X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=tools%2FclitkNormalizeImageFilterGenericFilter.txx;fp=tools%2FclitkNormalizeImageFilterGenericFilter.txx;h=99a43a464ad8157367caf9f5ed7e301b0736ac64;hb=bf97e857638ed65c07c8ee1835cf5373d6b381d6;hp=0000000000000000000000000000000000000000;hpb=69ca7b4f56b0873c4446859655712091b44e6434;p=clitk.git

diff --git a/tools/clitkNormalizeImageFilterGenericFilter.txx b/tools/clitkNormalizeImageFilterGenericFilter.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 clitkNormalizeImageFilterGenericFilter_txx
+#define clitkNormalizeImageFilterGenericFilter_txx
+
+/* =================================================
+ * @file   clitkNormalizeImageFilterGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date   29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkLabelStatisticsImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+    //--------------------------------------------------------------------
+    template<class args_info_type>
+    NormalizeImageFilterGenericFilter<args_info_type>::NormalizeImageFilterGenericFilter():
+        ImageToImageGenericFilter<Self>("NormalizeImageFilter")
+    {
+        InitializeImageType<2>();
+        InitializeImageType<3>();
+    }
+    //--------------------------------------------------------------------
+
+
+    //--------------------------------------------------------------------
+    template<class args_info_type>
+    template<unsigned int Dim>
+    void NormalizeImageFilterGenericFilter<args_info_type>::InitializeImageType()
+    {
+        ADD_DEFAULT_IMAGE_TYPES(Dim);
+    }
+    //--------------------------------------------------------------------
+
+
+    //--------------------------------------------------------------------
+    template<class args_info_type>
+    void NormalizeImageFilterGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+    {
+        mArgsInfo=a;
+        this->SetIOVerbose(mArgsInfo.verbose_flag);
+        if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+        if (mArgsInfo.input_given) {
+            this->SetInputFilename(mArgsInfo.input_arg);
+        }
+        if (mArgsInfo.output_given) {
+            this->SetOutputFilename(mArgsInfo.output_arg);
+        }
+        if (mArgsInfo.mask_given) {
+            this->AddInputFilename(mArgsInfo.mask_arg);
+        }
+    }
+    //--------------------------------------------------------------------
+
+    //--------------------------------------------------------------------
+    // Update with the number of dimensions and the pixeltype
+    //--------------------------------------------------------------------
+    template<class args_info_type>
+    template<class InputImageType>
+    void
+    NormalizeImageFilterGenericFilter<args_info_type>::UpdateWithInputImageType()
+    {
+
+        // Main filter
+        typedef typename InputImageType::PixelType InputPixelType;
+        typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
+        typedef itk::Image<unsigned char, OutputImageType::ImageDimension> MaskImageType;
+
+        // Reading input
+        typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+        typename MaskImageType::Pointer mask = NULL;
+        if(mArgsInfo.mask_given) {
+            mask = this->template GetInput<MaskImageType>(1);
+        }
+        else {
+            mask = MaskImageType::New();
+            mask->SetRegions(input->GetLargestPossibleRegion());
+            mask->SetOrigin(input->GetOrigin());
+            mask->SetSpacing(input->GetSpacing());
+            mask->Allocate();
+            mask->FillBuffer(1);
+        }
+
+        // Create output image
+        typename OutputImageType::Pointer outputImage = OutputImageType::New();
+        outputImage->SetRegions(input->GetLargestPossibleRegion());
+        outputImage->SetOrigin(input->GetOrigin());
+        outputImage->SetSpacing(input->GetSpacing());
+        outputImage->Allocate();
+        outputImage->FillBuffer(0.0);
+        // Set output iterator
+        typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
+        IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
+
+        // Filter
+        // Set iterator
+        typedef itk::ImageRegionIterator<InputImageType> IteratorType;
+        IteratorType it(input, input->GetLargestPossibleRegion());
+
+        // Set mask iterator
+        typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+        IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+
+        typedef itk::LabelStatisticsImageFilter< InputImageType, MaskImageType > LabelStatisticsImageFilterType;
+        typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
+        labelStatisticsImageFilter->SetLabelInput( mask );
+        labelStatisticsImageFilter->SetInput(input);
+        labelStatisticsImageFilter->Update();
+
+        //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
+
+        float minImg = labelStatisticsImageFilter->GetMinimum(1);
+        //std::cout << "minImg= " << minImg << std::endl;
+        float maxImg = labelStatisticsImageFilter->GetMaximum(1);
+        //std::cout << "maxImg= " << maxImg << std::endl;
+
+        it.GoToBegin();
+        ito.GoToBegin();
+        itm.GoToBegin();
+
+        while (!ito.IsAtEnd()) {
+            if(itm.Get() == 1) {
+                ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
+            }
+            ++it;
+            ++ito;
+            ++itm;
+        }
+        //
+        //
+        // Write/Save results
+        this->template SetNextOutput<OutputImageType>(outputImage);
+    }
+    //--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkNormalizeImageFilterGenericFilter_txx