tools/clitkImageGradientMagnitudeGenericFilter.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 clitkImageGradientMagnitudeGenericFilter_txx
  19 #define clitkImageGradientMagnitudeGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkImageGradientMagnitudeGenericFilter.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 "itkGradientMagnitudeImageFilter.h"
  32 #include "itkLabelStatisticsImageFilter.h"
  33 #include "itkMaskImageFilter.h"
  34 #include "itkMaskNegatedImageFilter.h"
  35 #include <clitkCommon.h>
  36
  37 namespace clitk
  38 {
  39
  40     //--------------------------------------------------------------------
  41     template<class args_info_type>
  42     ImageGradientMagnitudeGenericFilter<args_info_type>::ImageGradientMagnitudeGenericFilter():
  43         ImageToImageGenericFilter<Self>("ImageGradientMagnitude")
  44     {
  45         InitializeImageType<2>();
  46         InitializeImageType<3>();
  47     }
  48     //--------------------------------------------------------------------
  49
  50
  51     //--------------------------------------------------------------------
  52     template<class args_info_type>
  53     template<unsigned int Dim>
  54     void ImageGradientMagnitudeGenericFilter<args_info_type>::InitializeImageType()
  55     {
  56         ADD_DEFAULT_IMAGE_TYPES(Dim);
  57     }
  58     //--------------------------------------------------------------------
  59
  60
  61     //--------------------------------------------------------------------
  62     template<class args_info_type>
  63     void ImageGradientMagnitudeGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
  64     {
  65         mArgsInfo=a;
  66         this->SetIOVerbose(mArgsInfo.verbose_flag);
  67         if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  68
  69         if (mArgsInfo.input_given) {
  70             this->SetInputFilename(mArgsInfo.input_arg);
  71         }
  72         if (mArgsInfo.output_given) {
  73             this->SetOutputFilename(mArgsInfo.output_arg);
  74         }
  75         //
  76         if (mArgsInfo.normalize_flag) {
  77             this->m_NormalizeOutput = 1;
  78         }
  79         else {
  80             this->m_NormalizeOutput = 0;
  81         }
  82         if (mArgsInfo.mask_given) {
  83           this->AddInputFilename(mArgsInfo.mask_arg);
  84         }
  85     }
  86     //--------------------------------------------------------------------
  87
  88     //--------------------------------------------------------------------
  89     // Update with the number of dimensions and the pixeltype
  90     //--------------------------------------------------------------------
  91     template<class args_info_type>
  92     template<class InputImageType>
  93     void
  94     ImageGradientMagnitudeGenericFilter<args_info_type>::UpdateWithInputImageType()
  95     {
  96         // Main filter
  97         typedef typename InputImageType::PixelType InputPixelType;
  98         typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
  99         typedef itk::Image<unsigned char, OutputImageType::ImageDimension> MaskImageType;
 100
 101         // Reading input
 102         typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
 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 OutputImageType::Pointer outputImage = OutputImageType::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<OutputImageType> IteratorOutputType;
 127         IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
 128
 129         // Filter
 130         typedef itk::GradientMagnitudeImageFilter<InputImageType, OutputImageType> GradientMagnitudeImageFilterType;
 131         typename GradientMagnitudeImageFilterType::Pointer gradientFilter=GradientMagnitudeImageFilterType::New();
 132         gradientFilter->SetInput(input);
 133         gradientFilter->Update();
 134         // Set iterator
 135         typedef itk::ImageRegionIterator<OutputImageType> IteratorType;
 136         IteratorType it(gradientFilter->GetOutput(), gradientFilter->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< OutputImageType, MaskImageType > LabelStatisticsImageFilterType;
 147         typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
 148         labelStatisticsImageFilter->SetLabelInput( mask );
 149         labelStatisticsImageFilter->SetInput(gradientFilter->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(m_NormalizeOutput && itm.Get() == 1) {
 165                 ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
 166             }
 167             if (m_NormalizeOutput == 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<OutputImageType>(outputImage);
 177     }
 178     //--------------------------------------------------------------------
 179
 180
 181 }//end clitk
 182
 183 #endif //#define clitkImageGradientMagnitudeGenericFilter_txx