tools/clitkImageLaplacianGenericFilter.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18 #ifndef clitkImageLaplacianGenericFilter_txx
  19 #define clitkImageLaplacianGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkImageLaplacianGenericFilter.txx
  23  * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
  24  * @date   29 june 2009
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30 // itk include
  31 #include "itkCastImageFilter.h"
  32 #include "itkLaplacianImageFilter.h"
  33 #include "itkLaplacianRecursiveGaussianImageFilter.h"
  34 #include "itkLabelStatisticsImageFilter.h"
  35 #include "itkMaskImageFilter.h"
  36 #include "itkMaskNegatedImageFilter.h"
  37 #include <clitkCommon.h>
  38
  39 namespace clitk
  40 {
  41
  42 //--------------------------------------------------------------------
  43 template<class args_info_type>
  44 ImageLaplacianGenericFilter<args_info_type>::ImageLaplacianGenericFilter():
  45   ImageToImageGenericFilter<Self>("ImageLaplacian")
  46 {
  47   InitializeImageType<2>();
  48   InitializeImageType<3>();
  49 }
  50 //--------------------------------------------------------------------
  51
  52
  53 //--------------------------------------------------------------------
  54 template<class args_info_type>
  55 template<unsigned int Dim>
  56 void ImageLaplacianGenericFilter<args_info_type>::InitializeImageType()
  57 {
  58   ADD_DEFAULT_IMAGE_TYPES(Dim);
  59 }
  60 //--------------------------------------------------------------------
  61
  62
  63 //--------------------------------------------------------------------
  64 template<class args_info_type>
  65 void ImageLaplacianGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
  66 {
  67   mArgsInfo=a;
  68   this->SetIOVerbose(mArgsInfo.verbose_flag);
  69   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  70
  71   if (mArgsInfo.input_given) {
  72     this->SetInputFilename(mArgsInfo.input_arg);
  73   }
  74   if (mArgsInfo.output_given) {
  75     this->SetOutputFilename(mArgsInfo.output_arg);
  76   }
  77   if (mArgsInfo.mask_given) {
  78     this->AddInputFilename(mArgsInfo.mask_arg);
  79   }
  80 }
  81 //--------------------------------------------------------------------
  82
  83 //--------------------------------------------------------------------
  84 // Update with the number of dimensions and the pixeltype
  85 //--------------------------------------------------------------------
  86 template<class args_info_type>
  87 template<class InputImageType>
  88 void
  89 ImageLaplacianGenericFilter<args_info_type>::UpdateWithInputImageType()
  90 {
  91     // Main filter
  92     typedef typename InputImageType::PixelType InputPixelType;
  93     typedef itk::Image<float, InputImageType::ImageDimension> FloatImageType;
  94     typedef itk::Image<unsigned char, FloatImageType::ImageDimension> MaskImageType;
  95
  96     // Reading input
  97     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  98
  99     //Cast input to float
 100     typedef itk::CastImageFilter< InputImageType, FloatImageType > CastFilterType;
 101     typename CastFilterType::Pointer castFilter = CastFilterType::New();
 102     castFilter->SetInput(input);
 103     castFilter->Update();
 104
 105     typename MaskImageType::Pointer mask = NULL;
 106     if(mArgsInfo.mask_given) {
 107         mask = this->template GetInput<MaskImageType>(1);
 108     }
 109     else {
 110         mask = MaskImageType::New();
 111         mask->SetRegions(input->GetLargestPossibleRegion());
 112         mask->SetOrigin(input->GetOrigin());
 113         mask->SetSpacing(input->GetSpacing());
 114         mask->Allocate();
 115         mask->FillBuffer(1);
 116     }
 117
 118
 119     // Create output image
 120     typename FloatImageType::Pointer outputImage = FloatImageType::New();
 121     outputImage->SetRegions(input->GetLargestPossibleRegion());
 122     outputImage->SetOrigin(input->GetOrigin());
 123     outputImage->SetSpacing(input->GetSpacing());
 124     outputImage->Allocate();
 125     outputImage->FillBuffer(0.0);
 126     // Set output iterator
 127     typedef itk::ImageRegionIterator<FloatImageType> IteratorOutputType;
 128     IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
 129
 130     // Filter
 131     typename FloatImageType::Pointer outputLaplacianFilter;
 132     if (mArgsInfo.gaussian_filter_flag == 0) {
 133         //std::cout<<"gaussian filter flag == 0"<<std::endl;
 134         typedef itk::LaplacianImageFilter<FloatImageType, FloatImageType> LaplacianImageFilterType;
 135         typename LaplacianImageFilterType::Pointer laplacianFilter=LaplacianImageFilterType::New();
 136         laplacianFilter->SetInput(castFilter->GetOutput());
 137         laplacianFilter->Update();
 138         outputLaplacianFilter = laplacianFilter->GetOutput();
 139     }
 140     else {
 141         //std::cout<<"gaussian filter flag == 1"<<std::endl;
 142         typedef itk::LaplacianRecursiveGaussianImageFilter< FloatImageType, FloatImageType >  LaplacianImageFilterType;
 143         typename LaplacianImageFilterType::Pointer laplacianFilter=LaplacianImageFilterType::New();
 144         laplacianFilter->SetInput(castFilter->GetOutput());
 145         laplacianFilter->Update();
 146         //std::cout<<"sigma value="<<laplacianFilter->GetSigma()<<std::endl;
 147         outputLaplacianFilter = laplacianFilter->GetOutput();
 148     }
 149     // Set iterator
 150     typedef itk::ImageRegionIterator<FloatImageType> IteratorType;
 151     IteratorType it(outputLaplacianFilter, outputLaplacianFilter->GetLargestPossibleRegion());
 152
 153     // Set mask iterator
 154     typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
 155     IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
 156
 157     //typedef itk::MinimumMaximumImageCalculator <OutputImageType> ImageCalculatorFilterType;
 158     //typename ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
 159     //imageCalculatorFilter->SetImage(gradientFilter->GetOutput());
 160     //imageCalculatorFilter->Compute();
 161     typedef itk::LabelStatisticsImageFilter< FloatImageType, MaskImageType > LabelStatisticsImageFilterType;
 162     typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
 163     labelStatisticsImageFilter->SetLabelInput( mask );
 164     labelStatisticsImageFilter->SetInput(outputLaplacianFilter);
 165     labelStatisticsImageFilter->Update();
 166
 167     //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
 168
 169     float minImg = labelStatisticsImageFilter->GetMinimum(1);
 170     //std::cout << "minImg: " << minImg << std::endl;
 171     float maxImg = labelStatisticsImageFilter->GetMaximum(1);
 172     //std::cout << "maxImg: " << maxImg << std::endl;
 173
 174     it.GoToBegin();
 175     ito.GoToBegin();
 176     itm.GoToBegin();
 177
 178     while (!ito.IsAtEnd()) {
 179         if(mArgsInfo.normalize_flag && itm.Get() == 1) {
 180             ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
 181         }
 182         if (mArgsInfo.normalize_flag == 0 && itm.Get() == 1) {
 183             ito.Set((float) it.Get());
 184         }
 185         ++it;
 186         ++ito;
 187         ++itm;
 188     }
 189
 190     //typename OutputImageType::Pointer outputImage = gradientFilter->GetOutput();
 191     this->template SetNextOutput<FloatImageType>(outputImage);
 192 }
 193 //--------------------------------------------------------------------
 194
 195
 196 }//end clitk
 197
 198 #endif //#define clitkImageLaplacianGenericFilter_txx