target_link_libraries(clitkImageStatistics clitkCommon)
set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageStatistics)
- WRAP_GGO(clitkDVH_GGO_C clitkDVH.ggo)
- add_executable(clitkDVH clitkDVH.cxx clitkDVHGenericFilter.cxx ${clitkDVH_GGO_C})
- target_link_libraries(clitkDVH clitkVectorArithmLib clitkCommon)
- set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDVH)
-
WRAP_GGO(clitkVFConvert_GGO_C clitkVFConvert.ggo)
add_executable(clitkVFConvert clitkVFConvert.cxx clitkVFConvertGenericFilter.cxx ${clitkVFConvert_GGO_C})
target_link_libraries(clitkVFConvert clitkCommon )
+++ /dev/null
-/*=========================================================================
- Program: vv http://www.creatis.insa-lyon.fr/rio/vv
-
- 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
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the copyright notices for more information.
-
- It is distributed under dual licence
-
- - BSD See included LICENSE.txt file
- - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
-
-/* =================================================
- * @file clitkHGenericFilter.txx
- * @author Agata Krason <agata.krason@creatis.insa-lyon.fr>
- * @date 19 November 2013
- *
- * @brief Dose Histogram
- *
- ===================================================*/
-
-// clitk
-#include "clitkDVH_ggo.h"
-#include "clitkIO.h"
-#include "clitkDVHGenericFilter.h"
-
-//--------------------------------------------------------------------
-int main(int argc, char * argv[])
-{
-
- // Init command line
- GGO(clitkDVH, args_info);
- CLITK_INIT;
-
- // Filter
- clitk::DVHGenericFilter::Pointer genericFilter=clitk::DVHGenericFilter::New();
- genericFilter->SetArgsInfo(args_info);
- CLITK_TRY_CATCH_EXIT(genericFilter->Update());
-
- return EXIT_SUCCESS;
-}// end main
+++ /dev/null
-#File clitkDVH.ggo
-package "clitkDVH"
-version "2.0"
-purpose "Dose volume histogram"
-
-
-option "config" - "Config file" string no
-option "verbose" v "Verbose" flag off
-
-option "input" i "Input image filename" string yes multiple
-option "channel" c "Image channel to be used in statistics (-1 to process all channels)" int no default="-1"
-option "mask" m "Mask image filename (uchar)" string yes
-option "label" l "Label(s) in the mask image to consider" int no multiple default="1"
-option "histogram" - "Compute histogram, allows median calculation" string no
-option "dvhistogram" - "Compute dose volume histogram " string no
-option "bins" - "Number of histogram bins" int no default="80"
-option "lower" - "Lower histogram bound" double no default="0"
-option "upper" - "Upper histogram bound" double no default="80"
-option "allow_resize" r "Resize mask if different from input" flag off
-
-
-
+++ /dev/null
-/*=========================================================================
- Program: vv http://www.creatis.insa-lyon.fr/rio/vv
-
- 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
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the copyright notices for more information.
-
- It is distributed under dual licence
-
- - BSD See included LICENSE.txt file
- - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
-#ifndef clitkDVHGenericFilter_cxx
-#define clitkDVHGenericFilter_cxx
-
-#include "clitkDVHGenericFilter.h"
-
-namespace clitk
-{
-
- //-----------------------------------------------------------
- // Constructor
- //-----------------------------------------------------------
- DVHGenericFilter::DVHGenericFilter()
- {
- m_Verbose=false;
- m_InputFileName="";
- }
- //-----------------------------------------------------------
-
- //-----------------------------------------------------------
- // Update
- //-----------------------------------------------------------
- void DVHGenericFilter::Update()
- {
- // Read the Dimension and PixelType
- int Dimension, Components;
- std::string PixelType;
- ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
-
- if (m_ArgsInfo.channel_arg < -1 || m_ArgsInfo.channel_arg >= Components) {
- std::cout << "Invalid image channel" << std::endl;
- return;
- }
-
- if (m_ArgsInfo.mask_given) {
- int maskDimension, maskComponents;
- std::string maskPixelType;
- ReadImageDimensionAndPixelType(m_ArgsInfo.mask_arg, maskDimension, maskPixelType, maskComponents);
- if (!(maskDimension == Dimension || maskDimension == (Dimension - 1))) {
- std::cout << "Dimension of label mask must be equal to the (d)imension of the input image or d-1." << std::endl;
- return;
- }
- }
-
-
- // Call UpdateWithDim
- if (Dimension==2) {
- switch (Components) {
- case 1:
- UpdateWithDim<2,1>(PixelType);
- break;
- case 2:
- UpdateWithDim<2,2>(PixelType);
- break;
- case 3:
- UpdateWithDim<2,3>(PixelType);
- break;
- default:
- std::cout << "Unsupported number of channels" << std::endl;
- break;
- }
- }
- else if (Dimension==3) {
- switch (Components) {
- case 1:
- UpdateWithDim<3,1>(PixelType);
- break;
- case 2:
- UpdateWithDim<3,2>(PixelType);
- break;
- case 3:
- UpdateWithDim<3,3>(PixelType);
- break;
- default:
- std::cout << "Unsupported number of channels" << std::endl;
- break;
- }
- }
- else if (Dimension==4) {
- switch (Components) {
- case 1:
- UpdateWithDim<4,1>(PixelType);
- break;
- case 2:
- UpdateWithDim<4,2>(PixelType);
- break;
- case 3:
- UpdateWithDim<4,3>(PixelType);
- break;
- default:
- std::cout << "Unsupported number of channels" << std::endl;
- break;
- }
- }
- else {
- std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
- return;
- }
- }
-
-
-} //end clitk
-
-#endif //#define clitkDVHGenericFilter_cxx
+++ /dev/null
-/*=========================================================================
- Program: vv http://www.creatis.insa-lyon.fr/rio/vv
-
- 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
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the copyright notices for more information.
-
- It is distributed under dual licence
-
- - BSD See included LICENSE.txt file
- - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
-#ifndef CLITKDVHGENERICFILTER_H
-#define CLITKDVHGENERICFILTER_H
-
-// clitk include
-#include "clitkIO.h"
-#include "clitkCommon.h"
-#include "clitkImageCommon.h"
-#include "clitkImageToImageGenericFilter.h"
-#include "clitkDVH_ggo.h"
-
-// itk include
-#include "itkImage.h"
-#include "itkImageIOBase.h"
-#include "itkImageRegionIterator.h"
-#include "itkImageRegionConstIterator.h"
-#include "itkLightObject.h"
-#include "itkLabelStatisticsImageFilter.h"
-#include "itkLabelGeometryImageFilter.h"
-
-//--------------------------------------------------------------------
-namespace clitk
-{
-
-//template<class args_info_type>
-class ITK_EXPORT DVHGenericFilter: public itk::LightObject
-{
-
-public:
-
-
- //--------------------------------------------------------------------
- typedef DVHGenericFilter Self;
- typedef itk::LightObject Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- //--------------------------------------------------------------------
- // Method for creation through the object factory
- // and Run-time type information (and related methods)
- itkNewMacro(Self);
- itkTypeMacro(DVHGenericFilter, LightObject);
-
- //--------------------------------------------------------------------
- void SetArgsInfo(const args_info_clitkDVH & a)
- {
- m_ArgsInfo=a;
- m_Verbose=m_ArgsInfo.verbose_flag;
-
- if(m_ArgsInfo.input_given)
- m_InputFileName=m_ArgsInfo.input_arg[0];
- else if(m_ArgsInfo.inputs_num>0)
- m_InputFileName=m_ArgsInfo.inputs[0];
- else {
- std::cerr << "You must give an input file name" << std::endl;
- exit(1);
- }
- }
- //--------------------------------------------------------------------
- // Main function called each time the filter is updated
- //template<class InputImageType>
- //void UpdateWithInputImageType();
- void Update();
-
- // Set methods
- void SetDefaultPixelValue (double value) { mDefaultPixelValue = value ;}
- void SetTypeOfOperation (int value) { mTypeOfOperation = value ;}
- void SetScalar (double value) { mScalar = value ;}
- void EnableOverwriteInputImage(bool b);
-
- // Get methods
- double GetDefaultPixelValue () { return mDefaultPixelValue ;}
- int GetTypeOfOperation () { return mTypeOfOperation ;}
- double GetScalar () { return mScalar ;}
-
-protected:
-
- //--------------------------------------------------------------------
- // Constructor & Destructor
- DVHGenericFilter();
- ~DVHGenericFilter() {};
- // template<unsigned int Dim> void InitializeImageType();
- // args_info_type mArgsInfo;
-
- //--------------------------------------------------------------------
- // Tempated members
- //--------------------------------------------------------------------
- template<unsigned int Dimension, unsigned int Components> void UpdateWithDim(std::string PixelType);
- template <unsigned int Dimension, class PixelType, unsigned int Components> void UpdateWithDimAndPixelType();
-
- //--------------------------------------------------------------------
- // Data members
- //--------------------------------------------------------------------
- args_info_clitkDVH m_ArgsInfo;
- bool m_Verbose;
- std::string m_InputFileName;
-
- template<unsigned int Dim> void InitializeImageType();
- bool mIsOperationUseASecondImage;
- double mScalar;
- double mDefaultPixelValue;
- int mTypeOfOperation;
- bool mOverwriteInputImage;
- bool mOutputIsFloat;
-
- template<class Iter1, class Iter2> void ComputeImage(Iter1 it, Iter2 ito);
-
- template<class Iter1, class Iter2, class Iter3> void ComputeImage(Iter1 it1, Iter2 it2, Iter3 ito);
-
-
-}; // end class
-//--------------------------------------------------------------------
-
-} // end namespace clitk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkDVHGenericFilter.txx"
-#endif
-
-#endif // #define clitkDVHGenericFilter_h
+++ /dev/null
-/*=========================================================================
- Program: vv http://www.creatis.insa-lyon.fr/rio/vv
-
- 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
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the copyright notices for more information.
-
- It is distributed under dual licence
-
- - BSD See included LICENSE.txt file
- - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
-#ifndef clitkDVHGenericFilter_txx
-#define clitkDVHGenericFilter_txx
-
-/* =================================================
- * @file clitkDVHGenericFilter.txx
- * @author Agata Krason <agata.krason@creatis.insa-lyon.fr>
- * @date 20 November 2013
- *
- * @brief Dose volume and image histogram
- *
- ===================================================*/
-
-// itk include
-#include "itkBinaryThresholdImageFilter.h"
-#include "itkMaskImageFilter.h"
-#include "itkMaskNegatedImageFilter.h"
-#include "itkNthElementImageAdaptor.h"
-#include "itkJoinSeriesImageFilter.h"
-#include "itkMinimumMaximumImageCalculator.h"
-
-// clitk include
-#include <clitkCommon.h>
-#include "clitkImageCommon.h"
-#include "clitkDVHGenericFilter.h"
-#include "clitkCropLikeImageFilter.h"
-#include "clitkResampleImageWithOptionsFilter.h"
-
-//-------------------------------------------------------------------
-//
-namespace clitk
-{
-
-//-------------------------------------------------------------------
-template<unsigned int Dimension, unsigned int Components>
-void
-DVHGenericFilter::UpdateWithDim(std::string PixelType)
-{
- 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, 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, 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, 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 (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, float, Components>();
- }
-}
-
-
-//-------------------------------------------------------------------
-// Update with the number of dimensions and the pixeltype
-//-------------------------------------------------------------------
-template <unsigned int Dimension, class PixelType, unsigned int Components>
-void
-DVHGenericFilter::UpdateWithDimAndPixelType()
-{
-
- // ImageTypes
- 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->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<InputImageAdaptorType, LabelImageType> StatisticsImageFilterType;
- typename StatisticsImageFilterType::Pointer statisticsFilter=StatisticsImageFilterType::New();
- statisticsFilter->SetInput(input_adaptor);
-
- // Label image
- typename LabelImageType::Pointer labelImage;
- 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 {
- 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->SetGaussianFilteringEnabled(false);
- resampler->Update();
- labelImage = resampler->GetOutput();
- labelImage->GetSpacing();
- 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" << std::endl;
- exit(-1);
- }
- }
-
- }
-
- }
- 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);
-
- // 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;
- if (m_ArgsInfo.label_given)
- numberOfLabels=m_ArgsInfo.label_given;
- else
- numberOfLabels=1;
-
- 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];
- // Histogram
- if (m_ArgsInfo.histogram_given)
- {
- std::cout<<"--------------"<<std::endl;
- std::cout<<"| Label: |"<<label<<" |"<<std::endl;
- std::cout<<"--------------"<<std::endl;
-
- statisticsFilter->SetUseHistograms(true);
- statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
- }
-
- // DVHistogram
- if(m_ArgsInfo.dvhistogram_given)
- {
- statisticsFilter->SetUseHistograms(true);
- statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
- }
-
- statisticsFilter->Update();
-
- // 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);
-
- // Screen
- std::cout<<"Total volume : ";
- std::cout<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
- std::cout<<"Total volume : ";
- std::cout<<((statisticsFilter->GetCount(label))*spacing_cc)<<" [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[Gy] Volume_diff[No. of voxels]] Volume_cumul[No. of voxels] Volume_diff[%] Volume_cumul[%] Volume_diff[cc] Volume_cumul[cc]"<<std::endl;
- for( int i =0; i <m_ArgsInfo.bins_arg; i++)
- {
- double percentDiffVolume = ((dvhistogram->GetFrequency(i))*100)/(statisticsFilter->GetCount(label));
- double popCumulativeVolume = 0;
- for(int j=0; j<i; j++)
- {
- 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;
- std::cout<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<cumulativeVolume<<"\t "<<percentDiffVolume<<"\t "<<percentCumulativeVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<ccCumulativeVolume<<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<<((statisticsFilter->GetCount(label))*spacing_cc)<<" [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[Gy] Volume_diff[No. of voxels]] Volume_cumul[No. of voxels] Volume_diff[%] Volume_cumul[%] Volume_diff[cc] Volume_cumul[cc]"<<std::endl;
- for( int i =0; i <m_ArgsInfo.bins_arg; i++)
- {
- double percentDiffVolume = ((dvhistogram->GetFrequency(i))*100)/(statisticsFilter->GetCount(label));
- double popCumulativeVolume = 0;
- for(int j=0; j<i; j++)
- {
- 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;
- dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<cumulativeVolume<<"\t "<<percentDiffVolume<<"\t "<<percentCumulativeVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<ccCumulativeVolume<<std::endl;
- }
- }
- }
- }
-
- return;
-
-}
-
-}//end clitk
-
-#endif //#define clitkDVHGenericFilter_txx
option "mask" m "Mask image filename (uchar)" string no
option "label" l "Label(s) in the mask image to consider" int no multiple default="1"
option "histogram" - "Compute histogram, allows median calculation" string no
+option "dvhistogram" - "Compute dose volume histogram" string no
option "bins" - "Number of histogram bins" int no default="100"
option "lower" - "Lower histogram bound" double no default="-1000"
option "upper" - "Upper histogram bound" double no default="1000"
}
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;
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();
// Output
- if (m_Verbose) std::cout<<"N° of pixels: ";
- std::cout<<statisticsFilter->GetCount(label)<<std::endl;
-
+ 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;
-
+ 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) std::cout<<"Max: ";
- std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
-
+ std::cout<<statisticsFilter->GetMaximum(label)<<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<<"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);
+
+ // Screen
+ std::cout<<"# Total volume : ";
+ std::cout<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
+ std::cout<<"# Total volume : ";
+ std::cout<<((statisticsFilter->GetCount(label))*spacing_cc)<<" [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] #Dose_cumul[Gy] 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 = popCumulativeVolume + (dvhistogram->GetFrequency(i));
+ double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label)) ;
+ double ccCumulativeVolume = (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;
+ }
+ }
+
+ // 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<<((statisticsFilter->GetCount(label))*spacing_cc)<<" [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] #Dose_cumulative[Gy] 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 = popCumulativeVolume + (dvhistogram->GetFrequency(i));
+ double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label)) ;
+ double ccCumulativeVolume = (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;
+ }
+ }
+ }
}
}
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff