--- /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 clitkNormalizeImageFilterGenericFilter_txx
+#define clitkNormalizeImageFilterGenericFilter_txx
+
+/* =================================================
+ * @file clitkNormalizeImageFilterGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date 29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkLabelStatisticsImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ NormalizeImageFilterGenericFilter<args_info_type>::NormalizeImageFilterGenericFilter():
+ ImageToImageGenericFilter<Self>("NormalizeImageFilter")
+ {
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dim>
+ void NormalizeImageFilterGenericFilter<args_info_type>::InitializeImageType()
+ {
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ void NormalizeImageFilterGenericFilter<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.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
+ NormalizeImageFilterGenericFilter<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 = NULL;
+ 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
+ // Set iterator
+ typedef itk::ImageRegionIterator<InputImageType> IteratorType;
+ IteratorType it(input, input->GetLargestPossibleRegion());
+
+ // Set mask iterator
+ typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+ IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+
+ typedef itk::LabelStatisticsImageFilter< InputImageType, MaskImageType > LabelStatisticsImageFilterType;
+ typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
+ labelStatisticsImageFilter->SetLabelInput( mask );
+ labelStatisticsImageFilter->SetInput(input);
+ 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(itm.Get() == 1) {
+ ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
+ }
+ ++it;
+ ++ito;
+ ++itm;
+ }
+ //
+ //
+ // Write/Save results
+ this->template SetNextOutput<OutputImageType>(outputImage);
+ }
+ //--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkNormalizeImageFilterGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff