SWCPoint (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.util.PointInImage
- - sc.fiji.snt.util.SWCPoint

All Implemented Interfaces:

Comparable<SWCPoint>, SNTPoint
```
public class SWCPoint
extends PointInImage
implements 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)

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static StringReader`	`collectionAsReader(Collection<SWCPoint> points)` Converts a collection of SWC points into a Reader.
`int`	`compareTo(SWCPoint o)`
`boolean`	`equals(Object o)`
`static void`	`flush(Collection<SWCPoint> points, PrintWriter pw)` Prints a list of points as space-separated values.
`BrainAnnotation`	`getAnnotation()`
`Color`	`getColor()`
`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)
`String`	`getTags()`
`double`	`getX()`
`double`	`getY()`
`double`	`getZ()`
`int`	`hashCode()`
`void`	`setAnnotation(BrainAnnotation annotation)` Assigns a neuropil annotation (e.g., atlas compartment) to this point.
`void`	`setColor(Color color)`
`void`	`setPreviousPoint(SWCPoint previousPoint)` Sets the preceding node in the reconstruction
`void`	`setTags(String tags)`
`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
chebyshevDxTo, chebyshevXYdxTo, chebyshevZdxTo, clone, distanceSquaredTo, distanceSquaredTo, distanceTo, euclideanDxTo, getCoordinateOnAxis, getHemisphere, getPath, getUnscaledPoint, getUnscaledPoint, isReal, isSameLocation, scale, setHemisphere, setPath, transform

Methods inherited from class java.lang.Object
finalize, 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 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 String toString()
```
    Overrides:
    
    toString in class PointInImage
  - compareTo
```
public int compareTo(SWCPoint o)
```
    Specified by:
    
    compareTo in interface Comparable<SWCPoint>
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class PointInImage
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class PointInImage
  - collectionAsReader
```
public static StringReader collectionAsReader(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(Collection<SWCPoint> points,
                         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 List<SWCPoint> getNextPoints()
```
    Returns the list holding the subsequent nodes in the reconstructed structure after this one.
    
    Returns:
    
    the list of "next points"
  - setTags
```
public void setTags(String tags)
```
  - setColor
```
public void setColor(Color color)
```
  - getTags
```
public String getTags()
```
  - getColor
```
public Color getColor()
```

Class SWCPoint

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

id

type

parent

radius

Constructor Detail

SWCPoint

Method Detail

xSeparationFromPreviousPoint

ySeparationFromPreviousPoint

zSeparationFromPreviousPoint

toString

compareTo

equals

hashCode

collectionAsReader

flush

getX

getY

getZ

setAnnotation

getAnnotation

getPreviousPoint

setPreviousPoint

getNextPoints

setTags

setColor

getTags

getColor