/*=========================================================================
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
#ifndef clitkImageStatisticsGenericFilter_txx
#define clitkImageStatisticsGenericFilter_txx
-/* =================================================
- * @file clitkImageStatisticsGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
+#include "itkNthElementImageAdaptor.h"
+#include "itkJoinSeriesImageFilter.h"
+#include "itkImageRegionConstIterator.h"
+#include "clitkImageStatisticsGenericFilter.h"
+#include "clitkCropLikeImageFilter.h"
+#include "clitkResampleImageWithOptionsFilter.h"
namespace clitk
{
//-------------------------------------------------------------------
// Update with the number of dimensions
//-------------------------------------------------------------------
- template<unsigned int Dimension>
- void
+ template<unsigned int Dimension, unsigned int Components>
+ void
ImageStatisticsGenericFilter::UpdateWithDim(std::string PixelType)
{
- if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
+ 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>();
+ 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_char"){
+ 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>();
+ UpdateWithDimAndPixelType<Dimension, unsigned char, Components>();
+ }
+
+ else if(PixelType == "double"){
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, double, 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 (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, float>();
+ UpdateWithDimAndPixelType<Dimension, float, Components>();
}
}
//-------------------------------------------------------------------
// Update with the number of dimensions and the pixeltype
//-------------------------------------------------------------------
- template <unsigned int Dimension, class PixelType>
- void
+ template <unsigned int Dimension, class PixelType, unsigned int Components>
+ void
ImageStatisticsGenericFilter::UpdateWithDimAndPixelType()
{
// ImageTypes
- typedef itk::Image<PixelType, Dimension> InputImageType;
- typedef itk::Image<unsigned int, Dimension> LabelImageType;
- typedef itk::Image<PixelType, Dimension> OutputImageType;
-
+ 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->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<InputImageType, LabelImageType> StatisticsImageFilterType;
+ typedef itk::LabelStatisticsImageFilter<InputImageAdaptorType, LabelImageType> StatisticsImageFilterType;
typename StatisticsImageFilterType::Pointer statisticsFilter=StatisticsImageFilterType::New();
- statisticsFilter->SetInput(input);
+ statisticsFilter->SetInput(input_adaptor);
// Label image
typename LabelImageType::Pointer labelImage;
- if (m_ArgsInfo.mask_given)
- {
- typedef itk::ImageFileReader<LabelImageType> LabelImageReaderType;
- typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
- labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
- labelImageReader->Update();
- labelImage= labelImageReader->GetOutput();
+ if (m_ArgsInfo.mask_given) {
+ 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)
+ 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();
+
+ typename JoinImageFilterType::Pointer joinFilter = JoinImageFilterType::New();
+ 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();
}
- else
- {
- labelImage=LabelImageType::New();
- labelImage->SetRegions(input->GetLargestPossibleRegion());
- labelImage->SetOrigin(input->GetOrigin());
- labelImage->SetSpacing(input->GetSpacing());
- labelImage->Allocate();
- labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
+ else {
+ typedef itk::ImageFileReader<LabelImageType> LabelImageReaderType;
+ typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
+ 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 {
+ 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]);
+ }
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;
else
numberOfLabels=1;
- for (unsigned int k=0; k< numberOfLabels; k++)
- {
- label=m_ArgsInfo.label_arg[k];
-
- 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<<"-------------"<<std::endl;
-
- // Histograms
- if (m_ArgsInfo.histogram_given)
- {
- statisticsFilter->SetUseHistograms(true);
- statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
- }
- statisticsFilter->Update();
-
-
- // Output
- 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;
-
- if (m_Verbose) std::cout<<"SD: ";
- std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
-
- if (m_Verbose) std::cout<<"Variance: ";
- std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
-
- if (m_Verbose) std::cout<<"Min: ";
- std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
-
- if (m_Verbose) std::cout<<"Max: ";
- std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
-
- if (m_Verbose) std::cout<<"Sum: ";
- 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;
-
-
- // Histogram
- if (m_ArgsInfo.histogram_given)
- {
- if (m_Verbose) std::cout<<"Median: ";
- std::cout<<statisticsFilter->GetMedian(label)<<std::endl;
-
- typename StatisticsImageFilterType::HistogramPointer histogram =statisticsFilter->GetHistogram(label);
-
- // Screen
- if (m_Verbose) std::cout<<"Histogram: "<<std::endl;
- std::cout<<"# MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
- for( int i =0; i <m_ArgsInfo.bins_arg; i++)
- std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
-
- // Add to the file
- std::ofstream histogramFile(m_ArgsInfo.histogram_arg);
- histogramFile<<"#Histogram: "<<std::endl;
- histogramFile<<"#MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
- 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;
- }
+ unsigned int firstComponent = 0, lastComponent = 0;
+ if (m_ArgsInfo.channel_arg == -1) {
+ 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];
+
+ std::cout<<std::endl;
+ if (m_Verbose) std::cout<<"-------------"<<std::endl;
+ if (m_Verbose) std::cout<<"| Label: "<< (int) label<<" |"<<std::endl;
+ if (m_Verbose) std::cout<<"-------------"<<std::endl;
+
+ // Histograms
+ if (m_ArgsInfo.histogram_given) {
+ 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;
+ if (m_Verbose) std::cout<<"Mean: ";
+ std::cout<<statisticsFilter->GetMean(label)<<std::endl;
+ if (m_Verbose) std::cout<<"SD: ";
+ std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
+ if (m_Verbose) std::cout<<"Variance: ";
+ 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]<<" ";
+ std::cout<<std::endl;
+
+ // Histogram
+ if (m_ArgsInfo.histogram_given)
+ {
+ if (m_Verbose) std::cout<<"Median: ";
+ std::cout<<statisticsFilter->GetMedian(label)<<std::endl;
+
+ typename StatisticsImageFilterType::HistogramPointer histogram =statisticsFilter->GetHistogram(label);
+
+ // Screen
+ if (m_Verbose) std::cout<<"Histogram: "<<std::endl;
+ std::cout<<"# MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
+ for( int i =0; i <m_ArgsInfo.bins_arg; i++)
+ std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
+
+ // Add to the file
+ std::ofstream histogramFile(m_ArgsInfo.histogram_arg);
+ histogramFile<<"#Histogram: "<<std::endl;
+ histogramFile<<"#MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
+ 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;
+ }
+ }
}
-
+ }
+
return;
-
+
}
-
-
+
+
}//end clitk
#endif //#define clitkImageStatisticsGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff