`PathAndFillManager` Class Documentation#

Package: sc.fiji.snt

The PathAndFillManager is responsible for importing, handling and managing of Paths and Fills. Typically, a PathAndFillManager is accessed from a SNT instance, but accessing a PathAndFillManager directly is useful for batch/headless operations.

Methods#

Utilities Methods#

clear()#: Deletes all paths and fills.

Getters Methods#

getBoundingBox(boolean)#: Returns the BoundingBox enclosing all nodes of all existing Paths.

getCorrespondences(PathAndFillManager, double)#: For each point in this PathAndFillManager, find the corresponding point on the other one. If there’s no corresponding one, include a null instead. *

getLoadedFills()#

getPath(int)#: Returns the Path at the specified position in the PathAndFillManager list.

getPathFromID(int)#: Returns the Path with the specified id.

getPathFromName(String, boolean)#: Returns the Path with the specified name.

getPaths()#: Returns all the paths.

getPathsFiltered()#: Returns the ‘de facto’ Paths.

getPathsInROI(Roi)#

getPathsStructured(Collection)#

getPlugin()#: Gets the SNT instance.

getSWCFor(Collection)#: Converts a collection of connected Path objects into SWC points for export.

SWC is the standardized format used for neuromorphological data exchange. The conversion process:

Validates that paths form a proper tree structure with exactly one primary path (tree’s root) Uses breadth-first traversal to ensure correct parent-child relationships Assigns sequential SWC IDs starting from 1 Establishes proper parent references based on path connectivity Preserves path properties including SWC type, color, annotations, and custom tags

Path Requirements:

Must contain exactly one primary path (root of the tree) All non-primary paths must have valid parent relationships Paths must form a connected tree structure (no disconnected components) Empty paths (size == 0) are automatically skipped

getSelectedPaths()#: Gets all paths selected in the GUI

I/O Operations Methods#

static createFromFile(String, [I): Creates a PathAndFillManager instance from imported data

exportAllPathsAsSWC(String)#: Exports all as Paths as SWC file(s). Multiple files are created if multiple Trees exist.

exportFillsAsCSV(File)#: Export fills as CSV.

exportToCSV(File)#: Output some potentially useful information about all the Paths managed by this instance as a CSV (comma separated values) file.

exportTree(int, File)#

Other Methods#

addPath(Path)#

addPathAndFillListener(PathAndFillListener)#: Adds a PathAndFillListener. This is used by the interface to have changes in the path manager reported so that they can be reflected in the UI.

addTree(Tree, String)#: Adds a Tree. If an image is currently being traced, it is assumed it is large enough to contain the tree.

addTrees(Collection)#: Adds a collection of Trees.

allPointsIterator()#

anySelected()#: Checks whether at least one Path is currently selected in the UI.

assignSpatialSettings(ImagePlus)#

canvasResized()#

characters([C, int, int)#

contentAdded(Content)#

contentChanged(Content)#

contentRemoved(Content)#

contentSelected(Content)#

static createFromGraph(DirectedWeightedGraph, boolean): Create a new PathAndFillManager instance from the graph.

static createFromNodes(Collection): Creates a PathAndFillManager instance from a collection of reconstruction nodes.

declaration(String, String, String)#

deletePath(int)#: Deletes a path.

deletePaths([I)#: Delete paths by position.

dispose()#

downsampleAll(double)#: Downsamples alls path using Ramer–Douglas–Peucker simplification. Downsampling occurs only between branch points and terminal points.

endDocument()#

endElement(String, String, String)#

endPrefixMapping(String)#: Sets whether this PathAndFillManager instance should run headless.

error(SAXParseException)#

fatalError(SAXParseException)#

PathAndFillManager Class Documentation#