInfo.pad_arg)); + for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it) + f->AddSeed(*it); + f->SetRadius(size); + filter=f; + if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."< ImageFilterType; + typename ImageFilterType::Pointer f= ImageFilterType::New(); + + // Radius + typename InputImageType::SizeType size; + if(m_ArgsInfo.radius_given==Dimension) + for (unsigned int i=0; iSetMultiplier( m_ArgsInfo.multiplier_arg ); + f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg ); + for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it) + f->AddSeed(*it); + f->SetNumberOfIterations( m_ArgsInfo.iter_arg); + f->SetReplaceValue(static_cast(m_ArgsInfo.pad_arg)); + f->SetInitialNeighborhoodRadius(size[0]); + filter=f; + if(m_Verbose)std::cout<<"Using the confidence threshold connected image filter..."< ImageFilterType; + typename ImageFilterType::Pointer f= ImageFilterType::New(); + + // Radius + typename InputImageType::SizeType size; + if(m_ArgsInfo.radius_given==Dimension) + for (unsigned int i=0; iSetLower(m_ArgsInfo.lower_arg); + f->SetUpper(m_ArgsInfo.upper_arg); + f->SetLowerBorderIsGiven(m_ArgsInfo.adaptLower_flag); + f->SetLowerBorderIsGiven(m_ArgsInfo.adaptUpper_flag); + f->SetReplaceValue(static_cast(m_ArgsInfo.pad_arg)); + f->SetMultiplier(m_ArgsInfo.multiplier_arg); + f->SetMaximumSDIsGiven(m_ArgsInfo.maxSD_given); + if (m_ArgsInfo.maxSD_given) f->SetMaximumSD(m_ArgsInfo.maxSD_arg); + for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it) + f->AddSeed(*it); + f->SetRadius(size); + filter=f; + if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."< ImageFilterType; + typename ImageFilterType::Pointer f= ImageFilterType::New(); + + // // Radius + // typename InputImageType::SizeType size; + // if(m_ArgsInfo.radius_given==Dimension) + // for (unsigned int i=0; iSetVerbose(m_ArgsInfo.verbose_flag); + f->SetLower(m_ArgsInfo.lower_arg); + f->SetUpper(m_ArgsInfo.upper_arg); + f->SetMinimumLowerThreshold(m_ArgsInfo.minLower_arg); + f->SetMaximumUpperThreshold(m_ArgsInfo.maxUpper_arg); + f->SetAdaptLowerBorder(m_ArgsInfo.adaptLower_flag); + f->SetAdaptUpperBorder(m_ArgsInfo.adaptUpper_flag); + f->SetReplaceValue(static_cast(m_ArgsInfo.pad_arg)); + f->SetMultiplier(m_ArgsInfo.multiplier_arg); + f->SetThresholdStepSize(m_ArgsInfo.step_arg); + f->SetMinimumThresholdStepSize(m_ArgsInfo.minStep_arg); + f->SetFullyConnected(m_ArgsInfo.full_flag); + for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it) + f->AddSeed(*it); + filter=f; + if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<SetInput(input); + filter->Update(); + typename OutputImageType::Pointer output=filter->GetOutput(); + + // Output + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->SetFileName(m_ArgsInfo.output_arg); + writer->SetInput(output); + writer->Update(); + } + +}//end clitk + +#endif //#define clitkRegionGrowingGenericFilter_txx