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
- 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"
+//-----------------------------------------------------------
+// Constructor
+//-----------------------------------------------------------
+clitk::CropImageGenericFilter::CropImageGenericFilter():
+ ImageToImageGenericFilter<Self>("CropImage")
+{
+ cmdline_parser_clitkCropImage_init(&mArgsInfo);
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+}
+
+//--------------------------------------------------------------------
+template<unsigned int Dim>
+void clitk::CropImageGenericFilter::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+ ADD_DEFAULT_VEC_IMAGE_TYPES;
+}
+//--------------------------------------------------------------------
-namespace clitk
+//--------------------------------------------------------------------
+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 <class ImageType>
+typename clitk::CropImageGenericFilter::AutoCrop<ImageType>::ImagePointer
+clitk::CropImageGenericFilter::AutoCrop<ImageType>::Do(args_info_type &argsInfo, ImagePointer input)
+{
+ static const unsigned int PixelDimension = itk::PixelTraits<typename ImageType::PixelType>::Dimension;
+ return this->Do(argsInfo, input, static_cast< PixelDimType<PixelDimension> *>(NULL) );
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+template<unsigned int Dim>
+typename clitk::CropImageGenericFilter::AutoCrop<ImageType>::ImagePointer
+clitk::CropImageGenericFilter::AutoCrop<ImageType>::Do(args_info_type &, ImagePointer, PixelDimType<Dim> *)
+{
+ clitkExceptionMacro("Autocrop is not implemented for vector fields");
+ return ITK_NULLPTR;
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+typename clitk::CropImageGenericFilter::AutoCrop<ImageType>::ImagePointer
+clitk::CropImageGenericFilter::AutoCrop<ImageType>::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<ImageType> 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<class ImageType>
+void clitk::CropImageGenericFilter::UpdateWithInputImageType()
{
+ // Reading input
+ typename ImageType::Pointer input = this->template GetInput<ImageType>(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<ImageType> autoCrop;
+ output = autoCrop.Do(mArgsInfo, input);
+ }
+ 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<ImageType> 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();
+ }
+ else {
+ // ------------------------------------------------
+ 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; i<ImageType::ImageDimension; i++) {
+ lSize[i] = mArgsInfo.boundingBox_arg[2*i];
+ uSize[i] = input_region.GetSize()[i]-mArgsInfo.boundingBox_arg[2*i+1]-1;
+ }
+ }
+ else {
+ if (mArgsInfo.lower_given) {
+ for(unsigned int i=0; i<ImageType::ImageDimension; i++)
+ lSize[i]=static_cast<unsigned int >(mArgsInfo.lower_arg[i]);
+ }
+ else lSize.Fill(0);
+ if (mArgsInfo.upper_given) {
+ for(unsigned int i=0; i<ImageType::ImageDimension; i++)
+ uSize[i]=static_cast<unsigned int >(mArgsInfo.upper_arg[i]);
+ }
+ else uSize.Fill(0);
+ }
+ if (mArgsInfo.verbose_flag) {
+ std::cout << "lower " << lSize << " upper " << uSize << std::endl;
+ }
- //-----------------------------------------------------------
- // Constructor
- //-----------------------------------------------------------
- CropImageGenericFilter::CropImageGenericFilter()
- {
- m_Verbose=false;
- m_InputFileName="";
+ typedef itk::CropImageFilter<ImageType, ImageType> CropImageFilterType;
+ typename CropImageFilterType::Pointer filter=CropImageFilterType::New();
+ filter->SetInput(input);
+ filter->SetLowerBoundaryCropSize(lSize);
+ filter->SetUpperBoundaryCropSize(uSize);
+ filter->Update();
+ output = filter->GetOutput();
+ }
}
+ // Force origin if needed
+ if (mArgsInfo.origin_flag) {
+ typename ImageType::PointType origin;
+ origin.Fill(itk::NumericTraits<double>::Zero);
+ output->SetOrigin(origin);
+ }
- //-----------------------------------------------------------
- // Update
- //-----------------------------------------------------------
- void CropImageGenericFilter::Update()
- {
- // Read the Dimension and PixelType
- int Dimension, Components;
- std::string PixelType;
- ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
-
-
- // Call UpdateWithDim
- 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 4 Dimensions!!!"<<std::endl ;
- return;
- }
+ // 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<double>::Zero);
+ region.SetIndex(index);
+ output->SetRegions(region);
-} //end clitk
+ // Write/Save results
+ this->template SetNextOutput<ImageType>(output);
+}
+//--------------------------------------------------------------------
#endif //#define clitkCropImageGenericFilter_cxx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff