Package sc.fiji.snt.seed

Class SeedPoint

java.lang.Object

sc.fiji.snt.seed.SeedPoint

All Implemented Interfaces:

SNTPoint

public final class SeedPoint
extends Object
implements SNTPoint

Immutable candidate seed point used to bootstrap auto-tracing or as a visualization aid for the output of upstream point detectors (e.g., deep-learning probability maps + local-max suppression).

Coordinates are stored in physical units (same convention as PointInImage). Importers that receive voxel-indexed input are expected to convert at parse time using the active image's spacing.

Implements SNTPoint so seeds work polymorphically with the rest of SNT's spatial / analysis APIs. The core seed payload (x, y, z, confidence, radius, channel, frame, type, source) is immutable; only the BrainAnnotation and hemisphere fields are mutable, since they are typically populated after construction by atlas-lookup code.

Instances are cheap to copy; collections of millions of seeds are intended use cases.

Author:

Tiago Ferreira

See Also:

• SeedOverlay

Field Summary

Fields

Modifier and Type	Field	Description
final int	channel	1-based channel index, or CT_UNSET.
final double	confidence	Detector confidence in [0, 1].
static final int	CT_UNSET	Sentinel for missing/unspecified channel or frame.
final int	frame	1-based frame index, or CT_UNSET.
final double	radius	Estimated radius in physical units.
final String	source	Provenance label (e.g.
static final String	TAG_UNSET	Empty-string sentinel for unset type / source.
final String	type	Free-form semantic label (e.g.
final double	x	Physical X coordinate (calibrated).
final double	y	Physical Y coordinate (calibrated).
final double	z	Physical Z coordinate (calibrated). 0 for 2D images.

Constructor Summary

Constructors

Constructor	Description
SeedPoint(double x, double y, double z, double confidence, double radius)	Creates a seed without channel/frame assignment and no type/source.
SeedPoint(double x, double y, double z, double confidence, double radius, int channel, int frame)	Creates a seed with channel/frame assignment but no type/source.
SeedPoint(double x, double y, double z, double confidence, double radius, int channel, int frame, String type, String source)	Full constructor.

Method Summary

Modifier and Type	Method	Description
double[]	asArray()	Returns this seed as a double[]{x, y, z} array.
double	distanceSqTo(double px, double py, double pz)	Squared 3D Euclidean distance to a raw point (physical units).
double	distanceSqTo(SeedPoint other)	Squared 3D Euclidean distance to another seed (physical units).
BrainAnnotation	getAnnotation()
double	getCoordinateOnAxis(int axis)
char	getHemisphere()
double	getX()
double	getY()
double	getZ()
void	setAnnotation(BrainAnnotation annotation)	Assigns a neuropil annotation (e.g., atlas compartment) to this point.
void	setHemisphere(char lr)
PointInImage	toPointInImage()	Returns a PointInImage carrying this seed's coordinates and radius, useful when handing the seed to APIs that expect the concrete point class rather than the SNTPoint interface.
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

CT_UNSET

public static final int CT_UNSET

Sentinel for missing/unspecified channel or frame.

See Also:

• Constant Field Values

TAG_UNSET

public static final String TAG_UNSET

Empty-string sentinel for unset type / source.

See Also:

• Constant Field Values

x

public final double x

Physical X coordinate (calibrated).

y

public final double y

Physical Y coordinate (calibrated).

z

public final double z

Physical Z coordinate (calibrated). 0 for 2D images.

confidence

public final double confidence

Detector confidence in [0, 1].

radius

public final double radius

Estimated radius in physical units. 0 if unknown.

channel

public final int channel

1-based channel index, or CT_UNSET.

frame

public final int frame

1-based frame index, or CT_UNSET.

type

public final String type

Free-form semantic label (e.g. "soma", "tip", "branchpoint", "waypoint"). Set at import time by the upstream detector. Never null; TAG_UNSET when absent.

source

public final String source

Provenance label (e.g. "dl-detected", "user-added", "path-derived"). Records where the seed came from. Never null; TAG_UNSET when absent.

Constructor Details

SeedPoint

public SeedPoint(double x,
 double y,
 double z,
 double confidence,
 double radius)

Creates a seed without channel/frame assignment and no type/source.

Parameters:

x - physical X

y - physical Y

z - physical Z (0 for 2D)

confidence - detector confidence in [0, 1]

radius - physical radius (>= 0)

SeedPoint

public SeedPoint(double x,
 double y,
 double z,
 double confidence,
 double radius,
 int channel,
 int frame)

Creates a seed with channel/frame assignment but no type/source.

Parameters:

x - physical X

y - physical Y

z - physical Z (0 for 2D)

confidence - detector confidence in [0, 1]

radius - physical radius (>= 0)

channel - 1-based channel index, or CT_UNSET

frame - 1-based frame index, or CT_UNSET

SeedPoint

public SeedPoint(double x,
 double y,
 double z,
 double confidence,
 double radius,
 int channel,
 int frame,
 String type,
 String source)

Full constructor. null values for type or source are normalised to TAG_UNSET.

Parameters:

x - physical X

y - physical Y

z - physical Z (0 for 2D)

confidence - detector confidence in [0, 1]

radius - physical radius (>= 0)

channel - 1-based channel index, or CT_UNSET

frame - 1-based frame index, or CT_UNSET

type - semantic label, or TAG_UNSET

source - provenance label, or TAG_UNSET

Method Details

distanceSqTo

public double distanceSqTo(SeedPoint other)

Squared 3D Euclidean distance to another seed (physical units). Use the squared form for nearest-neighbor comparisons to avoid the sqrt; pass the result to Math.sqrt(double) when an actual distance is needed.

distanceSqTo

public double distanceSqTo(double px,
 double py,
 double pz)

Squared 3D Euclidean distance to a raw point (physical units).

asArray

public double[] asArray()

Returns this seed as a double[]{x, y, z} array.

toPointInImage

public PointInImage toPointInImage()

Returns a PointInImage carrying this seed's coordinates and radius, useful when handing the seed to APIs that expect the concrete point class rather than the SNTPoint interface.

getX

public double getX()

Specified by:

getX in interface SNTPoint

Returns:

the X-coordinate of the point

getY

public double getY()

Specified by:

getY in interface SNTPoint

Returns:

the Y-coordinate of the point

getZ

public double getZ()

Specified by:

getZ in interface SNTPoint

Returns:

the Z-coordinate of the point

getCoordinateOnAxis

public double getCoordinateOnAxis(int axis)

Specified by:

getCoordinateOnAxis in interface SNTPoint

Returns:

the coordinate on the specified axis

setAnnotation

public void setAnnotation(BrainAnnotation annotation)

Description copied from interface: SNTPoint

Assigns a neuropil annotation (e.g., atlas compartment) to this point.

Specified by:

setAnnotation in interface SNTPoint

Parameters:

annotation - the annotation to be assigned to this point

getAnnotation

public BrainAnnotation getAnnotation()

Specified by:

getAnnotation in interface SNTPoint

Returns:

the neuropil annotation assigned to this point

setHemisphere

public void setHemisphere(char lr)

Specified by:

setHemisphere in interface SNTPoint

getHemisphere

public char getHemisphere()

Specified by:

getHemisphere in interface SNTPoint

toString

public String toString()

Overrides:

toString in class Object