- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
-#ifndef clitkCropImageGenericFilter_txx
-#define clitkCropImageGenericFilter_txx
+ ======================================================================-====*/
-/* =================================================
- * @file clitkCropImageGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
+#include "clitkImageCommon.h"
-
-namespace clitk
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::CropImageGenericFilter<ArgsInfoType>::CropImageGenericFilter():
+ ImageToImageGenericFilter<Self>("CropImage")
{
-
- //-------------------------------------------------------------------
- // Update with the number of dimensions
- //-------------------------------------------------------------------
- template<unsigned int Dimension>
- void
- CropImageGenericFilter::UpdateWithDim(std::string PixelType, unsigned int Components)
- {
- if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<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_short"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, unsigned 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 == "char"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, signed char>();
- // }
- else {
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, float>();
- }
+ // Default values
+ cmdline_parser_clitkCropImage_init(&mArgsInfo);
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::CropImageGenericFilter<ArgsInfoType>::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);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::CropImageGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & 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);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::CropImageGenericFilter<ArgsInfoType>::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;
+
+ // ------------------------------------------------
+ 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;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetInput(input);
+ filter->SetBackgroundValue(mArgsInfo.BG_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();
+ }
+ 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;
+ }
}
-
- else if (Components==3)
- {
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
- UpdateWithDimAndPixelType<Dimension, itk::Vector<float, 3> >();
+ 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 std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
+ 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();
+ }
}
-
- //-------------------------------------------------------------------
- // Update with the number of dimensions and the pixeltype
- //-------------------------------------------------------------------
- template <unsigned int Dimension, class PixelType>
- void
- CropImageGenericFilter::UpdateWithDimAndPixelType()
- {
-
- // ImageTypes
- typedef itk::Image<PixelType, Dimension> InputImageType;
- typedef itk::Image<PixelType, Dimension> OutputImageType;
-
- // Read the input
- typedef itk::ImageFileReader<InputImageType> InputReaderType;
- typename InputReaderType::Pointer reader = InputReaderType::New();
- reader->SetFileName( m_InputFileName);
- reader->Update( );
- typename InputImageType::Pointer input= reader->GetOutput();
-
- // Filter
- typedef itk::CropImageFilter<InputImageType, OutputImageType> CropImageFilterType;
- typename CropImageFilterType::Pointer cropFilter=CropImageFilterType::New();
- cropFilter->SetInput(input);
- typename InputImageType::SizeType lSize, uSize;
-
- if (m_ArgsInfo.boundingBox_given)
- {
- for(unsigned int i=0;i<Dimension;i++)
- {
- lSize[i]=m_ArgsInfo.boundingBox_arg[2*i];
- uSize[i]=input->GetLargestPossibleRegion().GetSize()[i]-m_ArgsInfo.boundingBox_arg[2*i+1]-1;
- }
- }
- else
- {
-
- if (m_ArgsInfo.lower_given)
- for(unsigned int i=0;i<Dimension;i++)
- lSize[i]=static_cast<unsigned int >(m_ArgsInfo.lower_arg[i]);
- else lSize.Fill(0);
-
- if (m_ArgsInfo.upper_given)
- for(unsigned int i=0;i<Dimension;i++)
- uSize[i]=static_cast<unsigned int >(m_ArgsInfo.upper_arg[i]);
- else uSize.Fill(0);
- }
-
- cropFilter->SetLowerBoundaryCropSize(lSize);
- cropFilter->SetUpperBoundaryCropSize(uSize);
- cropFilter->Update();
- typename OutputImageType::Pointer output= cropFilter->GetOutput();
-
- // Origin?
- typename OutputImageType::PointType origin;
+ // Force origin if needed
+ if (mArgsInfo.origin_flag) {
+ typename ImageType::PointType origin;
origin.Fill(itk::NumericTraits<double>::Zero);
- if (m_ArgsInfo.origin_flag)
- {
- output->SetOrigin(origin);
- output->Update();
- if (m_Verbose) std::cout<<"Setting origin to "<< origin<<"..."<<std::endl;
- }
-
- // Output
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
- typename WriterType::Pointer writer = WriterType::New();
- writer->SetFileName(m_ArgsInfo.output_arg);
- writer->SetInput(output);
- writer->Update();
+ output->SetOrigin(origin);
}
+ // Write/Save results
+ this->template SetNextOutput<ImageType>(output);
+}
+//--------------------------------------------------------------------
+
-}//end clitk
-
-#endif //#define clitkCropImageGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff