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Merge topic 'AddVirtualImageDomain'
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6cd05a7 Fix another signed to unsigned comparison warning
26b9b88 address signed to unsigned integer comparison warning
60f8efc Adding check for virtual domain parameters
cdfbaf0 Adding registration test with multi-levels and virtual image
e5e4b3b Remove extraneous print statements.
821f089 Merge branch 'UpdateITKTo4.11-master' into AddVirtualImageDomain
60f345e ENH: adding methods and tests for Virtual image
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@blowekamp @kwrobot
blowekamp authored and kwrobot committed Dec 12, 2016
2 parents 55136ea + 6cd05a7 commit 0b49b1b
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Showing 3 changed files with 250 additions and 2 deletions.
17 changes: 17 additions & 0 deletions Code/Registration/include/sitkImageRegistrationMethod.h
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Original file line number Diff line number Diff line change
Expand Up @@ -177,6 +177,18 @@ namespace simple
{ return this->m_FixedInitialTransform; }
/**@}*/


/** \brief Set the virtual domain used for sampling
*
* @{
*/
SITK_RETURN_SELF_TYPE_HEADER SetVirtualDomain( const std::vector<uint32_t> &virtualSize,
const std::vector<double> &virtualOrigin,
const std::vector<double> &virtualSpacing,
const std::vector<double> &virtualDirection );
SITK_RETURN_SELF_TYPE_HEADER SetVirtualDomainFromImage( const Image &virtualImage );
/**@}*/

/** \brief Use normalized cross correlation using a small
* neighborhood for each voxel between two images, with speed
* optimizations for dense registration.
Expand Down Expand Up @@ -601,6 +613,11 @@ namespace simple
Transform m_MovingInitialTransform;
Transform m_FixedInitialTransform;

std::vector<uint32_t> m_VirtualDomainSize;
std::vector<double> m_VirtualDomainOrigin;
std::vector<double> m_VirtualDomainSpacing;
std::vector<double> m_VirtualDomainDirection;

// optimizer
enum OptimizerType { ConjugateGradientLineSearch,
RegularStepGradientDescent,
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52 changes: 52 additions & 0 deletions Code/Registration/src/sitkImageRegistrationMethod.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,47 @@ ImageRegistrationMethod::SetInitialTransform ( Transform &transform, bool inPlac
return *this;
}

ImageRegistrationMethod::Self&
ImageRegistrationMethod::SetVirtualDomain( const std::vector<uint32_t> &virtualSize,
const std::vector<double> &virtualOrigin,
const std::vector<double> &virtualSpacing,
const std::vector<double> &virtualDirection )
{
const size_t dim = virtualSize.size();

if ( virtualOrigin.size() != dim )
{
sitkExceptionMacro("Expected virtualOrigin to be of length " << dim << "!" );
}

if ( virtualSpacing.size() != dim )
{
sitkExceptionMacro("Expected virtualSpacing to be of length " << dim << "!" );
}

if ( virtualDirection.size() != dim*dim )
{
sitkExceptionMacro("Expected virtualDirection to be of length " << dim*dim << "!" );
}

this->m_VirtualDomainSize = virtualSize;
this->m_VirtualDomainOrigin = virtualOrigin;
this->m_VirtualDomainSpacing = virtualSpacing;
this->m_VirtualDomainDirection = virtualDirection;
return *this;
}

ImageRegistrationMethod::Self&
ImageRegistrationMethod::SetVirtualDomainFromImage( const Image &virtualImage )
{
this->m_VirtualDomainSize = virtualImage.GetSize();
this->m_VirtualDomainOrigin = virtualImage.GetOrigin();
this->m_VirtualDomainSpacing = virtualImage.GetSpacing();
this->m_VirtualDomainDirection = virtualImage.GetDirection();

return *this;
}

ImageRegistrationMethod::Self&
ImageRegistrationMethod::SetMetricAsANTSNeighborhoodCorrelation( unsigned int radius )
{
Expand Down Expand Up @@ -967,6 +1008,17 @@ ImageRegistrationMethod::SetupMetric(
metric->SetUseFixedImageGradientFilter( m_MetricUseFixedImageGradientFilter );
metric->SetUseMovingImageGradientFilter( m_MetricUseMovingImageGradientFilter );

if ( this->m_VirtualDomainSize.size() != 0 )
{
typename FixedImageType::SpacingType itkSpacing = sitkSTLVectorToITK<typename FixedImageType::SpacingType>(this->m_VirtualDomainSpacing);
typename FixedImageType::PointType itkOrigin = sitkSTLVectorToITK<typename FixedImageType::PointType>(this->m_VirtualDomainOrigin);
typename FixedImageType::DirectionType itkDirection = sitkSTLToITKDirection<typename FixedImageType::DirectionType>(this->m_VirtualDomainDirection);

typename FixedImageType::RegionType itkRegion;
itkRegion.SetSize( sitkSTLVectorToITK<typename FixedImageType::SizeType>( this->m_VirtualDomainSize ) );

metric->SetVirtualDomain( itkSpacing, itkOrigin, itkDirection, itkRegion );
}

typedef itk::InterpolateImageFunction< FixedImageType, double > FixedInterpolatorType;
typename FixedInterpolatorType::Pointer fixedInterpolator = CreateInterpolator(fixed, m_Interpolator);
Expand Down
183 changes: 181 additions & 2 deletions Testing/Unit/sitkImageRegistrationMethodTests.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ class sitkRegistrationMethodTest
const std::vector<double> &pt1,
const std::vector<unsigned int> &size)
{
sitk::GaussianImageSource source1;
sitk::GaussianImageSource source1;
source1.SetMean(pt0);
source1.SetScale(1.0);

Expand Down Expand Up @@ -162,7 +162,6 @@ TEST_F(sitkRegistrationMethodTest, Metric_Evaluate)
sitk::Image fixed = fixedBlobs;
sitk::Image moving = fixedBlobs;


sitk::ImageRegistrationMethod R;
R.SetInitialTransform(sitk::Transform(fixed.GetDimension(),sitk::sitkIdentity));

Expand Down Expand Up @@ -441,6 +440,186 @@ TEST_F(sitkRegistrationMethodTest, Mask_Test2)
}


TEST_F(sitkRegistrationMethodTest, VirtualDomain_Test)
{
// Test usage of setting virtual domain

sitk::ImageRegistrationMethod R;
R.SetInterpolator(sitk::sitkLinear);
//R.DebugOn();
sitk::Image virtualImage = MakeGaussianBlob( v2(32,32), std::vector<unsigned int>(2,64) );

R.SetVirtualDomainFromImage(virtualImage);

// transform to optimize
sitk::TranslationTransform tx(virtualImage.GetDimension());
tx.SetOffset(v2(3.2,-1.2));
R.SetInitialTransform(tx, false);

sitk::Image fixedImage = virtualImage;
fixedImage.SetOrigin(v2(100, 0));

// virtual image to fixed image
sitk::TranslationTransform fixedTransform(fixedImage.GetDimension());
fixedTransform.SetOffset(v2(100, 0));
R.SetFixedInitialTransform(fixedTransform);

sitk::Image movingImage = virtualImage;
movingImage.SetOrigin(v2(0, 200));

// transform from virtual domain to moving image with "optimizing" transform
sitk::TranslationTransform movingTransform(movingImage.GetDimension());
movingTransform.SetOffset(v2(0, 200));
R.SetMovingInitialTransform(movingTransform);

R.SetMetricAsCorrelation();

double minStep=1e-5;
unsigned int numberOfIterations=100;
double relaxationFactor=0.75;
double gradientMagnitudeTolerance = 1e-20;
R.SetOptimizerAsRegularStepGradientDescent(.1,
minStep,
numberOfIterations,
relaxationFactor,
gradientMagnitudeTolerance);


IterationUpdate cmd(R);
R.AddCommand(sitk::sitkIterationEvent, cmd);

sitk::Transform outTx = R.Execute(fixedImage, movingImage);


std::cout << "-------" << std::endl;
std::cout << outTx.ToString() << std::endl;
std::cout << "Optimizer stop condition: " << R.GetOptimizerStopConditionDescription() << std::endl;
std::cout << " Iteration: " << R.GetOptimizerIteration() << std::endl;
std::cout << " Metric value: " << R.GetMetricValue() << std::endl;

EXPECT_VECTOR_DOUBLE_NEAR(v2(0.0,0.0), outTx.GetParameters(), 1e-3);
EXPECT_GT( R.GetOptimizerIteration(), 1u );

}

TEST_F(sitkRegistrationMethodTest, VirtualDomain_MultiRes_Test)
{
// Test usage of setting virtual domain

sitk::ImageRegistrationMethod R;
R.SetInterpolator(sitk::sitkLinear);
//R.DebugOn();
sitk::Image virtualImage = MakeGaussianBlob( v3(32,32,32), std::vector<unsigned int>(3,64) );

R.SetVirtualDomainFromImage(virtualImage);

// transform to optimize
sitk::TranslationTransform tx(virtualImage.GetDimension());
tx.SetOffset(v3(5.21231, 3.2,-1.2));
R.SetInitialTransform(tx, false);

sitk::Image fixedImage = virtualImage;
fixedImage.SetOrigin(v3(1000, 100, 0));

// virtual image to fixed image
sitk::TranslationTransform fixedTransform(fixedImage.GetDimension());
fixedTransform.SetOffset(v3(1000, 100, 0));
R.SetFixedInitialTransform(fixedTransform);

sitk::Image movingImage = virtualImage;
movingImage.SetOrigin(v3(0, 200, 512));

// transform from virtual domain to moving image with "optimizing" transform
sitk::TranslationTransform movingTransform(movingImage.GetDimension());
movingTransform.SetOffset(v3(0, 200, 512));
R.SetMovingInitialTransform(movingTransform);

R.SetMetricAsMeanSquares();

double minStep=1e-3;
unsigned int numberOfIterations=10;
double relaxationFactor=0.6;
double gradientMagnitudeTolerance = 1e-10;
sitk::ImageRegistrationMethod::EstimateLearningRateType estimateLearningRate = sitk::ImageRegistrationMethod::Never;
R.SetOptimizerAsRegularStepGradientDescent(2,
minStep,
numberOfIterations,
relaxationFactor,
gradientMagnitudeTolerance,
estimateLearningRate);

std::vector<unsigned int> shrinkFactors(2);
shrinkFactors[0] = 8;
shrinkFactors[1] = 1;
R.SetShrinkFactorsPerLevel( shrinkFactors );
R.SetSmoothingSigmasPerLevel( v2(0.0, 0.0) );

R.SetOptimizerScalesFromJacobian();

IterationUpdate cmd(R);
R.AddCommand(sitk::sitkIterationEvent, cmd);

sitk::Transform outTx = R.Execute(fixedImage, movingImage);


std::cout << "-------" << std::endl;
std::cout << outTx.ToString() << std::endl;
std::cout << "Optimizer stop condition: " << R.GetOptimizerStopConditionDescription() << std::endl;
std::cout << " Iteration: " << R.GetOptimizerIteration() << std::endl;
std::cout << " Metric value: " << R.GetMetricValue() << std::endl;

EXPECT_VECTOR_DOUBLE_NEAR(v3(0.0,0.0,0.0), outTx.GetParameters(), 1e-1);
EXPECT_GT( R.GetOptimizerIteration(), 1u );

}



TEST_F(sitkRegistrationMethodTest, VirtualDomain_Parameters)
{

sitk::ImageRegistrationMethod R;
R.SetInterpolator(sitk::sitkLinear);

sitk::Image virtualImage = MakeGaussianBlob( v3(32,32,32), std::vector<unsigned int>(3,64) );

std::vector<uint32_t> size(3, 64);

EXPECT_NO_THROW(
R.SetVirtualDomain(size,
v3(0.0,0.0,0.0),
v3(1.0,1.0,1.0),
v9(1.0,0.0,0.0,
0.0,1.0,0.0,
0.0,0.0,1.0)) );

EXPECT_THROW(
R.SetVirtualDomain(size,
v2(0.0,0.0),
v3(1.0,1.0,1.0),
v9(1.0,0.0,0.0,
0.0,1.0,0.0,
0.0,0.0,1.0)),
sitk::GenericException);


EXPECT_THROW(
R.SetVirtualDomain(size,
v3(0.0,0.0,0.0),
v2(1.0,1.0),
v9(1.0,0.0,0.0,
0.0,1.0,0.0,
0.0,0.0,1.0)),
sitk::GenericException );

EXPECT_THROW(
R.SetVirtualDomain(size,
v3(0.0,0.0,0.0),
v3(1.0,1.0,1.0),
v3(1.0,0.0,0.0)),
sitk::GenericException );
}

TEST_F(sitkRegistrationMethodTest, OptimizerWeights_Test)
{
// Test the usage of optimizer weights
Expand Down

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