Uses of Class
fiji.plugin.trackmate.Settings

Packages that use Settings

Package	Description
fiji.plugin.trackmate
fiji.plugin.trackmate.action
fiji.plugin.trackmate.action.closegaps
fiji.plugin.trackmate.detection
fiji.plugin.trackmate.features
fiji.plugin.trackmate.gui.components
fiji.plugin.trackmate.gui.components.detector
fiji.plugin.trackmate.gui.wizard.descriptors
fiji.plugin.trackmate.io
fiji.plugin.trackmate.util
fiji.plugin.trackmate.visualization
fiji.plugin.trackmate.visualization.hyperstack
fiji.plugin.trackmate.visualization.trackscheme

Uses of Settings in fiji.plugin.trackmate

Fields in fiji.plugin.trackmate declared as Settings

Modifier and Type	Field and Description
protected Settings	TrackMate.settings

Methods in fiji.plugin.trackmate that return Settings

Modifier and Type	Method and Description
Settings	Settings.copyOn(ij.ImagePlus newImp) Copy a settings objects based on this instance, but configured to run on the specified image.
protected Settings	ManualTrackingPlugIn.createSettings(ij.ImagePlus imp)
protected Settings	TrackMatePlugIn.createSettings(ij.ImagePlus imp) Hook for subclassers: Creates the Settings instance that will be used to tune the TrackMate instance.
Settings	TrackMate.getSettings()

Methods in fiji.plugin.trackmate with parameters of type Settings

Modifier and Type	Method and Description
protected TrackMate	ManualTrackingPlugIn.createTrackMate(Model model, Settings settings)
protected TrackMate	TrackMatePlugIn.createTrackMate(Model model, Settings settings) Hook for subclassers: Creates the TrackMate instance that will be controlled in the GUI.

Constructors in fiji.plugin.trackmate with parameters of type Settings

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

Uses of Settings in fiji.plugin.trackmate.action

Methods in fiji.plugin.trackmate.action with parameters of type Settings

Modifier and Type	Method and Description
static void	ExportTracksToXML.export(Model model, Settings settings, File file) Static utility that silently exports tracks in a simplified xml format, describe in this class.
static void	ISBIChallengeExporter.exportToFile(Model model, Settings settings, File file)
static void	ISBIChallengeExporter.exportToFile(Model model, Settings settings, File file, Logger logger)
static ij.ImagePlus	ExtractTrackStackAction.trackStack(Settings settings, List<Spot> path, double radius, boolean do3d, Logger logger)

Uses of Settings in fiji.plugin.trackmate.action.closegaps

Methods in fiji.plugin.trackmate.action.closegaps that return Settings

Modifier and Type	Method and Description
static Settings	GapClosingMethod.makeSettingsForRoiAround(Spot spot, double neighborhoodFactor, Settings settings) Returns a new Settings object copied from the specified settings, but configured with a small ROI centered on the specified spot, with a radius proportional to the radius of the specified spot, and set to operate only on the frame in which the specified spot it.

Methods in fiji.plugin.trackmate.action.closegaps with parameters of type Settings

Modifier and Type	Method and Description
static Settings	GapClosingMethod.makeSettingsForRoiAround(Spot spot, double neighborhoodFactor, Settings settings) Returns a new Settings object copied from the specified settings, but configured with a small ROI centered on the specified spot, with a radius proportional to the radius of the specified spot, and set to operate only on the frame in which the specified spot it.

Uses of Settings in fiji.plugin.trackmate.detection

Methods in fiji.plugin.trackmate.detection with parameters of type Settings

Modifier and Type	Method and Description
ConfigurationPanel	HessianDetectorFactory.getDetectorConfigurationPanel(Settings lSettings, Model model)
ConfigurationPanel	ManualDetectorFactory.getDetectorConfigurationPanel(Settings settings, Model model)
ConfigurationPanel	LabelImageDetectorFactory.getDetectorConfigurationPanel(Settings lSettings, Model model)
ConfigurationPanel	MaskDetectorFactory.getDetectorConfigurationPanel(Settings lSettings, Model model)
ConfigurationPanel	ThresholdDetectorFactory.getDetectorConfigurationPanel(Settings lSettings, Model model)
ConfigurationPanel	LogDetectorFactory.getDetectorConfigurationPanel(Settings lSettings, Model model)
ConfigurationPanel	SpotDetectorFactoryBase.getDetectorConfigurationPanel(Settings settings, Model model) Returns a new GUI panel able to configure the settings suitable for this specific detector factory.
ConfigurationPanel	DogDetectorFactory.getDetectorConfigurationPanel(Settings lSettings, Model model)
static void	DetectionUtils.preview(Model model, Settings settings, SpotDetectorFactoryBase<?> detectorFactory, Map<String,Object> detectorSettings, int frame, Logger logger, Consumer<Boolean> buttonEnabler) Preview a detection results.

Uses of Settings in fiji.plugin.trackmate.features

Methods in fiji.plugin.trackmate.features with parameters of type Settings

Modifier and Type	Method and Description
static Map<String,String>	FeatureUtils.collectFeatureKeys(DisplaySettings.TrackMateObject target, Model model, Settings settings)

Constructors in fiji.plugin.trackmate.features with parameters of type Settings

Constructor and Description
EdgeFeatureCalculator(Model model, Settings settings, boolean doLogIt)
ModelFeatureUpdater(Model model, Settings settings) Constructs and activate a ModelFeatureUpdater.
SpotFeatureCalculator(Model model, Settings settings, boolean doLogIt)
TrackFeatureCalculator(Model model, Settings settings, boolean doLogIt)

Uses of Settings in fiji.plugin.trackmate.gui.components

Methods in fiji.plugin.trackmate.gui.components with parameters of type Settings

Modifier and Type	Method and Description
static CategoryJComboBox<DisplaySettings.TrackMateObject,String>	FeatureDisplaySelector.createComboBoxSelector(Model model, Settings settings) Return a CategoryJComboBox that lets a user select among all available features in TrackMate.

Constructors in fiji.plugin.trackmate.gui.components with parameters of type Settings

Constructor and Description
FeatureDisplaySelector(Model model, Settings settings, DisplaySettings displaySettings)
FilterGuiPanel(Model model, Settings settings, DisplaySettings.TrackMateObject target, List<FeatureFilter> filters, String defaultFeature, FeatureDisplaySelector featureSelector)

Uses of Settings in fiji.plugin.trackmate.gui.components.detector

Fields in fiji.plugin.trackmate.gui.components.detector declared as Settings

Modifier and Type	Field and Description
protected Settings	ThresholdDetectorConfigurationPanel.settings

Constructors in fiji.plugin.trackmate.gui.components.detector with parameters of type Settings

Constructor and Description
DogDetectorConfigurationPanel(Settings settings, Model model, String infoText, String detectorName)
HessianDetectorConfigurationPanel(Settings settings, Model model, String infoText, String detectorName) Creates a new HessianDetectorConfigurationPanel, a GUI able to configure settings suitable to HessianDetector and derived implementations.
LabelImageDetectorConfigurationPanel(Settings settings, Model model)
LogDetectorConfigurationPanel(Settings settings, Model model, String infoText, String detectorName) Creates a new LogDetectorConfigurationPanel, a GUI able to configure settings suitable to LogDetectorFactory and derived implementations.
MaskDetectorConfigurationPanel(Settings settings, Model model)
ThresholdDetectorConfigurationPanel(Settings settings, Model model)
ThresholdDetectorConfigurationPanel(Settings settings, Model model, String infoText, String detectorName) Creates a new ThresholdDetectorConfigurationPanel, a GUI able to configure settings suitable to a LogDetectorFactory and derived implementations.

Uses of Settings in fiji.plugin.trackmate.gui.wizard.descriptors

Constructors in fiji.plugin.trackmate.gui.wizard.descriptors with parameters of type Settings

Constructor and Description
SpotDetectorDescriptor(Settings settings, ConfigurationPanel configurationPanel, Logger logger)
SpotTrackerDescriptor(Settings settings, ConfigurationPanel configurationPanel, Logger logger)
StartDialogDescriptor(Settings settings, Logger logger)

Uses of Settings in fiji.plugin.trackmate.io

Methods in fiji.plugin.trackmate.io that return Settings

Modifier and Type	Method and Description
static Settings	SettingsPersistence.getDefaultSettings(ij.ImagePlus imp)
static Settings	SettingsPersistence.readLastUsedSettings(ij.ImagePlus imp, Logger logger)
Settings	TmXmlReader.readSettings(ij.ImagePlus imp)
Settings	TmXmlReader.readSettings(ij.ImagePlus imp, DetectorProvider detectorProvider, TrackerProvider trackerProvider, SpotAnalyzerProvider spotAnalyzerProvider, EdgeAnalyzerProvider edgeAnalyzerProvider, TrackAnalyzerProvider trackAnalyzerProvider, SpotMorphologyAnalyzerProvider spotMorphologyAnalyzerProvider) Reads the settings element of the file, and sets the fields of the specified Settings object according to the xml file content.

Methods in fiji.plugin.trackmate.io with parameters of type Settings

Modifier and Type	Method and Description
void	TmXmlWriter.appendSettings(Settings settings) Appends the content of a Settings object to the document.
protected org.jdom2.Element	TmXmlWriter.echoAnalyzers(Settings settings)
protected org.jdom2.Element	TmXmlWriter.echoDetectorSettings(Settings settings)
protected org.jdom2.Element	TmXmlWriter.echoImageInfo(Settings settings)
protected org.jdom2.Element	TmXmlWriter.echoInitialSpotFilter(Settings settings)
protected org.jdom2.Element	TmXmlWriter.echoSpotFilters(Settings settings)
protected org.jdom2.Element	TmXmlWriter.echoTrackerSettings(Settings settings)
protected org.jdom2.Element	TmXmlWriter.echoTrackFilters(Settings settings)
protected void	TmXmlReader.getDetectorSettings(org.jdom2.Element settingsElement, Settings settings, DetectorProvider provider) Update the given Settings object with the SpotDetectorFactory and settings map fields named detectorFactory and detectorSettings read within the XML file this reader is initialized with.
protected void	TmXmlReader.getTrackerSettings(org.jdom2.Element settingsElement, Settings settings, TrackerProvider provider) Update the given Settings object with SpotTracker proper settings map fields named trackerSettings and trackerFactory read within the XML file this reader is initialized with.
Collection<TrackMateModelView>	TmXmlReader.getViews(ViewProvider provider, Model model, Settings settings, SelectionModel selectionModel, DisplaySettings displaySettings) Returns the collection of views that were saved in this file.
static void	SettingsPersistence.saveLastUsedSettings(Settings settings, Logger logger)

Uses of Settings in fiji.plugin.trackmate.util

Methods in fiji.plugin.trackmate.util with parameters of type Settings

Modifier and Type	Method and Description
static String	TMUtils.getImagePathWithoutExtension(Settings settings) Returns a string of the name of the image without the extension, with the full path
static Interval	TMUtils.getInterval(ImgPlus<?> img, Settings settings) Returns an interval object that in the specified ImgPlus slice in a single time frame.
static Interval	TMUtils.getIntervalWithTime(ImgPlus<?> img, Settings settings) Returns an interval object that slices in the specified ImgPlus in a single channel (the channel dimension is dropped).
protected void	DetectionPreview.preview(Model model, Settings settings, SpotDetectorFactoryBase<?> detectorFactory, Map<String,Object> detectorSettings, int frame, String thresholdKey)
static File	TMUtils.proposeTrackMateSaveFile(Settings settings, Logger logger) Creates a default file path to save the TrackMate session to, based on the image TrackMate works on.
protected Pair<Model,Double>	DetectionPreview.runPreviewDetection(Settings settings, int frame, SpotDetectorFactoryBase<?> detectorFactory, Map<String,Object> detectorSettings, String thresholdKey) Runs the preview with the specified parameters.
DetectionPreview.Builder	DetectionPreview.Builder.settings(Settings settings) Sets the Settings object to use for preview.

Constructors in fiji.plugin.trackmate.util with parameters of type Settings

Constructor and Description
DetectionPreview(Model model, Settings settings, SpotDetectorFactoryBase<?> detectorFactory, Supplier<Map<String,Object>> detectionSettingsSupplier, Supplier<Integer> currentFrameSupplier, DoubleConsumer thresholdUpdater, String axisLabel, String thresholdKey)

Uses of Settings in fiji.plugin.trackmate.visualization

Methods in fiji.plugin.trackmate.visualization with parameters of type Settings

Modifier and Type	Method and Description
TrackMateModelView	ViewFactory.create(Model model, Settings settings, SelectionModel selectionModel, DisplaySettings displaySettings) Returns a new instance of the concrete view.

Uses of Settings in fiji.plugin.trackmate.visualization.hyperstack

Methods in fiji.plugin.trackmate.visualization.hyperstack with parameters of type Settings

Modifier and Type	Method and Description
TrackMateModelView	HyperStackDisplayerFactory.create(Model model, Settings settings, SelectionModel selectionModel, DisplaySettings displaySettings)

Uses of Settings in fiji.plugin.trackmate.visualization.trackscheme

Methods in fiji.plugin.trackmate.visualization.trackscheme with parameters of type Settings

Modifier and Type	Method and Description
TrackMateModelView	TrackSchemeFactory.create(Model model, Settings settings, SelectionModel selectionModel, DisplaySettings displaySettings)

Constructors in fiji.plugin.trackmate.visualization.trackscheme with parameters of type Settings

Constructor and Description
SpotImageUpdater(Settings settings) Instantiates a new spot image updater.