X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkCropImageGenericFilter.cxx;h=4f3bb231762ca6c6fe19fdc528a90a8c15b5456d;hb=05e26237e30a14a226cb4eb480a0eb9697f8ba06;hp=b8d77445eaa2dbd3f89703d18ca50167eb31a5c9;hpb=119a42cb1444930c78314e862e590f54c2f7678d;p=clitk.git diff --git a/tools/clitkCropImageGenericFilter.cxx b/tools/clitkCropImageGenericFilter.cxx old mode 100755 new mode 100644 index b8d7744..4f3bb23 --- a/tools/clitkCropImageGenericFilter.cxx +++ b/tools/clitkCropImageGenericFilter.cxx @@ -3,7 +3,7 @@ Authors belong to: - University of LYON http://www.universite-lyon.fr/ - - Léon Bérard cancer center http://oncora1.lyon.fnclcc.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 @@ -14,155 +14,190 @@ - BSD See included LICENSE.txt file - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html -======================================================================-====*/ +===========================================================================**/ #ifndef clitkCropImageGenericFilter_cxx #define clitkCropImageGenericFilter_cxx -/* ================================================= - * @file clitkCropImageGenericFilter.cxx - * @author - * @date - * - * @brief - * - ===================================================*/ - #include "clitkCropImageGenericFilter.h" - -namespace clitk +//----------------------------------------------------------- +// Constructor +//----------------------------------------------------------- +clitk::CropImageGenericFilter::CropImageGenericFilter(): + ImageToImageGenericFilter("CropImage") { + cmdline_parser_clitkCropImage_init(&mArgsInfo); + InitializeImageType<2>(); + InitializeImageType<3>(); + InitializeImageType<4>(); +} + +//-------------------------------------------------------------------- +template +void clitk::CropImageGenericFilter::InitializeImageType() +{ + ADD_DEFAULT_IMAGE_TYPES(Dim); + ADD_DEFAULT_VEC_IMAGE_TYPES; +} +//-------------------------------------------------------------------- - - //----------------------------------------------------------- - // Constructor - //----------------------------------------------------------- - CropImageGenericFilter::CropImageGenericFilter(): - ImageToImageGenericFilter("CropImage") - { - cmdline_parser_clitkCropImage_init(&mArgsInfo); - InitializeImageType<2>(); - InitializeImageType<3>(); - InitializeImageType<4>(); - } - - //-------------------------------------------------------------------- - template - void clitk::CropImageGenericFilter::InitializeImageType() - { - ADD_DEFAULT_IMAGE_TYPES(Dim); - //ADD_IMAGE_TYPE(Dim, uchar); - //ADD_IMAGE_TYPE(Dim, short); - // ADD_IMAGE_TYPE(Dim, uint); - // ADD_IMAGE_TYPE(Dim, ulong); - // ADD_IMAGE_TYPE(Dim, int); - // ADD_IMAGE_TYPE(Dim, float); - } - //-------------------------------------------------------------------- - - //-------------------------------------------------------------------- - void clitk::CropImageGenericFilter::SetArgsInfo(const args_info_type& a) - { - mArgsInfo=a; - SetIOVerbose(mArgsInfo.verbose_flag); - if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes(); - if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg); - if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg); +//-------------------------------------------------------------------- +void clitk::CropImageGenericFilter::SetArgsInfo(const args_info_type& a) +{ + mArgsInfo=a; + SetIOVerbose(mArgsInfo.verbose_flag); + if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes(); + if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg); + if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg); +} +//-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +template +typename clitk::CropImageGenericFilter::AutoCrop::ImagePointer +clitk::CropImageGenericFilter::AutoCrop::Do(args_info_type &argsInfo, ImagePointer input) +{ + static const unsigned int PixelDimension = itk::PixelTraits::Dimension; + return this->Do(argsInfo, input, static_cast< PixelDimType *>(NULL) ); +} +//-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +template +template +typename clitk::CropImageGenericFilter::AutoCrop::ImagePointer +clitk::CropImageGenericFilter::AutoCrop::Do(args_info_type &, ImagePointer, PixelDimType *) +{ + clitkExceptionMacro("Autocrop is not implemented for vector fields"); + return ITK_NULLPTR; +} +//-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +template +typename clitk::CropImageGenericFilter::AutoCrop::ImagePointer +clitk::CropImageGenericFilter::AutoCrop::Do(args_info_type &argsInfo, ImagePointer input, PixelDimType<1> *) +{ + if (argsInfo.boundingBox_given) + clitkExceptionMacro("Do not use --BG and --boundingBox at the same time"); + if (argsInfo.lower_given) + clitkExceptionMacro("Do not use --BG and --lower at the same time"); + if (argsInfo.upper_given) + clitkExceptionMacro("Do not use --BG and --upper at the same time"); + typedef clitk::AutoCropFilter FilterType; + typename FilterType::Pointer filter = FilterType::New(); + filter->SetInput(input); + filter->SetBackgroundValue(argsInfo.BG_arg); + filter->Update(); + return filter->GetOutput(); +} +//-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +// Update with the number of dimensions and the pixeltype +//-------------------------------------------------------------------- +template +void clitk::CropImageGenericFilter::UpdateWithInputImageType() +{ + // Reading input + typename ImageType::Pointer input = this->template GetInput(0); + typename ImageType::RegionType input_region = input->GetLargestPossibleRegion(); + + // Check options + if (mArgsInfo.BG_given && mArgsInfo.like_given) + clitkExceptionMacro("Do not use --BG and --like at the same time"); + if (mArgsInfo.updateOrigin_flag && !mArgsInfo.like_given) + clitkExceptionMacro("Use --updateOrigin with --like"); + + // Prepare output + typename ImageType::Pointer output; + + // ------------------------------------------------ + if (mArgsInfo.BG_given) { // AutoCrop filter + AutoCrop autoCrop; + output = autoCrop.Do(mArgsInfo, input); } - //-------------------------------------------------------------------- - - //-------------------------------------------------------------------- - // Update with the number of dimensions and the pixeltype - //-------------------------------------------------------------------- - template - void clitk::CropImageGenericFilter::UpdateWithInputImageType() - { - // Reading input - typename ImageType::Pointer input = this->template GetInput(0); - - // Check options - if (mArgsInfo.BG_given && mArgsInfo.like_given) - clitkExceptionMacro("Do not use --BG and --like at the same time"); - - // Prepare output - typename ImageType::Pointer output; - + else { // ------------------------------------------------ - if (mArgsInfo.BG_given) { // AutoCrop filter - if (mArgsInfo.boundingBox_given) - clitkExceptionMacro("Do not use --BG and --boundingBox at the same time"); - if (mArgsInfo.lower_given) - clitkExceptionMacro("Do not use --BG and --lower at the same time"); - if (mArgsInfo.upper_given) - clitkExceptionMacro("Do not use --BG and --upper at the same time"); - typedef clitk::AutoCropFilter FilterType; + if (mArgsInfo.like_given) { // CropLike filter + if (mArgsInfo.boundingBox_given) + clitkExceptionMacro("Do not use --like and --boundingBox at the same time"); + if (mArgsInfo.lower_given) + clitkExceptionMacro("Do not use --like and --lower at the same time"); + if (mArgsInfo.upper_given) + clitkExceptionMacro("Do not use --like and --upper at the same time"); + typedef clitk::CropLikeImageFilter FilterType; typename FilterType::Pointer filter = FilterType::New(); filter->SetInput(input); - filter->SetBackgroundValue(mArgsInfo.BG_arg); + filter->SetCropLikeFilename(mArgsInfo.like_arg); + filter->SetBackgroundValue(mArgsInfo.BGLike_arg); filter->Update(); output = filter->GetOutput(); } else { // ------------------------------------------------ - if (mArgsInfo.like_given) { // CropLike filter - if (mArgsInfo.boundingBox_given) - clitkExceptionMacro("Do not use --like and --boundingBox at the same time"); - if (mArgsInfo.lower_given) - clitkExceptionMacro("Do not use --like and --lower at the same time"); - if (mArgsInfo.upper_given) - clitkExceptionMacro("Do not use --like and --upper at the same time"); - typedef clitk::CropLikeImageFilter FilterType; - typename FilterType::Pointer filter = FilterType::New(); - filter->SetInput(input); - filter->SetCropLikeFilename(mArgsInfo.like_arg); - filter->SetBackgroundValue(mArgsInfo.BGLike_arg); - filter->Update(); - output = filter->GetOutput(); + typename ImageType::SizeType lSize; + typename ImageType::SizeType uSize; + if (mArgsInfo.verbose_flag) std::cout << "input region " << input_region << std::endl; + if (mArgsInfo.boundingBox_given) { + for(unsigned int i=0; iGetLargestPossibleRegion().GetSize()[i]-mArgsInfo.boundingBox_arg[2*i+1]-1; - } + if (mArgsInfo.lower_given) { + for(unsigned int i=0; i(mArgsInfo.lower_arg[i]); } - else { - if (mArgsInfo.lower_given) { - for(unsigned int i=0; i(mArgsInfo.lower_arg[i]); - } - else lSize.Fill(0); - if (mArgsInfo.upper_given) { - for(unsigned int i=0; i(mArgsInfo.upper_arg[i]); - } - else uSize.Fill(0); + else lSize.Fill(0); + if (mArgsInfo.upper_given) { + for(unsigned int i=0; i(mArgsInfo.upper_arg[i]); } - typedef itk::CropImageFilter CropImageFilterType; - typename CropImageFilterType::Pointer filter=CropImageFilterType::New(); - filter->SetInput(input); - filter->SetLowerBoundaryCropSize(lSize); - filter->SetUpperBoundaryCropSize(uSize); - filter->Update(); - output = filter->GetOutput(); + else uSize.Fill(0); + } + + if (mArgsInfo.verbose_flag) { + std::cout << "lower " << lSize << " upper " << uSize << std::endl; } - } - // Force origin if needed - if (mArgsInfo.origin_flag) { - typename ImageType::PointType origin; - origin.Fill(itk::NumericTraits::Zero); - output->SetOrigin(origin); + typedef itk::CropImageFilter CropImageFilterType; + typename CropImageFilterType::Pointer filter=CropImageFilterType::New(); + filter->SetInput(input); + filter->SetLowerBoundaryCropSize(lSize); + filter->SetUpperBoundaryCropSize(uSize); + filter->Update(); + output = filter->GetOutput(); } + } - // Write/Save results - this->template SetNextOutput(output); + // Force origin if needed + if (mArgsInfo.origin_flag) { + typename ImageType::PointType origin; + origin.Fill(itk::NumericTraits::Zero); + output->SetOrigin(origin); } - //-------------------------------------------------------------------- -} //end clitk + // adjust image origin and force index to zero + typename ImageType::RegionType region = output->GetLargestPossibleRegion(); + typename ImageType::IndexType index = region.GetIndex(); + typename ImageType::PointType origin = output->GetOrigin(); + typename ImageType::SpacingType spacing = output->GetSpacing(); + if (!mArgsInfo.BG_given && (!mArgsInfo.like_given || mArgsInfo.updateOrigin_flag)) { + if (mArgsInfo.verbose_flag) std::cout << "origin before crop " << origin << std::endl; + input->TransformIndexToPhysicalPoint(index,origin); + if (mArgsInfo.verbose_flag) std::cout << "origin after crop " << origin << std::endl; + output->SetOrigin(origin); + } + + index.Fill(itk::NumericTraits::Zero); + region.SetIndex(index); + output->SetRegions(region); + + // Write/Save results + this->template SetNextOutput(output); +} +//-------------------------------------------------------------------- #endif //#define clitkCropImageGenericFilter_cxx