sc.fiji.snt.util

Class PointInImage

java.lang.Object

sc.fiji.snt.util.PointInImage

All Implemented Interfaces:

SNTPoint

Direct Known Subclasses:

PointInCanvas, SWCPoint

public class PointInImage
extends java.lang.Object
implements SNTPoint

Defines a Point in an image, a node of a traced Path. Coordinates are always expressed in real-world coordinates.

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field and Description
Path	onPath The Path associated with this node, if any (optional field)
double	v A property associated with this point (e.g., voxel intensity) (optional field)
double	x The cartesian coordinate of this node
double	y The cartesian coordinate of this node
double	z The cartesian coordinate of this node

Constructor Summary

Constructors

Constructor and Description
PointInImage(double x, double y, double z)

Method Summary

Modifier and Type	Method and Description
double	distanceSquaredTo(double ox, double oy, double oz)
double	distanceSquaredTo(PointInImage o)
double	distanceTo(PointInImage o)
boolean	equals(java.lang.Object o)
BrainAnnotation	getAnnotation()
Path	getPath() Returns the Path associated with this node (if any)
PointInCanvas	getUnscaledPoint() Converts the coordinates of this point into pixel units if this point is associated with a Path.
PointInCanvas	getUnscaledPoint(int view) Converts the coordinates of this point into pixel units if this point is associated with a Path.
double	getX()
double	getY()
double	getZ()
int	hashCode()
boolean	isReal()
boolean	isSameLocation(PointInImage pim)
void	scale(double xScale, double yScale, double zScale) Scales this point coordinates.
void	setAnnotation(BrainAnnotation annotation) Assigns a neuropil annotation (e.g., atlas compartment) to this point.
void	setPath(Path onPath) Associates a Path with this node
java.lang.String	toString()
sholl.UPoint	toUPoint()
PointInImage	transform(PathTransformer transformer)

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

x

public double x

The cartesian coordinate of this node

y

public double y

The cartesian coordinate of this node

z

public double z

The cartesian coordinate of this node

v

public double v

A property associated with this point (e.g., voxel intensity) (optional field)

onPath

public Path onPath

The Path associated with this node, if any (optional field)

Constructor Detail

PointInImage

public PointInImage(double x,
                    double y,
                    double z)

Method Detail

distanceSquaredTo

public double distanceSquaredTo(double ox,
                                double oy,
                                double oz)

distanceSquaredTo

public double distanceSquaredTo(PointInImage o)

distanceTo

public double distanceTo(PointInImage o)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

transform

public PointInImage transform(PathTransformer transformer)

isReal

public boolean isReal()

isSameLocation

public boolean isSameLocation(PointInImage pim)

scale

public void scale(double xScale,
                  double yScale,
                  double zScale)

Scales this point coordinates.

Parameters:

xScale - the scaling factor for x coordinates

yScale - the scaling factor for y coordinates

zScale - the scaling factor for z coordinates

getUnscaledPoint

public PointInCanvas getUnscaledPoint()
                               throws java.lang.IllegalArgumentException

Converts the coordinates of this point into pixel units if this point is associated with a Path.

Returns:

this point in pixel coordinates

Throws:

java.lang.IllegalArgumentException - if this point is not associated with a Path

getUnscaledPoint

public PointInCanvas getUnscaledPoint(int view)

Converts the coordinates of this point into pixel units if this point is associated with a Path.

Parameters:

view - MultiDThreePanes.XY_PLANE, MultiDThreePanes.ZY_PLANE, etc.

Returns:

this point in pixel coordinates

Throws:

java.lang.IllegalArgumentException - if this point is not associated with a Path, or view was not recognized

toUPoint

public sholl.UPoint toUPoint()

getPath

public Path getPath()

Returns the Path associated with this node (if any)

Returns:

the path associated with this node or null if setPath(Path) has not been called.

setPath

public void setPath(Path onPath)

Associates a Path with this node

Parameters:

onPath - the Path to be associated with this node

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

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

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