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Merge pull request #135 from aghayoor/bfitSlicer
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ENH: Use BSplineTransformInitializer for BSpline Registration
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@aghayoor
aghayoor committed Aug 19, 2014
2 parents a28e356 + 577b2b7 commit d457e04
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Showing 3 changed files with 71 additions and 76 deletions.
1 change: 1 addition & 0 deletions BRAINSCommonLib/BRAINSFitHelperTemplate.h
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Expand Up @@ -52,6 +52,7 @@

#include "itkBSplineTransform.h"
#include "itkBSplineTransformParametersAdaptor.h"
#include "itkBSplineTransformInitializer.h"

#ifdef USE_ANTS
#include "BRAINSFitSyN.h"
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141 changes: 65 additions & 76 deletions BRAINSCommonLib/BRAINSFitHelperTemplate.hxx
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Expand Up @@ -1179,11 +1179,6 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
typedef itk::ImageRegistrationMethodv4<FixedImageType, MovingImageType> BSplineRegistrationType;
typename BSplineRegistrationType::Pointer bsplineRegistration = BSplineRegistrationType::New();

typename BSplineTransformType::Pointer initialBSplineTransform = BSplineTransformType::New();
// Initialize the BSpline transform
BSplineTransformType::PhysicalDimensionsType fixedPhysicalDimensions;
BSplineTransformType::MeshSizeType meshSize;
BSplineTransformType::OriginType fixedOrigin;

typename FixedImageType::Pointer initializationImage = FixedImageType::New();
if ( m_UseROIBSpline )
Expand Down Expand Up @@ -1259,30 +1254,37 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
initializationImage = this->m_FixedVolume;
}

typename BSplineTransformType::Pointer bsplineTx =
BSplineTransformType::New();
// Initialize the BSpline transform
// Using BSplineTransformInitializer
//
BSplineTransformType::MeshSizeType meshSize;
for( unsigned int i=0; i< SpaceDimension; i++ )
{
fixedOrigin[i] = initializationImage->GetOrigin()[i];
fixedPhysicalDimensions[i] = initializationImage->GetSpacing()[i]
* static_cast<double>( initializationImage->GetLargestPossibleRegion().GetSize()[i] - 1 );
meshSize[i] = m_SplineGridSize[i];
}

initialBSplineTransform->SetTransformDomainOrigin( fixedOrigin );
initialBSplineTransform->SetTransformDomainPhysicalDimensions( fixedPhysicalDimensions );
initialBSplineTransform->SetTransformDomainMeshSize( meshSize );
initialBSplineTransform->SetTransformDomainDirection( initializationImage->GetDirection() );
typedef itk::BSplineTransformInitializer< BSplineTransformType,
FixedImageType> InitializerType;
typename InitializerType::Pointer transformInitializer = InitializerType::New();

transformInitializer->SetTransform( bsplineTx );
transformInitializer->SetImage( initializationImage );
transformInitializer->SetTransformDomainMeshSize( meshSize );
transformInitializer->InitializeTransform();

typedef BSplineTransformType::ParametersType ParametersType;
const unsigned int numberOfParameters = initialBSplineTransform->GetNumberOfParameters();
ParametersType parameters( numberOfParameters );
parameters.Fill( 0.0 );
bsplineTx->SetIdentity();

initialBSplineTransform->SetParameters( parameters );
// std::cout << "Intial Parameters = " << std::endl
// << initialBSplineTransform->GetParameters() << std::endl;
std::cout << "Initialized BSpline transform is set to identity." << std::endl;
std::cout << " - Number of parameters = "
<< bsplineTx->GetNumberOfParameters() << std::endl << std::endl;
//std::cout << "Intial Parameters = " << std::endl
// << bsplineTx->GetParameters() << std::endl;

bsplineRegistration->SetInitialTransform( initialBSplineTransform );
bsplineRegistration->InPlaceOn();
bsplineRegistration->SetInitialTransform( bsplineTx );
bsplineRegistration->InPlaceOn(); // So bsplineTx is also the output transform
// of the registration filter.

// TODO: Expose these to the command line for consistancy.
const int m_MaximumNumberOfIterations = 1500;
Expand All @@ -1296,30 +1298,23 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)

LBFGSBOptimizerTypePointer LBFGSBoptimizer = LBFGSBOptimizerType::New();

/**
*
* Set the boundary condition for each variable, where
* select[i] = 0 if x[i] is unbounded,
* = 1 if x[i] has only a lower bound,
* = 2 if x[i] has both lower and upper bounds, and
* = 3 if x[1] has only an upper bound
*/
// TODO: For control points outside the fixed image mask, it might be good to
// constrian
// the parameters to something different than those control points inside the
// fixed image mask.
OptimizerBoundSelectionType boundSelect( initialBSplineTransform->GetNumberOfParameters() );
// TODO: For control points outside the fixed image mask, it might be good to
// constrian
// the parameters to something different than those control points inside the
// fixed image mask.

OptimizerBoundSelectionType boundSelect( bsplineTx->GetNumberOfParameters() );
if( vcl_abs(m_MaxBSplineDisplacement) < 1e-12 )
{
boundSelect.Fill(0);
boundSelect.Fill( LBFGSBOptimizerType::UNBOUNDED );
}
else
{
boundSelect.Fill(2);
boundSelect.Fill( LBFGSBOptimizerType::BOTHBOUNDED );
}
OptimizerBoundValueType upperBound( initialBSplineTransform->GetNumberOfParameters() );
OptimizerBoundValueType upperBound( bsplineTx->GetNumberOfParameters() );
upperBound.Fill(m_MaxBSplineDisplacement);
OptimizerBoundValueType lowerBound( initialBSplineTransform->GetNumberOfParameters() );
OptimizerBoundValueType lowerBound( bsplineTx->GetNumberOfParameters() );
lowerBound.Fill(-m_MaxBSplineDisplacement);

LBFGSBoptimizer->SetBoundSelection(boundSelect);
Expand All @@ -1343,19 +1338,21 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
{
if( this->m_CurrentGenericTransform.IsNotNull() )
{
std::cout << "Moving image is warped by initial transform, before it is passed to the BSpline registration." << std::endl;
std::cout << "\nMoving image is warped by initial transform, "
<< "before it is passed to the BSpline registration.\n" << std::endl;
typedef float VectorComponentType;
typedef itk::Vector<VectorComponentType, GenericTransformImageNS::SpaceDimension> VectorPixelType;
typedef itk::Image<VectorPixelType, GenericTransformImageNS::SpaceDimension> DisplacementFieldType;
typename MovingImageType::Pointer warpedMoving = GenericTransformImage<
MovingImageType,
MovingImageType,
DisplacementFieldType>( this->m_MovingVolume,
this->m_FixedVolume,
this->m_CurrentGenericTransform.GetPointer(),
m_BackgroundFillValue,
"Linear",
false );
typename MovingImageType::Pointer warpedMoving =
GenericTransformImage<
MovingImageType,
MovingImageType,
DisplacementFieldType>( this->m_MovingVolume,
this->m_FixedVolume,
this->m_CurrentGenericTransform.GetPointer(),
m_BackgroundFillValue,
"Linear",
false );

bsplineRegistration->SetMovingImage( 0, warpedMoving );

Expand All @@ -1365,16 +1362,17 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
dynamic_cast<MovingImageMaskType const *>( this->m_CostMetricObject->GetMovingImageMask() );
if( movingMask.IsNotNull() )
{
typename MaskImageType::Pointer warpedMovingMaskImage = GenericTransformImage<
MaskImageType,
MaskImageType,
DisplacementFieldType>(
ExtractConstPointerToImageMaskFromImageSpatialObject(movingMask).GetPointer(),
this->m_FixedVolume,
this->m_CurrentGenericTransform.GetPointer(),
m_BackgroundFillValue,
"Linear",
false );
typename MaskImageType::Pointer warpedMovingMaskImage =
GenericTransformImage<
MaskImageType,
MaskImageType,
DisplacementFieldType>(
ExtractConstPointerToImageMaskFromImageSpatialObject(movingMask).GetPointer(),
this->m_FixedVolume,
this->m_CurrentGenericTransform.GetPointer(),
m_BackgroundFillValue,
"Linear",
false );


typename MovingImageMaskType::ConstPointer warpedMask = ConvertMaskImageToSpatialMask( warpedMovingMaskImage.GetPointer() );
Expand Down Expand Up @@ -1438,42 +1436,33 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
bsplineRegistration->SetShrinkFactorsPerLevel( shrinkFactorsPerLevel );
bsplineRegistration->SetSmoothingSigmasAreSpecifiedInPhysicalUnits( true );
bsplineRegistration->SetMetricSamplingStrategy(
static_cast<typename BSplineRegistrationType::MetricSamplingStrategyType>( m_SamplingStrategy ) );
static_cast<typename BSplineRegistrationType::MetricSamplingStrategyType>( m_SamplingStrategy ) );
bsplineRegistration->SetMetricSamplingPercentage( m_SamplingPercentage );
bsplineRegistration->SetMetric( this->m_CostMetricObject );
bsplineRegistration->SetOptimizer( LBFGSBoptimizer );

try
{
std::cout << "*** Running bspline registration (meshSizeAtBaseLevel = " << meshSize << ") ***"
<< std::endl << std::endl;
<< std::endl << std::endl;
bsplineRegistration->Update();

std::cout << "Stop condition from LBFGSBoptimizer."
<< bsplineRegistration->GetOptimizer()->GetStopConditionDescription() << std::endl;
}
catch( itk::ExceptionObject & e )
{
itkGenericExceptionMacro( << "Exception caught: " << e << std::endl );
}

typename BSplineTransformType::Pointer outputBSplineTransform = BSplineTransformType::New();
outputBSplineTransform->SetFixedParameters( bsplineRegistration->GetOutput()->Get()->GetFixedParameters() );
outputBSplineTransform->SetParameters( bsplineRegistration->GetOutput()->Get()->GetParameters() );

if( outputBSplineTransform.IsNotNull() )
{
this->m_CurrentGenericTransform->AddTransform( outputBSplineTransform );
}
else
{
itkGenericExceptionMacro( << "******* Error: the BSpline output transform is null." << std::endl );
}
const LBFGSBOptimizerType::ConstPointer outputOptimizer =
dynamic_cast<const LBFGSBOptimizerType *>( bsplineRegistration->GetOptimizer() );
std::cout << "Stop condition from LBFGSBoptimizer." << outputOptimizer->GetStopConditionDescription() << std::endl;
// Add the optimized bspline tranform to the current generic transform
//
this->m_CurrentGenericTransform->AddTransform( bsplineTx );

if( this->m_DebugLevel > 4 )
{
std::cout << "Final Parameters = " << std::endl;
std::cout << outputBSplineTransform->GetParameters() << std::endl;
std::cout << bsplineTx->GetParameters() << std::endl;
}
}
else if( currentTransformType == "SyN" )
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5 changes: 5 additions & 0 deletions BRAINSCommonLib/genericRegistrationHelper.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -398,6 +398,11 @@ MultiModal3DMutualRegistrationHelper<TTransformType, TOptimizer, TFixedImage,
throw err;
}

std::cout << "METRIC THREADS USED: " << this->m_CostMetricObject->GetNumberOfThreadsUsed()
<< " of " << itk::MultiThreader::GetGlobalDefaultNumberOfThreads() << std::endl;
std::cout << "REGISTRATION THREADS USED: " << this->m_Registration->GetNumberOfThreads()
<< " of " << itk::MultiThreader::GetGlobalDefaultNumberOfThreads() << std::endl;

OptimizerPointer optimizer =
dynamic_cast<OptimizerPointer>( m_Registration->GetOptimizer() );
if( optimizer == NULL )
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