1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://www.centreleonberard.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ===========================================================================**/
18 #ifndef clitkImageStatisticsGenericFilter_txx
19 #define clitkImageStatisticsGenericFilter_txx
21 #include "itkNthElementImageAdaptor.h"
22 #include "itkJoinSeriesImageFilter.h"
24 #include "clitkImageStatisticsGenericFilter.h"
25 #include "clitkCropLikeImageFilter.h"
26 #include "clitkResampleImageWithOptionsFilter.h"
31 //-------------------------------------------------------------------
32 // Update with the number of dimensions
33 //-------------------------------------------------------------------
34 template<unsigned int Dimension, unsigned int Components>
36 ImageStatisticsGenericFilter::UpdateWithDim(std::string PixelType)
38 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<" with " << Components << " channel(s)..."<<std::endl;
40 if(PixelType == "short"){
41 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
42 UpdateWithDimAndPixelType<Dimension, signed short, Components>();
44 else if(PixelType == "unsigned_short"){
45 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
46 UpdateWithDimAndPixelType<Dimension, unsigned short, Components>();
49 else if (PixelType == "unsigned_char"){
50 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
51 UpdateWithDimAndPixelType<Dimension, unsigned char, Components>();
54 else if(PixelType == "double"){
55 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
56 UpdateWithDimAndPixelType<Dimension, double, Components>();
59 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
60 UpdateWithDimAndPixelType<Dimension, float, Components>();
65 //-------------------------------------------------------------------
66 // Update with the number of dimensions and the pixeltype
67 //-------------------------------------------------------------------
68 template <unsigned int Dimension, class PixelType, unsigned int Components>
70 ImageStatisticsGenericFilter::UpdateWithDimAndPixelType()
74 typedef unsigned char LabelPixelType;
75 typedef itk::Image<itk::Vector<PixelType, Components>, Dimension> InputImageType;
76 typedef itk::Image<LabelPixelType, Dimension> LabelImageType;
79 typedef itk::ImageFileReader<InputImageType> InputReaderType;
80 typename InputReaderType::Pointer reader = InputReaderType::New();
81 reader->SetFileName( m_InputFileName);
83 typename InputImageType::Pointer input= reader->GetOutput();
85 typedef itk::NthElementImageAdaptor<InputImageType, PixelType> InputImageAdaptorType;
86 typedef itk::Image<PixelType, Dimension> OutputImageType;
88 typename InputImageAdaptorType::Pointer input_adaptor = InputImageAdaptorType::New();
89 input_adaptor->SetImage(input);
92 typedef itk::LabelStatisticsImageFilter<InputImageAdaptorType, LabelImageType> StatisticsImageFilterType;
93 typename StatisticsImageFilterType::Pointer statisticsFilter=StatisticsImageFilterType::New();
94 statisticsFilter->SetInput(input_adaptor);
97 typename LabelImageType::Pointer labelImage;
98 if (m_ArgsInfo.mask_given) {
99 int maskDimension, maskComponents;
100 std::string maskPixelType;
101 ReadImageDimensionAndPixelType(m_ArgsInfo.mask_arg, maskDimension, maskPixelType, maskComponents);
103 if (maskDimension == Dimension - 1) {
104 // Due to a limitation of filter itk::LabelStatisticsImageFilter, InputImageType and LabelImageType
105 // must have the same image dimension. However, we want to support label images with Dl = Di - 1,
106 // so we need to replicate the label image as many times as the size along dimension Di.
108 std::cout << "Replicating label image to match input image's dimension... " << std::endl;
110 typedef itk::Image<LabelPixelType, Dimension - 1> ReducedLabelImageType;
111 typedef itk::ImageFileReader<ReducedLabelImageType> LabelImageReaderType;
112 typedef itk::JoinSeriesImageFilter<ReducedLabelImageType, LabelImageType> JoinImageFilterType;
114 typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
115 labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
116 labelImageReader->Update();
118 typename JoinImageFilterType::Pointer joinFilter = JoinImageFilterType::New();
119 typename InputImageType::SizeType size = input->GetLargestPossibleRegion().GetSize();
120 for (unsigned int i = 0; i < size[Dimension - 1]; i++)
121 joinFilter->PushBackInput(labelImageReader->GetOutput());
123 joinFilter->Update();
124 labelImage = joinFilter->GetOutput();
127 typedef itk::ImageFileReader<LabelImageType> LabelImageReaderType;
128 typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
129 labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
130 labelImageReader->Update();
131 labelImage= labelImageReader->GetOutput();
133 // Check mask sampling/size
134 if (!HaveSameSizeAndSpacing<LabelImageType, InputImageType>(labelImage, input)) {
135 if (m_ArgsInfo.allow_resize_flag) {
136 if (m_ArgsInfo.verbose_flag) {
137 std::cout << "Resize mask image like input" << std::endl;
139 typedef clitk::ResampleImageWithOptionsFilter<LabelImageType> ResamplerType;
140 typename ResamplerType::Pointer resampler = ResamplerType::New();
141 resampler->SetInput(labelImage);
142 resampler->SetOutputSpacing(input->GetSpacing());
143 resampler->SetGaussianFilteringEnabled(false);
145 labelImage = resampler->GetOutput();
146 //writeImage<LabelImageType>(labelImage, "test1.mha");
148 typedef clitk::CropLikeImageFilter<LabelImageType> FilterType;
149 typename FilterType::Pointer crop = FilterType::New();
150 crop->SetInput(labelImage);
151 crop->SetCropLikeImage(input);
153 labelImage = crop->GetOutput();
154 //writeImage<LabelImageType>(labelImage, "test2.mha");
158 std::cerr << "Mask image has a different size/spacing than input. Abort" << std::endl;
167 labelImage=LabelImageType::New();
168 labelImage->SetRegions(input->GetLargestPossibleRegion());
169 labelImage->SetOrigin(input->GetOrigin());
170 labelImage->SetSpacing(input->GetSpacing());
171 labelImage->Allocate();
172 labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
174 statisticsFilter->SetLabelInput(labelImage);
177 typename LabelImageType::PixelType label;
178 unsigned int numberOfLabels;
179 if (m_ArgsInfo.label_given)
180 numberOfLabels=m_ArgsInfo.label_given;
184 unsigned int firstComponent = 0, lastComponent = 0;
185 if (m_ArgsInfo.channel_arg == -1) {
187 lastComponent = Components - 1;
190 firstComponent = m_ArgsInfo.channel_arg;
191 lastComponent = m_ArgsInfo.channel_arg;
194 for (unsigned int c=firstComponent; c<=lastComponent; c++) {
195 if (m_Verbose) std::cout << std::endl << "Processing channel " << c << std::endl;
197 input_adaptor->SelectNthElement(c);
198 input_adaptor->Update();
200 for (unsigned int k=0; k< numberOfLabels; k++) {
201 label=m_ArgsInfo.label_arg[k];
203 std::cout<<std::endl;
204 if (m_Verbose) std::cout<<"-------------"<<std::endl;
205 if (m_Verbose) std::cout<<"| Label: "<<label<<" |"<<std::endl;
206 if (m_Verbose) std::cout<<"-------------"<<std::endl;
209 if (m_ArgsInfo.histogram_given) {
210 statisticsFilter->SetUseHistograms(true);
211 statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
213 statisticsFilter->Update();
216 if (m_Verbose) std::cout<<"N° of pixels: ";
217 std::cout<<statisticsFilter->GetCount(label)<<std::endl;
219 if (m_Verbose) std::cout<<"Mean: ";
220 std::cout<<statisticsFilter->GetMean(label)<<std::endl;
222 if (m_Verbose) std::cout<<"SD: ";
223 std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
225 if (m_Verbose) std::cout<<"Variance: ";
226 std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
228 if (m_Verbose) std::cout<<"Min: ";
229 std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
231 if (m_Verbose) std::cout<<"Max: ";
232 std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
234 if (m_Verbose) std::cout<<"Sum: ";
235 std::cout<<statisticsFilter->GetSum(label)<<std::endl;
237 if (m_Verbose) std::cout<<"Bounding box: ";
239 for(unsigned int i =0; i <statisticsFilter->GetBoundingBox(label).size(); i++)
240 std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
241 std::cout<<std::endl;
244 if (m_ArgsInfo.histogram_given)
246 if (m_Verbose) std::cout<<"Median: ";
247 std::cout<<statisticsFilter->GetMedian(label)<<std::endl;
249 typename StatisticsImageFilterType::HistogramPointer histogram =statisticsFilter->GetHistogram(label);
252 if (m_Verbose) std::cout<<"Histogram: "<<std::endl;
253 std::cout<<"# MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
254 for( int i =0; i <m_ArgsInfo.bins_arg; i++)
255 std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
258 std::ofstream histogramFile(m_ArgsInfo.histogram_arg);
259 histogramFile<<"#Histogram: "<<std::endl;
260 histogramFile<<"#MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
261 for( int i =0; i <m_ArgsInfo.bins_arg; i++)
262 histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
274 #endif //#define clitkImageStatisticsGenericFilter_txx