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 clitkBSplineCoefficientsToValuesGenericFilter_txx
19 #define clitkBSplineCoefficientsToValuesGenericFilter_txx
20 #include <itkAffineTransform.h>
22 /* =================================================
23 * @file clitkBSplineCoefficientsToValuesGenericFilter.txx
29 ===================================================*/
35 //-------------------------------------------------------------------
36 // Update with the number of dimensions
37 //-------------------------------------------------------------------
38 template<unsigned int Dimension>
40 BSplineCoefficientsToValuesGenericFilter::UpdateWithDim(std::string PixelType, unsigned int Components)
42 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
46 // if(PixelType == "short"){
47 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
48 // UpdateWithDimAndPixelType<Dimension, signed short>();
50 // else if(PixelType == "unsigned_short"){
51 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
52 // UpdateWithDimAndPixelType<Dimension, unsigned short>();
55 // else if (PixelType == "unsigned_char"){
56 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
57 // UpdateWithDimAndPixelType<Dimension, unsigned char>();
60 // else if (PixelType == "char"){
61 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
62 // UpdateWithDimAndPixelType<Dimension, signed char>();
65 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
66 UpdateWithDimAndPixelType<Dimension, float>();
73 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
74 UpdateWithDimAndVectorType<Dimension, itk::Vector<float, 3> >();
77 else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
82 //-------------------------------------------------------------------
83 // Update with the number of dimensions and the pixeltype
84 //-------------------------------------------------------------------
85 template <unsigned int Dimension, class PixelType>
87 BSplineCoefficientsToValuesGenericFilter::UpdateWithDimAndPixelType()
91 typedef itk::Image<PixelType, Dimension> InputImageType;
92 typedef itk::Image<PixelType, Dimension> OutputImageType;
95 typedef itk::ImageFileReader<InputImageType> InputReaderType;
96 typename InputReaderType::Pointer reader = InputReaderType::New();
97 reader->SetFileName( m_InputFileName);
99 typename InputImageType::Pointer input= reader->GetOutput();
102 typedef itk::ResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
103 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
106 if (m_ArgsInfo.like_given)
108 typename InputReaderType::Pointer likeReader=InputReaderType::New();
109 likeReader->SetFileName(m_ArgsInfo.like_arg);
110 likeReader->Update();
111 resampler->SetOutputParametersFromImage(likeReader->GetOutput());
112 if (m_Verbose)std::cout<<"Resampling output like "<<m_ArgsInfo.like_arg<<"..."<<std::endl;
117 typename OutputImageType::SizeType outputSize;
118 if (m_ArgsInfo.size_given)
120 for(unsigned int i=0; i< Dimension; i++)
121 outputSize[i]=m_ArgsInfo.size_arg[i];
123 else outputSize=input->GetLargestPossibleRegion().GetSize();
124 if (m_Verbose)std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
127 typename OutputImageType::SpacingType outputSpacing;
128 if (m_ArgsInfo.spacing_given)
130 for(unsigned int i=0; i< Dimension; i++)
131 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
133 else outputSpacing=input->GetSpacing();
134 if (m_Verbose)std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
137 typename OutputImageType::PointType outputOrigin;
138 if (m_ArgsInfo.origin_given)
140 for(unsigned int i=0; i< Dimension; i++)
141 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
143 else outputOrigin=input->GetOrigin();
144 if (m_Verbose)std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
147 resampler->SetSize( outputSize );
148 resampler->SetOutputSpacing( outputSpacing );
149 resampler->SetOutputOrigin( outputOrigin );
154 typedef itk::BSplineResampleImageFunction<InputImageType, double> InterpolatorType;
155 typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
156 interpolator->SetSplineOrder(m_ArgsInfo.order_arg);
159 resampler->SetInterpolator( interpolator);
160 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
161 resampler->SetInput( input );
168 catch(itk::ExceptionObject)
170 std::cerr<<"Error resampling the image"<<std::endl;
173 typename OutputImageType::Pointer output = resampler->GetOutput();
176 typedef itk::ImageFileWriter<OutputImageType> WriterType;
177 typename WriterType::Pointer writer = WriterType::New();
178 writer->SetFileName(m_ArgsInfo.output_arg);
179 writer->SetInput(output);
184 //-------------------------------------------------------------------
185 // Update with the number of dimensions and the Vectortype
186 //-------------------------------------------------------------------
187 template <unsigned int Dimension, class PixelType>
189 BSplineCoefficientsToValuesGenericFilter::UpdateWithDimAndVectorType()
193 typedef itk::Image<PixelType, Dimension> InputImageType;
194 typedef itk::Image<PixelType, Dimension> OutputImageType;
197 typedef itk::ImageFileReader<InputImageType> InputReaderType;
198 typename InputReaderType::Pointer reader = InputReaderType::New();
199 reader->SetFileName( m_InputFileName);
201 typename InputImageType::Pointer input= reader->GetOutput();
204 typedef itk::VectorResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
205 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
208 if (m_ArgsInfo.like_given)
210 typename InputReaderType::Pointer likeReader=InputReaderType::New();
211 likeReader->SetFileName(m_ArgsInfo.like_arg);
212 likeReader->Update();
215 resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
216 resampler->SetOutputSpacing(likeReader->GetOutput()->GetSpacing() );
217 resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
218 if (m_Verbose)std::cout<<"Resampling output like "<<m_ArgsInfo.like_arg<<"..."<<std::endl;
223 typename OutputImageType::SizeType outputSize;
224 if (m_ArgsInfo.size_given)
226 for(unsigned int i=0; i< Dimension; i++)
227 outputSize[i]=m_ArgsInfo.size_arg[i];
229 else outputSize=input->GetLargestPossibleRegion().GetSize();
230 if (m_Verbose)std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
233 typename OutputImageType::SpacingType outputSpacing;
234 if (m_ArgsInfo.spacing_given)
236 for(unsigned int i=0; i< Dimension; i++)
237 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
239 else outputSpacing=input->GetSpacing();
240 if (m_Verbose)std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
243 typename OutputImageType::PointType outputOrigin;
244 if (m_ArgsInfo.origin_given)
246 for(unsigned int i=0; i< Dimension; i++)
247 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
249 else outputOrigin=input->GetOrigin();
250 if (m_Verbose)std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
253 resampler->SetSize( outputSize );
254 resampler->SetOutputSpacing( outputSpacing );
255 resampler->SetOutputOrigin( outputOrigin );
260 typedef clitk::VectorBSplineResampleImageFunction<InputImageType, double> InterpolatorType;
261 typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
262 interpolator->SetSplineOrder(m_ArgsInfo.order_arg);
266 resampler->SetInterpolator( interpolator);
267 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
268 resampler->SetInput( input );
275 catch(itk::ExceptionObject)
277 std::cerr<<"Error resampling the image"<<std::endl;
280 typename OutputImageType::Pointer output = resampler->GetOutput();
281 //writeImage<OutputImageType>(output, "/home/jef/tmp/output1.mhd", true);
285 if(m_ArgsInfo.matrix_given)
287 #if ITK_VERSION_MAJOR >= 4
288 typedef itk::TransformToDisplacementFieldSource<OutputImageType, double> ConvertorType;
290 typedef itk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
292 typename ConvertorType::Pointer filter= ConvertorType::New();
293 filter->SetOutputParametersFromImage(output);
295 typedef itk::AffineTransform<double, Dimension> TransformType;
296 typename TransformType::Pointer transform =TransformType::New();
297 itk::Matrix<double, Dimension+1, Dimension+1> homMatrix= ReadMatrix<Dimension>( m_ArgsInfo.matrix_arg);
298 itk::Matrix<double, Dimension, Dimension> matrix =GetRotationalPartMatrix( homMatrix);
299 itk::Vector<double, Dimension> offset= GetTranslationPartMatrix( homMatrix);
300 transform->SetMatrix(matrix);
301 transform->SetOffset(offset);
302 filter->SetTransform(transform);
304 typename OutputImageType::Pointer output2=filter->GetOutput();
305 //writeImage<OutputImageType>(output2, "/home/jef/tmp/output2.mhd", true);
308 typedef itk::AddImageFilter< OutputImageType, OutputImageType, OutputImageType > AddType;
309 typename AddType::Pointer adder= AddType::New();
310 adder->SetInput(output);
311 adder->SetInput(1,output2);
313 output=adder->GetOutput();
318 typedef itk::ImageFileWriter<OutputImageType> WriterType;
319 typename WriterType::Pointer writer = WriterType::New();
320 writer->SetFileName(m_ArgsInfo.output_arg);
321 writer->SetInput(output);
327 #endif //#define clitkBSplineCoefficientsToValuesGenericFilter_txx