sc.fiji.snt.util

Class SWCPoint

java.lang.Object

sc.fiji.snt.util.PointInImage

sc.fiji.snt.util.SWCPoint

All Implemented Interfaces:

java.lang.Comparable<SWCPoint>, SNTPoint

public class SWCPoint
extends PointInImage
implements SNTPoint, java.lang.Comparable<SWCPoint>

Defines a node in an SWC reconstruction. The SWC file format is detailed here

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field and Description
int	id The sample number of this node
int	parent The parent id of this node
double	radius The radius of reconstructed structure at this node
int	type The SWC-type flag of this node (Path.SWC_SOMA, Path.SWC_DENDRITE, etc.)

Fields inherited from class sc.fiji.snt.util.PointInImage

onPath, v, x, y, z

Constructor Summary

Constructors

Constructor and Description
SWCPoint(int id, int type, double x, double y, double z, double radius, int parent)

Method Summary

Modifier and Type	Method and Description
static java.io.StringReader	collectionAsReader(java.util.Collection<SWCPoint> points) Converts a collection of SWC points into a Reader.
int	compareTo(SWCPoint o)
boolean	equals(java.lang.Object o)
static void	flush(java.util.Collection<SWCPoint> points, java.io.PrintWriter pw) Prints a list of points as space-separated values.
BrainAnnotation	getAnnotation()
java.util.List<SWCPoint>	getNextPoints() Returns the list holding the subsequent nodes in the reconstructed structure after this one.
SWCPoint	getPreviousPoint() Returns the preceding node (if any)
double	getX()
double	getY()
double	getZ()
void	setAnnotation(BrainAnnotation annotation) Assigns a neuropil annotation (e.g., atlas compartment) to this point.
void	setPreviousPoint(SWCPoint previousPoint) Sets the preceding node in the reconstruction
java.lang.String	toString()
double	xSeparationFromPreviousPoint() Returns the X-distance from previous point.
double	ySeparationFromPreviousPoint() Returns the Y-distance from previous point.
double	zSeparationFromPreviousPoint() Returns the Z-distance from previous point.

Methods inherited from class sc.fiji.snt.util.PointInImage

distanceSquaredTo, distanceSquaredTo, distanceTo, getPath, getUnscaledPoint, getUnscaledPoint, hashCode, isReal, isSameLocation, scale, setPath, toUPoint, transform

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface sc.fiji.snt.util.SNTPoint

average

Field Detail

id

public int id

The sample number of this node

type

public final int type

The SWC-type flag of this node (Path.SWC_SOMA, Path.SWC_DENDRITE, etc.)

parent

public int parent

The parent id of this node

radius

public double radius

The radius of reconstructed structure at this node

Constructor Detail

SWCPoint

public SWCPoint(int id,
                int type,
                double x,
                double y,
                double z,
                double radius,
                int parent)

Method Detail

xSeparationFromPreviousPoint

public double xSeparationFromPreviousPoint()

Returns the X-distance from previous point.

Returns:

the X-distance from previous point or Double.NaN if no previousPoint exists.

ySeparationFromPreviousPoint

public double ySeparationFromPreviousPoint()

Returns the Y-distance from previous point.

Returns:

the Y-distance from previous point or Double.NaN if no previousPoint exists.

zSeparationFromPreviousPoint

public double zSeparationFromPreviousPoint()

Returns the Z-distance from previous point.

Returns:

the Z-distance from previous point or Double.NaN if no previousPoint exists.

toString

public java.lang.String toString()

Overrides:

toString in class PointInImage

compareTo

public int compareTo(SWCPoint o)

Specified by:

compareTo in interface java.lang.Comparable<SWCPoint>

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class PointInImage

collectionAsReader

public static java.io.StringReader collectionAsReader(java.util.Collection<SWCPoint> points)

Converts a collection of SWC points into a Reader.

Parameters:

points - the collection of SWC points to be converted into a space/ tab separated String. Points should be sorted by sample number to ensure valid connectivity.

Returns:

the Reader

flush

public static void flush(java.util.Collection<SWCPoint> points,
                         java.io.PrintWriter pw)

Prints a list of points as space-separated values.

Parameters:

points - the collections of SWC points to be printed.

pw - the PrintWriter to write to.

See Also:

collectionAsReader(Collection)

getX

public double getX()

Specified by:

getX in interface SNTPoint

Overrides:

getX in class PointInImage

Returns:

the X-coordinate of the point

getY

public double getY()

Specified by:

getY in interface SNTPoint

Overrides:

getY in class PointInImage

Returns:

the Y-coordinate of the point

getZ

public double getZ()

Specified by:

getZ in interface SNTPoint

Overrides:

getZ in class PointInImage

Returns:

the Z-coordinate of the point

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

Overrides:

setAnnotation in class PointInImage

Parameters:

annotation - the annotation to be assigned to this point

getAnnotation

public BrainAnnotation getAnnotation()

Specified by:

getAnnotation in interface SNTPoint

Overrides:

getAnnotation in class PointInImage

Returns:

the neuropil annotation assigned to this point

getPreviousPoint

public SWCPoint getPreviousPoint()

Returns the preceding node (if any)

Returns:

the previous node or null if set by setPreviousPoint(SWCPoint) has not been called

setPreviousPoint

public void setPreviousPoint(SWCPoint previousPoint)

Sets the preceding node in the reconstruction

Parameters:

previousPoint - the previous node preceding this one

getNextPoints

public java.util.List<SWCPoint> getNextPoints()

Returns the list holding the subsequent nodes in the reconstructed structure after this one.

Returns:

the list of "next points"