X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=registration%2FclitkConvertBSplineDeformableTransformToVFGenericFilter.cxx;fp=registration%2FclitkConvertBSplineDeformableTransformToVFGenericFilter.cxx;h=0d3929a097a61a3669a126366ea32c5604bc574a;hb=657652a78c2e2717a6f77e027049173442ca29f0;hp=0000000000000000000000000000000000000000;hpb=8abe9edbdc63a33f8fbb1f321073b762e08be9aa;p=clitk.git

diff --git a/registration/clitkConvertBSplineDeformableTransformToVFGenericFilter.cxx b/registration/clitkConvertBSplineDeformableTransformToVFGenericFilter.cxx
new file mode 100755
index 0000000..0d3929a
--- /dev/null
+++ b/registration/clitkConvertBSplineDeformableTransformToVFGenericFilter.cxx
@@ -0,0 +1,417 @@
+/*=========================================================================
+  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