X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkImageStatisticsGenericFilter.txx;h=1995198234be2f07e4db47f3921dd9338e97482a;hb=d2264227eb56300989795b8fd305cc3e1cfbe081;hp=cf05bb65d642eb61680a3b49039c8619f4c0b5db;hpb=b96634936966a5da8c3d6ebb72b8954fb53b800a;p=clitk.git

diff --git a/tools/clitkImageStatisticsGenericFilter.txx b/tools/clitkImageStatisticsGenericFilter.txx
index cf05bb6..1995198 100644
--- a/tools/clitkImageStatisticsGenericFilter.txx
+++ b/tools/clitkImageStatisticsGenericFilter.txx
@@ -1,7 +1,7 @@
 /*=========================================================================
   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
 
-  Authors belong to: 
+  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
@@ -19,16 +19,11 @@
 #define clitkImageStatisticsGenericFilter_txx
 
 #include "itkNthElementImageAdaptor.h"
+#include "itkJoinSeriesImageFilter.h"
 
-/* =================================================
- * @file   clitkImageStatisticsGenericFilter.txx
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
-
+#include "clitkImageStatisticsGenericFilter.h"
+#include "clitkCropLikeImageFilter.h"
+#include "clitkResampleImageWithOptionsFilter.h"
 
 namespace clitk
 {
@@ -37,29 +32,29 @@ namespace clitk
   // Update with the number of dimensions
   //-------------------------------------------------------------------
   template<unsigned int Dimension, unsigned int Components>
-  void 
+  void
   ImageStatisticsGenericFilter::UpdateWithDim(std::string PixelType)
   {
     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<" with " << Components << " channel(s)..."<<std::endl;
 
-    if(PixelType == "short"){  
+    if(PixelType == "short"){
       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
-      UpdateWithDimAndPixelType<Dimension, signed short, Components>(); 
+      UpdateWithDimAndPixelType<Dimension, signed short, Components>();
+    }
+    else if(PixelType == "unsigned_short"){
+      if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
+      UpdateWithDimAndPixelType<Dimension, unsigned short, Components>();
     }
-    //    else if(PixelType == "unsigned_short"){  
-    //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
-    //       UpdateWithDimAndPixelType<Dimension, unsigned short>(); 
-    //     }
-    
-    else if (PixelType == "unsigned_char"){ 
+
+    else if (PixelType == "unsigned_char"){
       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
       UpdateWithDimAndPixelType<Dimension, unsigned char, Components>();
     }
-    
-    //     else if (PixelType == "char"){ 
-    //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
-    //       UpdateWithDimAndPixelType<Dimension, signed char>();
-    //     }
+
+    else if(PixelType == "double"){
+      if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
+      UpdateWithDimAndPixelType<Dimension, double, Components>();
+    }
     else {
       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
       UpdateWithDimAndPixelType<Dimension, float, Components>();
@@ -70,28 +65,29 @@ namespace clitk
   //-------------------------------------------------------------------
   // Update with the number of dimensions and the pixeltype
   //-------------------------------------------------------------------
-  template <unsigned int Dimension, class  PixelType, unsigned int Components> 
-  void 
+  template <unsigned int Dimension, class  PixelType, unsigned int Components>
+  void
   ImageStatisticsGenericFilter::UpdateWithDimAndPixelType()
   {
 
     // ImageTypes
+    typedef unsigned char LabelPixelType;
     typedef itk::Image<itk::Vector<PixelType, Components>, Dimension> InputImageType;
-    typedef itk::Image<unsigned int, Dimension> LabelImageType;
-    
+    typedef itk::Image<LabelPixelType, Dimension> LabelImageType;
+
     // Read the input
     typedef itk::ImageFileReader<InputImageType> InputReaderType;
     typename InputReaderType::Pointer reader = InputReaderType::New();
     reader->SetFileName( m_InputFileName);
     reader->Update();
     typename InputImageType::Pointer input= reader->GetOutput();
-    
+
     typedef itk::NthElementImageAdaptor<InputImageType, PixelType> InputImageAdaptorType;
     typedef itk::Image<PixelType, Dimension> OutputImageType;
 
     typename InputImageAdaptorType::Pointer input_adaptor = InputImageAdaptorType::New();
     input_adaptor->SetImage(input);
-    
+
     // Filter
     typedef itk::LabelStatisticsImageFilter<InputImageAdaptorType, LabelImageType> StatisticsImageFilterType;
     typename StatisticsImageFilterType::Pointer statisticsFilter=StatisticsImageFilterType::New();
@@ -100,13 +96,75 @@ namespace clitk
     // Label image
     typename LabelImageType::Pointer labelImage;
     if (m_ArgsInfo.mask_given) {
-      typedef itk::ImageFileReader<LabelImageType> LabelImageReaderType;
-      typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
-      labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
-      labelImageReader->Update();
-      labelImage= labelImageReader->GetOutput();
+      int maskDimension, maskComponents;
+      std::string maskPixelType;
+      ReadImageDimensionAndPixelType(m_ArgsInfo.mask_arg, maskDimension, maskPixelType, maskComponents);
+
+      if (maskDimension == Dimension - 1) {
+        // Due to a limitation of filter itk::LabelStatisticsImageFilter, InputImageType and LabelImageType
+        // must have the same image dimension. However, we want to support label images with Dl = Di - 1,
+        // so we need to replicate the label image as many times as the size along dimension Di.
+        if (m_Verbose)
+          std::cout << "Replicating label image to match input image's dimension... " << std::endl;
+
+        typedef itk::Image<LabelPixelType, Dimension - 1> ReducedLabelImageType;
+        typedef itk::ImageFileReader<ReducedLabelImageType> LabelImageReaderType;
+        typedef itk::JoinSeriesImageFilter<ReducedLabelImageType, LabelImageType> JoinImageFilterType;
+
+        typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
+        labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
+        labelImageReader->Update();
+
+        typename JoinImageFilterType::Pointer joinFilter = JoinImageFilterType::New();
+        typename InputImageType::SizeType size = input->GetLargestPossibleRegion().GetSize();
+        for (unsigned int i = 0; i < size[Dimension - 1]; i++)
+          joinFilter->PushBackInput(labelImageReader->GetOutput());
+
+        joinFilter->Update();
+        labelImage = joinFilter->GetOutput();
+      }
+      else {
+        typedef itk::ImageFileReader<LabelImageType> LabelImageReaderType;
+        typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
+        labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
+        labelImageReader->Update();
+        labelImage= labelImageReader->GetOutput();
+
+        // Check mask sampling/size
+        if (!HaveSameSizeAndSpacing<LabelImageType, InputImageType>(labelImage, input)) {
+          if (m_ArgsInfo.allow_resize_flag) {
+            if (m_ArgsInfo.verbose_flag) {
+              std::cout << "Resize mask image like input" << std::endl;
+            }
+            typedef clitk::ResampleImageWithOptionsFilter<LabelImageType> ResamplerType;
+            typename ResamplerType::Pointer resampler = ResamplerType::New();
+            resampler->SetInput(labelImage);
+            resampler->SetOutputSpacing(input->GetSpacing());
+            resampler->SetOutputOrigin(labelImage->GetOrigin());
+            resampler->SetGaussianFilteringEnabled(false);
+            resampler->Update();
+            labelImage = resampler->GetOutput();
+            //writeImage<LabelImageType>(labelImage, "test1.mha");
+
+            typedef clitk::CropLikeImageFilter<LabelImageType> FilterType;
+            typename FilterType::Pointer crop = FilterType::New();
+            crop->SetInput(labelImage);
+            crop->SetCropLikeImage(input);
+            crop->Update();
+            labelImage = crop->GetOutput();
+            //writeImage<LabelImageType>(labelImage, "test2.mha");
+
+          }
+          else {
+            std::cerr << "Mask image has a different size/spacing than input. Abort" << std::endl;
+            exit(-1);
+          }
+        }
+
+      }
+
     }
-    else { 
+    else {
       labelImage=LabelImageType::New();
       labelImage->SetRegions(input->GetLargestPossibleRegion());
       labelImage->SetOrigin(input->GetOrigin());
@@ -126,20 +184,20 @@ namespace clitk
 
     unsigned int firstComponent = 0, lastComponent = 0;
     if (m_ArgsInfo.channel_arg == -1) {
-      firstComponent = 0; 
+      firstComponent = 0;
       lastComponent = Components - 1;
     }
     else {
       firstComponent = m_ArgsInfo.channel_arg;
       lastComponent = m_ArgsInfo.channel_arg;
     }
-    
+
     for (unsigned int c=firstComponent; c<=lastComponent; c++) {
       if (m_Verbose) std::cout << std::endl << "Processing channel " << c << std::endl;
-      
+
       input_adaptor->SelectNthElement(c);
       input_adaptor->Update();
-      
+
       for (unsigned int k=0; k< numberOfLabels; k++) {
         label=m_ArgsInfo.label_arg[k];
 
@@ -178,7 +236,7 @@ namespace clitk
           std::cout<<statisticsFilter->GetSum(label)<<std::endl;
 
         if (m_Verbose) std::cout<<"Bounding box: ";
-        
+
         for(unsigned int i =0; i <statisticsFilter->GetBoundingBox(label).size(); i++)
           std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
         std::cout<<std::endl;
@@ -210,8 +268,8 @@ namespace clitk
     return;
 
   }
-  
-  
+
+
 }//end clitk
 
 #endif //#define clitkImageStatisticsGenericFilter_txx