TrackMate (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

Algorithm, Benchmark, MultiThreaded, Cancelable, Named
```
public class TrackMate
extends Object
implements Benchmark, MultiThreaded, Algorithm, Named, Cancelable
```
The TrackMate_ class runs on the currently active time-lapse image (2D or 3D) and both identifies and tracks bright spots over time.

Required input: A 2D or 3D time-lapse image with bright blobs.

Author:

Nicholas Perry, Johannes Schindelin, Jean-Yves Tinevez - Institut Pasteur - July 2010 - 2018, revised in 2021

Field Summary

Fields
Modifier and Type	Field and Description
`protected String`	`errorMessage`
`protected Model`	`model` The model this trackmate will shape.
`protected int`	`numThreads`
`static String`	`PLUGIN_NAME_STR`
`static String`	`PLUGIN_NAME_VERSION`
`protected long`	`processingTime`
`protected Settings`	`settings`

Constructor Summary

Constructors
Constructor and Description

TrackMate()

TrackMate(Model model, Settings settings)

TrackMate(Settings settings)

Constructors
Constructor and Description
`TrackMate()`
`TrackMate(Model model, Settings settings)`
`TrackMate(Settings settings)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`cancel(String reason)`
`boolean`	`checkInput()`
`boolean`	`computeEdgeFeatures(boolean doLogIt)` Calculate all features for all detected spots.
`boolean`	`computeSpotFeatures(boolean doLogIt)` Calculate all features for all detected spots.
`boolean`	`computeTrackFeatures(boolean doLogIt)` Calculate all features for all tracks.
`boolean`	`execDetection()` Execute the detection part.
`boolean`	`execInitialSpotFiltering()` Execute the initial spot filtering part.
`boolean`	`execSpotFiltering(boolean doLogIt)` Execute the spot feature filtering part.
`boolean`	`execTrackFiltering(boolean doLogIt)`
`boolean`	`execTracking()` Execute the tracking part.
`String`	`getCancelReason()`
`String`	`getErrorMessage()`
`Model`	`getModel()`
`String`	`getName()`
`int`	`getNumThreads()`
`long`	`getProcessingTime()`
`Settings`	`getSettings()`
`boolean`	`isCanceled()`
`boolean`	`process()`
`void`	`setName(String name)`
`void`	`setNumThreads()`
`void`	`setNumThreads(int numThreads)`
`String`	`toString()`

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

- Field Detail
  - PLUGIN_NAME_STR
```
public static final String PLUGIN_NAME_STR
```
    See Also:
    
    Constant Field Values
  - PLUGIN_NAME_VERSION
```
public static final String PLUGIN_NAME_VERSION
```
  - model
```
protected final Model model
```
    The model this trackmate will shape.
  - settings
```
protected final Settings settings
```
  - processingTime
```
protected long processingTime
```
  - errorMessage
```
protected String errorMessage
```
  - numThreads
```
protected int numThreads
```
- Constructor Detail
  - TrackMate
```
public TrackMate(Settings settings)
```
  - TrackMate
```
public TrackMate(Model model,
                 Settings settings)
```
  - TrackMate
```
public TrackMate()
```
- Method Detail
  - getModel
```
public Model getModel()
```
  - getSettings
```
public Settings getSettings()
```
  - computeSpotFeatures
```
public boolean computeSpotFeatures(boolean doLogIt)
```
    Calculate all features for all detected spots.
    Features are calculated for each spot, using their location, and the raw image. Features to be calculated and analyzers are taken from the settings field of this object.
    
    Parameters:
    
    doLogIt - if true, the Logger of the model will be notified.
    
    Returns:
    
    true if the calculation was performed successfully, false otherwise.
  - computeEdgeFeatures
```
public boolean computeEdgeFeatures(boolean doLogIt)
```
    Calculate all features for all detected spots.
    Features are calculated for each spot, using their location, and the raw image. Features to be calculated and analyzers are taken from the settings field of this object.
    
    Parameters:
    
    doLogIt - if true, the Logger of the model will be notified.
    
    Returns:
    
    true if the calculation was performed successfuly, false otherwise.
  - computeTrackFeatures
```
public boolean computeTrackFeatures(boolean doLogIt)
```
    Calculate all features for all tracks.
    
    Parameters:
    
    doLogIt - if true, messages will be sent to the logger.
    
    Returns:
    
    true if the computation completed without errors.
  - execTracking
```
public boolean execTracking()
```
    Execute the tracking part.
    This method links all the selected spots from the thresholding part using the selected tracking algorithm. This tracking process will generate a graph (more precisely a SimpleWeightedGraph) made of the spot election for its vertices, and edges representing the links.
    The ModelChangeListeners of the model will be notified when the successful process is over.
    
    Returns:
    
    true if the computation completed without errors.
  - execDetection
```
public boolean execDetection()
```
    Execute the detection part.
    This method configure the chosen Settings.detectorFactory with the source image and the detector settings and execute the detection process for all the frames set in the Settings object of the target model.
    
    Returns:
    
    true if the whole detection step has executed correctly.
  - execInitialSpotFiltering
```
public boolean execInitialSpotFiltering()
```
    Execute the initial spot filtering part.
    Because of the presence of noise, it is possible that some of the regional maxima found in the detection step have identified noise, rather than objects of interest. This can generates a very high number of spots, which is inconvenient to deal with when it comes to computing their features, or displaying them.
    Any SpotDetector is expected to at least compute the Spot.QUALITY value for each spot it creates, so it is possible to set up an initial filtering on this feature, prior to any other operation.
    This method simply takes all the detected spots, and discard those whose quality value is below the threshold set by Settings.initialSpotFilterValue. The spot field is overwritten, and discarded spots can't be recalled.
    The ModelChangeListeners of this model will be notified with a ModelChangeEvent.SPOTS_COMPUTED event.
    
    Returns:
    
    true if the computation completed without errors.
  - execSpotFiltering
```
public boolean execSpotFiltering(boolean doLogIt)
```
    Execute the spot feature filtering part.
    Because of the presence of noise, it is possible that some of the regional maxima found in the detection step have identified noise, rather than objects of interest. A filtering operation based on the calculated features in this step should allow to rule them out.
    This method simply takes all the detected spots, and mark as visible the spots whose features satisfy all of the filters in the Settings object.
    The ModelChangeListeners of this model will be notified with a ModelChangeEvent.SPOTS_FILTERED event.
    
    Parameters:
    
    doLogIt - if true, will send a message to the model logger.
    
    Returns:
    
    true if the computation completed without errors.
  - execTrackFiltering
```
public boolean execTrackFiltering(boolean doLogIt)
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - checkInput
```
public boolean checkInput()
```
    Specified by:
    
    checkInput in interface Algorithm
  - getErrorMessage
```
public String getErrorMessage()
```
    Specified by:
    
    getErrorMessage in interface Algorithm
  - process
```
public boolean process()
```
    Specified by:
    
    process in interface Algorithm
  - getNumThreads
```
public int getNumThreads()
```
    Specified by:
    
    getNumThreads in interface MultiThreaded
  - setNumThreads
```
public void setNumThreads()
```
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - setNumThreads
```
public void setNumThreads(int numThreads)
```
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - getProcessingTime
```
public long getProcessingTime()
```
    Specified by:
    
    getProcessingTime in interface Benchmark
  - getName
```
public String getName()
```
    Specified by:
    
    getName in interface Named
  - setName
```
public void setName(String name)
```
    Specified by:
    
    setName in interface Named
  - isCanceled
```
public boolean isCanceled()
```
    Specified by:
    
    isCanceled in interface Cancelable
  - cancel
```
public void cancel(String reason)
```
    Specified by:
    
    cancel in interface Cancelable
  - getCancelReason
```
public String getCancelReason()
```
    Specified by:
    
    getCancelReason in interface Cancelable

Class TrackMate

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

PLUGIN_NAME_STR

PLUGIN_NAME_VERSION

model

settings

processingTime

errorMessage

numThreads

Constructor Detail

TrackMate

TrackMate

TrackMate

Method Detail

getModel

getSettings

computeSpotFeatures

computeEdgeFeatures

computeTrackFeatures

execTracking

execDetection

execInitialSpotFiltering

execSpotFiltering

execTrackFiltering

toString

checkInput

getErrorMessage

process

getNumThreads

setNumThreads

setNumThreads

getProcessingTime

getName

setName

isCanceled

cancel

getCancelReason