- abortCurrentOperation() - Method in class sc.fiji.snt.SNTUI
-
- AbstractSearch - Class in sc.fiji.snt.tracing
-
- AbstractSearch(ImagePlus, int, long) - Constructor for class sc.fiji.snt.tracing.AbstractSearch
-
- AbstractSearch(RandomAccessibleInterval<? extends RealType<?>>, Calibration, int, long) - Constructor for class sc.fiji.snt.tracing.AbstractSearch
-
- AbstractSearch(SNT, ImagePlus) - Constructor for class sc.fiji.snt.tracing.AbstractSearch
-
- AbstractSearch(SNT, RandomAccessibleInterval<? extends RealType<?>>) - Constructor for class sc.fiji.snt.tracing.AbstractSearch
-
- accept(RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.Frangi
-
- accept(RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.Tubeness
-
- accessToValidImageData() - Method in class sc.fiji.snt.SNT
-
- acronym() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- acronym() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- acronym() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.FillManagerUI
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- activateFinishedPath - Variable in class sc.fiji.snt.SNT
-
- adapter - Variable in class sc.fiji.snt.viewer.geditor.SNTGraphComponent
-
- add(ProfileEntry) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- add(int, int, int, double, int, boolean) - Method in class sc.fiji.snt.Fill
-
- add(Path) - Method in class sc.fiji.snt.Path
-
- add(Path) - Method in class sc.fiji.snt.Tree
-
Adds a new Path to this Tree.
- add(Tree) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer using default options.
- add(List<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a list of trees while assigning each tree to a LUT index.
- add(Tree, ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer.
- add(Tree, String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer.
- add(Tree, String, ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- add(Tree, String, String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- add(Tree, String, String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- add(File[], String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a collection of trees or meshes from input files.
- add(Object) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Script friendly method to add a supported object (
Tree,
OBJMesh,
AbstractDrawable, etc.) to this viewer.
- addAsLinesTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addAsLinesTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addCenter() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- addChangeListener(PathChangeListener) - Method in class sc.fiji.snt.Path
-
- addCitationMessage() - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Allows users to visit the manuscript from a dialog prompt
- addClickableURLtoLabel(Component, String, Color) - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
- addColorBarLegend(String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a color bar legend (LUT ramp).
- addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- addColorBarLegend() - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a color bar legend (LUT ramp) to the viewer.
- addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a color bar legend (LUT ramp) from a ColorMapper.
- addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a color bar legend (LUT ramp) using default settings.
- addColorBarLegend(ColorTable, double, double, Font, int, int) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a color bar legend (LUT ramp).
- addColorChangedListener(ColorChangedListener) - Method in class sc.fiji.snt.gui.ColorChooserButton
-
- addColumn(String, double[]) - Method in class sc.fiji.snt.analysis.SNTTable
-
- addColumn(String, Collection<Double>) - Method in class sc.fiji.snt.analysis.SNTTable
-
- addDiscsTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addDiscsTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addFill(Fill) - Method in class sc.fiji.snt.PathAndFillManager
-
- addFillerThread(FillerThread) - Method in class sc.fiji.snt.SNT
-
- addGroup(Collection<Tree>, String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Adds a comparison group to the analysis queue.
- addGroup(Collection<Tree>, String, String...) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Adds a comparison group to the analysis queue.
- addHyperlink(String) - Method in class sc.fiji.snt.gui.EnhancedWaitForUserDialog
-
Deprecated.
- addHyperlinkMessage(String, Font, Color, String) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Appends a message to the specified dialog consisting of one or more lines
of text, and assigns a functional URL to it.
- addLabel(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds an annotation label to the scene.
- addListener(SigmaPaletteListener) - Method in class sc.fiji.snt.gui.SigmaPalette
-
- addListener(SNTListener) - Method in class sc.fiji.snt.SNT
-
- addMesh(OBJMesh) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Loads a Wavefront .OBJ file.
- addNode(PointInImage) - Method in class sc.fiji.snt.Path
-
Appends a node to this Path.
- addNode(DefaultSearchNode, boolean) - Method in class sc.fiji.snt.tracing.SearchThread
-
- addPath(Path) - Method in class sc.fiji.snt.PathAndFillManager
-
Adds a new path.
- addPath(Path, boolean) - Method in class sc.fiji.snt.PathAndFillManager
-
- addPath(Path, boolean, boolean) - Method in class sc.fiji.snt.PathAndFillManager
-
- addPath(Path, boolean, boolean, boolean) - Method in class sc.fiji.snt.PathAndFillManager
-
- addPath(Path, int, int) - Method in class sc.fiji.snt.PathAndFillManager
-
- addPathAndFillListener(PathAndFillListener) - Method in class sc.fiji.snt.PathAndFillManager
-
Adds a PathAndFillListener.
- addPathPointsToShollList(Path, double, double, double, List<ShollAnalysisDialog.ShollPoint>) - Static method in class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- addPoint(ShollPoint) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry
-
- addPointDouble(double, double, double) - Method in class sc.fiji.snt.Path
-
- addPoints(double[], double[], int) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- addPoints(double[], double[], double[], String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- addPoints(double[], double[], String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- addPoints(List<Number>, List<Number>, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- addPoints(List<Number>, List<Number>, List<Number>, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.AbstractSearch
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.BiSearch
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.ManualTracerThread
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.SearchThread
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.TubularGeodesicsTracer
-
- addSearchArtist(SearchArtist) - Method in class sc.fiji.snt.TracerCanvas
-
- addSeparator(JComponent, String, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- addSeparator(JComponent, JLabel, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- addSphere(String, double, double, double, Color, double) - Method in class sc.fiji.snt.SNT
-
- AddTextAnnotationCmd - Class in sc.fiji.snt.gui.cmds
-
Implements Reconstruction Viewer's 'Add Annotation Label...' commands.
- AddTextAnnotationCmd() - Constructor for class sc.fiji.snt.gui.cmds.AddTextAnnotationCmd
-
- addTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addTooltip(JComponent, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- addToResultsTable() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- addTree(Tree) - Method in class sc.fiji.snt.PathAndFillManager
-
- addTree(Tree) - Method in class sc.fiji.snt.SciViewSNT
-
Adds a tree to the associated SciView instance.
- addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a tree to this viewer.
- addTrees(Collection<Tree>, String, String...) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a collection of trees.
- addTrees(Collection<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a collection of trees.
- addTrees(Collection<Tree>, String, double) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a collection of trees.
- addTrees(Collection<Tree>, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- addVertex(double, double, double) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
- addViewer(Viewer3D) - Static method in class sc.fiji.snt.SNTUtils
-
- adjustListPlaceholder() - Method in class sc.fiji.snt.FillManagerUI
-
- aliases() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- aliases() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- aliases() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- ALL_FLAGS - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- ALL_PLOTS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- AllenCompartment - Class in sc.fiji.snt.annotation
-
Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate
Framework] annotation.
- AllenCompartment(UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
-
Instantiates a new ARA annotation from an UUID (as used by MouseLight's
database).
- AllenCompartment(int) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
-
Instantiates a new ARA annotation from its identifier.
- AllenCompartment(JSONObject, UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
-
- AllenUtils - Class in sc.fiji.snt.annotation
-
- allPathsShareSameSpatialCalibration() - Method in class sc.fiji.snt.PathAndFillManager
-
- allPointsIterator() - Method in class sc.fiji.snt.PathAndFillManager
-
- AllPointsIterator() - Constructor for class sc.fiji.snt.PathAndFillManager.AllPointsIterator
-
- alphaColor(Color, double) - Static method in class sc.fiji.snt.util.SNTColor
-
Adds an alpha component to a AWT color.
- analyze2D(int, int, double[], double, int, int, ImagePlus) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- analyze3D(int, int, int, double[], ImagePlus) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- analyzeProfile(double[], double[], boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Analyzes a sampled profile.
- AnalyzerCmd - Class in sc.fiji.snt.plugin
-
Command for measuring Tree(s).
- AnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.AnalyzerCmd
-
- analyzeTabularInput(ResultsTable, int, int, boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Instructs the plugin to parse the specified table expected to contain a
sampled profile.
- analyzeTabularInput(File, int, int, boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Instructs the plugin to parse the specified file expected to contain a
sampled profile.
- analyzeWithShollAnalysisPlugin(String, double) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- animateLayoutChange - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- annotate(String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Adds a subtitle to the chart.
- annotateCategory(String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified category (Category plots only)
- annotateCategory(String, String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified category (Category plots only).
- annotateLine(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a line annotation to this viewer.
- annotatePoint(double, double, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Highlights a point in a histogram/XY plot by drawing a labeled arrow at the
specified location.
- annotatePoint(double, double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Highlights a point in a histogram/XY plot by drawing a labeled arrow at the
specified location.
- annotatePoint(SNTPoint, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds an highlighting point annotation to this viewer.
- annotatePoint(SNTPoint, String, String, float) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds an highlighting point annotation to this viewer.
- annotatePoints(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a scatter (point cloud) annotation to this viewer.
- annotateSurface(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- annotateSurface(Collection<? extends SNTPoint>, String, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Computes a convex hull from a collection of points and adds it to the
scene as an annotation.
- annotateXline(double, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified X-value (XY plots and histograms).
- annotateXline(double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified X-value (XY plots and histograms).
- annotateYline(double, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified Y-value (XY plots and histograms).
- annotateYline(double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified Y-value (XY plots and histograms).
- Annotation3D - Class in sc.fiji.snt.viewer
-
An Annotation3D is a triangulated surface or a cloud of points (scatter)
rendered in
Viewer3D that can be used to highlight nodes in a
Tree or locations in a
mesh.
- Annotation3D(Viewer3D, Collection<Annotation3D>) - Constructor for class sc.fiji.snt.viewer.Annotation3D
-
- Annotation3D(Viewer3D, Collection<? extends SNTPoint>, int) - Constructor for class sc.fiji.snt.viewer.Annotation3D
-
- Annotation3D(Viewer3D, SNTPoint) - Constructor for class sc.fiji.snt.viewer.Annotation3D
-
- AnnotationGraph - Class in sc.fiji.snt.analysis.graph
-
- AnnotationGraph() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- AnnotationGraph(Collection<Tree>, String, double, int) - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- AnnotationGraphAdapter - Class in sc.fiji.snt.viewer.geditor
-
- AnnotationGraphAdapter(AnnotationGraph) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
-
- AnnotationGraphAdapter(AnnotationGraph, String) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
-
- AnnotationGraphComponent - Class in sc.fiji.snt.viewer.geditor
-
- AnnotationGraphComponent(AnnotationGraphAdapter, Context) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphComponent
-
- AnnotationGraphGeneratorCmd - Class in sc.fiji.snt.gui.cmds
-
- AnnotationGraphGeneratorCmd() - Constructor for class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd
-
- AnnotationGraphRecViewerCmd - Class in sc.fiji.snt.gui.cmds
-
- AnnotationGraphRecViewerCmd() - Constructor for class sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd
-
- AnnotationGraphUtils - Class in sc.fiji.snt.analysis.graph
-
Utilities for AnnotationGraph handling and manipulation.
- AnnotationGraphUtils() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraphUtils
-
- annotationsDescriptionChanged() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd
-
- AnnotationWeightedEdge - Class in sc.fiji.snt.analysis.graph
-
- AnnotationWeightedEdge() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge
-
- ANNULUS - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
Flag for annulus normalization (Semi-log/Log-log method)
- ANY_HEMISPHERE - Static variable in interface sc.fiji.snt.annotation.BrainAnnotation
-
- anyListeners() - Method in class sc.fiji.snt.SNT
-
- anyNodeUnderThreshold(int, int, int, double) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist
-
- anyNodeUnderThreshold(int, int, int, double) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist
-
- anyNodeUnderThreshold(int, int, int, double) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist
-
- anySelected() - Method in class sc.fiji.snt.PathAndFillManager
-
Checks whether at least one Path is currently selected in the UI.
- append(Iterator<? extends SNTPoint>) - Method in class sc.fiji.snt.util.BoundingBox
-
Computes the bounding box of the specified point cloud and appends it to this
bounding box, resizing it as needed.
- appendToLastRow(String, Object) - Method in class sc.fiji.snt.analysis.SNTTable
-
- applyCanvasOffset(double, double, double) - Method in class sc.fiji.snt.Tree
-
Specifies the offset to be used when rendering this Tree in a
TracerCanvas.
- applyDefaultTags(String...) - Method in class sc.fiji.snt.PathManagerUI
-
Applies a default (built-in) tag to selected Path(s).
- applyEdges(UnaryOperator<E>) - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
Apply the given operator over the edge set.
- applyIcon(AbstractButton, float, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
-
- applyLayout(mxIGraphLayout) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- applyProperties(Tree) - Method in class sc.fiji.snt.Tree
-
- applySelectionFilter(String, Number, Number) - Method in class sc.fiji.snt.PathManagerUI
-
Selects paths matching a morphometric criteria.
- applySelectionFilter(String) - Method in class sc.fiji.snt.PathManagerUI
-
Selects paths matching a text-based criteria.
- applySelectionFilter(String, Number) - Method in class sc.fiji.snt.PathManagerUI
-
Selects paths matching a morphometric criteria.
- applyStyle(SNTChart) - Method in class sc.fiji.snt.analysis.SNTChart
-
- applyTag(String) - Method in class sc.fiji.snt.PathManagerUI
-
Applies a custom tag/ color to selected Path(s).
- applyVertices(UnaryOperator<V>) - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
Apply the given operator over the vertex set.
- appTitle - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- AREA - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
Flag for area normalization (Semi-log/Log-log method)
- ArraySearchImage<V> - Class in sc.fiji.snt.tracing.image
-
- ArraySearchImage(Class<V>, int, int) - Constructor for class sc.fiji.snt.tracing.image.ArraySearchImage
-
- ArraySearchImageSupplier(Class<V>, int, int) - Constructor for class sc.fiji.snt.tracing.image.SupplierUtil.ArraySearchImageSupplier
-
- askUserConfirmation - Variable in class sc.fiji.snt.SNTUI
-
- asPath(double, double, double, String) - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- asPathReversed(double, double, double, String) - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- assessIfBranchesHaveBeenAssigned() - Method in class sc.fiji.snt.analysis.NodeStatistics
-
- assignBranches(Tree) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Associates the nodes being analyzed to the branches of the specified tree
- ASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper
-
Mapping property: Assigned Tree value
- ASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- assignEdgeWeightsEuclidean() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
For all edges, sets the Euclidean distance between the source and target
vertex as the weight.
- assignEditor(GraphEditor) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent
-
Assigns an editor.
- assignHemisphereTags(DirectedWeightedGraph) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignHemisphereTags(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignImage(ImagePlus) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- assignImage(ImagePlus) - Method in class sc.fiji.snt.Tree
-
Assigns the spatial calibration of an image to this Tree.
- assignListenerToHelpButton(String, ActionListener) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Adds a "Help" button and attaches the specified listener to it.
- assignPoints(Set<ShollPoint>) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry
-
- assignPopupToHelpButton(JPopupMenu) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Attaches the specified JPopupMenu to the GenericDialog "Help" button
renamed "More »".
- assignPopupToHelpButton(String, JPopupMenu) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Adds a "Help" button and attaches the specified JPopupMenu to it.
- assignProperty(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- assignSpatialSettings(ImagePlus) - Method in class sc.fiji.snt.PathAndFillManager
-
- assignToLeftHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignToRightHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignUniqueColors(Collection<Tree>) - Static method in class sc.fiji.snt.Tree
-
- assignUniqueColors(Collection<String>) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- assignValue(double) - Method in class sc.fiji.snt.Tree
-
Assigns a numeric property to this Tree.
- assignValues() - Method in class sc.fiji.snt.analysis.PathProfiler
-
- assignValues(int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- assignValues(Path) - Method in class sc.fiji.snt.analysis.PathProfiler
-
Retrieves pixel intensities at each node of the Path storing them as Path
values
- assignValues(Path, int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- assignValues(boolean) - Method in class sc.fiji.snt.SNTService
-
Assigns pixel intensities at each Path node, storing them as Path values.
- atGoal(int, int, int, boolean) - Method in class sc.fiji.snt.tracing.SearchThread
-
- atGoal(int, int, int, boolean) - Method in class sc.fiji.snt.tracing.TracerThread
-
- autoCanvasActivation - Variable in class sc.fiji.snt.SNT
-
- autoTrace(SNTPoint, SNTPoint, PointInImage) - Method in class sc.fiji.snt.SNT
-
Automatically traces a path from a point A to a point B.
- autoTrace(SNTPoint, SNTPoint, PointInImage, boolean) - Method in class sc.fiji.snt.SNT
-
- autoTrace(List<SNTPoint>, PointInImage) - Method in class sc.fiji.snt.SNT
-
Automatically traces a path from a list of points and adds it to the active
PathAndFillManager instance.
- autoTrace(List<SNTPoint>, PointInImage, boolean) - Method in class sc.fiji.snt.SNT
-
- availableLookAndFeels() - Static method in class sc.fiji.snt.gui.GuiUtils
-
- average(Collection<Color>) - Static method in class sc.fiji.snt.util.SNTColor
-
Averages a collection of colors
- average(Collection<T>) - Static method in interface sc.fiji.snt.util.SNTPoint
-
- AVG_BRANCH_LENGTH - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Flag for "Average branch length" analysis.
- AVG_CONTRACTION - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Flag for "Average contraction" statistics
- AVG_FRACTAL_DIMENSION - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Flag specifying "Average fractal dimension" statistics
- AVG_FRAGMENTATION - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Flag for "Average fragmentation" statistics
- AVG_PARTITION_ASYMMETRY - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Flag specifying "Average partition asymmetry" statistics
- AVG_REMOTE_ANGLE - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Flag specifying "Average remote bif. angle" statistics
- AVG_SPINE_DENSITY - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Flag for "Average spine/varicosity density" statistics.
- AVG_SPINE_DENSITY - Static variable in class sc.fiji.snt.analysis.TreeColorMapper
-
Flag for "Average spine/varicosity density" mapping.
- AVG_SPINE_DENSITY - Static variable in class sc.fiji.snt.analysis.TreeStatistics
-
Flag for "Average spine/varicosity density" statistics.
- AXES_NORMAL - Static variable in class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- AXON - Static variable in class sc.fiji.snt.io.MouseLightLoader
-
The Constant AXON.
- AXONAL - Static variable in interface sc.fiji.snt.TreeProperties
-
- g - Variable in class sc.fiji.snt.tracing.DefaultSearchNode
-
- gaussianCalculated(boolean) - Method in class sc.fiji.snt.SNTUI
-
- geSelectedPathsAsTree() - Method in class sc.fiji.snt.PathManagerUI
-
Gets the collection of paths listed in the Path Manager as a
Tree
object.
- get(BrainAnnotation) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Gets the list of nodes associated with the specified compartment (neuropil
label).
- get(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Gets the list of nodes associated with the specified compartment (neuropil
label).
- get() - Method in class sc.fiji.snt.tracing.image.SupplierUtil.ArraySearchImageSupplier
-
- get() - Method in class sc.fiji.snt.tracing.image.SupplierUtil.ListSearchImageSupplier
-
- get() - Method in class sc.fiji.snt.tracing.image.SupplierUtil.MapSearchImageSupplier
-
- get(int) - Method in class sc.fiji.snt.Tree
-
Returns the Path at the specified position.
- get() - Method in class sc.fiji.snt.util.CircleCursor3D
-
- get() - Method in class sc.fiji.snt.util.PathCursor
-
- get3DUniverse() - Method in class sc.fiji.snt.SNT
-
Deprecated.
- get3DViewerResamplingFactor() - Method in class sc.fiji.snt.SNTPrefs
-
- getActiveWindow() - Method in class sc.fiji.snt.SNT
-
- getAllFills() - Method in class sc.fiji.snt.PathAndFillManager
-
- getAllIDs() - Static method in class sc.fiji.snt.io.MouseLightQuerier
-
- getAllLoaders() - Static method in class sc.fiji.snt.io.MouseLightLoader
-
Gets the loaders for all the cells publicly available in the MouseLight database.
- getAllMetrics() - Static method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Gets the list of all supported metrics.
- getAllMetrics() - Static method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the list of all supported metrics.
- getAllMetrics() - Static method in class sc.fiji.snt.analysis.TreeStatistics
-
Gets the list of all supported metrics.
- getAllNeuronIDs() - Static method in class sc.fiji.snt.annotation.InsectBrainUtils
-
- getAllNeuronIDsOrganizedBySpecies() - Static method in class sc.fiji.snt.annotation.InsectBrainUtils
-
- getAllPathsRenderedInViewPort(TracerCanvas) - Method in class sc.fiji.snt.PathAndFillManager
-
- getAllSpecies() - Static method in class sc.fiji.snt.annotation.InsectBrainUtils
-
- getAnalyzer(boolean) - Method in class sc.fiji.snt.SNTService
-
Returns a
TreeAnalyzer instance constructed from current Paths.
- getAnalyzerMetrics() - Static method in class sc.fiji.snt.analysis.TreeStatistics
-
- getAncestor(int) - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Gets the nth ancestor of this compartment.
- getAncestor(int) - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- getAncestor(int) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- getAncestors() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Gets the ancestor ontologies of this compartment as a flat (non-hierarchical)
list.
- getAnnotatedFrequencies() - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Retrieves the count frequencies across brain compartment.
- getAnnotatedFrequencies(int) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Retrieves the count frequencies across brain compartment.
- getAnnotatedFrequencies(int, String) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Retrieves the count frequencies across brain compartment.
- getAnnotatedFrequenciesByHemisphere(int, Tree) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
- getAnnotatedFrequencyHistogram(int, String, Tree) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Retrieves the histogram of count frequencies across brain areas of the
specified ontology level across the specified hemisphere.
- getAnnotatedHistogram() - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Retrieves the histogram of count frequencies across brain areas.
- getAnnotatedHistogram(int) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Retrieves the histogram of count frequencies across brain areas of the
specified ontology level.
- getAnnotatedLength(int, String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getAnnotatedLength(int) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getAnnotatedLength(int) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
Retrieves the amount of cable length present on each brain compartment
innervated by the analyzed neuron.
- getAnnotatedLength(int, String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
Retrieves the amount of cable length present on each brain compartment
innervated by the analyzed neuron.
- getAnnotatedLength(DirectedWeightedGraph, int, char) - Static method in class sc.fiji.snt.analysis.TreeStatistics
-
- getAnnotatedLengthHistogram() - Method in class sc.fiji.snt.analysis.TreeStatistics
-
Retrieves the of cable length frequencies across brain areas.
- getAnnotatedLengthHistogram(int) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
Retrieves the histogram of cable length frequencies across brain areas of the
specified ontology level.
- getAnnotatedLengthHistogram(int, String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
Retrieves the histogram of cable length frequencies across brain areas of the
specified ontology level across the specified hemisphere.
- getAnnotatedLengthHistogram(Map<BrainAnnotation, Double>, int, String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- getAnnotatedLengthsByHemisphere(int) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getAnnotatedLengthsByHemisphere(int) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- getAnnotatedLengthsByHemisphere(DirectedWeightedGraph, int) - Static method in class sc.fiji.snt.analysis.TreeStatistics
-
- getAnnotatedLengthsByHemisphereHistogram(int) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- getAnnotatedNodes() - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Splits the nodes being analyzed into groups sharing the same brain
annotation.
- getAnnotatedNodes(int) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Splits the nodes being analyzed into groups sharing the same brain
annotation.
- getAnnotation() - Method in class sc.fiji.snt.util.PointInImage
-
- getAnnotation() - Method in interface sc.fiji.snt.util.SNTPoint
-
- getAnnotation() - Method in class sc.fiji.snt.util.SWCPoint
-
- getAnnotation(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Gets the annotation associated with the specified label.
- getAnnotationGraph() - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
-
- getAnnotations() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getAnnotations(int) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getAnnotations() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getAnnotations(int) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getAnnotations() - Method in class sc.fiji.snt.io.InsectBrainLoader
-
- getAnnotations() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Returns all annotations added to this viewer.
- getAnnotationsColor() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- getApproximatedVolume() - Method in class sc.fiji.snt.Path
-
Returns an estimated volume of this path.
- getApproximatedVolume() - Method in class sc.fiji.snt.Tree
-
Retrieves an approximate estimate of Tree's volume by approximating the
volume of each path, and summing to total.
- getAssignedValue() - Method in class sc.fiji.snt.Tree
-
Retrieves the numeric property assigned to this Tree.
- getAvailableLuts() - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper
-
Gets the available LUTs.
- getAvailableLuts() - Method in class sc.fiji.snt.analysis.NodeColorMapper
-
Gets the available LUTs.
- getAvailableLuts() - Method in class sc.fiji.snt.analysis.TreeColorMapper
-
Gets the available LUTs.
- getAverageSeparation() - Method in class sc.fiji.snt.SNT
-
- getAvgBifurcationRatio() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getAvgBranchLength() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets average length for all the branches of the analyzed tree.
- getAvgContraction() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets average
contraction for all the branches
of the analyzed tree.
- getAvgContractions() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getAvgFractalDimension() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the average fractal dimension of the analyzed tree.
- getAvgFragmentation() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getAvgFragmentations() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getAvgPartitionAsymmetry() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the average partition asymmetry of the analyzed tree.
- getAvgRemoteBifAngle() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the average remote bifurcation angle of the analyzed tree.
- getAxisDefiningMidSagittalPlane() - Static method in class sc.fiji.snt.annotation.AllenUtils
-
Gets the axis defining mid sagittal plane.
- getBarcode(String) - Method in class sc.fiji.snt.analysis.PersistenceAnalyzer
-
Gets the 'barcode' for the specified filter function.
- getBarycentre() - Method in class sc.fiji.snt.viewer.Annotation3D
-
Returns the center of this annotation bounding box.
- getBatchScriptsMenu() - Method in class sc.fiji.snt.gui.ScriptInstaller
-
Returns a UI list of SNT's 'Batch' scripts
- getBifurcationRatios() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getBooleanPrefs() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- getBottomPanel() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- getBoundingBox(boolean) - Method in class sc.fiji.snt.PathAndFillManager
-
Returns the BoundingBox enclosing all nodes of all existing Paths.
- getBoundingBox() - Method in class sc.fiji.snt.Tree
-
Gets the bounding box associated with this tree.
- getBoundingBox(boolean) - Method in class sc.fiji.snt.Tree
-
Gets the bounding box associated with this tree.
- getBoundingBox(String) - Method in class sc.fiji.snt.viewer.OBJMesh
-
Gets the minimum bounding box of this mesh.
- getBoxPlot(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).
- getBoxPlot(String, Collection<BrainAnnotation>) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Assembles a Box and Whisker Plot for the specified feature (absolute
measurements).
- getBoxPlot(String, Collection<BrainAnnotation>, double, boolean) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Assembles a Box and Whisker Plot for the specified feature.
- getBPs() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets the branch points (junctions) of the graph.
- getBPs() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
Gets the branch points (junctions) of the graph.
- getBrainAreasByStructureId() - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- getBrainAreasByUUID() - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- getBrainAreasList() - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- getBrainCompartments(int, String) - Static method in class sc.fiji.snt.annotation.InsectBrainUtils
-
- getBrainJSON(int) - Static method in class sc.fiji.snt.annotation.InsectBrainUtils
-
- getBrainMeshes(int, String) - Static method in class sc.fiji.snt.annotation.InsectBrainUtils
-
- getBranchCounts() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getBranches() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getBranches() - Method in class sc.fiji.snt.analysis.PathAnalyzer
-
- getBranches() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getBranches(int) - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getBranches() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets all the branches in the analyzed tree.
- getBranchPointCounts() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getBranchPointMap() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd
-
- getBranchPoints() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getBranchPoints() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the position of all the branch points in the analyzed tree.
- getBranchPoints(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the position of all the branch points in the analyzed tree associated
with the specified annotation.
- getBreadthFirstIterator() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets a BreadthFirstIterator, using the graph root as start vertex.
- getBreadthFirstIterator(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets a BreadthFirstIterator, using the specified start vertex.
- getButton(Container, String) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- getButton(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
-
- getButtonIcon(IconFactory.GLYPH, float) - Static method in class sc.fiji.snt.gui.IconFactory
-
- getButtonIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
-
- getCableLength(BrainAnnotation) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getCableLength() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the cable length.
- getCableLength(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the cable length associated with the specified compartment (neuropil
label).
- getCableLength(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the cable length associated with the specified compartment (neuropil
label).
- getCableLengthNorm(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the cable length associated with the specified compartment (neuropil
label) as a ratio of total length.
- getCalibration() - Method in class sc.fiji.snt.Path
-
Gets the spatial calibration of this Path.
- getCalibration() - Method in class sc.fiji.snt.util.BoundingBox
-
Creates a Calibration object using information from this BoundingBox
- getCanvasOffset() - Method in class sc.fiji.snt.Path
-
Returns the translation offset used to render this Path in a
TracerCanvas.
- getCategoryChart() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd
-
Returns the analysis chart.
- getCategoryChart() - Method in class sc.fiji.snt.plugin.StrahlerCmd
-
Returns the Strahler chart.
- getCenter() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
Returns the center coordinates
- getCenteredMaximum(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the average coordinates of all maxima.
- getCenteredMaximum() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getCenterFromChoice(String) - Static method in class sc.fiji.snt.plugin.ShollAnalysisTreeCmd
-
- getCenterX() - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped
-
- getCenterY() - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped
-
- getCentroid(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Retrieves the centroid from all pairs of data (radius, inters.
- getCentroid() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getCentroid() - Method in class sc.fiji.snt.util.BoundingBox
-
- getCentroid(String) - Method in class sc.fiji.snt.viewer.OBJMesh
-
Returns the spatial centroid of the specified (hemi)mesh.
- getChannel() - Method in class sc.fiji.snt.Path
-
Gets the hyperstack channel associated with this Path.
- getChannel() - Method in class sc.fiji.snt.SNT
-
- getChart() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd
-
- getChart() - Method in class sc.fiji.snt.plugin.StrahlerCmd
-
- getChart() - Method in class sc.fiji.snt.viewer.Viewer2D
-
Gets the current viewer as a
SNTChart object
- getChildren() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Gets the child ontologies of this compartment as a flat (non-hierarchical)
list.
- getChildren(int) - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Gets the child ontologies of this compartment as a flat (non-hierarchical)
list.
- getChildren() - Method in class sc.fiji.snt.Path
-
- getChoice(String, String, String[], String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getChosenTypes(Context) - Static method in class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd
-
- getCircumferencePoints(int, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- getCircumferencePoints(int, int, int) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- getClipboardText() - Static method in class sc.fiji.snt.plugin.ij1.Sholl_Utils
-
Deprecated.
Retrieves text from the system clipboard.
- getCol(String) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getColor(double) - Method in class sc.fiji.snt.analysis.ColorMapper
-
- getColor(String, Color) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getColor(String, Color, String...) - Method in class sc.fiji.snt.gui.GuiUtils
-
Simplified color chooser.
- getColor() - Method in class sc.fiji.snt.Path
-
Gets the color of this Path
- getColor(String) - Static method in class sc.fiji.snt.SNTUtils
-
- getColor() - Method in class sc.fiji.snt.util.SWCPoint
-
- getColorFilterMenu() - Method in class sc.fiji.snt.gui.PathManagerUISearchableBar
-
- getColorMap() - Method in class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd
-
- getColorRGB(double) - Method in class sc.fiji.snt.analysis.ColorMapper
-
- getColorRGB(String, Color, String...) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getColorRGB() - Method in class sc.fiji.snt.Path
-
Gets the color of this Path
- getColorString(Color) - Static method in class sc.fiji.snt.SNTUtils
-
- getColorTable() - Method in class sc.fiji.snt.analysis.ColorMapper
-
- getColorTable(String) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper
-
- getColorTable(String) - Method in class sc.fiji.snt.analysis.NodeColorMapper
-
- getColorTable() - Method in class sc.fiji.snt.analysis.NodeColorMapper
-
- getColorTable(String) - Method in class sc.fiji.snt.analysis.TreeColorMapper
-
- getCommentString() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- getCompartment(int) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
Constructs a compartment from its CCF id
- getCompartment(String) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
Constructs a compartment from its CCF name or acronym
- getCompartment(String) - Method in class sc.fiji.snt.gui.cmds.MLImporterCmd
-
- getComponents() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
- getConfirmation(String, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getConfirmation(String, String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getConfirmation(String, String) - Method in class sc.fiji.snt.SNT
-
- getConfirmation2(String, String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getConfirmationAndOption(String, String, String, boolean) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getConsole() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- getContext() - Method in class sc.fiji.snt.SNT
-
- getContext() - Static method in class sc.fiji.snt.SNTUtils
-
Convenience method to access the context of the running Fiji instance (mainly
for IJ1 plugins.
- getContraction() - Method in class sc.fiji.snt.Path
-
Returns the ratio between the "Euclidean distance" of this path and its
length.
- getCoordinateOnAxis(int) - Method in class sc.fiji.snt.util.PointInImage
-
Gets the coordinate along the specified axis.
- getCoordinateOnAxis(int) - Method in interface sc.fiji.snt.util.SNTPoint
-
- getCorrespondences(PathAndFillManager, double) - Method in class sc.fiji.snt.PathAndFillManager
-
For each point in this PathAndFillManager, find the corresponding point on
the other one.
- getCostType() - Method in class sc.fiji.snt.SNT
-
- getCountAtRadius(double) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- getCountMap() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd
-
- getCriticalValue() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getCtSlice(Dataset, int, int) - Static method in class sc.fiji.snt.util.ImgUtils
-
Get a view of the
Dataset at the specified channel and frame.
- getCtSlice3d(Dataset, int, int) - Static method in class sc.fiji.snt.util.ImgUtils
-
Get a 3D view of a
Dataset at the specified channel and frame.
- getCurrentFile() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- getCurrentPath() - Method in class sc.fiji.snt.SNT
-
- getCursorPos() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- getDataset() - Method in class sc.fiji.snt.SNT
-
- getDateUploaded() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getDecimalFormat(double, int) - Static method in class sc.fiji.snt.SNTUtils
-
- getDefaultBooleanPrefs() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- getDefaultLookAndFeel() - Static method in class sc.fiji.snt.SNTPrefs
-
- getDefaultMetrics() - Static method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- getDefaultName(Path) - Method in class sc.fiji.snt.PathAndFillManager
-
- getDefaultSigma(SNT) - Static method in class sc.fiji.snt.util.SigmaUtils
-
- getDefaultThickness() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Returns the default line thickness.
- getDefaultTransparency() - Method in class sc.fiji.snt.TracerCanvas
-
- getDefColor() - Method in class sc.fiji.snt.viewer.Viewer3D
-
- getDendriteMaximum() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getDepth() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getDepth() - Method in class sc.fiji.snt.SNT
-
- getDepthFirstIterator() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets a DepthFirstIterator, using the graph root as start vertex.
- getDepthFirstIterator(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets a DepthFirstIterator, using the specified start vertex.
- getDepthFirstIterator() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
- getDepthFirstIterator(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
- getDescription() - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- getDescription() - Method in enum sc.fiji.snt.SNT.CostType
-
- getDescriptiveStatistics(String) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
- getDescriptiveStats(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getDescriptiveStats(String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- getDescriptors() - Static method in class sc.fiji.snt.analysis.PersistenceAnalyzer
-
Gets a list of supported descriptor functions.
- getDeterminationRatio() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getDiagonal() - Method in class sc.fiji.snt.util.BoundingBox
-
Gets the box diagonal
- getDiagram(String) - Method in class sc.fiji.snt.analysis.PersistenceAnalyzer
-
Gets the persistence diagram.
- getDiagramNodes(String) - Method in class sc.fiji.snt.analysis.PersistenceAnalyzer
-
Gets the persistence diagram nodes.
- getDimensions() - Method in class sc.fiji.snt.util.BoundingBox
-
Gets this BoundingBox dimensions in real world units.
- getDimensions(boolean) - Method in class sc.fiji.snt.util.BoundingBox
-
Gets this BoundingBox dimensions.
- getDisabledComponentColor() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Returns the foreground color of disabled components.
- getDisabledComponentColor() - Static method in class sc.fiji.snt.gui.GuiUtils
-
- getDistanceAtPoint(double, double, double) - Method in class sc.fiji.snt.tracing.FillerThread
-
- getDistinctColors(int) - Static method in class sc.fiji.snt.util.SNTColor
-
Returns distinct colors based on Kenneth Kelly's 22 colors of maximum
contrast (black and white excluded).
- getDnDFileChooser() - Static method in class sc.fiji.snt.gui.GuiUtils
-
- getDOI() - Method in class sc.fiji.snt.io.MouseLightLoader
-
- getDouble(String, String, Number) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getDoubleFromHashMap(String, double) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- getDoublePosition(int) - Method in class sc.fiji.snt.util.CircleCursor3D
-
- getDoublePosition(int) - Method in class sc.fiji.snt.util.PathCursor
-
- getDrawable() - Method in class sc.fiji.snt.viewer.Annotation3D
-
Returns the AbstractDrawable associated with this annotation.
- getDrawable() - Method in class sc.fiji.snt.viewer.OBJMesh
-
Returns the DrawableVBO associated with this mesh
- getDrawDiametersXY() - Method in class sc.fiji.snt.SNT
-
- getEdgeColor(E) - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- getEdgeColorRGBMap() - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- getEditableNodeIndex() - Method in class sc.fiji.snt.Path
-
Gets the position of the node tagged as 'editable', if any.
- getEditingNode() - Method in class sc.fiji.snt.SNT
-
- getEditingPath() - Method in class sc.fiji.snt.SNT
-
- getEditor() - Method in class sc.fiji.snt.viewer.GraphViewer
-
- getElapsedTime(long) - Static method in class sc.fiji.snt.SNTUtils
-
- getEnclosingRadius(boolean, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the largest radius associated with at least the number of
specified counts.
- getEnclosingRadius(double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getExitReason() - Method in class sc.fiji.snt.tracing.SearchThread
-
- getF(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getFFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getFFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getFile() - Method in class sc.fiji.snt.gui.GuiUtils.JTextFieldFile
-
- getFill() - Method in class sc.fiji.snt.tracing.FillerThread
-
- getFilledBinaryImp() - Method in class sc.fiji.snt.SNT
-
- getFilledDistanceImp() - Method in class sc.fiji.snt.SNT
-
- getFilledImp() - Method in class sc.fiji.snt.SNT
-
- getFillerStack() - Method in class sc.fiji.snt.FillConverter
-
- getFillManager() - Method in class sc.fiji.snt.SNTUI
-
Gets the Fill Manager dialog.
- getFillWindowLocation() - Method in class sc.fiji.snt.SNTPrefs
-
- getFilteredImageFile() - Method in class sc.fiji.snt.SNT
-
Returns the file of the 'secondary image', if any.
- getFilterType() - Method in class sc.fiji.snt.SNT
-
- getFitted() - Method in class sc.fiji.snt.Path
-
Gets the fitted version ('flavor') of this Path.
- getFitYvalues() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the ordinates of the sampled linear plot of fitted data.
- getFitYvalues() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getFitYvalues() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
- getFitYvalues(boolean) - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
- getFloatPosition(int) - Method in class sc.fiji.snt.util.CircleCursor3D
-
- getFloatPosition(int) - Method in class sc.fiji.snt.util.PathCursor
-
- getFractalDimension() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the fractal dimension of each branch in the analyzed tree.
- getFrame() - Method in class sc.fiji.snt.Path
-
Gets the hyperstack frame position associated with this Path.
- getFrame() - Method in class sc.fiji.snt.SNT
-
- getFullName() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getG(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getGFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getGFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getGraph() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getGraph() - Method in class sc.fiji.snt.Tree
-
Assembles a DirectedGraph from this Tree.
- getGraph(boolean) - Method in class sc.fiji.snt.Tree
-
Assembles a DirectedGraph from this Tree.
- getGraphComponent() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- getGraphics2D(Graphics) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- getGraphOutline() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- getGraphs() - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
- getGroup() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Gets the collection of Trees being analyzed.
- getGroups() - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Gets the group identifiers currently queued for analysis.
- getGroupStats(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Gets the group statistics.
- getHandle() - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- getHeapHandle(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getHeapHandleFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getHeapHandleFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getHeight() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getHeight() - Method in class sc.fiji.snt.SNT
-
- getHemisphere() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getHemisphere() - Method in class sc.fiji.snt.util.PointInImage
-
- getHemisphere() - Method in interface sc.fiji.snt.util.SNTPoint
-
- getHemisphereFlag(String) - Static method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- getHeuristicType() - Method in class sc.fiji.snt.SNT
-
- getHighestBranchOrder() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getHighestOntologyDepth() - Static method in class sc.fiji.snt.annotation.AllenUtils
-
Gets the maximum number of ontology levels in the Allen CCF.
- getHighestPathOrder() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getHighestPathOrder() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd
-
- getHistogram(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Gets the relative frequencies histogram for a univariate measurement.
- getHistogram(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getHistogram(String) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Gets the relative frequencies histogram for a univariate measurement.
- getHistogram(String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
Retrieves the histogram of relative frequencies histogram for a univariate
measurement.
- getHistogram(String, AnalysisUtils.HistogramDatasetPlus) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- getIcon(IconFactory.GLYPH, float, Color) - Static method in class sc.fiji.snt.gui.IconFactory
-
Creates a new icon from a Font Awesome glyph.
- getIconHeight() - Method in class sc.fiji.snt.gui.FADerivedIcon
-
- getIconWidth() - Method in class sc.fiji.snt.gui.FADerivedIcon
-
- getID() - Method in class sc.fiji.snt.io.MouseLightLoader
-
- getID() - Method in class sc.fiji.snt.Path
-
Gets the identifier of this Path
- getID() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Returns this Viewer's id.
- getIDs(AllenCompartment) - Static method in class sc.fiji.snt.io.MouseLightQuerier
-
- getIDs(Collection<AllenCompartment>) - Static method in class sc.fiji.snt.io.MouseLightQuerier
-
- getIDs(String, boolean) - Static method in class sc.fiji.snt.io.MouseLightQuerier
-
Returns a list of IDs associated with the specified identifier
- getIDs(Collection<String>, boolean) - Static method in class sc.fiji.snt.io.MouseLightQuerier
-
- getIgnoreCalibration() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- getImagePlus() - Method in class sc.fiji.snt.SNT
-
- getImagePlus(int) - Method in class sc.fiji.snt.SNT
-
Gets the Image associated with a view pane.
- getImpContainer(int, int) - Method in class sc.fiji.snt.Tree
-
Gets an empty image capable of holding the skeletonized version of this tree.
- getImpDiagonalLength(boolean, boolean) - Method in class sc.fiji.snt.SNT
-
- getImpInstances() - Method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd
-
- getIndexOfInters(boolean, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the closest index of the intersections data associated with the
specified value
- getIndexOfRadius(double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the closest index of sampled distances associated with the
specified value
- getInnerBranches() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getInnerBranches() - Method in class sc.fiji.snt.analysis.PathAnalyzer
-
- getInnerBranches() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getInnerLength() - Method in class sc.fiji.snt.analysis.PathAnalyzer
-
- getInnerLength() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the cable length of inner branches
- getIntercept() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
Returns the intercept of the estimated regression line,
- getIntersectingRadii(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the number of intersecting radii.
- getIntersectingRadii() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getIntFromHashMap(String, int) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- getIntPosition(int) - Method in class sc.fiji.snt.util.CircleCursor3D
-
- getIntPosition(int) - Method in class sc.fiji.snt.util.PathCursor
-
- getIsotropicVoxelSize() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- getJFreeChart() - Method in class sc.fiji.snt.viewer.Viewer2D
-
- getJSON() - Method in class sc.fiji.snt.io.MouseLightLoader
-
Gets all the data associated with this reconstruction as a JSON object.
- getJTree() - Method in class sc.fiji.snt.PathManagerUI
-
- getJunctionNodes() - Method in class sc.fiji.snt.Path
-
This is a version of
Path.findJunctions() ensuring that a junction node
is only retrieved once even if multiple child paths are associated with it.
- getKStest() - Method in class sc.fiji.snt.analysis.sholl.math.Comparator
-
- getKurtosis(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the kurtosis.
- getKurtosis() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getLabel() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
Returns the label identifying this subgraph.
- getLabel() - Method in class sc.fiji.snt.Tree
-
Returns the identifying label of this tree.
- getLabel() - Method in class sc.fiji.snt.viewer.Annotation3D
-
Gets the annotation label
- getLabel() - Method in class sc.fiji.snt.viewer.OBJMesh
-
- getLabelsImage(ImagePlus, ColorTable) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
Gets the labels image.
- getLandscape(String, int, int) - Method in class sc.fiji.snt.analysis.PersistenceAnalyzer
-
Gets the persistence landscape as an N-dimensional vector, where N == numLandscapes x resolution.
- getLength() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge
-
- getLength() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge
-
- getLength() - Method in class sc.fiji.snt.Path
-
Gets the length of this Path
- getLengthMap() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd
-
- getLengths() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getLibraryPane() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- getLinearStats() - Method in class sc.fiji.snt.analysis.ShollAnalyzer
-
- getListIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
-
- getLoadedData() - Method in class sc.fiji.snt.SNT
-
- getLoadedDataAsImp() - Method in class sc.fiji.snt.SNT
-
Retrieves the pixel data of the main image currently loaded in memory as an
ImagePlus object.
- getLoadedFills() - Method in class sc.fiji.snt.PathAndFillManager
-
- getLongestPath(boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
- getLongestPathVertices(boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
- getLongPosition(int) - Method in class sc.fiji.snt.util.CircleCursor3D
-
- getLongPosition(int) - Method in class sc.fiji.snt.util.PathCursor
-
- getLookAndFeel() - Static method in class sc.fiji.snt.SNTPrefs
-
- getLut(ColorTable) - Static method in class sc.fiji.snt.SNTUtils
-
- getLUTs() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- getMainImagePlusWithoutChecks() - Method in class sc.fiji.snt.SNT
-
- getManagerPanel() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Returns a reference to 'RV Controls' panel.
- getMask() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- getMaskBackground() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
Returns the background color of the Sholl mask image
- getMaskProcessor(boolean, double[]) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
Creates a 2D 'Sholl heatmap' by applying measured values to the foreground
pixels of a copy of the analyzed image.
- getMaskType() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
Returns the type of data to be used in Sholl mask.
- getMax(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the largest value of intersection count.
- getMax() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getMaxDistanceSquared() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getMaxEvaluations() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Gets the function evaluation limit for solvers
- getMaxima(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns a list of all the points in the linear Sholl profile associated
with the highest intersections count
- getMaxima() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getMaximaRadii() - Method in class sc.fiji.snt.analysis.ShollAnalyzer
-
- getMaxOntologyDepth() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- getMaxRadius() - Method in class sc.fiji.snt.PathFitter
-
Gets the current max radius
- getMean(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the arithmetic mean.
- getMean() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getMeanRadius() - Method in class sc.fiji.snt.Path
-
Gets the path mean radius.
- getMeanValueOfPolynomialFit(String, double, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Gets the mean value of polynomial fit.
- getMeanValueOfPolynomialFit(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the mean value of polynomial fit using the default integration
method (Simpson's).
- getMedian(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the median.
- getMedian() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getMenuIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
-
- getMenuItemHeight() - Static method in class sc.fiji.snt.gui.GuiUtils
-
- getMenuItems(JMenuBar) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- getMenuItems(JPopupMenu) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- getMesh() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- getMesh() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- getMesh() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- getMesh(String) - Static method in class sc.fiji.snt.annotation.VFBUtils
-
Retrieves the mesh associated with the specified VFB id.
- getMesh(String, ColorRGB) - Static method in class sc.fiji.snt.annotation.VFBUtils
-
Retrieves the mesh associated with the specified VFB id.
- getMesh(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Gets the mesh associated with the specified label.
- getMeshes() - Method in class sc.fiji.snt.io.InsectBrainLoader
-
- getMeshes() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Returns all meshes added to this viewer.
- getMeshes(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Returns all meshes added to this viewer.
- getMethod() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getMethodDescription() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getMethodFlag(String) - Static method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getMetric() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- getMetric(String) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Computes the specified metric.
- getMetric() - Method in class sc.fiji.snt.Fill
-
- getMetricInternal(String) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getMetrics() - Static method in class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- getMetrics() - Static method in class sc.fiji.snt.analysis.graph.GraphColorMapper
-
Gets the list of supported mapping metrics.
- getMetrics() - Static method in class sc.fiji.snt.analysis.MultiTreeColorMapper
-
Gets the list of supported mapping metrics.
- getMetrics() - Static method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Gets the list of most commonly used metrics.
- getMetrics() - Static method in class sc.fiji.snt.analysis.NodeColorMapper
-
Gets the list of supported mapping metrics.
- getMetrics() - Static method in class sc.fiji.snt.analysis.NodeStatistics
-
Gets the list of supported metrics.
- getMetrics() - Static method in class sc.fiji.snt.analysis.ProfileProcessor
-
- getMetrics() - Static method in class sc.fiji.snt.analysis.ShollAnalyzer
-
- getMetrics() - Static method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets a list of supported metrics.
- getMetrics() - Static method in class sc.fiji.snt.analysis.TreeColorMapper
-
Gets the list of supported mapping metrics.
- getMetrics() - Static method in class sc.fiji.snt.analysis.TreeStatistics
-
Gets the list of most commonly used metrics.
- getMetrics() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- getMetricWithoutChecks(String) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getMin(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the lowest value of intersection count.
- getMin() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getMinimumSeparation() - Method in class sc.fiji.snt.Path
-
- getMinimumSeparation() - Method in class sc.fiji.snt.SNT
-
- getMinMax() - Method in class sc.fiji.snt.analysis.ColorMapper
-
Returns the mapping bounds
- getMinMax() - Method in class sc.fiji.snt.analysis.NodeColorMapper
-
- getMIP(ImagePlus) - Static method in class sc.fiji.snt.SNTUtils
-
- getMorphoFilterMenu() - Method in class sc.fiji.snt.gui.PathManagerUISearchableBar
-
- getMultipleChoices(String, String, String[]) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getMultipleTrees() - Method in class sc.fiji.snt.PathManagerUI
-
- getMultipleTreesInASingleContainer() - Method in class sc.fiji.snt.PathManagerUI
-
- getMultiScaleSettings() - Method in class sc.fiji.snt.gui.SigmaPalette
-
- getMultiViewer() - Method in class sc.fiji.snt.analysis.MultiTreeColorMapper
-
- getMultiViewer() - Method in class sc.fiji.snt.analysis.TreeColorMapper
-
- getN(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Gets the number of Trees in a specified group.
- getN() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
- getName() - Method in class sc.fiji.snt.Path
-
Gets this Path's name.
- getNBranches() - Method in class sc.fiji.snt.analysis.PathAnalyzer
-
- getNBranches() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the number of branches in the analyzed tree.
- getNbranchPoints(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the number of branch points in the analyzed tree associated with the
specified annotation.
- getNbranchPointsNorm(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the percentage of branch points in the analyzed tree associated with the
specified annotation
- getNeuronCount() - Static method in class sc.fiji.snt.io.MouseLightLoader
-
Gets the number of cells publicly available in the MouseLight database.
- getNeuronCount() - Static method in class sc.fiji.snt.io.MouseLightQuerier
-
Gets the number of cells publicly available in the MouseLight database.
- getNeuronID() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getNeuronInfo() - Method in class sc.fiji.snt.io.InsectBrainLoader
-
- getNextPoints() - Method in class sc.fiji.snt.util.SWCPoint
-
Returns the list holding the subsequent nodes in the reconstructed structure
after this one.
- getNextRow(String) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getNFittedPaths() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getNode() - Method in class sc.fiji.snt.NearPoint
-
- getNode(int) - Method in class sc.fiji.snt.Path
-
Gets the node at the specified position.
- getNodeAnnotation(int) - Method in class sc.fiji.snt.Path
-
Returns the neuropil annotation associated with this node.
- getNodeColor(int) - Method in class sc.fiji.snt.Path
-
Gets the node color.
- getNodeColors() - Method in class sc.fiji.snt.Path
-
Gets the node colors.
- getNodeHemisphereFlag(int) - Method in class sc.fiji.snt.Path
-
Returns the hemisphere flag associated with this node.
- getNodeIndex(PointInImage) - Method in class sc.fiji.snt.Path
-
Gets the first node index associated with the specified image coordinates.
- getNodeList() - Method in class sc.fiji.snt.Fill
-
- getNodeRadius(int) - Method in class sc.fiji.snt.Path
-
Gets the radius of the specified node.
- getNodes() - Method in class sc.fiji.snt.analysis.NodeColorMapper
-
- getNodes() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getNodes() - Method in class sc.fiji.snt.io.MouseLightLoader
-
Extracts the nodes (single-point soma, axonal and dendritic arbor) of the
loaded neuron.
- getNodes(String) - Method in class sc.fiji.snt.io.MouseLightLoader
-
Script-friendly method to extract the nodes of a cellular compartment.
- getNodes() - Method in class sc.fiji.snt.Path
-
Gets the nodes of this path.
- getNodes() - Method in class sc.fiji.snt.Tree
-
Gets all the nodes (path points) forming this tree.
- getNodesAsImage() - Method in class sc.fiji.snt.tracing.BiSearch
-
- getNodesAsImage() - Method in class sc.fiji.snt.tracing.FillerThread
-
- getNodesAsImageFromGoal() - Method in class sc.fiji.snt.tracing.SearchThread
-
- getNodesAsImageFromStart() - Method in class sc.fiji.snt.tracing.SearchThread
-
- getNodesAsSWCPoints() - Method in class sc.fiji.snt.Tree
-
- getNodeStatistics() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets a NodeStatistics instance for the vertex set
- getNodeStatistics(String) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets a NodeStatistics instance for the nodes in the vertex set of the specified type
- getNodeStatistics(String) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
- getNodeStatistics() - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- getNodeStatistics(String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- getNodeUnscaled() - Method in class sc.fiji.snt.NearPoint
-
- getNodeValue(int) - Method in class sc.fiji.snt.Path
-
Returns the "value" property of this node.
- getNodeWithoutChecks(int) - Method in class sc.fiji.snt.Path
-
- getNormalizedMeasurement(String) - Method in class sc.fiji.snt.analysis.MultiTreeColorMapper
-
- getNormalizedMeasurement(String, boolean) - Static method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getNormalizedMeasurement(String) - Static method in class sc.fiji.snt.analysis.NodeStatistics
-
- getNormalizedMeasurement(String) - Method in class sc.fiji.snt.analysis.TreeColorMapper
-
- getNormalizedMeasurement(String) - Static method in class sc.fiji.snt.analysis.TreeStatistics
-
- getNormalizer() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getNormalizerDescription() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getNormalizerFlag(String) - Static method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getNormStats() - Method in class sc.fiji.snt.analysis.ShollAnalyzer
-
- getNoSpinesOrVaricosities() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the number of spines/varicosities that have been (manually) assigned to
tree being analyzed.
- getNPaths() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the no.
- getNtips(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the number of end points in the analyzed tree associated with the
specified annotation.
- getNtipsNorm(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the percentage of end points in the analyzed tree associated with the
specified annotation
- getObj() - Method in class sc.fiji.snt.viewer.OBJMesh
-
Returns the OBJFile associated with this mesh
- getOneMinusErfZFudge() - Method in class sc.fiji.snt.SNT
-
- getOntologies() - Static method in class sc.fiji.snt.annotation.AllenUtils
-
Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.
- getOntologies(int, boolean) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
Gets a flat (non-hierarchical) list of all the compartments of the specified
ontology depth.
- getOntologyDepth() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Gets the ontology depth of this compartment.
- getOntologyDepth() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- getOntologyDepth() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- getOptions(String, String[], boolean[], String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getOrCreateSciViewSNT() - Method in class sc.fiji.snt.SNTService
-
- getOrder() - Method in class sc.fiji.snt.Path
-
Gets the "bifurcation" (branching) order of this Path.
- getOriginalFilename() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getOriginalValueOfmxCell(String) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- getOutOfBoundsTransparency() - Method in class sc.fiji.snt.TracerCanvas
-
- getOverlay() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- getPaintScaleLegend(String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- getPaintScaleLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- getParent() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Gets the parent of this compartment.
- getParent() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- getParent() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- getParent() - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg
-
- getParent() - Method in interface sc.fiji.snt.gui.SigmaPaletteListener
-
- getParentStructureId() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- getParsedTree() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Returns the set of parsed Paths.
- getPartitionAsymmetry() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the partition asymmetry at each bifurcation point in the analyzed tree.
- getPath() - Method in class sc.fiji.snt.NearPoint
-
- getPath(int) - Method in class sc.fiji.snt.PathAndFillManager
-
Returns the Path at the specified position in the PathAndFillManager list.
- getPath() - Method in class sc.fiji.snt.PathFitter
-
- getPath() - Method in class sc.fiji.snt.util.PointInImage
-
Returns the Path associated with this node (if any)
- getPathAndFillManager() - Method in class sc.fiji.snt.PathManagerUI
-
- getPathAndFillManager() - Method in class sc.fiji.snt.SNT
-
- getPathAndFillManager() - Method in class sc.fiji.snt.SNTService
-
- getPathFrom3DViewerName(String) - Method in class sc.fiji.snt.PathAndFillManager
-
- getPathFromID(int) - Method in class sc.fiji.snt.PathAndFillManager
-
Returns the Path with the specified id.
- getPathFromName(String, boolean) - Method in class sc.fiji.snt.PathAndFillManager
-
Returns the Path with the specified name.
- getPathIndex(Path) - Method in class sc.fiji.snt.PathAndFillManager
-
Gets the index of a Path.
- getPathManager() - Method in class sc.fiji.snt.SNTUI
-
Gets the Path Manager dialog.
- getPaths() - Method in class sc.fiji.snt.PathAndFillManager
-
Returns all the paths.
- getPaths() - Method in class sc.fiji.snt.SNTService
-
Gets the paths currently listed in the Path Manager
- getPaths3DDisplay() - Method in class sc.fiji.snt.SNT
-
Deprecated.
- getPathsFiltered() - Method in class sc.fiji.snt.PathAndFillManager
-
Returns the 'de facto' Paths.
- getPathsInROI(Roi) - Method in class sc.fiji.snt.PathAndFillManager
-
- getPathsStructured() - Method in class sc.fiji.snt.PathAndFillManager
-
- getPathsStructured(Collection<Path>) - Method in class sc.fiji.snt.PathAndFillManager
-
- getPathWindowLocation() - Method in class sc.fiji.snt.SNTPrefs
-
- getPersistentConfirmation(String, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getPersistentWarning(String, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getPixelDepth() - Method in class sc.fiji.snt.SNT
-
- getPixelHeight() - Method in class sc.fiji.snt.SNT
-
- getPixels(int[][]) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D
-
- getPixelWidth() - Method in class sc.fiji.snt.SNT
-
- getPlane() - Method in class sc.fiji.snt.TracerCanvas
-
Returns the MultiDThreePanes plane associated with this canvas.
- getPlot() - Method in class sc.fiji.snt.analysis.PathProfiler
-
Gets the plot profile as an IJ1
Plot.
- getPlot(int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- getPlot(Path) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- getPlot(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Gets the current plot as a
XYPlot object
- getPlotOutput() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
Returns the flag for outputPlots.
- getPlugin() - Method in class sc.fiji.snt.PathAndFillManager
-
Gets the SNT instance.
- getPlugin() - Method in class sc.fiji.snt.SNTService
-
Returns a reference to the active
SNT plugin.
- getPluginInstance() - Static method in class sc.fiji.snt.SNTUtils
-
- getPoint3fList() - Method in class sc.fiji.snt.Path
-
- getPointDouble(int, double[]) - Method in class sc.fiji.snt.Path
-
- getPointInCanvas(int) - Method in class sc.fiji.snt.Path
-
- getPointInCanvas2D(int, TracerCanvas) - Method in class sc.fiji.snt.Path
-
- getPolygonCentroid(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the centroid from all (radius, inters.
- getPolygonCentroid() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getPolynomial() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Gets the polynomial function.
- getPolynomialAsString() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns a string describing the polynomial fit
- getPolynomialDegree() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the degree of the polynomial.
- getPolynomialMaxima(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates local maxima (critical points at which the derivative of the
polynomial is zero) within the specified interval.
- getPredecessor() - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- getPredecessorFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getPredecessorFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getPreferredSize() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent
-
- getPrefs() - Method in class sc.fiji.snt.SNT
-
- getPreviousEditingPath() - Method in class sc.fiji.snt.SNT
-
- getPreviousPoint() - Method in class sc.fiji.snt.util.SWCPoint
-
Returns the preceding node (if any)
- getPrimaryBranches() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getPrimaryBranches() - Method in class sc.fiji.snt.analysis.PathAnalyzer
-
- getPrimaryBranches(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns intersection counts at the smallest radius (inferred no.
- getPrimaryBranches() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getPrimaryBranches() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Retrieves the primary branches of the analyzed Tree.
- getPrimaryLength() - Method in class sc.fiji.snt.analysis.PathAnalyzer
-
- getPrimaryLength() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the cable length of primary branches.
- getPrimaryPaths() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Retrieves all the Paths in the analyzed Tree tagged as primary.
- getProfile() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
- getProfile() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- getProfile() - Method in interface sc.fiji.snt.analysis.sholl.parsers.Parser
-
- getProfile() - Method in class sc.fiji.snt.analysis.sholl.parsers.TabularParser
-
- getProfile() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
- getProfile() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd
-
- getProperties() - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- getProperties() - Method in class sc.fiji.snt.Tree
-
Returns the Properties instance holding the persistent set of properties.
- getR() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getRadii(double, double, double) - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils
-
- getRamificationIndex(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the ramification index (the highest intersections count divided by
the n.
- getRamificationIndex() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getRange(String, String, float[]) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getRatioMap() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd
-
- getReadableVersion() - Static method in class sc.fiji.snt.SNTUtils
-
- getReader(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader
-
Gets the SWC data associated with the specified cell ID as a reader
- getReader(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader
-
Gets the SWC data ('CNG version') associated with the specified cell ID as
a reader
- getReader(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader
-
- getRealLengthString() - Method in class sc.fiji.snt.Path
-
- getRecentDir() - Method in class sc.fiji.snt.SNTPrefs
-
- getReconstructionFiles(File, String) - Static method in class sc.fiji.snt.SNTUtils
-
Retrieves a list of reconstruction files stored in a common directory
matching the specified criteria.
- getReconstructionURL(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader
-
Gets the URL of the SWC file associated with the specified cell ID.
- getReconstructionURL(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader
-
Gets the URL of the SWC file ('CNG version') associated with the specified
cell ID.
- getReconstructionURL(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader
-
- getReconstructionViewer(boolean) - Method in class sc.fiji.snt.SNTUI
-
Gets the Reconstruction Viewer.
- getRecViewer() - Method in class sc.fiji.snt.SNTService
-
Returns a reference to the active Reconstruction Viewer (either stand-alone
or SNT-associated instance).
- getRecViewer(int) - Method in class sc.fiji.snt.SNTService
-
Returns a reference to an opened Reconstruction Viewer (standalone instance).
- getReductionFactor() - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutScaled
-
- getRefBrain(String) - Static method in class sc.fiji.snt.annotation.VFBUtils
-
Retrieves the surface mesh of an adult Drosophila template brain.
- getRefBrain() - Static method in class sc.fiji.snt.annotation.ZBAtlasUtils
-
Retrieves the surface mesh (outline) of the zebrafish template brain.
- getRegression() - Method in class sc.fiji.snt.analysis.sholl.math.Comparator
-
- getRegression() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getRegressionGradient() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getRegressionIntercept() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getRegressionRSquare() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getRemoteBifAngles() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the angle between each bifurcation point and its children in the simplified graph,
which comprise either branch points or terminal nodes.
- getReplaceExistingPaths() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- getResult(Callable<T>) - Static method in class sc.fiji.snt.gui.SwingSafeResult
-
- getResult() - Method in class sc.fiji.snt.tracing.BiSearch
-
- getResult() - Method in class sc.fiji.snt.tracing.FillerThread
-
- getResult() - Method in class sc.fiji.snt.tracing.ManualTracerThread
-
- getResult() - Method in interface sc.fiji.snt.tracing.SearchInterface
-
- getResult() - Method in class sc.fiji.snt.tracing.TracerThread
-
- getResult() - Method in class sc.fiji.snt.tracing.TubularGeodesicsTracer
-
- getROIs(Path) - Method in class sc.fiji.snt.analysis.RoiConverter
-
- getROIs() - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- getROIs(ImagePlus) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- getRoot() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets the root of this graph.
- getRoot() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
Gets the root of this graph.
- getRoot() - Method in class sc.fiji.snt.Tree
-
Gets the first node of the main primary path of this tree
- getRootAssociatedBranches() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getRootMesh(ColorRGB) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
Retrieves the surface contours for the Allen Mouse Brain Atlas (CCF), bundled
with SNT.
- getRootNumber() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- getRSquaredOfFit(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns RSquared of the polynomial fit.
- getRSquaredOfFit() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getSampledCounts() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getSampledDistances() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getSampleInfo() - Method in class sc.fiji.snt.io.MouseLightLoader
-
- getSanitizedUnit(String) - Static method in class sc.fiji.snt.SNTUtils
-
- getSaveDir() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent
-
- getScaledPoint() - Method in class sc.fiji.snt.util.PointInCanvas
-
Converts the pixels coordinates of this point into a physical location if
this point is associated with a Path.
- getScientificNotationAwarePrecision() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
Retrieves precision according to Analyze>Set Measurements...
- getSciView() - Method in class sc.fiji.snt.SciViewSNT
-
Gets the SciView instance currently in use.
- getSciViewSNT() - Method in class sc.fiji.snt.SNTService
-
- getSciViewSNT(boolean) - Method in class sc.fiji.snt.SNTUI
-
Gets the active getSciViewSNT (SciView<>SNT bridge) instance.
- getScriptsMenu() - Method in class sc.fiji.snt.gui.ScriptInstaller
-
Returns a UI list with all the bundled non-demo SNT scripts
- getScriptsMenu(Pattern, String...) - Method in class sc.fiji.snt.gui.ScriptInstaller
-
Returns a UI list with the bundled SNT scripts (specified directories only).
- getSearch() - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist
-
- getSearch() - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist
-
- getSearch() - Method in interface sc.fiji.snt.tracing.artist.SearchArtist
-
- getSearch() - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist
-
- getSearchable() - Method in class sc.fiji.snt.PathManagerUI
-
- getSearchImageType() - Method in class sc.fiji.snt.SNT
-
- getSearchType() - Method in class sc.fiji.snt.SNT
-
- getSecondaryData() - Method in class sc.fiji.snt.SNT
-
- getSecondaryDataAsImp() - Method in class sc.fiji.snt.SNT
-
Retrieves the 'secondary image' data currently loaded in memory as an
ImagePlus object.
- getSecondaryImageMinMax() - Method in class sc.fiji.snt.SNT
-
- getSecondaryMaxima() - Method in class sc.fiji.snt.analysis.ShollAnalyzer
-
- getSection(int, int) - Method in class sc.fiji.snt.Path
-
Gets a section between two nodes of this Path.
- getSelectedColor() - Method in class sc.fiji.snt.gui.ColorChooserButton
-
- getSelectedPaths() - Method in class sc.fiji.snt.PathAndFillManager
-
Gets all paths selected in the GUI
- getSelectedPaths(boolean) - Method in class sc.fiji.snt.PathManagerUI
-
Gets the paths currently selected in the Manager's
JTree list.
- getSelectedPaths() - Method in class sc.fiji.snt.SNT
-
- getSelectedPaths() - Method in class sc.fiji.snt.SNTService
-
Gets the paths currently selected in the Path Manager list.
- getSelectedPathsOrganizedByTrees(boolean) - Method in class sc.fiji.snt.PathManagerUI
-
Gets the paths currently selected in the Manager's
JTree list as
Trees.
- getSelectedPathsRenderedInViewPort(TracerCanvas) - Method in class sc.fiji.snt.PathAndFillManager
-
- getSelectedSWCColor() - Method in class sc.fiji.snt.gui.ColorMenu
-
- getSex() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getShapes() - Static method in class sc.fiji.snt.analysis.ProfileProcessor
-
- getShollAnalyzer() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getShollAnalyzer() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getShollDecay() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getShollRegressionCoefficient() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getShollTable() - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Returns a reference to the plugin's "Sholl Results" table displaying
summary statistics.
- getShortestPath(SWCPoint, SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets the shortest path between source and target vertex as a
Path object.
- getShortestPathVertices(SWCPoint, SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets the shortest path between source and target vertex as a
Deque of SWCPoint objects.
- getShortName() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getSimplifiedGraph() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Returns a simplified graph in which slab nodes are removed and the graph
is represented only by root, branch nodes and leaves.
- getSimplifiedGraph(DirectedWeightedGraph) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils
-
Deprecated.
- getSinglePane() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- getSinglePointPaths() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getSingleSelectedPath() - Method in class sc.fiji.snt.SNT
-
- getSingleTree() - Method in class sc.fiji.snt.PathManagerUI
-
- getSingleValueMetrics() - Method in class sc.fiji.snt.analysis.ShollAnalyzer
-
- getSkeleton() - Method in class sc.fiji.snt.Tree
-
Retrieves the rasterized skeleton of this tree at 1:1 scaling.
- getSkeleton2() - Method in class sc.fiji.snt.Tree
-
Retrieves the rasterized skeleton of this tree at 1:1 scaling.
- getSkeleton2D() - Method in class sc.fiji.snt.Tree
-
Retrieves a 2D projection of the rasterized skeleton of this tree at 1:1
scaling.
- getSkewness(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the skewness.
- getSkewness() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getSlice(int) - Method in class sc.fiji.snt.tracing.image.SearchImageStack
-
- getSlope() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
- getSNT() - Method in class sc.fiji.snt.PathManagerUI
-
- getSomaCompartment() - Method in class sc.fiji.snt.io.MouseLightLoader
-
- getSomaLocation() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getSomaLocation() - Method in class sc.fiji.snt.io.MouseLightLoader
-
- getSomaNodes() - Method in class sc.fiji.snt.Tree
-
- getSource() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge
-
- getSource() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge
-
- getSourceGraph() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- getSourcePaths() - Method in class sc.fiji.snt.Fill
-
- getSourcePathsStringHuman() - Method in class sc.fiji.snt.Fill
-
- getSourcePathsStringMachine() - Method in class sc.fiji.snt.Fill
-
- getSpacingUnits() - Method in class sc.fiji.snt.SNT
-
- getSpeciesCommonName() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getSpeciesID() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getSpeciesNeuronIDs(int) - Static method in class sc.fiji.snt.annotation.InsectBrainUtils
-
- getSpeciesScientificName() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo
-
- getSpineOrVaricosityCount() - Method in class sc.fiji.snt.Path
-
- getSpineOrVaricosityDensity() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the overall density of spines/varicosities associated with this tree
- getStandardizedCompartment(String) - Static method in interface sc.fiji.snt.TreeProperties
-
- getStandardizedMetric(String) - Static method in class sc.fiji.snt.analysis.NodeStatistics
-
- getStartJoins() - Method in class sc.fiji.snt.Path
-
- getStartJoinsPoint() - Method in class sc.fiji.snt.Path
-
- getState() - Method in class sc.fiji.snt.SNTUI
-
Gets the current UI state.
- getState(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getStateFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getStateFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getStatistics(boolean) - Method in class sc.fiji.snt.SNTService
-
- getStats() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- getStats() - Method in class sc.fiji.snt.SNT
-
- getStatsSecondary() - Method in class sc.fiji.snt.SNT
-
- getStrahlerAnalyzer() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getStrahlerAnalyzer() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getStrahlerBifurcationRatio() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getStrahlerNumber() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getString(String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- getStringFromHashMap(String, String) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- getStructureIdPath() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- getSubgraph(Set<SWCPoint>) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Returns the subgraph defined by the supplied subset of vertices, including their edges.
- getSucceeded() - Method in class sc.fiji.snt.PathFitter
-
Checks whether the fit succeeded.
- getSuggestedSuffix() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- getSum(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the sum.
- getSum() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getSummaryStats(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getSummaryStats(String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- getSumSq(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the sum of the squared values.
- getSumSq() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getSWC() - Method in class sc.fiji.snt.io.MouseLightLoader
-
Gets all the data associated with this reconstruction in the SWC format.
- getSWCcolor(int) - Static method in class sc.fiji.snt.Path
-
Gets the default SWC colors used by SNT.
- getSWCFileForIndex(String, int) - Method in class sc.fiji.snt.PathAndFillManager
-
- getSWCFor(Collection<Path>) - Method in class sc.fiji.snt.PathAndFillManager
-
- getSWCForOld(Collection<Path>) - Method in class sc.fiji.snt.PathAndFillManager
-
Gets the list of SWCPoints associated with a collection of Paths.
- getSWCType() - Method in class sc.fiji.snt.Path
-
Gets the SWC type.
- getSWCTypeMap() - Static method in class sc.fiji.snt.Tree
-
Returns the SWC Type flags used by SNT.
- getSWCtypeName(int, boolean) - Static method in class sc.fiji.snt.Path
-
Gets the SWC type label associated with the specified type flag.
- getSWCtypeNames() - Static method in class sc.fiji.snt.Path
-
- getSWCtypes() - Static method in class sc.fiji.snt.Path
-
- getSWCTypes() - Method in class sc.fiji.snt.Tree
-
Extracts the SWC-type flags present in this Tree.
- getSWCTypesAsString() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getTabbedPaneIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
-
- getTable() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the table currently being used by the Analyzer
- getTable() - Method in class sc.fiji.snt.PathManagerUI
-
- getTable() - Method in class sc.fiji.snt.plugin.StrahlerCmd
-
Gets the Strahler table.
- getTable() - Method in class sc.fiji.snt.SNTService
-
Returns a reference to SNT's main table of measurements.
- getTags() - Method in class sc.fiji.snt.util.SWCPoint
-
- getTangent(int, int, double[]) - Method in class sc.fiji.snt.Path
-
- getTarget() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge
-
- getTarget() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge
-
- getTemp(String, boolean) - Method in class sc.fiji.snt.SNTPrefs
-
- getTemp(String, String) - Method in class sc.fiji.snt.SNTPrefs
-
- getTerminalBranches() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getTerminalBranches() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Retrieves the terminal branches of the analyzed Tree.
- getTerminalLength() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the cable length of terminal branches
- getText() - Method in class sc.fiji.snt.gui.GuiUtils.JTextFieldFile
-
- getTextWindow(String) - Static method in class sc.fiji.snt.plugin.ij1.Sholl_Utils
-
Deprecated.
- getThreads() - Static method in class sc.fiji.snt.SNTPrefs
-
- getThreshold() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- getThreshold() - Method in class sc.fiji.snt.Fill
-
- getThreshold() - Method in class sc.fiji.snt.tracing.FillerThread
-
- getTips() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets the end points (tips) of the graph.
- getTips() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
Gets the end points (tips) of the subgraph.
- getTips() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- getTips() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the position of all the tips in the analyzed tree.
- getTips(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Gets the position of all the tips in the analyzed tree associated with the
specified annotation.
- getTitle() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
- getTitle() - Method in class sc.fiji.snt.viewer.Viewer2D
-
Gets the plot display title.
- getToolTipForCell(Object) - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
-
- getToolTipForCell(Object) - Method in class sc.fiji.snt.viewer.geditor.TreeGraphAdapter
-
- getTree() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Returns a new tree associated with this graph, using the current state of the
graph to build the tree.
- getTree(boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Returns a tree associated with this graph.
- getTree() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
Returns the tree associated with the parent's graph
- getTree() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
Returns the tree associated with this parser
- getTree(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader
-
Gets the collection of Paths for the specified cell ID
- getTree() - Method in class sc.fiji.snt.io.InsectBrainLoader
-
Gets the collection of Paths for the specified cell ID
- getTree(String, ColorRGB) - Method in class sc.fiji.snt.io.MouseLightLoader
-
Extracts a cell compartment as a collection of Paths.
- getTree(String) - Method in class sc.fiji.snt.io.MouseLightLoader
-
Script-friendly method to extract a compartment as a collection of Paths.
- getTree() - Method in class sc.fiji.snt.io.MouseLightLoader
-
Script-friendly method to extract the entire neuron as a collection of Paths.
- getTree(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader
-
Gets the collection of Paths for the specified cell ID
- getTree(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader
-
- getTree(boolean) - Method in class sc.fiji.snt.SNTService
-
Gets the collection of paths listed in the Path Manager as a
Tree
object.
- getTree() - Method in class sc.fiji.snt.SNTService
-
Gets the collection of paths listed in the Path Manager as a
Tree
object.
- getTree(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Gets the tree associated with the specified label.
- getTreeAsSceneryNode(Tree) - Method in class sc.fiji.snt.SciViewSNT
-
Gets the specified Tree as a Scenery Node.
- getTreeID() - Method in class sc.fiji.snt.Path
-
Gets the identifier of the
Tree associated to this Path (if any).
- getTreeLabel() - Method in class sc.fiji.snt.Path
-
- getTreeModel(boolean) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
Retrieves the Allen CCF hierarchical tree data.
- getTreePath() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
Gets the tree path of this compartment.
- getTrees() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- getTrees() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Return the connected components of this graph as a list of
Trees
- getTrees() - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
Generates a list of
Trees from the skeleton image.
- getTrees() - Method in class sc.fiji.snt.PathAndFillManager
-
Returns all the paths associated with this PathAndFillManager instance,
grouped by Tree.
- getTrees() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Returns all trees added to this viewer.
- getTrees(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Returns all trees added to this viewer.
- getTreeWithSamePathStructure() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Attempt to build a new Tree with the same
Path hierarchy as the source Tree.
- getType() - Method in class sc.fiji.snt.event.SNTEvent
-
- getType() - Method in class sc.fiji.snt.viewer.Annotation3D
-
Gets the type of this annotation.
- getUI() - Method in class sc.fiji.snt.SNT
-
Gets the main UI.
- getUI() - Method in class sc.fiji.snt.SNTService
-
Returns a reference to SNT's UI.
- getUIState() - Method in class sc.fiji.snt.SNT
-
- getUndoManager() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- getUnique3Dgroups(ArrayList<ShollPoint>) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D
-
- getUniquelySuffixedFile(File) - Static method in class sc.fiji.snt.SNTUtils
-
- getUniquelySuffixedTifFile(File) - Static method in class sc.fiji.snt.SNTUtils
-
- getUnit() - Method in class sc.fiji.snt.util.BoundingBox
-
Gets the length unit of voxel spacing
- getUnscaledNodesInViewPort(TracerCanvas) - Method in class sc.fiji.snt.Path
-
- getUnscaledPoint() - Method in class sc.fiji.snt.util.PointInImage
-
Converts the coordinates of this point into pixel units if this point is
associated with a Path.
- getUnscaledPoint(int) - Method in class sc.fiji.snt.util.PointInImage
-
Converts the coordinates of this point into pixel units if this point is
associated with a Path.
- getUnSelectedPathsRenderedInViewPort(TracerCanvas) - Method in class sc.fiji.snt.PathAndFillManager
-
- getUseFitted() - Method in class sc.fiji.snt.Path
-
Gets whether the fitted 'flavor' of this Path is in use.
- getUseSubVolumeStats() - Method in class sc.fiji.snt.SNT
-
- getUUID() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- getValue(int, int) - Method in class sc.fiji.snt.tracing.image.ArraySearchImage
-
- getValue(int, int) - Method in class sc.fiji.snt.tracing.image.ListSearchImage
-
- getValue(int, int) - Method in class sc.fiji.snt.tracing.image.MapSearchImage
-
- getValue(int, int) - Method in interface sc.fiji.snt.tracing.image.SearchImage
-
- getValues(Path) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- getValues(Path, int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- getValues() - Method in class sc.fiji.snt.analysis.ProfileProcessor
-
The profile values, or null if they have not been processed yet.
- getVariance(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Calculates the variance.
- getVariance() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
- getVertexColor(V) - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- getVertexColorRGBMap() - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- getVertexValue(V) - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- getVertexValueMap() - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- getVertices() - Method in class sc.fiji.snt.viewer.OBJMesh
-
Returns the mesh vertices.
- getVertices(String) - Method in class sc.fiji.snt.viewer.OBJMesh
-
Returns the mesh vertices.
- getViewers() - Static method in class sc.fiji.snt.SNTUtils
-
- getViewPort() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- getVolume() - Method in class sc.fiji.snt.Fill
-
Returns the Fill volume.
- getVolume() - Method in class sc.fiji.snt.viewer.Annotation3D
-
- getVolume() - Method in class sc.fiji.snt.viewer.OBJMesh
-
- getWeight() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge
-
- getWeight() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge
-
- getWidth() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
- getWidth() - Method in class sc.fiji.snt.SNT
-
- getX() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getX() - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- getX() - Method in interface sc.fiji.snt.tracing.SearchNode
-
- getX() - Method in class sc.fiji.snt.util.PointInImage
-
- getX() - Method in interface sc.fiji.snt.util.SNTPoint
-
- getX() - Method in class sc.fiji.snt.util.SWCPoint
-
- getXOffset() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- getXScale() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- getXUnscaled(int) - Method in class sc.fiji.snt.Path
-
- getXUnscaledDouble(int) - Method in class sc.fiji.snt.Path
-
- getXvalues() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the abscissae of the sampled linear plot for sampled data.
- getXvalues() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
Returns the abscissae of the Semi-log /Log-log plot for sampled data.
- getXvalues() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
- getXYCanvas() - Method in class sc.fiji.snt.SNT
-
- getXYPlot() - Method in class sc.fiji.snt.analysis.PathProfiler
-
- getXYPlot(int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- getXZCanvas() - Method in class sc.fiji.snt.SNT
-
- getY() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getY() - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- getY() - Method in interface sc.fiji.snt.tracing.SearchNode
-
- getY() - Method in class sc.fiji.snt.util.PointInImage
-
- getY() - Method in interface sc.fiji.snt.util.SNTPoint
-
- getY() - Method in class sc.fiji.snt.util.SWCPoint
-
- getYOffset() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- getYScale() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- getYUnscaled(int) - Method in class sc.fiji.snt.Path
-
- getYUnscaledDouble(int) - Method in class sc.fiji.snt.Path
-
- getYvalues() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Returns the ordinates of the sampled linear plot of sampled data.
- getYvalues() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats
-
Returns the ordinates of the Semi-log/Log-log plot for sampled data.
- getYvalues() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
- getYvalues(boolean) - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
- getZ() - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- getZ() - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- getZ() - Method in interface sc.fiji.snt.tracing.SearchNode
-
- getZ() - Method in class sc.fiji.snt.util.PointInImage
-
- getZ() - Method in interface sc.fiji.snt.util.SNTPoint
-
- getZ() - Method in class sc.fiji.snt.util.SWCPoint
-
- getZFudge() - Method in class sc.fiji.snt.tracing.cost.OneMinusErf
-
- getZOffset() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- getZScale() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- getZUnscaled(int) - Method in class sc.fiji.snt.Path
-
- getZUnscaledDouble(int) - Method in class sc.fiji.snt.Path
-
- getZYCanvas() - Method in class sc.fiji.snt.SNT
-
- getZYXZ(ImagePlus, int) - Static method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- goal_x - Variable in class sc.fiji.snt.tracing.BiSearch
-
- goal_y - Variable in class sc.fiji.snt.tracing.BiSearch
-
- goal_z - Variable in class sc.fiji.snt.tracing.BiSearch
-
- graph - Variable in class sc.fiji.snt.analysis.graph.GraphColorMapper
-
- GraphAdapterMapperCmd - Class in sc.fiji.snt.plugin
-
- GraphAdapterMapperCmd() - Constructor for class sc.fiji.snt.plugin.GraphAdapterMapperCmd
-
- GraphColorMapper<V,E extends org.jgrapht.graph.DefaultWeightedEdge> - Class in sc.fiji.snt.analysis.graph
-
- GraphColorMapper(Context) - Constructor for class sc.fiji.snt.analysis.graph.GraphColorMapper
-
- GraphColorMapper() - Constructor for class sc.fiji.snt.analysis.graph.GraphColorMapper
-
- graphComponent - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- GraphEditor - Class in sc.fiji.snt.viewer.geditor
-
- GraphEditor(String, mxGraphComponent) - Constructor for class sc.fiji.snt.viewer.geditor.GraphEditor
-
- GraphGeneratorCmd - Class in sc.fiji.snt.gui.cmds
-
Command for displaying the contents of Path Manager in the "SNT Graph Viewer"
- GraphGeneratorCmd() - Constructor for class sc.fiji.snt.gui.cmds.GraphGeneratorCmd
-
- graphLayout(String) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
Creates an action that executes the specified layout.
- graphOrder() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- graphOutline - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- GraphUtils - Class in sc.fiji.snt.analysis.graph
-
Utilities for Graph handling.
- GraphViewer - Class in sc.fiji.snt.viewer
-
- GraphViewer(SNTGraph<?, ? extends DefaultWeightedEdge>) - Constructor for class sc.fiji.snt.viewer.GraphViewer
-
- GroupAnalyzerCmd - Class in sc.fiji.snt.plugin
-
Command for Comparing Groups of Tree(s).
- GroupAnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.GroupAnalyzerCmd
-
- GroupedTreeStatistics - Class in sc.fiji.snt.analysis
-
Computes statistics from
Tree groups.
- GroupedTreeStatistics() - Constructor for class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Instantiates a new grouped tree statistics.
- groupPositions(int[][]) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D
-
- GUESS_LOG_METHOD - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- GUESS_SLOG - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
Flag for automatic choice between Semi-log/Log-log analysis
- guessResamplingFactor() - Method in class sc.fiji.snt.SNT
-
- guessTracesFileType(String) - Method in class sc.fiji.snt.PathAndFillManager
-
- GuiUtils - Class in sc.fiji.snt.gui
-
Misc.
- GuiUtils(Component) - Constructor for class sc.fiji.snt.gui.GuiUtils
-
- GuiUtils() - Constructor for class sc.fiji.snt.gui.GuiUtils
-
- guiUtils - Variable in class sc.fiji.snt.PathManagerUI
-
- guiUtils - Variable in class sc.fiji.snt.SNTUI
-
- GuiUtils.JTextFieldFile - Class in sc.fiji.snt.gui
-
- S_SHELL - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
Flag for spherical shell normalization (Semi-log/Log-log method)
- sampleImage() - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils
-
Returns the plugin's sample image (File>Samples>ddaC Neuron).
- sampleImage() - Static method in class sc.fiji.snt.plugin.ij1.Sholl_Utils
-
- SAMPLES_PER_RADIUS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- save(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- save(File) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- save(String) - Method in class sc.fiji.snt.analysis.SNTTable
-
- save(File) - Method in class sc.fiji.snt.analysis.SNTTable
-
- save(String) - Method in class sc.fiji.snt.io.MouseLightLoader
-
Convenience method to save JSON data.
- save(File) - Method in class sc.fiji.snt.io.MouseLightLoader
-
Convenience method to save JSON data.
- save(String) - Method in class sc.fiji.snt.SNTService
-
Saves all the existing paths to a file.
- save(String) - Method in class sc.fiji.snt.Tree
-
Saves this Tree to a .TRACES (XML, compressed) file.
- save(String) - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- SAVE_DIR_KEY - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- SAVE_FILES - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- saveAllPathsToSwc(String) - Method in class sc.fiji.snt.SNTUI
-
- saveAsJSON(String) - Method in class sc.fiji.snt.io.MouseLightLoader
-
Convenience method to save JSON data to a local directory.
- saveAsPNG(File) - Method in class sc.fiji.snt.analysis.SNTChart
-
- saveAsPNG(String) - Method in class sc.fiji.snt.analysis.SNTChart
-
- saveAsSWC(String) - Method in class sc.fiji.snt.io.MouseLightLoader
-
Convenience method to save SWC data to a local directory.
- saveAsSWC(String) - Method in class sc.fiji.snt.Tree
-
Saves this Tree to an SWC file.
- saveDir - Variable in class sc.fiji.snt.viewer.geditor.SNTGraphComponent
-
- saveFile(String, File, List<String>) - Method in class sc.fiji.snt.gui.GuiUtils
-
- saveFile(String, String, String) - Method in class sc.fiji.snt.SNTUI
-
- saveFill() - Method in class sc.fiji.snt.SNT
-
- SaveMeasurementsCmd - Class in sc.fiji.snt.gui
-
Implements the 'Save Tables and Analysis Plots...' command: A single prompt for saving all
tables, plots and charts currently open.
- SaveMeasurementsCmd() - Constructor for class sc.fiji.snt.gui.SaveMeasurementsCmd
-
- savePluginPrefs(boolean) - Method in class sc.fiji.snt.SNTPrefs
-
- saveSilently(File) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
- saveSnapshot() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Saves a snapshot of current scene as a PNG image.
- saveSnapshot(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Saves a snapshot of current scene as a PNG image to the specified path.
- saveSnapshot(File) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- saveStartupPrefs() - Method in class sc.fiji.snt.SNTPrefs
-
Deprecated.
- saveStringPreferences() - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- saveTable() - Method in class sc.fiji.snt.PathManagerUI
-
- saveTable(Table<?, ?>, char, boolean, boolean, File) - Static method in class sc.fiji.snt.SNTUtils
-
- savetoFileOrFileSeries(File) - Method in class sc.fiji.snt.PathAndFillManager
-
- saveToXML(File) - Method in class sc.fiji.snt.SNTUI
-
- sc.fiji.snt - package sc.fiji.snt
-
SNT core classes
- sc.fiji.snt.analysis - package sc.fiji.snt.analysis
-
- sc.fiji.snt.analysis.graph - package sc.fiji.snt.analysis.graph
-
Classes for handling neuronal reconstructions as graphs
- sc.fiji.snt.analysis.sholl - package sc.fiji.snt.analysis.sholl
-
Sholl analysis of Images, pre-sampled data and
Trees.
- sc.fiji.snt.analysis.sholl.gui - package sc.fiji.snt.analysis.sholl.gui
-
GUI customizations (image overlays, plots, etc.) required for Sholl Analysis.
- sc.fiji.snt.analysis.sholl.math - package sc.fiji.snt.analysis.sholl.math
-
Statistical analysis of Sholl data
- sc.fiji.snt.analysis.sholl.parsers - package sc.fiji.snt.analysis.sholl.parsers
-
Parsers to retrieve Profiles from multiple sources (2D/3D images, reconstructions, and tables)
- sc.fiji.snt.annotation - package sc.fiji.snt.annotation
-
Classes handling neuropil annotations and atlases metadata.
- sc.fiji.snt.event - package sc.fiji.snt.event
-
Utilities for TrakEM2 interaction
- sc.fiji.snt.filter - package sc.fiji.snt.filter
-
- sc.fiji.snt.gui - package sc.fiji.snt.gui
-
Customizations and commands for SNT's GUI.
- sc.fiji.snt.gui.cmds - package sc.fiji.snt.gui.cmds
-
Scijava-based GUIs for SNT built-in commands.
- sc.fiji.snt.hyperpanes - package sc.fiji.snt.hyperpanes
-
Classes implementing SNT's XY, ZY, and XZ canvases.
- sc.fiji.snt.io - package sc.fiji.snt.io
-
Classes for importing reconstructions into SNT.
- sc.fiji.snt.plugin - package sc.fiji.snt.plugin
-
SNT add-ons as IJ2 commands
- sc.fiji.snt.plugin.ij1 - package sc.fiji.snt.plugin.ij1
-
- sc.fiji.snt.tracing - package sc.fiji.snt.tracing
-
- sc.fiji.snt.tracing.artist - package sc.fiji.snt.tracing.artist
-
- sc.fiji.snt.tracing.cost - package sc.fiji.snt.tracing.cost
-
- sc.fiji.snt.tracing.heuristic - package sc.fiji.snt.tracing.heuristic
-
- sc.fiji.snt.tracing.image - package sc.fiji.snt.tracing.image
-
- sc.fiji.snt.util - package sc.fiji.snt.util
-
Miscellaneous SNT utilities, including classes defining reconstruction nodes.
- sc.fiji.snt.viewer - package sc.fiji.snt.viewer
-
Visualization of reconstructions
- sc.fiji.snt.viewer.geditor - package sc.fiji.snt.viewer.geditor
-
- scale(double, double, double, boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Scales the point coordinates of each vertex by the specified factors.
- scale(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- scale(double, double, double) - Method in class sc.fiji.snt.Tree
-
Scales the tree by the specified factors.
- scale(double, double, double, double) - Method in class sc.fiji.snt.Tree
-
Scales the tree by the specified factors.
- scale(double, double, double) - Method in class sc.fiji.snt.util.PointInImage
-
Scales this point coordinates.
- scale(Set<ShollPoint>, Calibration) - Static method in class sc.fiji.snt.util.ShollPoint
-
- scaled() - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- scaledMicrometer(double, int) - Static method in class sc.fiji.snt.gui.GuiUtils
-
Returns a more human readable representation of a length in micrometers.
- scaleEdgeWidths(double, double, String) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- SCATTER - Static variable in class sc.fiji.snt.viewer.Annotation3D
-
- SciViewSNT - Class in sc.fiji.snt
-
Bridges SNT to
SciView, allowing
Trees to be rendered as scenery objects
- SciViewSNT(Context) - Constructor for class sc.fiji.snt.SciViewSNT
-
Instantiates a new SciViewSNT instance.
- SciViewSNT(SciView) - Constructor for class sc.fiji.snt.SciViewSNT
-
Instantiates SciViewSNT from an existing SciView instance.
- SciViewSNT(SNT) - Constructor for class sc.fiji.snt.SciViewSNT
-
- sciViewSNT - Variable in class sc.fiji.snt.SNTUI
-
- ScriptInstaller - Class in sc.fiji.snt.gui
-
Utility class for discovery of SNT scripts
- ScriptInstaller(Context, Component) - Constructor for class sc.fiji.snt.gui.ScriptInstaller
-
- ScriptInstaller(Context, SNTUI) - Constructor for class sc.fiji.snt.gui.ScriptInstaller
-
- scrollTo(int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- SearchArtist - Interface in sc.fiji.snt.tracing.artist
-
- SearchArtistFactory - Class in sc.fiji.snt.tracing.artist
-
- SearchArtistFactory() - Constructor for class sc.fiji.snt.tracing.artist.SearchArtistFactory
-
- searchArtists - Variable in class sc.fiji.snt.TracerCanvas
-
- SearchImage<V> - Interface in sc.fiji.snt.tracing.image
-
General interface for data structures used to keep track
of encountered nodes during image-based searches.
- SearchImageStack<V extends SearchNode> - Class in sc.fiji.snt.tracing.image
-
A stack of
SearchImages, backed by a
Int2ObjectOpenHashMap.
- SearchImageStack() - Constructor for class sc.fiji.snt.tracing.image.SearchImageStack
-
- SearchImageStack(Supplier<SearchImage<V>>) - Constructor for class sc.fiji.snt.tracing.image.SearchImageStack
-
- searchImageType - Variable in class sc.fiji.snt.SNT
-
- SearchInterface - Interface in sc.fiji.snt.tracing
-
Tracer classes implementing searches between two points should implement this
interface.
- SearchNode - Interface in sc.fiji.snt.tracing
-
- SearchProgressCallback - Interface in sc.fiji.snt
-
- searchStatus - Variable in class sc.fiji.snt.tracing.DefaultSearchNode
-
- SearchThread - Class in sc.fiji.snt.tracing
-
Implements a common thread that explores the image using a variety of
strategies, e.g., to trace tubular structures or surfaces.
- SearchThread(RandomAccessibleInterval<? extends RealType<?>>, Calibration, boolean, boolean, int, long, SNT.SearchImageType, Cost) - Constructor for class sc.fiji.snt.tracing.SearchThread
-
- SearchThread(SNT, RandomAccessibleInterval<? extends RealType<?>>, Cost) - Constructor for class sc.fiji.snt.tracing.SearchThread
-
- SearchThreadArtist - Class in sc.fiji.snt.tracing.artist
-
- SearchThreadArtist(SearchThread, Color, Color) - Constructor for class sc.fiji.snt.tracing.artist.SearchThreadArtist
-
- SECLAYER_KEY - Static variable in class sc.fiji.snt.gui.cmds.PathFitterCmd
-
- secondaryData - Variable in class sc.fiji.snt.SNT
-
- secondaryImageFile - Variable in class sc.fiji.snt.SNT
-
- selectAll() - Method in class sc.fiji.snt.PathManagerUI
-
- selectColor(Color) - Method in class sc.fiji.snt.gui.ColorMenu
-
- selectedColor - Variable in class sc.fiji.snt.SNT
-
- selectedColor3f - Variable in class sc.fiji.snt.SNT
-
- selectionExists() - Method in class sc.fiji.snt.PathManagerUI
-
- selectNone() - Method in class sc.fiji.snt.gui.ColorMenu
-
- selectPath(Path, boolean) - Method in class sc.fiji.snt.SNT
-
- selectSWCColor(SNTColor) - Method in class sc.fiji.snt.gui.ColorMenu
-
- SEMI_LOG - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
Flag for imposing Semi-log analysis
- SEND_TO_TRAKEM2 - Static variable in class sc.fiji.snt.event.SNTEvent
-
- set(String, String, Object) - Method in class sc.fiji.snt.analysis.SNTTable
-
- set(String, int, Object) - Method in class sc.fiji.snt.analysis.SNTTable
-
- set(int, int, Object) - Method in class sc.fiji.snt.analysis.SNTTable
-
- set2DDisplayCanvas(boolean) - Method in class sc.fiji.snt.SNTPrefs
-
- set3DUniverse(Image3DUniverse) - Method in class sc.fiji.snt.SNT
-
- set3DViewerResamplingFactor(int) - Method in class sc.fiji.snt.SNTPrefs
-
- setAcronym(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setAliases(String[]) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setAlternateShells(Color, Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setAlternateShells() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setAnalysisScope() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd
-
- setAnimationEnabled(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Toggles the Viewer's animation.
- setAnnotation(BrainAnnotation) - Method in class sc.fiji.snt.util.PointInImage
-
- setAnnotation(BrainAnnotation) - Method in interface sc.fiji.snt.util.SNTPoint
-
Assigns a neuropil annotation (e.g., atlas compartment) to this point.
- setAnnotation(BrainAnnotation) - Method in class sc.fiji.snt.util.SWCPoint
-
- setAnnotationsColor(Color) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- setAnnotationsColorAllPanes(Color) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- setAutoDismiss(JDialog) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- setAWTColor(Color) - Method in class sc.fiji.snt.util.SNTColor
-
Re-assigns a AWT color.
- setAxesVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart
-
- setAxesVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- setAxesVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- setBaseColor(Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setBooleanPrefs(int) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setBottomPaneVisible(boolean) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- setBoundingBox(BoundingBox) - Method in class sc.fiji.snt.Tree
-
Associates a bounding box to this tree.
- setBoundingBoxColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Annotation3D
-
Determines whether the mesh bounding box should be displayed.
- setBoundingBoxColor(ColorRGB) - Method in class sc.fiji.snt.viewer.OBJMesh
-
Determines whether the mesh bounding box should be displayed.
- setBoundingBoxColor(String) - Method in class sc.fiji.snt.viewer.OBJMesh
-
Determines whether the mesh bounding box should be displayed.
- setBounds(float, float, float, float, float, float) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Sets a manual bounding box for the scene.
- setCanvasLabel(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
Sets the string to be rendered on canvas' upper left corner.
- setCanvasLabelAllPanes(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- setCanvasOffset(PointInCanvas) - Method in class sc.fiji.snt.Path
-
Specifies a translation offset when rendering this Path in a
TracerCanvas.
- setCellColorsFromGraph() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- setCenter(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setCenter(double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D
-
- setCenter(int) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
Computes the center of the Profile.
- setCenter(PointInImage) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
Sets the center of the profile.
- setCenter(ShollPoint) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- setCenter(int, int, int) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Sets the analysis center.
- setCenterFromROI() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setCenterFromROI() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd
-
- setCenterPx(int, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setCenterPx(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D
-
- setCenterSource(boolean) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped
-
- setChildren(Set<Path>) - Method in class sc.fiji.snt.Path
-
- setClosedColor(Color) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist
-
- setClosedColor(Color) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist
-
- setClosedColor(Color) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist
-
- setColor(Color) - Method in class sc.fiji.snt.Path
-
Sets this path color.
- setColor(ColorRGB) - Method in class sc.fiji.snt.Path
-
Sets this path color.
- setColor(ColorRGB) - Method in class sc.fiji.snt.Tree
-
Assigns a color to all the paths in this tree.
- setColor(String) - Method in class sc.fiji.snt.Tree
-
Assigns a color to all the paths in this tree.
- setColor(String, double) - Method in class sc.fiji.snt.Tree
-
Assigns a color to all the paths in this tree.
- setColor(Color) - Method in class sc.fiji.snt.util.SWCPoint
-
- setColor(ColorRGB, double) - Method in class sc.fiji.snt.viewer.Annotation3D
-
Assigns a color to the annotation.
- setColor(String, double) - Method in class sc.fiji.snt.viewer.Annotation3D
-
Script friendly method to assign a color to the annotation.
- setColor(String) - Method in class sc.fiji.snt.viewer.Annotation3D
-
Script friendly method to assign a color to the annotation.
- setColor(String, double) - Method in class sc.fiji.snt.viewer.OBJMesh
-
Script friendly method to assign a color to the mesh.
- setColor(ColorRGB, double) - Method in class sc.fiji.snt.viewer.OBJMesh
-
Assigns a color to the mesh.
- setColorBarLegend(String, double, double) - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- setColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- setColorCode(boolean) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped
-
- setColorImage(ImagePlus) - Method in class sc.fiji.snt.SNT
-
Deprecated.
- setColors(String...) - Method in class sc.fiji.snt.analysis.SNTChart
-
(Re)colors existing dataset series
- setColors(ColorTable) - Method in class sc.fiji.snt.analysis.SNTChart
-
(Re)colors existing dataset series
- setColorTable(ColorTable) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped
-
- setCommentString(String) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setConnectComponents(boolean) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
Whether to merge broken components in the skeleton result
- setContext(Context) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
- setContext(Context) - Method in class sc.fiji.snt.analysis.SNTTable
-
Sets a SciJava context to this table.
- setContext(Context) - Static method in class sc.fiji.snt.SNTUtils
-
- setContext(Context) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- setContext(Context) - Method in class sc.fiji.snt.viewer.GraphViewer
-
- setCostType(SNT.CostType) - Method in class sc.fiji.snt.SNT
-
- setCrosshairs(double, double, double, boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
Deprecated.
- setCTposition(int, int) - Method in class sc.fiji.snt.Path
-
Sets the hyperstack position of this Path
- setCurrentFile(File) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- setCurrentPath(Path) - Method in class sc.fiji.snt.SNT
-
- setCursorText(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
Sets the string to be appended to the current cursor.
- setCursorTextAllPanes(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- setDebug(boolean) - Method in class sc.fiji.snt.util.Logger
-
- setDebugMode(boolean) - Static method in class sc.fiji.snt.SNTUtils
-
Enables/disables debug mode
- setDefaultColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Sets the default (fallback) color for plotting paths.
- setDefaultColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Sets the default color for rendering
Trees.
- setDefaultDirectoryForSaveAs(File) - Method in class sc.fiji.snt.analysis.SNTChart
-
- setDefaultThickness(float) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Sets the line thickness for rendering
Trees that have no specified
radius.
- setDefaultTransparency(int) - Method in class sc.fiji.snt.TracerCanvas
-
- setDescription(String) - Method in class sc.fiji.snt.gui.GuiUtils.JTextFieldFile
-
- setDescription(String, boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Associates the analysis with an identifier.
- setDeselectedColor(Color) - Method in class sc.fiji.snt.SNT
-
- setDetailedSummary(boolean) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
Sets whether extensive metrics should be listed when outputting summaries.
- setDimensions(int, int, int) - Method in class sc.fiji.snt.util.BoundingBox
-
Sets the dimensions of this bounding box using uncalibrated (pixel)
lengths.
- setDrawCrosshairs(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- setDrawCrosshairsAllPanes(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- setDrawDiametersXY(boolean) - Method in class sc.fiji.snt.SNT
-
- setDrawingThreshold(double) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist
-
- setDrawingThreshold(double) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist
-
- setEdgeColor(E, ColorRGB) - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- setEdgeColor(AnnotationWeightedEdge, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
-
- setEdgeColor(E, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- setEdgeColor(E, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.SNTPseudographAdapter
-
- setEdgeColor(SWCWeightedEdge, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.TreeGraphAdapter
-
- setEditableNode(int) - Method in class sc.fiji.snt.Path
-
Tags the specified point position as 'editable'.
- setEditableNodeLocked(boolean) - Method in class sc.fiji.snt.Path
-
- setEditingPath(Path) - Method in class sc.fiji.snt.SNT
-
- setEnableCurveFitting(boolean) - Method in class sc.fiji.snt.analysis.ShollAnalyzer
-
Sets whether curve fitting computations should be performed.
- setEnableDarkMode(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Enables/disables "Dark Mode" mode
- setEnableDebugMode(boolean) - Method in class sc.fiji.snt.SNTUI
-
Enables/disables debug mode
- setEnableDebugMode(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Enables/disables debug mode
- setEnabledNone() - Method in class sc.fiji.snt.FillManagerUI
-
- setEnabledWhileFilling() - Method in class sc.fiji.snt.FillManagerUI
-
- setEnabledWhileNotFilling() - Method in class sc.fiji.snt.FillManagerUI
-
- setEnableEdgeLabels(boolean) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- setEnableVertexLabels(boolean) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- setExportPath(String) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- setExportPath(String, boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- setFFromGoal(double) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setFFromStart(double) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setFillList(List<Fill>) - Method in class sc.fiji.snt.FillManagerUI
-
- setFillList(List<Fill>) - Method in class sc.fiji.snt.PathManagerUI
-
- setFillList(List<Fill>) - Method in class sc.fiji.snt.SNT
-
- setFillListVisible(boolean) - Method in class sc.fiji.snt.SNTUI
-
- setFillThreshold(double) - Method in class sc.fiji.snt.SNT
-
Sets the fill threshold distance.
- setFillThresholdFrom(double, double, double) - Method in class sc.fiji.snt.SNT
-
- setFillTransparent(boolean) - Method in class sc.fiji.snt.FillManagerUI
-
- setFillTransparent(boolean) - Method in class sc.fiji.snt.SNT
-
- setFilterType(SNT.FilterType) - Method in class sc.fiji.snt.SNT
-
- setFindAndReplaceMenuItem(JMenuItem) - Method in class sc.fiji.snt.gui.SNTSearchableBar
-
- setFitted(Path) - Method in class sc.fiji.snt.Path
-
- setFittedCircles(int, double[], double[], double[], double[], double[], double[], double[]) - Method in class sc.fiji.snt.Path
-
- setFlag(int) - Method in class sc.fiji.snt.util.ShollPoint
-
- setFont(Font, float, ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Sets the font for label annotations
- setFontSize(float) - Method in class sc.fiji.snt.analysis.SNTChart
-
Sets the font size to all components of this chart.
- setFontSize(float, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Sets the font size for this chart.
- setFrame(int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- setFrameSize(int, int) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Resizes the viewer to the specified dimensions.
- setFrom(double, double, BiSearchNode, boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setFrom(DefaultSearchNode) - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- setFromGoal(double, double, BiSearchNode) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setFromStart(double, double, BiSearchNode) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setGFromGoal(double) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setGFromStart(double) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setGradientShells(Color, Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setGridlinesVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart
-
- setGridlinesVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- setGridlinesVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- setGuessedTangents(int) - Method in class sc.fiji.snt.Path
-
- setGuiUtils(GuiUtils) - Method in class sc.fiji.snt.gui.SNTSearchableBar
-
- setHandle(AddressableHeap.Handle<DefaultSearchNode, Void>) - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- setHeadless(boolean) - Method in class sc.fiji.snt.PathAndFillManager
-
Sets whether this PathAndFillManager instance should run headless.
- setHeapHandle(AddressableHeap.Handle<BiSearchNode, Void>, boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setHeapHandleFromGoal(AddressableHeap.Handle<BiSearchNode, Void>) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setHeapHandleFromStart(AddressableHeap.Handle<BiSearchNode, Void>) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setHemiShells(String) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setHemisphere(Object) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setHemisphere(char) - Method in class sc.fiji.snt.util.PointInImage
-
- setHemisphere(char) - Method in interface sc.fiji.snt.util.SNTPoint
-
- setHeuristicType(SNT.HeuristicType) - Method in class sc.fiji.snt.SNT
-
- setID(int) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setIdentifier(String) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- setIDs(int, int) - Method in class sc.fiji.snt.Path
-
- setImp(ImagePlus) - Method in class sc.fiji.snt.PathFitter
-
Sets the target image
- setInteractiveMode(boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Instructs the plugin to run in headless mode or with user interaction.
- setIsIntDensityProfile(boolean) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- setIsLoading(boolean) - Static method in class sc.fiji.snt.SNTUtils
-
- setIsPrimary(boolean) - Method in class sc.fiji.snt.Path
-
- setLabel(String) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
Sets an identifying label for this subgraph.
- setLabel(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
Sets an identifying label for the group of Trees being analyzed.
- setLabel(String) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Sets a descriptive label to this statistic analysis to be used in histograms,
etc.
- setLabel(String) - Method in class sc.fiji.snt.Tree
-
Sets an identifying label for this Tree.
- setLabel(String) - Method in class sc.fiji.snt.viewer.Annotation3D
-
- setLabel(String) - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- setLabel(String) - Method in class sc.fiji.snt.viewer.OBJMesh
-
- setLabelLocation(float, float) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Sets the location for annotation labels
- setLayoutColumns(int) - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- setLegend(String, double, double) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- setLegend(String, String, double, double) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- setLegend(ColorTable, String, double, double) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- setLengthThreshold(double) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
The minimum component length necessary to avoid pruning.
- setLocationRelativeTo(Component) - Method in class sc.fiji.snt.gui.SNTCommandFinder
-
- setLockCursor(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- setLockCursorAllPanes(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- setLookAndFeel() - Static method in class sc.fiji.snt.gui.GuiUtils
-
- setLookAndFeel(String, boolean, Component...) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- setLookAndFeel(String) - Static method in class sc.fiji.snt.SNTPrefs
-
- setLookAndFeel(String) - Method in class sc.fiji.snt.SNTUI
-
- setLookAndFeel(String) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- setLookAndFeel(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- setMaskBackground(int) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
Sets the background color of the Sholl mask
- setMaskType(int) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
Sets the type of data to be used in Sholl mask.
- setMaxConnectDist(double) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
The maximum allowable distance between nearest neighbors to be considered for a merge
- setMaxEvaluations(int) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Sets the the function evaluation limit for solvers.
- setMaxRadius(int) - Method in class sc.fiji.snt.PathFitter
-
Sets the max radius (side search) for constraining the fit.
- setMetric(ProfileProcessor.Metric) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- setMetric(ProfileProcessor.Metric) - Method in class sc.fiji.snt.analysis.ProfileProcessor
-
Sets the metric to be computed for each local neighborhood.
- setMetric(SNT.CostType) - Method in class sc.fiji.snt.Fill
-
- setMetric(int, boolean) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setMinMax(double, double) - Method in class sc.fiji.snt.analysis.ColorMapper
-
Sets the LUT mapping bounds.
- setMinMax(double, double) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper
-
- setMinMax(double, double) - Method in class sc.fiji.snt.analysis.NodeColorMapper
-
- setMinNBins(int) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Sets the minimum number of bins when assembling histograms.
- setModified(boolean) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- setName(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setName(String) - Method in class sc.fiji.snt.Path
-
Sets this Path's name.
- setNDimensions(int) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- setNodeAnnotation(BrainAnnotation, int) - Method in class sc.fiji.snt.Path
-
Assigns an annotation to an existing node.
- setNodeColor(Color, int) - Method in class sc.fiji.snt.Path
-
Sets the node color.
- setNodeColor(ColorRGB, int) - Method in class sc.fiji.snt.Path
-
Sets the node color.
- setNodeColors(Color[]) - Method in class sc.fiji.snt.Path
-
Sets the node colors.
- setNodeDiameter(double) - Method in class sc.fiji.snt.TracerCanvas
-
Sets the baseline for rendering diameter of path nodes
- setNodeHemisphere(char, int) - Method in class sc.fiji.snt.Path
-
Assigns an hemisphere to an existing node.
- setNodeIndicesAsDistances(boolean) - Method in class sc.fiji.snt.analysis.PathProfiler
-
Sets whether the profile abscissae should be reported in real-word units
(the default) or node indices (zero-based).
- setNodeValue(double, int) - Method in class sc.fiji.snt.Path
-
Assigns the "value" property to this node.
- setNodeValues(double[]) - Method in class sc.fiji.snt.Path
-
Sets the path "values", the array containing the numeric property assigned
to path nodes, typically voxel intensities.
- setNoPlots(boolean) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setNoTable(boolean) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setObjColor(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setObjPath(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setOpacity(double) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist
-
- setOpenColor(Color) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist
-
- setOpenColor(Color) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist
-
- setOpenColor(Color) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist
-
- setOptions(ShollOptions) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Assigns options to the plugin.
- setOrder(int) - Method in class sc.fiji.snt.Path
-
- setOrigin(PointInImage) - Method in class sc.fiji.snt.util.BoundingBox
-
Sets the origin for this box, i.e., its (xMin, yMin, zMin) vertex.
- setOriginOpposite(PointInImage) - Method in class sc.fiji.snt.util.BoundingBox
-
Sets the origin opposite for this box, i.e., its (xMax, yMax, zMax) vertex.
- setOrigIP(ImagePlus) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
Sets the original ImagePlus to be used during voxel-based loop pruning.
- setOutlineVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart
-
- setOutlineVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- setOutlineVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- setOutOfBoundsTransparency(int) - Method in class sc.fiji.snt.TracerCanvas
-
- setPaneOwner(PaneOwner) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- setParent(BrainAnnotation) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setParent(Window) - Method in class sc.fiji.snt.gui.SigmaPalette
-
- setPath(Path) - Method in class sc.fiji.snt.util.PointInImage
-
Associates a Path with this node
- setPathList(List<Path>, Path, boolean) - Method in class sc.fiji.snt.FillManagerUI
-
- setPathList(List<Path>, Path, boolean) - Method in class sc.fiji.snt.PathManagerUI
-
- setPathList(List<Path>, Path, boolean) - Method in class sc.fiji.snt.SNT
-
- setPaths3DDisplay(int) - Method in class sc.fiji.snt.SNT
-
Deprecated.
- setPathUnfinished(boolean) - Method in class sc.fiji.snt.SNT
-
- setPlotLabels(boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Controls the inclusion of fitting details in Sholl plots.
- setPlotLabels(String) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- setPlotOutput(int) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
Sets the flag for output plots.
- setPlugin(SNT) - Static method in class sc.fiji.snt.SNTUtils
-
- setPointsColor(Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setPointsLUT(String, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setPointsLUT(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setPointsLUT(ColorTable, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setPointsOpacity(double) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setPolynomialFitRange(int, int) - Method in class sc.fiji.snt.analysis.ShollAnalyzer
-
Sets the polynomial fit range for linear Sholl statistics.
- setPos(long, long) - Method in class sc.fiji.snt.util.CircleCursor3D
-
- setPosition(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setPosition(int, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D
-
- setPosition(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D
-
- setPosition(int, int, int) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setPrecision(int) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Sets the precision used to calculate metrics from fitted data, such as
Nav and Nm.
- setPrecision(String) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- setPredecessor(DefaultSearchNode) - Method in class sc.fiji.snt.tracing.DefaultSearchNode
-
- setPredecessorFromGoal(BiSearchNode) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setPredecessorFromStart(BiSearchNode) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setPreferredSize(int, int) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Sets the preferred size of the plot to a constant value.
- setPreviousPoint(SWCPoint) - Method in class sc.fiji.snt.util.SWCPoint
-
Sets the preceding node in the reconstruction
- setPrimaryBranches(int) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats
-
Sets the number of primary branches associated with this profile, used to
calculate ramification indices.
- setPrimaryBranches(double) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- setProfile(Profile) - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd
-
- setProgressCallback(int, MultiTaskProgress) - Method in class sc.fiji.snt.PathFitter
-
- setPromptChoice(int, boolean) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setProperties(Properties) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- setPruneByLength(boolean) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
Sets whether or not to prune components below a threshold length from the result.
- setPruneEnds(boolean) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
Sets whether or not to prune branches which end in end-points from the result.
- setPruneMode(int) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
Sets the loop pruning strategy.
- setRadii(double[]) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setRadii(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setRadii(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D
-
- setRadii(double, double, double, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D
-
- setRadii(double[]) - Method in class sc.fiji.snt.Path
-
Assigns radii to this Path
- setRadii(double) - Method in class sc.fiji.snt.Tree
-
Assigns a fixed radius to all the nodes in this tree.
- setRadiiSpan(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D
-
- setRadius(int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- setRadius(int) - Method in class sc.fiji.snt.analysis.ProfileProcessor
-
- setRadius(double) - Method in class sc.fiji.snt.Path
-
Assigns a fixed radius to all the nodes of this Path
- setRadius(double, int) - Method in class sc.fiji.snt.Path
-
- setRecentDir(File) - Method in class sc.fiji.snt.SNTPrefs
-
- setReconstructionViewer(Viewer3D) - Method in class sc.fiji.snt.SNTUI
-
- setReductionFactor(double) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutScaled
-
- setReplaceNodes(boolean) - Method in class sc.fiji.snt.PathFitter
-
Sets whether fitting should occur "in place".
- setRetrieveIntDensities(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setRoot(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Sets the root of the tree.
- setSaveCompressedTraces(boolean) - Method in class sc.fiji.snt.SNTPrefs
-
- setSaveWinLocations(boolean) - Method in class sc.fiji.snt.SNTPrefs
-
- setSceneUpdatesEnabled(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Sets whether the scene should update (refresh) every time a new
reconstruction (or mesh) is added/removed from the scene.
- setSciView(SciView) - Method in class sc.fiji.snt.SciViewSNT
-
Sets the SciView to be used.
- setSciViewSNT(SciViewSNT) - Method in class sc.fiji.snt.SNTUI
-
- setScope(int) - Method in class sc.fiji.snt.PathFitter
-
Sets the fitting scope.
- setSearcheableObjectDescription(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar
-
- setSearchImageType(SNT.SearchImageType) - Method in class sc.fiji.snt.SNT
-
- setSearchType(SNT.SearchType) - Method in class sc.fiji.snt.SNT
-
- setSecondaryImage(File) - Method in class sc.fiji.snt.SNT
-
Specifies the 'secondary image' to be used during a tracing session.
- setSecondaryImageMinMax(float, float) - Method in class sc.fiji.snt.SNT
-
- setSelected(boolean) - Method in class sc.fiji.snt.Path
-
- setSelected(Collection<Path>, Object) - Method in class sc.fiji.snt.PathAndFillManager
-
- setSelectedColor(Color, boolean) - Method in class sc.fiji.snt.gui.ColorChooserButton
-
- setSelectedColor(Color) - Method in class sc.fiji.snt.SNT
-
- setSelectedPaths(Collection<Path>, Object) - Method in class sc.fiji.snt.FillManagerUI
-
- setSelectedPaths(Collection<Path>, Object) - Method in class sc.fiji.snt.PathManagerUI
-
- setSelectedPaths(Collection<Path>, Object) - Method in class sc.fiji.snt.SNT
-
- setSex(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setShape(ProfileProcessor.Shape) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- setShape(ProfileProcessor.Shape) - Method in class sc.fiji.snt.analysis.ProfileProcessor
-
Sets the shape to be iterated.
- setShellsColor(Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setShellsLUT(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setShellsLUT(String, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setShellsLUT(ColorTable, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setShellsOpacity(double) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setShellsThickness(int) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- setShortestPath(boolean) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
Sets whether or not to calculate the longest shortest-path in the skeleton result.
- setShowAnnotatedView(boolean) - Method in class sc.fiji.snt.PathFitter
-
Sets whether an interactive image of the result should be displayed.
- setShowOnlyActiveCTposPaths(boolean, boolean) - Method in class sc.fiji.snt.SNT
-
- setShowOnlySelectedPaths(boolean, boolean) - Method in class sc.fiji.snt.SNT
-
- setShowOnlySelectedPaths(boolean) - Method in class sc.fiji.snt.SNT
-
- setSigmaPaletteListener(SigmaPaletteListener) - Method in class sc.fiji.snt.SNTUI
-
- setSigmas(List<Double>) - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg
-
- setSigmas(List<Double>) - Method in interface sc.fiji.snt.gui.SigmaPaletteListener
-
- setSilent(boolean) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
Setting this to false will display both the tagged skeleton image and the shortest path image (if the
shortest path calculation is enabled).
- setSinglePane(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- setSize(float) - Method in class sc.fiji.snt.viewer.Annotation3D
-
Sets the annotation width.
- setSkipBitmapOptions(boolean) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setSkipSingleVoxels(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D
-
- setSkipSomaticSegments(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
If primary paths start far-away from the soma (expected to be defined by a
single-point (soma centroid)), should segments between the soma and neurite
be ignored.
- setSnapshotDir(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Sets the directory for storing snapshots.
- setSomasDisplayed(Collection<String>, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Toggles the visibility of somas for subset of trees.
- setSomasDisplayed(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Toggles the visibility of somas for all trees in the scene.
- setSortMidLevel(boolean) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped
-
- setSourcePaths(Path[]) - Method in class sc.fiji.snt.Fill
-
- setSourcePaths(Set<Path>) - Method in class sc.fiji.snt.Fill
-
- setSourcePaths(Collection<Path>) - Method in class sc.fiji.snt.tracing.FillerThread
-
- setSpacing(double, double, double, String) - Method in class sc.fiji.snt.Fill
-
- setSpacing(Calibration) - Method in class sc.fiji.snt.Path
-
- setSpacing(double, double, double, String) - Method in class sc.fiji.snt.util.BoundingBox
-
Sets the voxel spacing.
- setSpatialCalibration(Calibration) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- setSpeciesID(int) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setSpineOrVaricosityCount(int) - Method in class sc.fiji.snt.Path
-
- setSplitDendritesFromAxons(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Sets whether axons and dendrites should be imported as separated objects.
- setStartJoin(Path, PointInImage) - Method in class sc.fiji.snt.Path
-
- setState(BiSearchNode.State, boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setStateFromGoal(BiSearchNode.State) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setStateFromStart(BiSearchNode.State) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setStatus(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar
-
- setStatusLabelPlaceholder(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar
-
- setStepRadius(double) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Sets the radius step size (shell spacing).
- setStepSize(double) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
Sets the radius step size.
- setStopAtThreshold(boolean) - Method in class sc.fiji.snt.tracing.FillerThread
-
- setStringPreference(String, double) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setStringPreference(String, int) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setStringPreference(String, String) - Method in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- setStrokeWidth(int) - Method in class sc.fiji.snt.analysis.RoiConverter
-
Sets the line width of converted segment paths.
- setSWCType(int) - Method in class sc.fiji.snt.Path
-
Sets the SWC type.
- setSWCType(int, boolean) - Method in class sc.fiji.snt.Path
-
- setSWCType(String) - Method in class sc.fiji.snt.Tree
-
Assigns an SWC type label to all the Paths in this Tree.
- setSWCType(int) - Method in class sc.fiji.snt.util.SNTColor
-
Re-assigns a SWC type integer flag
- setTable(DefaultGenericTable) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Sets the Analyzer table.
- setTable(DefaultGenericTable, String) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Sets the table.
- setTags(String) - Method in class sc.fiji.snt.util.SWCPoint
-
- setTemp(String, boolean) - Method in class sc.fiji.snt.SNTPrefs
-
- setTemp(String, String) - Method in class sc.fiji.snt.SNTPrefs
-
- setTemporaryPath(Path) - Method in class sc.fiji.snt.SNT
-
- setText(String) - Method in class sc.fiji.snt.gui.GuiUtils.JTextFieldFile
-
- setThreads(int) - Static method in class sc.fiji.snt.SNTPrefs
-
- setThreshold(double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- setThreshold(double) - Method in class sc.fiji.snt.Fill
-
- setThreshold(int, int) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Sets the threshold limits.
- setThreshold(double) - Method in class sc.fiji.snt.tracing.FillerThread
-
- setTitle(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
- setTitle(String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Sets the plot display title.
- setTmpMsgTimeOut(int) - Method in class sc.fiji.snt.gui.GuiUtils
-
- setTransparency(double) - Method in class sc.fiji.snt.viewer.OBJMesh
-
Changes the transparency of this mesh.
- setTreeColor(Collection<String>, String, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Recolors a subset of rendered trees.
- setTreeColor(Collection<String>, ColorRGB, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Recolors a subset of rendered trees.
- setTreeLabel(String) - Method in class sc.fiji.snt.Path
-
- setTreeThickness(Collection<String>, float, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Applies a constant thickness (line width) to a subset of rendered trees.
- setTreeThickness(float) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Applies a constant thickness to all rendered trees.
- setTreeThickness(float, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Applies a constant thickness (line width) to all rendered trees.Note that by
default, trees are rendered using their nodes' diameter.
- setType(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setType(int) - Method in class sc.fiji.snt.Tree
-
Assigns an SWC type label to all the Paths in this Tree.
- setUnit(String) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Sets the unit for sampling distances.
- setUnit(String) - Method in class sc.fiji.snt.util.BoundingBox
-
Sets the default length unit for voxel spacing (typically um, for SWC
reconstructions)
- setUseFitted(boolean) - Method in class sc.fiji.snt.Path
-
Sets whether the fitted flavor of this Path should be used.
- setUseSubVolumeStats(boolean) - Method in class sc.fiji.snt.SNT
-
- setUUID(UUID) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- setValue(int, int, V) - Method in class sc.fiji.snt.tracing.image.ArraySearchImage
-
- setValue(int, int, V) - Method in class sc.fiji.snt.tracing.image.ListSearchImage
-
- setValue(int, int, V) - Method in class sc.fiji.snt.tracing.image.MapSearchImage
-
- setValue(int, int, V) - Method in interface sc.fiji.snt.tracing.image.SearchImage
-
- setVerbose(boolean) - Method in class sc.fiji.snt.analysis.SkeletonConverter
-
- setVerbose(boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- setVertexColor(V, ColorRGB) - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- setVertexColor(BrainAnnotation, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
-
- setVertexColor(V, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- setVertexColor(V, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.SNTPseudographAdapter
-
- setVertexColor(SWCPoint, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.TreeGraphAdapter
-
- setVertexValue(V, double) - Method in class sc.fiji.snt.analysis.graph.SNTGraph
-
- setView(int) - Method in class sc.fiji.snt.analysis.RoiConverter
-
Sets the exporting view for segment paths (XY by default).
- setViewMode(Viewer3D.ViewMode) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Renders the scene from a specified camera angle.
- setViewMode(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Renders the scene from a specified camera angle (script-friendly).
- setViewPoint(double, double) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Renders the scene from a specified camera angle using polar coordinates
relative to the the center of the scene.
- setViewPointCC(double, double) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- setVisible(boolean) - Method in class sc.fiji.snt.gui.SNTCommandFinder
-
- setVisible(String, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Toggles the visibility of a rendered Tree, a loaded OBJ mesh, or an
annotation.
- setVolume(double) - Method in class sc.fiji.snt.viewer.OBJMesh
-
- setWidth(int) - Method in class sc.fiji.snt.analysis.PathStraightener
-
- setX(int) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setY(int) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setZ(int) - Method in class sc.fiji.snt.tracing.BiSearchNode
-
- setZFudge(double) - Method in class sc.fiji.snt.tracing.cost.OneMinusErf
-
Scale factor for intensity z-score.
- setZoom(double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- setZPositionAllPanes(int, int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- SHELL - Static variable in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- Sholl_Analysis - Class in sc.fiji.snt.plugin.ij1
-
- Sholl_Analysis() - Constructor for class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- SHOLL_COUNTS - Static variable in class sc.fiji.snt.analysis.TreeColorMapper
-
Flag for "Sholl inters. (root centered)" mapping.
- SHOLL_LOG - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- SHOLL_N - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- SHOLL_NS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- SHOLL_SLOG - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- Sholl_Utils - Class in sc.fiji.snt.plugin.ij1
-
- Sholl_Utils() - Constructor for class sc.fiji.snt.plugin.ij1.Sholl_Utils
-
Deprecated.
- ShollAnalysisBulkTreeCmd - Class in sc.fiji.snt.plugin
-
- ShollAnalysisBulkTreeCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisBulkTreeCmd
-
- ShollAnalysisDialog - Class in sc.fiji.snt.gui
-
Deprecated.
- ShollAnalysisDialog(double, double, double, SNT) - Constructor for class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- ShollAnalysisDialog.ShollPoint - Class in sc.fiji.snt.gui
-
Deprecated.
- ShollAnalysisDialog.ShollResults - Class in sc.fiji.snt.gui
-
Deprecated.
- ShollAnalysisImgCmd - Class in sc.fiji.snt.plugin
-
Implements the Analyze:Sholl:Sholl Analysis (From Image)...
- ShollAnalysisImgCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisImgCmd
-
- ShollAnalysisPlugin - Class in sc.fiji.snt.plugin.ij1
-
Deprecated.
- ShollAnalysisPlugin() - Constructor for class sc.fiji.snt.plugin.ij1.ShollAnalysisPlugin
-
Deprecated.
- ShollAnalysisPrefsCmd - Class in sc.fiji.snt.plugin
-
Implements the "Sholl Options" command
- ShollAnalysisPrefsCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd
-
- ShollAnalysisTreeCmd - Class in sc.fiji.snt.plugin
-
Implements SNT's commands for Sholl Analysis of
Trees.
- ShollAnalysisTreeCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisTreeCmd
-
- ShollAnalyzer - Class in sc.fiji.snt.analysis
-
Class to retrieve Sholl metrics from a
Tree.
- ShollAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.ShollAnalyzer
-
Instantiates a new Sholl analyzer using default settings, i.e., focused on
Tree's root; using sampling step size of average inter-node distance; curve
fitting enabled; and all other parameters left to defaults/auto-discovery.
- ShollOptions - Class in sc.fiji.snt.plugin.ij1
-
Deprecated.
- ShollOptions(boolean) - Constructor for class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- ShollOptions() - Constructor for class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- ShollOverlay - Class in sc.fiji.snt.analysis.sholl.gui
-
- ShollOverlay(Profile) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- ShollOverlay(Profile, ImagePlus) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- ShollOverlay(Profile, ImagePlus, boolean) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- ShollPlot - Class in sc.fiji.snt.analysis.sholl.gui
-
- ShollPlot(String, String, String) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
Constructs a new empty Plot.
- ShollPlot(Profile) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- ShollPlot(ShollStats) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- ShollPlot(ShollStats, boolean) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- ShollPlot(Profile...) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- ShollPlot(String, String, String, ShollStats, boolean, boolean) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- ShollPoint - Class in sc.fiji.snt.util
-
Convenience flavor of
PointInImage defining 2D/3D points for Sholll Analysis.
- ShollPoint(PointInImage) - Constructor for class sc.fiji.snt.util.ShollPoint
-
- ShollPoint(double, double, double) - Constructor for class sc.fiji.snt.util.ShollPoint
-
- ShollPoint(double, double) - Constructor for class sc.fiji.snt.util.ShollPoint
-
- ShollPoint(int, int, int, Calibration) - Constructor for class sc.fiji.snt.util.ShollPoint
-
- ShollPoint(int, int, Calibration) - Constructor for class sc.fiji.snt.util.ShollPoint
-
- ShollPoint(int, int, int, int) - Constructor for class sc.fiji.snt.util.ShollPoint
-
- ShollResults(List<ShollAnalysisDialog.ShollPoint>, ImagePlus, boolean, int, double, double, double, String, int, int, double, boolean) - Constructor for class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- ShollStats - Interface in sc.fiji.snt.analysis.sholl.math
-
Methods and constants common to Profile analyzers.
- ShollTable - Class in sc.fiji.snt.analysis.sholl.gui
-
Implementation of
SNTTable for Sholl metrics and Profile lists.
- ShollTable() - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
Instantiates a new empty table.
- ShollTable(Profile) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
Instantiates a new table from a
Profile
- ShollTable(ShollStats...) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
- ShollUtils - Class in sc.fiji.snt.analysis.sholl
-
Static utilities.
- ShortcutWindowCmd - Class in sc.fiji.snt.gui.cmds
-
A command that displays a shortcut window of most popular commands, inspired
by the Bio-Formats Plugins Shortcut Window.
- ShortcutWindowCmd() - Constructor for class sc.fiji.snt.gui.cmds.ShortcutWindowCmd
-
- show() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph
-
Displays this graph in a new instance of SNT's "Dendrogram Viewer".
- show() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Displays this graph in a new instance of SNT's "Dendrogram Viewer".
- show() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
Displays this graph in a new instance of SNT's "Dendrogram Viewer".
- show(DirectedWeightedGraph) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils
-
Displays a graph in SNT's "Dendrogram Viewer" featuring UI commands for
interactive visualization and export options.
- show(int, int) - Method in class sc.fiji.snt.analysis.SNTChart
-
- show() - Method in class sc.fiji.snt.analysis.SNTChart
-
- show() - Method in class sc.fiji.snt.Tree
-
- show() - Method in class sc.fiji.snt.viewer.GraphViewer
-
Displays a graph in SNT's "Graph Viewer" featuring UI commands for
interactive visualization and export options.
- show() - Method in class sc.fiji.snt.viewer.MultiViewer2D
-
- show() - Method in class sc.fiji.snt.viewer.Viewer2D
-
Displays the current plot on a dedicated frame
- show() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Displays the Viewer and returns a reference to its frame.
- show(int, int) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Displays the viewer under specified dimensions.
- show2D() - Method in class sc.fiji.snt.Tree
-
- show3D() - Method in class sc.fiji.snt.Tree
-
- SHOW_MASK - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- SHOW_SEARCH_OPTIONS - Static variable in class sc.fiji.snt.gui.SNTSearchableBar
-
- ShowCorrespondencesCmd - Class in sc.fiji.snt.gui.cmds
-
Command for highlighting the correspondences between two reconstructions in
the Legacy 3D Viewer
- ShowCorrespondencesCmd() - Constructor for class sc.fiji.snt.gui.cmds.ShowCorrespondencesCmd
-
- showCorrespondencesTo(File, Color, double) - Method in class sc.fiji.snt.SNT
-
Deprecated.
- showGraphPopupMenu(MouseEvent) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- showHTMLDialog(String, String) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- showHTMLDialog(String, String, boolean) - Method in class sc.fiji.snt.gui.GuiUtils
-
- showMessage(String, String) - Method in class sc.fiji.snt.SNT
-
- showMessage(String, String) - Method in class sc.fiji.snt.SNTUI
-
- showMIPOverlays(double) - Method in class sc.fiji.snt.SNT
-
Overlays a semi-transparent MIP (8-bit scaled) of the data being traced
over the tracing canvas(es).
- showMIPOverlays(boolean, double) - Method in class sc.fiji.snt.SNT
-
- showMouseThreshold(double) - Method in class sc.fiji.snt.FillManagerUI
-
- showOnlyActiveCTposPaths - Variable in class sc.fiji.snt.SNT
-
- showOnlySelectedPaths - Variable in class sc.fiji.snt.SNT
-
- showOutlinePopupMenu(MouseEvent) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- showPartsNearby - Variable in class sc.fiji.snt.SNTUI
-
- showPlot() - Method in class sc.fiji.snt.viewer.Viewer2D
-
- showProgress(int, int) - Method in class sc.fiji.snt.viewer.Viewer3D.ManagerPanel
-
Updates the progress bar.
- showScrollableDialog() - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Adds AWT scroll bars to the dialog before displaying it, when not running
headless.
- showStatus(int, int, String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- showStatus(int, int, String) - Method in interface sc.fiji.snt.hyperpanes.PaneOwner
-
- showStatus(int, int, String) - Method in class sc.fiji.snt.SNT
-
- showStatus(String, boolean) - Method in class sc.fiji.snt.SNTUI
-
Updates the status bar.
- SigmaPalette - Class in sc.fiji.snt.gui
-
Implements SNT 'Sigma wizard'.
- SigmaPalette(SNT) - Constructor for class sc.fiji.snt.gui.SigmaPalette
-
- SigmaPaletteListener - Interface in sc.fiji.snt.gui
-
- SigmaUtils - Class in sc.fiji.snt.util
-
- similarCalibrations(Calibration, Calibration) - Static method in class sc.fiji.snt.SNTUtils
-
- single_pane - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- singleSlice - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- size() - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- size() - Method in class sc.fiji.snt.Path
-
Returns the number of nodes of this path
- size() - Method in class sc.fiji.snt.PathAndFillManager
-
Returns the number of Paths in the PathAndFillManager list.
- size() - Method in class sc.fiji.snt.tracing.image.SearchImageStack
-
- size() - Method in class sc.fiji.snt.Tree
-
Retrieves the number of paths in this tree.
- SkeletonConverter - Class in sc.fiji.snt.analysis
-
Class for generation of
Trees from a skeletonized
ImagePlus.
- SkeletonConverter(ImagePlus) - Constructor for class sc.fiji.snt.analysis.SkeletonConverter
-
- SkeletonConverter(ImagePlus, boolean) - Constructor for class sc.fiji.snt.analysis.SkeletonConverter
-
- SkeletonConverterCmd - Class in sc.fiji.snt.plugin
-
- SkeletonConverterCmd() - Constructor for class sc.fiji.snt.plugin.SkeletonConverterCmd
-
- skeletonize(ImagePlus) - Static method in class sc.fiji.snt.analysis.SkeletonConverter
-
Convenience method to skeletonize an 8-bit image using
Skeletonize3D_.
- skeletonize(ImagePlus, int) - Method in class sc.fiji.snt.Tree
-
Skeletonizes (rasterizes) this tree on the specified image using Bresenham’s
Algorithm (3D).
- SkeletonizerCmd - Class in sc.fiji.snt.plugin
-
Convenience command for converting Paths into skeleton images
- SkeletonizerCmd() - Constructor for class sc.fiji.snt.plugin.SkeletonizerCmd
-
- SKEWNESS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- SKIP_BITMAP_OPTIONS_LABEL - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- SKIP_SINGLE_VOXELS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- smallButton(String) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- snapCursor - Variable in class sc.fiji.snt.SNT
-
- snapWindowXYsizeSpinner - Variable in class sc.fiji.snt.SNTUI
-
- snapWindowZsizeSpinner - Variable in class sc.fiji.snt.SNTUI
-
- snt - Variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd
-
- SNT - Class in sc.fiji.snt
-
Implements the SNT plugin.
- SNT(Context, ImagePlus) - Constructor for class sc.fiji.snt.SNT
-
Instantiates SNT in 'Tracing Mode'.
- SNT(Context, PathAndFillManager) - Constructor for class sc.fiji.snt.SNT
-
Instantiates SNT in 'Analysis Mode'
- SNT.CostType - Enum in sc.fiji.snt
-
- SNT.FilterType - Enum in sc.fiji.snt
-
- SNT.HeuristicType - Enum in sc.fiji.snt
-
- SNT.SearchImageType - Enum in sc.fiji.snt
-
- SNT.SearchType - Enum in sc.fiji.snt
-
- SNT_PAUSED - Static variable in class sc.fiji.snt.SNTUI
-
Flag specifying all SNT are temporarily disabled (all user interactions are
waived back to ImageJ)
- SNTChart - Class in sc.fiji.snt.analysis
-
Extension of
ChartFrame with convenience methods for plot annotations.
- SNTChart(String, JFreeChart) - Constructor for class sc.fiji.snt.analysis.SNTChart
-
- SNTChart(String, XYPlot) - Constructor for class sc.fiji.snt.analysis.SNTChart
-
- SNTChart(String, CategoryChart<?>) - Constructor for class sc.fiji.snt.analysis.SNTChart
-
- SNTChart(String, JFreeChart, Dimension) - Constructor for class sc.fiji.snt.analysis.SNTChart
-
- SNTColor - Class in sc.fiji.snt.util
-
A simple class for handling Colors including the ability to map an AWT Color
to a SWC type integer tag.
- SNTColor(Color, int) - Constructor for class sc.fiji.snt.util.SNTColor
-
Instantiates a new SNT color.
- SNTColor(Color) - Constructor for class sc.fiji.snt.util.SNTColor
-
Instantiates a new SNT color without SWC type association
- SNTCommandFinder - Class in sc.fiji.snt.gui
-
- SNTCommandFinder(SNTUI) - Constructor for class sc.fiji.snt.gui.SNTCommandFinder
-
- SNTCommandFinder() - Constructor for class sc.fiji.snt.gui.SNTCommandFinder
-
- SNTEvent - Class in sc.fiji.snt.event
-
- SNTEvent(int) - Constructor for class sc.fiji.snt.event.SNTEvent
-
- SNTGraph<V,E extends org.jgrapht.graph.DefaultWeightedEdge> - Class in sc.fiji.snt.analysis.graph
-
- SNTGraph(Supplier<V>, Supplier<E>, GraphType) - Constructor for class sc.fiji.snt.analysis.graph.SNTGraph
-
- SNTGraphAdapter<V,E extends org.jgrapht.graph.DefaultWeightedEdge> - Class in sc.fiji.snt.viewer.geditor
-
- SNTGraphAdapter(SNTGraph<V, E>) - Constructor for class sc.fiji.snt.viewer.geditor.SNTGraphAdapter
-
- SNTGraphComponent - Class in sc.fiji.snt.viewer.geditor
-
- SNTGraphComponent(SNTGraphAdapter<?, ? extends DefaultWeightedEdge>, Context) - Constructor for class sc.fiji.snt.viewer.geditor.SNTGraphComponent
-
- SNTListener - Interface in sc.fiji.snt.event
-
- SNTLoaderCmd - Class in sc.fiji.snt.gui.cmds
-
Command for Launching SNT
- SNTLoaderCmd() - Constructor for class sc.fiji.snt.gui.cmds.SNTLoaderCmd
-
- SNTPoint - Interface in sc.fiji.snt.util
-
Classes extend this interface implement a point in a 3D space, always using
real world coordinates.
- SNTPrefs - Class in sc.fiji.snt
-
Class handling SNT preferences.
- SNTPrefs(SNT) - Constructor for class sc.fiji.snt.SNTPrefs
-
- SNTPseudograph<V,E extends org.jgrapht.graph.DefaultWeightedEdge> - Class in sc.fiji.snt.analysis.graph
-
- SNTPseudograph(Class<? extends E>) - Constructor for class sc.fiji.snt.analysis.graph.SNTPseudograph
-
- SNTPseudographAdapter<V,E extends org.jgrapht.graph.DefaultWeightedEdge> - Class in sc.fiji.snt.viewer.geditor
-
- SNTPseudographAdapter(SNTPseudograph<V, E>) - Constructor for class sc.fiji.snt.viewer.geditor.SNTPseudographAdapter
-
- SNTPseudographComponent - Class in sc.fiji.snt.viewer.geditor
-
- SNTPseudographComponent(SNTPseudographAdapter<?, ? extends DefaultWeightedEdge>, Context) - Constructor for class sc.fiji.snt.viewer.geditor.SNTPseudographComponent
-
- SNTSearchableBar - Class in sc.fiji.snt.gui
-
Implements a SearchableBar following SNT's UI.
- SNTSearchableBar(Searchable) - Constructor for class sc.fiji.snt.gui.SNTSearchableBar
-
- SNTSearchableBar(Searchable, String) - Constructor for class sc.fiji.snt.gui.SNTSearchableBar
-
- sntService - Variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd
-
- sntService - Variable in class sc.fiji.snt.gui.cmds.PrefsCmd
-
- SNTService - Class in sc.fiji.snt
-
Service for accessing and scripting the active instance of
SNT.
- SNTService() - Constructor for class sc.fiji.snt.SNTService
-
- SNTTable - Class in sc.fiji.snt.analysis
-
Extension of DefaultGenericTable with (minor) scripting conveniences.
- SNTTable() - Constructor for class sc.fiji.snt.analysis.SNTTable
-
- SNTTable(String) - Constructor for class sc.fiji.snt.analysis.SNTTable
-
- SNTUI - Class in sc.fiji.snt
-
Implements SNT's main dialog.
- SNTUI(SNT) - Constructor for class sc.fiji.snt.SNTUI
-
- SNTUtils - Class in sc.fiji.snt
-
Static utilities for SNT
- SOMA - Static variable in class sc.fiji.snt.io.MouseLightLoader
-
The Constant SOMA.
- SOMATIC - Static variable in interface sc.fiji.snt.TreeProperties
-
- somehowJoins - Variable in class sc.fiji.snt.Path
-
- somehowJoinsAsString() - Method in class sc.fiji.snt.Path
-
- sortedMappedTrees() - Method in class sc.fiji.snt.analysis.MultiTreeColorMapper
-
- sortVertices() - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped
-
- sortVertices(Object[], String) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutSorted
-
- source() - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- spacing_units - Variable in class sc.fiji.snt.Fill
-
- spacing_units - Variable in class sc.fiji.snt.Path
-
- spacing_units - Variable in class sc.fiji.snt.SNT
-
- spacing_units - Variable in class sc.fiji.snt.tracing.AbstractSearch
-
- spacing_units - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer
-
- spacingUnit - Variable in class sc.fiji.snt.util.BoundingBox
-
- spatialCalibration() - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- SPHERE - Static variable in class sc.fiji.snt.analysis.PathProfiler
-
- SpineExtractorCmd - Class in sc.fiji.snt.plugin
-
Command for obtaining spine/varicosity counts from multi-point ROIs
- SpineExtractorCmd() - Constructor for class sc.fiji.snt.plugin.SpineExtractorCmd
-
- splitByHemisphere(DirectedWeightedGraph) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- splitIntoBlocks(RandomAccessibleInterval<T>, long[]) - Static method in class sc.fiji.snt.util.ImgUtils
-
Partition the source rai into a list of
IntervalView with given dimensions.
- SRC_IMG - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties
-
- SRC_TABLE - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties
-
- SRC_TRACES - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties
-
- start - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- START_RADIUS_KEY - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- start_x - Variable in class sc.fiji.snt.tracing.BiSearch
-
- start_x_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer
-
- start_y - Variable in class sc.fiji.snt.tracing.BiSearch
-
- start_y_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer
-
- start_z - Variable in class sc.fiji.snt.tracing.BiSearch
-
- start_z_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer
-
- startBallName - Static variable in class sc.fiji.snt.SNT
-
- started_at - Variable in class sc.fiji.snt.tracing.SearchThread
-
- startElement(String, String, String, Attributes) - Method in class sc.fiji.snt.PathAndFillManager
-
- startFilling() - Method in class sc.fiji.snt.SNT
-
- STARTING_RADIUS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- startJoins - Variable in class sc.fiji.snt.Path
-
- startJoinsPoint - Variable in class sc.fiji.snt.Path
-
- startRadius() - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- startRadiusStepSizeChanged() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd
-
- startSholl(PointInImage) - Method in class sc.fiji.snt.SNT
-
- startUI() - Method in class sc.fiji.snt.SNT
-
- status(String, boolean) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd
-
- status(String) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- status(String, boolean) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- statusBar - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- statusService - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- statusService - Variable in class sc.fiji.snt.analysis.TreeAnalyzer
-
- statusService - Variable in class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd
-
- statusService - Variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd
-
- statusService - Variable in class sc.fiji.snt.SNT
-
- STEP_SIZE_KEY - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- stepSize() - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- stopBeingEdited() - Method in class sc.fiji.snt.Path
-
- stopFilling() - Method in class sc.fiji.snt.SNT
-
- STRAHLER_NUMBER - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper
-
- STRAHLER_NUMBER - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- STRAHLER_NUMBER - Static variable in class sc.fiji.snt.analysis.TreeColorMapper
-
Flag for "Horton-Strahler number" mapping.
- STRAHLER_RATIO - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- StrahlerAnalyzer - Class in sc.fiji.snt.analysis
-
Class to perform Horton-Strahler analysis on a
Tree.
- StrahlerAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.StrahlerAnalyzer
-
- StrahlerCmd - Class in sc.fiji.snt.plugin
-
Command to perform Horton-Strahler analysis on a
Tree.
- StrahlerCmd() - Constructor for class sc.fiji.snt.plugin.StrahlerCmd
-
Instantiates a new StrahlerCmd.
- StrahlerCmd(Tree) - Constructor for class sc.fiji.snt.plugin.StrahlerCmd
-
Instantiates a new StrahlerCmd.
- straighten() - Method in class sc.fiji.snt.analysis.PathStraightener
-
- straighten(int) - Method in class sc.fiji.snt.analysis.PathStraightener
-
- stringPrefs - Variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- stringToColor(String) - Static method in class sc.fiji.snt.util.SNTColor
-
Returns an AWT Color from a (#)RRGGBB(AA) hex string.
- STRIP - Static variable in class sc.fiji.snt.viewer.Annotation3D
-
- stripExtension(String) - Static method in class sc.fiji.snt.SNTUtils
-
- subgraph - Variable in class sc.fiji.snt.analysis.graph.GraphColorMapper
-
- subTree(String...) - Method in class sc.fiji.snt.Tree
-
Extracts the subset of paths matching the specified criteria (script friendly
method)
- subTree(int...) - Method in class sc.fiji.snt.Tree
-
Extracts the subset of paths matching the specified criteria.
- subVolume(RandomAccessibleInterval<T>, long, long, long, long, long, long, int) - Static method in class sc.fiji.snt.util.ImgUtils
-
Get a 3D sub-volume of an image, given two corner points and specified padding.
- succeeded() - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- SUCCESS - Static variable in class sc.fiji.snt.tracing.SearchThread
-
- successful() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser
-
- successful() - Method in interface sc.fiji.snt.analysis.sholl.parsers.Parser
-
- successful() - Method in class sc.fiji.snt.analysis.sholl.parsers.TabularParser
-
- successful() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser
-
- SUM - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer
-
- SUM_INTERS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- sumEdgeWeights() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph
-
Gets the sum of all edge weights.
- sumEdgeWeights() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
Gets the sum of all edge weights.
- sumEdgeWeights(boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
-
Gets the sum of all edge weights.
- summarize(ShollTable, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
- summarize(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable
-
- summarize(boolean) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Outputs a summary of the current analysis to the Analyzer table using the
default Tree label.
- summarize(String, boolean) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Outputs a summary of the current analysis to the Analyzer table.
- SupplierUtil - Class in sc.fiji.snt.tracing.image
-
- SupplierUtil.ArraySearchImageSupplier<V extends SearchNode> - Class in sc.fiji.snt.tracing.image
-
- SupplierUtil.ListSearchImageSupplier<V extends SearchNode> - Class in sc.fiji.snt.tracing.image
-
- SupplierUtil.MapSearchImageSupplier<V extends SearchNode> - Class in sc.fiji.snt.tracing.image
-
- SURFACE - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
Flag for surface normalization (Semi-log/Log-log method)
- SURFACE - Static variable in class sc.fiji.snt.viewer.Annotation3D
-
- SURFACE_AND_VOLUME - Static variable in class sc.fiji.snt.viewer.Annotation3D
-
- swapAxes(int, int) - Method in class sc.fiji.snt.Tree
-
Swaps the coordinates of two axes in this Tree.
- SWC_APICAL_DENDRITE - Static variable in class sc.fiji.snt.Path
-
Flag specifying the SWC type 'apical dendrite'.
- SWC_APICAL_DENDRITE_LABEL - Static variable in class sc.fiji.snt.Path
-
- SWC_AXON - Static variable in class sc.fiji.snt.Path
-
Flag specifying the SWC type 'axon'.
- SWC_AXON_LABEL - Static variable in class sc.fiji.snt.Path
-
- SWC_CUSTOM - Static variable in class sc.fiji.snt.Path
-
Flag specifying the SWC type 'custom'.
- SWC_CUSTOM_LABEL - Static variable in class sc.fiji.snt.Path
-
- SWC_DENDRITE - Static variable in class sc.fiji.snt.Path
-
Flag specifying the SWC type '(basal) dendrite'.
- SWC_DENDRITE_LABEL - Static variable in class sc.fiji.snt.Path
-
- SWC_END_POINT - Static variable in class sc.fiji.snt.Path
-
Deprecated.
- SWC_END_POINT_LABEL - Static variable in class sc.fiji.snt.Path
-
- SWC_FORK_POINT - Static variable in class sc.fiji.snt.Path
-
Deprecated.
- SWC_FORK_POINT_LABEL - Static variable in class sc.fiji.snt.Path
-
- SWC_SOMA - Static variable in class sc.fiji.snt.Path
-
Flag specifying the SWC type 'soma'.
- SWC_SOMA_LABEL - Static variable in class sc.fiji.snt.Path
-
- SWC_TYPE_IGNORED - Static variable in class sc.fiji.snt.util.SNTColor
-
- SWC_UNDEFINED - Static variable in class sc.fiji.snt.Path
-
Flag specifying the SWC type 'undefined'.
- SWC_UNDEFINED_LABEL - Static variable in class sc.fiji.snt.Path
-
- SWCImportOptionsDialog - Class in sc.fiji.snt.gui
-
Implements a dialog for importing SWC files into SNT with advanced options.
- SWCImportOptionsDialog(JDialog, String) - Constructor for class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- SWCPoint - Class in sc.fiji.snt.util
-
Defines a node in an SWC reconstruction.
- SWCPoint(int, int, double, double, double, double, int) - Constructor for class sc.fiji.snt.util.SWCPoint
-
- SWCTypeFilterCmd - Class in sc.fiji.snt.gui.cmds
-
- SWCTypeFilterCmd() - Constructor for class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd
-
- SWCTypeOptionsCmd - Class in sc.fiji.snt.gui.cmds
-
- SWCTypeOptionsCmd() - Constructor for class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd
-
- SWCWeightedEdge - Class in sc.fiji.snt.analysis.graph
-
An extremely simple implementation of a weighted edge for Tree:Directed
Graph conversions.
- SWCWeightedEdge() - Constructor for class sc.fiji.snt.analysis.graph.SWCWeightedEdge
-
- SwingSafeResult - Class in sc.fiji.snt.gui
-
Utility class that ensures EDT execution.
- SwingSafeResult() - Constructor for class sc.fiji.snt.gui.SwingSafeResult
-
- symDifference(AnnotationGraph, AnnotationGraph) - Static method in class sc.fiji.snt.analysis.graph.AnnotationGraphUtils
-
- syncPathManagerList() - Method in class sc.fiji.snt.SciViewSNT
-
(Re)loads the current list of Paths in the Path Manager list.
- syncPathManagerList() - Method in class sc.fiji.snt.viewer.Viewer3D
-
(Re)loads the current list of Paths in the Path Manager list.
- syncSpatialSettingsWithPlugin() - Method in class sc.fiji.snt.PathAndFillManager
-