#ifndef clitkImageStatisticsGenericFilter_txx
#define clitkImageStatisticsGenericFilter_txx
+#include "itkNthElementImageAdaptor.h"
+
/* =================================================
* @file clitkImageStatisticsGenericFilter.txx
* @author
//-------------------------------------------------------------------
// Update with the number of dimensions
//-------------------------------------------------------------------
- template<unsigned int Dimension>
+ 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 (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;
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 == "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>
+ template <unsigned int Dimension, class PixelType, unsigned int Components>
void
ImageStatisticsGenericFilter::UpdateWithDimAndPixelType()
{
// ImageTypes
- typedef itk::Image<PixelType, Dimension> InputImageType;
+ typedef itk::Image<itk::Vector<PixelType, Components>, Dimension> InputImageType;
typedef itk::Image<unsigned int, Dimension> LabelImageType;
- typedef itk::Image<PixelType, Dimension> OutputImageType;
// Read the input
typedef itk::ImageFileReader<InputImageType> InputReaderType;
reader->SetFileName( m_InputFileName);
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();
- }
- 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]);
- }
+ 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();
+ }
+ 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]);
+ }
statisticsFilter->SetLabelInput(labelImage);
// For each Label
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;
+ 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;
+ }
- 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;
- }
+ 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: "<<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;
+ }
}
-
+ }
+
return;
-
+
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff