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 "itkLabelStatisticsImageFilter.h"
  34 #include "itkMaskImageFilter.h"
  35 #include "itkMaskNegatedImageFilter.h"
  36 #include <clitkCommon.h>
  37
  38 namespace clitk
  39 {
  40
  41 //--------------------------------------------------------------------
  42 template<class args_info_type>
  43 ImageLaplacianGenericFilter<args_info_type>::ImageLaplacianGenericFilter():
  44   ImageToImageGenericFilter<Self>("ImageLaplacian")
  45 {
  46   InitializeImageType<2>();
  47   InitializeImageType<3>();
  48 }
  49 //--------------------------------------------------------------------
  50
  51
  52 //--------------------------------------------------------------------
  53 template<class args_info_type>
  54 template<unsigned int Dim>
  55 void ImageLaplacianGenericFilter<args_info_type>::InitializeImageType()
  56 {
  57   ADD_DEFAULT_IMAGE_TYPES(Dim);
  58 }
  59 //--------------------------------------------------------------------
  60
  61
  62 //--------------------------------------------------------------------
  63 template<class args_info_type>
  64 void ImageLaplacianGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
  65 {
  66   mArgsInfo=a;
  67   this->SetIOVerbose(mArgsInfo.verbose_flag);
  68   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  69
  70   if (mArgsInfo.input_given) {
  71     this->SetInputFilename(mArgsInfo.input_arg);
  72   }
  73   if (mArgsInfo.output_given) {
  74     this->SetOutputFilename(mArgsInfo.output_arg);
  75   }
  76   if (mArgsInfo.mask_given) {
  77     this->AddInputFilename(mArgsInfo.mask_arg);
  78   }
  79 }
  80 //--------------------------------------------------------------------
  81
  82 //--------------------------------------------------------------------
  83 // Update with the number of dimensions and the pixeltype
  84 //--------------------------------------------------------------------
  85 template<class args_info_type>
  86 template<class InputImageType>
  87 void
  88 ImageLaplacianGenericFilter<args_info_type>::UpdateWithInputImageType()
  89 {
  90     // Main filter
  91     typedef typename InputImageType::PixelType InputPixelType;
  92     typedef itk::Image<float, InputImageType::ImageDimension> FloatImageType;
  93     typedef itk::Image<unsigned char, FloatImageType::ImageDimension> MaskImageType;
  94
  95     // Reading input
  96     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  97
  98     //Cast input to float
  99     typedef itk::CastImageFilter< InputImageType, FloatImageType > CastFilterType;
 100     typename CastFilterType::Pointer castFilter = CastFilterType::New();
 101     castFilter->SetInput(input);
 102     castFilter->Update();
 103
 104     typename MaskImageType::Pointer mask = NULL;
 105     if(mArgsInfo.mask_given) {
 106         mask = this->template GetInput<MaskImageType>(1);
 107     }
 108     else {
 109         mask = MaskImageType::New();
 110         mask->SetRegions(input->GetLargestPossibleRegion());
 111         mask->SetOrigin(input->GetOrigin());
 112         mask->SetSpacing(input->GetSpacing());
 113         mask->Allocate();
 114         mask->FillBuffer(1);
 115     }
 116
 117
 118     // Create output image
 119     typename FloatImageType::Pointer outputImage = FloatImageType::New();
 120     outputImage->SetRegions(input->GetLargestPossibleRegion());
 121     outputImage->SetOrigin(input->GetOrigin());
 122     outputImage->SetSpacing(input->GetSpacing());
 123     outputImage->Allocate();
 124     outputImage->FillBuffer(0.0);
 125     // Set output iterator
 126     typedef itk::ImageRegionIterator<FloatImageType> IteratorOutputType;
 127     IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
 128
 129     // Filter
 130     typedef itk::LaplacianImageFilter<FloatImageType, FloatImageType> LaplacianImageFilterType;
 131     typename LaplacianImageFilterType::Pointer laplacianFilter=LaplacianImageFilterType::New();
 132     laplacianFilter->SetInput(castFilter->GetOutput());
 133     laplacianFilter->Update();
 134     // Set iterator
 135     typedef itk::ImageRegionIterator<FloatImageType> IteratorType;
 136     IteratorType it(laplacianFilter->GetOutput(), laplacianFilter->GetOutput()->GetLargestPossibleRegion());
 137
 138     // Set mask iterator
 139     typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
 140     IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
 141
 142     //typedef itk::MinimumMaximumImageCalculator <OutputImageType> ImageCalculatorFilterType;
 143     //typename ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
 144     //imageCalculatorFilter->SetImage(gradientFilter->GetOutput());
 145     //imageCalculatorFilter->Compute();
 146     typedef itk::LabelStatisticsImageFilter< FloatImageType, MaskImageType > LabelStatisticsImageFilterType;
 147     typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
 148     labelStatisticsImageFilter->SetLabelInput( mask );
 149     labelStatisticsImageFilter->SetInput(laplacianFilter->GetOutput());
 150     labelStatisticsImageFilter->Update();
 151
 152     //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
 153
 154     float minImg = labelStatisticsImageFilter->GetMinimum(1);
 155     //std::cout << "minImg: " << minImg << std::endl;
 156     float maxImg = labelStatisticsImageFilter->GetMaximum(1);
 157     //std::cout << "maxImg: " << maxImg << std::endl;
 158
 159     it.GoToBegin();
 160     ito.GoToBegin();
 161     itm.GoToBegin();
 162
 163     while (!ito.IsAtEnd()) {
 164         if(mArgsInfo.normalize_flag && itm.Get() == 1) {
 165             ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
 166         }
 167         if (mArgsInfo.normalize_flag == 0 && itm.Get() == 1) {
 168             ito.Set((float) it.Get());
 169         }
 170         ++it;
 171         ++ito;
 172         ++itm;
 173     }
 174
 175     //typename OutputImageType::Pointer outputImage = gradientFilter->GetOutput();
 176     this->template SetNextOutput<FloatImageType>(outputImage);
 177 }
 178 //--------------------------------------------------------------------
 179
 180
 181 }//end clitk
 182
 183 #endif //#define clitkImageLaplacianGenericFilter_txx