--- /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://oncora1.lyon.fnclcc.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 clitkConvertBSplineDeformableTransformToVFGenericFilter_cxx
+#define clitkConvertBSplineDeformableTransformToVFGenericFilter_cxx
+
+/* =================================================
+ * @file clitkConvertBSplineDeformableTransformToVFGenericFilter.cxx
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include "clitkConvertBSplineDeformableTransformToVFGenericFilter.h"
+
+
+namespace clitk
+{
+
+
+ //-----------------------------------------------------------
+ // Constructor
+ //-----------------------------------------------------------
+ ConvertBSplineDeformableTransformToVFGenericFilter::ConvertBSplineDeformableTransformToVFGenericFilter()
+ {
+ m_Verbose=false;
+ m_InputFileName="";
+ }
+
+ //-------------------------------------------------------------------
+ // Update with the number of dimensions
+ //-------------------------------------------------------------------
+ template<>
+ void
+ ConvertBSplineDeformableTransformToVFGenericFilter::UpdateWithDim<3>(std::string PixelType, int Components)
+ {
+ // Components
+ if (Components !=3)
+ {
+ std::cerr<<"Number of components is "<<Components<<"! Only 3 components is supported."<<std::endl;
+ return;
+ }
+ if (PixelType != "double")
+ {
+ std::cerr<<"PixelType is "<<PixelType<<"! Only double coefficient images are supported."<<std::endl;
+ std::cerr<<"Reading image as double..."<<std::endl;
+ }
+
+ // ImageTypes
+ const unsigned int Dimension=3;
+ typedef itk::Vector<double, Dimension> InputPixelType;
+ typedef itk::Vector<float, Dimension> OutputPixelType;
+ typedef itk::Image<InputPixelType, Dimension> InputImageType;
+ typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
+
+ // Read the input
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ InputReaderType::Pointer reader = InputReaderType::New();
+ reader->SetFileName( m_InputFileName);
+ reader->Update();
+ InputImageType::Pointer input= reader->GetOutput();
+
+
+ // -----------------------------------------------
+ // Filter
+ // -----------------------------------------------
+ typedef itk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
+ ConvertorType::Pointer filter= ConvertorType::New();
+
+ //Output image info
+ if (m_ArgsInfo.like_given)
+ {
+ typedef itk::ImageFileReader<OutputImageType> ReaderType;
+ ReaderType::Pointer reader2=ReaderType::New();
+ reader2->SetFileName(m_ArgsInfo.like_arg);
+ reader2->Update();
+
+ OutputImageType::Pointer image=reader2->GetOutput();
+ filter->SetOutputParametersFromImage(image);
+ }
+ else
+ {
+ unsigned int i=0;
+ if(m_ArgsInfo.origin_given)
+ {
+ OutputImageType::PointType origin;
+ for(i=0;i<Dimension;i++)
+ origin[i]=m_ArgsInfo.origin_arg[i];
+ filter->SetOutputOrigin(origin);
+ }
+ if (m_ArgsInfo.spacing_given)
+ {
+ OutputImageType::SpacingType spacing;
+ for(i=0;i<Dimension;i++)
+ spacing[i]=m_ArgsInfo.spacing_arg[i];
+ filter->SetOutputSpacing(spacing);
+ }
+ if (m_ArgsInfo.spacing_given)
+ {
+ OutputImageType::SizeType size;
+ for(i=0;i<Dimension;i++)
+ size[i]=m_ArgsInfo.size_arg[i];
+ filter->SetOutputSize(size);
+ }
+ }
+
+ if (m_Verbose)
+ {
+ std::cout<< "Setting output origin to "<<filter->GetOutputOrigin()<<"..."<<std::endl;
+ std::cout<< "Setting output spacing to "<<filter->GetOutputSpacing()<<"..."<<std::endl;
+ std::cout<< "Setting output size to "<<filter->GetOutputSize()<<"..."<<std::endl;
+ }
+
+
+ // -----------------------------------------------
+ // Transform
+ // -----------------------------------------------
+ typedef clitk::BSplineDeformableTransform< double, Dimension, Dimension> TransformType;
+ TransformType::Pointer transform=TransformType::New();
+
+ // Spline orders: Default is cubic splines
+ InputImageType::RegionType::SizeType splineOrders ;
+ splineOrders.Fill(3);
+ if (m_ArgsInfo.order_given)
+ for(unsigned int i=0; i<Dimension;i++)
+ splineOrders[i]=m_ArgsInfo.order_arg[i];
+ if (m_Verbose) std::cout<<"Setting the spline orders to "<<splineOrders<<"..."<<std::endl;
+
+ // Mask
+ typedef itk::ImageMaskSpatialObject< Dimension > MaskType;
+ MaskType::Pointer spatialObjectMask=NULL;
+ if (m_ArgsInfo.mask_given)
+ {
+ typedef itk::Image< unsigned char, Dimension > ImageMaskType;
+ typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
+ MaskReaderType::Pointer maskReader = MaskReaderType::New();
+ maskReader->SetFileName(m_ArgsInfo.mask_arg);
+
+ try
+ {
+ maskReader->Update();
+ }
+ catch( itk::ExceptionObject & err )
+ {
+ std::cerr << "ExceptionObject caught while reading mask !" << std::endl;
+ std::cerr << err << std::endl;
+ return;
+ }
+ if (m_Verbose)std::cout <<"Mask was read..." <<std::endl;
+
+ // Set the image to the spatialObject
+ spatialObjectMask = MaskType::New();
+ spatialObjectMask->SetImage( maskReader->GetOutput() );
+ }
+
+
+ // Samplingfactors
+ InputImageType::SizeType samplingFactors;
+ for (unsigned int i=0; i< Dimension; i++)
+ {
+ samplingFactors[i]= (int) ( input->GetSpacing()[i]/ filter->GetOutputSpacing()[i]);
+ if (m_Verbose) std::cout<<"Setting sampling factor "<<i<<" to "<<samplingFactors[i]<<"..."<<std::endl;
+ }
+
+
+ // Set
+ transform->SetSplineOrders(splineOrders);
+ transform->SetMask(spatialObjectMask);
+ transform->SetLUTSamplingFactors(samplingFactors);
+ transform->SetCoefficientImage(input);
+ filter->SetTransform(transform);
+
+
+ // -----------------------------------------------
+ // Update
+ // -----------------------------------------------
+ if (m_Verbose)std::cout<< "Converting the BSpline transform..."<<std::endl;
+ try
+ {
+ filter->Update();
+ }
+ catch (itk::ExceptionObject)
+ {
+ std::cerr<<"Error: Exception thrown during execution convertion filter!"<<std::endl;
+ }
+
+ OutputImageType::Pointer output=filter->GetOutput();
+
+
+ // -----------------------------------------------
+ // Output
+ // -----------------------------------------------
+ typedef itk::ImageFileWriter<OutputImageType> WriterType;
+ WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(m_ArgsInfo.output_arg);
+ writer->SetInput(output);
+ writer->Update();
+
+ }
+
+
+ //-------------------------------------------------------------------
+ // Update with the number of dimensions
+ //-------------------------------------------------------------------
+ template<>
+ void
+ ConvertBSplineDeformableTransformToVFGenericFilter::UpdateWithDim<4>(std::string PixelType, int Components)
+ {
+ // Components
+ if (Components !=3)
+ {
+ std::cerr<<"Number of components is "<<Components<<"! Only 3 components is supported."<<std::endl;
+ return;
+ }
+ if (PixelType != "double")
+ {
+ std::cerr<<"PixelType is "<<PixelType<<"! Only double coefficient images are supported."<<std::endl;
+ std::cerr<<"Reading image as double..."<<std::endl;
+ }
+
+ // ImageTypes
+ const unsigned int Dimension=4;
+ const unsigned int SpaceDimension=3;
+ typedef itk::Vector<double, SpaceDimension> InputPixelType;
+ typedef itk::Vector<float, SpaceDimension> OutputPixelType;
+ typedef itk::Image<InputPixelType, Dimension> InputImageType;
+ typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
+
+ // Read the input
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ InputReaderType::Pointer reader = InputReaderType::New();
+ reader->SetFileName( m_InputFileName);
+ reader->Update();
+ InputImageType::Pointer input= reader->GetOutput();
+
+
+ // -----------------------------------------------
+ // Filter
+ // -----------------------------------------------
+ typedef clitk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
+ ConvertorType::Pointer filter= ConvertorType::New();
+
+ //Output image info
+ if (m_ArgsInfo.like_given)
+ {
+ typedef itk::ImageFileReader<OutputImageType> ReaderType;
+ ReaderType::Pointer reader2=ReaderType::New();
+ reader2->SetFileName(m_ArgsInfo.like_arg);
+ reader2->Update();
+
+ OutputImageType::Pointer image=reader2->GetOutput();
+ filter->SetOutputParametersFromImage(image);
+ }
+ else
+ {
+ unsigned int i=0;
+ if(m_ArgsInfo.origin_given)
+ {
+ OutputImageType::PointType origin;
+ for(i=0;i<Dimension;i++)
+ origin[i]=m_ArgsInfo.origin_arg[i];
+ filter->SetOutputOrigin(origin);
+ }
+ if (m_ArgsInfo.spacing_given)
+ {
+ OutputImageType::SpacingType spacing;
+ for(i=0;i<Dimension;i++)
+ spacing[i]=m_ArgsInfo.spacing_arg[i];
+ filter->SetOutputSpacing(spacing);
+ }
+ if (m_ArgsInfo.spacing_given)
+ {
+ OutputImageType::SizeType size;
+ for(i=0;i<Dimension;i++)
+ size[i]=m_ArgsInfo.size_arg[i];
+ filter->SetOutputSize(size);
+ }
+ }
+ //Output image info
+ if (m_Verbose)
+ {
+ std::cout<< "Setting output origin to "<<filter->GetOutputOrigin()<<"..."<<std::endl;
+ std::cout<< "Setting output spacing to "<<filter->GetOutputSpacing()<<"..."<<std::endl;
+ std::cout<< "Setting output size to "<<filter->GetOutputSize()<<"..."<<std::endl;
+ }
+
+
+ // -----------------------------------------------
+ // Transform
+ // -----------------------------------------------
+ typedef clitk::ShapedBLUTSpatioTemporalDeformableTransform< double, Dimension, Dimension > TransformType;
+ TransformType::Pointer transform=TransformType::New();
+ transform->SetTransformShape(m_ArgsInfo.shape_arg);
+
+ // Spline orders: Default is cubic splines
+ InputImageType::RegionType::SizeType splineOrders ;
+ splineOrders.Fill(3);
+ if (m_ArgsInfo.order_given)
+ for(unsigned int i=0; i<Dimension;i++)
+ splineOrders[i]=m_ArgsInfo.order_arg[i];
+ if (m_Verbose) std::cout<<"Setting the spline orders to "<<splineOrders<<"..."<<std::endl;
+
+ // Mask
+ typedef itk::ImageMaskSpatialObject< Dimension > MaskType;
+ MaskType::Pointer spatialObjectMask=NULL;
+ if (m_ArgsInfo.mask_given)
+ {
+ typedef itk::Image< unsigned char, Dimension > ImageMaskType;
+ typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
+ MaskReaderType::Pointer maskReader = MaskReaderType::New();
+ maskReader->SetFileName(m_ArgsInfo.mask_arg);
+
+ try
+ {
+ maskReader->Update();
+ }
+ catch( itk::ExceptionObject & err )
+ {
+ std::cerr << "ExceptionObject caught while reading mask !" << std::endl;
+ std::cerr << err << std::endl;
+ return;
+ }
+ if (m_Verbose)std::cout <<"Mask was read..." <<std::endl;
+
+ // Set the image to the spatialObject
+ spatialObjectMask = MaskType::New();
+ spatialObjectMask->SetImage( maskReader->GetOutput() );
+ }
+
+
+ // Samplingfactors
+ InputImageType::SizeType samplingFactors;
+ for (unsigned int i=0; i< Dimension; i++)
+ {
+ samplingFactors[i]= (int) ( input->GetSpacing()[i]/ filter->GetOutputSpacing()[i]);
+ if (m_Verbose) std::cout<<"Setting sampling factor "<<i<<" to "<<samplingFactors[i]<<"..."<<std::endl;
+ }
+ if( !(m_ArgsInfo.shape_arg%2) )samplingFactors[Dimension-1]=5;
+
+ // Set
+ transform->SetSplineOrders(splineOrders);
+ transform->SetMask(spatialObjectMask);
+ transform->SetLUTSamplingFactors(samplingFactors);
+ transform->SetCoefficientImage(input);
+ filter->SetTransform(transform);
+
+
+ // -----------------------------------------------
+ // Update
+ // -----------------------------------------------
+ if (m_Verbose)std::cout<< "Converting the BSpline transform..."<<std::endl;
+ try
+ {
+ filter->Update();
+ }
+ catch (itk::ExceptionObject)
+ {
+ std::cerr<<"Error: Exception thrown during execution convertion filter!"<<std::endl;
+ }
+
+ OutputImageType::Pointer output=filter->GetOutput();
+
+
+ // -----------------------------------------------
+ // Output
+ // -----------------------------------------------
+ typedef itk::ImageFileWriter<OutputImageType> WriterType;
+ WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(m_ArgsInfo.output_arg);
+ writer->SetInput(output);
+ writer->Update();
+
+ }
+
+
+
+ //-----------------------------------------------------------
+ // Update
+ //-----------------------------------------------------------
+ void ConvertBSplineDeformableTransformToVFGenericFilter::Update()
+ {
+
+ // Read the Dimension and PixelType
+ int Dimension, Components;
+ std::string PixelType;
+ ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
+
+ // Call UpdateWithDim
+ //if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
+ if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
+ else if (Dimension==4) UpdateWithDim<4>(PixelType, Components);
+ else
+ {
+ std::cout<<"Error, Only for 3 Dimensions!!!"<<std::endl ;
+ return;
+ }
+ }
+
+} //end clitk
+
+#endif //#define clitkConvertBSplineDeformableTransformToVFGenericFilter_cxx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff