// itk include
#include "itkGradientMagnitudeImageFilter.h"
+#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
+#include "itkLabelStatisticsImageFilter.h"
#include "itkMaskImageFilter.h"
#include "itkMaskNegatedImageFilter.h"
#include <clitkCommon.h>
namespace clitk
{
-//--------------------------------------------------------------------
-template<class args_info_type>
-ImageGradientMagnitudeGenericFilter<args_info_type>::ImageGradientMagnitudeGenericFilter():
- ImageToImageGenericFilter<Self>("ImageGradientMagnitude")
-{
- InitializeImageType<2>();
- InitializeImageType<3>();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class args_info_type>
-template<unsigned int Dim>
-void ImageGradientMagnitudeGenericFilter<args_info_type>::InitializeImageType()
-{
- ADD_DEFAULT_IMAGE_TYPES(Dim);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class args_info_type>
-void ImageGradientMagnitudeGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
-{
- mArgsInfo=a;
- this->SetIOVerbose(mArgsInfo.verbose_flag);
- if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
-
- if (mArgsInfo.input_given) {
- this->SetInputFilename(mArgsInfo.input_arg);
- }
- if (mArgsInfo.output_given) {
- this->SetOutputFilename(mArgsInfo.output_arg);
- }
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-// Update with the number of dimensions and the pixeltype
-//--------------------------------------------------------------------
-template<class args_info_type>
-template<class InputImageType>
-void
-ImageGradientMagnitudeGenericFilter<args_info_type>::UpdateWithInputImageType()
-{
-
- // Reading input
- typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
-
- // Main filter
- typedef typename InputImageType::PixelType PixelType;
- typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
-
- // Filter
- typedef itk::GradientMagnitudeImageFilter<InputImageType, OutputImageType> GradientMagnitudeImageFilterType;
- typename GradientMagnitudeImageFilterType::Pointer gradientFilter=GradientMagnitudeImageFilterType::New();
- gradientFilter->SetInput(input);
- gradientFilter->Update();
-
- typename OutputImageType::Pointer outputImage = gradientFilter->GetOutput();
- this->template SetNextOutput<OutputImageType>(outputImage);
-}
-//--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ ImageGradientMagnitudeGenericFilter<args_info_type>::ImageGradientMagnitudeGenericFilter():
+ ImageToImageGenericFilter<Self>("ImageGradientMagnitude")
+ {
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dim>
+ void ImageGradientMagnitudeGenericFilter<args_info_type>::InitializeImageType()
+ {
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ void ImageGradientMagnitudeGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+ {
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ this->SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ this->SetOutputFilename(mArgsInfo.output_arg);
+ }
+ //
+ if (mArgsInfo.normalize_flag) {
+ this->m_NormalizeOutput = 1;
+ }
+ else {
+ this->m_NormalizeOutput = 0;
+ }
+ if (mArgsInfo.mask_given) {
+ this->AddInputFilename(mArgsInfo.mask_arg);
+ }
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ // Update with the number of dimensions and the pixeltype
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<class InputImageType>
+ void
+ ImageGradientMagnitudeGenericFilter<args_info_type>::UpdateWithInputImageType()
+ {
+ // Main filter
+ typedef typename InputImageType::PixelType InputPixelType;
+ typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
+ typedef itk::Image<unsigned char, OutputImageType::ImageDimension> MaskImageType;
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ typename MaskImageType::Pointer mask = ITK_NULLPTR;
+ if(mArgsInfo.mask_given) {
+ mask = this->template GetInput<MaskImageType>(1);
+ }
+ else {
+ mask = MaskImageType::New();
+ mask->SetRegions(input->GetLargestPossibleRegion());
+ mask->SetOrigin(input->GetOrigin());
+ mask->SetSpacing(input->GetSpacing());
+ mask->Allocate();
+ mask->FillBuffer(1);
+ }
+
+
+ // Create output image
+ typename OutputImageType::Pointer outputImage = OutputImageType::New();
+ outputImage->SetRegions(input->GetLargestPossibleRegion());
+ outputImage->SetOrigin(input->GetOrigin());
+ outputImage->SetSpacing(input->GetSpacing());
+ outputImage->Allocate();
+ outputImage->FillBuffer(0.0);
+ // Set output iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
+ IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
+
+ // Filter
+ typename OutputImageType::Pointer outputGradientFilter;
+ if (mArgsInfo.gaussian_filter_flag == 0) {
+ typedef itk::GradientMagnitudeImageFilter<InputImageType, OutputImageType> GradientMagnitudeImageFilterType;
+ typename GradientMagnitudeImageFilterType::Pointer gradientFilter=GradientMagnitudeImageFilterType::New();
+ gradientFilter->SetInput(input);
+ gradientFilter->Update();
+ outputGradientFilter = gradientFilter->GetOutput();
+ }
+ else {
+ typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<InputImageType, OutputImageType> GradientMagnitudeImageFilterType;
+ typename GradientMagnitudeImageFilterType::Pointer gradientFilter=GradientMagnitudeImageFilterType::New();
+ gradientFilter->SetInput(input);
+ gradientFilter->Update();
+ //std::cout<<"sigma value="<<gradientFilter->GetSigma()<<std::endl;
+ outputGradientFilter = gradientFilter->GetOutput();
+ }
+ // Set iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorType;
+ IteratorType it(outputGradientFilter, outputGradientFilter->GetLargestPossibleRegion());
+
+ // Set mask iterator
+ typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+ IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+
+ //typedef itk::MinimumMaximumImageCalculator <OutputImageType> ImageCalculatorFilterType;
+ //typename ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
+ //imageCalculatorFilter->SetImage(outputGradientFilter);
+ //imageCalculatorFilter->Compute();
+ typedef itk::LabelStatisticsImageFilter< OutputImageType, MaskImageType > LabelStatisticsImageFilterType;
+ typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
+ labelStatisticsImageFilter->SetLabelInput( mask );
+ labelStatisticsImageFilter->SetInput(outputGradientFilter);
+ labelStatisticsImageFilter->Update();
+
+ //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
+
+ float minImg = labelStatisticsImageFilter->GetMinimum(1);
+ //std::cout << "minImg: " << minImg << std::endl;
+ float maxImg = labelStatisticsImageFilter->GetMaximum(1);
+ //std::cout << "maxImg: " << maxImg << std::endl;
+
+ it.GoToBegin();
+ ito.GoToBegin();
+ itm.GoToBegin();
+
+ while (!ito.IsAtEnd()) {
+ if(m_NormalizeOutput && itm.Get() == 1) {
+ ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
+ }
+ if (m_NormalizeOutput == 0 && itm.Get() == 1) {
+ ito.Set((float) it.Get());
+ }
+ ++it;
+ ++ito;
+ ++itm;
+ }
+
+ //typename OutputImageType::Pointer outputImage = outputGradientFilter;
+ this->template SetNextOutput<OutputImageType>(outputImage);
+ }
+ //--------------------------------------------------------------------
}//end clitk
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff