cosmetic for .ggo

[clitk.git] / tools / clitkImageStatisticsGenericFilter.txx

diff --git a/tools/clitkImageStatisticsGenericFilter.txx b/tools/clitkImageStatisticsGenericFilter.txx
index 5d462407437554b29aa753d6fffce21c2f5d5c39..82a11ab5355a86134a3a6cc666ff9136b04dc423 100644 (file)
--- a/tools/clitkImageStatisticsGenericFilter.txx
+++ b/tools/clitkImageStatisticsGenericFilter.txx
@@ -20,6 +20,7 @@
 
 #include "itkNthElementImageAdaptor.h"
 #include "itkJoinSeriesImageFilter.h"
+#include "itkImageRegionConstIterator.h"
 
 #include "clitkImageStatisticsGenericFilter.h"
 #include "clitkCropLikeImageFilter.h"
@@ -156,7 +157,7 @@ namespace clitk
 
           }
           else {
-            std::cerr << "Mask image has a different size/spacing than input. Abort" << std::endl;
+            std::cerr << "Mask image has a different size/spacing than input. Abort. (Use option to resize)" << std::endl;
             exit(-1);
           }
         }
@@ -166,9 +167,11 @@ namespace clitk
     }
     else {
       labelImage=LabelImageType::New();
+      labelImage->SetDirection(input->GetDirection());
       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]);
     }
@@ -212,7 +215,7 @@ namespace clitk
 
         std::cout<<std::endl;
         if (m_Verbose) std::cout<<"-------------"<<std::endl;
-        if (m_Verbose) std::cout<<"| Label: "<<label<<"  |"<<std::endl;
+        if (m_Verbose) std::cout<<"| Label: "<< (int) label<<"  |"<<std::endl;
         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 
         // Histograms
@@ -230,8 +233,21 @@ namespace clitk
 
         statisticsFilter->Update();
 
+        //find localization for max and min (the last pixel found)
+        typename InputImageType::IndexType minIndex, maxIndex;
+        if (m_Verbose && m_Localize) {
+          itk::ImageRegionConstIterator<InputImageAdaptorType> imageIterator(input_adaptor,input_adaptor->GetLargestPossibleRegion());
+          while(!imageIterator.IsAtEnd()) {
+            if (imageIterator.Get() == statisticsFilter->GetMinimum(label))
+              minIndex = imageIterator.GetIndex();
+            if (imageIterator.Get() == statisticsFilter->GetMaximum(label))
+              maxIndex = imageIterator.GetIndex();
+            ++imageIterator;
+          }
+        }
+
         // Output
-       if (m_Verbose) std::cout<<"N° of pixels: ";
+        if (m_Verbose) std::cout<<"N° of pixels: ";
         std::cout<<statisticsFilter->GetCount(label)<<std::endl;
         if (m_Verbose) std::cout<<"Mean: ";
         std::cout<<statisticsFilter->GetMean(label)<<std::endl;
@@ -241,10 +257,20 @@ namespace clitk
         std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
         if (m_Verbose) std::cout<<"Min: ";
         std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
+        if (m_Verbose && m_Localize) {
+          std::cout<<"        in voxel of index: ";
+          std::cout<<minIndex<<std::endl;
+        }
         if (m_Verbose) std::cout<<"Max: ";
         std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
+        if (m_Verbose && m_Localize) {
+          std::cout<<"        in voxel of index: ";
+          std::cout<<maxIndex<<std::endl;
+        }
         if (m_Verbose) std::cout<<"Sum: ";
         std::cout<<statisticsFilter->GetSum(label)<<std::endl;
+        if (m_Verbose) std::cout<<"Volume (cc): ";
+        std::cout<<statisticsFilter->GetCount(label)*spacing_cc<<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]<<" ";
@@ -276,12 +302,14 @@ namespace clitk
         if(m_ArgsInfo.dvhistogram_given)
         {
             typename StatisticsImageFilterType::HistogramPointer dvhistogram = statisticsFilter->GetHistogram(label);
+            double totalVolumeCC = ((statisticsFilter->GetCount(label))*spacing_cc);
+            double totalVolume = statisticsFilter->GetCount(label);
 
             // Screen
             std::cout<<"# Total volume : ";
-            std::cout<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
+            std::cout<<totalVolume<<" [No. of voxels]"<<std::endl;
             std::cout<<"# Total volume : ";
-            std::cout<<((statisticsFilter->GetCount(label))*spacing_cc)<<" [cc]"<<std::endl;
+            std::cout<<totalVolumeCC<<" [cc]"<<std::endl;
             std::cout<<"# Dose mean: ";
             std::cout<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
             std::cout<<"# Dose min: ";
@@ -289,7 +317,7 @@ namespace clitk
             std::cout<<"# Dose max: ";
             std::cout<<statisticsFilter->GetMaximum(label)<<" [Gy]"<<std::endl;
             std::cout<<" "<<std::endl;
-            std::cout<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] #Dose_cumul[Gy] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
+            std::cout<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
             for( int i =0; i <m_ArgsInfo.bins_arg; i++)
             {
               double popCumulativeVolume = 0;
@@ -297,17 +325,11 @@ namespace clitk
               {
                  popCumulativeVolume+=(dvhistogram->GetFrequency(j));
               }
-              double cumulativeVolume = popCumulativeVolume + (dvhistogram->GetFrequency(i));
+              double cumulativeVolume = (totalVolume - (popCumulativeVolume + (dvhistogram->GetFrequency(i))));
               double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label)) ;
-              double ccCumulativeVolume = (popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc;
+              double ccCumulativeVolume = (totalVolumeCC -((popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc));
               double percentDiffVolume = dvhistogram->GetFrequency(i)*100/(statisticsFilter->GetCount(label));
-              if(i == 0)
-              {
-                 std::cout<<dvhistogram->GetBinMax(0,i)<<"\t  "<<dvhistogram->GetFrequency(i)<<"\t  "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<m_ArgsInfo.bins_arg<<"\t "<<cumulativeVolume<<"\t  "<<percentCumulativeVolume<<"\t  "<<ccCumulativeVolume<<"\t "<<std::endl;
-              }else
-              {
-                 std::cout<<dvhistogram->GetBinMax(0,i)<<"\t  "<<dvhistogram->GetFrequency(i)<<"\t  "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<dvhistogram->GetBinMin(0,m_ArgsInfo.bins_arg-i)<<"\t "<<cumulativeVolume<<"\t  "<<percentCumulativeVolume<<"\t  "<<ccCumulativeVolume<<"\t "<<std::endl;
-              }
+              std::cout<<dvhistogram->GetBinMax(0,i)<<"\t  "<<dvhistogram->GetFrequency(i)<<"\t  "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<"\t "<<cumulativeVolume<<"\t  "<<percentCumulativeVolume<<"\t  "<<ccCumulativeVolume<<"\t "<<std::endl;
             }
 
             // Add to the file
@@ -315,7 +337,7 @@ namespace clitk
             dvhistogramFile<<"# Total volume : ";
             dvhistogramFile<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
             dvhistogramFile<<"# Total volume : ";
-            dvhistogramFile<<((statisticsFilter->GetCount(label))*spacing_cc)<<" [cc]"<<std::endl;
+            dvhistogramFile<<totalVolumeCC<<" [cc]"<<std::endl;
             dvhistogramFile<<"# Dose mean: ";
             dvhistogramFile<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
             dvhistogramFile<<"# Dose min: ";
@@ -323,7 +345,7 @@ namespace clitk
             dvhistogramFile<<"# Dose max: ";
             dvhistogramFile<<statisticsFilter->GetMaximum(label)<<" [Gy]"<<std::endl;
             dvhistogramFile<<"  "<<std::endl;
-            dvhistogramFile<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] #Dose_cumulative[Gy] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
+            dvhistogramFile<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
             for( int i =0; i <m_ArgsInfo.bins_arg; i++)
             {
                double popCumulativeVolume = 0;
@@ -331,17 +353,11 @@ namespace clitk
                {
                  popCumulativeVolume+=(dvhistogram->GetFrequency(j));
                }
-               double cumulativeVolume = popCumulativeVolume + (dvhistogram->GetFrequency(i));
-               double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label)) ;
-               double ccCumulativeVolume = (popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc;
+               double cumulativeVolume = (totalVolume - (popCumulativeVolume + (dvhistogram->GetFrequency(i))));
+               double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label));
+               double ccCumulativeVolume = (totalVolumeCC -((popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc));
                double percentDiffVolume = ((dvhistogram->GetFrequency(i))*100)/(statisticsFilter->GetCount(label));
-               if(i == 0)
-               {
-                 dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t  "<<dvhistogram->GetFrequency(i)<<"\t  "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<m_ArgsInfo.bins_arg<<"\t "<<cumulativeVolume<<"\t  "<<percentCumulativeVolume<<"\t  "<<ccCumulativeVolume<<std::endl;
-               }else
-               {
-                 dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t  "<<dvhistogram->GetFrequency(i)<<"\t  "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<dvhistogram->GetBinMin(0,m_ArgsInfo.bins_arg-i)<<"\t "<<cumulativeVolume<<"\t  "<<percentCumulativeVolume<<"\t  "<<ccCumulativeVolume<<std::endl;
-               }
+               dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t  "<<dvhistogram->GetFrequency(i)<<"\t  "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t  "<<ccCumulativeVolume<<std::endl;
            }
         }
       }