X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkImageStatisticsGenericFilter.txx;h=82a11ab5355a86134a3a6cc666ff9136b04dc423;hb=05306a598620f8eecd320abc606d1cff4b96f333;hp=70d25bd39c7122b79a91ac27168727fe754aa2d4;hpb=e8c23e7104a4eb289cbc3d65a244a1a1586458af;p=clitk.git

diff --git a/tools/clitkImageStatisticsGenericFilter.txx b/tools/clitkImageStatisticsGenericFilter.txx
index 70d25bd..82a11ab 100644
--- 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"
@@ -166,6 +167,7 @@ namespace clitk
     }
     else {
       labelImage=LabelImageType::New();
+      labelImage->SetDirection(input->GetDirection());
       labelImage->SetRegions(input->GetLargestPossibleRegion());
       labelImage->SetOrigin(input->GetOrigin());
       labelImage->SetSpacing(input->GetSpacing());
@@ -175,6 +177,15 @@ namespace clitk
     }
     statisticsFilter->SetLabelInput(labelImage);
 
+    // Check/compute spacing
+    const typename LabelImageType::SpacingType& spacing = input->GetSpacing();
+    double spacing_cc = (spacing[0]*spacing[1]*spacing[2])/1000;
+    // std::cout<<"Spacing x : " << spacing[0]<<std::endl;
+    // std::cout<<"Spacing y :  " << spacing[1]<<std::endl;
+    // std::cout<<"Spacing z :  " << spacing[2]<<std::endl;
+    // std::cout <<"spacing_cc : " << spacing_cc << std::endl;
+
+
     // For each Label
     typename LabelImageType::PixelType label;
     unsigned int numberOfLabels;
@@ -212,34 +223,57 @@ namespace clitk
           statisticsFilter->SetUseHistograms(true);
           statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
         }
+
+        // DVH
+        if(m_ArgsInfo.dvhistogram_given)
+        {
+          statisticsFilter->SetUseHistograms(true);
+          statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
+        }
+
         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: ";
-          std::cout<<statisticsFilter->GetCount(label)<<std::endl;
-
+        std::cout<<statisticsFilter->GetCount(label)<<std::endl;
         if (m_Verbose) std::cout<<"Mean: ";
-          std::cout<<statisticsFilter->GetMean(label)<<std::endl;
-
+        std::cout<<statisticsFilter->GetMean(label)<<std::endl;
         if (m_Verbose) std::cout<<"SD: ";
-          std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
-
+        std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
         if (m_Verbose) std::cout<<"Variance: ";
-          std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
-
+        std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
         if (m_Verbose) std::cout<<"Min: ";
-          std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
-
+        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;
-
+        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;
-
+        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]<<" ";
+            std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
         std::cout<<std::endl;
 
         // Histogram
@@ -263,6 +297,69 @@ namespace clitk
           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
             histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
         }
+
+        // DVH
+        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<<totalVolume<<" [No. of voxels]"<<std::endl;
+            std::cout<<"# Total volume : ";
+            std::cout<<totalVolumeCC<<" [cc]"<<std::endl;
+            std::cout<<"# Dose mean: ";
+            std::cout<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
+            std::cout<<"# Dose min: ";
+            std::cout<<statisticsFilter->GetMinimum(label)<<" [Gy]"<<std::endl;
+            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] 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;
+              for(int j=0; j<i; j++)
+              {
+                 popCumulativeVolume+=(dvhistogram->GetFrequency(j));
+              }
+              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));
+              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
+            std::ofstream dvhistogramFile(m_ArgsInfo.dvhistogram_arg);
+            dvhistogramFile<<"# Total volume : ";
+            dvhistogramFile<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
+            dvhistogramFile<<"# Total volume : ";
+            dvhistogramFile<<totalVolumeCC<<" [cc]"<<std::endl;
+            dvhistogramFile<<"# Dose mean: ";
+            dvhistogramFile<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
+            dvhistogramFile<<"# Dose min: ";
+            dvhistogramFile<<statisticsFilter->GetMinimum(label)<<" [Gy]"<<std::endl;
+            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] 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;
+               for(int j=0; j<i; j++)
+               {
+                 popCumulativeVolume+=(dvhistogram->GetFrequency(j));
+               }
+               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));
+               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;
+           }
+        }
       }
     }