#include "itkNthElementImageAdaptor.h"
#include "itkJoinSeriesImageFilter.h"
+#include "itkImageRegionConstIterator.h"
#include "clitkImageStatisticsGenericFilter.h"
#include "clitkCropLikeImageFilter.h"
}
else {
labelImage=LabelImageType::New();
+ labelImage->SetDirection(input->GetDirection());
labelImage->SetRegions(input->GetLargestPossibleRegion());
labelImage->SetOrigin(input->GetOrigin());
labelImage->SetSpacing(input->GetSpacing());
}
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;
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
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
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;
+ }
+ }
}
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff