| Package | Description |
|---|---|
| sc.fiji.snt |
SNT core classes
|
| sc.fiji.snt.analysis |
Analysis of
Trees. |
| sc.fiji.snt.analysis.graph |
Classes for handling neuronal reconstructions as graphs
|
| sc.fiji.snt.gui |
Customizations and commands for SNT's GUI.
|
| sc.fiji.snt.tracing | |
| sc.fiji.snt.util |
Miscellaneous SNT utilities, including classes defining reconstruction nodes.
|
| Modifier and Type | Field and Description |
|---|---|
protected Path |
SNT.currentPath |
protected Path |
Path.fitted |
protected Path |
Path.fittedVersionOf |
protected Path |
Path.startJoins |
protected Path |
SNT.temporaryPath |
| Modifier and Type | Field and Description |
|---|---|
protected ArrayList<Path> |
Path.children |
protected ArrayList<Path> |
Path.somehowJoins |
| Modifier and Type | Method and Description |
|---|---|
Path |
SNT.autoTrace(List<SNTPoint> pointList,
PointInImage forkPoint)
Automatically traces a path from a list of points and adds it to the active
PathAndFillManager instance. |
Path |
SNT.autoTrace(List<SNTPoint> pointList,
PointInImage forkPoint,
boolean headless) |
Path |
SNT.autoTrace(SNTPoint start,
SNTPoint end,
PointInImage forkPoint)
Automatically traces a path from a point A to a point B.
|
Path |
SNT.autoTrace(SNTPoint start,
SNTPoint end,
PointInImage forkPoint,
boolean headless) |
Path |
PathFitter.call()
Takes the signal from the image specified in the constructor to fit
cross-section circles around the nodes of input path.
|
Path |
Path.clone() |
Path |
Path.clone(boolean includeImmediateChildren) |
Path |
Path.createPath()
Returns a new Path with this Path's attributes (e.g.
|
Path |
Tree.get(int index)
Returns the Path at the specified position.
|
Path |
SNT.getCurrentPath() |
protected Path |
SNT.getEditingPath() |
Path |
Path.getFitted()
Gets the fitted version ('flavor') of this Path.
|
Path |
PathFitter.getPath() |
Path |
NearPoint.getPath() |
Path |
PathAndFillManager.getPath(int i)
Returns the Path at the specified position in the PathAndFillManager list.
|
protected Path |
PathAndFillManager.getPathFrom3DViewerName(String name) |
Path |
PathAndFillManager.getPathFromID(int id)
Returns the Path with the specified id.
|
Path |
PathAndFillManager.getPathFromName(String name,
boolean caseSensitive)
Returns the Path with the specified name.
|
Path[] |
PathAndFillManager.getPathsStructured() |
Path[] |
PathAndFillManager.getPathsStructured(Collection<Path> paths) |
protected Path |
SNT.getPreviousEditingPath() |
Path |
Path.getSection(int startIndex,
int endIndex)
Gets a section between two nodes of this Path.
|
protected Path |
SNT.getSingleSelectedPath() |
Path |
Path.getStartJoins() |
Path |
Path.reversed() |
Path |
Path.transform(PathTransformer transformation,
ij.ImagePlus template,
ij.ImagePlus model) |
| Modifier and Type | Method and Description |
|---|---|
protected List<Path> |
PathAndFillManager.getAllPathsRenderedInViewPort(TracerCanvas canvas) |
ArrayList<Path> |
Path.getChildren() |
List<Path> |
SNTService.getPaths()
Gets the paths currently listed in the Path Manager
|
ArrayList<Path> |
PathAndFillManager.getPaths()
Returns all the paths.
|
List<Path> |
PathAndFillManager.getPathsFiltered()
Returns the 'de facto' Paths.
|
Collection<Path> |
PathAndFillManager.getPathsInROI(Roi roi) |
Collection<Path> |
SNTService.getSelectedPaths()
Gets the paths currently selected in the Path Manager list.
|
Collection<Path> |
SNT.getSelectedPaths() |
Set<Path> |
PathAndFillManager.getSelectedPaths()
Gets all paths selected in the GUI
|
List<Path> |
PathManagerUI.getSelectedPaths(boolean ifNoneSelectedGetAll)
Gets the paths currently selected in the Manager's
JTree list. |
protected List<Path> |
PathAndFillManager.getSelectedPathsRenderedInViewPort(TracerCanvas canvas) |
Set<Path> |
Fill.getSourcePaths() |
protected List<Path> |
PathAndFillManager.getUnSelectedPathsRenderedInViewPort(TracerCanvas canvas) |
ArrayList<Path> |
Tree.list()
Gets all the paths from this tree.
|
static List<Path> |
SNTUtils.randomPaths()
Generates a list of random paths.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
Tree.add(Path p)
Adds a new Path to this Tree.
|
void |
Path.add(Path other) |
void |
PathAndFillManager.addPath(Path p)
Adds a new path.
|
void |
PathAndFillManager.addPath(Path p,
boolean retainTags) |
void |
PathAndFillManager.addPath(Path p,
boolean forceNewName,
boolean forceNewId) |
protected void |
PathAndFillManager.addPath(Path p,
boolean forceNewName,
boolean forceNewId,
boolean assumeMaxUsedTreeID) |
void |
PathAndFillManager.addPath(Path p,
int id,
int treeID) |
int |
Path.compareTo(Path o) |
boolean |
PathAndFillManager.deletePath(Path p)
Deletes a path.
|
protected boolean |
PathAndFillManager.exportAllPathsAsSWC(Path[] primaryPaths,
String baseFilename) |
protected boolean |
PathAndFillManager.exportConnectedStructureAsSWC(Path primaryPath,
File swcFile) |
static String |
PathManagerUI.extractTagsFromPath(Path p) |
protected String |
PathAndFillManager.getDefaultName(Path p) |
int |
PathAndFillManager.getPathIndex(Path p)
Gets the index of a Path.
|
int |
Tree.indexOf(Path path)
Returns the index of the specified Path in this Tree.
|
boolean |
Path.isConnectedTo(Path other) |
boolean |
PathAndFillManager.isSelected(Path path)
Checks if a Path is currently selected in the GUI.
|
boolean |
Tree.remove(Path p)
Removes a path from this tree.
|
protected void |
SNT.replaceCurrentPath(Path path) |
void |
PathAndFillManager.resetListeners(Path justAdded) |
protected void |
PathAndFillManager.resetListeners(Path justAdded,
boolean expandAll) |
void |
SNT.selectPath(Path p,
boolean addToExistingSelection) |
void |
SNT.setCurrentPath(Path path) |
protected void |
SNT.setEditingPath(Path path) |
protected void |
Path.setFitted(Path p) |
void |
SNT.setPathList(List<Path> pathList,
Path justAdded,
boolean expandAll) |
void |
PathManagerUI.setPathList(List<Path> pathList,
Path justAdded,
boolean expandAll) |
void |
FillManagerUI.setPathList(List<Path> pathList,
Path justAdded,
boolean expandAll) |
void |
Fill.setSourcePaths(Path[] newSourcePaths) |
void |
Path.setStartJoin(Path other,
PointInImage joinPoint) |
void |
SNT.setTemporaryPath(Path path) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
PathAndFillManager.deletePaths(Collection<Path> paths)
Deletes a collection of paths.
|
Path[] |
PathAndFillManager.getPathsStructured(Collection<Path> paths) |
List<SWCPoint> |
PathAndFillManager.getSWCFor(Collection<Path> paths) |
List<SWCPoint> |
PathAndFillManager.getSWCForOld(Collection<Path> paths)
Gets the list of SWCPoints associated with a collection of Paths.
|
void |
SNT.initPathsToFill(Set<Path> fromPaths) |
ij.ImagePlus |
SNT.makePathVolume(Collection<Path> paths) |
NearPoint |
PathAndFillManager.nearestPointOnAnyPath(Collection<Path> paths,
PointInCanvas pic,
double distanceLimit) |
protected NearPoint |
PathAndFillManager.nearestPointOnAnyPath(Collection<Path> paths,
PointInImage pim,
double distanceLimitSquared,
boolean unScaledPositions) |
protected static String |
Path.pathsToIDListString(ArrayList<Path> a) |
void |
Tree.replaceAll(List<Path> paths)
Replaces all Paths in this Tree.
|
protected void |
Path.setChildren(Set<Path> pathsLeft) |
void |
SNT.setPathList(List<Path> pathList,
Path justAdded,
boolean expandAll) |
void |
PathManagerUI.setPathList(List<Path> pathList,
Path justAdded,
boolean expandAll) |
void |
FillManagerUI.setPathList(List<Path> pathList,
Path justAdded,
boolean expandAll) |
protected void |
PathAndFillManager.setSelected(Collection<Path> selectedPaths,
Object sourceOfMessage) |
void |
SNT.setSelectedPaths(Collection<Path> selectedPathsSet,
Object source) |
void |
PathManagerUI.setSelectedPaths(Collection<Path> selectedPaths,
Object source) |
void |
FillManagerUI.setSelectedPaths(Collection<Path> selectedPathSet,
Object source) |
void |
Fill.setSourcePaths(Set<Path> newSourcePaths) |
protected void |
Path.unsetPrimaryForConnected(HashSet<Path> pathsExplored) |
| Constructor and Description |
|---|
NearPoint(PointInImage nearPoint,
Path path,
int indexInPath) |
NearPoint(PointInImage nearPoint,
Path path,
int indexInPath,
boolean unScaledPositions) |
PathFitter(ij.ImagePlus imp,
Path path)
Instantiates a new PathFitter.
|
PathFitter(SNT plugin,
Path path)
Instantiates a new PathFitter.
|
| Constructor and Description |
|---|
Tree(Collection<Path> paths)
Instantiates a new Tree from a set of paths.
|
| Modifier and Type | Field and Description |
|---|---|
protected List<Path> |
TreeAnalyzer.innerBranches |
protected ArrayList<Path> |
TreeColorMapper.paths |
protected List<Path> |
TreeAnalyzer.primaryBranches |
protected List<Path> |
TreeAnalyzer.terminalBranches |
| Modifier and Type | Method and Description |
|---|---|
List<Path> |
TreeAnalyzer.getBranches()
Gets all the branches in the analyzed tree.
|
Map<Integer,List<Path>> |
StrahlerAnalyzer.getBranches() |
List<Path> |
PathAnalyzer.getBranches() |
List<Path> |
MultiTreeStatistics.getBranches() |
List<Path> |
StrahlerAnalyzer.getBranches(int order) |
List<Path> |
TreeAnalyzer.getInnerBranches()
Retrieves the branches of highest
Strahler order in the Tree. |
List<Path> |
PathAnalyzer.getInnerBranches() |
List<Path> |
MultiTreeStatistics.getInnerBranches() |
List<Path> |
TreeAnalyzer.getPrimaryBranches()
Retrieves the primary branches of the analyzed Tree.
|
List<Path> |
PathAnalyzer.getPrimaryBranches() |
List<Path> |
MultiTreeStatistics.getPrimaryBranches() |
List<Path> |
TreeAnalyzer.getPrimaryPaths()
Retrieves all the Paths in the analyzed Tree tagged as primary.
|
List<Path> |
StrahlerAnalyzer.getRootAssociatedBranches() |
List<Path> |
TreeAnalyzer.getTerminalBranches()
Retrieves the terminal branches of the analyzed Tree.
|
List<Path> |
MultiTreeStatistics.getTerminalBranches() |
| Modifier and Type | Method and Description |
|---|---|
void |
PathProfiler.assignValues(Path p)
Retrieves pixel intensities at each node of the Path storing them as Path
values |
<T extends RealType<T>> |
PathProfiler.assignValues(Path p,
int channel) |
Plot |
PathProfiler.getPlot(Path path) |
List<PolygonRoi> |
RoiConverter.getROIs(Path path) |
Map<String,List<Double>> |
PathProfiler.getValues(Path p)
Gets the profile for the specified path as a map of lists, with distances (or
indices) stored under
PathProfiler.X_VALUES ("x-values") and intensities
under PathProfiler.Y_VALUES ("y-values"). |
Map<String,List<Double>> |
PathProfiler.getValues(Path p,
int channel) |
static <T extends RealType<T>> |
ProfileProcessor.profilePathNodes(RandomAccessible<T> rai,
Path path,
double[] values)
Get the intensities for the point coordinates of a Path
|
| Constructor and Description |
|---|
PathProfiler(Path path,
Dataset dataset) |
PathProfiler(Path path,
ij.ImagePlus imp)
Instantiates a new Profiler from a single path
|
PathStraightener(Path path,
ij.ImagePlus imp)
Instantiates a new PathStraightener
|
PathStraightener(Path path,
SNT snt)
Instantiates a new PathStraightener
|
ProfileProcessor(RandomAccessibleInterval<T> rai,
Path path) |
RoiConverter(Path path,
ij.ImagePlus imp)
Instantiates a new Converter.
|
| Constructor and Description |
|---|
PathAnalyzer(Collection<Path> paths,
String label) |
TreeAnalyzer(Collection<Path> paths,
String label)
Instantiates a new Tree analyzer from a collection of paths.
|
| Modifier and Type | Method and Description |
|---|---|
Path |
DirectedWeightedGraph.getLongestPath(boolean useDirected)
Return the sequence of nodes representing the
longest shortest-path
in the graph, as a
Path. |
Path |
DirectedWeightedGraph.getShortestPath(SWCPoint v1,
SWCPoint v2)
Gets the shortest path between source and target vertex as a
Path object. |
| Modifier and Type | Method and Description |
|---|---|
static void |
ShollAnalysisDialog.addPathPointsToShollList(Path p,
double x_start,
double y_start,
double z_start,
List<ShollAnalysisDialog.ShollPoint> shollPointsList)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
void |
PathManagerUISearchableBar.doMorphoFiltering(Collection<Path> paths,
String property,
Number min,
Number max) |
| Modifier and Type | Field and Description |
|---|---|
protected Path |
BiSearch.result |
| Modifier and Type | Method and Description |
|---|---|
Path |
DefaultSearchNode.asPath(double x_spacing,
double y_spacing,
double z_spacing,
String spacing_units) |
Path |
DefaultSearchNode.asPathReversed(double x_spacing,
double y_spacing,
double z_spacing,
String spacing_units) |
Path |
TubularGeodesicsTracer.getResult() |
Path |
TracerThread.getResult() |
Path |
SearchInterface.getResult() |
Path |
ManualTracerThread.getResult() |
Path |
FillerThread.getResult() |
Path |
BiSearch.getResult() |
protected Path |
BiSearch.reconstructPath(double x_spacing,
double y_spacing,
double z_spacing,
String spacing_units) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
TracerThread.foundGoal(Path pathToGoal) |
protected void |
SearchThread.foundGoal(Path pathToGoal) |
| Modifier and Type | Method and Description |
|---|---|
void |
FillerThread.setSourcePaths(Collection<Path> newSourcePaths) |
| Modifier and Type | Field and Description |
|---|---|
Path |
PointInImage.onPath
The Path associated with this node, if any (optional field)
|
| Modifier and Type | Method and Description |
|---|---|
Path |
PointInImage.getPath()
Returns the Path associated with this node (if any)
|
| Modifier and Type | Method and Description |
|---|---|
void |
PointInImage.setPath(Path onPath)
Associates a Path with this node
|
| Constructor and Description |
|---|
PathCursor(RandomAccessible<T> accessible,
Path path) |
PointInCanvas(double x,
double y,
double z,
Path onPath) |
PointInImage(double x,
double y,
double z,
Path onPath) |
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