-
Notifications
You must be signed in to change notification settings - Fork 9
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #171 from ANTsX/HessianObjectness
WIP: Add hessian objectness interface to itk filter.
- Loading branch information
Showing
3 changed files
with
183 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,157 @@ | ||
| #include <exception> | ||
| #include <vector> | ||
| #include <string> | ||
| #include <algorithm> | ||
| #include <ants.h> | ||
| #include "antsUtilities.h" | ||
| #include "ReadWriteData.h" | ||
|
|
||
| #include "itkHessianToObjectnessMeasureImageFilter.h" | ||
| #include "itkMultiScaleHessianBasedMeasureImageFilter.h" | ||
| #include "itkSymmetricSecondRankTensor.h" | ||
| #include "itkNumericTraits.h" | ||
|
|
||
| #include "RcppANTsR.h" | ||
|
|
||
|
|
||
| template<class PrecisionType, unsigned int Dimension> | ||
| SEXP HessianObjectnessHelper( | ||
| SEXP r_inputImage, | ||
| SEXP r_outputImage, | ||
| unsigned int objectDimension, | ||
| bool isBrightObject, | ||
| float sigmaMin, | ||
| float sigmaMax, | ||
| unsigned int numberOfSigmaSteps, | ||
| bool useSigmaLogarithmicSpacing, | ||
| float alpha, | ||
| float beta, | ||
| float gamma, | ||
| bool setScaleObjectnessMeasure ) | ||
| { | ||
|
|
||
| using ImageType = itk::Image<PrecisionType, Dimension>; | ||
| using ImagePointerType = typename ImageType::Pointer; | ||
|
|
||
| typename ImageType::Pointer inputImage = Rcpp::as< ImagePointerType >( r_inputImage ); | ||
| typename ImageType::Pointer outputImage = Rcpp::as< ImagePointerType >( r_outputImage ); | ||
|
|
||
| using PixelType = typename ImageType::PixelType; | ||
| const unsigned int ImageDimension = ImageType::ImageDimension; | ||
| using RealPixelType = typename itk::NumericTraits<PixelType>::RealType; | ||
|
|
||
| using HessianPixelType = itk::SymmetricSecondRankTensor<RealPixelType, ImageDimension>; | ||
| using HessianImageType = itk::Image<HessianPixelType, ImageDimension>; | ||
| using ObjectnessFilterType = itk::HessianToObjectnessMeasureImageFilter<HessianImageType, ImageType>; | ||
| using MultiScaleEnhancementFilterType = itk::MultiScaleHessianBasedMeasureImageFilter<ImageType, HessianImageType, ImageType>; | ||
|
|
||
| typename ObjectnessFilterType::Pointer objectnessFilter = ObjectnessFilterType::New(); | ||
| objectnessFilter->SetScaleObjectnessMeasure( setScaleObjectnessMeasure ); | ||
| objectnessFilter->SetBrightObject( isBrightObject ); | ||
| objectnessFilter->SetAlpha( alpha ); | ||
| objectnessFilter->SetBeta( beta ); | ||
| objectnessFilter->SetGamma( gamma ); | ||
| objectnessFilter->SetObjectDimension( objectDimension ); | ||
|
|
||
| typename MultiScaleEnhancementFilterType::Pointer multiScaleEnhancementFilter = MultiScaleEnhancementFilterType::New(); | ||
| multiScaleEnhancementFilter->SetInput( inputImage ); | ||
| if( useSigmaLogarithmicSpacing ) | ||
| { | ||
| multiScaleEnhancementFilter->SetSigmaStepMethodToLogarithmic(); | ||
| } | ||
| else | ||
| { | ||
| multiScaleEnhancementFilter->SetSigmaStepMethodToEquispaced(); | ||
| } | ||
| multiScaleEnhancementFilter->SetSigmaMinimum( sigmaMin ); | ||
| multiScaleEnhancementFilter->SetSigmaMaximum( sigmaMax ); | ||
| multiScaleEnhancementFilter->SetNumberOfSigmaSteps( numberOfSigmaSteps ); | ||
| multiScaleEnhancementFilter->SetHessianToMeasureFilter( objectnessFilter ); | ||
| multiScaleEnhancementFilter->Update(); | ||
|
|
||
| outputImage = multiScaleEnhancementFilter->GetOutput(); | ||
| outputImage->Update(); | ||
| outputImage->DisconnectPipeline(); | ||
|
|
||
| r_outputImage = Rcpp::wrap( outputImage ); | ||
| return( r_outputImage ); | ||
| } | ||
|
|
||
| // [[Rcpp::export]] | ||
| SEXP hessianObjectnessR( | ||
| SEXP r_inputImage, | ||
| SEXP r_objectDimension, | ||
| SEXP r_isBrightObject, | ||
| SEXP r_sigmaMin, | ||
| SEXP r_sigmaMax, | ||
| SEXP r_numberOfSigmaSteps, | ||
| SEXP r_useSigmaLogarithmicSpacing, | ||
| SEXP r_alpha, | ||
| SEXP r_beta, | ||
| SEXP r_gamma, | ||
| SEXP r_setScaleObjectnessMeasure ) | ||
| { | ||
| try | ||
| { | ||
| Rcpp::S4 inputImage( r_inputImage ); | ||
| Rcpp::S4 s4_outputImage( r_inputImage ); | ||
| SEXP outputImage; | ||
|
|
||
| unsigned int imageDimension = Rcpp::as<int>( inputImage.slot( "dimension" ) ); | ||
| std::string pixelType = Rcpp::as<std::string>( inputImage.slot( "pixeltype" ) ); | ||
|
|
||
| unsigned int objectDimension = Rcpp::as<int>( r_objectDimension ); | ||
| bool isBrightObject = Rcpp::as<bool>( r_isBrightObject ); | ||
| float sigmaMin = Rcpp::as<float>( r_sigmaMin ); | ||
| float sigmaMax = Rcpp::as<float>( r_sigmaMax ); | ||
| unsigned int numberOfSigmaSteps = Rcpp::as<int>( r_numberOfSigmaSteps ); | ||
| bool useSigmaLogarithmicSpacing = Rcpp::as<bool>( r_useSigmaLogarithmicSpacing ); | ||
| float alpha = Rcpp::as<float>( r_alpha ); | ||
| float beta = Rcpp::as<float>( r_beta ); | ||
| float gamma = Rcpp::as<float>( r_gamma ); | ||
| bool setScaleObjectnessMeasure = Rcpp::as<bool>( r_setScaleObjectnessMeasure ); | ||
|
|
||
| if( pixelType.compare( "float" ) == 0 && imageDimension == 2 ) | ||
| { | ||
| typedef float PrecisionType; | ||
| const unsigned int ImageDimension = 2; | ||
|
|
||
| outputImage = HessianObjectnessHelper<PrecisionType, ImageDimension>( | ||
| inputImage, s4_outputImage, objectDimension, isBrightObject, sigmaMin, | ||
| sigmaMax, numberOfSigmaSteps, useSigmaLogarithmicSpacing, alpha, | ||
| beta, gamma, setScaleObjectnessMeasure ); | ||
| return( outputImage ); | ||
| } | ||
| else if( pixelType.compare( "float" ) == 0 && imageDimension == 3 ) | ||
| { | ||
| typedef float PrecisionType; | ||
| const unsigned int ImageDimension = 3; | ||
|
|
||
| outputImage = HessianObjectnessHelper<PrecisionType, ImageDimension>( | ||
| inputImage, s4_outputImage, objectDimension, isBrightObject, sigmaMin, | ||
| sigmaMax, numberOfSigmaSteps, useSigmaLogarithmicSpacing, alpha, | ||
| beta, gamma, setScaleObjectnessMeasure ); | ||
| } | ||
| else | ||
| { | ||
| Rcpp::stop( "Unsupported image dimension or pixeltype." ); | ||
| } | ||
| } | ||
|
|
||
| catch( itk::ExceptionObject & err ) | ||
| { | ||
| Rcpp::Rcout << "ITK ExceptionObject caught!" << std::endl; | ||
| forward_exception_to_r( err ); | ||
| } | ||
| catch( const std::exception& exc ) | ||
| { | ||
| Rcpp::Rcout << "STD ExceptionObject caught!" << std::endl; | ||
| forward_exception_to_r( exc ); | ||
| } | ||
| catch( ... ) | ||
| { | ||
| Rcpp::stop( "C++ exception (unknown reason)" ); | ||
| } | ||
|
|
||
| return Rcpp::wrap( NA_REAL ); // should not be reached | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters