Model objects

Tree, Branch, and Point

This page documents the core data structures that represent a 3D neuronal reconstruction in Dynamo: Tree, Branch, and Point. These classes model soma-rooted trees, ordered branch point lists, and per-node metadata, and are used by the GUI and by programmatic workflows.

Tree Class

The Tree class represents a 3D neuronal reconstruction, anchored at a soma (rootPoint) and composed of multiple Branch objects. It provides methods to query, edit, and traverse the dendritic/axonal tree, as well as utilities for distance calculations and cloning.

Attributes

Name

Type

Description

rootPoint

Optional[Point]

Soma / root node of the tree.

branches

List[Branch]

All branches in the tree. Each branch contains an ordered list of points.

transform

Transform

Image-to-world transform (identity; scaling from FullState.projectOptions.pixelSizes).

_parentState

Optional[UIState]

Internal link back to the UIState.

Core Methods

Lookup

  • getPointByID(pointID, includeDisconnected=False) → Optional[Point]

  • getBranchByID(branchID) → Optional[Branch]

  • flattenPoints(includeDisconnected=False) → List[Point]

Editing

  • addBranch(branch) → int — Add branch, return index.

  • removeBranch(branch) → None — Remove branch (must be empty).

  • removePointByID(pointID) → Optional[Point] — Remove a point and cleanup.

  • reparentPoint(childPoint, newParent, newBranchID=None) → Optional[str] — Reparent a point and descendants.

  • movePoint(pointID, newLocation, downstream=False) → None — Move point (and optionally downstream).

Traversal & Tree Manipulation

  • nextPointFilteredWithCount(sourcePoint, filterFunc, delta) → (Optional[Point], int)

  • continueParentBranchIfFirst(point) → None

  • updateAllPrimaryBranches(point=None) → None

  • updateAllBranchesMinimalAngle(point=None) → None

Geometry & Distance

  • worldCoordPoints(points) → coordinates in world units.

  • spatialDist(p1, p2) → float, Euclidean distance.

  • spatialAndTreeDist(p1, p2) → (euclidean, path).

  • spatialRadius() → max Euclidean radius.

  • spatialAndTreeRadius() → max (euclidean, path) radius.

  • closestPointTo(location, zFilter=False) → Optional[Point].

  • closestPointToWorldLocation(worldLocation) → Optional[Point].

Cloning & Cleanup

  • clearAndCopyFrom(otherTree, idMaker) → None.

  • cleanBranchIDs() → None.

  • cleanEmptyBranches() → int (branches removed).

Branch Class

Branch represents a single connected segment of a neuronal tree, starting at a parentPoint and containing an ordered list of Point objects. It provides indexing, editing, labeling queries, subtree traversal, and world-space length utilities.

Attributes

Name

Type

Description

id

str

Branch identifier.

_parentTree

Tree

Owning tree (set by Tree.addBranch).

parentPoint

Optional[Point]

Node where this branch originates.

points

List[Point]

Ordered list of points.

isEnded, colorData

—

Reserved placeholders.

reparentTo

Optional[Point]

Temporary hook for reparenting.

Core Methods

Indexing & Queries

  • indexInParent() → index in tree.branches.

  • indexForPointID(pointID) / indexForPoint(point) → position or -1.

  • isEmpty() → bool.

  • hasChildren() → bool.

  • hasPointWithAnnotation(annotation, recurseUp=False) → bool.

  • isAxon(axonLabel='axon', recurseUp=True) → bool.

  • isBasal(basalLabel='basal', recurseUp=True) → bool.

  • isFilo(maxLength) → (bool, length).

  • getOrder(centrifugal=False) → int.

Editing

  • addPoint(point) → index.

  • insertPointBefore(point, index) → index.

  • removePointLocally(point) → Optional[Point].

  • setParentPoint(parentPoint) → None.

Traversal & Subtree

  • flattenSubtreePoints(startIdx=0) → list of points.

  • subtreeContainsID(pointID) → bool.

Lengths (world space)

  • worldLengths(fromIdx=0) → (total, toLastBranchPoint).

  • cumulativeWorldLengths() → list of distances.

  • pointsWithParentIfExists() → list of points.

Utilities

  • _lastPointWithChildren(points) → index or -1.

  • _lastPointWithLabel(points, label) → index or -1.

Point Class

Point represents a node in 3D pixel space. It links to its owning branch, can have child branches, and carries optional radius and annotations. World-space methods require access to FullState for scaling.

Attributes

Name

Type

Description

id

str

Unique identifier.

location

Point3D

(x, y, z) in pixels.

radius

Optional[float]

Radius in pixels.

parentBranch

Optional[Branch]

Owning branch.

annotation

str

Free-text label.

children

List[Branch]

Child branches.

manuallyMarked

Optional[bool]

Flag for curation.

hilighted

Optional[bool]

Deprecated.

Core Methods

Topology & Position

  • isRoot() → bool.

  • indexInParent() → int.

  • isLastInBranch() → bool.

  • removeChildrenByID(branchID) → None.

Traversal

  • nextPointInBranch(delta=1, noWrap=False) → Optional[Point].

  • pathFromRoot() → list of points.

Subtree

  • flattenSubtreePoints() → list of points.

  • subtreeContainsID(pointID) → bool.

Geometry

  • radiusFromAncestors() → float.

  • longestDistanceToLeaf() → float.

  • returnWorldRadius(fullState) → float.