Uses of Class
fiji.plugin.trackmate.Logger

Packages that use Logger

Package	Description
fiji.plugin.trackmate
fiji.plugin.trackmate.action
fiji.plugin.trackmate.action.autonaming
fiji.plugin.trackmate.action.closegaps
fiji.plugin.trackmate.action.fit
fiji.plugin.trackmate.detection
fiji.plugin.trackmate.detection.semiauto
fiji.plugin.trackmate.gui.components
fiji.plugin.trackmate.gui.wizard.descriptors
fiji.plugin.trackmate.io
fiji.plugin.trackmate.tracking
fiji.plugin.trackmate.tracking.jaqaman	Classes that implements the tracking logic of the framework described first in:
fiji.plugin.trackmate.tracking.kalman
fiji.plugin.trackmate.tracking.kdtree
fiji.plugin.trackmate.tracking.overlap
fiji.plugin.trackmate.util
fiji.plugin.trackmate.util.cli
fiji.plugin.trackmate.visualization.hyperstack
fiji.plugin.trackmate.visualization.trackscheme

Uses of Logger in fiji.plugin.trackmate

Subclasses of Logger in fiji.plugin.trackmate

Modifier and Type	Class and Description
static class	Logger.SlaveLogger A logger that wraps a master logger and uses it to echo any received message.
static class	Logger.StringBuilderLogger This Logger outputs to a StringBuilder given at construction.

Fields in fiji.plugin.trackmate declared as Logger

Modifier and Type	Field and Description
static Logger	Logger.DEFAULT_LOGGER This Logger simply outputs to the standard output and standard error.
static Logger	Logger.IJ_LOGGER This Logger outputs to the ImageJ log window, and to the ImageJ toolbar to report progress.
static Logger	Logger.IJTOOLBAR_LOGGER This Logger outputs everything to the ImageJ toolbar.
static Logger	Logger.VOID_LOGGER This logger discard any message.

Methods in fiji.plugin.trackmate that return Logger

Modifier and Type	Method and Description
Logger	Model.getLogger() Return the logger currently set for this model.

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

Modifier and Type	Method and Description
void	Model.setLogger(Logger logger) Set the logger that will receive the messages from the processes occurring within this trackmate.

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

Constructor and Description
SlaveLogger(Logger master, double progressStart, double progressRange) Create a new slave logger that will report progress to its master in the following way: If a sub-process reports a progress of val, then the master logger will receive the progress value progressStart + progressRange * val.

Uses of Logger in fiji.plugin.trackmate.action

Fields in fiji.plugin.trackmate.action declared as Logger

Modifier and Type	Field and Description
protected Logger	AbstractTMAction.logger

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

Modifier and Type	Method and Description
static ij.ImagePlus	CaptureOverlayAction.capture(ij.ImagePlus imp, int first, int last, Logger log) Generates a new ImagePlus of type RGB, 2D over time, made by capturing each time frame of the specified ImagePlus.
static ij.ImagePlus	CaptureOverlayAction.capture(TrackMate trackmate, int first, int last, Logger logger) Generates a new ImagePlus of type RGB, 2D over time, made by capturing each time frame of the TrackMate display.
static ij.ImagePlus	LabelImgExporter.createLabelImagePlus(Model model, ij.ImagePlus imp, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static ij.ImagePlus	LabelImgExporter.createLabelImagePlus(Model model, int[] dimensions, double[] calibration, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static ij.ImagePlus	LabelImgExporter.createLabelImagePlus(TrackMate trackmate, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static Img<FloatType>	LabelImgExporter.createLabelImg(Model model, long[] dimensions, double[] calibration, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label Img of FloatType where the spots of the specified model are painted with their shape, with an ID pixel value.
static <T extends RealType<T> & NativeType<T>> ImgPlus<T>	LabelImgExporter.createLabelImg(SpotCollection spots, long[] dimensions, double[] calibration, boolean exportSpotsAsDots, LabelImgExporter.LabelIdPainting labelIdPainting, T outputType, Logger logger) Creates a new label ImgPlus of FloatType where the spots are painted with an ID.
static String	CTCExporter.exportAll(String exportRootFolder, TrackMate trackmate, CTCExporter.ExportType exportType, Logger logger)
static void	CTCExporter.exportOriginalImageData(String exportRootFolder, int saveId, ij.ImagePlus imp, Logger logger)
static void	CTCExporter.exportOriginalImageData(String exportRootFolder, int saveId, TrackMate trackmate, Logger logger)
static void	CTCExporter.exportSegmentationData(String exportRootFolder, int saveId, CTCExporter.ExportType exportType, TrackMate trackmate, Logger logger) Writes the segmentation ground-truth files.
static void	CTCExporter.exportSettingsFile(String exportRootFolder, int saveId, TrackMate trackmate, Logger logger) Saves the settings part as XML for reference.
static void	ISBIChallengeExporter.exportToFile(Model model, Settings settings, File file, Logger logger)
static String	CTCExporter.exportTrackingData(String exportRootFolder, int saveId, CTCExporter.ExportType exportType, TrackMate trackmate, Logger logger)
static void	RecomputeFeatureAction.recompute(TrackMate trackmate, Logger logger)
void	TrackMateAction.setLogger(Logger logger) Sets the logger that will receive logs when this action is executed.
void	AbstractTMAction.setLogger(Logger logger)
static ij.ImagePlus	ExtractTrackStackAction.trackStack(Settings settings, List<Spot> path, double radius, boolean do3d, Logger logger)
static ij.ImagePlus	ExtractTrackStackAction.trackStack(TrackMate trackmate, Spot spot, boolean do3d, Logger logger)
static ij.ImagePlus	ExtractTrackStackAction.trackStack(TrackMate trackmate, Spot start, Spot end, boolean do3d, Logger logger)

Constructors in fiji.plugin.trackmate.action with parameters of type Logger

Constructor and Description
IJRoiExporter(ij.ImagePlus imp, Logger logger)

Uses of Logger in fiji.plugin.trackmate.action.autonaming

Constructors in fiji.plugin.trackmate.action.autonaming with parameters of type Logger

Constructor and Description
AutoNamingController(TrackMate trackmate, Logger logger)

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

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

Modifier and Type	Method and Description
void	CloseGapsByLinearInterpolation.execute(TrackMate trackmate, Logger logger)
void	CloseGapsByDetection.execute(TrackMate trackmate, Logger logger)
void	GapClosingMethod.execute(TrackMate trackmate, Logger logger) Performs the gap closing.

Constructors in fiji.plugin.trackmate.action.closegaps with parameters of type Logger

Constructor and Description
CloseGapsController(TrackMate trackmate, Logger logger)

Uses of Logger in fiji.plugin.trackmate.action.fit

Methods in fiji.plugin.trackmate.action.fit with parameters of type Logger

Modifier and Type	Method and Description
void	SpotGaussianFitter3DFixedRadius.process(Iterable<Spot> spots, Logger logger)
void	SpotGaussianFitter2DFixedRadius.process(Iterable<Spot> spots, Logger logger)
void	SpotGaussianFitter3D.process(Iterable<Spot> spots, Logger logger)
void	SpotGaussianFitter2D.process(Iterable<Spot> spots, Logger logger)
void	SpotFitter.process(Iterable<Spot> spots, Logger logger)
void	AbstractSpotFitter.process(Iterable<Spot> spots, Logger logger)

Constructors in fiji.plugin.trackmate.action.fit with parameters of type Logger

Constructor and Description
SpotFitterController(TrackMate trackmate, SelectionModel selectionModel, Logger logger)

Uses of Logger in fiji.plugin.trackmate.detection

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

Modifier and Type	Method and Description
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 Logger in fiji.plugin.trackmate.detection.semiauto

Fields in fiji.plugin.trackmate.detection.semiauto declared as Logger

Modifier and Type	Field and Description
protected Logger	AbstractSemiAutoTracker.logger

Constructors in fiji.plugin.trackmate.detection.semiauto with parameters of type Logger

Constructor and Description
AbstractSemiAutoTracker(Model model, SelectionModel selectionModel, Logger logger)
SemiAutoTracker(Model model, SelectionModel selectionModel, ij.ImagePlus imp, Logger logger)

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

Methods in fiji.plugin.trackmate.gui.components that return Logger

Modifier and Type	Method and Description
Logger	FilterGuiPanel.getLogger()
Logger	LogPanel.getLogger()

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

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

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

Uses of Logger in fiji.plugin.trackmate.io

Fields in fiji.plugin.trackmate.io declared as Logger

Modifier and Type	Field and Description
protected Logger	TmXmlWriter.logger

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

Modifier and Type	Method and Description
static File	IOUtils.askForFileForLoading(File file, String title, Frame parent, Logger logger) Prompts the user for a xml file to load from.
static File	IOUtils.askForFolder(File file, String title, Frame parent, Logger logger) Prompts the user for a target folder.
static boolean	IOUtils.readBooleanAttribute(org.jdom2.Element element, String name, Logger logger)
static boolean	IOUtils.readBooleanAttribute(org.jdom2.Element element, String name, Logger logger, boolean defaultValue)
static double	IOUtils.readDoubleAttribute(org.jdom2.Element element, String name, Logger logger)
static double	IOUtils.readDoubleAttribute(org.jdom2.Element element, String name, Logger logger, double defaultValue)
static double	IOUtils.readFloatAttribute(org.jdom2.Element element, String name, Logger logger)
static int	IOUtils.readIntAttribute(org.jdom2.Element element, String name, Logger logger) Read and return an integer attribute from a JDom Element, and substitute a default value of 0 if the attribute is not found or of the wrong type.
static int	IOUtils.readIntAttribute(org.jdom2.Element element, String name, Logger logger, int defaultValue)
static Settings	SettingsPersistence.readLastUsedSettings(ij.ImagePlus imp, Logger logger)
static void	SettingsPersistence.saveLastUsedSettings(Settings settings, Logger logger)

Constructors in fiji.plugin.trackmate.io with parameters of type Logger

Constructor and Description
TGMMImporter(File file, List<AffineTransform3D> transforms, Logger logger)
TGMMImporter(File file, List<AffineTransform3D> transforms, Pattern framePattern, Logger logger)
TmXmlWriter(File file, Logger logger) Creates a new XML file writer for TrackMate.

Uses of Logger in fiji.plugin.trackmate.tracking

Methods in fiji.plugin.trackmate.tracking with parameters of type Logger

Modifier and Type	Method and Description
void	SpotTracker.setLogger(Logger logger) Sets the Logger instance that will receive messages from this SpotTracker.

Uses of Logger in fiji.plugin.trackmate.tracking.jaqaman

Fields in fiji.plugin.trackmate.tracking.jaqaman declared as Logger

Modifier and Type	Field and Description
protected Logger	SparseLAPFrameToFrameTracker.logger

Methods in fiji.plugin.trackmate.tracking.jaqaman with parameters of type Logger

Modifier and Type	Method and Description
void	SegmentTracker.setLogger(Logger logger)
void	SparseLAPFrameToFrameTracker.setLogger(Logger logger)
void	SparseLAPTracker.setLogger(Logger logger)

Constructors in fiji.plugin.trackmate.tracking.jaqaman with parameters of type Logger

Constructor and Description
JaqamanLinker(CostMatrixCreator<K,J> costMatrixCreator, Logger logger) Creates a new linker for the specified cost matrix creator.
SegmentTracker(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph, Map<String,Object> fullsettings, Logger logger)

Uses of Logger in fiji.plugin.trackmate.tracking.kalman

Methods in fiji.plugin.trackmate.tracking.kalman with parameters of type Logger

Modifier and Type	Method and Description
void	AdvancedKalmanTracker.setLogger(Logger logger)
void	KalmanTracker.setLogger(Logger logger)

Uses of Logger in fiji.plugin.trackmate.tracking.kdtree

Fields in fiji.plugin.trackmate.tracking.kdtree declared as Logger

Modifier and Type	Field and Description
protected Logger	NearestNeighborTracker.logger

Methods in fiji.plugin.trackmate.tracking.kdtree with parameters of type Logger

Modifier and Type	Method and Description
void	NearestNeighborTracker.setLogger(Logger logger)

Uses of Logger in fiji.plugin.trackmate.tracking.overlap

Methods in fiji.plugin.trackmate.tracking.overlap with parameters of type Logger

Modifier and Type	Method and Description
void	OverlapTracker.setLogger(Logger logger)

Uses of Logger in fiji.plugin.trackmate.util

Subclasses of Logger in fiji.plugin.trackmate.util

Modifier and Type	Class and Description
class	LogRecorder

Methods in fiji.plugin.trackmate.util that return Logger

Modifier and Type	Method and Description
Logger	JLabelLogger.getLogger()
Logger	DetectionPreview.getLogger()

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

Modifier and Type	Method and Description
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.

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

Constructor and Description
LogRecorder(Logger source)

Uses of Logger in fiji.plugin.trackmate.util.cli

Constructors in fiji.plugin.trackmate.util.cli with parameters of type Logger

Constructor and Description
LoggerTailerListener(Logger logger)

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

Methods in fiji.plugin.trackmate.visualization.hyperstack that return Logger

Modifier and Type	Method and Description
Logger	SpotEditToolConfigPanel.getLogger() Returns the Logger that outputs on this config panel.

Constructors in fiji.plugin.trackmate.visualization.hyperstack with parameters of type Logger

Constructor and Description
ModelEditActions(ij.ImagePlus imp, Model model, SelectionModel selectionModel, Logger logger)

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

Fields in fiji.plugin.trackmate.visualization.trackscheme declared as Logger

Modifier and Type	Field and Description
protected Logger	TrackSchemeFrame.logger