- Made clitkPadImage generic (no support for 4D images for the moment).
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkJacobianImage)
WRAP_GGO(clitkPadImage_GGO_C clitkPadImage.ggo)
- ADD_EXECUTABLE(clitkPadImage clitkPadImage.cxx ${clitkPadImage_GGO_C})
+ ADD_EXECUTABLE(clitkPadImage clitkPadImage.cxx clitkPadImageGenericFilter.cxx ${clitkPadImage_GGO_C})
TARGET_LINK_LIBRARIES(clitkPadImage clitkCommon ${ITK_LIBRARIES})
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkPadImage)
-#include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
-#include "itkConstantPadImageFilter.h"
#include "clitkCommon.h"
#include "clitkPadImage_ggo.h"
-#include <string>
-#include "itkMath.h"
+#include "clitkPadImageGenericFilter.h"
-enum
-{
- ERR_SUCCESS = 0,
- ERR_NOT_SAME_SPACING = -1,
- ERR_NOT_LIKE_LARGER = -2
-};
-
-typedef unsigned int DimType;
-
-template <class ImageType, class PadBoundType, DimType dim>
-int pad_like(typename ImageType::Pointer input, const std::string& likeFile, PadBoundType* padLower, PadBoundType* padUpper)
-{
- typedef typename ImageType::SpacingType SpacingType;
- typedef typename ImageType::RegionType RegionType;
- typedef typename ImageType::SizeType SizeType;
- typedef typename ImageType::IndexType IndexType;
- typedef typename ImageType::PointType PointType;
- typedef typename ImageType::PointValueType PointValueType;
-
- typedef itk::ImageFileReader<ImageType> ImageReaderType;
- typename ImageReaderType::Pointer reader = ImageReaderType::New();
- reader->SetFileName(likeFile);
- reader->Update();
-
- typename ImageType::Pointer like_image = reader->GetOutput();
-
- SpacingType spacing = input->GetSpacing(), like_spacing = like_image->GetSpacing();
- if (spacing != like_spacing) {
- std::cerr << "Like-image must have same spacing as input: " << spacing << " " << like_spacing << std::endl;
- return ERR_NOT_SAME_SPACING;
- }
-
- SizeType size = input->GetLargestPossibleRegion().GetSize(), like_size = like_image->GetLargestPossibleRegion().GetSize();
- PointType origin = input->GetOrigin(), like_origin = like_image->GetOrigin();
-
- PointType lower_bound, like_lower_bound;
- PointType upper_bound, like_upper_bound;
- PointValueType auxl = 0, auxu = 0;
- for (DimType i = 0; i < dim; i++) {
- lower_bound[i] = origin[i];
- like_lower_bound[i] = like_origin[i];
- auxl = itk::Math::Round<PointValueType>(((lower_bound[i] - like_lower_bound[i])/spacing[i]));
-
- upper_bound[i] = (lower_bound[i] + size[i]*spacing[i]);
- like_upper_bound[i] = (like_lower_bound[i] + like_size[i]*spacing[i]);
- auxu = itk::Math::Round<PointValueType>(((like_upper_bound[i] - upper_bound[i])/spacing[i]));
-
- if (auxl < 0 || auxu < 0) {
- std::cerr << "Like-image's bounding box must be larger than input's" << std::endl;
- return ERR_NOT_LIKE_LARGER;
- }
-
- padLower[i] = (PadBoundType)auxl;
- padUpper[i] = (PadBoundType)auxu;
- }
-
- return ERR_SUCCESS;
-}
+// template <class ImageType, class PadBoundType, unsigned int dim>
+// int pad_like(typename ImageType::Pointer input, const std::string& likeFile, PadBoundType* padLower, PadBoundType* padUpper)
+// {
+// typedef typename ImageType::SpacingType SpacingType;
+// typedef typename ImageType::RegionType RegionType;
+// typedef typename ImageType::SizeType SizeType;
+// typedef typename ImageType::IndexType IndexType;
+// typedef typename ImageType::PointType PointType;
+// typedef typename ImageType::PointValueType PointValueType;
+//
+// typedef itk::ImageFileReader<ImageType> ImageReaderType;
+// typename ImageReaderType::Pointer reader = ImageReaderType::New();
+// reader->SetFileName(likeFile);
+// reader->Update();
+//
+// typename ImageType::Pointer like_image = reader->GetOutput();
+//
+// SpacingType spacing = input->GetSpacing(), like_spacing = like_image->GetSpacing();
+// if (spacing != like_spacing) {
+// std::cerr << "Like-image must have same spacing as input: " << spacing << " " << like_spacing << std::endl;
+// return ERR_NOT_SAME_SPACING;
+// }
+//
+// SizeType size = input->GetLargestPossibleRegion().GetSize(), like_size = like_image->GetLargestPossibleRegion().GetSize();
+// PointType origin = input->GetOrigin(), like_origin = like_image->GetOrigin();
+//
+// PointType lower_bound, like_lower_bound;
+// PointType upper_bound, like_upper_bound;
+// PointValueType auxl = 0, auxu = 0;
+// for (unsigned int i = 0; i < dim; i++) {
+// lower_bound[i] = origin[i];
+// like_lower_bound[i] = like_origin[i];
+// auxl = itk::Math::Round<PointValueType>(((lower_bound[i] - like_lower_bound[i])/spacing[i]));
+//
+// upper_bound[i] = (lower_bound[i] + size[i]*spacing[i]);
+// like_upper_bound[i] = (like_lower_bound[i] + like_size[i]*spacing[i]);
+// auxu = itk::Math::Round<PointValueType>(((like_upper_bound[i] - upper_bound[i])/spacing[i]));
+//
+// if (auxl < 0 || auxu < 0) {
+// std::cerr << "Like-image's bounding box must be larger than input's" << std::endl;
+// return ERR_NOT_LIKE_LARGER;
+// }
+//
+// padLower[i] = (PadBoundType)auxl;
+// padUpper[i] = (PadBoundType)auxu;
+// }
+//
+// return ERR_SUCCESS;
+// }
int main(int argc, char** argv)
{
- const DimType dim = 3;
+/* const DimType dim = 3;
typedef short PixelType;
typedef itk::Image<PixelType, dim> ImageType;
typedef itk::ImageFileReader<ImageType> ImageReaderType;
typedef itk::ImageFileWriter<ImageType> ImageWriterType;
typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
- typedef PadFilterType::SizeValueType PadBoundType;
+ typedef PadFilterType::SizeValueType PadBoundType;*/
GGO(clitkPadImage, args_info);
-
- ImageReaderType::Pointer reader = ImageReaderType::New();
- reader->SetFileName(args_info.input_arg);
- reader->Update();
-
- PadBoundType pad_lower[dim], pad_upper[dim];
- ImageType::Pointer input = reader->GetOutput();
- if (args_info.like_given) {
- int err = pad_like<ImageType, PadBoundType, dim>(input, args_info.like_arg, pad_lower, pad_upper);
- if (err) {
- std::cerr << "Error processing like image." << std::endl;
- return err;
- }
- }
- else {
- for (DimType i = 0; i < dim; i++) {
- pad_lower[i] = args_info.lower_arg[i];
- pad_upper[i] = args_info.upper_arg[i];
- }
+
+ // Filter
+ typedef clitk::PadImageGenericFilter FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+
+ try {
+ filter->Update();
+ } catch(std::runtime_error e) {
+ std::cout << e.what() << std::endl;
}
- PadFilterType::Pointer filter = PadFilterType::New();
- filter->SetPadLowerBound(pad_lower);
- filter->SetPadUpperBound(pad_upper);
- filter->SetInput(input);
- filter->SetConstant(args_info.value_arg);
- filter->Update();
-
- ImageType::Pointer output = filter->GetOutput();
- ImageWriterType::Pointer writer = ImageWriterType::New();
- writer->SetInput(output);
- writer->SetFileName(args_info.output_arg);
- writer->Update();
+// ImageReaderType::Pointer reader = ImageReaderType::New();
+// reader->SetFileName(args_info.input_arg);
+// reader->Update();
+//
+// PadBoundType pad_lower[dim], pad_upper[dim];
+// ImageType::Pointer input = reader->GetOutput();
+// if (args_info.like_given) {
+// int err = pad_like<ImageType, PadBoundType, dim>(input, args_info.like_arg, pad_lower, pad_upper);
+// if (err) {
+// std::cerr << "Error processing like image." << std::endl;
+// return err;
+// }
+// }
+// else {
+// for (DimType i = 0; i < dim; i++) {
+// pad_lower[i] = args_info.lower_arg[i];
+// pad_upper[i] = args_info.upper_arg[i];
+// }
+// }
+//
+// PadFilterType::Pointer filter = PadFilterType::New();
+// filter->SetPadLowerBound(pad_lower);
+// filter->SetPadUpperBound(pad_upper);
+// filter->SetInput(input);
+// filter->SetConstant(args_info.value_arg);
+// filter->Update();
+//
+// ImageType::Pointer output = filter->GetOutput();
+// ImageWriterType::Pointer writer = ImageWriterType::New();
+// writer->SetInput(output);
+// writer->SetFileName(args_info.output_arg);
+// writer->Update();
- return ERR_SUCCESS;
+ return EXIT_SUCCESS;
}
-#File clitkCropImage.ggo
-package "clitkCropImage"
+#File clitkPadImage.ggo
+package "clitkPadImage"
version "1.0"
purpose "Pad an image according to a given extends or like another image"
--- /dev/null
+/*=========================================================================
+ 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 clitkPadImageGenericFilter_cxx
+#define clitkPadImageGenericFilter_cxx
+
+/* =================================================
+ * @file clitkPadImageGenericFilter.cxx
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include "clitkPadImageGenericFilter.h"
+
+// itk
+#include <itkConstantPadImageFilter.h>
+
+
+namespace clitk
+{
+
+
+ //-----------------------------------------------------------
+ // Constructor
+ //-----------------------------------------------------------
+ PadImageGenericFilter::PadImageGenericFilter():
+ ImageToImageGenericFilter<Self>("PadImage")
+ {
+ cmdline_parser_clitkPadImage_init(&mArgsInfo);
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ //InitializeImageType<4>();
+ }
+
+ //--------------------------------------------------------------------
+ template<unsigned int Dim>
+ void PadImageGenericFilter::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 PadImageGenericFilter::SetArgsInfo(const args_info_type& a)
+ {
+ mArgsInfo=a;
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ 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 ImageType>
+ void PadImageGenericFilter::UpdateWithInputImageType()
+ {
+ typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
+ typedef typename PadFilterType::SizeValueType PadBoundType;
+
+ // Reading input
+ typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
+
+ const unsigned int dim = ImageType::ImageDimension;
+ PadBoundType pad_lower[dim], pad_upper[dim];
+ if (mArgsInfo.like_given) {
+ int err = PadLike<ImageType, PadBoundType, ImageType::ImageDimension>(input, pad_lower, pad_upper);
+ if (err) {
+ std::cerr << "Error processing like image." << std::endl;
+ return;
+ }
+ }
+ else {
+ if (mArgsInfo.lower_given != dim || mArgsInfo.upper_given != dim)
+ {
+ std::cerr << "The number of lower and upper padding parameters must be equal to the image dimension." << std::endl;
+ return;
+ }
+
+ for (unsigned int i = 0; i < dim; i++) {
+ pad_lower[i] = mArgsInfo.lower_arg[i];
+ pad_upper[i] = mArgsInfo.upper_arg[i];
+ }
+ }
+
+ typename PadFilterType::Pointer filter = PadFilterType::New();
+ filter->SetPadLowerBound(pad_lower);
+ filter->SetPadUpperBound(pad_upper);
+ filter->SetInput(input);
+ filter->SetConstant(mArgsInfo.value_arg);
+ filter->Update();
+
+ // Prepare output
+ typename ImageType::Pointer output;
+ output = filter->GetOutput();
+
+ // Write/Save results
+ this->template SetNextOutput<ImageType>(output);
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ // Update with the number of dimensions and the pixeltype
+ //--------------------------------------------------------------------
+ template <class ImageType, class PadBoundType, unsigned int dim>
+ int PadImageGenericFilter::PadLike(typename ImageType::Pointer input, PadBoundType* padLower, PadBoundType* padUpper)
+ {
+ if (mArgsInfo.verbose_flag)
+ std::cout << "PadLike - IN" << std::endl;
+
+ typedef typename ImageType::SpacingType SpacingType;
+ typedef typename ImageType::RegionType RegionType;
+ typedef typename ImageType::SizeType SizeType;
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::PointType PointType;
+ typedef typename ImageType::PointValueType PointValueType;
+
+ if (mArgsInfo.verbose_flag)
+ std::cout << "Reading like image: " << mArgsInfo.like_arg << ::endl;
+
+ typedef itk::ImageFileReader<ImageType> ImageReaderType;
+ typename ImageReaderType::Pointer reader = ImageReaderType::New();
+ reader->SetFileName(mArgsInfo.like_arg);
+ reader->Update();
+
+ typename ImageType::Pointer like_image = reader->GetOutput();
+
+ if (mArgsInfo.verbose_flag)
+ std::cout << "Calculating padding." << std::endl;
+
+ SpacingType spacing = input->GetSpacing(), like_spacing = like_image->GetSpacing();
+ if (spacing != like_spacing) {
+ std::cerr << "Like-image must have same spacing as input: " << spacing << " " << like_spacing << std::endl;
+ return ERR_NOT_SAME_SPACING;
+ }
+
+ SizeType size = input->GetLargestPossibleRegion().GetSize(), like_size = like_image->GetLargestPossibleRegion().GetSize();
+ PointType origin = input->GetOrigin(), like_origin = like_image->GetOrigin();
+
+ PointType lower_bound, like_lower_bound;
+ PointType upper_bound, like_upper_bound;
+ PointValueType auxl = 0, auxu = 0;
+ for (unsigned int i = 0; i < dim; i++) {
+ lower_bound[i] = origin[i];
+ like_lower_bound[i] = like_origin[i];
+ auxl = itk::Math::Round<PointValueType>(((lower_bound[i] - like_lower_bound[i])/spacing[i]));
+
+ upper_bound[i] = (lower_bound[i] + size[i]*spacing[i]);
+ like_upper_bound[i] = (like_lower_bound[i] + like_size[i]*spacing[i]);
+ auxu = itk::Math::Round<PointValueType>(((like_upper_bound[i] - upper_bound[i])/spacing[i]));
+
+ if (auxl < 0 || auxu < 0) {
+ std::cerr << "Like-image's bounding box must be larger than input's" << std::endl;
+ return ERR_NOT_LIKE_LARGER;
+ }
+
+ padLower[i] = (PadBoundType)auxl;
+ padUpper[i] = (PadBoundType)auxu;
+ }
+
+ if (mArgsInfo.verbose_flag)
+ std::cout << "PadLike - OUT" << std::endl;
+ return ERR_SUCCESS;
+ }
+} //end clitk
+
+#endif //#define clitkPadImageGenericFilter_cxx
--- /dev/null
+/*=========================================================================
+ 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 CLITKPADIMAGEGENERICFILTER_H
+#define CLITKPADIMAGEGENERICFILTER_H
+
+// clitk
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkPadImage_ggo.h"
+
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ class ITK_EXPORT PadImageGenericFilter:
+ public ImageToImageGenericFilter<PadImageGenericFilter>
+ {
+ public:
+ enum
+ {
+ ERR_SUCCESS = 0,
+ ERR_NOT_SAME_SPACING = -1,
+ ERR_NOT_LIKE_LARGER = -2
+ };
+
+ //--------------------------------------------------------------------
+ PadImageGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef PadImageGenericFilter Self;
+ typedef ImageToImageGenericFilter<PadImageGenericFilter> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef args_info_clitkPadImage args_info_type;
+
+ //--------------------------------------------------------------------
+ itkNewMacro(Self);
+ itkTypeMacro( PadImageGenericFilter, LightObject );
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type& a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class ImageType>
+ void UpdateWithInputImageType();
+
+ protected:
+ template<unsigned int Dim> void InitializeImageType();
+
+ template <class ImageType, class PadBoundType, unsigned int dim>
+ int PadLike(typename ImageType::Pointer input, PadBoundType* padLower, PadBoundType* padUpper);
+
+ args_info_type mArgsInfo;
+
+ };// end class
+ //--------------------------------------------------------------------
+} // end namespace clitk
+
+#endif // #define CLITKPADIMAGEGENERICFILTER_H
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff