This library provides classes related to computations on GPU hardware via the CUDA and potentially OpenCL programming paradigms. More...

Collaboration diagram for cmtkGPU library:

Classes
class	cmtk::DeviceArrayTemplate< DeviceArrayGPU >
	Resource managing class template for type-specific memory allocated on a GPU device through . More...
class	cmtk::DeviceArrayCUDA
	Resource managing class for raw memory allocated on a GPU device through CUDA. More...
class	cmtk::DeviceArrayCUDA::bad_alloc
	Exception for failed allocation. More...
class	cmtk::DeviceContextCL
	Device context wrapper for OpenCL. More...
class	cmtk::DeviceHistogram
	Device memory representation of a uniform volume with static helper functions. More...
class	cmtk::DeviceMemory< T, DeviceMemoryGPU >
	Resource managing class template for type-specific memory allocated on a GPU device through . More...
class	cmtk::DeviceMemoryCL
	Resource managing class for raw memory allocated on a GPU device through OpenCL. More...
class	cmtk::DeviceMemoryCUDA
	Resource managing class for raw memory allocated on a GPU device through CUDA. More...
class	cmtk::DeviceUniformVolume
	Device memory representation of a uniform volume with static helper functions. More...
class	cmtk::DeviceUniformVolumeArray
	Representation of a uniform volume as 3D texture in device memory. More...
class	cmtk::EntropyMinimizationIntensityCorrectionFunctionalDevice< NOrderAdd, NOrderMul >
	Base class for GPU implementation entropy-minimzation MR bias correction functional using Device. More...
class	cmtk::ImagePairAffineRegistrationFunctionalDevice
	Functional for affine registration of two images on the GPU. More...
class	cmtk::ImageSymmetryPlaneFunctionalDevice
	Functional for finding a symmetry plane in 3-D volumes using GPU support. More...
class	cmtk::SimpleLevelsetDevice
	Class for computing a simple levelset evolution on the GPU. More...
Namespaces
namespace	cmtk
Typedefs
typedef DeviceArrayTemplate < DeviceArrayCL >	cmtk::DeviceArray
typedef SmartConstPointer< Self >	cmtk::DeviceArrayCUDA::SmartConstPtr
	Smart pointer-to-const.
typedef SmartPointer< Self >	cmtk::DeviceArrayCUDA::SmartPtr
	Smart pointer.
typedef struct cudaArray *	cmtk::DeviceArrayCUDA::DeviceArrayPointer
	Device array pointer.
typedef SmartPointer< Self >	cmtk::DeviceHistogram::SmartPtr
	Smart pointer to this class.
typedef SmartPointer< Self >	cmtk::DeviceUniformVolume::SmartPtr
	Smart pointer to this class.
typedef SmartPointer< Self >	cmtk::DeviceUniformVolumeArray::SmartPtr
	Smart pointer to this class.
typedef SimpleLevelset	cmtk::SimpleLevelsetDevice::Superclass
	Parent class.
Functions
	cmtk::DeviceArrayCUDA::DeviceArrayCUDA (const FixedVector< 3, int > &dims3)
	Constructor: allocate array through CUDA.
virtual	cmtk::DeviceArrayCUDA::~DeviceArrayCUDA ()
	Destructor: free array through CUDA.
void	cmtk::DeviceArrayCUDA::CopyToDevice (const float *data)
	Copy host linear memory to device.
void	cmtk::DeviceArrayCUDA::CopyOnDeviceToArray (const float *data)
	Copy from linear device memory to device array.
void	cmtk::DeviceArrayCUDA::CopyOnDeviceToLinear (float *data)
	Copy from device array to linear device memory.
DeviceArrayPointer	cmtk::DeviceArrayCUDA::GetArrayOnDevice ()
	Get device array pointer.
static Self::SmartPtr	cmtk::DeviceHistogram::Create (const size_t numberOfBins)
	Create device representation of volume object.
DeviceMemory< float > &	cmtk::DeviceHistogram::GetDataOnDevice ()
	Return device data pointer.
const DeviceMemory< float > &	cmtk::DeviceHistogram::GetDataOnDevice () const
	Return device data pointer.
void	cmtk::DeviceHistogram::Reset ()
	Reset histogram, i.e., set all bins to zero.
void	cmtk::DeviceHistogram::Populate (const DeviceMemory< float > &dataOnDevice, const float rangeFrom, const float rangeTo, const bool logScale=false)
	Populate histogram from data on device.
void	cmtk::DeviceHistogram::Populate (const DeviceMemory< float > &dataOnDevice, const DeviceMemory< int > &maskOnDevice, const float rangeFrom, const float rangeTo, const bool logScale=false)
	Populate histogram from data on device using binary mask.
float	cmtk::DeviceHistogram::GetEntropy () const
	Get entropy.
	cmtk::DeviceHistogram::DeviceHistogram (const size_t numberOfBins)
	Constructor.
void	cmtkDeviceHistogramPopulate (float histPtr, const float dataPtr, const float rangeFrom, const float rangeTo, const bool logScale, const int numberOfBins, const int numberOfSamples)
	Populate histogram from data, entirely on device.
void	cmtkDeviceHistogramPopulate (float histPtr, const float dataPtr, const int *maskPtr, const float rangeFrom, const float rangeTo, const bool logScale, const int numberOfBins, const int numberOfSamples)
	Populate histogram from data using binary mask, entirely on device.
void	cmtkDeviceHistogramEntropy (float result, const float dataPtr, int numberOfBins)
	Compute entropy from histogram on device.
void	cmtk::DeviceImageConvolution (float dest, const int dims3, void array, const int kernelLengthX, const float kernelX, const int kernelLengthY, const float kernelY, const int kernelLengthZ, const float kernelZ)
	Convolution of a 3D image (CUDA array) with a separable 3D kernel.
void	cmtk::DeviceImageConvolutionInPlace (const int dims3, void array, const int kernelLengthX, const float kernelX, const int kernelLengthY, const float kernelY, const int kernelLengthZ, const float *kernelZ)
	In-place convolution of a 3D image (CUDA array) with a separable 3D kernel.
void	cmtk::DeviceThresholdData (float *dest, const int n, const float lowerThreshold, const float upperThreshold)
	Threshold data on device.
static Self::SmartPtr	cmtk::DeviceUniformVolume::Create (const UniformVolume &volume, const size_t padDataToMultiple=1)
	Create device representation of volume object.
DeviceMemory < UniformVolumeOnDevice > &	cmtk::DeviceUniformVolume::GetOnDevice ()
	Return device representation of volume.
DeviceMemory< float > &	cmtk::DeviceUniformVolume::GetDataOnDevice ()
	Return device data pointer.
	cmtk::DeviceUniformVolume::DeviceUniformVolume (const UniformVolume &volume, const size_t padDataToMultiple=1)
	Constructor.
static Self::SmartPtr	cmtk::DeviceUniformVolumeArray::Create (const UniformVolume &volume)
	Create device representation of volume object.
DeviceArray::SmartPtr &	cmtk::DeviceUniformVolumeArray::GetDeviceArrayPtr ()
	Get volume array on device.
	cmtk::DeviceUniformVolumeArray::DeviceUniformVolumeArray (const UniformVolume &volume)
	Constructor.
template<unsigned int NDegreeMul>
EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr	cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice (const unsigned int polynomialDegreeAdd)
	Create functional templated over polynomial degrees.
EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr	cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice (const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul)
	Create functional templated over polynomial degrees.
EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr	cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice (const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul, EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr oldFunctional)
	Create functional templated over polynomial degrees with initialization from old functional.
	cmtk::SimpleLevelsetDevice::SimpleLevelsetDevice (UniformVolume::SmartConstPtr &volume)
	Constructor.
virtual void	cmtk::SimpleLevelsetDevice::Evolve (const int numberOfIterations, const bool forceIterations=false)
	Levelset evolution on GPU.
static Self &	cmtk::DeviceContextCL::GetGlobalContext ()
	Get the global context instance.
Variables
FixedVector< 3, int >	cmtk::DeviceArrayCUDA::m_Dims
	Array dimensions.
DeviceArrayPointer	cmtk::DeviceArrayCUDA::m_DeviceArrayPtr
	Opaque pointer to array on device.
size_t	cmtk::DeviceHistogram::m_NumberOfBins
	User-selected number of bins.
size_t	cmtk::DeviceHistogram::m_NumberOfBinsPadded
	Number of bins after padding to power of 2.
DeviceMemory< float >::SmartPtr	cmtk::DeviceHistogram::m_OnDeviceData
	Managed device memory pointer to histogram data.
DeviceMemory< float >::SmartPtr	cmtk::DeviceHistogram::m_OnDeviceResult
	Managed device memory pointer to result of histogram operations.
DeviceMemory < UniformVolumeOnDevice > ::SmartPtr	cmtk::DeviceUniformVolume::m_OnDevice
	Managed device memory pointer to parameter block.
DeviceMemory< float >::SmartPtr	cmtk::DeviceUniformVolume::m_OnDeviceData
	Managed device memory pointer to volume data.
DeviceArray::SmartPtr	cmtk::DeviceUniformVolumeArray::m_DeviceArrayPointer
	Device array pointer.

Detailed Description

This library provides classes related to computations on GPU hardware via the CUDA and potentially OpenCL programming paradigms.

Typedef Documentation

typedef DeviceArrayTemplate<DeviceArrayCL> cmtk::DeviceArray

Definition at line 92 of file cmtkDeviceArray.h.

typedef struct cudaArray* cmtk::DeviceArrayCUDA::DeviceArrayPointer [inherited]

Device array pointer.

Definition at line 66 of file cmtkDeviceArrayCUDA.h.

typedef SmartConstPointer<Self> cmtk::DeviceArrayCUDA::SmartConstPtr [inherited]

Smart pointer-to-const.

Definition at line 60 of file cmtkDeviceArrayCUDA.h.

typedef SmartPointer<Self> cmtk::DeviceUniformVolume::SmartPtr [inherited]

Smart pointer to this class.

Definition at line 56 of file cmtkDeviceUniformVolume.h.

typedef SmartPointer<Self> cmtk::DeviceHistogram::SmartPtr [inherited]

Smart pointer to this class.

Definition at line 53 of file cmtkDeviceHistogram.h.

typedef SmartPointer<Self> cmtk::DeviceUniformVolumeArray::SmartPtr [inherited]

Smart pointer to this class.

Definition at line 55 of file cmtkDeviceUniformVolumeArray.h.

typedef SmartPointer<Self> cmtk::DeviceArrayCUDA::SmartPtr [inherited]

Smart pointer.

Definition at line 63 of file cmtkDeviceArrayCUDA.h.

typedef SimpleLevelset cmtk::SimpleLevelsetDevice::Superclass [inherited]

Parent class.

Definition at line 56 of file cmtkSimpleLevelsetDevice.h.

Function Documentation

void cmtkDeviceHistogramEntropy	(	float *	result,
		const float *	dataPtr,
		int	numberOfBins
	)

Compute entropy from histogram on device.

Definition at line 37 of file cmtkDeviceHistogram_kernels.cxx.

Referenced by cmtk::DeviceHistogram::GetEntropy().

void cmtkDeviceHistogramPopulate	(	float *	histPtr,
		const float *	dataPtr,
		const float	rangeFrom,
		const float	rangeTo,
		const bool	logScale,
		const int	numberOfBins,
		const int	numberOfSamples
	)

Populate histogram from data, entirely on device.

Parameters:

histPtr	Device pointer to histogram data (output).
dataPtr	Device pointer to input image data.
rangeFrom	Histogram range from this value.
rangeTo	Histogram range to this value.
logScale	Use log scale for value-to-bin mapping to make entropy scale-invariant.
numberOfBins	Number of histogram bins.
numberOfSamples	Number of data samples

Definition at line 42 of file cmtkDeviceHistogram_kernels.cxx.

Referenced by cmtk::DeviceHistogram::Populate().

void cmtkDeviceHistogramPopulate	(	float *	histPtr,
		const float *	dataPtr,
		const int *	maskPtr,
		const float	rangeFrom,
		const float	rangeTo,
		const bool	logScale,
		const int	numberOfBins,
		const int	numberOfSamples
	)

Populate histogram from data using binary mask, entirely on device.

Parameters:

histPtr	Device pointer to histogram data (output).
dataPtr	Device pointer to input image data.
maskPtr	Device pointer to binary mask data (0=background, 1=foreground).
rangeFrom	Histogram range from this value.
rangeTo	Histogram range to this value.
logScale	Use log scale for value-to-bin mapping to make entropy scale-invariant.
numberOfBins	Number of histogram bins.
numberOfSamples	Number of data samples

Definition at line 47 of file cmtkDeviceHistogram_kernels.cxx.

void cmtk::DeviceArrayCUDA::CopyOnDeviceToArray ( const float * data ) [inherited]

Copy from linear device memory to device array.

Definition at line 70 of file cmtkDeviceArrayCUDA.cxx.

References cmtkCheckCallCUDA.

void cmtk::DeviceArrayCUDA::CopyOnDeviceToLinear ( float * data ) [inherited]

Copy from device array to linear device memory.

Definition at line 84 of file cmtkDeviceArrayCUDA.cxx.

References cmtkCheckCallCUDA.

void cmtk::DeviceArrayCUDA::CopyToDevice ( const float * data ) [inherited]

Copy host linear memory to device.

Definition at line 56 of file cmtkDeviceArrayCUDA.cxx.

References cmtkCheckCallCUDA.

static Self::SmartPtr cmtk::DeviceUniformVolume::Create	(	const UniformVolume &	volume,
		const size_t	padDataToMultiple = `1`
	)		`[inline, static, inherited]`

Create device representation of volume object.

Parameters:

padDataToMultiple Allocate device memory for data as multiple of this value.

Definition at line 59 of file cmtkDeviceUniformVolume.h.

Referenced by cmtk::DeviceUniformVolume::DeviceUniformVolume().

static Self::SmartPtr cmtk::DeviceUniformVolumeArray::Create ( const UniformVolume & volume ) [inline, static, inherited]

Create device representation of volume object.

Definition at line 58 of file cmtkDeviceUniformVolumeArray.h.

static Self::SmartPtr cmtk::DeviceHistogram::Create ( const size_t numberOfBins ) [inline, static, inherited]

Create device representation of volume object.

Parameters:

numberOfBins Allocate device memory for data as multiple of this value.

Definition at line 56 of file cmtkDeviceHistogram.h.

EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice	(	const unsigned int	polynomialDegreeAdd,
		const unsigned int	polynomialDegreeMul
	)

Create functional templated over polynomial degrees.

Definition at line 78 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalDevice.cxx.

References cmtk::Console::printf(), and cmtk::StdErr.

template<unsigned int NDegreeMul>

EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice ( const unsigned int polynomialDegreeAdd )

Create functional templated over polynomial degrees.

Definition at line 46 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalDevice.cxx.

References cmtk::Console::printf(), and cmtk::StdErr.

Referenced by cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice().

EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice	(	const unsigned int	polynomialDegreeAdd,
		const unsigned int	polynomialDegreeMul,
		EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr	oldFunctional
	)

Create functional templated over polynomial degrees with initialization from old functional.

This function creates a new functional and copies the polynomial coefficients from an existing functional of equal or lower polynomial degrees into the correct locations of the new functional's parameter vector. This is for incremental computation.

Definition at line 110 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalDevice.cxx.

References cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice(), and cmtk::Vector< T >::SetAll().

cmtk::DeviceArrayCUDA::DeviceArrayCUDA ( const FixedVector< 3, int > & dims3 ) [inherited]

Constructor: allocate array through CUDA.

Definition at line 39 of file cmtkDeviceArrayCUDA.cxx.

References cmtkCheckCallCUDA, cmtk::DeviceArrayCUDA::m_DeviceArrayPtr, and cmtk::DeviceArrayCUDA::m_Dims.

cmtk::DeviceHistogram::DeviceHistogram ( const size_t numberOfBins ) [private, inherited]

Constructor.

Definition at line 38 of file cmtkDeviceHistogram.cxx.

References cmtk::Memory::GetNextPowerOfTwo().

void cmtk::DeviceImageConvolution	(	float *	dest,
		const int *	dims3,
		void *	array,
		const int	kernelLengthX,
		const float *	kernelX,
		const int	kernelLengthY,
		const float *	kernelY,
		const int	kernelLengthZ,
		const float *	kernelZ
	)

Convolution of a 3D image (CUDA array) with a separable 3D kernel.

Warning:: Even though the convolution result is ultimately stored out-of-place in the given target memory, the input array's content is destroyed in the process.

Referenced by cmtk::SimpleLevelsetDevice::Evolve().

void cmtk::DeviceImageConvolutionInPlace	(	const int *	dims3,
		void *	array,
		const int	kernelLengthX,
		const float *	kernelX,
		const int	kernelLengthY,
		const float *	kernelY,
		const int	kernelLengthZ,
		const float *	kernelZ
	)

In-place convolution of a 3D image (CUDA array) with a separable 3D kernel.

void cmtk::DeviceThresholdData	(	float *	dest,
		const int	n,
		const float	lowerThreshold,
		const float	upperThreshold
	)

Threshold data on device.

cmtk::DeviceUniformVolume::DeviceUniformVolume	(	const UniformVolume &	volume,
		const size_t	padDataToMultiple = `1`
	)		`[private, inherited]`

Constructor.

Definition at line 34 of file cmtkDeviceUniformVolume.cxx.

References cmtk::DeviceUniformVolume::Create(), cmtk::DataGrid::GetNumberOfPixels(), cmtk::UniformVolumeOnDevice::m_Data, cmtk::UniformVolume::m_Delta, cmtk::UniformVolumeOnDevice::m_Delta, cmtk::DataGrid::m_Dims, cmtk::UniformVolumeOnDevice::m_Dims, cmtk::DeviceUniformVolume::m_OnDevice, cmtk::DeviceUniformVolume::m_OnDeviceData, cmtk::DeviceMemory< T, DeviceMemoryGPU >::Ptr(), and cmtk::TYPE_FLOAT.

cmtk::DeviceUniformVolumeArray::DeviceUniformVolumeArray ( const UniformVolume & volume ) [private, inherited]

Constructor.

Definition at line 36 of file cmtkDeviceUniformVolumeArray.cxx.

References cmtk::Memory::DeleteArray(), cmtk::DeviceUniformVolumeArray::m_DeviceArrayPointer, and cmtk::TYPE_FLOAT.

void cmtk::SimpleLevelsetDevice::Evolve	(	const int	numberOfIterations,
		const bool	forceIterations = `false`
	)		`[virtual, inherited]`

Levelset evolution on GPU.

Parameters:

numberOfIterations	Number of iterations
forceIterations	If this is set, evolution continues until maximum iteration count is reached, even when convergence is detected

Definition at line 49 of file cmtkSimpleLevelsetDevice.cxx.

References cmtk::DeviceMemory< T, DeviceMemoryGPU >::CopyToHost(), cmtk::DeviceImageConvolution(), cmtk::DeviceMemory< T, DeviceMemoryGPU >::Ptr(), cmtk::SimpleLevelsetDeviceUpdateInsideOutside(), and cmtk::SimpleLevelsetDeviceUpdateLevelset().

DeviceArrayPointer cmtk::DeviceArrayCUDA::GetArrayOnDevice ( ) [inline, inherited]

Get device array pointer.

Definition at line 87 of file cmtkDeviceArrayCUDA.h.

DeviceMemory<float>& cmtk::DeviceHistogram::GetDataOnDevice ( ) [inline, inherited]

Return device data pointer.

Definition at line 62 of file cmtkDeviceHistogram.h.

const DeviceMemory<float>& cmtk::DeviceHistogram::GetDataOnDevice ( ) const [inline, inherited]

Return device data pointer.

Definition at line 68 of file cmtkDeviceHistogram.h.

DeviceMemory<float>& cmtk::DeviceUniformVolume::GetDataOnDevice ( ) [inline, inherited]

Return device data pointer.

Definition at line 71 of file cmtkDeviceUniformVolume.h.

DeviceArray::SmartPtr& cmtk::DeviceUniformVolumeArray::GetDeviceArrayPtr ( ) [inline, inherited]

Get volume array on device.

Definition at line 64 of file cmtkDeviceUniformVolumeArray.h.

float cmtk::DeviceHistogram::GetEntropy ( ) const [inherited]

Get entropy.

Definition at line 77 of file cmtkDeviceHistogram.cxx.

References cmtkDeviceHistogramEntropy().

cmtk::DeviceContextCL::GetGlobalContext ( ) [static, inherited]

Get the global context instance.

Definition at line 78 of file cmtkDeviceContextCL.h.

DeviceMemory<UniformVolumeOnDevice>& cmtk::DeviceUniformVolume::GetOnDevice ( ) [inline, inherited]

Return device representation of volume.

Definition at line 65 of file cmtkDeviceUniformVolume.h.

void cmtk::DeviceHistogram::Populate	(	const DeviceMemory< float > &	dataOnDevice,
		const float	rangeFrom,
		const float	rangeTo,
		const bool	logScale = `false`
	)		`[inherited]`

Populate histogram from data on device.

Definition at line 63 of file cmtkDeviceHistogram.cxx.

References cmtkDeviceHistogramPopulate(), cmtk::DeviceMemory< T, DeviceMemoryGPU >::GetNumberOfItems(), and cmtk::DeviceMemory< T, DeviceMemoryGPU >::Ptr().

void cmtk::DeviceHistogram::Populate	(	const DeviceMemory< float > &	dataOnDevice,
		const DeviceMemory< int > &	maskOnDevice,
		const float	rangeFrom,
		const float	rangeTo,
		const bool	logScale = `false`
	)		`[inherited]`