From 0ebe428ddf5c84373c3eb814e9465f048b1e7d48 Mon Sep 17 00:00:00 2001 From: Romulo Pinho Date: Wed, 18 Jan 2012 18:28:16 +0100 Subject: [PATCH] Invert VF from B-Spline coefficients - Interpolate VF first, from coeffs, using --like image --- tools/clitkInvertVF.ggo | 2 +- tools/clitkInvertVFGenericFilter.h | 1 + tools/clitkInvertVFGenericFilter.txx | 91 ++++++++++++++++++++++++++++ 3 files changed, 93 insertions(+), 1 deletion(-) diff --git a/tools/clitkInvertVF.ggo b/tools/clitkInvertVF.ggo index 19c451a..92970bb 100644 --- a/tools/clitkInvertVF.ggo +++ b/tools/clitkInvertVF.ggo @@ -11,7 +11,7 @@ option "threads" - "Number of threads (default=min(8, #CPU))" in option "input" i "Input VF filename" string yes option "output" o "Output VF filename" string yes -option "type" t "Type of filter: 0=clitk (fast forward splat using linear kernels), 1= itk (grid subsumpling with controllable precision)" int no default="0" +option "type" t "Type of filter: 0=clitk (fast forward splat using linear kernels), 1=clitk (like 0, but input images are B-Spline coefficients), 2= itk (grid subsumpling with controllable precision)" int no default="0" option "threadSafe" - "Clitk: use thread safe algorithm" flag off option "pad" p "Clitk: edge padding value (1 or N number of values!, defautls to zeros)" double multiple no option "sampling" s "Itk: subsampling factor" int no default="20" diff --git a/tools/clitkInvertVFGenericFilter.h b/tools/clitkInvertVFGenericFilter.h index 012524c..cdaf86f 100644 --- a/tools/clitkInvertVFGenericFilter.h +++ b/tools/clitkInvertVFGenericFilter.h @@ -99,6 +99,7 @@ namespace clitk //---------------------------------------- template void UpdateWithDim(std::string PixelType); template void UpdateWithDimAndPixelType(); + template typename DisplacementFieldType::Pointer CoeffsToDVF(std::string fileName, std::string likeFileName); //---------------------------------------- diff --git a/tools/clitkInvertVFGenericFilter.txx b/tools/clitkInvertVFGenericFilter.txx index 558b341..5cd12c4 100644 --- a/tools/clitkInvertVFGenericFilter.txx +++ b/tools/clitkInvertVFGenericFilter.txx @@ -19,6 +19,12 @@ #define clitkInvertVFGenericFilter_txx #include "itkVectorResampleImageFilter.h" +#include "clitkBSplineDeformableTransform.h" +#if ITK_VERSION_MAJOR >= 4 +#include "itkTransformToDisplacementFieldSource.h" +#else +#include "itkTransformToDeformationFieldSource.h" +#endif /* ================================================= * @file clitkInvertVFGenericFilter.txx @@ -100,6 +106,65 @@ InvertVFGenericFilter::UpdateWithDim(std::string PixelType) // } } +//------------------------------------------------------------------- +// Convert Coefficient image to DVF +//------------------------------------------------------------------- +template +template +typename DisplacementFieldType::Pointer +InvertVFGenericFilter::CoeffsToDVF(std::string fileName, std::string likeFileName) +{ + typedef clitk::BSplineDeformableTransform TransformType; + typedef typename TransformType::CoefficientImageType CoefficientImageType; + + typedef itk::ImageFileReader CoeffReaderType; + typename CoeffReaderType::Pointer reader = CoeffReaderType::New(); + reader->SetFileName(fileName); + reader->Update(); + + typename TransformType::Pointer transform = TransformType::New(); + transform->SetCoefficientImage(reader->GetOutput()); + +#if ITK_VERSION_MAJOR >= 4 + typedef itk::TransformToDisplacementFieldSource ConvertorType; +#else + typedef itk::TransformToDeformationFieldSource ConvertorType; +#endif + + typedef itk::ImageIOBase ImageIOType; + typename ImageIOType::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(likeFileName.c_str(), itk::ImageIOFactory::ReadMode); + imageIO->SetFileName(likeFileName); + imageIO->ReadImageInformation(); + + typename ConvertorType::Pointer convertor= ConvertorType::New(); + typename ConvertorType::SizeType output_size; + typename ConvertorType::SpacingType output_spacing; + typename ConvertorType::OriginType output_origin; + typename ConvertorType::DirectionType output_direction; + for (unsigned int i = 0; i < DisplacementFieldType::ImageDimension; i++) { + output_size[i] = imageIO->GetDimensions(i); + output_spacing[i] = imageIO->GetSpacing(i); + output_origin[i] = imageIO->GetOrigin(i); + for (unsigned int j = 0; j < DisplacementFieldType::ImageDimension; j++) + output_direction[i][j] = imageIO->GetDirection(i)[j]; + } + + if (m_Verbose) { + std::cout << "Interpolating coefficients with grid:" << std::endl; + std::cout << output_size << output_spacing << std::endl; + } + + convertor->SetNumberOfThreads(1); + convertor->SetTransform(transform); + convertor->SetOutputOrigin(output_origin); + convertor->SetOutputSpacing(output_spacing); + convertor->SetOutputSize(output_size); + convertor->SetOutputDirection(output_direction); + convertor->Update(); + + return convertor->GetOutput(); +} + //------------------------------------------------------------------- // Update with the number of dimensions and the pixeltype @@ -172,6 +237,31 @@ InvertVFGenericFilter::UpdateWithDimAndPixelType() } case 1: { + // Create the InvertVFFilter + typedef clitk::InvertVFFilter FilterType; + typename FilterType::Pointer filter =FilterType::New(); + if (m_ArgsInfo.like_given) { + filter->SetInput(CoeffsToDVF(m_InputFileName, m_ArgsInfo.like_arg)); + } + + filter->SetVerbose(m_Verbose); + if (m_ArgsInfo.threads_given) filter->SetNumberOfThreads(m_ArgsInfo.threads_arg); + if (m_ArgsInfo.pad_given) { + PixelType pad; + if (m_ArgsInfo.pad_given != (pad.GetNumberOfComponents()) ) + pad.Fill(m_ArgsInfo.pad_arg[0]); + else + for(unsigned int i=0; iSetThreadSafe(m_ArgsInfo.threadSafe_flag); + filter->Update(); + output=filter->GetOutput(); + + break; + } + + case 2: { // Create the InverseDeformationFieldFilter #if ITK_VERSION_MAJOR >= 4 typedef itk::InverseDisplacementFieldImageFilter FilterType; @@ -190,6 +280,7 @@ InvertVFGenericFilter::UpdateWithDimAndPixelType() break; } + } // Output -- 2.45.1