A B C D E F G I J K L M N O P R S T U V W X Y
All Classes All Packages

A

AboutController - Class in sc.fiji.filamentdetector.gui.controller

AboutController(Context) - Constructor for class sc.fiji.filamentdetector.gui.controller.AboutController

AbstractAnalyzer - Class in sc.fiji.filamentdetector.analyzer

AbstractAnalyzer() - Constructor for class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

AbstractAnalyzerController - Class in sc.fiji.filamentdetector.gui.controller.analyzer

AbstractAnalyzerController(Context) - Constructor for class sc.fiji.filamentdetector.gui.controller.analyzer.AbstractAnalyzerController

AbstractController - Class in sc.fiji.filamentdetector.gui.controller

AbstractController() - Constructor for class sc.fiji.filamentdetector.gui.controller.AbstractController

AbstractDataExporter<T> - Class in sc.fiji.filamentdetector.exporter

AbstractDataExporter(Context) - Constructor for class sc.fiji.filamentdetector.exporter.AbstractDataExporter

AbstractFilamentDetector - Class in sc.fiji.filamentdetector.detection

AbstractFilamentDetector() - Constructor for class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

AbstractFilamentDetectorController - Class in sc.fiji.filamentdetector.gui.controller.detection

AbstractFilamentDetectorController() - Constructor for class sc.fiji.filamentdetector.gui.controller.detection.AbstractFilamentDetectorController

AbstractFilamentsTracker - Class in sc.fiji.filamentdetector.tracking

AbstractFilamentsTracker() - Constructor for class sc.fiji.filamentdetector.tracking.AbstractFilamentsTracker

AbstractFilamentsTrackerController - Class in sc.fiji.filamentdetector.gui.controller.tracking

AbstractFilamentsTrackerController() - Constructor for class sc.fiji.filamentdetector.gui.controller.tracking.AbstractFilamentsTrackerController

AbstractLineDrawer - Class in sc.fiji.filamentdetector.kymograph.linedrawer

AbstractLineDrawer() - Constructor for class sc.fiji.filamentdetector.kymograph.linedrawer.AbstractLineDrawer

add(RealPoint, RealPoint) - Static method in class sc.fiji.filamentdetector.GeometryUtils

add(Filament) - Method in class sc.fiji.filamentdetector.model.Filaments

add(Filament) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

add(Filament) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

add(Filaments) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

add(Filaments) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

add(TrackedFilament) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

add(TrackedFilament) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

add(TrackedFilaments) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

add(TrackedFilaments) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

addFilament(Filament) - Method in class sc.fiji.filamentdetector.gui.view.FilamentsTableView

addLink(Filament, Filament) - Method in class sc.fiji.filamentdetector.model.TrackedFilaments

addTrackedFilament(TrackedFilament) - Method in class sc.fiji.filamentdetector.gui.view.TrackedFilamentsTableView

analyze() - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

analyze() - Method in class sc.fiji.filamentdetector.analyzer.LengthOverTimeAnalyzer

analyze() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

analyze() - Method in class sc.fiji.filamentdetector.analyzer.TipFitterAnalyzer

AnalyzeController - Class in sc.fiji.filamentdetector.gui.controller

AnalyzeController(Context, FilamentWorkflow) - Constructor for class sc.fiji.filamentdetector.gui.controller.AnalyzeController

Analyzer - Interface in sc.fiji.filamentdetector.analyzer

AnalyzerController - Interface in sc.fiji.filamentdetector.gui.controller.analyzer

AnalyzerService - Class in sc.fiji.filamentdetector.analyzer

AnalyzerService() - Constructor for class sc.fiji.filamentdetector.analyzer.AnalyzerService

autoScaleImage() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

autoScaleImage() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

AverageFilamentLineDrawer - Class in sc.fiji.filamentdetector.kymograph.linedrawer

AverageFilamentLineDrawer() - Constructor for class sc.fiji.filamentdetector.kymograph.linedrawer.AverageFilamentLineDrawer

B

BBoxLAPFilamentsTracker - Class in sc.fiji.filamentdetector.tracking

BBoxLAPFilamentsTracker() - Constructor for class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

BBoxLAPFilamentsTrackerController - Class in sc.fiji.filamentdetector.gui.controller.tracking

BBoxLAPFilamentsTrackerController(Context, FilamentsTracker) - Constructor for class sc.fiji.filamentdetector.gui.controller.tracking.BBoxLAPFilamentsTrackerController

BoundingBoxOverlapCostFunction - Class in sc.fiji.filamentdetector.tracking.lap

BoundingBoxOverlapCostFunction() - Constructor for class sc.fiji.filamentdetector.tracking.lap.BoundingBoxOverlapCostFunction

build() - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

build(LineDrawer) - Method in class sc.fiji.filamentdetector.kymograph.LineGenerator

buildTracks(SimpleWeightedGraph<Filament, DefaultWeightedEdge>) - Method in class sc.fiji.filamentdetector.model.TrackedFilaments

C

Calibrations - Class in sc.fiji.filamentdetector

Calibrations(Context, Dataset) - Constructor for class sc.fiji.filamentdetector.Calibrations

channelToUse(String) - Method in class sc.fiji.filamentdetector.Calibrations

checkInput() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

clearSelection() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

clearSelection() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

COLOR - sc.fiji.filamentdetector.overlay.ImageDisplayMode

ColorService - Interface in sc.fiji.filamentdetector.overlay

compareTo(Filament) - Method in class sc.fiji.filamentdetector.model.Filament

COMPOSITE - sc.fiji.filamentdetector.overlay.ImageDisplayMode

contains(Filament) - Method in class sc.fiji.filamentdetector.model.TrackedFilaments

Controller - Interface in sc.fiji.filamentdetector.gui.controller

copy() - Method in class sc.fiji.filamentdetector.model.Filament

cropAlongAxis(ImgPlus<? extends RealType<?>>, AxisType, long) - Method in class sc.fiji.filamentdetector.ImageUtilService

CSVFilamentExporter - Class in sc.fiji.filamentdetector.exporter

CSVFilamentExporter(Context, Calibrations) - Constructor for class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

CSVTrackedFilamentExporter - Class in sc.fiji.filamentdetector.exporter

CSVTrackedFilamentExporter(Context, Calibrations) - Constructor for class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

D

DataExporter<T> - Interface in sc.fiji.filamentdetector.exporter

DataExporterController - Class in sc.fiji.filamentdetector.gui.controller

DataExporterController(Context, FilamentWorkflow) - Constructor for class sc.fiji.filamentdetector.gui.controller.DataExporterController

DEFAULT_COLOR - Static variable in class sc.fiji.filamentdetector.model.Filament

DefaultColorService - Class in sc.fiji.filamentdetector.overlay

DefaultColorService() - Constructor for class sc.fiji.filamentdetector.overlay.DefaultColorService

DefaultFilamentOverlayService - Class in sc.fiji.filamentdetector.overlay

DefaultFilamentOverlayService() - Constructor for class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

description - Variable in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

description - Variable in class sc.fiji.filamentdetector.kymograph.linedrawer.AbstractLineDrawer

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.analyzer.LengthOverTimeAnalyzer

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.analyzer.TipFitterAnalyzer

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.kymograph.linedrawer.AverageFilamentLineDrawer

DESCRIPTION - Static variable in class sc.fiji.filamentdetector.kymograph.linedrawer.LongestFilamentLineDrawer

DetailedFilamentController - Class in sc.fiji.filamentdetector.gui.controller

DetailedFilamentController(Filament) - Constructor for class sc.fiji.filamentdetector.gui.controller.DetailedFilamentController

DetailedTrackedFilamentController - Class in sc.fiji.filamentdetector.gui.controller

DetailedTrackedFilamentController(TrackedFilament) - Constructor for class sc.fiji.filamentdetector.gui.controller.DetailedTrackedFilamentController

detect() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

detect() - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

detect() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

detect() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

detect(int) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

detect(int) - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

detect(int) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

detect(ActionEvent) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

detectCurrentFrame() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

detectCurrentFrame() - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

detectCurrentFrame() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

detectCurrentFrame() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

detectCurrentFrame(int) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

detectCurrentFrame(int) - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

detectCurrentFrame(int) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

DetectFilamentController - Class in sc.fiji.filamentdetector.gui.controller

DetectFilamentController(Context, FilamentWorkflow) - Constructor for class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

detectFrame(int) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

detectFrame(int) - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

detectFrame(int) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

detectFrame(int, int) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

detectFrame(int, int) - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

detectFrame(int, int) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

DetectionParametersUpdatedEvent - Class in sc.fiji.filamentdetector.gui.event

DetectionParametersUpdatedEvent() - Constructor for class sc.fiji.filamentdetector.gui.event.DetectionParametersUpdatedEvent

detectTips() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

disableOverlay(boolean) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

disableOverlay(boolean) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

distance(RealPoint, RealPoint) - Static method in class sc.fiji.filamentdetector.GeometryUtils

distanceFromCenter(Filament) - Method in class sc.fiji.filamentdetector.model.Filament

draw(TrackedFilament) - Method in class sc.fiji.filamentdetector.kymograph.linedrawer.AverageFilamentLineDrawer

draw(TrackedFilament) - Method in interface sc.fiji.filamentdetector.kymograph.linedrawer.LineDrawer

draw(TrackedFilament) - Method in class sc.fiji.filamentdetector.kymograph.linedrawer.LongestFilamentLineDrawer

E

export(Filaments, File) - Method in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

export(Filaments, File) - Method in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

export(Filaments, File) - Method in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

export(TrackedFilaments, File) - Method in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

export(TrackedFilaments, File) - Method in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

export(T, File) - Method in interface sc.fiji.filamentdetector.exporter.DataExporter

exportToROIManager() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

exportToROIManager() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

extendTip(double[], double) - Method in class sc.fiji.filamentdetector.kymograph.LineGenerator

extendTips(double[], double, double) - Method in class sc.fiji.filamentdetector.kymograph.LineGenerator

EXTENSION - Static variable in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

EXTENSION - Static variable in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

EXTENSION - Static variable in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

EXTENSION - Static variable in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

EXTENSION - Static variable in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

EXTENSION_DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

EXTENSION_DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

EXTENSION_DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

EXTENSION_DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

EXTENSION_DESCRIPTION - Static variable in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

EXTENSION_FILTERS - Static variable in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

EXTENSION_FILTERS - Static variable in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

EXTENSION_FILTERS - Static variable in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

EXTENSION_FILTERS - Static variable in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

EXTENSION_FILTERS - Static variable in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

F

Filament - Class in sc.fiji.filamentdetector.model

Filament(double[], double[], int) - Constructor for class sc.fiji.filamentdetector.model.Filament

Filament(float[], float[], int) - Constructor for class sc.fiji.filamentdetector.model.Filament

Filament(List<RealPoint>, int) - Constructor for class sc.fiji.filamentdetector.model.Filament

FilamentDetector - Interface in sc.fiji.filamentdetector.detection

FilamentDetectorController - Interface in sc.fiji.filamentdetector.gui.controller.detection

FilamentDetectorPlugin - Class in sc.fiji.filamentdetector

FilamentDetectorPlugin() - Constructor for class sc.fiji.filamentdetector.FilamentDetectorPlugin

FilamentDetectorService - Class in sc.fiji.filamentdetector.detection

FilamentDetectorService() - Constructor for class sc.fiji.filamentdetector.detection.FilamentDetectorService

FilamentFactory - Class in sc.fiji.filamentdetector.model

FilamentFactory() - Constructor for class sc.fiji.filamentdetector.model.FilamentFactory

FilamentGraphSegmentSplitter - Class in sc.fiji.filamentdetector.tracking.lap

FilamentGraphSegmentSplitter(Graph<Filament, DefaultWeightedEdge>, boolean) - Constructor for class sc.fiji.filamentdetector.tracking.lap.FilamentGraphSegmentSplitter

FilamentModel - Class in sc.fiji.filamentdetector.gui.model

FilamentModel(Filament) - Constructor for class sc.fiji.filamentdetector.gui.model.FilamentModel

FilamentOverlayService - Interface in sc.fiji.filamentdetector.overlay

Filaments - Class in sc.fiji.filamentdetector.model

Filaments() - Constructor for class sc.fiji.filamentdetector.model.Filaments

filamentSelected(FilamentSelectedEvent) - Method in class sc.fiji.filamentdetector.gui.view.FilamentsTableView

filamentSelected(TrackedFilamentSelectedEvent) - Method in class sc.fiji.filamentdetector.gui.view.TrackedFilamentsTableView

FilamentSelectedEvent - Class in sc.fiji.filamentdetector.event

FilamentSelectedEvent(Filament) - Constructor for class sc.fiji.filamentdetector.event.FilamentSelectedEvent

FilamentsExporter<Filaments> - Class in sc.fiji.filamentdetector.exporter

FilamentsExporter(Context) - Constructor for class sc.fiji.filamentdetector.exporter.FilamentsExporter

FilamentsTableView - Class in sc.fiji.filamentdetector.gui.view

FilamentsTableView(Context, Filaments) - Constructor for class sc.fiji.filamentdetector.gui.view.FilamentsTableView

FilamentsTracker - Interface in sc.fiji.filamentdetector.tracking

FilamentsTrackerController - Interface in sc.fiji.filamentdetector.gui.controller.tracking

FilamentTipFitter - Class in sc.fiji.filamentdetector.analyzer.tipfitter

FilamentTipFitter(Context) - Constructor for class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

FilamentTrackerService - Class in sc.fiji.filamentdetector.tracking

FilamentTrackerService() - Constructor for class sc.fiji.filamentdetector.tracking.FilamentTrackerService

filamentWorkflow - Variable in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

FilamentWorkflow - Class in sc.fiji.filamentdetector

FilamentWorkflow(Context, ImageDisplay) - Constructor for class sc.fiji.filamentdetector.FilamentWorkflow

FilesUtils - Class in sc.fiji.filamentdetector

FilesUtils() - Constructor for class sc.fiji.filamentdetector.FilesUtils

filter(ActionEvent) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

filter(FilterFilamentEvent) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

filter(FilterTrackedFilamentEvent) - Method in class sc.fiji.filamentdetector.gui.controller.TrackingFilamentController

filterFilament(FilteringParameters) - Method in class sc.fiji.filamentdetector.FilamentWorkflow

FilterFilamentEvent - Class in sc.fiji.filamentdetector.event

FilterFilamentEvent(FilteringParameters) - Constructor for class sc.fiji.filamentdetector.event.FilterFilamentEvent

FilteringParameters - Class in sc.fiji.filamentdetector.detection

FilteringParameters() - Constructor for class sc.fiji.filamentdetector.detection.FilteringParameters

FilteringTrackedFilamentsParameters - Class in sc.fiji.filamentdetector.tracking

FilteringTrackedFilamentsParameters() - Constructor for class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

filterTrackedFilament(FilteringTrackedFilamentsParameters) - Method in class sc.fiji.filamentdetector.FilamentWorkflow

FilterTrackedFilamentEvent - Class in sc.fiji.filamentdetector.event

FilterTrackedFilamentEvent(FilteringTrackedFilamentsParameters) - Constructor for class sc.fiji.filamentdetector.event.FilterTrackedFilamentEvent

fit() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

frameComparator - Static variable in class sc.fiji.filamentdetector.model.Filament

fromLine(Line, int) - Static method in class sc.fiji.filamentdetector.model.FilamentFactory

fromPolyline(Polyline, int) - Static method in class sc.fiji.filamentdetector.model.FilamentFactory

G

GeometryUtils - Class in sc.fiji.filamentdetector

GeometryUtils() - Constructor for class sc.fiji.filamentdetector.GeometryUtils

getAlternativeCostForSource(Filament) - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getAlternativeCostForTarget(Filament) - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getAnalyzerInfo() - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

getAnalyzerInfo() - Method in class sc.fiji.filamentdetector.analyzer.LengthOverTimeAnalyzer

getAnalyzerInfo() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

getAnalyzerInfo() - Method in class sc.fiji.filamentdetector.analyzer.TipFitterAnalyzer

getAnalyzers() - Method in class sc.fiji.filamentdetector.analyzer.AnalyzerService

getAverageX() - Method in class sc.fiji.filamentdetector.model.Tip

getAverageY() - Method in class sc.fiji.filamentdetector.model.Tip

getBBoxTracker() - Method in class sc.fiji.filamentdetector.tracking.FilamentTrackerService

getBorderLimit() - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

getBoundingBox() - Method in class sc.fiji.filamentdetector.model.Filament

getCalibrations() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getChannelIndex() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

getChannelIndex() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getChannelList() - Method in class sc.fiji.filamentdetector.Calibrations

getChannelToUse() - Method in class sc.fiji.filamentdetector.Calibrations

getChannelToUseIndex() - Method in class sc.fiji.filamentdetector.Calibrations

getColor() - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

getColor() - Method in class sc.fiji.filamentdetector.gui.model.TrackedFilamentModel

getColor() - Method in class sc.fiji.filamentdetector.model.Filament

getColor() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

getColor(int) - Method in interface sc.fiji.filamentdetector.overlay.ColorService

getColor(int) - Method in class sc.fiji.filamentdetector.overlay.DefaultColorService

getColorAlpha() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

getColorAlpha() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

getColorAsHex() - Method in class sc.fiji.filamentdetector.model.Filament

getColorAsHex() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

getContext() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getCostFunctionFor(Map<String, Double>) - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getCostThreshold() - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

getData() - Method in class sc.fiji.filamentdetector.Calibrations

getDataset() - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

getDataset() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

getDataset() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getDataset() - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

getDescription() - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

getDescription() - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

getDescription() - Method in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

getDescription() - Method in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

getDescription() - Method in interface sc.fiji.filamentdetector.exporter.DataExporter

getDescription() - Method in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

getDescription() - Method in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

getDescription() - Method in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

getDescription() - Method in class sc.fiji.filamentdetector.kymograph.linedrawer.AbstractLineDrawer

getDescription() - Method in interface sc.fiji.filamentdetector.kymograph.linedrawer.LineDrawer

getDetailPane() - Method in class sc.fiji.filamentdetector.gui.view.FilamentsTableView

getDetailPane() - Method in class sc.fiji.filamentdetector.gui.view.TrackedFilamentsTableView

getDetectors() - Method in class sc.fiji.filamentdetector.detection.FilamentDetectorService

getDetectors() - Method in class sc.fiji.filamentdetector.tracking.FilamentTrackerService

getDispX() - Method in class sc.fiji.filamentdetector.model.Tip

getDispY() - Method in class sc.fiji.filamentdetector.model.Tip

getDistanceRatio(double, double, double, double, double) - Method in class sc.fiji.filamentdetector.kymograph.LineGenerator

getDt() - Method in class sc.fiji.filamentdetector.Calibrations

getDx() - Method in class sc.fiji.filamentdetector.Calibrations

getDy() - Method in class sc.fiji.filamentdetector.Calibrations

getDz() - Method in class sc.fiji.filamentdetector.Calibrations

getEndOffsetLength() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

getEndTip() - Method in class sc.fiji.filamentdetector.model.Filament

getEndTipAsArray() - Method in class sc.fiji.filamentdetector.model.Filament

getErrorMessage() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getExtension() - Method in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

getExtension() - Method in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

getExtension() - Method in interface sc.fiji.filamentdetector.exporter.DataExporter

getExtension() - Method in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

getExtension() - Method in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

getExtension() - Method in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

getExtensionDescription() - Method in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

getExtensionDescription() - Method in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

getExtensionDescription() - Method in interface sc.fiji.filamentdetector.exporter.DataExporter

getExtensionDescription() - Method in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

getExtensionDescription() - Method in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

getExtensionDescription() - Method in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

getExtensionFilters() - Method in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

getExtensionFilters() - Method in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

getExtensionFilters() - Method in interface sc.fiji.filamentdetector.exporter.DataExporter

getExtensionFilters() - Method in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

getExtensionFilters() - Method in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

getExtensionFilters() - Method in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

getFilament() - Method in class sc.fiji.filamentdetector.event.FilamentSelectedEvent

getFilament() - Method in class sc.fiji.filamentdetector.gui.controller.DetailedFilamentController

getFilament() - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

getFilamentByFrame(double) - Method in class sc.fiji.filamentdetector.model.TrackedFilament

getFilamentDetector() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getFilaments() - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

getFilaments() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

getFilaments() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getFilaments() - Method in class sc.fiji.filamentdetector.gui.view.FilamentsTableView

getFilaments() - Method in class sc.fiji.filamentdetector.tracking.AbstractFilamentsTracker

getFilaments() - Method in interface sc.fiji.filamentdetector.tracking.FilamentsTracker

getFilamentsTracker() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getFilamentWidth() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

getFilamentWidth() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

getFilamentWorkflow() - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

getFilamentWorkflow() - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

getFileNameWithoutExtension(File) - Static method in class sc.fiji.filamentdetector.FilesUtils

getFileNameWithoutExtension(String) - Static method in class sc.fiji.filamentdetector.FilesUtils

getFilteringParameters() - Method in class sc.fiji.filamentdetector.event.FilterFilamentEvent

getFilteringTrackedFilamentsParameters() - Method in class sc.fiji.filamentdetector.event.FilterTrackedFilamentEvent

getFirstPoint() - Method in class sc.fiji.filamentdetector.model.Filament

getFitter() - Method in class sc.fiji.filamentdetector.analyzer.TipFitterAnalyzer

getFrame() - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

getFrame() - Method in class sc.fiji.filamentdetector.model.Filament

getFrames() - Method in class sc.fiji.filamentdetector.model.Tip

getFrames() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

getFXMLPath() - Method in class sc.fiji.filamentdetector.gui.controller.AbstractController

getHighContrast() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getId() - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

getId() - Method in class sc.fiji.filamentdetector.gui.model.TrackedFilamentModel

getId() - Method in class sc.fiji.filamentdetector.model.Filament

getId() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

getIDs() - Method in class sc.fiji.filamentdetector.model.TrackedFilaments

getIJ2RidgeFilamentDetector() - Method in class sc.fiji.filamentdetector.detection.FilamentDetectorService

getImageDisplay() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getImageDisplay() - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

getImageDisplay() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

getImageDisplay() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getImageDisplay() - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

getImageDisplay() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

getImageDisplay() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

getIndexByID(int) - Method in class sc.fiji.filamentdetector.model.Filaments

getInfoPane() - Method in class sc.fiji.filamentdetector.gui.view.FilamentsTableView

getInfoPane() - Method in class sc.fiji.filamentdetector.gui.view.TrackedFilamentsTableView

getIntensities(Context, ImageDisplay, double, double) - Method in class sc.fiji.filamentdetector.model.Filament

getIntensitiesAsArray(Context, ImageDisplay, double, double) - Method in class sc.fiji.filamentdetector.model.Filament

getIntensityThreshold() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

getKymographParameters() - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

getKymographs() - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

getLastPoint() - Method in class sc.fiji.filamentdetector.model.Filament

getLength() - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

getLength() - Method in class sc.fiji.filamentdetector.model.Filament

getLength() - Method in interface sc.fiji.filamentdetector.overlay.ColorService

getLength() - Method in class sc.fiji.filamentdetector.overlay.DefaultColorService

getLengthOverTimeAnalyzer() - Method in class sc.fiji.filamentdetector.analyzer.AnalyzerService

getLengths() - Method in class sc.fiji.filamentdetector.model.Filament

getLengths() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

getLineDrawer() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

getLineFitLength() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getLineLength() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

getLinePointsFromNumberOfPoints(RealPoint, RealPoint, int) - Static method in class sc.fiji.filamentdetector.GeometryUtils

getLinePointsFromSpacing(RealPoint, RealPoint, double) - Static method in class sc.fiji.filamentdetector.GeometryUtils

getLineThickness() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

getLineThickness() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

getLineWidth() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getLineWidth() - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

getLineWidth() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getLowContrast() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getLowerThresh() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getLowerThreshold() - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

getLowerValue() - Method in class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

getLut() - Method in interface sc.fiji.filamentdetector.overlay.ColorService

getLut() - Method in class sc.fiji.filamentdetector.overlay.DefaultColorService

getMaxFrame() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

getMaxFrameGap() - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

getMaxLength() - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

getMaxLength() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getMaxSinuosity() - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

getMaxSize() - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

getMinLength() - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

getMinLength() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getMinSinuosity() - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

getMinSize() - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

getMinusTip() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

getNaiveNucleationAnalyzer() - Method in class sc.fiji.filamentdetector.analyzer.AnalyzerService

getName() - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

getName() - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

getName() - Method in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

getName() - Method in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

getName() - Method in interface sc.fiji.filamentdetector.exporter.DataExporter

getName() - Method in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

getName() - Method in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

getName() - Method in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

getName() - Method in class sc.fiji.filamentdetector.kymograph.linedrawer.AbstractLineDrawer

getName() - Method in interface sc.fiji.filamentdetector.kymograph.linedrawer.LineDrawer

getName() - Method in class sc.fiji.filamentdetector.tracking.AbstractFilamentsTracker

getNumThreads() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getOverlapOption() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getPane() - Method in class sc.fiji.filamentdetector.gui.controller.AbstractController

getPane() - Method in interface sc.fiji.filamentdetector.gui.controller.Controller

getParallelLines(List<RealPoint>, double, double) - Static method in class sc.fiji.filamentdetector.GeometryUtils

getPixelSpacing() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

getPlusTip() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

getPointOnVectorFromDistance(double[], double[], double) - Static method in class sc.fiji.filamentdetector.GeometryUtils

getPointOnVectorFromDistance(float[], float[], double) - Static method in class sc.fiji.filamentdetector.GeometryUtils

getPointOnVectorFromDistance(RealPoint, RealPoint, double) - Static method in class sc.fiji.filamentdetector.GeometryUtils

getPolynomDegree() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getPreventPaneSwitch() - Method in class sc.fiji.filamentdetector.event.PreventPanelSwitchEvent

getProcessingTime() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getRelativePositionFromEnd() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getRemoveFilamentLabel() - Method in class sc.fiji.filamentdetector.gui.controller.DetailedFilamentController

getRemoveFilamentLabel() - Method in class sc.fiji.filamentdetector.gui.controller.DetailedTrackedFilamentController

getResult() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getResultMessage() - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

getResultMessage() - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

getResults() - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

getResults() - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

getRidgeFilamentDetector() - Method in class sc.fiji.filamentdetector.detection.FilamentDetectorService

getRoi() - Method in class sc.fiji.filamentdetector.model.Filament

getSeeds() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getSegmentEnds() - Method in class sc.fiji.filamentdetector.tracking.lap.FilamentGraphSegmentSplitter

getSegmentMiddles() - Method in class sc.fiji.filamentdetector.tracking.lap.FilamentGraphSegmentSplitter

getSegmentStarts() - Method in class sc.fiji.filamentdetector.tracking.lap.FilamentGraphSegmentSplitter

getSide1Filaments() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getSide2Filaments() - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

getSigma() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getSimplifyToleranceDistance() - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

getSimplifyToleranceDistance() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

getSinuosity() - Method in class sc.fiji.filamentdetector.model.Filament

getSize() - Method in class sc.fiji.filamentdetector.gui.model.TrackedFilamentModel

getSize() - Method in class sc.fiji.filamentdetector.model.Filament

getSizeT() - Method in class sc.fiji.filamentdetector.Calibrations

getSizeX() - Method in class sc.fiji.filamentdetector.Calibrations

getSizeY() - Method in class sc.fiji.filamentdetector.Calibrations

getSizeZ() - Method in class sc.fiji.filamentdetector.Calibrations

getSourceImage() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getSourceList() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getStartOffsetLength() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

getStartTip() - Method in class sc.fiji.filamentdetector.model.Filament

getStartTipAsArray() - Method in class sc.fiji.filamentdetector.model.Filament

getStdX() - Method in class sc.fiji.filamentdetector.model.Tip

getStdY() - Method in class sc.fiji.filamentdetector.model.Tip

getTargetList() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

getTipDiameter() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

getTipDiameter() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

getTipFitterAnalyzer() - Method in class sc.fiji.filamentdetector.analyzer.AnalyzerService

getTipLength() - Method in class sc.fiji.filamentdetector.model.Filament

getTips() - Method in class sc.fiji.filamentdetector.model.Filament

getTitledPane(String) - Method in class sc.fiji.filamentdetector.gui.controller.MainController

getTrackedFilament() - Method in class sc.fiji.filamentdetector.event.TrackedFilamentSelectedEvent

getTrackedFilament() - Method in class sc.fiji.filamentdetector.gui.controller.DetailedTrackedFilamentController

getTrackedFilament() - Method in class sc.fiji.filamentdetector.gui.model.TrackedFilamentModel

getTrackedFilament() - Method in class sc.fiji.filamentdetector.kymograph.LineGenerator

getTrackedFilament(Filament) - Method in class sc.fiji.filamentdetector.model.TrackedFilaments

getTrackedFilaments() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

getTrackedFilaments() - Method in class sc.fiji.filamentdetector.gui.view.TrackedFilamentsTableView

getTrackedFilaments() - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

getTrackedFilaments() - Method in class sc.fiji.filamentdetector.tracking.AbstractFilamentsTracker

getTrackedFilaments() - Method in interface sc.fiji.filamentdetector.tracking.FilamentsTracker

getUnitT() - Method in class sc.fiji.filamentdetector.Calibrations

getUnitX() - Method in class sc.fiji.filamentdetector.Calibrations

getUnitY() - Method in class sc.fiji.filamentdetector.Calibrations

getUnitZ() - Method in class sc.fiji.filamentdetector.Calibrations

getUpperThresh() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

getUpperThreshold() - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

getUpperValue() - Method in class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

getValue() - Method in class sc.fiji.filamentdetector.gui.fxwidgets.SliderLabelSynchronizer

getX() - Method in class sc.fiji.filamentdetector.model.Tip

getXCoordinates() - Method in class sc.fiji.filamentdetector.model.Filament

getXCoordinatesAsFloat() - Method in class sc.fiji.filamentdetector.model.Filament

getY() - Method in class sc.fiji.filamentdetector.model.Tip

getYCoordinates() - Method in class sc.fiji.filamentdetector.model.Filament

getYCoordinatesAsFloat() - Method in class sc.fiji.filamentdetector.model.Filament

GRAYSCALE - sc.fiji.filamentdetector.overlay.ImageDisplayMode

guessIntensityThresholdFromImage() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

GUIStatusService - Class in sc.fiji.filamentdetector.gui

GUIStatusService() - Constructor for class sc.fiji.filamentdetector.gui.GUIStatusService

GUIUtils - Class in sc.fiji.filamentdetector.gui

GUIUtils() - Constructor for class sc.fiji.filamentdetector.gui.GUIUtils

I

IJ1RoiFilamentExporter - Class in sc.fiji.filamentdetector.exporter

IJ1RoiFilamentExporter(Context) - Constructor for class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

IJ2RidgeDetectionFilamentDetector - Class in sc.fiji.filamentdetector.detection

IJ2RidgeDetectionFilamentDetector() - Constructor for class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

IJ2RidgeDetectionFilamentDetectorController - Class in sc.fiji.filamentdetector.gui.controller.detection

IJ2RidgeDetectionFilamentDetectorController(Context, FilamentDetector) - Constructor for class sc.fiji.filamentdetector.gui.controller.detection.IJ2RidgeDetectionFilamentDetectorController

ImageDisplayMode - Enum in sc.fiji.filamentdetector.overlay

ImageNotFoundEvent - Class in sc.fiji.filamentdetector.event

ImageNotFoundEvent() - Constructor for class sc.fiji.filamentdetector.event.ImageNotFoundEvent

ImageUtilService - Class in sc.fiji.filamentdetector

ImageUtilService() - Constructor for class sc.fiji.filamentdetector.ImageUtilService

importLinesfromROIManager(MouseEvent) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

info() - Method in class sc.fiji.filamentdetector.model.Filament

info() - Method in class sc.fiji.filamentdetector.model.Filaments

initDetectionComboBox() - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

initFX(JFXPanel) - Method in class sc.fiji.filamentdetector.gui.MainAppFrame

initialize() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

initialize() - Method in class sc.fiji.filamentdetector.gui.MainAppFrame

Create the JFXPanel that make the link between Swing (IJ) and JavaFX plugin.

initialize() - Method in interface sc.fiji.filamentdetector.overlay.ColorService

initialize() - Method in class sc.fiji.filamentdetector.overlay.DefaultColorService

initialize(String) - Method in interface sc.fiji.filamentdetector.overlay.ColorService

initialize(String) - Method in class sc.fiji.filamentdetector.overlay.DefaultColorService

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.AboutController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.AnalyzeController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.analyzer.LengthOverTimeAnalyzerController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.analyzer.NaiveNucleationAnalyzerController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.analyzer.TipFitterAnalyzerController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.DataExporterController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.DetailedFilamentController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.DetailedTrackedFilamentController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.detection.IJ2RidgeDetectionFilamentDetectorController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.detection.RidgeDetectionFilamentDetectorController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.KymographBuilderController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.MainController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.tracking.BBoxLAPFilamentsTrackerController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.TrackingFilamentController

initialize(URL, ResourceBundle) - Method in class sc.fiji.filamentdetector.gui.controller.WelcomeController

initPane() - Method in class sc.fiji.filamentdetector.gui.controller.AnalyzeController

initPane() - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

initPane() - Method in class sc.fiji.filamentdetector.gui.controller.KymographBuilderController

initPane() - Method in class sc.fiji.filamentdetector.gui.controller.TrackingFilamentController

initTrackerComboBox() - Method in class sc.fiji.filamentdetector.gui.controller.TrackingFilamentController

insideBbox(double[]) - Method in class sc.fiji.filamentdetector.model.Filament

insideBbox(double[]) - Method in class sc.fiji.filamentdetector.model.TrackedFilament

interpolateFilaments() - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

isBlockReorder() - Method in class sc.fiji.filamentdetector.gui.fxwidgets.ReorderableListCell

isBuildOneRandomKymograph() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

isColorizedNucleatedSeeds() - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

isDarkLine() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

isDetectJunctions() - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

isDetectOnlyCurrentFrame() - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

isDetectOnlyCurrentFrame() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

isDisableFiltering() - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

isDisableFiltering() - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

isDoCorrectPosition() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

isDoEstimateWidth() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

isDoExtendLine() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

isDrawBoundingBoxes() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

isDrawBoundingBoxes() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

isDrawMinusTips() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

isDrawMinusTips() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

isDrawPlusTips() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

isDrawPlusTips() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

isEvent(Event) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.SliderLabelSynchronizer

isEvent(Event) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

isInterpolateFilaments() - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

isSaveKymographLines() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

isSaveKymographs() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

isSaveResults() - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

isSaveResults() - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

isShowKymographs() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

isSimplifyFilaments() - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

isSimplifyFilaments() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

J

JaqamanFilamentSegmentCostMatrixCreator - Class in sc.fiji.filamentdetector.tracking.lap

JaqamanFilamentSegmentCostMatrixCreator(Graph<Filament, DefaultWeightedEdge>, Map<String, Object>) - Constructor for class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

Instantiates a cost matrix creator for the top-left quadrant of the segment linking cost matrix.

JSONFilamentExporter - Class in sc.fiji.filamentdetector.exporter

JSONFilamentExporter(Context, Calibrations) - Constructor for class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

JSONTrackedFilamentExporter - Class in sc.fiji.filamentdetector.exporter

JSONTrackedFilamentExporter(Context, Calibrations) - Constructor for class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

K

KymographBuilderController - Class in sc.fiji.filamentdetector.gui.controller

KymographBuilderController(Context, FilamentWorkflow) - Constructor for class sc.fiji.filamentdetector.gui.controller.KymographBuilderController

KymographGenerator - Class in sc.fiji.filamentdetector.kymograph

KymographGenerator(Context) - Constructor for class sc.fiji.filamentdetector.kymograph.KymographGenerator

KymographParameters - Class in sc.fiji.filamentdetector.kymograph

KymographParameters() - Constructor for class sc.fiji.filamentdetector.kymograph.KymographParameters

kymographsHasBeenSaved() - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

L

lastFilamentIs(Filament) - Method in class sc.fiji.filamentdetector.model.TrackedFilament

LengthOverTimeAnalyzer - Class in sc.fiji.filamentdetector.analyzer

LengthOverTimeAnalyzer() - Constructor for class sc.fiji.filamentdetector.analyzer.LengthOverTimeAnalyzer

LengthOverTimeAnalyzerController - Class in sc.fiji.filamentdetector.gui.controller.analyzer

LengthOverTimeAnalyzerController(Context, LengthOverTimeAnalyzer) - Constructor for class sc.fiji.filamentdetector.gui.controller.analyzer.LengthOverTimeAnalyzerController

LineDrawer - Interface in sc.fiji.filamentdetector.kymograph.linedrawer

LineGenerator - Class in sc.fiji.filamentdetector.kymograph

LineGenerator(double, double, double) - Constructor for class sc.fiji.filamentdetector.kymograph.LineGenerator

linkingCost(Filament, Filament) - Method in class sc.fiji.filamentdetector.tracking.lap.BoundingBoxOverlapCostFunction

liveDetectionClicked(MouseEvent) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

loadAbout() - Method in class sc.fiji.filamentdetector.gui.controller.MainController

loadAnalyzer() - Method in class sc.fiji.filamentdetector.gui.controller.MainController

loadDataExporter() - Method in class sc.fiji.filamentdetector.gui.controller.MainController

loadDetectFilament() - Method in class sc.fiji.filamentdetector.gui.controller.MainController

loadFXML(String, Controller) - Static method in class sc.fiji.filamentdetector.gui.GUIUtils

loadImageCalibrations() - Method in class sc.fiji.filamentdetector.gui.controller.WelcomeController

loadKymographBuilder() - Method in class sc.fiji.filamentdetector.gui.controller.MainController

loadPane() - Method in class sc.fiji.filamentdetector.gui.controller.AbstractController

loadPane() - Method in interface sc.fiji.filamentdetector.gui.controller.Controller

loadPanes() - Method in class sc.fiji.filamentdetector.gui.controller.MainController

loadTrackingFilament() - Method in class sc.fiji.filamentdetector.gui.controller.MainController

loadWelcome() - Method in class sc.fiji.filamentdetector.gui.controller.MainController

LongestFilamentLineDrawer - Class in sc.fiji.filamentdetector.kymograph.linedrawer

LongestFilamentLineDrawer() - Constructor for class sc.fiji.filamentdetector.kymograph.linedrawer.LongestFilamentLineDrawer

M

MainAppFrame - Class in sc.fiji.filamentdetector.gui

MainAppFrame(ImageJ, FilamentWorkflow) - Constructor for class sc.fiji.filamentdetector.gui.MainAppFrame

MainController - Class in sc.fiji.filamentdetector.gui.controller

MainController(Context, FilamentWorkflow) - Constructor for class sc.fiji.filamentdetector.gui.controller.MainController

matchTips() - Method in class sc.fiji.filamentdetector.model.TrackedFilament

mouseClicked(MouseEvent) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

mouseEntered(MouseEvent) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

mouseExited(MouseEvent) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

mousePressed(MouseEvent) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

mouseReleased(MouseEvent) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

N

NaiveNucleationAnalyzer - Class in sc.fiji.filamentdetector.analyzer

NaiveNucleationAnalyzer() - Constructor for class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

NaiveNucleationAnalyzerController - Class in sc.fiji.filamentdetector.gui.controller.analyzer

NaiveNucleationAnalyzerController(Context, NaiveNucleationAnalyzer) - Constructor for class sc.fiji.filamentdetector.gui.controller.analyzer.NaiveNucleationAnalyzerController

name - Variable in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

name - Variable in class sc.fiji.filamentdetector.kymograph.linedrawer.AbstractLineDrawer

NAME - Static variable in class sc.fiji.filamentdetector.analyzer.LengthOverTimeAnalyzer

NAME - Static variable in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

NAME - Static variable in class sc.fiji.filamentdetector.analyzer.TipFitterAnalyzer

NAME - Static variable in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

NAME - Static variable in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

NAME - Static variable in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

NAME - Static variable in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

NAME - Static variable in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

NAME - Static variable in class sc.fiji.filamentdetector.kymograph.linedrawer.AverageFilamentLineDrawer

NAME - Static variable in class sc.fiji.filamentdetector.kymograph.linedrawer.LongestFilamentLineDrawer

nKymographs() - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

O

onEvent(StatusEvent) - Method in class sc.fiji.filamentdetector.gui.GUIStatusService

P

pane - Variable in class sc.fiji.filamentdetector.gui.controller.AbstractController

plotPoints(double[]) - Static method in class sc.fiji.filamentdetector.GeometryUtils

plotPoints(double[], double[]) - Static method in class sc.fiji.filamentdetector.GeometryUtils

plotPoints(List<RealPoint>) - Static method in class sc.fiji.filamentdetector.GeometryUtils

PLUGIN_NAME - Static variable in class sc.fiji.filamentdetector.FilamentDetectorPlugin

positionWindow(JFrame, Component) - Static method in class sc.fiji.filamentdetector.gui.GUIUtils

Positions a JFrame more or less cleverly next a Component.

PreventPanelSwitchEvent - Class in sc.fiji.filamentdetector.event

PreventPanelSwitchEvent(boolean) - Constructor for class sc.fiji.filamentdetector.event.PreventPanelSwitchEvent

process() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

R

refresh() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

refresh() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

refreshData(MouseEvent) - Method in class sc.fiji.filamentdetector.gui.controller.DataExporterController

remove(Filament) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

remove(Filament) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

remove(Filaments) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

remove(Filaments) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

remove(TrackedFilament) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

remove(TrackedFilament) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

remove(TrackedFilaments) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

remove(TrackedFilaments) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

removeFilamentLabel - Variable in class sc.fiji.filamentdetector.gui.controller.DetailedFilamentController

removeFilamentLabel - Variable in class sc.fiji.filamentdetector.gui.controller.DetailedTrackedFilamentController

ReorderableListCell - Class in sc.fiji.filamentdetector.gui.fxwidgets

ReorderableListCell() - Constructor for class sc.fiji.filamentdetector.gui.fxwidgets.ReorderableListCell

ReorderablePaneListView - Class in sc.fiji.filamentdetector.gui.fxwidgets

ReorderablePaneListView() - Constructor for class sc.fiji.filamentdetector.gui.fxwidgets.ReorderablePaneListView

ReorderablePaneListView(List<T>) - Constructor for class sc.fiji.filamentdetector.gui.fxwidgets.ReorderablePaneListView

reset() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

reset() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

resultMessage - Variable in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

results - Variable in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

reverseCoordinates() - Method in class sc.fiji.filamentdetector.model.Filament

RidgeDetectionFilamentDetector - Class in sc.fiji.filamentdetector.detection

RidgeDetectionFilamentDetector() - Constructor for class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

RidgeDetectionFilamentDetectorController - Class in sc.fiji.filamentdetector.gui.controller.detection

RidgeDetectionFilamentDetectorController(Context, FilamentDetector) - Constructor for class sc.fiji.filamentdetector.gui.controller.detection.RidgeDetectionFilamentDetectorController

run() - Method in class sc.fiji.filamentdetector.FilamentDetectorPlugin

runPostAnalysisAction() - Method in interface sc.fiji.filamentdetector.gui.controller.analyzer.AnalyzerController

runPostAnalysisAction() - Method in class sc.fiji.filamentdetector.gui.controller.analyzer.LengthOverTimeAnalyzerController

runPostAnalysisAction() - Method in class sc.fiji.filamentdetector.gui.controller.analyzer.NaiveNucleationAnalyzerController

runPostAnalysisAction() - Method in class sc.fiji.filamentdetector.gui.controller.analyzer.TipFitterAnalyzerController

S

saveResults - Variable in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

sc.fiji.filamentdetector - module sc.fiji.filamentdetector

sc.fiji.filamentdetector - package sc.fiji.filamentdetector

sc.fiji.filamentdetector.analyzer - package sc.fiji.filamentdetector.analyzer

sc.fiji.filamentdetector.analyzer.tipfitter - package sc.fiji.filamentdetector.analyzer.tipfitter

sc.fiji.filamentdetector.detection - package sc.fiji.filamentdetector.detection

sc.fiji.filamentdetector.event - package sc.fiji.filamentdetector.event

sc.fiji.filamentdetector.exporter - package sc.fiji.filamentdetector.exporter

sc.fiji.filamentdetector.gui - package sc.fiji.filamentdetector.gui

sc.fiji.filamentdetector.gui.controller - package sc.fiji.filamentdetector.gui.controller

sc.fiji.filamentdetector.gui.controller.analyzer - package sc.fiji.filamentdetector.gui.controller.analyzer

sc.fiji.filamentdetector.gui.controller.detection - package sc.fiji.filamentdetector.gui.controller.detection

sc.fiji.filamentdetector.gui.controller.tracking - package sc.fiji.filamentdetector.gui.controller.tracking

sc.fiji.filamentdetector.gui.event - package sc.fiji.filamentdetector.gui.event

sc.fiji.filamentdetector.gui.fxwidgets - package sc.fiji.filamentdetector.gui.fxwidgets

sc.fiji.filamentdetector.gui.model - package sc.fiji.filamentdetector.gui.model

sc.fiji.filamentdetector.gui.view - package sc.fiji.filamentdetector.gui.view

sc.fiji.filamentdetector.kymograph - package sc.fiji.filamentdetector.kymograph

sc.fiji.filamentdetector.kymograph.linedrawer - package sc.fiji.filamentdetector.kymograph.linedrawer

sc.fiji.filamentdetector.model - package sc.fiji.filamentdetector.model

sc.fiji.filamentdetector.overlay - package sc.fiji.filamentdetector.overlay

sc.fiji.filamentdetector.tracking - package sc.fiji.filamentdetector.tracking

sc.fiji.filamentdetector.tracking.lap - package sc.fiji.filamentdetector.tracking.lap

serializeCoordinates(double[]) - Method in class sc.fiji.filamentdetector.exporter.AbstractDataExporter

serializeCoordinates(double[], double) - Method in class sc.fiji.filamentdetector.exporter.AbstractDataExporter

setBlockReorder(boolean) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.ReorderableListCell

setBorderLimit(double) - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

setBuildOneRandomKymograph(boolean) - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

setChannelIndex(int) - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

setChannelIndex(int) - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

setChannelList(List<String>) - Method in class sc.fiji.filamentdetector.Calibrations

setChannelToUseIndex(int) - Method in class sc.fiji.filamentdetector.Calibrations

setColor(Color) - Method in class sc.fiji.filamentdetector.model.Filament

setColor(Color) - Method in class sc.fiji.filamentdetector.model.TrackedFilament

setColor(StringProperty) - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

setColor(StringProperty) - Method in class sc.fiji.filamentdetector.gui.model.TrackedFilamentModel

setColorAlpha(int) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setColorAlpha(int) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setColorizedNucleatedSeeds(boolean) - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

setCostThreshold(double) - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

setDarkLine(boolean) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setDataset(Dataset) - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

setDataset(Dataset) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

setDescription(String) - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

setDescription(String) - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

setDescription(String) - Method in class sc.fiji.filamentdetector.kymograph.linedrawer.AbstractLineDrawer

setDescription(String) - Method in interface sc.fiji.filamentdetector.kymograph.linedrawer.LineDrawer

setDetectJunctions(boolean) - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

setDetectOnlyCurrentFrame(boolean) - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

setDetectOnlyCurrentFrame(boolean) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

setDisableFiltering(boolean) - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

setDisableFiltering(boolean) - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

setDoCorrectPosition(boolean) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setDoEstimateWidth(boolean) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setDoExtendLine(boolean) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setDrawBoundingBoxes(boolean) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setDrawBoundingBoxes(boolean) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setDrawMinusTips(boolean) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setDrawMinusTips(boolean) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setDrawPlusTips(boolean) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setDrawPlusTips(boolean) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setDt(double) - Method in class sc.fiji.filamentdetector.Calibrations

setDx(double) - Method in class sc.fiji.filamentdetector.Calibrations

setDy(double) - Method in class sc.fiji.filamentdetector.Calibrations

setDz(double) - Method in class sc.fiji.filamentdetector.Calibrations

setEndOffsetLength(double) - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

setFilamentDetector(FilamentDetector) - Method in class sc.fiji.filamentdetector.FilamentWorkflow

setFilaments(Filaments) - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

setFilaments(Filaments) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

setFilaments(Filaments) - Method in class sc.fiji.filamentdetector.gui.view.FilamentsTableView

setFilaments(Filaments) - Method in class sc.fiji.filamentdetector.tracking.AbstractFilamentsTracker

setFilaments(Filaments) - Method in interface sc.fiji.filamentdetector.tracking.FilamentsTracker

setFilamentsTracker(FilamentsTracker) - Method in class sc.fiji.filamentdetector.FilamentWorkflow

setFilamentWidth(int) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setFilamentWidth(int) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setFilamentWorkflow(FilamentWorkflow) - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

setFilamentWorkflow(FilamentWorkflow) - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

setFrame(IntegerProperty) - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

setFXMLPath(String) - Method in class sc.fiji.filamentdetector.gui.controller.AbstractController

setHighContrast(double) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setId(IntegerProperty) - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

setId(IntegerProperty) - Method in class sc.fiji.filamentdetector.gui.model.TrackedFilamentModel

setImageDisplay(ImageDisplay) - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

setImageDisplay(ImageDisplay) - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

setImageDisplay(ImageDisplay) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

setImageDisplay(ImageDisplay) - Method in class sc.fiji.filamentdetector.FilamentWorkflow

setImageDisplay(ImageDisplay) - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

setImageDisplay(ImageDisplay) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setImageDisplay(ImageDisplay) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setIntensityThreshold(double) - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

setInterpolateFilaments(boolean) - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

setLength(DoubleProperty) - Method in class sc.fiji.filamentdetector.gui.model.FilamentModel

setLineDrawer(LineDrawer) - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

setLineFitLength(double) - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

setLineLength(double) - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

setLineThickness(double) - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

setLineThickness(double) - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

setLineWidth(double) - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

setLineWidth(double) - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

setLineWidth(double) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setLowContrast(double) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setLowerThresh(double) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setLowerThreshold(double) - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

setLowerTooltip(String) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

setLowerValue(double) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

setMaxFrame(int) - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

setMaxFrameGap(double) - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

setMaxLength(double) - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

setMaxLength(double) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setMaxSinuosity(double) - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

setMaxSize(double) - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

setMinLength(double) - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

setMinLength(double) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setMinSinuosity(double) - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

setMinSize(double) - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

setName(String) - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

setName(String) - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

setName(String) - Method in class sc.fiji.filamentdetector.kymograph.linedrawer.AbstractLineDrawer

setName(String) - Method in interface sc.fiji.filamentdetector.kymograph.linedrawer.LineDrawer

setName(String) - Method in class sc.fiji.filamentdetector.tracking.AbstractFilamentsTracker

setNumThreads() - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

setNumThreads(int) - Method in class sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

setOverlapOption(OverlapOption) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setPane(Pane) - Method in class sc.fiji.filamentdetector.gui.controller.AbstractController

setPane(Pane) - Method in interface sc.fiji.filamentdetector.gui.controller.Controller

setPixelSpacing(double) - Method in class sc.fiji.filamentdetector.analyzer.NaiveNucleationAnalyzer

setPolynomDegree(int) - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

setRelativePositionFromEnd(double) - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

setSaveKymographLines(boolean) - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

setSaveKymographs(boolean) - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

setSaveResults(boolean) - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

setSaveResults(boolean) - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

setSeeds(TrackedFilaments) - Method in class sc.fiji.filamentdetector.analyzer.tipfitter.FilamentTipFitter

setSelected(Filament, boolean, boolean) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setSelected(Filament, boolean, boolean) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setSelected(TrackedFilament, boolean, boolean) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setSelected(TrackedFilament, boolean, boolean) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setShowKymographs(boolean) - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

setSigma(double) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setSimplifyFilaments(boolean) - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

setSimplifyFilaments(boolean) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

setSimplifyToleranceDistance(double) - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

setSimplifyToleranceDistance(double) - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

setSize(IntegerProperty) - Method in class sc.fiji.filamentdetector.gui.model.TrackedFilamentModel

setStartOffsetLength(double) - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

setTextField(Object) - Method in class sc.fiji.filamentdetector.gui.GUIStatusService

setTipDiameter(int) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setTipDiameter(int) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

setTooltip(String) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.SliderLabelSynchronizer

setTrackedFilament(TrackedFilament) - Method in class sc.fiji.filamentdetector.kymograph.LineGenerator

setTrackedFilaments(TrackedFilaments) - Method in class sc.fiji.filamentdetector.gui.view.TrackedFilamentsTableView

setTrackedFilaments(TrackedFilaments) - Method in class sc.fiji.filamentdetector.kymograph.KymographGenerator

setTrackedFilaments(TrackedFilaments) - Method in class sc.fiji.filamentdetector.tracking.AbstractFilamentsTracker

setTrackedFilaments(TrackedFilaments) - Method in interface sc.fiji.filamentdetector.tracking.FilamentsTracker

setUpperThresh(double) - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

setUpperThreshold(double) - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

setUpperTooltip(String) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

setUpperValue(double) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

setValue(double) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.SliderLabelSynchronizer

setViewMode(ImageDisplayMode) - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

setViewMode(ImageDisplayMode) - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

simplify(double) - Method in class sc.fiji.filamentdetector.model.Filament

simplify(double) - Method in class sc.fiji.filamentdetector.model.Filaments

simplifyFilaments() - Method in class sc.fiji.filamentdetector.detection.AbstractFilamentDetector

simplifyFilaments() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

SliderLabelSynchronizer - Class in sc.fiji.filamentdetector.gui.fxwidgets

SliderLabelSynchronizer(Slider, TextField) - Constructor for class sc.fiji.filamentdetector.gui.fxwidgets.SliderLabelSynchronizer

subtract(RealPoint, RealPoint) - Static method in class sc.fiji.filamentdetector.GeometryUtils

T

Tip - Class in sc.fiji.filamentdetector.model

Tip(double[], double[], int[]) - Constructor for class sc.fiji.filamentdetector.model.Tip

TipFitterAnalyzer - Class in sc.fiji.filamentdetector.analyzer

TipFitterAnalyzer() - Constructor for class sc.fiji.filamentdetector.analyzer.TipFitterAnalyzer

TipFitterAnalyzerController - Class in sc.fiji.filamentdetector.gui.controller.analyzer

TipFitterAnalyzerController(Context, TipFitterAnalyzer) - Constructor for class sc.fiji.filamentdetector.gui.controller.analyzer.TipFitterAnalyzerController

toString() - Method in class sc.fiji.filamentdetector.analyzer.AbstractAnalyzer

toString() - Method in interface sc.fiji.filamentdetector.analyzer.Analyzer

toString() - Method in interface sc.fiji.filamentdetector.detection.FilamentDetector

toString() - Method in class sc.fiji.filamentdetector.detection.FilteringParameters

toString() - Method in class sc.fiji.filamentdetector.detection.IJ2RidgeDetectionFilamentDetector

toString() - Method in class sc.fiji.filamentdetector.detection.RidgeDetectionFilamentDetector

toString() - Method in class sc.fiji.filamentdetector.exporter.CSVFilamentExporter

toString() - Method in class sc.fiji.filamentdetector.exporter.CSVTrackedFilamentExporter

toString() - Method in interface sc.fiji.filamentdetector.exporter.DataExporter

toString() - Method in class sc.fiji.filamentdetector.exporter.IJ1RoiFilamentExporter

toString() - Method in class sc.fiji.filamentdetector.exporter.JSONFilamentExporter

toString() - Method in class sc.fiji.filamentdetector.exporter.JSONTrackedFilamentExporter

toString() - Method in class sc.fiji.filamentdetector.kymograph.KymographParameters

toString() - Method in class sc.fiji.filamentdetector.kymograph.linedrawer.AbstractLineDrawer

toString() - Method in interface sc.fiji.filamentdetector.kymograph.linedrawer.LineDrawer

toString() - Method in class sc.fiji.filamentdetector.model.Filament

toString() - Method in class sc.fiji.filamentdetector.model.Filaments

toString() - Method in class sc.fiji.filamentdetector.model.Tip

toString() - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

toString() - Method in interface sc.fiji.filamentdetector.tracking.FilamentsTracker

toString() - Method in class sc.fiji.filamentdetector.tracking.FilteringTrackedFilamentsParameters

track() - Method in class sc.fiji.filamentdetector.FilamentWorkflow

track() - Method in class sc.fiji.filamentdetector.tracking.BBoxLAPFilamentsTracker

track() - Method in interface sc.fiji.filamentdetector.tracking.FilamentsTracker

TrackedFilament - Class in sc.fiji.filamentdetector.model

TrackedFilament() - Constructor for class sc.fiji.filamentdetector.model.TrackedFilament

TrackedFilamentModel - Class in sc.fiji.filamentdetector.gui.model

TrackedFilamentModel(TrackedFilament) - Constructor for class sc.fiji.filamentdetector.gui.model.TrackedFilamentModel

TrackedFilaments - Class in sc.fiji.filamentdetector.model

TrackedFilaments() - Constructor for class sc.fiji.filamentdetector.model.TrackedFilaments

TrackedFilaments(Context) - Constructor for class sc.fiji.filamentdetector.model.TrackedFilaments

TrackedFilamentSelectedEvent - Class in sc.fiji.filamentdetector.event

TrackedFilamentSelectedEvent(TrackedFilament) - Constructor for class sc.fiji.filamentdetector.event.TrackedFilamentSelectedEvent

TrackedFilamentsExporter<TrackedFilaments> - Class in sc.fiji.filamentdetector.exporter

TrackedFilamentsExporter(Context) - Constructor for class sc.fiji.filamentdetector.exporter.TrackedFilamentsExporter

TrackedFilamentsTableView - Class in sc.fiji.filamentdetector.gui.view

TrackedFilamentsTableView(Context, TrackedFilaments) - Constructor for class sc.fiji.filamentdetector.gui.view.TrackedFilamentsTableView

TrackingFilamentController - Class in sc.fiji.filamentdetector.gui.controller

TrackingFilamentController(Context, FilamentWorkflow) - Constructor for class sc.fiji.filamentdetector.gui.controller.TrackingFilamentController

U

update(Event) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.SliderLabelSynchronizer

update(Event) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

updateDetectionParameters(Event) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

updateDetectionParameters(DetectionParametersUpdatedEvent) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

updateFilteringParameters(Event) - Method in class sc.fiji.filamentdetector.gui.controller.DetectFilamentController

updateItem(Pane, boolean) - Method in class sc.fiji.filamentdetector.gui.fxwidgets.ReorderableListCell

updateLineWidth() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

updateLineWidth() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

updateNFilamentsField() - Method in class sc.fiji.filamentdetector.gui.view.FilamentsTableView

updateNFilamentsField() - Method in class sc.fiji.filamentdetector.gui.view.TrackedFilamentsTableView

updateParameters() - Method in class sc.fiji.filamentdetector.gui.controller.KymographBuilderController

updateParameters(Event) - Method in class sc.fiji.filamentdetector.gui.controller.detection.IJ2RidgeDetectionFilamentDetectorController

updateParameters(Event) - Method in class sc.fiji.filamentdetector.gui.controller.detection.RidgeDetectionFilamentDetectorController

updateTransparency() - Method in class sc.fiji.filamentdetector.overlay.DefaultFilamentOverlayService

updateTransparency() - Method in interface sc.fiji.filamentdetector.overlay.FilamentOverlayService

UpperLowerSynchronizer - Class in sc.fiji.filamentdetector.gui.fxwidgets

UpperLowerSynchronizer(Slider, TextField, Slider, TextField) - Constructor for class sc.fiji.filamentdetector.gui.fxwidgets.UpperLowerSynchronizer

userCheckImpDimensions(ImageJ, Dataset) - Static method in class sc.fiji.filamentdetector.gui.GUIUtils

V

valueOf(String) - Static method in enum sc.fiji.filamentdetector.overlay.ImageDisplayMode

Returns the enum constant of this type with the specified name.

values() - Static method in enum sc.fiji.filamentdetector.overlay.ImageDisplayMode

Returns an array containing the constants of this enum type, in the order they are declared.

VERSION - Static variable in class sc.fiji.filamentdetector.FilamentDetectorPlugin

W

WelcomeController - Class in sc.fiji.filamentdetector.gui.controller

WelcomeController(Context, FilamentWorkflow) - Constructor for class sc.fiji.filamentdetector.gui.controller.WelcomeController

X

xIndex - Static variable in class sc.fiji.filamentdetector.model.Filament

Y

yIndex - Static variable in class sc.fiji.filamentdetector.model.Filament

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