X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkMaskOfIntegratedIntensityGenericFilter.txx;fp=tools%2FclitkMaskOfIntegratedIntensityGenericFilter.txx;h=3096d87cebdc89e10a009a3518778107f33caf23;hb=64e548f2c8c2976f9573855e438437c9447d5d34;hp=0000000000000000000000000000000000000000;hpb=43f2c99b1e1f826d2c1c78b97aef4798bd56398c;p=clitk.git

diff --git a/tools/clitkMaskOfIntegratedIntensityGenericFilter.txx b/tools/clitkMaskOfIntegratedIntensityGenericFilter.txx
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+/*=========================================================================
+  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 clitkMaskOfIntegratedIntensityGenericFilter_txx
+#define clitkMaskOfIntegratedIntensityGenericFilter_txx
+
+// itk include
+#include "itkIntensityWindowingImageFilter.h"
+#include "itkLabelStatisticsImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+#include <numeric>
+
+namespace clitk
+{
+
+  //--------------------------------------------------------------------
+  template<class args_info_type>
+  MaskOfIntegratedIntensityGenericFilter<args_info_type>::MaskOfIntegratedIntensityGenericFilter():
+    ImageToImageGenericFilter<Self>("MaskOfIntegratedIntensity")
+  {
+    InitializeImageType<2>();
+    InitializeImageType<3>();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class args_info_type>
+  template<unsigned int Dim>
+  void MaskOfIntegratedIntensityGenericFilter<args_info_type>::InitializeImageType()
+  {
+    ADD_DEFAULT_IMAGE_TYPES(Dim);
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class args_info_type>
+  void MaskOfIntegratedIntensityGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+  {
+    mArgsInfo=a;
+    this->SetIOVerbose(mArgsInfo.verbose_flag);
+    if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+    this->SetInputFilename(mArgsInfo.input_arg);
+    this->SetOutputFilename(mArgsInfo.output_arg);
+    this->SetPercentage(mArgsInfo.percentage_arg);
+
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  //  https://stackoverflow.com/questions/1577475/c-sorting-and-keeping-track-of-indexes
+  template <typename T>
+  std::vector<size_t> sort_indexes(const std::vector<T> &v) {
+
+    // initialize original index locations
+    std::vector<size_t> idx(v.size());
+    iota(idx.begin(), idx.end(), 0);
+
+    // sort indexes based on comparing values in v
+    std::sort(idx.begin(), idx.end(),
+              [&v](size_t i1, size_t i2) {return v[i1] > v[i2];});
+
+    return idx;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  // Update with the number of dimensions and the pixeltype
+  //--------------------------------------------------------------------
+  template<class args_info_type>
+  template<class InputImageType>
+  void
+  MaskOfIntegratedIntensityGenericFilter<args_info_type>::UpdateWithInputImageType()
+  {
+    // Main filter
+    typedef typename InputImageType::PixelType InputPixelType;
+    typedef itk::Image<unsigned char, InputImageType::ImageDimension> MaskImageType;
+
+    // Reading input
+    typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+    typename MaskImageType::Pointer mask;
+    mask = MaskImageType::New();
+    mask->SetRegions(input->GetLargestPossibleRegion());
+    mask->SetOrigin(input->GetOrigin());
+    mask->SetSpacing(input->GetSpacing());
+    mask->Allocate();
+    mask->FillBuffer(0);
+
+    // Get a vector of all values (will be easier to sort)
+    // And compute total sum of values
+    std::vector<double> values;
+    typedef itk::ImageRegionIterator<InputImageType> IteratorInputType;
+    IteratorInputType iter(input, input->GetLargestPossibleRegion());
+    iter.GoToBegin();
+    double total = 0.0;
+    while (!iter.IsAtEnd()) {
+      values.push_back(iter.Get());
+      total += iter.Get();
+      ++iter;
+    }
+
+    // Sort (reverse)
+    auto indices = sort_indexes(values);
+
+    // Get max index of pixel to reach xx percent
+    double current = 0.0;
+    double max = GetPercentage()/100.0*total;
+    int i=0;
+    auto n = input->GetLargestPossibleRegion().GetNumberOfPixels();
+    std::vector<int> should_keep(values.size());;
+    std::fill(should_keep.begin(), should_keep.end(), 0);
+    while (current<max and i<n) { // loop by decreasing pixel values
+      current += values[indices[i]];
+      should_keep[indices[i]] = 1.0;
+      ++i;
+    }
+    int nb = i;
+
+    // Set mask values
+    typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+    IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+    iter.GoToBegin();
+    itm.GoToBegin();
+    i = 0;
+    while (!iter.IsAtEnd()) {
+      if (should_keep[i]) itm.Set(1);
+      ++iter;
+      ++itm;
+      ++i;
+    }
+
+    // Verbose option
+    if (this->m_IOVerbose)
+      std::cout << "Sum of pixel values : " << total << std::endl
+                << "Percentage          : " << GetPercentage() << "%" << std::endl
+                << "Number of pixels    : " << nb << "/" << n << std::endl
+                << "Number of pixels    : " << nb/n*100.0 << "%" << std::endl;
+
+    // Write/Save results
+    this->template SetNextOutput<MaskImageType>(mask);
+  }
+  //--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkMaskOfIntegratedIntensityGenericFilter_txx