Inheritance diagram for Seg3D::IntensityCorrectionFilterAlgo:

Public Types
typedef itk::GradientMagnitudeImageFilter< FLOAT_IMAGE_TYPE, FLOAT_IMAGE_TYPE >	GMagFilterType

typedef itk::GradientImageFilter< FLOAT_IMAGE_TYPE >	GradientFilterType

typedef GradientFilterType::OutputImageType	GradientImageType

typedef GradientImageType::PixelType	GradientPixelType

typedef itk::ImageRegionIterator< GradientImageType >	GradientImageIterator

Public Types inherited from Seg3D::ITKFilter
typedef itk::Image< unsigned short, 3 >	USHORT_IMAGE_TYPE

typedef itk::Image< unsigned int, 3 >	UINT_IMAGE_TYPE

typedef itk::Image< float, 3 >	FLOAT_IMAGE_TYPE

typedef itk::Image< unsigned char, 3 >	UCHAR_IMAGE_TYPE

typedef Core::ITKImageDataT< float >	FLOAT_CONTAINER_TYPE

typedef Core::ITKImageDataT< unsigned int >	UINT_CONTAINER_TYPE

typedef Core::ITKImageDataT< unsigned short >	USHORT_CONTAINER_TYPE

typedef Core::ITKImageDataT< unsigned char >	UCHAR_CONTAINER_TYPE

Public Member Functions
float	getAx (float w, float nx, float ny, float nz, int order_index)

float	getAy (float w, float nx, float ny, float nz, int order_index)

float	getAz (float w, float nx, float ny, float nz, int order_index)

this	get_itk_image_from_layer (this->src_layer_, input_image)

	if (!input_data_block)

dgfilter	SetInput (input_image->get_image())

dgfilter	SetVariance (1.0)

dgfilter	SetMaximumKernelWidth (8)

dgfilter	SetUseImageSpacingOff ()

this	forward_abort_to_filter (dgfilter, this->dst_layer_)

this	observe_itk_progress (dgfilter, this->dst_layer_, 0.0, 0.05)

	catch (...)

	if (this->check_abort()) return

FLOAT_CONTAINER_TYPE::Handle	dg_image (new FLOAT_CONTAINER_TYPE( dgfilter->GetOutput()))

	if (!dg_image)

	for (size_t j=0;j< size;j++)

	for (size_t j=0;j< size;j++) data[j]

	if (this->check_abort()) return

gmag_filter	SetInput (dg_image->get_image())

this	forward_abort_to_filter (gmag_filter, this->dst_layer_)

this	observe_itk_progress (gmag_filter, this->dst_layer_, 0.1, 0.05)

	catch (...)

	if (this->check_abort()) return

FLOAT_CONTAINER_TYPE::Handle	gmag_image (new FLOAT_CONTAINER_TYPE( gmag_filter->GetOutput()))

	if (!gmag_image)

	if (!gmag_data_block)

	for (size_t j=0;j< size;j++) data[j]

	if (this->check_abort()) return

gradient_filter	SetInput (gmag_image->get_image())

this	forward_abort_to_filter (gradient_filter, this->dst_layer_)

this	observe_itk_progress (gradient_filter, this->dst_layer_, 0.2, 0.05)

	catch (...)

	if (this->check_abort()) return

GradientImageIterator	grad_iter (gradient_image, gradient_image->GetLargestPossibleRegion())

	while (!grad_iter.IsAtEnd())

vnl_matrix< float >	ATA (order, order, 0)

vnl_matrix< float >	uT (order, 1, 0)

	for (size_t z=0;z< size_z;z++)

	if (this->check_abort()) return

this dst_layer_	update_progress (0.7f)

	if (this->check_abort()) return

this dst_layer_	update_progress (0.85f)

	if (this->check_abort()) return

	if (this->check_abort()) return

this dst_layer_	update_progress (0.9f)

	for (size_t z=0;z< size_z;z++)

	for (size_t j=0;j< size;j++)

	catch (...)

	if (this->check_abort()) return

this dst_layer_	update_progress (0.99f)

	if (this->preserve_data_format_)

virtual std::string	get_filter_name () const

virtual std::string	get_layer_prefix () const

Public Member Functions inherited from Seg3D::LayerFilter
virtual void	raise_abort () override

virtual bool	check_abort () override

void	raise_stop ()

bool	check_stop ()

virtual void	abort_and_wait () override

void	connect_abort (const LayerHandle &layer)

void	connect_stop (const LayerHandle &layer)

Core::NotifierHandle	get_notifier ()

bool	find_layer (const std::string &layer_id, LayerHandle &layer)

bool	lock_for_use (LayerHandle layer)

bool	lock_for_processing (LayerHandle layer)

bool	lock_for_deletion (LayerHandle layer)

bool	create_and_lock_data_layer_from_layer (LayerHandle src_layer, LayerHandle &dst_layer)

bool	create_and_lock_data_layer (const Core::GridTransform &grid_trans, LayerHandle src_layer, LayerHandle &dst_layer)

bool	create_cropped_large_volume_layer (const Core::GridTransform &crop_trans, LayerHandle src_layer, LayerHandle &dst_layer)

bool	create_and_lock_mask_layer_from_layer (LayerHandle src_layer, LayerHandle &dst_layer)

bool	create_and_lock_mask_layer_from_layer (LayerHandle src_layer, LayerHandle &dst_layer, std::string dst_name)

bool	create_and_lock_mask_layer (const Core::GridTransform &grid_trans, LayerHandle src_layer, LayerHandle &dst_layer)

bool	dispatch_unlock_layer (LayerHandle layer)

bool	dispatch_delete_layer (LayerHandle layer)

bool	dispatch_insert_data_volume_into_layer (LayerHandle layer, Core::DataVolumeHandle data, bool update_histogram)

bool	dispatch_insert_mask_volume_into_layer (LayerHandle layer, Core::MaskVolumeHandle mask)

void	create_undo_redo_and_provenance_record (Core::ActionContextHandle context, Core::ActionHandle action, bool split_prov=false)

bool	update_provenance_action_string (Core::ActionHandle action)

void	set_sandbox (SandboxID sandbox)

SandboxID	get_sandbox ()

void	report_error (const std::string &error)

Layer::filter_key_type	get_key () const

Public Attributes
LayerHandle	src_layer_

LayerHandle	dst_layer_

int	order_

double	edge_

bool	preserve_data_format_

TYPED_CONTAINER_TYPE::Handle	input_image

Core::DataBlockHandle	input_data_block = Core::ITKDataBlock::New( input_image )

DGFilterType::Pointer	dgfilter = DGFilterType::New()

	try

Core::DataBlockHandle	dg_data_block = Core::ITKDataBlock::New( dg_image )

float	data_min = std::numeric_limits<float>::max()

float	data_max = std::numeric_limits<float>::min()

size_t	size = dg_data_block->get_size()

GMagFilterType::Pointer	gmag_filter = GMagFilterType::New()

Core::DataBlockHandle	gmag_data_block = Core::ITKDataBlock::New( gmag_image )

const float	inv_edge_sqr = 1.0 / ( this->edge_ * this->edge_ )

GradientFilterType::Pointer	gradient_filter = GradientFilterType::New()

GradientImageType::Pointer	gradient_image = gradient_filter->GetOutput()

size_t	size_x = input_image->get_nx()

size_t	size_y = input_image->get_ny()

size_t	size_z = input_image->get_nz()

float	xscale = static_cast<float>( size_x + size_y + size_z ) / 8.0f

float	yscale = static_cast<float>( size_x + size_y + size_z ) / 8.0f

float	zscale = static_cast<float>( size_x + size_y + size_z ) / 8.0f

float	xcenter = static_cast<float>( size_x ) / 2.0

float	ycenter = static_cast<float>( size_y ) / 2.0

float	zcenter = static_cast<float>( size_z ) / 2.0

float *	W = reinterpret_cast<float*>( gmag_data_block->get_data() )

float *	res = reinterpret_cast<float*>( dg_data_block->get_data() )

VALUE_TYPE *	input = reinterpret_cast<VALUE_TYPE*>( input_data_block->get_data() )

size_t	j = 0

	gradient_image = 0
	Clear memory for image.

const int	order = order_counts[ this->order_ ]

vnl_matrix< float >	ATA_inv = vnl_matrix_inverse<float>(ATA)

vnl_matrix< float >	alphaM = ATA_inv * uT

vnl_vector< float >	alpha = alphaM.get_column(0)

size_t	i = 0

float	new_data_min = std::numeric_limits<float>::max()

float	new_data_max = std::numeric_limits<float>::min()

float	factor = ( data_max - data_min ) / ( new_data_max - new_data_min )

	else

Static Public Attributes
static int	order_counts [5] = { 0, 3, 9, 19, 34 }

Additional Inherited Members
Static Public Member Functions inherited from Core::Runnable
static void	Start (RunnableHandle runnable)

Protected Member Functions inherited from Seg3D::ITKFilter
template<class T >
bool	get_itk_image_from_layer (const LayerHandle &layer, typename Core::ITKImageDataT< T >::Handle &image, bool invert=false)

template<class T >
bool	get_itk_image_from_mask_layer (const LayerHandle &layer, typename Core::ITKImageDataT< T >::Handle &image, double label=1.0)

template<class T >
bool	insert_itk_image_into_layer (const LayerHandle &layer, typename itk::Image< T, 3 > *itk_image)

template<class T >
bool	insert_itk_image_pointer_into_layer (const LayerHandle &layer, typename itk::Image< T, 3 >::Pointer itk_image)

template<class T >
bool	insert_itk_positive_labels_into_mask_layer (const LayerHandle &layer, typename itk::Image< T, 3 > *itk_image, bool invert=false)

template<class T >
bool	insert_itk_positive_labels_pointer_into_mask_layer (const LayerHandle &layer, typename itk::Image< T, 3 >::Pointer itk_image, bool invert=false)

template<class T >
bool	insert_itk_label_into_mask_layer (const LayerHandle &layer, typename itk::Image< T, 3 > *itk_image, T label)

template<class T >
bool	insert_itk_label_pointer_into_mask_layer (const LayerHandle &layer, typename itk::Image< T, 3 >::Pointer itk_image, T label)

template<class T >
bool	convert_and_insert_itk_image_into_layer (const LayerHandle &layer, typename itk::Image< T, 3 > *itk_image, Core::DataType data_type)

template<class T >
bool	convert_and_insert_itk_image_pointer_into_layer (const LayerHandle &layer, typename itk::Image< T, 3 >::Pointer itk_image, Core::DataType data_type)

template<class T >
void	forward_abort_to_filter (T filter_pointer, LayerHandle layer)

template<class T >
void	observe_itk_progress (T filter_pointer, const LayerHandle &layer, float progress_start=0.0, float progress_amount=1.0)

template<class T >
void	observe_itk_iterations (T filter_pointer, boost::function< void(itk::Object *) > iteration_fcn)

template<class T >
void	limit_number_of_itk_threads (T filter_pointer)

virtual void	handle_abort ()

virtual void	handle_stop ()

Protected Member Functions inherited from Seg3D::LayerFilter
virtual void	run_filter ()=0

virtual void	run ()

Member Function Documentation

virtual std::string Seg3D::IntensityCorrectionFilterAlgo::get_filter_name ( ) const

inlinevirtual

GET_FILTER_NAME: This functions returns the name of the filter that is used in the error report.

Implements Seg3D::LayerFilter.

virtual std::string Seg3D::IntensityCorrectionFilterAlgo::get_layer_prefix ( ) const

inlinevirtual

GET_LAYER_PREFIX: This function returns the name of the filter. The latter is prepended to the new layer name, when a new layer is generated.

Implements Seg3D::LayerFilter.

Member Data Documentation

Seg3D::IntensityCorrectionFilterAlgo::else

Initial value:

{
      this->insert_itk_image_pointer_into_layer<float>( this->dst_layer_, 
        dg_image->get_image() )

TYPED_CONTAINER_TYPE::Handle Seg3D::IntensityCorrectionFilterAlgo::input_image

Initial value:

{
    
    typedef itk::DiscreteGaussianImageFilter< TYPED_IMAGE_TYPE, FLOAT_IMAGE_TYPE > DGFilterType

Seg3D::IntensityCorrectionFilterAlgo::try

Initial value:

{

dgfilter->Update()

The documentation for this class was generated from the following file:

Application/Filters/Actions/ActionIntensityCorrectionFilter.cc

Public Types

Public Member Functions

Public Attributes

Static Public Attributes

Additional Inherited Members

Member Function Documentation

Member Data Documentation