Utilities Methods#

General utility methods and helper functions.

Total methods in this category: 341

AllenCompartment #

acronym()#

Signature: acronym() -> String

Returns: (str) the compartment’s acronym

aliases()#

Signature: aliases() -> String;

Returns: (Any) the compartment’s alias(es)

id()#

Signature: id() -> int

Returns: (int) the compartment’s unique id

includes(arg0)#

Signature: includes(BrainAnnotation) -> boolean

Parameters:

arg0 (Any)

Returns: bool

name()#

Signature: name() -> String

Returns: (str) the compartment’s name

BiSearch #

pointsConsideredInSearch()#

Signature: pointsConsideredInSearch() -> long

Returns: int

printStatus()#

Signature: printStatus() -> void

Returns: None

reportFinished(arg0)#

Signature: reportFinished(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

run()#

Signature: run() -> void

Returns: None

BiSearchNode #

heapDecreaseKey(arg0)#

Signature: heapDecreaseKey(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

heapInsert(arg0, arg1)#

Signature: heapInsert(AddressableHeap, boolean) -> void

Parameters:

arg0 (Any)
arg1 (bool)

Returns: None

BoundingBox #

append(arg0)#

Computes the bounding box of the specified point cloud and appends it to this bounding box, resizing it as needed.

Signature: append(Iterator) -> void

Parameters:

arg0 (Any): - the iterator of the points Collection

Returns: None

clone()#

Creates a copy of this BoundingBox.

Signature: clone() -> Object

Returns: Any

combine(arg0)#

Combines this bounding box with another one. It is assumed both boxes share the same voxel spacing/Calibration.

Signature: combine(BoundingBox) -> void

Parameters:

arg0 (BoundingBox): - the bounding box to be combined.

Returns: None

contains(arg0)#

Signature: contains(SNTPoint) -> boolean

Parameters:

arg0 (SNTPoint)

Returns: bool

contains2D(arg0)#

Signature: contains2D(SNTPoint) -> boolean

Parameters:

arg0 (SNTPoint)

Returns: bool

depth()#

Signature: depth() -> double

Returns: float

height()#

Signature: height() -> double

Returns: float

inferSpacing(arg0)#

Infers the voxel spacing of this box from the inter-node distances of a Collection of SWCPoints.

Signature: inferSpacing(Collection) -> void

Parameters:

arg0 (List[Any]): - the point collection

Returns: None

intersection(arg0)#

Retrieves the intersection cuboid between this bounding with another bounding box. It is assumed both boxes share the same voxel spacing/Calibration.

Signature: intersection(BoundingBox) -> BoundingBox

Parameters:

arg0 (BoundingBox): - the second bounding box.

Returns: (BoundingBox) The intersection cuboid.

origin()#

Retrieves the origin of this box.

Signature: origin() -> PointInImage

Returns: (PointInImage) the origin

originOpposite()#

Retrieves the origin opposite of this box.

Signature: originOpposite() -> PointInImage

Returns: (PointInImage) the origin

scale(arg0)#

Signature: scale([D) -> BoundingBox

Parameters:

arg0 (Any)

Returns: BoundingBox

shift(arg0)#

Signature: shift([D) -> BoundingBox

Parameters:

arg0 (Any)

Returns: BoundingBox

toBoundingBox3d()#

Signature: toBoundingBox3d() -> BoundingBox3d

Returns: Any

unscaledOrigin()#

Retrieves the origin of this box in unscaled (“pixel” units)

Signature: unscaledOrigin() -> PointInImage

Returns: (PointInImage) the unscaled origin

unscaledOriginOpposite()#

Retrieves the origin opposite of this box in unscaled (“pixel” units)

Signature: unscaledOriginOpposite() -> PointInImage

Returns: (PointInImage) the unscaled origin opposite

width()#

Signature: width() -> double

Returns: float

ConvexHull2D #

intersection(arg0)#

Signature: intersection(AbstractConvexHull;) -> AbstractConvexHull

Parameters:

arg0 (Any)

Returns: Any

intersectionBox(arg0)#

Signature: intersectionBox(AbstractConvexHull;) -> BoundingBox

Parameters:

arg0 (Any)

Returns: BoundingBox

ConvexHull3D #

intersection(arg0)#

Signature: intersection(AbstractConvexHull;) -> ConvexHull3D

Parameters:

arg0 (Any)

Returns: ConvexHull3D

intersectionBox(arg0)#

Signature: intersectionBox(AbstractConvexHull;) -> BoundingBox

Parameters:

arg0 (Any)

Returns: BoundingBox

ConvexHullAnalyzer #

context()#

Signature: context() -> Context

Returns: Any

dump(arg0)#

Signature: dump(SNTTable) -> void

Parameters:

arg0 (SNTTable)

Returns: None

get(arg0)#: Gets the value of a specific convex hull metric.

Retrieves the computed value for the specified metric name. The metric must be one of the supported metrics returned by supportedMetrics().

Signature: get(String) -> double

Parameters:

arg0 (str): - the name of the metric to retrieve

Returns: (float) the computed value for the metric

run()#

Signature: run() -> void

Returns: None

DefaultSearchNode #

compareTo(arg0)#

Signature: compareTo(DefaultSearchNode) -> int

Parameters:

arg0 (Any)

Returns: int

Fill #

add(arg0, arg1, arg2, arg3, arg4, arg5)#

Adds a node to the filled structure.

Signature: add(int, int, int, double, int, boolean) -> void

Parameters:

arg0 (int): - the x-coordinate of the node
arg1 (int)
arg2 (int)
arg3 (float)
arg4 (int)
arg5 (bool)

Returns: None

FillConverter #

convert(arg0, arg1)#

Map values between the input and output at fill voxel positions.

Signature: convert(RandomAccessible, RandomAccessible) -> void

Parameters:

arg0 (Any): - the input rai
arg1 (Any)

Returns: None

convertBinary(arg0)#

Set 1 at fill voxel positions.

Signature: convertBinary(RandomAccessible) -> void

Parameters:

arg0 (Any): - the output rai

Returns: None

convertDistance(arg0)#

Map the node distance measure to fill voxel positions. This corresponds to the g-score of a node assigned during the Dijkstra search. This value is stored as Double.

Signature: convertDistance(RandomAccessible) -> void

Parameters:

arg0 (Any): - the output rai

Returns: None

convertLabels(arg0)#

Map the fill component label to fill voxel positions. The concrete IntegerType should be chosen based on the cardinality of the given Collection of FillerThreads. For example, if there are less than 256 FillerThreads, choose UnsignedByteType. If there are more than 255 but less than 65536, choose UnsignedShortType, etc. Fill components are assigned labels based on their order in the collection. If you want to ensure labels are assigned based on insertion order, make sure to use an ordered collection such as List or LinkedHashSet. The first component will have label == 1, the second label == 2, and so on. The label 0 is not assigned to any voxel positions. 0-valued voxels may already exist in the output image.

Signature: convertLabels(RandomAccessible) -> void

Parameters:

arg0 (Any): - the output rai

Returns: None

FillerThread #

createNewNode(arg0, arg1, arg2, arg3, arg4, arg5, arg6)#

Signature: createNewNode(int, int, int, double, double, DefaultSearchNode, byte) -> DefaultSearchNode

Parameters:

arg0 (int)
arg1 (int)
arg2 (int)
arg3 (float)
arg4 (float)
arg5 (Any)
arg6 (int)

Returns: Any

pointsConsideredInSearch()#

Signature: pointsConsideredInSearch() -> long

Returns: int

printStatus()#

Signature: printStatus() -> void

Returns: None

reportFinished(arg0)#

Signature: reportFinished(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

run()#

Signature: run() -> void

Returns: None

Frangi #

accept(arg0)#

Signature: accept(RandomAccessibleInterval) -> void

Parameters:

arg0 (Any)

Returns: None

andThen(arg0)#

Signature: andThen(Consumer) -> Consumer

Parameters:

arg0 (Any)

Returns: Any

in()#

Signature: in() -> Object

Returns: Any

initialize()#

Signature: initialize() -> void

Returns: None

ops()#

Signature: ops() -> OpEnvironment

Returns: Any

out()#

Signature: out() -> Object

Returns: Any

run()#

Signature: run() -> void

Returns: None

GroupedTreeStatistics #

anovaPValue(arg0)#

Computes the one-way ANOVA P-value for all the groups being analyzed. It is assumed that data fulfills basic assumptions on normality, variance homogeneity, sample size, etc.

Signature: anovaPValue(String) -> double

Parameters:

arg0 (str): - the measurement (N_NODES, NODE_RADIUS, etc.)

Returns: (float) the p-value

tTest(arg0, arg1, arg2)#

Computes a two-sample, two-tailed t-test P-value for two of groups being analyzed. It is assumed that data fulfills basic assumptions on normality, variance homogeneity, etc.

Signature: tTest(String, String, String) -> double

Parameters:

arg0 (str): - the measurement (N_NODES, NODE_RADIUS, etc.)
arg1 (str)
arg2 (str)

Returns: (float) the p-value

InsectBrainCompartment #

acronym()#

Signature: acronym() -> String

Returns: (str) the compartment’s acronym

aliases()#

Signature: aliases() -> String;

Returns: (Any) the compartment’s alias(es)

id()#

Signature: id() -> int

Returns: (int) the compartment’s unique id

name()#

Signature: name() -> String

Returns: (str) the compartment’s name

InsectBrainLoader #

idExists()#

Checks whether the neuron to be loaded was found in the database.

Signature: idExists() -> boolean

Returns: (bool) true, if the neuron id specified in the constructor was found in the database

InteractiveTracerCanvas #

action(arg0, arg1)#

Signature: action(Event, Object) -> boolean

Parameters:

arg0 (Any)
arg1 (Any)

Returns: bool

add(arg0)#

Signature: add(PopupMenu) -> void

Parameters:

arg0 (Any)

Returns: None

applyComponentOrientation(arg0)#

Signature: applyComponentOrientation(ComponentOrientation) -> void

Parameters:

arg0 (Any)

Returns: None

areFocusTraversalKeysSet(arg0)#

Signature: areFocusTraversalKeysSet(int) -> boolean

Parameters:

arg0 (int)

Returns: bool

bounds()#

Signature: bounds() -> Rectangle

Returns: Any

checkImage(arg0, arg1)#

Signature: checkImage(Image, ImageObserver) -> int

Parameters:

arg0 (Any)
arg1 (Any)

Returns: int

contains(arg0, arg1)#

Signature: contains(int, int) -> boolean

Parameters:

arg0 (int)
arg1 (int)

Returns: bool

createBufferStrategy(arg0, arg1)#

Signature: createBufferStrategy(int, BufferCapabilities) -> void

Parameters:

arg0 (int)
arg1 (Any)

Returns: None

createImage(arg0, arg1)#

Signature: createImage(int, int) -> Image

Parameters:

arg0 (int)
arg1 (int)

Returns: Any

createVolatileImage(arg0, arg1, arg2)#

Signature: createVolatileImage(int, int, ImageCapabilities) -> VolatileImage

Parameters:

arg0 (int)
arg1 (int)
arg2 (Any)

Returns: Any

cursorOverImage()#

Signature: cursorOverImage() -> boolean

Returns: bool

deliverEvent(arg0)#

Signature: deliverEvent(Event) -> void

Parameters:

arg0 (Any)

Returns: None

disable()#

Signature: disable() -> void

Returns: None

dispatchEvent(arg0)#

Signature: dispatchEvent(AWTEvent) -> void

Parameters:

arg0 (Any)

Returns: None

doLayout()#

Signature: doLayout() -> void

Returns: None

enable()#

Signature: enable() -> void

Returns: None

firePropertyChange(arg0, arg1, arg2)#

Signature: firePropertyChange(String, byte, byte) -> void

Parameters:

arg0 (str)
arg1 (int)
arg2 (int)

Returns: None

fitToWindow()#

Signature: fitToWindow() -> void

Returns: None

MouseLightLoader #

idExists()#

Checks if the neuron ID exists in the database.

Signature: idExists() -> boolean

Returns: (bool) true if the ID exists, false otherwise

save(arg0)#

Convenience method to save JSON data.

Signature: save(String) -> boolean

Parameters:

arg0 (str): - the output directory or the output file

Returns: (bool) true, if successful

MultiTreeColorMapper #

map(arg0, arg1)#

Description copied from class: ColorMapper

Signature: map(String, ColorTable) -> void

Parameters:

arg0 (str): - the measurement to be mapped
arg1 (Any)

Returns: None

mapRootDistanceToCentroid(arg0, arg1)#

Signature: mapRootDistanceToCentroid(AllenCompartment, ColorTable) -> void

Parameters:

arg0 (Any)
arg1 (Any)

Returns: None

mapTrees(arg0, arg1)#

Signature: mapTrees(List, String) -> void

Parameters:

arg0 (List[Any])
arg1 (str)

Returns: None

sortedMappedTrees()#

Signature: sortedMappedTrees() -> List

Returns: List[Any]

MultiTreeStatistics #

context()#

Signature: context() -> Context

Returns: Any

dispose()#

Description copied from class: TreeStatistics

Signature: dispose() -> void

Returns: None

MultiViewer2D #

save(arg0)#

Signature: save(String) -> void

Parameters:

arg0 (str)

Returns: None

show()#

Signature: show() -> JFrame

Returns: Any

MultiViewer3D #

show()#

Signature: show() -> JFrame

Returns: Any

NodeColorMapper #

map(arg0, arg1)#

Maps nodes after the specified measurement. Mapping bounds are automatically determined.

Signature: map(String, ColorTable) -> void

Parameters:

arg0 (str): - the measurement (X_COORDINATES, Y_COORDINATES, etc.)
arg1 (Any)

Returns: None

NodeProfiler #

context()#

Signature: context() -> Context

Returns: Any

initialize()#

Signature: initialize() -> void

Returns: None

resolveInput(arg0)#

Signature: resolveInput(String) -> void

Parameters:

arg0 (str)

Returns: None

resolveOutput(arg0)#

Signature: resolveOutput(String) -> void

Parameters:

arg0 (str)

Returns: None

run()#

Signature: run() -> void

Returns: None

uncancel()#

Signature: uncancel() -> void

Returns: None

unresolveInput(arg0)#

Signature: unresolveInput(String) -> void

Parameters:

arg0 (str)

Returns: None

unresolveOutput(arg0)#

Signature: unresolveOutput(String) -> void

Parameters:

arg0 (str)

Returns: None

NodeStatistics #

assignBranches(arg0)#

Associates the nodes being analyzed to the branches of the specified tree

Signature: assignBranches(Tree) -> void

Parameters:

arg0 (Tree): - the association tree

Returns: None

filter(arg0, arg1, arg2)#

Filters the current pool of nodes matching a measurement-based criterion.

Signature: filter(String, double, double) -> List

Parameters:

arg0 (str): - the measurement (X_COORDINATES, Y_COORDINATES, BRANCH_ORDER, etc.)
arg1 (float)
arg2 (float)

Returns: (List[Any]) the filtered list.

get(arg0, arg1)#

Gets the list of nodes associated with the specified compartment (neuropil label).

Signature: get(BrainAnnotation, boolean) -> List

Parameters:

arg0 (Any)
arg1 (bool)

Returns: List[Any]

Path #

add(arg0)#

Signature: add(Path) -> void

Parameters:

arg0 (Path)

Returns: None

clone()#: Creates a copy of this Path with optional inclusion of immediate children.

This method creates a clone of this path and optionally includes clones of its immediate child paths. When children are included, they are properly reconnected to the cloned parent path, maintaining the parent-child relationships. Note that only immediate children are cloned - grandchildren and deeper descendants are not included.

Limitations: This method only clones the immediate children and does not recursively clone the entire subtree. For complex tree structures, consider using Tree.clone() instead.

Signature: clone() -> Object

Returns: Any

compareTo(arg0)#

Signature: compareTo(Object) -> int

Parameters:

arg0 (Any)

Returns: int

contains(arg0)#

Checks if this path contains the specified point within the given tolerance.

Signature: contains(PointInImage) -> boolean

Parameters:

arg0 (PointInImage): - the point to check

Returns: (bool) true if the path contains the point within tolerance

detachFromParent()#: Detaches this path from its parent, converting it into an independent primary path.

Removes the parent-child relationship established by setBranchFrom(Path, PointInImage) In

Clears the parent path reference and branch point Removes this path from the parent’s children collection Updates bidirectional references for tree traversal Resets the path order to -1 (no hierarchical position) Converts this path from a branch to a primary path

Signature: detachFromParent() -> void

Returns: None

downsample(arg0)#: Downsamples this path (in-place) by reducing the number of nodes while preserving its overall shape.

This method reduces the density of nodes in the path by removing redundant points expected to not significantly contribute to the path’s shape. The downsampling is performed using the Douglas-Peucker algorithm, which preserves fidelity within the specified tolerance.

The method operates on the segments flanked by anchor points (junctions, start, and end points). Each segment is downsampled independently, and the results are combined to form the final downsampled path. Node radii are averaged appropriately for retained points

Thread Safety: This method is synchronized to prevent concurrent modification of the path structure during the downsampling operation.

Signature: downsample(double) -> void

Parameters:

arg0 (float): - the target spacing between nodes after downsampling. This parameter controls the aggressiveness of the downsampling - smaller values preserve more detail, larger values result in more aggressive simplification. Must be greater than zero.

Returns: None

findJunctionIndices()#

Returns the indices of nodes which are indicated to be a join, either in this Path object, or any other that starts or ends on it.

Signature: findJunctionIndices() -> TreeSet

Returns: (Set[Any]) the indices of junction nodes, naturally sorted

findJunctions()#

Returns the nodes which are indicated to be a join (junction/branch point), either in this Path object, or any other that starts or ends on it.

Signature: findJunctions() -> List

Returns: (List[Any]) the list of nodes as PointInImage objects

firstNode()#

Returns the first node of this path.

Signature: firstNode() -> PointInImage

Returns: (PointInImage) the root node, or null if path is empty

PathAndFillManager #

allPointsIterator()#

Signature: allPointsIterator() -> Iterator

Returns: Any

anySelected()#

Checks whether at least one Path is currently selected in the UI.

Signature: anySelected() -> boolean

Returns: (bool) true, if successful

assignSpatialSettings(arg0)#

Signature: assignSpatialSettings(ImagePlus) -> void

Parameters:

arg0 (Any)

Returns: None

characters(arg0, arg1, arg2)#

Signature: characters([C, int, int) -> void

Parameters:

arg0 (Any)
arg1 (int)
arg2 (int)

Returns: None

clear()#

Deletes all paths and fills.

Signature: clear() -> void

Returns: None

declaration(arg0, arg1, arg2)#

Signature: declaration(String, String, String) -> void

Parameters:

arg0 (str)
arg1 (str)
arg2 (str)

Returns: None

dispose()#

Signature: dispose() -> void

Returns: None

downsampleAll(arg0)#

Downsamples alls path using Ramer–Douglas–Peucker simplification. Downsampling occurs only between branch points and terminal points.

Signature: downsampleAll(double) -> void

Parameters:

arg0 (float): - the maximum permitted distance between nodes.

Returns: None

endDocument()#

Signature: endDocument() -> void

Returns: None

endElement(arg0, arg1, arg2)#

Signature: endElement(String, String, String) -> void

Parameters:

arg0 (str)
arg1 (str)
arg2 (str)

Returns: None

endPrefixMapping(arg0)#

Sets whether this PathAndFillManager instance should run headless.

Signature: endPrefixMapping(String) -> void

Parameters:

arg0 (str): - true to activate headless calls, otherwise false

Returns: None

error(arg0)#

Signature: error(SAXParseException) -> void

Parameters:

arg0 (Any)

Returns: None

fatalError(arg0)#

Signature: fatalError(SAXParseException) -> void

Parameters:

arg0 (Any)

Returns: None

PathFitter #

applyFit()#

Sets the fallback strategy for radii at locations in which fitting failed

Signature: applyFit() -> void

Returns: None

applySettings(arg0)#

Signature: applySettings(PathFitter) -> void

Parameters:

arg0 (Any)

Returns: None

call()#

Takes the signal from the image specified in the constructor to fit cross-section circles around the nodes of input path. Computation of fit is confined to the neighborhood specified by setMaxRadius(int). Note that connectivity of path may need to be rebuilt upon fit.

Signature: call() -> Object

Returns: Any

PathManagerUI #

action(arg0, arg1)#

Signature: action(Event, Object) -> boolean

Parameters:

arg0 (Any)
arg1 (Any)

Returns: bool

add(arg0, arg1)#

Runs a menu command with options.

Signature: add(String, Component) -> Component

Parameters:

arg0 (str)
arg1 (Any)

Returns: Any

applyComponentOrientation(arg0)#

Signature: applyComponentOrientation(ComponentOrientation) -> void

Parameters:

arg0 (Any)

Returns: None

applyDefaultTags(arg0)#

Applies a default (built-in) tag to selected Path(s).

Signature: applyDefaultTags(String;) -> void

Parameters:

arg0 (Any): - The tags to be applied to selected Paths, as listed in the “Tag” menu, e.g., “Traced Channel”, “Traced Frame”, “No. of Spine/Varicosity Markers”, etc.

Returns: None

applyResourceBundle(arg0)#

Signature: applyResourceBundle(String) -> void

Parameters:

arg0 (str)

Returns: None

applySelectionFilter(arg0, arg1)#

Selects paths matching a morphometric criteria.

Signature: applySelectionFilter(String, Number) -> void

Parameters:

arg0 (str)
arg1 (Union[int, float])

Returns: None

applyTag(arg0)#

Applies a custom tag/ color to selected Path(s).

Signature: applyTag(String) -> void

Parameters:

arg0 (str): - The tag (or color) to be applied to selected Paths. Specifying “null color” will remove color tags from selected paths.

Returns: None

areFocusTraversalKeysSet(arg0)#

Signature: areFocusTraversalKeysSet(int) -> boolean

Parameters:

arg0 (int)

Returns: bool

bounds()#

Signature: bounds() -> Rectangle

Returns: Any

checkImage(arg0, arg1)#

Signature: checkImage(Image, ImageObserver) -> int

Parameters:

arg0 (Any)
arg1 (Any)

Returns: int

contains(arg0, arg1)#

Signature: contains(int, int) -> boolean

Parameters:

arg0 (int)
arg1 (int)

Returns: bool

countComponents()#

Signature: countComponents() -> int

Returns: int

createBufferStrategy(arg0, arg1)#

Signature: createBufferStrategy(int, BufferCapabilities) -> void

Parameters:

arg0 (int)
arg1 (Any)

Returns: None

createImage(arg0, arg1)#

Signature: createImage(int, int) -> Image

Parameters:

arg0 (int)
arg1 (int)

Returns: Any

createVolatileImage(arg0, arg1, arg2)#

Signature: createVolatileImage(int, int, ImageCapabilities) -> VolatileImage

Parameters:

arg0 (int)
arg1 (int)
arg2 (Any)

Returns: Any

deliverEvent(arg0)#

Signature: deliverEvent(Event) -> void

Parameters:

arg0 (Any)

Returns: None

disable()#

Signature: disable() -> void

Returns: None

dispatchEvent(arg0)#

Signature: dispatchEvent(AWTEvent) -> void

Parameters:

arg0 (Any)

Returns: None

dispose()#

Signature: dispose() -> void

Returns: None

doLayout()#

Signature: doLayout() -> void

Returns: None

PathProfiler #

assignValues(arg0, arg1)#

Retrieves pixel intensities at each node of the Path storing them as Path values

Signature: assignValues(Path, int) -> void

Parameters:

arg0 (Path)
arg1 (int)

Returns: None

context()#

Signature: context() -> Context

Returns: Any

findMaxima(arg0, arg1)#: Finds the maxima in the profile of the specified path.

A maxima (peak) will only be considered if protruding more than the profile’s standard deviation from the ridge to a higher maximum

Signature: findMaxima(Path, int) -> [I

Parameters:

arg0 (Path): - the channel to be parsed (base-0 index)

arg1 (int)

Returns: (Any) the indices of the maxima

findMinima(arg0, arg1)#: Finds the minima in the profile of the specified path.

A maxima (peak) will only be considered if protruding less than the profile’s standard deviation from the ridge to a lower minimum

Signature: findMinima(Path, int) -> [I

Parameters:

arg0 (Path): - the channel to be parsed (base-0 index)

arg1 (int)

Returns: (Any) the indices of the minima

initialize()#

Signature: initialize() -> void

Returns: None

resolveInput(arg0)#

Signature: resolveInput(String) -> void

Parameters:

arg0 (str)

Returns: None

resolveOutput(arg0)#

Signature: resolveOutput(String) -> void

Parameters:

arg0 (str)

Returns: None

run()#

Signature: run() -> void

Returns: None

PathStatistics #

context()#

Signature: context() -> Context

Returns: Any

dispose()#

Signature: dispose() -> void

Returns: None

PathStraightener #

straighten()#

Signature: straighten() -> ImagePlus

Returns: Any

PointInImage #

chebyshevDxTo(arg0)#

Signature: chebyshevDxTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

chebyshevXYdxTo(arg0)#

Signature: chebyshevXYdxTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

chebyshevZdxTo(arg0)#

Signature: chebyshevZdxTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

clone()#: Creates a copy of this PointInImage.

This method creates a copy of the point including all properties such as coordinates, value, annotation, and hemisphere information.

Signature: clone() -> PointInImage

Returns: (PointInImage) a new PointInImage that is a copy of this point

distanceSquaredTo(arg0)#

Signature: distanceSquaredTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

distanceTo(arg0)#

Signature: distanceTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

euclideanDxTo(arg0)#

Signature: euclideanDxTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

scale(arg0, arg1, arg2)#

Scales this point coordinates.

Signature: scale(double, double, double) -> void

Parameters:

arg0 (float): - the scaling factor for x coordinates
arg1 (float)
arg2 (float)

Returns: None

transform(arg0)#

Signature: transform(PathTransformer) -> PointInImage

Parameters:

arg0 (Any)

Returns: PointInImage

RootAngleAnalyzer #

balancingFactor()#

Returns the balancing factor, computed from centripetalBias().

Signature: balancingFactor() -> double

Returns: (float) the balancing factor (dimensionless, range: [0, 1]).

centripetalBias()#

Returns the strength of the centripetal bias, also known as κ. κ is defined as the concentration of the von Mises fit of the root angle distribution. κ= 0 indicate no bias (root angles are distributed uniformly). K->∞ indicate that all neurites point directly toward the root of the tree

Signature: centripetalBias() -> double

Returns: (float) Returns the centripetal bias, or κ (dimensionless, range: [0, ∞[).

max()#

Signature: max() -> double

Returns: (float) Returns the largest of root angles (in degrees).

mean()#

Signature: mean() -> double

Returns: (float) Returns the arithmetic mean of root angles (in degrees).

meanDirection()#

Returns the mean direction of the fitted von Mises distribution.

Signature: meanDirection() -> double

Returns: (float) the mean direction (in degrees).

min()#

Signature: min() -> double

Returns: (float) Returns the smallest of root angles (in degrees).

SNT #

accessToValidImageData()#

Signature: accessToValidImageData() -> boolean

Returns: bool

autoTrace(arg0, arg1, arg2)#

Automatically traces a path from a point A to a point B. See autoTrace(List, PointInImage) for details.

Signature: autoTrace(SNTPoint, SNTPoint, PointInImage) -> Path

Parameters:

arg0 (SNTPoint)
arg1 (SNTPoint)
arg2 (PointInImage)

Returns: Path

changeUIState(arg0)#

Signature: changeUIState(int) -> void

Parameters:

arg0 (int)

Returns: None

closeAndResetAllPanes()#

Signature: closeAndResetAllPanes() -> void

Returns: None

confirmTemporary(arg0)#

Signature: confirmTemporary(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

createCanvas(arg0, arg1)#

Signature: createCanvas(ImagePlus, int) -> InteractiveTracerCanvas

Parameters:

arg0 (Any)
arg1 (int)

Returns: Any

editModeAllowed()#

Assesses if activation of ‘Edit Mode’ is possible.

Signature: editModeAllowed() -> boolean

Returns: (bool) true, if possible, false otherwise

findPointInStack(arg0, arg1, arg2, arg3)#

Signature: findPointInStack(int, int, int, [I) -> void

Parameters:

arg0 (int)
arg1 (int)
arg2 (int)
arg3 (Any)

Returns: None

findPointInStackPrecise(arg0, arg1, arg2, arg3)#

Signature: findPointInStackPrecise(double, double, int, [D) -> void

Parameters:

arg0 (float)
arg1 (float)
arg2 (int)
arg3 (Any)

Returns: None

finished(arg0, arg1)#

Signature: finished(SearchInterface, boolean) -> void

Parameters:

arg0 (Any)
arg1 (bool)

Returns: None

flushSecondaryData()#

Signature: flushSecondaryData() -> void

Returns: None

SNTChart #

action(arg0, arg1)#

Signature: action(Event, Object) -> boolean

Parameters:

arg0 (Any)
arg1 (Any)

Returns: bool

actionPerformed(arg0)#

Shows a bivariate histogram (two-dimensional histogram) from two DescriptiveStatistics objects. The number of bins is automatically determined using the Freedman-Diaconis rule.

Signature: actionPerformed(ActionEvent) -> void

Parameters:

arg0 (Any): - DescriptiveStatistics for the first distribution

Returns: None

add(arg0, arg1)#

Signature: add(String, Component) -> Component

Parameters:

arg0 (str)
arg1 (Any)

Returns: Any

annotate(arg0)#

Adds a subtitle to the chart.

Signature: annotate(String) -> void

Parameters:

arg0 (str): - the subtitle text

Returns: None

annotateCategory(arg0, arg1, arg2)#

Annotates the specified category (Category plots only).

Signature: annotateCategory(String, String, String) -> void

Parameters:

arg0 (str)
arg1 (str)
arg2 (str)

Returns: None

annotatePoint(arg0, arg1, arg2)#

Highlights a point in a histogram/XY plot by drawing a labeled arrow at the specified location.

Signature: annotatePoint([D, String, String) -> void

Parameters:

arg0 (Any): - the array holding the focal point coordinates of the profile
arg1 (str)
arg2 (str)

Returns: None

annotateXline(arg0, arg1, arg2)#

Annotates the specified X-value (XY plots and histograms).

Signature: annotateXline(double, String, String) -> void

Parameters:

arg0 (float)
arg1 (str)
arg2 (str)

Returns: None

annotateYline(arg0, arg1)#

Annotates the specified Y-value (XY plots and histograms).

Signature: annotateYline(double, String) -> void

Parameters:

arg0 (float): - the Y value to be annotated.
arg1 (str)

Returns: None

applyComponentOrientation(arg0)#

Signature: applyComponentOrientation(ComponentOrientation) -> void

Parameters:

arg0 (Any)

Returns: None

applyStyle(arg0)#

Signature: applyStyle(SNTChart) -> void

Parameters:

arg0 (SNTChart)

Returns: None

areFocusTraversalKeysSet(arg0)#

Saves this chart.

Signature: areFocusTraversalKeysSet(int) -> boolean

Parameters:

arg0 (int): - the path of the output file (null not permitted). Its filename extension (“.svg”, “.png”, “.pdf”), determines the file format.

Returns: (bool) true if file was successfully saved, false otherwise

bounds()#

Signature: bounds() -> Rectangle

Returns: Any

chartChanged(arg0)#

Signature: chartChanged(ChartChangeEvent) -> void

Parameters:

arg0 (Any)

Returns: None

chartProgress(arg0)#

Signature: chartProgress(ChartProgressEvent) -> void

Parameters:

arg0 (Any)

Returns: None

checkImage(arg0, arg1)#

Signature: checkImage(Image, ImageObserver) -> int

Parameters:

arg0 (Any)
arg1 (Any)

Returns: int

SNTColor #

type()#

Retrieves the SWC type

Signature: type() -> int

Returns: (int) the SWC type integer flag

SNTService #

assignValues(arg0)#

Assigns pixel intensities at each Path node, storing them as Path values. Assigned intensities are those of the channel and time point currently being traced. Assumes SNT has been initialized with a valid image.

Signature: assignValues(boolean) -> void

Parameters:

arg0 (bool): - If true, only selected paths will be assigned values, otherwise voxel intensities will be assigned to all paths

Returns: None

compareTo(arg0)#

Signature: compareTo(Object) -> int

Parameters:

arg0 (Any)

Returns: int

context()#

Signature: context() -> Context

Returns: Any

demoImage(arg0)#

Returns one of the demo images bundled with SNT image associated with the demo (fractal) tree.

Signature: demoImage(String) -> ImagePlus

Parameters:

arg0 (str): - a string describing the type of demo image. Options include: ‘fractal’ for the L-system toy neuron; ‘ddaC’ for the C4 ddaC drosophila neuron (demo image initially distributed with the Sholl plugin); ‘OP1’/’OP_1’ for the DIADEM OP_1 dataset; ‘cil701’ and ‘cil810’ for the respective Cell Image Library entries, and ‘binary timelapse’ for a small 4-frame sequence of neurite growth

Returns: (Any) the demo image, or null if data could no be retrieved

demoTree(arg0)#

Returns a demo tree.

Signature: demoTree(String) -> Tree

Parameters:

arg0 (str): - a string describing the type of demo tree. Either ‘fractal’ for the L-system toy neuron, ‘pyramidal’ for the dendritic arbor of mouse pyramidal cell (MouseLight’s cell AA0001), ‘OP1’for the DIADEM OP_1 reconstruction, or ‘DG’ for the dentate gyrus granule cell (Neuromorpho’s Beining archive)

Returns: Tree

demoTrees()#

Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database). NB: Data is cached locally. No internet connection required.

Signature: demoTrees() -> List

Returns: (List[Any]) the list of Trees, corresponding to the dendritic arbors of cells “AA0001”, “AA0002”, “AA0003”, “AA0004” (MouseLight database IDs).

dispose()#

Quits SNT. Does nothing if SNT is currently not running.

Signature: dispose() -> void

Returns: None

initialize(arg0, arg1)#

Initializes SNT.

Signature: initialize(ImagePlus, boolean) -> SNT

Parameters:

arg0 (Any)
arg1 (bool)

Returns: Any

log()#

Signature: log() -> LogService

Returns: Any

registerEventHandlers()#

Signature: registerEventHandlers() -> void

Returns: None

save(arg0)#

Saves all the existing paths to a file.

Signature: save(String) -> boolean

Parameters:

arg0 (str): - the saving output file path. If

Returns: (bool) true, if paths exist and file was successfully written.

SNTTable #

add(arg0, arg1)#

Signature: add(int, Object) -> void

Parameters:

arg0 (int)
arg1 (Any)

Returns: None

appendColumn()#

Signature: appendColumn() -> Column

Returns: Any

appendColumns(arg0)#

Signature: appendColumns(String;) -> List

Parameters:

arg0 (Any)

Returns: List[Any]

appendRow(arg0)#

Signature: appendRow(String) -> void

Parameters:

arg0 (str)

Returns: None

appendRows(arg0)#

Signature: appendRows(String;) -> void

Parameters:

arg0 (Any)

Returns: None

appendToLastRow(arg0, arg1)#: Appends a value to the last row in the specified column.

If the table is empty, a new row is created first. The value is then set in the specified column of the last row.

Signature: appendToLastRow(String, Object) -> void

Parameters:

arg0 (str): - the column header

arg1 (Any)

Returns: None

clear()#

Signature: clear() -> void

Returns: None

clone()#

Signature: clone() -> Object

Returns: Any

contains(arg0)#

Signature: contains(Object) -> boolean

Parameters:

arg0 (Any)

Returns: bool

containsAll(arg0)#

Signature: containsAll(Collection) -> boolean

Parameters:

arg0 (List[Any])

Returns: bool

createOrUpdateDisplay()#: Creates a new display or updates an existing one.

If no display exists, creates a new table display window. If a display already exists, updates it with the current table contents.

Signature: createOrUpdateDisplay() -> void

Returns: None

ensureCapacity(arg0)#

Signature: ensureCapacity(int) -> void

Parameters:

arg0 (int)

Returns: None

fillEmptyCells(arg0)#: Fills all empty cells in the table with the specified value.

Iterates through all cells in the table and replaces null values with the provided replacement value.

Signature: fillEmptyCells(Object) -> void

Parameters:

arg0 (Any): - the value to use for filling empty cells

Returns: None

forEach(arg0)#

Signature: forEach(Consumer) -> void

Parameters:

arg0 (Any)

Returns: None

geColumnHeaders(arg0)#

Signature: geColumnHeaders(String) -> List

Parameters:

arg0 (str)

Returns: List[Any]

geColumnStats(arg0, arg1, arg2)#

Signature: geColumnStats(int, int, int) -> SummaryStatistics

Parameters:

arg0 (int)
arg1 (int)
arg2 (int)

Returns: Any

geRowStats(arg0, arg1, arg2)#

Signature: geRowStats(String, int, int) -> SummaryStatistics

Parameters:

arg0 (str)
arg1 (int)
arg2 (int)

Returns: Any

get(arg0)#

Signature: get(int) -> Column

Parameters:

arg0 (int)

Returns: Any

SNTUI #

action(arg0, arg1)#

Signature: action(Event, Object) -> boolean

Parameters:

arg0 (Any)
arg1 (Any)

Returns: bool

add(arg0, arg1)#

Updates the status bar.

Signature: add(String, Component) -> Component

Parameters:

arg0 (str)
arg1 (Any)

Returns: Any

applyComponentOrientation(arg0)#

Signature: applyComponentOrientation(ComponentOrientation) -> void

Parameters:

arg0 (Any)

Returns: None

applyResourceBundle(arg0)#

Signature: applyResourceBundle(String) -> void

Parameters:

arg0 (str)

Returns: None

areFocusTraversalKeysSet(arg0)#

Signature: areFocusTraversalKeysSet(int) -> boolean

Parameters:

arg0 (int)

Returns: bool

bounds()#

Signature: bounds() -> Rectangle

Returns: Any

changeState(arg0)#

Changes this UI to a new state. Does nothing if newState is the current UI state

Signature: changeState(int) -> void

Parameters:

arg0 (int): - the new state, e.g., READY, TRACING_PAUSED, etc.

Returns: None

checkImage(arg0, arg1)#

Signature: checkImage(Image, ImageObserver) -> int

Parameters:

arg0 (Any)
arg1 (Any)

Returns: int

contains(arg0, arg1)#

Signature: contains(int, int) -> boolean

Parameters:

arg0 (int)
arg1 (int)

Returns: bool

countComponents()#

Gets the current UI state.

Signature: countComponents() -> int

Returns: (int) the current UI state, e.g., READY, RUNNING_CMD, etc.

createBufferStrategy(arg0, arg1)#

Signature: createBufferStrategy(int, BufferCapabilities) -> void

Parameters:

arg0 (int)
arg1 (Any)

Returns: None

createImage(arg0, arg1)#

Signature: createImage(int, int) -> Image

Parameters:

arg0 (int)
arg1 (int)

Returns: Any

createVolatileImage(arg0, arg1, arg2)#

Signature: createVolatileImage(int, int, ImageCapabilities) -> VolatileImage

Parameters:

arg0 (int)
arg1 (int)
arg2 (Any)

Returns: Any

deliverEvent(arg0)#

Signature: deliverEvent(Event) -> void

Parameters:

arg0 (Any)

Returns: None

disable()#

Signature: disable() -> void

Returns: None

dispatchEvent(arg0)#

Signature: dispatchEvent(AWTEvent) -> void

Parameters:

arg0 (Any)

Returns: None

dispose()#

Signature: dispose() -> void

Returns: None

doLayout()#

Signature: doLayout() -> void

Returns: None

enable()#

Signature: enable() -> void

Returns: None

error(arg0)#

Signature: error(String) -> void

Parameters:

arg0 (str)

Returns: None

findComponentAt(arg0)#

Signature: findComponentAt(Point) -> Component

Parameters:

arg0 (Any)

Returns: Any

SWCPoint #

chebyshevDxTo(arg0)#

Signature: chebyshevDxTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

chebyshevXYdxTo(arg0)#

Signature: chebyshevXYdxTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

chebyshevZdxTo(arg0)#

Signature: chebyshevZdxTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

clone()#

Signature: clone() -> PointInImage

Returns: PointInImage

compareTo(arg0)#

Signature: compareTo(SWCPoint) -> int

Parameters:

arg0 (SWCPoint)

Returns: int

distanceSquaredTo(arg0)#

Signature: distanceSquaredTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

distanceTo(arg0)#

Signature: distanceTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

euclideanDxTo(arg0)#

Signature: euclideanDxTo(PointInImage) -> double

Parameters:

arg0 (PointInImage)

Returns: float

previous()#

Returns the preceding node (if any)

Signature: previous() -> SWCPoint

Returns: (SWCPoint) the previous node or null if set by setPrevious(SWCPoint) has not been called

scale(arg0, arg1, arg2)#

Signature: scale(double, double, double) -> void

Parameters:

arg0 (float)
arg1 (float)
arg2 (float)

Returns: None

transform(arg0)#

Signature: transform(PathTransformer) -> PointInImage

Parameters:

arg0 (Any)

Returns: PointInImage

xSeparationFromPreviousPoint()#

Returns the X-distance from previous point.

Signature: xSeparationFromPreviousPoint() -> double

Returns: (float) the X-distance from previous point or Double.NaN if no previousPoint exists.

ySeparationFromPreviousPoint()#

Returns the Y-distance from previous point.

Signature: ySeparationFromPreviousPoint() -> double

Returns: (float) the Y-distance from previous point or Double.NaN if no previousPoint exists.

zSeparationFromPreviousPoint()#

Returns the Z-distance from previous point.

Signature: zSeparationFromPreviousPoint() -> double

Returns: (float) the Z-distance from previous point or Double.NaN if no previousPoint exists.

SearchThread #

createNewNode(arg0, arg1, arg2, arg3, arg4, arg5, arg6)#

Signature: createNewNode(int, int, int, double, double, DefaultSearchNode, byte) -> DefaultSearchNode

Parameters:

arg0 (int)
arg1 (int)
arg2 (int)
arg3 (float)
arg4 (float)
arg5 (Any)
arg6 (int)

Returns: Any

pointsConsideredInSearch()#

Signature: pointsConsideredInSearch() -> long

Returns: int

printStatus()#

Signature: printStatus() -> void

Returns: None

reportFinished(arg0)#

Signature: reportFinished(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

run()#

Signature: run() -> void

Returns: None

StrahlerAnalyzer #

dispose()#

Clears internal caches and mappings to free memory.

Signature: dispose() -> void

Returns: None

TracerCanvas #

action(arg0, arg1)#

Signature: action(Event, Object) -> boolean

Parameters:

arg0 (Any)
arg1 (Any)

Returns: bool

add(arg0)#

Signature: add(PopupMenu) -> void

Parameters:

arg0 (Any)

Returns: None

applyComponentOrientation(arg0)#

Signature: applyComponentOrientation(ComponentOrientation) -> void

Parameters:

arg0 (Any)

Returns: None

areFocusTraversalKeysSet(arg0)#

Signature: areFocusTraversalKeysSet(int) -> boolean

Parameters:

arg0 (int)

Returns: bool

bounds()#

Signature: bounds() -> Rectangle

Returns: Any

checkImage(arg0, arg1)#

Signature: checkImage(Image, ImageObserver) -> int

Parameters:

arg0 (Any)
arg1 (Any)

Returns: int

contains(arg0, arg1)#

Signature: contains(int, int) -> boolean

Parameters:

arg0 (int)
arg1 (int)

Returns: bool

createBufferStrategy(arg0, arg1)#

Signature: createBufferStrategy(int, BufferCapabilities) -> void

Parameters:

arg0 (int)
arg1 (Any)

Returns: None

createImage(arg0, arg1)#

Signature: createImage(int, int) -> Image

Parameters:

arg0 (int)
arg1 (int)

Returns: Any

createVolatileImage(arg0, arg1, arg2)#

Signature: createVolatileImage(int, int, ImageCapabilities) -> VolatileImage

Parameters:

arg0 (int)
arg1 (int)
arg2 (Any)

Returns: Any

cursorOverImage()#

Signature: cursorOverImage() -> boolean

Returns: bool

deliverEvent(arg0)#

Signature: deliverEvent(Event) -> void

Parameters:

arg0 (Any)

Returns: None

disable()#

Signature: disable() -> void

Returns: None

dispatchEvent(arg0)#

Signature: dispatchEvent(AWTEvent) -> void

Parameters:

arg0 (Any)

Returns: None

doLayout()#

Signature: doLayout() -> void

Returns: None

enable()#

Signature: enable() -> void

Returns: None

firePropertyChange(arg0, arg1, arg2)#

Signature: firePropertyChange(String, byte, byte) -> void

Parameters:

arg0 (str)
arg1 (int)
arg2 (int)

Returns: None

fitToWindow()#

Signature: fitToWindow() -> void

Returns: None

TracerThread #

createNewNode(arg0, arg1, arg2, arg3, arg4, arg5, arg6)#

Signature: createNewNode(int, int, int, double, double, DefaultSearchNode, byte) -> DefaultSearchNode

Parameters:

arg0 (int)
arg1 (int)
arg2 (int)
arg3 (float)
arg4 (float)
arg5 (Any)
arg6 (int)

Returns: Any

pointsConsideredInSearch()#

Signature: pointsConsideredInSearch() -> long

Returns: int

printStatus()#

Signature: printStatus() -> void

Returns: None

reportFinished(arg0)#

Signature: reportFinished(boolean) -> void

Parameters:

arg0 (bool)

Returns: None

run()#

Signature: run() -> void

Returns: None

Tree #

add(arg0)#

Adds a new Path to this Tree.

Signature: add(Path) -> boolean

Parameters:

arg0 (Path): - the Path to be added

Returns: (bool) true, if Path successful added

applyCanvasOffset(arg0, arg1, arg2)#

Specifies the offset to be used when rendering this Tree in a TracerCanvas. Path coordinates remain unaltered.

Signature: applyCanvasOffset(double, double, double) -> void

Parameters:

arg0 (float): - the x offset (in pixels)
arg1 (float)
arg2 (float)

Returns: None

applyProperties(arg0)#

Applies properties from another Tree to this Tree.

Signature: applyProperties(Tree) -> void

Parameters:

arg0 (Tree): - the Tree whose properties should be copied

Returns: None

assignImage(arg0)#

Assigns spatial calibration from a Dataset to this Tree.

Signature: assignImage(Dataset) -> void

Parameters:

arg0 (Any): - the Dataset providing the spatial calibration. Null allowed.

Returns: None

assignValue(arg0)#

Assigns a numeric property to this Tree.

Signature: assignValue(double) -> void

Parameters:

arg0 (float): - the value to be assigned to this Tree.

Returns: None

clone()#: Creates a deep copy of this Tree.

This method creates a complete copy of the tree including all paths and their relationships. Each path is cloned individually, and then the parent-child relationships are reconstructed in the cloned tree. This ensures that the cloned tree maintains the same structure as the original while being completely independent.

Signature: clone() -> Tree

Returns: (Tree) a new Tree that is a deep copy of this tree

downsample(arg0)#: Downsamples the tree, i.e., reduces the density of its nodes by increasing internode spacing.

Note that 1) upsampling is not supported (cf. {upsample(double)}, and 2) the position of nodes at branch points and tips remains unaltered during downsampling, as per Path.downsample(double).

Signature: downsample(double) -> void

Parameters:

arg0 (float): - the maximum allowed distance between path nodes.

Returns: None

get(arg0)#

Returns the Path at the specified position.

Signature: get(int) -> Path

Parameters:

arg0 (int): - index of the element to return

Returns: (Path) the element at the specified position

indexOf(arg0)#

Returns the index of the specified Path in this Tree.

Signature: indexOf(Path) -> int

Parameters:

arg0 (Path): - the Path to be searched for

Returns: (int) the path index, or -1 if it was not found

is3D()#

Assesses whether this Tree has depth.

Signature: is3D() -> boolean

Returns: (bool) true, if is 3D

list()#

Gets all the paths from this tree.

Signature: list() -> ArrayList

Returns: (List[Any]) the paths forming this tree

TreeColorMapper #

map(arg0, arg1, arg2)#

Colorizes a tree after the specified measurement. Mapping bounds are automatically determined.

Signature: map(Tree, String, String) -> void

Parameters:

arg0 (Tree)
arg1 (str)
arg2 (str)

Returns: None

mapTrees(arg0, arg1)#

Colorizes a list of trees, with each tree being assigned a LUT index.

Signature: mapTrees(List, String) -> void

Parameters:

arg0 (List[Any]): - the list of trees to be colorized
arg1 (str)

Returns: None

TreeStatistics #

context()#

Signature: context() -> Context

Returns: Any

dispose()#

Clears internal caches and mappings to free memory.

Signature: dispose() -> void

Returns: None

Tubeness #

accept(arg0)#

Signature: accept(RandomAccessibleInterval) -> void

Parameters:

arg0 (Any)

Returns: None

andThen(arg0)#

Signature: andThen(Consumer) -> Consumer

Parameters:

arg0 (Any)

Returns: Any

in()#

Signature: in() -> Object

Returns: Any

initialize()#

Signature: initialize() -> void

Returns: None

ops()#

Signature: ops() -> OpEnvironment

Returns: Any

out()#

Signature: out() -> Object

Returns: Any

run(arg0)#

Signature: run(Object) -> Object

Parameters:

arg0 (Any)

Returns: Any

Viewer2D #

add(arg0)#

Appends a tree to the viewer rendered after the specified measurement.

Signature: add(Object) -> void

Parameters:

arg0 (Any): - the tree to be plotted

Returns: None

map(arg0, arg1, arg2)#

Signature: map(Tree, String, String) -> void

Parameters:

arg0 (Tree)
arg1 (str)
arg2 (str)

Returns: None

mapTrees(arg0, arg1)#

Signature: mapTrees(List, String) -> void

Parameters:

arg0 (List[Any])
arg1 (str)

Returns: None

show()#

Displays the current plot on a dedicated frame *

Signature: show() -> void

Returns: None

Viewer3D #

add(arg0, arg1)#

Script friendly method to add a supported object (Tree, OBJMesh, AbstractDrawable, etc.) to this viewer. Note that collections of supported objects are also supported, which is an effective way of adding multiple items since the scene is only rebuilt once all items have been added.

Signature: add(File;, String) -> void

Parameters:

arg0 (Any)
arg1 (str)

Returns: None

annotateLine(arg0, arg1)#

Adds a line annotation to this viewer.

Signature: annotateLine(Collection, String) -> Annotation3D

Parameters:

arg0 (List[Any]): - the collection of points in the line annotation (at least 2 elements required). Start and end of line are highlighted if 2 points are specified.
arg1 (str)

Returns: (Any) the Annotation3D or null if collection contains less than 2 elements

annotateMidPlane(arg0, arg1, arg2)#

Signature: annotateMidPlane(BoundingBox, int, String) -> Annotation3D

Parameters:

arg0 (BoundingBox)
arg1 (int)
arg2 (str)

Returns: Any

annotatePlane(arg0, arg1, arg2)#

Signature: annotatePlane(SNTPoint, SNTPoint, String) -> Annotation3D

Parameters:

arg0 (SNTPoint)
arg1 (SNTPoint)
arg2 (str)

Returns: Any

annotatePoint(arg0, arg1)#

Adds a highlighting point annotation to this viewer.

Signature: annotatePoint(SNTPoint, String) -> Annotation3D

Parameters:

arg0 (SNTPoint): - the node to be highlighted
arg1 (str)

Returns: (Any) the Annotation3D

annotatePoints(arg0, arg1)#

Adds a scatter (point cloud) annotation to this viewer.

Signature: annotatePoints(Collection, String) -> Annotation3D

Parameters:

arg0 (List[Any]): - the collection of points in the annotation
arg1 (str)

Returns: (Any) the Annotation3D

annotateSurface(arg0, arg1, arg2)#

Computes a convex hull from a collection of points and adds it to the scene as an annotation.

Signature: annotateSurface(Collection, String, boolean) -> Annotation3D

Parameters:

arg0 (List[Any])
arg1 (str)
arg2 (bool)

Returns: Any

dispose()#

Closes and releases all the resources used by this viewer.

Signature: dispose() -> void

Returns: None

duplicate()#: Creates a duplicate of this viewer containing only visible objects.

This method creates a new Viewer3D instance and copies all currently visible objects (trees, meshes, annotations) from this viewer to the new one. The duplicate viewer maintains the same visual settings and object properties but operates independently from the original.

Signature: duplicate() -> Viewer3D

Returns: (Viewer3D) a new Viewer3D instance containing copies of all visible objects

freeze()#

Does not allow scene to be interactive. Only static orthogonal views allowed.

Signature: freeze() -> void

Returns: None

logSceneControls()#

Logs API calls controlling the scene (view point, bounds, etc.) to Script Recorder (or Console if Script Recorder is not running). Useful for programmatic control of animations.

Signature: logSceneControls() -> void

Returns: None

mergeAnnotations(arg0, arg1)#

Merges a collection of annotations into a single object.

Signature: mergeAnnotations(Collection, String) -> Annotation3D

Parameters:

arg0 (List[Any]): - the collection of annotations.
arg1 (str)

Returns: (Any) the merged Annotation3D

rebuild(arg0)#

Rebuilds (repaints) a scene object (e.g., a Tree after being modified elsewhere)

Signature: rebuild(Object) -> void

Parameters:

arg0 (Any): - the object to be re-rendered (or its label)

Returns: None

recordRotation(arg0, arg1, arg2)#

Records an animated rotation of the scene as a sequence of images.

Signature: recordRotation(float, int, File) -> void

Parameters:

arg0 (float): - the rotation angle (e.g., 360 for a full rotation)
arg1 (int)
arg2 (str)

Returns: None

WekaModelLoader #

context()#

Signature: context() -> Context

Returns: Any

initialize()#

Signature: initialize() -> void

Returns: None

resolveInput(arg0)#

Signature: resolveInput(String) -> void

Parameters:

arg0 (str)

Returns: None

resolveOutput(arg0)#

Signature: resolveOutput(String) -> void

Parameters:

arg0 (str)

Returns: None

run()#

Signature: run() -> void

Returns: None

uncancel()#

Signature: uncancel() -> void

Returns: None

unresolveInput(arg0)#

Signature: unresolveInput(String) -> void

Parameters:

arg0 (str)

Returns: None

unresolveOutput(arg0)#

Signature: unresolveOutput(String) -> void

Parameters:

arg0 (str)

Returns: None

Category index generated on 2026-01-02 23:09:09