de.mpg.biochem.mars.image

Class Peak

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.image.Peak

All Implemented Interfaces:

JsonConvertibleRecord, net.imglib2.EuclideanSpace, net.imglib2.RealLocalizable

public class Peak
extends AbstractJsonConvertibleRecord
implements net.imglib2.RealLocalizable

Stores information about detected 2D intensity peaks. Implements RealLocalizable to allow for KDTree searches. Depending on the implementation, Peaks can be assigned a UID, colorName, Rsquared, as well as t and c position. All parameters from subpixel localization are included as well as error margins. Peaks can be linked to other peaks. The valid parameter is used for convenience in tracking algorithms.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	AREA
static java.lang.String	BASELINE
static java.lang.String	CIRCULARITY
static java.lang.String	HEIGHT
static java.util.concurrent.atomic.AtomicLong	idGenerator
static java.lang.String	INTENSITY
static java.lang.String	MEAN_BACKGROUND
static java.lang.String	MEDIAN_BACKGROUND
static java.lang.String	PERIMETER
static java.lang.String	R2
static java.lang.String	SIGMA
static java.lang.String	T
static java.lang.String	UNCORRECTED_INTENSITY
static java.lang.String	X
static java.lang.String	Y

Constructor Summary

Constructors

Constructor and Description
Peak(double[] values)
Peak(double x, double y)
Peak(double x, double y, double height, double baseline, double sigma, int t)
Peak(double x, double y, int t)
Peak(com.fasterxml.jackson.core.JsonParser jParser)
Peak(Peak peak)
Peak(java.lang.String trackUID, double x, double y)

Method Summary

Modifier and Type	Method and Description
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
Peak	getBackwardLink()
long	getBackwardLinkID()
double	getBaseline()
int	getC()
java.lang.String	getColorName()
double	getDoublePosition(int arg0)
float	getFloatPosition(int arg0)
Peak	getForwardLink()
long	getForwardLinkID()
double	getHeight()
long	getID()
double	getIntensity()
double	getMeanBackground()
double	getMedianBackground()
java.util.Map<java.lang.String,java.lang.Double>	getProperties()
double	getRSquared()
PeakShape	getShape()
double	getSigma()
int	getT()
java.lang.String	getTrackUID()
double	getX()
double	getY()
boolean	isValid()
void	localize(double[] arg0)
void	localize(float[] arg0)
int	numDimensions()
void	reset()
void	reset(double x, double y, int t)
void	setBackwardLink(Peak link)
void	setBackwardLinkID(long backwardLinkID)
void	setC(int c)
void	setColorName(java.lang.String colorName)
void	setForwardLink(Peak link)
void	setForwardLinkID(long forwardLinkID)
void	setID(long id)
void	setIntensity(double intensity)
void	setMeanBackground(double meanBackground)
void	setMedianBackground(double medianBackground)
void	setProperty(java.lang.String name, java.lang.Double value)
void	setRsquared(double R2value)
void	setShape(PeakShape peakShape)
void	setT(int t)
void	setTrackUID(java.lang.String trackUID)
void	setValid(boolean valid)
void	setValues(double[] values)
void	setX(double x)
void	setY(double y)

Methods inherited from class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.imglib2.RealLocalizable

localize, positionAsDoubleArray, positionAsRealPoint

Field Detail

idGenerator

public static final java.util.concurrent.atomic.AtomicLong idGenerator

X

public static final java.lang.String X

See Also:

Constant Field Values

Y

public static final java.lang.String Y

See Also:

Constant Field Values

T

public static final java.lang.String T

See Also:

Constant Field Values

HEIGHT

public static final java.lang.String HEIGHT

See Also:

Constant Field Values

BASELINE

public static final java.lang.String BASELINE

See Also:

Constant Field Values

SIGMA

public static final java.lang.String SIGMA

See Also:

Constant Field Values

R2

public static final java.lang.String R2

See Also:

Constant Field Values

MEDIAN_BACKGROUND

public static final java.lang.String MEDIAN_BACKGROUND

See Also:

Constant Field Values

INTENSITY

public static final java.lang.String INTENSITY

See Also:

Constant Field Values

AREA

public static final java.lang.String AREA

See Also:

Constant Field Values

PERIMETER

public static final java.lang.String PERIMETER

See Also:

Constant Field Values

CIRCULARITY

public static final java.lang.String CIRCULARITY

See Also:

Constant Field Values

UNCORRECTED_INTENSITY

public static final java.lang.String UNCORRECTED_INTENSITY

See Also:

Constant Field Values

MEAN_BACKGROUND

public static final java.lang.String MEAN_BACKGROUND

See Also:

Constant Field Values

Constructor Detail

Peak

public Peak(com.fasterxml.jackson.core.JsonParser jParser)
     throws java.io.IOException

Throws:

java.io.IOException

Peak

public Peak(double[] values)

Peak

public Peak(double x,
            double y,
            double height,
            double baseline,
            double sigma,
            int t)

Peak

public Peak(double x,
            double y,
            int t)

Peak

public Peak(java.lang.String trackUID,
            double x,
            double y)

Peak

public Peak(double x,
            double y)

Peak

public Peak(Peak peak)

Method Detail

reset

public void reset()

reset

public void reset(double x,
                  double y,
                  int t)

getX

public double getX()

setX

public void setX(double x)

getY

public double getY()

setY

public void setY(double y)

getHeight

public double getHeight()

getBaseline

public double getBaseline()

getSigma

public double getSigma()

getShape

public PeakShape getShape()

setShape

public void setShape(PeakShape peakShape)

isValid

public boolean isValid()

setValid

public void setValid(boolean valid)

setID

public void setID(long id)

getID

public long getID()

setTrackUID

public void setTrackUID(java.lang.String trackUID)

getTrackUID

public java.lang.String getTrackUID()

getT

public int getT()

setT

public void setT(int t)

getC

public int getC()

setC

public void setC(int c)

setColorName

public void setColorName(java.lang.String colorName)

getColorName

public java.lang.String getColorName()

getProperties

public java.util.Map<java.lang.String,java.lang.Double> getProperties()

setProperty

public void setProperty(java.lang.String name,
                        java.lang.Double value)

setValues

public void setValues(double[] values)

setForwardLink

public void setForwardLink(Peak link)

getForwardLink

public Peak getForwardLink()

setForwardLinkID

public void setForwardLinkID(long forwardLinkID)

getForwardLinkID

public long getForwardLinkID()

setBackwardLink

public void setBackwardLink(Peak link)

getBackwardLink

public Peak getBackwardLink()

setBackwardLinkID

public void setBackwardLinkID(long backwardLinkID)

getBackwardLinkID

public long getBackwardLinkID()

setIntensity

public void setIntensity(double intensity)

getIntensity

public double getIntensity()

setMedianBackground

public void setMedianBackground(double medianBackground)

getMedianBackground

public double getMedianBackground()

setMeanBackground

public void setMeanBackground(double meanBackground)

getMeanBackground

public double getMeanBackground()

setRsquared

public void setRsquared(double R2value)

getRSquared

public double getRSquared()

numDimensions

public int numDimensions()

Specified by:

numDimensions in interface net.imglib2.EuclideanSpace

getDoublePosition

public double getDoublePosition(int arg0)

Specified by:

getDoublePosition in interface net.imglib2.RealLocalizable

getFloatPosition

public float getFloatPosition(int arg0)

Specified by:

getFloatPosition in interface net.imglib2.RealLocalizable

localize

public void localize(float[] arg0)

Specified by:

localize in interface net.imglib2.RealLocalizable

localize

public void localize(double[] arg0)

Specified by:

localize in interface net.imglib2.RealLocalizable

createIOMaps

protected void createIOMaps()

Description copied from class: AbstractJsonConvertibleRecord

Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.

Specified by:

createIOMaps in class AbstractJsonConvertibleRecord