Settings (Fiji Javadocs 0-SNAPSHOT API)

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

```
public class Settings
extends Object
```
This class is used to store user settings for the TrackMate trackmate. It is simply made of public fields

Field Summary

Fields
Modifier and Type	Field and Description
`SpotDetectorFactoryBase<?>`	`detectorFactory` The name of the detector factory to use.
`Map<String,Object>`	`detectorSettings` Settings map for `SpotDetector`.
`double`	`dt` Target channel for detection, 1-based.
`double`	`dx`
`double`	`dy`
`double`	`dz`
`protected List<EdgeAnalyzer>`	`edgeAnalyzers` The `EdgeAnalyzer`s that will be used to compute edge features.
`protected String`	`errorMessage`
`int`	`height`
`String`	`imageFileName`
`String`	`imageFolder`
`ij.ImagePlus`	`imp` The ImagePlus to operate on.
`Double`	`initialSpotFilterValue` The initial quality filter value that is used to clip spots of low quality from spots.
`int`	`nframes`
`int`	`nslices`
`Roi`	`roi` The region of interest (ROI).
`protected List<SpotAnalyzerFactoryBase<?>>`	`spotAnalyzerFactories` The `SpotAnalyzerFactory`s that will be used to compute spot features.
`protected List<FeatureFilter>`	`spotFilters` The feature filter list.
`int`	`tend` The time-frame index, 0-based, of the last time-point to process.
`protected List<TrackAnalyzer>`	`trackAnalyzers` The `TrackAnalyzer`s that will be used to compute track features.
`SpotTrackerFactory`	`trackerFactory` The the tracker to use.
`Map<String,Object>`	`trackerSettings` Settings map for `SpotTracker`.
`protected List<FeatureFilter>`	`trackFilters` The track filter list that is used to prune track and spots.
`int`	`tstart` The time-frame index, 0-based, of the first time-point to process.
`int`	`width`
`int`	`xend` The highest pixel X position, 0-based, of the volume to process.
`int`	`xstart` The lowest pixel X position, 0-based, of the volume to process.
`int`	`yend` The lowest pixel Y position, 0-based, of the volume to process.
`int`	`ystart` The lowest pixel Y position, 0-based, of the volume to process.
`int`	`zend` The lowest pixel Z position, 0-based, of the volume to process.
`int`	`zstart` The lowest pixel Z position, 0-based, of the volume to process.

Constructor Summary

Constructors
Constructor and Description

Settings()

Constructors
Constructor and Description
`Settings()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAllAnalyzers()` All the spot analyzers, edge analyzers and track analyzers discovered at runtime.
`void`	`addEdgeAnalyzer(EdgeAnalyzer edgeAnalyzer)` Adds a `EdgeAnalyzer` to the `List` of edge analyzers configured.
`void`	`addEdgeAnalyzer(int index, EdgeAnalyzer edgeAnalyzer)` Adds a `EdgeAnalyzer` to the `List` of edge analyzers configured, at the specified index.
`void`	`addSpotAnalyzerFactory(int index, SpotAnalyzerFactory<?> spotAnalyzer)` Adds a `SpotAnalyzerFactory` to the `List` of spot analyzers configured, at the specified index.
`void`	`addSpotAnalyzerFactory(SpotAnalyzerFactoryBase<?> spotAnalyzer)` Adds a `SpotAnalyzerFactory` to the `List` of spot analyzers configured.
`void`	`addSpotFilter(FeatureFilter filter)` Add a filter to the list of spot filters.
`void`	`addTrackAnalyzer(int index, TrackAnalyzer trackAnalyzer)` Adds a `TrackAnalyzer` to the `List` of track analyzers configured, at the specified index.
`void`	`addTrackAnalyzer(TrackAnalyzer trackAnalyzer)` Adds a `TrackAnalyzer` to the `List` of track analyzers configured.
`void`	`addTrackFilter(FeatureFilter filter)` Add a filter to the list of track filters.
`boolean`	`checkValidity()`
`void`	`clearEdgeAnalyzers()` Remove any `EdgeAnalyzer` to this object.
`void`	`clearSpotAnalyzerFactories()` Remove any `SpotAnalyzerFactory` to this object.
`void`	`clearSpotFilters()` Remove all spot filters stored in this model.
`void`	`clearTrackAnalyzers()` Remove any `TrackAnalyzer` to this object.
`void`	`clearTrackFilters()` Remove all track filters stored in this model.
`void`	`defaultParameters()` Initialize the detection and tracking part with default parameters.
`List<EdgeAnalyzer>`	`getEdgeAnalyzers()` Returns a copy of the list of `EdgeAnalyzer`s configured in this settings object.
`String`	`getErrorMessage()`
`List<SpotAnalyzerFactoryBase<?>>`	`getSpotAnalyzerFactories()` Returns a copy of the list of `SpotAnalyzerFactory`s configured in this settings object.
`List<FeatureFilter>`	`getSpotFilters()`
`List<TrackAnalyzer>`	`getTrackAnalyzers()` Returns a copy of the list of `TrackAnalyzer`s configured in this settings object.
`List<FeatureFilter>`	`getTrackFilters()`
`static void`	`prettyPrintFeatureAnalyzer(List<? extends FeatureAnalyzer> analyzers, StringBuilder str)`
`boolean`	`removeEdgeAnalyzer(EdgeAnalyzer edgeAnalyzer)` Removes the specified `EdgeAnalyzer` from the analyzers configured.
`boolean`	`removeSpotAnalyzerFactory(SpotAnalyzerFactory<?> spotAnalyzer)` Removes the specified `SpotAnalyzerFactory` from the analyzers configured.
`void`	`removeSpotFilter(FeatureFilter filter)`
`boolean`	`removeTrackAnalyzer(TrackAnalyzer trackAnalyzer)` Removes the specified `TrackAnalyzer` from the analyzers configured.
`void`	`removeTrackFilter(FeatureFilter filter)`
`void`	`setFrom(ij.ImagePlus imp)`
`void`	`setSpotFilters(List<FeatureFilter> spotFilters)`
`void`	`setTrackFilters(List<FeatureFilter> trackFilters)`
`String`	`toString()`
`String`	`toStringFeatureAnalyzersInfo()`
`String`	`toStringImageInfo()` Returns a string description of the target image.

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

- Field Detail
  - imp
```
public ij.ImagePlus imp
```
    The ImagePlus to operate on. Will also be used by some TrackMateModelView as a GUI target.
  - roi
```
public Roi roi
```
    The region of interest (ROI). This will be used to crop the image and to discard found spots outside the ROI. If null, the whole image is considered.
  - tstart
```
public int tstart
```
    The time-frame index, 0-based, of the first time-point to process.
  - tend
```
public int tend
```
    The time-frame index, 0-based, of the last time-point to process.
  - xstart
```
public int xstart
```
    The lowest pixel X position, 0-based, of the volume to process.
  - xend
```
public int xend
```
    The highest pixel X position, 0-based, of the volume to process.
  - ystart
```
public int ystart
```
    The lowest pixel Y position, 0-based, of the volume to process.
  - yend
```
public int yend
```
    The lowest pixel Y position, 0-based, of the volume to process.
  - zstart
```
public int zstart
```
    The lowest pixel Z position, 0-based, of the volume to process.
  - zend
```
public int zend
```
    The lowest pixel Z position, 0-based, of the volume to process.
  - dt
```
public double dt
```
    Target channel for detection, 1-based.
  - dx
```
public double dx
```
  - dy
```
public double dy
```
  - dz
```
public double dz
```
  - width
```
public int width
```
  - height
```
public int height
```
  - nslices
```
public int nslices
```
  - nframes
```
public int nframes
```
  - imageFolder
```
public String imageFolder
```
  - imageFileName
```
public String imageFileName
```
  - detectorFactory
```
public SpotDetectorFactoryBase<?> detectorFactory
```
    The name of the detector factory to use. It will be used to generate SpotDetector for each target frame.
  - trackerFactory
```
public SpotTrackerFactory trackerFactory
```
    The the tracker to use.
  - detectorSettings
```
public Map<String,Object> detectorSettings
```
    Settings map for SpotDetector.
    
    See Also:
    
    DetectorKeys
  - trackerSettings
```
public Map<String,Object> trackerSettings
```
    Settings map for SpotTracker.
    
    See Also:
    
    TrackerKeys
  - spotFilters
```
protected List<FeatureFilter> spotFilters
```
    The feature filter list.
  - initialSpotFilterValue
```
public Double initialSpotFilterValue
```
    The initial quality filter value that is used to clip spots of low quality from spots.
  - trackFilters
```
protected List<FeatureFilter> trackFilters
```
    The track filter list that is used to prune track and spots.
  - errorMessage
```
protected String errorMessage
```
  - spotAnalyzerFactories
```
protected List<SpotAnalyzerFactoryBase<?>> spotAnalyzerFactories
```
    The SpotAnalyzerFactorys that will be used to compute spot features. They are ordered in a List in case some analyzers requires the results of another analyzer to proceed.
  - edgeAnalyzers
```
protected List<EdgeAnalyzer> edgeAnalyzers
```
    The EdgeAnalyzers that will be used to compute edge features. They are ordered in a List in case some analyzers requires the results of another analyzer to proceed.
  - trackAnalyzers
```
protected List<TrackAnalyzer> trackAnalyzers
```
    The TrackAnalyzers that will be used to compute track features. They are ordered in a List in case some analyzers requires the results of another analyzer to proceed.
- Constructor Detail
  - Settings
```
public Settings()
```
- Method Detail
  - setFrom
```
public void setFrom(ij.ImagePlus imp)
```
  - toStringImageInfo
```
public String toStringImageInfo()
```
    Returns a string description of the target image.
    
    Returns:
    
    a string representation of the target image.
  - toStringFeatureAnalyzersInfo
```
public String toStringFeatureAnalyzersInfo()
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - checkValidity
```
public boolean checkValidity()
```
  - getErrorMessage
```
public String getErrorMessage()
```
  - addAllAnalyzers
```
public void addAllAnalyzers()
```
    All the spot analyzers, edge analyzers and track analyzers discovered at runtime. This method is a convenience for scripting, that simply discovers and adds all the analyzers it can find.
  - defaultParameters
```
public void defaultParameters()
```
    Initialize the detection and tracking part with default parameters. These parameters are not mean to be used for all cases and need to be tuned for the actual tracking problem.
  - clearSpotAnalyzerFactories
```
public void clearSpotAnalyzerFactories()
```
    Remove any SpotAnalyzerFactory to this object.
  - getSpotAnalyzerFactories
```
public List<SpotAnalyzerFactoryBase<?>> getSpotAnalyzerFactories()
```
    Returns a copy of the list of SpotAnalyzerFactorys configured in this settings object. They are returned in an ordered list, to enforce processing order in case some analyzers requires the results of another analyzers to proceed.
    
    Returns:
    
    the list of SpotAnalyzerFactorys.
  - addSpotAnalyzerFactory
```
public void addSpotAnalyzerFactory(SpotAnalyzerFactoryBase<?> spotAnalyzer)
```
    Adds a SpotAnalyzerFactory to the List of spot analyzers configured.
    
    Parameters:
    
    spotAnalyzer - the SpotAnalyzer to add, at the end of the list.
  - addSpotAnalyzerFactory
```
public void addSpotAnalyzerFactory(int index,
                                   SpotAnalyzerFactory<?> spotAnalyzer)
```
    Adds a SpotAnalyzerFactory to the List of spot analyzers configured, at the specified index.
    
    Parameters:
    
    index - index at which the analyzer is to be inserted.
    
    spotAnalyzer - the SpotAnalyzer to add, at the specified index in the list.
  - removeSpotAnalyzerFactory
```
public boolean removeSpotAnalyzerFactory(SpotAnalyzerFactory<?> spotAnalyzer)
```
    Removes the specified SpotAnalyzerFactory from the analyzers configured.
    
    Parameters:
    
    spotAnalyzer - the SpotAnalyzerFactory to remove.
    
    Returns:
    
    true if the specified SpotAnalyzerFactory was in the list and was removed.
  - clearEdgeAnalyzers
```
public void clearEdgeAnalyzers()
```
    Remove any EdgeAnalyzer to this object.
  - getEdgeAnalyzers
```
public List<EdgeAnalyzer> getEdgeAnalyzers()
```
    Returns a copy of the list of EdgeAnalyzers configured in this settings object. They are returned in an ordered list, to enforce processing order in case some analyzers requires the results of another analyzers to proceed.
    
    Returns:
    
    the list of EdgeAnalyzers.
  - addEdgeAnalyzer
```
public void addEdgeAnalyzer(EdgeAnalyzer edgeAnalyzer)
```
    Adds a EdgeAnalyzer to the List of edge analyzers configured.
    
    Parameters:
    
    edgeAnalyzer - the EdgeAnalyzer to add, at the end of the list.
  - addEdgeAnalyzer
```
public void addEdgeAnalyzer(int index,
                            EdgeAnalyzer edgeAnalyzer)
```
    Adds a EdgeAnalyzer to the List of edge analyzers configured, at the specified index.
    
    Parameters:
    
    index - index at which the analyzer is to be inserted.
    
    edgeAnalyzer - the EdgeAnalyzer to add, at the specified index in the list.
  - removeEdgeAnalyzer
```
public boolean removeEdgeAnalyzer(EdgeAnalyzer edgeAnalyzer)
```
    Removes the specified EdgeAnalyzer from the analyzers configured.
    
    Parameters:
    
    edgeAnalyzer - the EdgeAnalyzer to remove.
    
    Returns:
    
    true if the specified EdgeAnalyzer was in the list and was removed.
  - clearTrackAnalyzers
```
public void clearTrackAnalyzers()
```
    Remove any TrackAnalyzer to this object.
  - getTrackAnalyzers
```
public List<TrackAnalyzer> getTrackAnalyzers()
```
    Returns a copy of the list of TrackAnalyzers configured in this settings object. They are returned in an ordered list, to enforce processing order in case some analyzers requires the results of another analyzers to proceed.
    
    Returns:
    
    the list of TrackAnalyzers.
  - addTrackAnalyzer
```
public void addTrackAnalyzer(TrackAnalyzer trackAnalyzer)
```
    Adds a TrackAnalyzer to the List of track analyzers configured.
    
    Parameters:
    
    trackAnalyzer - the TrackAnalyzer to add, at the end of the list.
  - addTrackAnalyzer
```
public void addTrackAnalyzer(int index,
                             TrackAnalyzer trackAnalyzer)
```
    Adds a TrackAnalyzer to the List of track analyzers configured, at the specified index.
    
    Parameters:
    
    index - index at which the analyzer is to be inserted.
    
    trackAnalyzer - the TrackAnalyzer to add, at the specified index in the list.
  - removeTrackAnalyzer
```
public boolean removeTrackAnalyzer(TrackAnalyzer trackAnalyzer)
```
    Removes the specified TrackAnalyzer from the analyzers configured.
    
    Parameters:
    
    trackAnalyzer - the TrackAnalyzer to remove.
    
    Returns:
    
    true if the specified TrackAnalyzer was in the list and was removed.
  - addSpotFilter
```
public void addSpotFilter(FeatureFilter filter)
```
    Add a filter to the list of spot filters.
    
    Parameters:
    
    filter - the filter to add.
  - removeSpotFilter
```
public void removeSpotFilter(FeatureFilter filter)
```
  - clearSpotFilters
```
public void clearSpotFilters()
```
    Remove all spot filters stored in this model.
  - getSpotFilters
```
public List<FeatureFilter> getSpotFilters()
```
  - setSpotFilters
```
public void setSpotFilters(List<FeatureFilter> spotFilters)
```
  - addTrackFilter
```
public void addTrackFilter(FeatureFilter filter)
```
    Add a filter to the list of track filters.
    
    Parameters:
    
    filter - the filter to add.
  - removeTrackFilter
```
public void removeTrackFilter(FeatureFilter filter)
```
  - clearTrackFilters
```
public void clearTrackFilters()
```
    Remove all track filters stored in this model.
  - getTrackFilters
```
public List<FeatureFilter> getTrackFilters()
```
  - setTrackFilters
```
public void setTrackFilters(List<FeatureFilter> trackFilters)
```
  - prettyPrintFeatureAnalyzer
```
public static final void prettyPrintFeatureAnalyzer(List<? extends FeatureAnalyzer> analyzers,
                                                    StringBuilder str)
```

Class Settings

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

imp

roi

tstart

tend

xstart

xend

ystart

yend

zstart

zend

dt

dx

dy

dz

width

height

nslices

nframes

imageFolder

imageFileName

detectorFactory

trackerFactory

detectorSettings

trackerSettings

spotFilters

initialSpotFilterValue

trackFilters

errorMessage

spotAnalyzerFactories

edgeAnalyzers

trackAnalyzers

Constructor Detail

Settings

Method Detail

setFrom

toStringImageInfo

toStringFeatureAnalyzersInfo

toString

checkValidity

getErrorMessage

addAllAnalyzers

defaultParameters

clearSpotAnalyzerFactories

getSpotAnalyzerFactories

addSpotAnalyzerFactory

addSpotAnalyzerFactory

removeSpotAnalyzerFactory

clearEdgeAnalyzers

getEdgeAnalyzers

addEdgeAnalyzer

addEdgeAnalyzer

removeEdgeAnalyzer

clearTrackAnalyzers

getTrackAnalyzers

addTrackAnalyzer

addTrackAnalyzer

removeTrackAnalyzer

addSpotFilter

removeSpotFilter

clearSpotFilters

getSpotFilters

setSpotFilters

addTrackFilter

removeTrackFilter

clearTrackFilters

getTrackFilters

setTrackFilters

prettyPrintFeatureAnalyzer