de.unihalle.informatik.MiToBo.features

Class MorphologyAnalyzer2DInProData

java.lang.Object

de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData

public class MorphologyAnalyzer2DInProData
extends Object

Data type for protrusion/indentation analysis of region contours.

Author:

Birgit Moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	MorphologyAnalyzer2DInProData.InflectionPoint Class to represent inflection points.
class	MorphologyAnalyzer2DInProData.InProContourSegment Class to represent concave/convex segments along a contour.
static class	MorphologyAnalyzer2DInProData.SegmentType Type of segment to distinguish between indentation and protrusions.

Field Summary

Fields

Modifier and Type	Field and Description
(package private) double	avgApicalIndentationLength Average of apical indentations lengths.
(package private) double	avgApicalProtrusionLength Average of apical protrusion lengths.
(package private) double	avgBasalIndentationLength Average of basal indentation lengths.
(package private) double	avgBasalProtrusionLength Average of basal protrusion lengths.
(package private) double	avgBaselineIndentationLength Average length of indentations baselines.
(package private) double	avgBaselineProtrusionLength Average length of protrusion baselines.
(package private) double	avgEquatorIndentationLength Average length of indentation equators.
(package private) double	avgEquatorProtrusionLength Average length of protrusion equators.
(package private) double	avgIndentationLength Average length of indentations.
(package private) double	avgProtrusionLength Average length of protrusions.
private MTBContour2D	contour Analyzed region contour.
private int	contourID ID of the contour.
private LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment>	indentationSegs List of indentation segments along the contour.
private LinkedList<MorphologyAnalyzer2DInProData.InflectionPoint>	inflectionPoints List of inflection points along the contour.
(package private) double	nonProtrusionArea Non-protrusion area in cell region.
(package private) int	numberOfProtrusions Number of detected protrusions along contour.
private LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment>	protrusionSegs List of protrusion segments along the contour.

Constructor Summary

Constructors

Constructor and Description
MorphologyAnalyzer2DInProData(MTBContour2D c, int id) Default constructor.

Method Summary

Modifier and Type	Method and Description
void	addIndentationSegments(LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment> is) Add list of indentation segments to object.
void	addInflectionPoints(LinkedList<MorphologyAnalyzer2DInProData.InflectionPoint> ip) Add list of inflection points to object.
void	addProtrusionSegments(LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment> ps) Add list of protrusion segments to object.
MTBContour2D	getContour() Get a reference to the contour.
int	getContourID() Get the contour ID.
LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment>	getIndentationSegments() Get list of indentation segments.
LinkedList<MorphologyAnalyzer2DInProData.InflectionPoint>	getInflectionPoints() Get list of inflection points.
LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment>	getProtrusionSegments() Get list of protrusion segments.

Methods inherited from class java.lang.Object

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

Field Detail

contour

private MTBContour2D contour

Analyzed region contour.

contourID

private int contourID

ID of the contour.

protrusionSegs

private LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment> protrusionSegs

List of protrusion segments along the contour.

indentationSegs

private LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment> indentationSegs

List of indentation segments along the contour.

inflectionPoints

private LinkedList<MorphologyAnalyzer2DInProData.InflectionPoint> inflectionPoints

List of inflection points along the contour.

numberOfProtrusions

int numberOfProtrusions

Number of detected protrusions along contour.

avgEquatorProtrusionLength

double avgEquatorProtrusionLength

Average length of protrusion equators.

avgEquatorIndentationLength

double avgEquatorIndentationLength

Average length of indentation equators.

avgProtrusionLength

double avgProtrusionLength

Average length of protrusions.

avgBaselineProtrusionLength

double avgBaselineProtrusionLength

Average length of protrusion baselines.

avgApicalProtrusionLength

double avgApicalProtrusionLength

Average of apical protrusion lengths.

avgBasalProtrusionLength

double avgBasalProtrusionLength

Average of basal protrusion lengths.

nonProtrusionArea

double nonProtrusionArea

Non-protrusion area in cell region.

avgIndentationLength

double avgIndentationLength

Average length of indentations.

avgBaselineIndentationLength

double avgBaselineIndentationLength

Average length of indentations baselines.

avgApicalIndentationLength

double avgApicalIndentationLength

Average of apical indentations lengths.

avgBasalIndentationLength

double avgBasalIndentationLength

Average of basal indentation lengths.

Constructor Detail

MorphologyAnalyzer2DInProData

public MorphologyAnalyzer2DInProData(MTBContour2D c,
                                     int id)

Default constructor.

Parameters:

c - Contour.

id - ID of contour.

Method Detail

addIndentationSegments

public void addIndentationSegments(LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment> is)

Add list of indentation segments to object.

Parameters:

is - List of segments.

addProtrusionSegments

public void addProtrusionSegments(LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment> ps)

Add list of protrusion segments to object.

Parameters:

ps - List of segments.

addInflectionPoints

public void addInflectionPoints(LinkedList<MorphologyAnalyzer2DInProData.InflectionPoint> ip)

Add list of inflection points to object.

Parameters:

ip - List of points.

getContour

public MTBContour2D getContour()

Get a reference to the contour.

Returns:

Reference to contour.

getContourID

public int getContourID()

Get the contour ID.

Returns:

ID of contour.

getIndentationSegments

public LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment> getIndentationSegments()

Get list of indentation segments.

Returns:

List of segments.

getProtrusionSegments

public LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment> getProtrusionSegments()

Get list of protrusion segments.

Returns:

List of segments.

getInflectionPoints

public LinkedList<MorphologyAnalyzer2DInProData.InflectionPoint> getInflectionPoints()

Get list of inflection points.

Returns:

List of points.