SpotCollection (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.SpotCollection

All Implemented Interfaces:

MultiThreaded
```
public class SpotCollection
extends Object
implements MultiThreaded
```
A utility class that wrap the SortedMap we use to store the spots contained in each frame with a few utility methods.
Internally we rely on ConcurrentSkipListMap to allow concurrent access without clashes.
This class is MultiThreaded. There are a few processes that can benefit from multithreaded computation (filter(Collection), filter(FeatureFilter)

Author:

Jean-Yves Tinevez - Feb 2011 -2013. Revised December 2020.

Field Summary

Fields
Modifier and Type Field and Description

static Double ONE

static String VISIBILITY

static Double ZERO

Fields
Modifier and Type	Field and Description
`static Double`	`ONE`
`static String`	`VISIBILITY`
`static Double`	`ZERO`

Constructor Summary

Constructors
Constructor and Description

SpotCollection()
Construct a new empty spot collection.

Constructors
Constructor and Description
`SpotCollection()` Construct a new empty spot collection.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`add(Spot spot, Integer frame)` Adds the given spot to this collection, at the specified frame, and mark it as visible.
`void`	`clear()` Removes all the content from this collection.
`void`	`crop()` Remove all the non-visible spots of this collection.
`void`	`filter(Collection<FeatureFilter> filters)` Filters out the content of this collection using the specified `FeatureFilter` collection.
`void`	`filter(FeatureFilter featurefilter)` Filters out the content of this collection using the specified `FeatureFilter`.
`Integer`	`firstKey()` Returns the first (lowest) frame currently in this collection.
`static SpotCollection`	`fromCollection(Iterable<Spot> spots)` Creates a new `SpotCollection` containing only the specified spots.
`static SpotCollection`	`fromMap(Map<Integer,Set<Spot>> source)` Creates a new `SpotCollection` from a copy of the specified map of sets.
`Spot`	`getClosestSpot(Spot location, int frame, boolean visibleSpotsOnly)` Returns the closest `Spot` to the given location (encoded as a Spot), contained in the frame `frame`.
`int`	`getNSpots(boolean visibleSpotsOnly)` Returns the total number of spots in this collection, over all frames.
`int`	`getNSpots(int frame, boolean visibleSpotsOnly)` Returns the number of spots at the given frame.
`int`	`getNumThreads()`
`Spot`	`getSpotAt(Spot location, int frame, boolean visibleSpotsOnly)` Returns the `Spot` at the given location (encoded as a Spot), contained in the frame `frame`.
`Iterable<Spot>`	`iterable(boolean visibleSpotsOnly)` A convenience methods that returns an `Iterable` wrapper for this collection as a whole.
`Iterable<Spot>`	`iterable(int frame, boolean visibleSpotsOnly)` A convenience methods that returns an `Iterable` wrapper for a specific frame of this spot collection.
`Iterator<Spot>`	`iterator(boolean visibleSpotsOnly)` Return an iterator that iterates over all the spots contained in this collection.
`Iterator<Spot>`	`iterator(Integer frame, boolean visibleSpotsOnly)` Return an iterator that iterates over the spots in the specified frame.
`NavigableSet<Integer>`	`keySet()` Returns a NavigableSet view of the frames contained in this collection.
`Integer`	`lastKey()` Returns the last (highest) frame currently in this collection.
`void`	`put(int frame, Collection<Spot> spots)` Stores the specified spots as the content of the specified frame.
`boolean`	`remove(Spot spot, Integer frame)` Removes the given spot from this collection, at the specified frame.
`Spot`	`search(int ID)` Retrieves and returns the `Spot` object in this collection with the specified ID.
`void`	`setNumThreads()`
`void`	`setNumThreads(int numThreads)`
`void`	`setVisible(boolean visible)` Marks all the content of this collection as visible or invisible.
`String`	`toString()`

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

- Field Detail
  - ZERO
```
public static final Double ZERO
```
  - ONE
```
public static final Double ONE
```
  - VISIBILITY
```
public static final String VISIBILITY
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SpotCollection
```
public SpotCollection()
```
    Construct a new empty spot collection.
- Method Detail
  - search
```
public Spot search(int ID)
```
    Retrieves and returns the Spot object in this collection with the specified ID. Returns null if the spot cannot be found. All spots, visible or not, are searched for.
    
    Parameters:
    
    ID - the ID to look for.
    
    Returns:
    
    the spot with the specified ID or null if this spot does not exist or does not belong to this collection.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - add
```
public void add(Spot spot,
                Integer frame)
```
    Adds the given spot to this collection, at the specified frame, and mark it as visible.
    If the frame does not exist yet in the collection, it is created and added. Upon adding, the added spot has its feature Spot.FRAME updated with the passed frame value.
    
    Parameters:
    
    spot - the spot to add.
    
    frame - the frame to add it to.
  - remove
```
public boolean remove(Spot spot,
                      Integer frame)
```
    Removes the given spot from this collection, at the specified frame.
    If the spot frame collection does not exist yet, nothing is done and false is returned. If the spot cannot be found in the frame content, nothing is done and false is returned.
    
    Parameters:
    
    spot - the spot to remove.
    
    frame - the frame to remove it from.
    
    Returns:
    
    true if the spot was succesfully removed.
  - setVisible
```
public void setVisible(boolean visible)
```
    Marks all the content of this collection as visible or invisible.
    
    Parameters:
    
    visible - if true, all spots will be marked as visible.
  - filter
```
public final void filter(FeatureFilter featurefilter)
```
    Filters out the content of this collection using the specified FeatureFilter. Spots that are filtered out are marked as invisible, and visible otherwise.
    
    Parameters:
    
    featurefilter - the filter to use.
  - filter
```
public final void filter(Collection<FeatureFilter> filters)
```
    Filters out the content of this collection using the specified FeatureFilter collection. Spots that are filtered out are marked as invisible, and visible otherwise. To be marked as visible, a spot must pass all of the specified filters (AND chaining).
    
    Parameters:
    
    filters - the filter collection to use.
  - getClosestSpot
```
public final Spot getClosestSpot(Spot location,
                                 int frame,
                                 boolean visibleSpotsOnly)
```
    Returns the closest Spot to the given location (encoded as a Spot), contained in the frame frame. If the frame has no spot, return null.
    
    Parameters:
    
    location - the location to search for.
    
    frame - the frame to inspect.
    
    visibleSpotsOnly - if true, will only search though visible spots. If false, will search through all spots.
    
    Returns:
    
    the closest spot to the specified location, member of this collection.
  - getSpotAt
```
public final Spot getSpotAt(Spot location,
                            int frame,
                            boolean visibleSpotsOnly)
```
    Returns the Spot at the given location (encoded as a Spot), contained in the frame frame. A spot is returned only if there exists a spot such that the given location is within the spot radius. Otherwise null is returned.
    
    Parameters:
    
    location - the location to search for.
    
    frame - the frame to inspect.
    
    visibleSpotsOnly - if true, will only search though visible spots. If false, will search through all spots.
    
    Returns:
    
    the closest spot such that the specified location is within its radius, member of this collection, or null is such a spots cannot be found.
  - getNSpots
```
public final int getNSpots(boolean visibleSpotsOnly)
```
    Returns the total number of spots in this collection, over all frames.
    
    Parameters:
    
    visibleSpotsOnly - if true, will only count visible spots. If false count all spots.
    
    Returns:
    
    the total number of spots in this collection.
  - getNSpots
```
public int getNSpots(int frame,
                     boolean visibleSpotsOnly)
```
    Returns the number of spots at the given frame.
    
    Parameters:
    
    frame - the frame.
    
    visibleSpotsOnly - if true, will only count visible spots. If false count all spots.
    
    Returns:
    
    the number of spots at the given frame.
  - iterator
```
public Iterator<Spot> iterator(boolean visibleSpotsOnly)
```
    Return an iterator that iterates over all the spots contained in this collection.
    
    Parameters:
    
    visibleSpotsOnly - if true, the returned iterator will only iterate through visible spots. If false, it will iterate over all spots.
    
    Returns:
    
    an iterator that iterates over this collection.
  - iterator
```
public Iterator<Spot> iterator(Integer frame,
                               boolean visibleSpotsOnly)
```
    Return an iterator that iterates over the spots in the specified frame.
    
    Parameters:
    
    visibleSpotsOnly - if true, the returned iterator will only iterate through visible spots. If false, it will iterate over all spots.
    
    frame - the frame to iterate over.
    
    Returns:
    
    an iterator that iterates over the content of a frame of this collection.
  - iterable
```
public Iterable<Spot> iterable(boolean visibleSpotsOnly)
```
    A convenience methods that returns an Iterable wrapper for this collection as a whole.
    
    Parameters:
    
    visibleSpotsOnly - if true, the iterable will contains only visible spots. Otherwise, it will contain all the spots.
    
    Returns:
    
    an iterable view of this spot collection.
  - iterable
```
public Iterable<Spot> iterable(int frame,
                               boolean visibleSpotsOnly)
```
    A convenience methods that returns an Iterable wrapper for a specific frame of this spot collection. The iterable is backed-up by the actual collection content, so modifying it can have unexpected results.
    
    Parameters:
    
    visibleSpotsOnly - if true, the iterable will contains only visible spots of the specified frame. Otherwise, it will contain all the spots of the specified frame.
    
    frame - the frame of the content the returned iterable will wrap.
    
    Returns:
    
    an iterable view of the content of a single frame of this spot collection.
  - put
```
public void put(int frame,
                Collection<Spot> spots)
```
    Stores the specified spots as the content of the specified frame. The added spots are all marked as not visible. Their Spot.FRAME is updated to be the specified frame.
    
    Parameters:
    
    frame - the frame to store these spots at. The specified spots replace the previous content of this frame, if any.
    
    spots - the spots to store.
  - firstKey
```
public Integer firstKey()
```
    Returns the first (lowest) frame currently in this collection.
    
    Returns:
    
    the first (lowest) frame currently in this collection.
  - lastKey
```
public Integer lastKey()
```
    Returns the last (highest) frame currently in this collection.
    
    Returns:
    
    the last (highest) frame currently in this collection.
  - keySet
```
public NavigableSet<Integer> keySet()
```
    Returns a NavigableSet view of the frames contained in this collection. The set's iterator returns the keys in ascending order. The set is backed by the map, so changes to the map are reflected in the set, and vice-versa. The set supports element removal, which removes the corresponding mapping from the map, via the Iterator.remove, Set.remove, removeAll, retainAll, and clear operations. It does not support the add or addAll operations.
    The view's iterator is a "weakly consistent" iterator that will never throw ConcurrentModificationException, and guarantees to traverse elements as they existed upon construction of the iterator, and may (but is not guaranteed to) reflect any modifications subsequent to construction.
    
    Returns:
    
    a navigable set view of the frames in this collection.
  - clear
```
public void clear()
```
    Removes all the content from this collection.
  - setNumThreads
```
public void setNumThreads()
```
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - setNumThreads
```
public void setNumThreads(int numThreads)
```
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - getNumThreads
```
public int getNumThreads()
```
    Specified by:
    
    getNumThreads in interface MultiThreaded
  - crop
```
public void crop()
```
    Remove all the non-visible spots of this collection.
  - fromCollection
```
public static SpotCollection fromCollection(Iterable<Spot> spots)
```
    Creates a new SpotCollection containing only the specified spots. Their frame origin is retrieved from their Spot.FRAME feature, so it must be set properly for all spots. All the spots of the new collection have the same visibility that the one they carry.
    
    Parameters:
    
    spots - the spot collection to build from.
    
    Returns:
    
    a new SpotCollection instance.
  - fromMap
```
public static SpotCollection fromMap(Map<Integer,Set<Spot>> source)
```
    Creates a new SpotCollection from a copy of the specified map of sets. The spots added this way are completely untouched. In particular, their VISIBILITY feature is left untouched, which makes this method suitable to de-serialize a SpotCollection.
    
    Parameters:
    
    source - the map to buidl the spot collection from.
    
    Returns:
    
    a new SpotCollection.

Class SpotCollection

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ZERO

ONE

VISIBILITY

Constructor Detail

SpotCollection

Method Detail

search

toString

add

remove

setVisible

filter

filter

getClosestSpot

getSpotAt

getNSpots

getNSpots

iterator

iterator

iterable

iterable

put

firstKey

lastKey

keySet

clear

setNumThreads

setNumThreads

getNumThreads

crop

fromCollection

fromMap