--- /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
+===========================================================================**/
+
+// clitk
+#include "clitkMaskOfIntegratedIntensity_ggo.h"
+#include "clitkMaskOfIntegratedIntensityGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkMaskOfIntegratedIntensity, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::MaskOfIntegratedIntensityGenericFilter<args_info_clitkMaskOfIntegratedIntensity> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /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 CLITKMaskOfIntegratedIntensityGENERICFILTER_H
+#define CLITKMaskOfIntegratedIntensityGENERICFILTER_H
+
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ template<class args_info_type>
+ class ITK_EXPORT MaskOfIntegratedIntensityGenericFilter:
+ public ImageToImageGenericFilter<MaskOfIntegratedIntensityGenericFilter<args_info_type> >
+ {
+
+ public:
+
+ //--------------------------------------------------------------------
+ MaskOfIntegratedIntensityGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef MaskOfIntegratedIntensityGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(MaskOfIntegratedIntensityGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ void SetPercentage(double p) { mPercentage = p; }
+ double GetPercentage() const { return mPercentage; }
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+ protected:
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+ double mPercentage;
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkMaskOfIntegratedIntensityGenericFilter.txx"
+#endif
+
+#endif // #define clitkMaskOfIntegratedIntensityGenericFilter_h
--- /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 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
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff