A B C D E F G H I J L M N O P Q R S T U V W X Y Z

T

TAG_FILENAME - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Flag for "Tags/filename" mapping.

tearDown() - Method in class sc.fiji.snt.Tracing2DTest

tearDown() - Method in class sc.fiji.snt.Tracing3DTest

tempMsg(String) - Method in class sc.fiji.snt.gui.GuiUtils

terminate() - Method in class sc.fiji.snt.analysis.sholl.TreeParser

testAnalyzer() - Method in class sc.fiji.snt.TreeAnalyzerTest

testTracing() - Method in class sc.fiji.snt.Tracing2DTest

testTracing() - Method in class sc.fiji.snt.Tracing3DTest

textField(String) - Method in class sc.fiji.snt.gui.GuiUtils

threadStatus(SearchInterface, int) - Method in class sc.fiji.snt.FillManagerUI

threadStatus(SearchInterface, int) - Method in interface sc.fiji.snt.SearchProgressCallback

threadStatus(SearchInterface, int) - Method in class sc.fiji.snt.SNT

TIMED_OUT - Static variable in class sc.fiji.snt.SearchThread

toString() - Method in class sc.fiji.snt.annotation.AllenCompartment

toString() - Method in class sc.fiji.snt.HessianCaller

toString() - Method in class sc.fiji.snt.NearPoint

toString() - Method in class sc.fiji.snt.Path

This toString() method shows details of the path which is actually being displayed, not necessarily this path object.

toString() - Method in class sc.fiji.snt.SearchNode

toString() - Method in class sc.fiji.snt.util.PointInImage

toString() - Method in class sc.fiji.snt.util.SWCPoint

TOTAL_LENGTH - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Cable length

TOTAL_N_BRANCH_POINTS - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Count of all branch points

TOTAL_N_TIPS - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Count of all tips (end points)

toUPoint() - Method in class sc.fiji.snt.util.PointInImage

TracerThread - Class in sc.fiji.snt

SNT's default tracer thread: explores between two points in an image, doing an A* search with a choice of distance measures.

TracerThread(SNT, int, int, int, int, int, int) - Constructor for class sc.fiji.snt.TracerThread

TracerThread(ImagePlus, float, float, int, long, int, int, int, int, int, int, boolean, boolean, ComputeCurvatures, double, float[][], boolean) - Constructor for class sc.fiji.snt.TracerThread

TracerThread(ImagePlus, float, float, int, int, int, int, int, int, boolean, boolean, ComputeCurvatures, double) - Constructor for class sc.fiji.snt.TracerThread

Tracing2DTest - Class in sc.fiji.snt

Tracing2DTest() - Constructor for class sc.fiji.snt.Tracing2DTest

Tracing3DTest - Class in sc.fiji.snt

Tracing3DTest() - Constructor for class sc.fiji.snt.Tracing3DTest

TRACING_PAUSED - Static variable in class sc.fiji.snt.SNTUI

Flag specifying tracing functions are (currently) disabled.

transform(PathTransformer, ImagePlus, ImagePlus) - Method in class sc.fiji.snt.Path

transform(PathTransformer) - Method in class sc.fiji.snt.util.PointInImage

transformationFinished(View) - Method in class sc.fiji.snt.PathAndFillManager

transformationStarted(View) - Method in class sc.fiji.snt.PathAndFillManager

transformationUpdated(View) - Method in class sc.fiji.snt.PathAndFillManager

transformPaths(PathTransformer, ImagePlus, ImagePlus) - Method in class sc.fiji.snt.PathAndFillManager

transformPoint(double, double, double, double[]) - Method in interface sc.fiji.snt.PathTransformer

transformPoint(double, double, double, int[]) - Method in interface sc.fiji.snt.PathTransformer

transformPoint(int, int, int, int[]) - Method in interface sc.fiji.snt.PathTransformer

transformPoint(int, int, int, double[]) - Method in interface sc.fiji.snt.PathTransformer

translate(double, double, double) - Method in class sc.fiji.snt.Tree

Translates the tree by the specified offset.

translate(SNTPoint) - Method in class sc.fiji.snt.viewer.OBJMesh

Translates the vertices of this mesh by the specified offset.

translate(Tree, SNTPoint) - Method in class sc.fiji.snt.viewer.Viewer3D

Translates the specified Tree.

translate(Collection<String>, SNTPoint) - Method in class sc.fiji.snt.viewer.Viewer3D

Translates the specified collection of Trees.

TranslateReconstructionsCmd - Class in sc.fiji.snt.gui.cmds

Implements Reconstruction Viewer's 'Translate...' command.

TranslateReconstructionsCmd() - Constructor for class sc.fiji.snt.gui.cmds.TranslateReconstructionsCmd

Tree - Class in sc.fiji.snt

Utility class to access a Collection of Paths.

Tree() - Constructor for class sc.fiji.snt.Tree

Instantiates a new empty Tree.

Tree(Collection<Path>) - Constructor for class sc.fiji.snt.Tree

Instantiates a new Tree from a set of paths.

Tree(Collection<SWCPoint>, String) - Constructor for class sc.fiji.snt.Tree

Instantiates a Tree from a collection of reconstruction nodes.

Tree(String) - Constructor for class sc.fiji.snt.Tree

Instantiates a new tree from a SWC, TRACES or JSON file.

Tree(String, int...) - Constructor for class sc.fiji.snt.Tree

Instantiates a new tree from a filtered SWC, TRACES or JSON file.

TreeAnalyzer - Class in sc.fiji.snt.analysis

Class for analysis of Trees

TreeAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.TreeAnalyzer

Instantiates a new Tree analyzer.

TreeAnalyzerTest - Class in sc.fiji.snt

Tests for TreeAnalyzers

TreeAnalyzerTest() - Constructor for class sc.fiji.snt.TreeAnalyzerTest

TreeColorMapper - Class in sc.fiji.snt.analysis

Class for color coding Trees.

TreeColorMapper(Context) - Constructor for class sc.fiji.snt.analysis.TreeColorMapper

Instantiates the Colorizer.

TreeColorMapper() - Constructor for class sc.fiji.snt.analysis.TreeColorMapper

Instantiates the Colorizer.

TreeMapperCmd - Class in sc.fiji.snt.plugin

Command for color coding trees according to their properties using TreeColorMapper with options to display result in Viewer2D and Viewer3D

TreeMapperCmd() - Constructor for class sc.fiji.snt.plugin.TreeMapperCmd

TreeParser - Class in sc.fiji.snt.analysis.sholl

A Parser for extracting Sholl Profiles from a Tree.

TreeParser(Tree) - Constructor for class sc.fiji.snt.analysis.sholl.TreeParser

Instantiates a new Tree Parser.

TreeStatistics - Class in sc.fiji.snt.analysis

Computes summary and descriptive statistics from univariate properties of a Tree.

TreeStatistics(Tree) - Constructor for class sc.fiji.snt.analysis.TreeStatistics

Instantiates a new instance from a collection of Paths

TubularGeodesicsTracer - Class in sc.fiji.snt

A tracer thread for FijiITKInterface.TubularGeodesics (assumes the tubularity add-on to be installed)

TubularGeodesicsTracer(File, float, float, float, float, float, float, double, double, double, String) - Constructor for class sc.fiji.snt.TubularGeodesicsTracer

type() - Method in class sc.fiji.snt.util.SNTColor

Retrieves the SWC type

type - Variable in class sc.fiji.snt.util.SWCPoint

The SWC-type flag of this node (Path.SWC_SOMA, Path.SWC_DENDRITE, etc.)

A B C D E F G H I J L M N O P Q R S T U V W X Y Z