Add clitkMergeRootFiles

[clitk.git] / tools / clitkImageStatisticsGenericFilter.txx

diff --git a/tools/clitkImageStatisticsGenericFilter.txx b/tools/clitkImageStatisticsGenericFilter.txx
index 9931fa0b0e048bad7fbcd59dde0d0b0ea944791d..f5c82356dff35c50bd2a3c841d9dc07ae820bdea 100644 (file)
--- a/tools/clitkImageStatisticsGenericFilter.txx
+++ b/tools/clitkImageStatisticsGenericFilter.txx
@@ -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
 {
@@ -48,20 +41,20 @@ namespace clitk
       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
       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>(); 
-    //     }
+    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_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>();
@@ -106,6 +99,7 @@ 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,
@@ -135,6 +129,37 @@ 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->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);
+          }
+        }
+
       }
 
     }
@@ -186,7 +211,6 @@ namespace clitk
           statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
         }
         statisticsFilter->Update();
-        if (m_Verbose) std::cout<<"FINISHED!";
 
         // Output
         if (m_Verbose) std::cout<<"N° of pixels: ";