X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkImageStatisticsGenericFilter.txx;h=fabc429aef76a65c60c9fc5d031a80635ed8e6b3;hb=69e0d4a169d9b95536a0f45377bdb208814cf89b;hp=a0d2abfc609e101ece56b5b1e6606f13939f0064;hpb=cd04d8c797defe2fdaff3d1fa09928b22dd6edc4;p=clitk.git

diff --git a/tools/clitkImageStatisticsGenericFilter.txx b/tools/clitkImageStatisticsGenericFilter.txx
index a0d2abf..fabc429 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
@@ -21,16 +21,9 @@
 #include "itkNthElementImageAdaptor.h"
 #include "itkJoinSeriesImageFilter.h"
 
-/* =================================================
- * @file   clitkImageStatisticsGenericFilter.txx
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
 #include "clitkImageStatisticsGenericFilter.h"
-
+#include "clitkCropLikeImageFilter.h"
+#include "clitkResampleImageWithOptionsFilter.h"
 
 namespace clitk
 {
@@ -39,36 +32,28 @@ 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"){  
+    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>(); 
+      UpdateWithDimAndPixelType<Dimension, unsigned short, Components>();
     }
-    
-    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 == "unsigned_int"){ 
-//       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_int..." << std::endl;
-//       UpdateWithDimAndPixelType<Dimension, unsigned int, 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"){  
+
+    else if(PixelType == "double"){
       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
-      UpdateWithDimAndPixelType<Dimension, double, Components>(); 
+      UpdateWithDimAndPixelType<Dimension, double, Components>();
     }
     else {
       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
@@ -80,8 +65,8 @@ 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()
   {
 
@@ -89,20 +74,20 @@ namespace clitk
     typedef unsigned char LabelPixelType;
     typedef itk::Image<itk::Vector<PixelType, Components>, Dimension> InputImageType;
     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();
@@ -114,17 +99,18 @@ namespace clitk
       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) 
+        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();
@@ -133,7 +119,7 @@ namespace clitk
         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();
       }
@@ -143,14 +129,47 @@ namespace clitk
         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. (Use option to resize)" << std::endl;
+            exit(-1);
+          }
+        }
+
       }
 
     }
-    else { 
+    else {
       labelImage=LabelImageType::New();
       labelImage->SetRegions(input->GetLargestPossibleRegion());
       labelImage->SetOrigin(input->GetOrigin());
       labelImage->SetSpacing(input->GetSpacing());
+      labelImage->SetDirection(input->GetDirection());
       labelImage->Allocate();
       labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
     }
@@ -166,20 +185,20 @@ 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];
 
@@ -218,7 +237,7 @@ 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;
@@ -250,8 +269,8 @@ namespace clitk
     return;
 
   }
-  
-  
+
+
 }//end clitk
 
 #endif //#define clitkImageStatisticsGenericFilter_txx