#ifndef clitkCropImageGenericFilter_cxx
#define clitkCropImageGenericFilter_cxx
-/* =================================================
- * @file clitkCropImageGenericFilter.cxx
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
-
#include "clitkCropImageGenericFilter.h"
-
-namespace clitk
+//-----------------------------------------------------------
+// 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;
+}
+//--------------------------------------------------------------------
-
- //-----------------------------------------------------------
- // Constructor
- //-----------------------------------------------------------
- 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_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 <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);
}
- //--------------------------------------------------------------------
-
- //--------------------------------------------------------------------
- // 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);
-
- // 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<ImageType> 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<ImageType> 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<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();
+ 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 {
- // ------------------------------------------------
- typename ImageType::SizeType lSize;
- typename ImageType::SizeType uSize;
- if (mArgsInfo.boundingBox_given) {
- for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
- lSize[i] = mArgsInfo.boundingBox_arg[2*i];
- uSize[i] = input->GetLargestPossibleRegion().GetSize()[i]-mArgsInfo.boundingBox_arg[2*i+1]-1;
- }
+ if (mArgsInfo.lower_given) {
+ for(unsigned int i=0; i<ImageType::ImageDimension; i++)
+ lSize[i]=static_cast<unsigned int >(mArgsInfo.lower_arg[i]);
}
- 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);
+ 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]);
}
- 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();
+ 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<double>::Zero);
- output->SetOrigin(origin);
+ 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();
}
+ }
- // Write/Save results
- this->template SetNextOutput<ImageType>(output);
+ // Force origin if needed
+ if (mArgsInfo.origin_flag) {
+ typename ImageType::PointType origin;
+ origin.Fill(itk::NumericTraits<double>::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<double>::Zero);
+ region.SetIndex(index);
+ output->SetRegions(region);
+
+ // Write/Save results
+ this->template SetNextOutput<ImageType>(output);
+}
+//--------------------------------------------------------------------
#endif //#define clitkCropImageGenericFilter_cxx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff