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://oncora1.lyon.fnclcc.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
21 /* =================================================
22 * @file clitkBSplineCoefficientsToValuesGenericFilter.txx
28 ===================================================*/
34 //-------------------------------------------------------------------
35 // Update with the number of dimensions
36 //-------------------------------------------------------------------
37 template<unsigned int Dimension>
39 BSplineCoefficientsToValuesGenericFilter::UpdateWithDim(std::string PixelType, unsigned int Components)
41 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
45 // if(PixelType == "short"){
46 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
47 // UpdateWithDimAndPixelType<Dimension, signed short>();
49 // else if(PixelType == "unsigned_short"){
50 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
51 // UpdateWithDimAndPixelType<Dimension, unsigned short>();
54 // else if (PixelType == "unsigned_char"){
55 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
56 // UpdateWithDimAndPixelType<Dimension, unsigned char>();
59 // else if (PixelType == "char"){
60 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
61 // UpdateWithDimAndPixelType<Dimension, signed char>();
64 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
65 UpdateWithDimAndPixelType<Dimension, float>();
72 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
73 UpdateWithDimAndVectorType<Dimension, itk::Vector<float, 3> >();
76 else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
81 //-------------------------------------------------------------------
82 // Update with the number of dimensions and the pixeltype
83 //-------------------------------------------------------------------
84 template <unsigned int Dimension, class PixelType>
86 BSplineCoefficientsToValuesGenericFilter::UpdateWithDimAndPixelType()
90 typedef itk::Image<PixelType, Dimension> InputImageType;
91 typedef itk::Image<PixelType, Dimension> OutputImageType;
94 typedef itk::ImageFileReader<InputImageType> InputReaderType;
95 typename InputReaderType::Pointer reader = InputReaderType::New();
96 reader->SetFileName( m_InputFileName);
98 typename InputImageType::Pointer input= reader->GetOutput();
101 typedef itk::ResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
102 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
105 if (m_ArgsInfo.like_given)
107 typename InputReaderType::Pointer likeReader=InputReaderType::New();
108 likeReader->SetFileName(m_ArgsInfo.like_arg);
109 likeReader->Update();
110 resampler->SetOutputParametersFromImage(likeReader->GetOutput());
111 if (m_Verbose)std::cout<<"Resampling output like "<<m_ArgsInfo.like_arg<<"..."<<std::endl;
116 typename OutputImageType::SizeType outputSize;
117 if (m_ArgsInfo.size_given)
119 for(unsigned int i=0; i< Dimension; i++)
120 outputSize[i]=m_ArgsInfo.size_arg[i];
122 else outputSize=input->GetLargestPossibleRegion().GetSize();
123 if (m_Verbose)std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
126 typename OutputImageType::SpacingType outputSpacing;
127 if (m_ArgsInfo.spacing_given)
129 for(unsigned int i=0; i< Dimension; i++)
130 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
132 else outputSpacing=input->GetSpacing();
133 if (m_Verbose)std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
136 typename OutputImageType::PointType outputOrigin;
137 if (m_ArgsInfo.origin_given)
139 for(unsigned int i=0; i< Dimension; i++)
140 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
142 else outputOrigin=input->GetOrigin();
143 if (m_Verbose)std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
146 resampler->SetSize( outputSize );
147 resampler->SetOutputSpacing( outputSpacing );
148 resampler->SetOutputOrigin( outputOrigin );
153 typedef itk::BSplineResampleImageFunction<InputImageType, double> InterpolatorType;
154 typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
155 interpolator->SetSplineOrder(m_ArgsInfo.order_arg);
158 resampler->SetInterpolator( interpolator);
159 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
160 resampler->SetInput( input );
167 catch(itk::ExceptionObject)
169 std::cerr<<"Error resampling the image"<<std::endl;
172 typename OutputImageType::Pointer output = resampler->GetOutput();
175 typedef itk::ImageFileWriter<OutputImageType> WriterType;
176 typename WriterType::Pointer writer = WriterType::New();
177 writer->SetFileName(m_ArgsInfo.output_arg);
178 writer->SetInput(output);
183 //-------------------------------------------------------------------
184 // Update with the number of dimensions and the Vectortype
185 //-------------------------------------------------------------------
186 template <unsigned int Dimension, class PixelType>
188 BSplineCoefficientsToValuesGenericFilter::UpdateWithDimAndVectorType()
192 typedef itk::Image<PixelType, Dimension> InputImageType;
193 typedef itk::Image<PixelType, Dimension> OutputImageType;
196 typedef itk::ImageFileReader<InputImageType> InputReaderType;
197 typename InputReaderType::Pointer reader = InputReaderType::New();
198 reader->SetFileName( m_InputFileName);
200 typename InputImageType::Pointer input= reader->GetOutput();
203 typedef itk::VectorResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
204 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
207 if (m_ArgsInfo.like_given)
209 typename InputReaderType::Pointer likeReader=InputReaderType::New();
210 likeReader->SetFileName(m_ArgsInfo.like_arg);
211 likeReader->Update();
214 resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
215 resampler->SetOutputSpacing(likeReader->GetOutput()->GetSpacing() );
216 resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
217 if (m_Verbose)std::cout<<"Resampling output like "<<m_ArgsInfo.like_arg<<"..."<<std::endl;
222 typename OutputImageType::SizeType outputSize;
223 if (m_ArgsInfo.size_given)
225 for(unsigned int i=0; i< Dimension; i++)
226 outputSize[i]=m_ArgsInfo.size_arg[i];
228 else outputSize=input->GetLargestPossibleRegion().GetSize();
229 if (m_Verbose)std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
232 typename OutputImageType::SpacingType outputSpacing;
233 if (m_ArgsInfo.spacing_given)
235 for(unsigned int i=0; i< Dimension; i++)
236 outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
238 else outputSpacing=input->GetSpacing();
239 if (m_Verbose)std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
242 typename OutputImageType::PointType outputOrigin;
243 if (m_ArgsInfo.origin_given)
245 for(unsigned int i=0; i< Dimension; i++)
246 outputOrigin[i]=m_ArgsInfo.origin_arg[i];
248 else outputOrigin=input->GetOrigin();
249 if (m_Verbose)std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
252 resampler->SetSize( outputSize );
253 resampler->SetOutputSpacing( outputSpacing );
254 resampler->SetOutputOrigin( outputOrigin );
259 typedef clitk::VectorBSplineResampleImageFunction<InputImageType, double> InterpolatorType;
260 typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
261 interpolator->SetSplineOrder(m_ArgsInfo.order_arg);
265 resampler->SetInterpolator( interpolator);
266 resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
267 resampler->SetInput( input );
274 catch(itk::ExceptionObject)
276 std::cerr<<"Error resampling the image"<<std::endl;
279 typename OutputImageType::Pointer output = resampler->GetOutput();
280 //writeImage<OutputImageType>(output, "/home/jef/tmp/output1.mhd", true);
284 if(m_ArgsInfo.matrix_given)
286 typedef itk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
287 typename ConvertorType::Pointer filter= ConvertorType::New();
288 filter->SetOutputParametersFromImage(output);
290 typedef itk::AffineTransform<double, Dimension> TransformType;
291 typename TransformType::Pointer transform =TransformType::New();
292 itk::Matrix<double, Dimension+1, Dimension+1> homMatrix= ReadMatrix<Dimension>( m_ArgsInfo.matrix_arg);
293 itk::Matrix<double, Dimension, Dimension> matrix =GetRotationalPartMatrix( homMatrix);
294 itk::Vector<double, Dimension> offset= GetTranslationPartMatrix( homMatrix);
295 transform->SetMatrix(matrix);
296 transform->SetOffset(offset);
297 filter->SetTransform(transform);
299 typename OutputImageType::Pointer output2=filter->GetOutput();
300 //writeImage<OutputImageType>(output2, "/home/jef/tmp/output2.mhd", true);
303 typedef itk::AddImageFilter< OutputImageType, OutputImageType, OutputImageType > AddType;
304 typename AddType::Pointer adder= AddType::New();
305 adder->SetInput(output);
306 adder->SetInput(1,output2);
308 output=adder->GetOutput();
313 typedef itk::ImageFileWriter<OutputImageType> WriterType;
314 typename WriterType::Pointer writer = WriterType::New();
315 writer->SetFileName(m_ArgsInfo.output_arg);
316 writer->SetInput(output);
322 #endif //#define clitkBSplineCoefficientsToValuesGenericFilter_txx