Spot (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- net.imglib2.AbstractEuclideanSpace
- - fiji.plugin.trackmate.Spot

All Implemented Interfaces:

Comparable<Spot>, EuclideanSpace, RealLocalizable
```
public class Spot
extends AbstractEuclideanSpace
implements RealLocalizable, Comparable<Spot>
```
A RealLocalizable implementation, used in TrackMate to represent a detection.
On top of being a RealLocalizable, it can store additional numerical named features, with a Map-like syntax. Constructors enforce the specification of the spot location in 3D space (if Z is unused, put 0), the spot radius, and the spot quality. This somewhat cumbersome syntax is made to avoid any bad surprise with missing features in a subsequent use. The spot temporal features (FRAME and POSITION_T) are set upon adding to a SpotCollection.
Each spot received at creation a unique ID (as an int), used later for saving, retrieving and loading. Interfering with this value will predictively cause undesired behavior.

Author:

Jean-Yves Tinevez <jeanyves.tinevez@gmail.com> 2010, 2013

Field Summary

Fields
Modifier and Type	Field and Description
`static Map<String,Dimension>`	`FEATURE_DIMENSIONS` The 7 privileged spot feature dimensions.
`static Map<String,String>`	`FEATURE_NAMES` The 7 privileged spot feature names.
`static Map<String,String>`	`FEATURE_SHORT_NAMES` The 7 privileged spot feature short names.
`static Collection<String>`	`FEATURES` The 7 privileged spot features that must be set by a spot detector: `QUALITY`, `POSITION_X`, `POSITION_Y`, `POSITION_Z`, `POSITION_Z`, `RADIUS`, `FRAME` .
`static String`	`FRAME` The name of the frame feature.
`static Comparator<Spot>`	`frameComparator` A comparator used to sort spots by ascending frame.
`static AtomicInteger`	`IDcounter`
`static Map<String,Boolean>`	`IS_INT` The 7 privileged spot feature isInt flags.
`static Comparator<Spot>`	`nameComparator` A comparator used to sort spots by name.
`static String[]`	`POSITION_FEATURES` The position features.
`static String`	`POSITION_T` The name of the spot T position feature.
`static String`	`POSITION_X` The name of the spot X position feature.
`static String`	`POSITION_Y` The name of the spot Y position feature.
`static String`	`POSITION_Z` The name of the spot Z position feature.
`static String`	`QUALITY` The name of the spot quality feature.
`static String`	`RADIUS` The name of the radius spot feature.
`static Comparator<Spot>`	`timeComparator` A comparator used to sort spots by ascending time feature.

Fields inherited from class net.imglib2.AbstractEuclideanSpace
n

Constructor Summary

Constructors
Constructor and Description
`Spot(double x, double y, double z, double radius, double quality)` Creates a new spot, and gives it a default name.
`Spot(double x, double y, double z, double radius, double quality, String name)` Creates a new spot.
`Spot(int ID)` Blank constructor meant to be used when loading a spot collection from a file.
`Spot(RealLocalizable location, double radius, double quality)` Creates a new spot, taking its 3D coordinates from a `RealLocalizable`.
`Spot(RealLocalizable location, double radius, double quality, String name)` Creates a new spot, taking its 3D coordinates from a `RealLocalizable`.
`Spot(Spot spot)` Creates a new spot, taking its location, its radius, its quality value and its name from the specified spot.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(Spot o)`
`double`	`diffTo(Spot s, String feature)` Returns the difference of the feature value for this spot with the one of the specified spot.
`String`	`echo()` Return a string representation of this spot, with calculated features.
`boolean`	`equals(Object other)`
`static Comparator<Spot>`	`featureComparator(String feature)` A comparator used to sort spots by ascending feature values.
`double`	`getDoublePosition(int d)`
`Double`	`getFeature(String feature)` Returns the value corresponding to the specified spot feature.
`Map<String,Double>`	`getFeatures()` Exposes the storage map of features for this spot.
`float`	`getFloatPosition(int d)`
`String`	`getName()`
`SpotRoi`	`getRoi()`
`int`	`hashCode()`
`int`	`ID()`
`void`	`localize(double[] position)`
`void`	`localize(float[] position)`
`double`	`normalizeDiffTo(Spot s, String feature)` Returns the absolute normalized difference of the feature value of this spot with the one of the given spot.
`void`	`putFeature(String feature, Double value)` Stores the specified feature value for this spot.
`void`	`setName(String name)` Set the name of this Spot.
`void`	`setRoi(SpotRoi roi)`
`double`	`squareDistanceTo(RealLocalizable s)` Returns the square distance from this spot to the specified spot.
`String`	`toString()`

Methods inherited from class net.imglib2.AbstractEuclideanSpace
numDimensions

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.imglib2.RealLocalizable
localize, positionAsDoubleArray, positionAsRealPoint

Methods inherited from interface net.imglib2.EuclideanSpace
numDimensions

- Field Detail
  - IDcounter
```
public static AtomicInteger IDcounter
```
  - QUALITY
```
public static final String QUALITY
```
    The name of the spot quality feature.
    
    See Also:
    
    Constant Field Values
  - RADIUS
```
public static final String RADIUS
```
    The name of the radius spot feature.
    
    See Also:
    
    Constant Field Values
  - POSITION_X
```
public static final String POSITION_X
```
    The name of the spot X position feature.
    
    See Also:
    
    Constant Field Values
  - POSITION_Y
```
public static final String POSITION_Y
```
    The name of the spot Y position feature.
    
    See Also:
    
    Constant Field Values
  - POSITION_Z
```
public static final String POSITION_Z
```
    The name of the spot Z position feature.
    
    See Also:
    
    Constant Field Values
  - POSITION_T
```
public static final String POSITION_T
```
    The name of the spot T position feature.
    
    See Also:
    
    Constant Field Values
  - FRAME
```
public static final String FRAME
```
    The name of the frame feature.
    
    See Also:
    
    Constant Field Values
  - POSITION_FEATURES
```
public static final String[] POSITION_FEATURES
```
    The position features.
  - FEATURES
```
public static final Collection<String> FEATURES
```
    The 7 privileged spot features that must be set by a spot detector: QUALITY, POSITION_X, POSITION_Y, POSITION_Z, POSITION_Z, RADIUS, FRAME .
  - FEATURE_NAMES
```
public static final Map<String,String> FEATURE_NAMES
```
    The 7 privileged spot feature names.
  - FEATURE_SHORT_NAMES
```
public static final Map<String,String> FEATURE_SHORT_NAMES
```
    The 7 privileged spot feature short names.
  - FEATURE_DIMENSIONS
```
public static final Map<String,Dimension> FEATURE_DIMENSIONS
```
    The 7 privileged spot feature dimensions.
  - IS_INT
```
public static final Map<String,Boolean> IS_INT
```
    The 7 privileged spot feature isInt flags.
  - timeComparator
```
public static final Comparator<Spot> timeComparator
```
    A comparator used to sort spots by ascending time feature.
  - frameComparator
```
public static final Comparator<Spot> frameComparator
```
    A comparator used to sort spots by ascending frame.
  - nameComparator
```
public static final Comparator<Spot> nameComparator
```
    A comparator used to sort spots by name. The comparison uses numerical natural sorting, So that "Spot_4" comes before "Spot_122".
- Constructor Detail
  - Spot
```
public Spot(double x,
            double y,
            double z,
            double radius,
            double quality,
            String name)
```
    Creates a new spot.
    
    Parameters:
    
    x - the spot X coordinates, in image units.
    
    y - the spot Y coordinates, in image units.
    
    z - the spot Z coordinates, in image units.
    
    radius - the spot radius, in image units.
    
    quality - the spot quality.
    
    name - the spot name.
  - Spot
```
public Spot(double x,
            double y,
            double z,
            double radius,
            double quality)
```
    Creates a new spot, and gives it a default name.
    
    Parameters:
    
    x - the spot X coordinates, in image units.
    
    y - the spot Y coordinates, in image units.
    
    z - the spot Z coordinates, in image units.
    
    radius - the spot radius, in image units.
    
    quality - the spot quality.
  - Spot
```
public Spot(RealLocalizable location,
            double radius,
            double quality,
            String name)
```
    Creates a new spot, taking its 3D coordinates from a RealLocalizable. The RealLocalizable must have at least 3 dimensions, and must return coordinates in image units.
    
    Parameters:
    
    location - the RealLocalizable that contains the spot locatiob.
    
    radius - the spot radius, in image units.
    
    quality - the spot quality.
    
    name - the spot name.
  - Spot
```
public Spot(RealLocalizable location,
            double radius,
            double quality)
```
    Creates a new spot, taking its 3D coordinates from a RealLocalizable. The RealLocalizable must have at least 3 dimensions, and must return coordinates in image units. The spot will get a default name.
    
    Parameters:
    
    location - the RealLocalizable that contains the spot locatiob.
    
    radius - the spot radius, in image units.
    
    quality - the spot quality.
  - Spot
```
public Spot(Spot spot)
```
    Creates a new spot, taking its location, its radius, its quality value and its name from the specified spot.
    
    Parameters:
    
    spot - the spot to read from.
  - Spot
```
public Spot(int ID)
```
    Blank constructor meant to be used when loading a spot collection from a file. Will mess with the IDcounter field, so this constructor should not be used for normal spot creation.
    
    Parameters:
    
    ID - the spot ID to set
- Method Detail
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - compareTo
```
public int compareTo(Spot o)
```
    Specified by:
    
    compareTo in interface Comparable<Spot>
  - equals
```
public boolean equals(Object other)
```
    Overrides:
    
    equals in class Object
  - setRoi
```
public void setRoi(SpotRoi roi)
```
  - getRoi
```
public SpotRoi getRoi()
```
  - getName
```
public String getName()
```
    Returns:
    
    the name for this Spot.
  - setName
```
public void setName(String name)
```
    Set the name of this Spot.
    
    Parameters:
    
    name - the name to use.
  - ID
```
public int ID()
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - echo
```
public String echo()
```
    Return a string representation of this spot, with calculated features.
    
    Returns:
    
    a string representation of the spot.
  - getFeatures
```
public Map<String,Double> getFeatures()
```
    Exposes the storage map of features for this spot. Altering the returned map will alter the spot.
    
    Returns:
    
    a map of Strings to Doubles.
  - getFeature
```
public Double getFeature(String feature)
```
    Returns the value corresponding to the specified spot feature.
    
    Parameters:
    
    feature - The feature string to retrieve the stored value for.
    
    Returns:
    
    the feature value, as a Double. Will be null if it has not been set.
  - putFeature
```
public void putFeature(String feature,
                       Double value)
```
    Stores the specified feature value for this spot.
    
    Parameters:
    
    feature - the name of the feature to store, as a String.
    
    value - the value to store, as a Double. Using null will have unpredicted outcomes.
  - diffTo
```
public double diffTo(Spot s,
                     String feature)
```
    Returns the difference of the feature value for this spot with the one of the specified spot. By construction, this operation is anti-symmetric ( A.diffTo(B) = - B.diffTo(A)).
    Will generate a NullPointerException if one of the spots does not store the named feature.
    
    Parameters:
    
    s - the spot to compare to.
    
    feature - the name of the feature to use for calculation.
    
    Returns:
    
    the difference in feature value.
  - normalizeDiffTo
```
public double normalizeDiffTo(Spot s,
                              String feature)
```
    Returns the absolute normalized difference of the feature value of this spot with the one of the given spot.
    If a and b are the feature values, then the absolute normalized difference is defined as Math.abs( a - b) / ( (a+b)/2 ).
    By construction, this operation is symmetric ( A.normalizeDiffTo(B) = B.normalizeDiffTo(A)).
    Will generate a NullPointerException if one of the spots does not store the named feature.
    
    Parameters:
    
    s - the spot to compare to.
    
    feature - the name of the feature to use for calculation.
    
    Returns:
    
    the absolute normalized difference feature value.
  - squareDistanceTo
```
public double squareDistanceTo(RealLocalizable s)
```
    Returns the square distance from this spot to the specified spot.
    
    Parameters:
    
    s - the spot to compute the square distance to.
    
    Returns:
    
    the square distance as a double.
  - localize
```
public void localize(float[] position)
```
    Specified by:
    
    localize in interface RealLocalizable
  - localize
```
public void localize(double[] position)
```
    Specified by:
    
    localize in interface RealLocalizable
  - getFloatPosition
```
public float getFloatPosition(int d)
```
    Specified by:
    
    getFloatPosition in interface RealLocalizable
  - getDoublePosition
```
public double getDoublePosition(int d)
```
    Specified by:
    
    getDoublePosition in interface RealLocalizable
  - featureComparator
```
public static final Comparator<Spot> featureComparator(String feature)
```
    A comparator used to sort spots by ascending feature values.
    
    Parameters:
    
    feature - the feature to use for comparison. It is the caller responsibility to ensure that all spots have the target feature.
    
    Returns:
    
    a new Comparator.

Class Spot

Field Summary

Fields inherited from class net.imglib2.AbstractEuclideanSpace

Constructor Summary

Method Summary

Methods inherited from class net.imglib2.AbstractEuclideanSpace

Methods inherited from class java.lang.Object

Methods inherited from interface net.imglib2.RealLocalizable

Methods inherited from interface net.imglib2.EuclideanSpace

Field Detail

IDcounter

QUALITY

RADIUS

POSITION_X

POSITION_Y

POSITION_Z

POSITION_T

FRAME

POSITION_FEATURES

FEATURES

FEATURE_NAMES

FEATURE_SHORT_NAMES

FEATURE_DIMENSIONS

IS_INT

timeComparator

frameComparator

nameComparator

Constructor Detail

Spot

Spot

Spot

Spot

Spot

Spot

Method Detail

hashCode

compareTo

equals

setRoi

getRoi

getName

setName

ID

toString

echo

getFeatures

getFeature

putFeature

diffTo

normalizeDiffTo

squareDistanceTo

localize

localize

getFloatPosition

getDoublePosition

featureComparator