Propagate labels along a vector field. More...

#include <highres-cortex/propagate_along_field.hh>

Classes
class	AbortedAdvection
	Exception raised by certain members if an advection cannot be completed. More...

Public Member Functions
	PropagateAlongField (const boost::shared_ptr< VectorField3d > &vector_field)

	PropagateAlongField (const carto::VolumeRef< float > &fieldx, const carto::VolumeRef< float > &fieldy, const carto::VolumeRef< float > &fieldz)
	Provide the field as separate scalar components.

virtual	~PropagateAlongField ()

void	setVerbose (int verbosity=1)
	Indicate progress on stderr.

void	setStep (float step)
	Move in steps of the specified size (millimetres).

void	setMaxIter (unsigned int max_iter)
	Abort following the gradient after a number of iterations.

template<typename Tlabel>
Tlabel	ascend_until_nonzero (const Point3df &start_point, const carto::VolumeRef< Tlabel > &seeds, Tlabel ignore_label) const
	Move along the field until a nonzero label is found.

template<typename Tlabel>
carto::VolumeRef< Tlabel >	propagate_regions (const carto::VolumeRef< Tlabel > &seeds, Tlabel target_label=0) const
	Propagate labelled regions down a vector field.

template<typename Tlabel>
std::pair< carto::VolumeRef< Tlabel >, carto::VolumeRef< float > >	propagate_regions_keeping_dests (const carto::VolumeRef< Tlabel > &seeds, Tlabel target_label=0) const
	Propagate regions, keeping track of the provenance of each voxel.

template<class TVisitor, typename Tlabel>
bool	visitor_ascension (const Point3df &start_point, const carto::VolumeRef< Tlabel > &seeds, Tlabel ignore_label, TVisitor &visitor) const
	Visit each point along the advection path.

template<typename Tlabel>
float	integrate_field_along_advection (const Point3df &start_point, const carto::VolumeRef< Tlabel > &seeds, const boost::shared_ptr< ScalarField > &field, Tlabel ignore_label) const
	Return the integral of a scalar field along an advection path.

template<typename Tlabel>
carto::VolumeRef< float >	integrate_from_region (const carto::VolumeRef< Tlabel > &seeds, const boost::shared_ptr< ScalarField > &field, Tlabel target_label=0) const

Static Public Attributes
static const float	default_step

static const unsigned int	default_max_iter

Detailed Description

Propagate labels along a vector field.

From a given starting point, the field is followed in fixed-size steps until a seed is reached, or the maximum number of iterations is exceeded.

Definition at line 55 of file propagate_along_field.hh.

Constructor & Destructor Documentation

◆ PropagateAlongField() [1/2]

yl::PropagateAlongField::PropagateAlongField ( const boost::shared_ptr< VectorField3d > & vector_field )

explicit

◆ PropagateAlongField() [2/2]

yl::PropagateAlongField::PropagateAlongField	(	const carto::VolumeRef< float > &	fieldx,
		const carto::VolumeRef< float > &	fieldy,
		const carto::VolumeRef< float > &	fieldz )

Provide the field as separate scalar components.

The field will be linearly interpolated.

◆ ~PropagateAlongField()

virtual yl::PropagateAlongField::~PropagateAlongField ( )

virtual

Member Function Documentation

◆ ascend_until_nonzero()

template<typename Tlabel>

Tlabel yl::PropagateAlongField::ascend_until_nonzero	(	const Point3df &	start_point,
		const carto::VolumeRef< Tlabel > &	seeds,
		Tlabel	ignore_label ) const

Move along the field until a nonzero label is found.

start_point is to be specified in millimetre coordinates.
seeds is interpreted as for propagate_regions().
ignore_label counts as propagation region.

Return the value of the seed encountered, or zero in the following cases:

the path leads outside of the image;
the maximum number of iterations is exceeded (e.g. the path loops);
a vector field value is encountered that is too close to zero, or infinite, or NaN.

◆ integrate_field_along_advection()

template<typename Tlabel>

float yl::PropagateAlongField::integrate_field_along_advection	(	const Point3df &	start_point,
		const carto::VolumeRef< Tlabel > &	seeds,
		const boost::shared_ptr< ScalarField > &	field,
		Tlabel	ignore_label ) const

Return the integral of a scalar field along an advection path.

Exceptions

AbortedAdvection is thrown if the advection cannot be completed.

◆ integrate_from_region()

template<typename Tlabel>

carto::VolumeRef< float > yl::PropagateAlongField::integrate_from_region	(	const carto::VolumeRef< Tlabel > &	seeds,
		const boost::shared_ptr< ScalarField > &	field,
		Tlabel	target_label = 0 ) const

◆ propagate_regions()

template<typename Tlabel>

carto::VolumeRef< Tlabel > yl::PropagateAlongField::propagate_regions	(	const carto::VolumeRef< Tlabel > &	seeds,
		Tlabel	target_label = 0 ) const

Propagate labelled regions down a vector field.

The labels are interpreted as follows:

zero: propagation zone,
positive: seed, propagation is stopped and the target voxel is given the seed's value (except if the label is target_label),
negative: forbidden region, propagation is stopped and the target voxel remains unset.

An optional target_label can be given, in which case the propagation is started only from thus labelled voxels.

◆ propagate_regions_keeping_dests()

template<typename Tlabel>

std::pair< carto::VolumeRef< Tlabel >, carto::VolumeRef< float > > yl::PropagateAlongField::propagate_regions_keeping_dests	(	const carto::VolumeRef< Tlabel > &	seeds,
		Tlabel	target_label = 0 ) const

Propagate regions, keeping track of the provenance of each voxel.

See also: propagate_regions()

The second output volume is the same size as the input seeds volume, except is has 3 time points which represent x, y, and z coordinates of the point of origin, respectively.

◆ setMaxIter()

void yl::PropagateAlongField::setMaxIter ( unsigned int max_iter )

Abort following the gradient after a number of iterations.

This is to prevent infinite looping when the propagation falls in a local minimum or loops over itself. By default this is default_max_iter.

◆ setStep()

void yl::PropagateAlongField::setStep ( float step )

Move in steps of the specified size (millimetres).

The default step size is default_step.

◆ setVerbose()

void yl::PropagateAlongField::setVerbose ( int verbosity = 1 )

Indicate progress on stderr.

0: be silent
1: show progress and statistics
2: show aborted field ascensions
more: for debugging, see source code and debug_output.

◆ visitor_ascension()

template<class TVisitor, typename Tlabel>

bool yl::PropagateAlongField::visitor_ascension	(	const Point3df &	start_point,
		const carto::VolumeRef< Tlabel > &	seeds,
		Tlabel	ignore_label,
		TVisitor &	visitor ) const

Visit each point along the advection path.

Return values

true	if the advection succeeds (reaches a goal region).
false	if the advection it is stopped early and fails.

Member Data Documentation

◆ default_max_iter

const unsigned int yl::PropagateAlongField::default_max_iter

static

Definition at line 140 of file propagate_along_field.hh.

◆ default_step

const float yl::PropagateAlongField::default_step

static

Definition at line 139 of file propagate_along_field.hh.

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

highres-cortex/propagate_along_field.hh

Classes

Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PropagateAlongField() [1/2]

◆ PropagateAlongField() [2/2]

◆ ~PropagateAlongField()

Member Function Documentation

◆ ascend_until_nonzero()

◆ integrate_field_along_advection()

◆ integrate_from_region()

◆ propagate_regions()

◆ propagate_regions_keeping_dests()

◆ setMaxIter()

◆ setStep()

◆ setVerbose()

◆ visitor_ascension()

Member Data Documentation

◆ default_max_iter

◆ default_step