Class OtoProfile

java.lang.Object

OtoProfile

public class OtoProfile
extends java.lang.Object

OtoProfile Transforms the otolith profile to enhance the rings

Author:

Vitor Vaz da Silva

Constructor Summary

Constructors

Constructor and Description
OtoProfile(Point[] pontos, ij.ImagePlus image) OtoProfile Creates an object with a initial profile

Method Summary

Modifier and Type	Method and Description
void	buildSegments() buildSegments Convert the profile into segments
java.util.ArrayList<Segment>[]	countRings(java.util.ArrayList<Segment> an, Option op, int ch) countRings Count identified otolith rings from @param an segments using @param op options on @param ch channel
java.util.ArrayList<Segment>	filterSegments(int ch) filterSegments Filter the segments of channel @param ch by connecting segments with same derivative sign
double[]	getDistances() getDistances Return all point distance
double[]	getPointsFromChannel(int ch) getPointsFromChannel Get profile points from channel @param ch
java.util.ArrayList<Segment>	getSegments() getSegments Return the segment list
void	joinSegments() joinSegments Connect segments forming a continuous connected segment
Point[]	points() points Profile points
Point[]	runFilter() runFilter Apply the filer to the profile
Point[]	segmentsToPoints() segmentsToPoints Convert segments to points
void	setFilter(Filter f) setFilter Set filter
void	setSegments(java.util.ArrayList<Segment> an) setSegments Set segment list to @param an
void	smoothSegments(double grain, int ch) smoothSegments Remove segments with heights in channel @param ch below @param grain.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OtoProfile

public OtoProfile(Point[] pontos,
                  ij.ImagePlus image)

OtoProfile Creates an object with a initial profile

Parameters:

pontos -

image -

Method Detail

points

public Point[] points()

points Profile points

Returns:

setFilter

public void setFilter(Filter f)

setFilter Set filter

Parameters:

f -

runFilter

public Point[] runFilter()

runFilter Apply the filer to the profile

Returns:

getPointsFromChannel

public double[] getPointsFromChannel(int ch)

getPointsFromChannel Get profile points from channel @param ch

Parameters:

ch -

Returns:

buildSegments

public void buildSegments()

buildSegments Convert the profile into segments

smoothSegments

public void smoothSegments(double grain,
                           int ch)

smoothSegments Remove segments with heights in channel @param ch below @param grain.

Parameters:

grain -

ch -

joinSegments

public void joinSegments()

joinSegments Connect segments forming a continuous connected segment

segmentsToPoints

public Point[] segmentsToPoints()

segmentsToPoints Convert segments to points

Returns:

getSegments

public java.util.ArrayList<Segment> getSegments()

getSegments Return the segment list

Returns:

setSegments

public void setSegments(java.util.ArrayList<Segment> an)

setSegments Set segment list to @param an

Parameters:

an -

getDistances

public double[] getDistances()

getDistances Return all point distance

Returns:

countRings

public java.util.ArrayList<Segment>[] countRings(java.util.ArrayList<Segment> an,
                                                 Option op,
                                                 int ch)

countRings Count identified otolith rings from @param an segments using @param op options on @param ch channel

Parameters:

an -

op -

ch -

Returns:

filterSegments

public java.util.ArrayList<Segment> filterSegments(int ch)

filterSegments Filter the segments of channel @param ch by connecting segments with same derivative sign

Parameters:

ch -

Returns: