Getters Methods#

Methods that retrieve values or properties from objects.

Total methods in this category: 544

AllenCompartment#

getAncestor(arg0)#

Gets the nth ancestor of this compartment.

Signature: getAncestor(int) -> AllenCompartment

Parameters:

  • arg0 (int): - the ancestor level as negative 1-based index. E.g.,

Returns: (Any) the nth ancestor

getAncestors()#

Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.

Signature: getAncestors() -> List

Returns: (List[Any]) the “flattened” list of ancestors

getChildren(arg0)#

Gets the child ontologies of this compartment as a flat (non-hierarchical) list.

Signature: getChildren(int) -> List

Parameters:

  • arg0 (int): - maximum depth that should be considered.

Returns: (List[Any]) the “flattened” ontologies list

getMesh()#

Signature: getMesh() -> OBJMesh

Returns: (Any) the mesh associated with this compartment

getOntologyDepth()#

Gets the ontology depth of this compartment.

Signature: getOntologyDepth() -> int

Returns: (int) the ontological depth of this compartment, i.e., its ontological distance relative to the root (e.g., a compartment of hierarchical level 9, has a depth of 8).

getParent()#

Gets the parent of this compartment.

Signature: getParent() -> BrainAnnotation

Returns: Any

getTreePath()#

Gets the tree path of this compartment. The TreePath is the list of parent compartments that uniquely identify this compartment in the ontologies hierarchical tree. The elements of the list are ordered with the root (‘Whole Brain’) as the first element of the list. In practice, this is equivalent to appending this compartment to the list returned by getAncestors().

Signature: getTreePath() -> List

Returns: (List[Any]) the tree path that uniquely identifies this compartment as a node in the CCF ontologies tree

getUUID()#

Signature: getUUID() -> UUID

Returns: Any

isChildOf(arg0)#

Assesses if this annotation is a child of a specified compartment.

Signature: isChildOf(BrainAnnotation) -> boolean

Parameters:

  • arg0 (Any): - the compartment to be tested

Returns: (bool) true, if successful, i.e., parentCompartment is not this compartment and getTreePath() contains parentCompartment

isMeshAvailable()#

Checks whether a mesh is known to be available for this compartment.

Signature: isMeshAvailable() -> boolean

Returns: (bool) true, if a mesh is available.

isParentOf(arg0)#

Assesses if this annotation is the parent of the specified compartment.

Signature: isParentOf(BrainAnnotation) -> boolean

Parameters:

  • arg0 (Any): - the compartment to be tested

Returns: (bool) true, if successful, i.e., childCompartment is not this compartment and is present in getChildren()

Annotation3D#

getBarycentre()#

Returns the center of this annotation bounding box.

Signature: getBarycentre() -> SNTPoint

Returns: (SNTPoint) the barycentre of this annotation. All coordinates are set to Double.NaN if the bounding box is not available.

getColor()#

Signature: getColor() -> ColorRGB

Returns: Any

getDrawable()#

Returns the AbstractDrawable associated with this annotation.

Signature: getDrawable() -> Drawable

Returns: (Any) the AbstractDrawable

getLabel()#

Gets the annotation label

Signature: getLabel() -> String

Returns: (str) the label, as listed in Reconstruction Viewer’s list.

getType()#

Gets the type of this annotation.

Signature: getType() -> String

Returns: (str) the annotation type. Either cloud (point cloud), surface, line, plane, or mixed (composite shape).

getVolume()#

Signature: getVolume() -> double

Returns: float

isColorCodeAllowed()#

Signature: isColorCodeAllowed() -> boolean

Returns: bool

setSize(arg0)#

Sets the annotation width.

Signature: setSize(Number) -> void

Parameters:

  • arg0 (Union[int, float]): - the new width. A negative value will set width to Viewer3D’s default.

Returns: None

BiSearch#

getNodesAsImage()#

Signature: getNodesAsImage() -> SearchImageStack

Returns: Any

getResult()#

Signature: getResult() -> Path

Returns: Path

BiSearchNode#

getF(arg0)#

Signature: getF(boolean) -> double

Parameters:

  • arg0 (bool)

Returns: float

getFFromGoal()#

Signature: getFFromGoal() -> double

Returns: float

getFFromStart()#

Signature: getFFromStart() -> double

Returns: float

getG(arg0)#

Signature: getG(boolean) -> double

Parameters:

  • arg0 (bool)

Returns: float

getGFromGoal()#

Signature: getGFromGoal() -> double

Returns: float

getGFromStart()#

Signature: getGFromStart() -> double

Returns: float

getHeapHandle(arg0)#

Signature: getHeapHandle(boolean) -> AddressableHeap$Handle

Parameters:

  • arg0 (bool)

Returns: Any

getHeapHandleFromGoal()#

Signature: getHeapHandleFromGoal() -> AddressableHeap$Handle

Returns: Any

getHeapHandleFromStart()#

Signature: getHeapHandleFromStart() -> AddressableHeap$Handle

Returns: Any

getPredecessorFromGoal()#

Signature: getPredecessorFromGoal() -> BiSearchNode

Returns: BiSearchNode

getPredecessorFromStart()#

Signature: getPredecessorFromStart() -> BiSearchNode

Returns: BiSearchNode

getState(arg0)#

Signature: getState(boolean) -> BiSearchNode$State

Parameters:

  • arg0 (bool)

Returns: Any

getStateFromGoal()#

Signature: getStateFromGoal() -> BiSearchNode$State

Returns: Any

getStateFromStart()#

Signature: getStateFromStart() -> BiSearchNode$State

Returns: Any

getX()#

Signature: getX() -> int

Returns: int

getY()#

Signature: getY() -> int

Returns: int

getZ()#

Signature: getZ() -> int

Returns: int

BoundingBox#

getCalibration()#

Creates a Calibration object using information from this BoundingBox

Signature: getCalibration() -> Calibration

Returns: (Any) the Calibration object

getCentroid()#

Signature: getCentroid() -> SNTPoint

Returns: SNTPoint

getDiagonal()#

Gets the box diagonal

Signature: getDiagonal() -> double

Returns: (float) the diagonal of BoundingBox

getDimensions()#

Gets this BoundingBox dimensions.

Signature: getDimensions() -> [D

Returns: Any

getUnit()#

Gets the length unit of voxel spacing

Signature: getUnit() -> String

Returns: (str) the unit

hasDimensions()#

Signature: hasDimensions() -> boolean

Returns: bool

isScaled()#

Checks whether this BoundingBox is spatially calibrated, i.e., if voxel spacing has been specified

Signature: isScaled() -> boolean

Returns: (bool) true, if voxel spacing has been specified

ConvexHull2D#

boundarySize()#

Signature: boundarySize() -> double

Returns: float

getPolygon()#

Signature: getPolygon() -> Polygon2D

Returns: Any

size()#

Signature: size() -> double

Returns: float

ConvexHull3D#

boundarySize()#

Signature: boundarySize() -> double

Returns: float

getMesh()#

Signature: getMesh() -> Mesh

Returns: Any

size()#

Signature: size() -> double

Returns: float

ConvexHullAnalyzer#

cancel(arg0)#

Signature: cancel(String) -> void

Parameters:

  • arg0 (str)

Returns: None

getAnalysis()#

Gets all computed convex hull analysis metrics.

Returns a map containing all the computed convex hull metrics and their values. The metrics are computed lazily and cached for subsequent calls. If the hull cannot be computed, all metrics return NaN.

Signature: getAnalysis() -> Map

Returns: (Dict[str, Any]) a map of metric names to their computed values

getBoundarySize()#

Gets the boundary size (perimeter for 2D hulls or surface area for 3D hulls) of the convex hull.

Signature: getBoundarySize() -> double

Returns: (float) the boundary size of the convex hull

getBoxivity()#

Gets the boxivity of the convex hull, which measures how box-like the convex hull is. Values closer to 1 indicate a more box-like shape.

Signature: getBoxivity() -> double

Returns: (float) the boxivity value

getCancelReason()#

Signature: getCancelReason() -> String

Returns: str

getCentroid()#

Signature: getCentroid() -> PointInImage

Returns: PointInImage

getCompactness()#

Signature: getCompactness() -> double

Returns: float

getContext()#

Signature: getContext() -> Context

Returns: Any

getEccentricity()#

Signature: getEccentricity() -> double

Returns: float

getElongation()#

Gets the elongation of the convex hull, which measures how elongated the convex hull is. Higher values indicate more elongated shapes.

Signature: getElongation() -> double

Returns: (float) the elongation value

getHull()#

Gets the convex hull object being analyzed. The hull is initialized if needed.

Signature: getHull() -> AbstractConvexHull

Returns: (Any) the convex hull object

getRoundness()#

Gets the roundness of the convex hull, which measures how round or circular the convex hull is. Values closer to 1 indicate a more round shape.

Signature: getRoundness() -> double

Returns: (float) the roundness value

getSize()#

Gets the size (area or volume) of the convex hull, which is the area for 2D hulls or the volume for 3D hulls.

Signature: getSize() -> double

Returns: (float) the size of the convex hull

getTree()#

Gets the tree being analyzed.

Signature: getTree() -> Tree

Returns: (Tree) the tree being analyzed, or null if the analyzer was created directly from a convex hull.

getUnit(arg0)#

Returns the physical unit associated with the specified metric.

Signature: getUnit(String) -> String

Parameters:

  • arg0 (str): - the supported metric to be queried (case-sensitive)

Returns: (str) physical unit

isCanceled()#

Signature: isCanceled() -> boolean

Returns: bool

DefaultSearchNode#

getHandle()#

Signature: getHandle() -> AddressableHeap$Handle

Returns: Any

getPredecessor()#

Signature: getPredecessor() -> DefaultSearchNode

Returns: Any

getX()#

Signature: getX() -> int

Returns: int

getY()#

Signature: getY() -> int

Returns: int

getZ()#

Signature: getZ() -> int

Returns: int

Fill#

getEstimatedMeanRadius()#

Returns the estimated mean radius of the fill, assuming a cylindric shape

Signature: getEstimatedMeanRadius() -> double

Returns: (float) the estimated mean radius

getMetric()#

Signature: getMetric() -> SNT$CostType

Returns: Any

getNodeList()#

Returns the list of nodes in the filled structure.

Signature: getNodeList() -> List

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

getSourcePaths()#

Returns the set of source paths for the filled structure.

Signature: getSourcePaths() -> Set

Returns: (Set[Any]) the set of source paths

getSourcePathsStringHuman()#

Signature: getSourcePathsStringHuman() -> String

Returns: str

getSourcePathsStringMachine()#

Signature: getSourcePathsStringMachine() -> String

Returns: str

getThreshold()#

Signature: getThreshold() -> double

Returns: float

getVolume()#

Returns the Fill volume. It assumes that the volume is just the number of sub-threshold nodes multiplied by x_spacing * y_spacing * z_spacing.

Signature: getVolume() -> double

Returns: (float) the volume

FillConverter#

getFillerStack()#

Merges the input FillerThreads into a single SearchImageStack. When a filled voxel position is present in multiple filler instances, the node with the lowest g-score is chosen for inclusion in the merged stack.

Signature: getFillerStack() -> SearchImageStack

Returns: (Any) the merged filler stack

FillerThread#

getDistanceAtPoint(arg0, arg1, arg2)#

Signature: getDistanceAtPoint(double, double, double) -> double

Parameters:

  • arg0 (float)

  • arg1 (float)

  • arg2 (float)

Returns: float

getExitReason()#

Signature: getExitReason() -> int

Returns: int

getFill()#

Signature: getFill() -> Fill

Returns: Any

getNodesAsImage()#

Signature: getNodesAsImage() -> SearchImageStack

Returns: Any

getNodesAsImageFromGoal()#

Signature: getNodesAsImageFromGoal() -> SearchImageStack

Returns: Any

getNodesAsImageFromStart()#

Signature: getNodesAsImageFromStart() -> SearchImageStack

Returns: Any

getResult()#

Signature: getResult() -> Path

Returns: Path

getThreshold()#

Signature: getThreshold() -> double

Returns: float

FlyCircuitLoader#

getReader(arg0)#

Gets the SWC data associated with the specified cell ID as a reader

Signature: getReader(String) -> BufferedReader

Parameters:

  • arg0 (str): - the ID of the cell to be retrieved

Returns: (Any) the character stream containing the data, or null if cell ID was not found or could not be retrieved

getReconstructionURL(arg0)#

Gets the URL of the SWC file associated with the specified cell ID.

Signature: getReconstructionURL(String) -> String

Parameters:

  • arg0 (str): - the ID of the cell to be retrieved

Returns: (str) the reconstruction URL

getTree(arg0)#

Gets the collection of Paths for the specified cell ID

Signature: getTree(String) -> Tree

Parameters:

  • arg0 (str): - the ID of the cell to be retrieved

Returns: (Tree) the data for the specified cell as a Tree, or null if data could not be retrieved

isDatabaseAvailable()#

Checks whether a connection to the FlyCircuit database can be established.

Signature: isDatabaseAvailable() -> boolean

Returns: (bool) true, if an HHTP connection could be established, false otherwise

Frangi#

getArity()#

Signature: getArity() -> int

Returns: int

getIndependentInstance()#

Signature: getIndependentInstance() -> UnaryComputerOp

Returns: Any

GroupedTreeStatistics#

getBoxPlot(arg0, arg1)#

Assembles a Box and Whisker Plot for the specified feature.

Signature: getBoxPlot(String, Collection) -> SNTChart

Parameters:

  • arg0 (str): - the feature (“Cable length”, “No. of branch points”, “No. of tips”, etc.). Note that the majority of TreeStatistics.getAllMetrics() metrics are currently not supported.

  • arg1 (List[Any])

Returns: (SNTChart) the box plot

getFlowPlot(arg0, arg1, arg2, arg3)#

Assembles a Flow plot (aka Sankey diagram) for the specified feature.

Signature: getFlowPlot(String, int, double, boolean) -> SNTChart

Parameters:

  • arg0 (str)

  • arg1 (int)

  • arg2 (float)

  • arg3 (bool)

Returns: SNTChart

getGroupStats(arg0)#

Gets the group statistics.

Signature: getGroupStats(String) -> MultiTreeStatistics

Parameters:

  • arg0 (str): - the unique label identifying the group

Returns: (MultiTreeStatistics) the group statistics or null if no group is mapped to groupLabel

getGroups()#

Gets the group identifiers currently queued for analysis.

Signature: getGroups() -> List

Returns: (List[Any]) the group identifiers

getHistogram(arg0)#

Gets the relative frequencies histogram for a univariate measurement. The number of bins is determined using the Freedman-Diaconis rule.

Signature: getHistogram(String) -> SNTChart

Parameters:

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

Returns: (SNTChart) the frame holding the histogram

getN(arg0)#

Gets the number of Trees in a specified group.

Signature: getN(String) -> int

Parameters:

  • arg0 (str): - the unique label identifying the group

Returns: (int) the number of Trees or -1 if no group is mapped to groupLabel

getPolarHistogram(arg0)#

Gets the relative frequencies histogram for a univariate measurement as a polar (rose) plot assuming a data range between [0-360]. The number of bins is determined using the Freedman-Diaconis rule.

Signature: getPolarHistogram(String) -> SNTChart

Parameters:

  • arg0 (str): - the measurement (e.g., MultiTreeStatistics.AVG_REMOTE_ANGLE

Returns: (SNTChart) the frame holding the histogram

InsectBrainCompartment#

getAncestor(arg0)#

Signature: getAncestor(int) -> BrainAnnotation

Parameters:

  • arg0 (int): - the ancestor level as negative 1-based index. E.g.,

Returns: (Any) the ancestor of this compartment at the nth level

getMesh()#

Signature: getMesh() -> OBJMesh

Returns: (Any) the mesh associated with this compartment

getOntologyDepth()#

Signature: getOntologyDepth() -> int

Returns: int

getParent()#

Signature: getParent() -> BrainAnnotation

Returns: (Any) the parent of this compartment

isChildOf(arg0)#

Signature: isChildOf(BrainAnnotation) -> boolean

Parameters:

  • arg0 (Any)

Returns: (bool) whether this compartment is a sub-compartment of annotation

isMeshAvailable()#

Signature: isMeshAvailable() -> boolean

Returns: (bool) whether a mesh is available for this compartment

isParentOf(arg0)#

Signature: isParentOf(BrainAnnotation) -> boolean

Parameters:

  • arg0 (Any)

Returns: (bool) whether this compartment is a parentCompartment of annotation

InsectBrainLoader#

getAnnotations()#

Gets the brain compartment annotations for this neuron.

Signature: getAnnotations() -> List

Returns: (List[Any]) list of InsectBrainCompartment annotations, or null if not available

getMeshes()#

Gets the 3D meshes associated with this neuron’s brain compartments.

Signature: getMeshes() -> List

Returns: (List[Any]) list of OBJMesh objects representing brain compartments

getNeuronInfo()#

Signature: getNeuronInfo() -> InsectBrainLoader$NeuronInfo

Returns: Any

getTree()#

Gets the collection of Paths for the specified cell ID

Signature: getTree() -> Tree

Returns: (Tree) the data for the specified cell as a Tree, or null if data could not be retrieved

InteractiveTracerCanvas#

getAccessibleContext()#

Signature: getAccessibleContext() -> AccessibleContext

Returns: Any

getAlignmentX()#

Signature: getAlignmentX() -> float

Returns: float

getAlignmentY()#

Signature: getAlignmentY() -> float

Returns: float

getAnnotationsColor()#

Signature: getAnnotationsColor() -> Color

Returns: Any

getBackground()#

Signature: getBackground() -> Color

Returns: Any

getBaseline(arg0, arg1)#

Signature: getBaseline(int, int) -> int

Parameters:

  • arg0 (int)

  • arg1 (int)

Returns: int

MouseLightLoader#

getDOI()#

Gets the DOI for this neuron.

Signature: getDOI() -> String

Returns: (str) the DOI string, or null if not available

getID()#

Gets the neuron ID for this loader.

Signature: getID() -> String

Returns: (str) the neuron ID

getJSON()#

Gets all the data associated with this reconstruction as a JSON object.

Signature: getJSON() -> JSONObject

Returns: (Any) the JSON data (null if data could not be retrieved).

getNodes()#

Script-friendly method to extract the nodes of a cellular compartment.

Signature: getNodes() -> TreeSet

Returns: Set[Any]

getSWC()#

Gets all the data associated with this reconstruction in the SWC format.

Signature: getSWC() -> String

Returns: (str) the SWC data (null if data could not be retrieved).

getSampleInfo()#

Gets sample information for this neuron.

Signature: getSampleInfo() -> String

Returns: (str) the sample information as a JSON string, or null if not available

getSomaCompartment()#

Gets the brain compartment containing the soma.

Signature: getSomaCompartment() -> AllenCompartment

Returns: (Any) the AllenCompartment containing the soma

getSomaLocation()#

Gets the soma location for this neuron.

Signature: getSomaLocation() -> SWCPoint

Returns: (SWCPoint) the SWCPoint representing the soma location

getTree()#

Script-friendly method to extract the entire neuron as a collection of Paths.

Signature: getTree() -> Tree

Returns: (Tree) the neuron as a Tree, or null if data could not be retrieved

static getNeuronCount()

Gets the number of cells publicly available in the MouseLight database.

Signature: static getNeuronCount() -> int

Returns: (int) the number of available cells, or -1 if the database could not be reached.

MouseLightQuerier#

static getNeuronCount()

Gets the number of cells publicly available in the MouseLight database.

Signature: static getNeuronCount() -> int

Returns: (int) the number of available cells, or -1 if the database could not be reached.

MultiTreeColorMapper#

getAvailableLuts()#

Signature: getAvailableLuts() -> Set

Returns: Set[Any]

getColor(arg0)#

Signature: getColor(double) -> Color

Parameters:

  • arg0 (float)

Returns: Any

getColorRGB(arg0)#

Signature: getColorRGB(double) -> ColorRGB

Parameters:

  • arg0 (float)

Returns: Any

getColorTable(arg0)#

Signature: getColorTable(String) -> ColorTable

Parameters:

  • arg0 (str)

Returns: Any

getMinMax()#

Signature: getMinMax() -> [D

Returns: Any

getMultiViewer()#

Description copied from class: TreeColorMapper

Signature: getMultiViewer() -> MultiViewer2D

Returns: (MultiViewer2D) the multi-viewer instance

getNaNColor()#

Signature: getNaNColor() -> Color

Returns: Any

isIntegerScale()#

Signature: isIntegerScale() -> boolean

Returns: bool

isNodeMapping()#

Signature: isNodeMapping() -> boolean

Returns: bool

MultiTreeStatistics#

cancel(arg0)#

Main method for testing and demonstration purposes.

Creates a MultiTreeStatistics instance using demo data and displays various analysis plots including histograms and flow plots. This method is primarily used for development and debugging.

Signature: cancel(String) -> void

Parameters:

  • arg0 (str): - command line arguments (not used)

Returns: None

getAnnotatedLength(arg0)#

Description copied from class: TreeStatistics

Signature: getAnnotatedLength(int) -> Map

Parameters:

  • arg0 (int): - the ontological depth of the compartments to be considered

Returns: (Dict[str, Any]) the map containing the brain compartments as keys, and cable lengths as values.

getAnnotatedLengthHistogram(arg0)#

Signature: getAnnotatedLengthHistogram(int) -> SNTChart

Parameters:

  • arg0 (int)

Returns: SNTChart

getAnnotatedLengthsByHemisphere(arg0)#

Description copied from class: TreeStatistics

Signature: getAnnotatedLengthsByHemisphere(int) -> Map

Parameters:

  • arg0 (int): - the ontological depth of the compartments to be considered

Returns: (Dict[str, Any]) the map containing the brain compartments as keys, and cable lengths per hemisphere as values.

getAnnotations()#

Description copied from class: TreeStatistics

Signature: getAnnotations() -> Set

Returns: Set[Any]

getAvgBranchLength()#

Signature: getAvgBranchLength() -> double

Returns: float

getAvgContraction()#

Signature: getAvgContraction() -> double

Returns: float

getAvgFractalDimension()#

Signature: getAvgFractalDimension() -> double

Returns: float

getAvgFragmentation()#

Signature: getAvgFragmentation() -> double

Returns: float

getAvgPartitionAsymmetry()#

Signature: getAvgPartitionAsymmetry() -> double

Returns: float

getAvgRemoteBifAngle()#

Signature: getAvgRemoteBifAngle() -> double

Returns: float

getBoxPlot(arg0)#

Signature: getBoxPlot(String) -> SNTChart

Parameters:

  • arg0 (str)

Returns: SNTChart

getBranchPoints()#

Description copied from class: TreeStatistics

Signature: getBranchPoints() -> Set

Returns: (Set[Any]) the branch points positions

getBranches()#

Description copied from class: TreeStatistics

Signature: getBranches() -> List

Returns: (List[Any]) the list of branches as Path objects.

getCableLength()#

Description copied from class: TreeStatistics

Signature: getCableLength() -> double

Returns: float

getCableLengthNorm(arg0)#

Signature: getCableLengthNorm(BrainAnnotation) -> double

Parameters:

  • arg0 (Any)

Returns: float

getCancelReason()#

Signature: getCancelReason() -> String

Returns: str

getContext()#

Signature: getContext() -> Context

Returns: Any

getConvexAnalyzer()#

Signature: getConvexAnalyzer() -> ConvexHullAnalyzer

Returns: Any

getConvexHullMetric(arg0)#

Signature: getConvexHullMetric(String) -> double

Parameters:

  • arg0 (str)

Returns: float

getDepth()#

Signature: getDepth() -> double

Returns: float

getDescriptiveStats(arg0)#

Description copied from class: TreeStatistics

Signature: getDescriptiveStats(String) -> DescriptiveStatistics

Parameters:

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

Returns: (Any) the DescriptiveStatistics object.

getFlowPlot(arg0, arg1, arg2, arg3, arg4)#

Description copied from class: TreeStatistics

Signature: getFlowPlot(String, Collection, String, double, boolean) -> SNTChart

Parameters:

  • arg0 (str)

  • arg1 (List[Any])

  • arg2 (str)

  • arg3 (float)

  • arg4 (bool)

Returns: SNTChart

getFractalDimension()#

Signature: getFractalDimension() -> List

Returns: List[Any]

getGroup()#

Gets the collection of Trees being analyzed.

Signature: getGroup() -> Collection

Returns: (List[Any]) the Tree group

getHeight()#

Signature: getHeight() -> double

Returns: float

getHighestPathOrder()#

Signature: getHighestPathOrder() -> int

Returns: int

getHistogram(arg0)#

Description copied from class: TreeStatistics

Signature: getHistogram(String) -> SNTChart

Parameters:

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

Returns: (SNTChart) the frame holding the histogram

getInnerBranches()#

Description copied from class: TreeStatistics

Signature: getInnerBranches() -> List

Returns: (List[Any]) the list containing the “inner” branches. Note that these branches (Path segments) will not carry any connectivity information.

getInnerLength()#

Signature: getInnerLength() -> double

Returns: float

getMetric(arg0)#

Signature: getMetric(String) -> Number

Parameters:

  • arg0 (str)

Returns: Union[int, float]

NeuroMorphoLoader#

getReader(arg0)#

Gets the SWC data (‘CNG version’) associated with the specified cell ID as a reader

Signature: getReader(String) -> BufferedReader

Parameters:

  • arg0 (str): - the ID of the cell to be retrieved

Returns: (Any) the character stream containing the data, or null if cell ID was not found or could not be retrieved

getReconstructionURL(arg0)#

Gets the URL of the SWC file (‘CNG version’) associated with the specified cell ID.

Signature: getReconstructionURL(String) -> String

Parameters:

  • arg0 (str): - the ID of the cell to be retrieved

Returns: (str) the reconstruction URL, or null if cell ID was not found or could not be retrieved

getTree(arg0)#

Gets the collection of Paths for the specified cell ID

Signature: getTree(String) -> Tree

Parameters:

  • arg0 (str): - the ID of the cell to be retrieved

Returns: (Tree) the data (‘CNG version’) for the specified cell as a Tree, or null if data could not be retrieved

isDatabaseAvailable()#

Checks whether a connection to the NeuroMorpho database can be established.

Signature: isDatabaseAvailable() -> boolean

Returns: (bool) true, if an HHTP connection could be established, false otherwise

NodeColorMapper#

getAvailableLuts()#

Gets the available LUTs.

Signature: getAvailableLuts() -> Set

Returns: (Set[Any]) the set of keys, corresponding to the set of LUTs available

getColor(arg0)#

Signature: getColor(double) -> Color

Parameters:

  • arg0 (float)

Returns: Any

getColorRGB(arg0)#

Signature: getColorRGB(double) -> ColorRGB

Parameters:

  • arg0 (float)

Returns: Any

getColorTable(arg0)#

Description copied from class: ColorMapper

Signature: getColorTable(String) -> ColorTable

Parameters:

  • arg0 (str)

Returns: Any

getMinMax()#

Description copied from class: ColorMapper

Signature: getMinMax() -> [D

Returns: (Any) a two-element array with current {minimum, maximum} mapping bounds

getNaNColor()#

Signature: getNaNColor() -> Color

Returns: Any

getNodes()#

Gets the collection of nodes being mapped.

Signature: getNodes() -> Collection

Returns: (List[Any]) the collection of SNTPoint nodes

getNodesByColor()#

Signature: getNodesByColor() -> Map

Returns: Dict[str, Any]

isIntegerScale()#

Signature: isIntegerScale() -> boolean

Returns: bool

NodeProfiler#

cancel(arg0)#

Signature: cancel(String) -> void

Parameters:

  • arg0 (str)

Returns: None

getCancelReason()#

Signature: getCancelReason() -> String

Returns: str

getContext()#

Signature: getContext() -> Context

Returns: Any

getDelegateObject()#

Signature: getDelegateObject() -> Object

Returns: Any

getInfo()#

Signature: getInfo() -> DynamicCommandInfo

Returns: Any

getInput(arg0)#

Signature: getInput(String) -> Object

Parameters:

  • arg0 (str)

Returns: Any

getInputs()#

Signature: getInputs() -> Map

Returns: Dict[str, Any]

getOutput(arg0)#

Signature: getOutput(String) -> Object

Parameters:

  • arg0 (str)

Returns: Any

getOutputs()#

Signature: getOutputs() -> Map

Returns: Dict[str, Any]

getPlot(arg0, arg1)#

Signature: getPlot(Path, int) -> Plot

Parameters:

  • arg0 (Path)

  • arg1 (int)

Returns: Any

getTable(arg0, arg1)#

Signature: getTable(Path, int) -> SNTTable

Parameters:

  • arg0 (Path)

  • arg1 (int)

Returns: SNTTable

getValues(arg0, arg1, arg2)#

Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)

Signature: getValues(Path, int, int) -> SortedMap

Parameters:

  • arg0 (Path)

  • arg1 (int)

  • arg2 (int)

Returns: Any

isCanceled()#

Signature: isCanceled() -> boolean

Returns: bool

isInputResolved(arg0)#

Signature: isInputResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

isOutputResolved(arg0)#

Signature: isOutputResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

isResolved(arg0)#

Signature: isResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

NodeStatistics#

getAnnotatedFrequencies()#

Retrieves the count frequencies across brain compartment.

Signature: getAnnotatedFrequencies() -> Map

Returns: Dict[str, Any]

getAnnotatedFrequenciesByHemisphere(arg0, arg1)#

Signature: getAnnotatedFrequenciesByHemisphere(int, Tree) -> Map

Parameters:

  • arg0 (int)

  • arg1 (Tree)

Returns: Dict[str, Any]

getAnnotatedFrequencyHistogram(arg0, arg1, arg2)#

Retrieves the histogram of count frequencies across brain areas of the specified ontology level across the specified hemisphere.

Signature: getAnnotatedFrequencyHistogram(int, String, Tree) -> SNTChart

Parameters:

  • arg0 (int): - the ontological depth of the compartments to be considered

  • arg1 (str)

  • arg2 (Tree)

Returns: (SNTChart) the annotated frequencies histogram

getAnnotatedHistogram()#

Retrieves the histogram of count frequencies across brain areas of the specified ontology level.

Signature: getAnnotatedHistogram() -> SNTChart

Returns: SNTChart

getAnnotatedNodes(arg0)#

Splits the nodes being analyzed into groups sharing the same brain annotation.

Signature: getAnnotatedNodes(int) -> Map

Parameters:

  • arg0 (int): - the ontological depth of the compartments to be considered

Returns: (Dict[str, Any]) the map containing the brain annotations as keys, and list of nodes as values.

getDescriptiveStatistics(arg0)#

Computes the DescriptiveStatistics for the specified measurement.

Signature: getDescriptiveStatistics(String) -> DescriptiveStatistics

Parameters:

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

Returns: (Any) the DescriptiveStatistics object.

getHistogram(arg0)#

Gets the relative frequencies histogram for a univariate measurement. The number of bins is determined using the Freedman-Diaconis rule.

Signature: getHistogram(String) -> SNTChart

Parameters:

  • arg0 (str): - the measurement (X_COORDINATES, RADIUS, etc.)

Returns: (SNTChart) the frame holding the histogram

Path#

getAngle(arg0)#

Computes the angle between the specified node and its two flanking neighbors.

With B being the specified node, A its previous neighbor, and C is next neighbor, computes the angle between the vectors AB, and BC.

Signature: getAngle(int) -> double

Parameters:

  • arg0 (int)

Returns: (float) the angle in degrees (0-360 range) or Double.NaN if specified node does not have sufficient neighbors

getApproximatedSurface()#

Returns an estimated surface area of this path, treating each inter-node segment as a frustum.

Signature: getApproximatedSurface() -> double

Returns: (float) the approximate surface area (in physical units), or 0 if this Path has no radii

getApproximatedVolume()#

Returns an estimated volume of this path.

The most accurate volume of each path segment would be the volume of a convex hull of two arbitrarily oriented and sized circles in space. This is tough to work out analytically, and this precision isn’t really warranted given the errors introduced in the fitting process, the tracing in the first place, etc. So, this method produces an approximate volume assuming that the volume of each of these parts is that of a truncated cone (Frustum) , with circles of the same size (i.e., as if the circles had simply been reoriented to be parallel and have a common normal vector)

For more accurate measurements of the volumes of a neuron, you should use the filling interface.

Signature: getApproximatedVolume() -> double

Returns: (float) the approximate fitted volume (in physical units), or NaN if this Path has no radii

getBranchPoint()#

Gets the branch point (junction) where this path starts, i.e., connects to its parent path.

Signature: getBranchPoint() -> PointInImage

Returns: (PointInImage) the start junction point, or null if this is a primary path

getBranchPointIndex()#

Gets the index of the branch point in the parent path.

Signature: getBranchPointIndex() -> int

Returns: (int) the branch point index, or -1 if this is a primary path

getBranchPoints()#

This is a version of findJunctions() ensuring that a junction node is only retrieved once even if multiple child paths are associated with it.

Signature: getBranchPoints() -> Set

Returns: (Set[Any]) the junction nodes

getCalibration()#

Gets the spatial calibration of this Path.

Signature: getCalibration() -> Calibration

Returns: (Any) the calibration details associated with this Path

getCanvasOffset()#

Returns the translation offset used to render this Path in a TracerCanvas.

Signature: getCanvasOffset() -> PointInCanvas

Returns: (Any) the rendering offset (in pixel coordinates)

getChannel()#

Gets the hyperstack channel associated with this Path.

Signature: getChannel() -> int

Returns: (int) the channel position of this path (1-based index). Note that if the channel associated with a path is not known, it is assumed to be 1;

getChildren()#

Gets the list of child paths that branch from this path.

Returns the collection of paths that have this path as their parent. The returned list is the actual internal list, so modifications to it will affect the path’s structure.

Signature: getChildren() -> List

Returns: (List[Any]) the List of child paths. May be empty if this path has no children, but never null.

getColor()#

Gets the color of this Path

Signature: getColor() -> Color

Returns: (Any) the color, or null if no color has been assigned to this Path

getColorRGB()#

Gets the color of this Path

Signature: getColorRGB() -> ColorRGB

Returns: (Any) the color, or null if no color has been assigned to this Path

getContraction()#

Returns the ratio between the “Euclidean distance” of this path and its length. The Euclidean distance of this path is defined as the distance between this Path’s start and end point.

Signature: getContraction() -> double

Returns: (float) the Contraction of this Path, or NaN if this Path has no length

getEditableNodeIndex()#

Gets the position of the node tagged as ‘editable’, if any.

Signature: getEditableNodeIndex() -> int

Returns: (int) the index of the point currently tagged as editable, or -1 if no such point exists

getExtensionAngle3D(arg0)#

Returns a single angle representing the 3D extension direction. This is the angle between the path’s direction vector and a reference vector.

Signature: getExtensionAngle3D(boolean) -> double

Parameters:

  • arg0 (bool): - the reference vector to measure angle from (e.g., new Vector3d(0, 0, 1) for vertical reference, or new Vector3d(1, 0, 0) for horizontal)

Returns: (float) the acute angle in degrees (0-180°), or Double.NaN if path has only one point

getExtensionAngleFromHorizontal()#

Returns the angle between the path’s 3D direction and the horizontal axis.

Signature: getExtensionAngleFromHorizontal() -> double

Returns: (float) angle from horizontal in degrees (09° = vertical, 0° = horizontal), or Double.NaN if path has only one point.

getExtensionAngleFromVertical()#

Returns the angle between the path’s 3D direction and the vertical axis.

Signature: getExtensionAngleFromVertical() -> double

Returns: (float) angle from vertical in degrees (0° = vertical, 90° = horizontal), or Double.NaN if path has only one point, or 90° if path is 2D

getExtensionAngleXY()#

Returns the overall extension angle of this path in the XY plane. The angle is obtained from the slope of a linear regression across all the path nodes.

Signature: getExtensionAngleXY() -> double

Returns: (float) the overall ‘extension’ angle in degrees [0-360[ of this path in the XY plane.

getExtensionAngleXZ()#

Returns the overall extension angle of this path in the XZ plane. The angle is obtained from the slope of a linear regression across all the path nodes.

Signature: getExtensionAngleXZ() -> double

Returns: (float) the overall ‘extension’ angle in degrees [0-360[ in the XZ plane or NaN if path is 2D.

getExtensionAngleZY()#

Returns the overall extension angle of this path in the ZY plane. The angle is obtained from the slope of a linear regression across all the path nodes.

Signature: getExtensionAngleZY() -> double

Returns: (float) the overall ‘extension’ angle in degrees [0-360[ in the ZY plane or NaN if path is 2D.

getExtensionAngles3D()#

Returns the complete 3D orientation of this path’s extension direction as spherical coordinates using navigation/compass convention.

This method provides both horizontal direction (azimuth) and vertical inclination (elevation) of the path’s overall extension direction.

Signature: getExtensionAngles3D() -> [D

Returns: (Any) double array containing [azimuth, elevation] in degrees, where:

azimuth (index 0): Compass bearing in XY plane (0-360°) following navigation convention:

0° = North (negative Y direction in image coordinates) 90° = East (positive X direction) 180° = South (positive Y direction in image coordinates) 270° = West (negative X direction)

elevation (index 1): Vertical angle from XY plane (-90° to +90°):

0° = horizontal (parallel to XY plane) +90° = pointing straight up (positive Z direction) -90° = pointing straight down (negative Z direction)

Returns null if path has only one point or extension direction cannot be determined

getExtensionDirection3D()#

Returns the 3D extension direction vector of this path using linear regression. The vector represents the overall direction from start to end of the path, fitted through all its nodes.

Signature: getExtensionDirection3D() -> Vector3d

Returns: (Any) the normalized Vector3d (length of 1) representing the extension direction, or null if path has only one point

getFitted()#

Gets the fitted version (‘flavor’) of this Path.

Signature: getFitted() -> Path

Returns: (Path) the fitted version, or null if this Path has not been fitted

getFractalDimension()#

Gets the fractal dimension of this path.

Signature: getFractalDimension() -> double

Returns: (float) the fractal dimension of this path or Double.NaN if this path has less than 5 nodes

getFrame()#

Gets the hyperstack frame position associated with this Path.

Signature: getFrame() -> int

Returns: (int) the frame position of this path (1-based index). Note that if the frame associated with a path is not known, it is assumed to be 1;

PathAndFillManager#

getBoundingBox(arg0)#

Returns the BoundingBox enclosing all nodes of all existing Paths.

Signature: getBoundingBox(boolean) -> BoundingBox

Parameters:

  • arg0 (bool): - If true, BoundingBox dimensions will be computed for all the existing Paths. If false, the last computed BoundingBox will be returned. Also, if BoundingBox is not scaled, its spacing will be computed from the smallest inter-node distance of an arbitrary ‘ large’ Path. Computations of Path boundaries typically occur during import operations.

Returns: (BoundingBox) the BoundingBox enclosing existing nodes, or an ‘empty’ BoundingBox if no computation of boundaries has not yet occurred. Output is never null.

getCorrespondences(arg0, arg1)#

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

Signature: getCorrespondences(PathAndFillManager, double) -> List

Parameters:

  • arg0 (Any): - the other PathAndFillManager holding the corresponding Paths

  • arg1 (float)

Returns: (List[Any]) the cloud of NearPoint correspondences

getLoadedFills()#

Signature: getLoadedFills() -> Map

Returns: Dict[str, Any]

getPath(arg0)#

Returns the Path at the specified position in the PathAndFillManager list.

Signature: getPath(int) -> Path

Parameters:

  • arg0 (int): - the index of the Path

Returns: (Path) the Path at the specified index

getPathFromID(arg0)#

Returns the Path with the specified id.

Signature: getPathFromID(int) -> Path

Parameters:

  • arg0 (int): - the id of the Path to be retrieved

Returns: (Path) the Path with the specified id, or null if id was not found.

getPathFromName(arg0, arg1)#

Returns the Path with the specified name.

Signature: getPathFromName(String, boolean) -> Path

Parameters:

  • arg0 (str): - the name of the Path to be retrieved

  • arg1 (bool)

Returns: (Path) the Path with the specified name, or null if name was not found.

getPaths()#

Returns all the paths.

Signature: getPaths() -> ArrayList

Returns: (List[Any]) the paths associated with this PathAndFillManager instance.

getPathsFiltered()#

Returns the ‘de facto’ Paths.

Signature: getPathsFiltered() -> List

Returns: (List[Any]) the paths associated with this PathAndFillManager instance excluding those that are null or fitted version of o paths.

getPathsInROI(arg0)#

Signature: getPathsInROI(Roi) -> Collection

Parameters:

  • arg0 (Any)

Returns: List[Any]

getPathsStructured(arg0)#

Signature: getPathsStructured(Collection) -> Path;

Parameters:

  • arg0 (List[Any])

Returns: Any

getPlugin()#

Gets the SNT instance.

Signature: getPlugin() -> SNT

Returns: (Any) the SNT instance associated with this PathManager (if any)

getSWCFor(arg0)#

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

Signature: getSWCFor(Collection) -> List

Parameters:

  • arg0 (List[Any]): - the collection of Path objects to convert. Must contain exactly one primary path and form a connected tree structure. Empty paths are automatically skipped. Cannot be null or empty.

Returns: (List[Any]) a list of SWCPoint objects representing the neuronal structure in SWC format. Points are ordered by their sequential SWC IDs, with proper parent-child relationships established. The list is never null but may be empty if all input paths are empty.

getSelectedPaths()#

Gets all paths selected in the GUI

Signature: getSelectedPaths() -> Set

Returns: (Set[Any]) the collection of selected paths

PathFitter#

getPath()#

Signature: getPath() -> Path

Returns: (Path) the path being fitted

getSucceeded()#

Checks whether the fit succeeded.

Signature: getSucceeded() -> boolean

Returns: (bool) true if fit was successful, false otherwise

PathProfiler#

cancel(arg0)#

Signature: cancel(String) -> void

Parameters:

  • arg0 (str)

Returns: None

getCancelReason()#

Signature: getCancelReason() -> String

Returns: str

getContext()#

Signature: getContext() -> Context

Returns: Any

getDelegateObject()#

Signature: getDelegateObject() -> Object

Returns: Any

getInfo()#

Signature: getInfo() -> DynamicCommandInfo

Returns: Any

getInput(arg0)#

Signature: getInput(String) -> Object

Parameters:

  • arg0 (str)

Returns: Any

getInputs()#

Signature: getInputs() -> Map

Returns: Dict[str, Any]

getOutput(arg0)#

Signature: getOutput(String) -> Object

Parameters:

  • arg0 (str)

Returns: Any

getOutputs()#

Signature: getOutputs() -> Map

Returns: Dict[str, Any]

getPlot()#

Gets the plot profile as an ImageJ plot (all channels included).

Signature: getPlot() -> Plot

Returns: (Any) the plot

getValues(arg0)#

Gets the profile for the specified path as a map of lists, with distances (or indices) stored under X_VALUES (“x-values”) and intensities under Y_VALUES (“y-values”).

Signature: getValues(Path) -> Map

Parameters:

  • arg0 (Path): - the path to be profiled

Returns: (Dict[str, Any]) the profile map

getXYPlot(arg0)#

Gets the plot profile as an PlotService plot. It is recommended to call DynamicCommand.setContext(org.scijava.Context) beforehand.

Signature: getXYPlot(int) -> XYPlot

Parameters:

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

Returns: (Any) the plot

isCanceled()#

Signature: isCanceled() -> boolean

Returns: bool

isInputResolved(arg0)#

Signature: isInputResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

isOutputResolved(arg0)#

Signature: isOutputResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

isResolved(arg0)#

Signature: isResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

PathResult#

getErrorMessage()#

Signature: getErrorMessage() -> String

Returns: str

getNumberOfPoints()#

Signature: getNumberOfPoints() -> int

Returns: int

getPath()#

Signature: getPath() -> [F

Returns: Any

getSuccess()#

Signature: getSuccess() -> boolean

Returns: bool

PathStatistics#

cancel(arg0)#

Measures specified metrics for each individual path and creates a detailed table.

This method generates a comprehensive measurement table where each row represents an individual path and columns contain the requested morphometric measurements. This is particularly useful for comparative analysis of path properties or for exporting detailed morphometric data.

The generated table includes:

Path identification information (name, SWC type) All requested morphometric measurements Optional summary statistics (if summarize is true)

Signature: cancel(String) -> void

Parameters:

  • arg0 (str): - the collection of metric names to measure for each path. If null or empty, a default “safe” set of metrics is used

Returns: None

getAnnotatedLength(arg0, arg1)#

Signature: getAnnotatedLength(int, String) -> Map

Parameters:

  • arg0 (int)

  • arg1 (str)

Returns: Dict[str, Any]

getAnnotatedLengthHistogram(arg0)#

Signature: getAnnotatedLengthHistogram(int) -> SNTChart

Parameters:

  • arg0 (int)

Returns: SNTChart

getAnnotatedLengthsByHemisphere(arg0)#

Signature: getAnnotatedLengthsByHemisphere(int) -> Map

Parameters:

  • arg0 (int)

Returns: Dict[str, Any]

getAnnotations(arg0)#

Signature: getAnnotations(int) -> Set

Parameters:

  • arg0 (int)

Returns: Set[Any]

getAvgBranchLength()#

Gets the total length of terminal branches.

Calculates the sum of lengths of all terminal branches as defined by getTerminalBranches().

Signature: getAvgBranchLength() -> double

Returns: (float) the total length of terminal branches

getAvgContraction()#

Signature: getAvgContraction() -> double

Returns: float

getAvgFractalDimension()#

Signature: getAvgFractalDimension() -> double

Returns: float

getAvgFragmentation()#

Signature: getAvgFragmentation() -> double

Returns: float

getAvgPartitionAsymmetry()#

Signature: getAvgPartitionAsymmetry() -> double

Returns: float

getAvgRemoteBifAngle()#

Signature: getAvgRemoteBifAngle() -> double

Returns: float

getBranchPoints(arg0, arg1)#

Signature: getBranchPoints(BrainAnnotation, boolean) -> Set

Parameters:

  • arg0 (Any)

  • arg1 (bool)

Returns: Set[Any]

getBranches()#

Gets all the paths being analyzed as branches.

In PathStatistics, all paths are considered as branches since each path represents a distinct structural element.

Signature: getBranches() -> List

Returns: (List[Any]) the list of all paths

getCableLength(arg0)#

Signature: getCableLength(BrainAnnotation) -> double

Parameters:

  • arg0 (Any)

Returns: float

getCableLengthNorm(arg0)#

Signature: getCableLengthNorm(BrainAnnotation) -> double

Parameters:

  • arg0 (Any)

Returns: float

getCancelReason()#

Signature: getCancelReason() -> String

Returns: str

getContext()#

Signature: getContext() -> Context

Returns: Any

getConvexAnalyzer()#

Signature: getConvexAnalyzer() -> ConvexHullAnalyzer

Returns: Any

getConvexHullMetric(arg0)#

Signature: getConvexHullMetric(String) -> double

Parameters:

  • arg0 (str)

Returns: float

getDepth()#

Signature: getDepth() -> double

Returns: float

getDescriptiveStats(arg0)#

Signature: getDescriptiveStats(String) -> DescriptiveStatistics

Parameters:

  • arg0 (str)

Returns: Any

getFlowPlot(arg0, arg1)#

Signature: getFlowPlot(String, Collection) -> SNTChart

Parameters:

  • arg0 (str)

  • arg1 (List[Any])

Returns: SNTChart

getFractalDimension()#

Signature: getFractalDimension() -> List

Returns: List[Any]

getHeight()#

Signature: getHeight() -> double

Returns: float

getHighestPathOrder()#

Gets the number of branches (paths) being analyzed.

Returns the total count of paths in this PathStatistics instance.

Signature: getHighestPathOrder() -> int

Returns: (int) the number of paths

getHistogram(arg0)#

Signature: getHistogram(String) -> SNTChart

Parameters:

  • arg0 (str)

Returns: SNTChart

getInnerBranches()#

Gets the inner branches from the analyzed paths.

In PathStatistics, inner branches are equivalent to primary branches.

Signature: getInnerBranches() -> List

Returns: (List[Any]) the list of inner branches (same as primary branches)

getInnerLength()#

Gets the total length of inner branches.

In PathStatistics, this returns the same value as getPrimaryLength().

Signature: getInnerLength() -> double

Returns: (float) the total length of inner branches

getMetric(arg0, arg1)#

Gets a specific metric value for an individual path.

This method provides direct access to morphometric properties of individual paths, including geometric measurements, connectivity information, and structural characteristics. It supports all standard path metrics plus PathStatistics-specific measurements.

Supported metrics include:

Geometric: length, volume, surface area, mean radius Structural: number of nodes, branch points, children Angular: extension angles in XY, XZ, ZY planes Morphological: contraction, fractal dimension, spine density Metadata: path ID, channel, frame, order

Signature: getMetric(String, Path) -> Number

Parameters:

  • arg0 (str)

  • arg1 (Path)

Returns: Union[int, float]

PersistenceAnalyzer#

getBarcode(arg0)#

Gets the persistence barcode for the specified filter function.

The barcode is a simplified representation of the persistence diagram that contains only the persistence values (death - birth) for each topological feature, akin to a one-dimensional summary of branch significance.

Interpretation:

High values: Morphologically significant branches Low values: Minor branches or potential noise Distribution: The spread of values indicates branching complexity

Special Properties:

All values are non-negative (|death - birth|) For geodesic descriptor: sum of all values equals total cable length Number of values equals number of tips in the tree

Example Usage: ``` List<Double> barcode = analyzer.getBarcode(“geodesic”);

// Find most significant branches barcode.sort(Collections.reverseOrder()); System.out.println(“Top 5 most persistent branches:”); for (int i = 0; i < Math.min(5, barcode.size()); i++) {

System.out.println(“Branch “ + (i+1) + “: “ + barcode.get(i));

}#

Signature: getBarcode(String) -> List

Parameters:

  • arg0 (str): - A descriptor for the filter function as per getDescriptors() (case-insensitive). Supported values: “geodesic”, “radial”, “centrifugal”, “path order”, “x”, “y”, “z”.

Returns: (List[Any]) the barcode as a list of persistence values (death - birth). Each value represents the “lifespan” or significance of a topological feature (branch).

Example:

List<Double> barcode = analyzer.getBarcode("geodesic");

// Find most significant branches
barcode.sort(Collections.reverseOrder());
System.out.println("Top 5 most persistent branches:");
for (int i = 0; i < Math.min(5, barcode.size()); i++) {
    System.out.println("Branch " + (i+1) + ": " + barcode.get(i));
}
getDiagram(arg0)#

Gets the persistence diagram for the specified filter function.

The persistence diagram is the core output of the analysis, consisting of birth-death pairs that represent the “lifespan” of topological features (branches) during the filtration process. Each point in the diagram corresponds to a branch in the neuronal tree.

Structure: Returns a list where each inner list contains exactly two values:

Birth [0]: The filter value where the branch appears (branch point) Death [1]: The filter value where the branch disappears (tip)

Properties:

Number of points = Number of tips in the tree All values are non-negative For geodesic descriptor: sum of all (death-birth) = total cable length High persistence (death-birth) indicates morphologically significant branches

Example usage: ``` List<List<Double>> diagram = analyzer.getDiagram(“geodesic”); for (List<Double> point : diagram) {

double birth = point.get(0); double death = point.get(1); double persistence = death - birth; System.out.println(“Branch: persistence = “ + persistence);

}#

Signature: getDiagram(String) -> List

Parameters:

  • arg0 (str): - A descriptor for the filter function as per getDescriptors() (case-insensitive). Supported values: “geodesic”, “radial”, “centrifugal”, “path order”, “x”, “y”, “z”. Alternative names like “reverse strahler” for “centrifugal” are also accepted.

Returns: (List[Any]) the persistence diagram as a list of [birth, death] pairs. Each inner list contains exactly two Double values representing the birth and death of a topological feature.

Example:

List<List<Double>> diagram = analyzer.getDiagram("geodesic");
for (List<Double> point : diagram) {
    double birth = point.get(0);
    double death = point.get(1);
    double persistence = death - birth;
    System.out.println("Branch: persistence = " + persistence);
}
getDiagramNodes(arg0)#

Gets the tree nodes associated with each point in the persistence diagram.

This method returns the actual SWCPoint nodes from the neuronal tree that correspond to each birth-death pair in the persistence diagram. This allows you to map topological features back to specific locations in the original morphology.

Structure: Returns a list where each inner list contains exactly two nodes:

Birth Node [0]: The branch point where the topological feature appears Death Node [1]: The tip node where the topological feature disappears

Correspondence: The order of node pairs matches the order of birth-death pairs returned by getDiagram(String), allowing direct correlation between topological features and their spatial locations.

Example Usage: ``` List<List<Double>> diagram = analyzer.getDiagram(“geodesic”); List<List<SWCPoint>> nodes = analyzer.getDiagramNodes(“geodesic”);

for (int i = 0; i < diagram.size(); i++) {

List<Double> birthDeath = diagram.get(i); List<SWCPoint> nodesPair = nodes.get(i);

double persistence = birthDeath.get(1) - birthDeath.get(0); SWCPoint branchPoint = nodesPair.get(0); SWCPoint tipPoint = nodesPair.get(1);

System.out.printf(“Branch with persistence %.2f: from (%.1f,%.1f,%.1f) to (%.1f,%.1f,%.1f)%n”,

persistence, branchPoint.getX(), branchPoint.getY(), branchPoint.getZ(), tipPoint.getX(), tipPoint.getY(), tipPoint.getZ());

}#

Signature: getDiagramNodes(String) -> List

Parameters:

  • arg0 (str): - A descriptor for the filter function as per getDescriptors() (case-insensitive). Supported values: “geodesic”, “radial”, “centrifugal”, “path order”, “x”, “y”, “z”.

Returns: (List[Any]) the persistence diagram nodes as a list of [birth_node, death_node] pairs. Each inner list contains exactly two SWCPoint objects representing the spatial locations of the topological feature.

Example:

List<List<Double>> diagram = analyzer.getDiagram("geodesic");
List<List<SWCPoint>> nodes = analyzer.getDiagramNodes("geodesic");

for (int i = 0; i < diagram.size(); i++) {
    List<Double> birthDeath = diagram.get(i);
    List<SWCPoint> nodesPair = nodes.get(i);

    double persistence = birthDeath.get(1) - birthDeath.get(0);
    SWCPoint branchPoint = nodesPair.get(0);
    SWCPoint tipPoint = nodesPair.get(1);

    System.out.printf("Branch with persistence %.2f: from (%.1f,%.1f,%.1f) to (%.1f,%.1f,%.1f)%n",
                      persistence,
                      branchPoint.getX(), branchPoint.getY(), branchPoint.getZ(),
                      tipPoint.getX(), tipPoint.getY(), tipPoint.getZ());
}
getLandscape(arg0, arg1, arg2)#

Gets the persistence landscape as a vectorized representation.

Persistence landscapes transform persistence diagrams into a vector space representation that The landscape is a collection of piecewise-linear functions that capture the “shape” of the persistence diagram in a stable, vectorized format.

Mathematical Background: Each point (birth, death) in the persistence diagram contributes a “tent” function to the landscape. The k-th landscape function at any point is the k-th largest value among all tent functions at that point. This creates a stable, multi-resolution representation of the topological features.

Output Structure: Returns a 1D array of length numLandscapes × resolution where the first resolution values represent the first landscape function, the next resolution values represent the second landscape function, and so on.

Signature: getLandscape(String, int, int) -> [D

Parameters:

  • arg0 (str): - A descriptor for the filter function as per getDescriptors() (case-insensitive). Supported values: “geodesic”, “radial”, “centrifugal”, “path order”, “x”, “y”, “z”.

  • arg1 (int)

  • arg2 (int)

Returns: (Any) the persistence landscape as a 1D array of length numLandscapes × resolution. All values are non-negative and scaled by √2 for proper L² normalization.

PointInImage#

getAnnotation()#

Signature: getAnnotation() -> BrainAnnotation

Returns: (Any) the neuropil annotation assigned to this point

getCoordinateOnAxis(arg0)#

Gets the coordinate along the specified axis.

Signature: getCoordinateOnAxis(int) -> double

Parameters:

  • arg0 (int): - the axis. Either Tree.X_AXIS, Tree.Y_AXIS, or Tree.Z_AXIS

Returns: (float) the coordinate on the specified axis

getHemisphere()#

Signature: getHemisphere() -> char

Returns: str

getPath()#

Returns the Path associated with this node (if any)

Signature: getPath() -> Path

Returns: (Path) the path associated with this node or null if setPath(Path) has not been called.

getUnscaledPoint(arg0)#

Converts the coordinates of this point into pixel units if this point is associated with a Path.

Signature: getUnscaledPoint(int) -> PointInCanvas

Parameters:

  • arg0 (int): - MultiDThreePanes.XY_PLANE, MultiDThreePanes.ZY_PLANE, etc.

Returns: (Any) this point in pixel coordinates

getX()#

Signature: getX() -> double

Returns: (float) the X-coordinate of the point

getY()#

Signature: getY() -> double

Returns: (float) the Y-coordinate of the point

getZ()#

Signature: getZ() -> double

Returns: (float) the Z-coordinate of the point

isReal()#

Signature: isReal() -> boolean

Returns: bool

isSameLocation(arg0)#

Signature: isSameLocation(PointInImage) -> boolean

Parameters:

  • arg0 (PointInImage)

Returns: bool

RemoteSWCLoader#

getReader(arg0)#

Signature: getReader(String) -> BufferedReader

Parameters:

  • arg0 (str)

Returns: Any

getReconstructionURL(arg0)#

Signature: getReconstructionURL(String) -> String

Parameters:

  • arg0 (str)

Returns: str

getTree(arg0)#

Signature: getTree(String) -> Tree

Parameters:

  • arg0 (str)

Returns: Tree

isDatabaseAvailable()#

Signature: isDatabaseAvailable() -> boolean

Returns: bool

RootAngleAnalyzer#

getAnalysis()#

Signature: getAnalysis() -> Map

Returns: Dict[str, Any]

getAngles()#

Signature: getAngles() -> List

Returns: (List[Any]) the list of root angles sorted from leaves to root (in degrees).

getCramerVonMisesStatistic()#

Computes the Cramér-von Mises statistic between computed root angles and fitted von Mises distribution. A value of 0 indicates a perfect fit between the empirical distribution and the theoretical distribution, and larger values indicate a greater discrepancy between the two distributions.

Signature: getCramerVonMisesStatistic() -> double

Returns: (float) the Cramér-von Mises statistic. Range: [0, ∞[ (dimensionless).

getDensityPlot()#

Signature: getDensityPlot() -> SNTChart

Returns: SNTChart

getDescriptiveStatistics()#

Signature: getDescriptiveStatistics() -> DescriptiveStatistics

Returns: (Any) the descriptive statistics of the root angles (in degrees).

getHistogram(arg0)#

Signature: getHistogram(boolean) -> SNTChart

Parameters:

  • arg0 (bool)

Returns: SNTChart

getTaggedGraph()#

Signature: getTaggedGraph() -> DirectedWeightedGraph

Returns: (DirectedWeightedGraph) the graph of the tree being parsed. Vertices are tagged with the root angles (See: PointInImage.v).

getTaggedTree(arg0, arg1, arg2)#

Returns a recolored copy of the analyzed tree with the root angles assigned to its node values.

Signature: getTaggedTree(ColorTable, double, double) -> Tree

Parameters:

  • arg0 (Any)

  • arg1 (float)

  • arg2 (float)

Returns: Tree

SNT#

cancelPath()#

Cancels the temporary path.

Signature: cancelPath() -> void

Returns: None

cancelSearch(arg0)#

Signature: cancelSearch(boolean) -> void

Parameters:

  • arg0 (bool)

Returns: None

cancelTemporary()#

Signature: cancelTemporary() -> void

Returns: None

getAverageSeparation()#

Signature: getAverageSeparation() -> double

Returns: float

getChannel()#

Signature: getChannel() -> int

Returns: int

getContext()#

Signature: getContext() -> Context

Returns: Any

getCostType()#

Signature: getCostType() -> SNT$CostType

Returns: Any

getCurrentPath()#

Signature: getCurrentPath() -> Path

Returns: Path

getDataset()#

Signature: getDataset() -> Dataset

Returns: Any

getDepth()#

Signature: getDepth() -> int

Returns: int

getDrawDiameters()#

Signature: getDrawDiameters() -> boolean

Returns: bool

getFilledBinaryImp()#

Signature: getFilledBinaryImp() -> ImagePlus

Returns: Any

getFilledDistanceImp()#

Signature: getFilledDistanceImp() -> ImagePlus

Returns: Any

getFilledImp()#

Signature: getFilledImp() -> ImagePlus

Returns: Any

getFilledLabelImp()#

Signature: getFilledLabelImp() -> ImagePlus

Returns: Any

getFilterType()#

Signature: getFilterType() -> SNT$FilterType

Returns: Any

getFrame()#

Signature: getFrame() -> int

Returns: int

getHeight()#

Signature: getHeight() -> int

Returns: int

getHeuristicType()#

Signature: getHeuristicType() -> SNT$HeuristicType

Returns: Any

getImagePlus()#

Gets the Image associated with a view pane.

Signature: getImagePlus() -> ImagePlus

Returns: Any

getLoadedData()#

Signature: getLoadedData() -> RandomAccessibleInterval

Returns: Any

getLoadedDataAsImp()#

Retrieves the pixel data of the main image currently loaded in memory as an ImagePlus object. Returned image is always a single channel image.

Signature: getLoadedDataAsImp() -> ImagePlus

Returns: (Any) the loaded data corresponding to the C,T position currently being traced, or null if no image data has been loaded into memory.

getLoadedIterable()#

Signature: getLoadedIterable() -> IterableInterval

Returns: Any

SNTColor#

isTypeDefined()#

Checks if an SWC type has been defined.

Signature: isTypeDefined() -> boolean

Returns: (bool) true, if an SWC integer flag has been specified

SNTPoint#

getAnnotation()#

Signature: getAnnotation() -> BrainAnnotation

Returns: (Any) the neuropil annotation assigned to this point

getCoordinateOnAxis(arg0)#

Signature: getCoordinateOnAxis(int) -> double

Parameters:

  • arg0 (int)

Returns: (float) the coordinate on the specified axis

getHemisphere()#

Signature: getHemisphere() -> char

Returns: str

getX()#

Signature: getX() -> double

Returns: (float) the X-coordinate of the point

getY()#

Signature: getY() -> double

Returns: (float) the Y-coordinate of the point

getZ()#

Signature: getZ() -> double

Returns: (float) the Z-coordinate of the point

SNTService#

getContext()#

Signature: getContext() -> Context

Returns: Any

getIdentifier()#

Signature: getIdentifier() -> String

Returns: str

getInfo()#

Signature: getInfo() -> PluginInfo

Returns: Any

getInstance()#

Returns a reference to the active SNT instance.

Signature: getInstance() -> SNT

Returns: (Any) the SNT instance

getLocation()#

Signature: getLocation() -> String

Returns: str

getOrCreateSciViewSNT()#

Signature: getOrCreateSciViewSNT() -> SciViewSNT

Returns: Any

getPathAndFillManager()#

Returns the PathAndFillManager associated with the current SNT instance.

Signature: getPathAndFillManager() -> PathAndFillManager

Returns: (Any) the PathAndFillManager instance

getPaths()#

Gets the paths currently listed in the Path Manager

Signature: getPaths() -> List

Returns: (List[Any]) all the listed paths, or null if the Path Manager is empty

getPriority()#

Signature: getPriority() -> double

Returns: float

getRecViewer(arg0)#

Returns a reference to an opened Reconstruction Viewer (standalone instance). *

Signature: getRecViewer(int) -> Viewer3D

Parameters:

  • arg0 (int): - the unique numeric ID of the Reconstruction Viewer to be retrieved (as used by the “Script This Viewer” command, and typically displayed in the Viewer’s window title)

Returns: (Viewer3D) The standalone Viewer3D instance, or null if id was not recognized

getSciViewSNT()#

Signature: getSciViewSNT() -> SciViewSNT

Returns: Any

getSelectedPaths()#

Gets the paths currently selected in the Path Manager list.

Signature: getSelectedPaths() -> Collection

Returns: (List[Any]) the paths currently selected, or null if no selection exists

getStatistics(arg0)#

Returns a TreeStatistics instance constructed from current Paths.

Signature: getStatistics(boolean) -> TreeStatistics

Parameters:

  • arg0 (bool): - If true only selected paths will be considered

Returns: (TreeStatistics) the TreeStatistics instance

getTable()#

Returns a reference to SNT’s main table of measurements.

Signature: getTable() -> SNTTable

Returns: (SNTTable) SNT measurements table (a DefaultGenericTable)

getTree()#

Gets the collection of paths listed in the Path Manager as a Tree object.

Signature: getTree() -> Tree

Returns: (Tree) the Tree holding the Path collection

getTrees()#

Gets the collection of paths listed in the Path Manager as a Tree object.

Signature: getTrees() -> Collection

Returns: (List[Any]) the Tree holding the Path collection

getUI()#

Returns a reference to SNT’s UI.

Signature: getUI() -> SNTUI

Returns: (Any) the SNTUI window, or null if SNT is not running, or is running without GUI

getVersion()#

Signature: getVersion() -> String

Returns: str

isActive()#

Gets whether SNT is running.

Signature: isActive() -> boolean

Returns: (bool) true if this SNTService is active, tied to the active instance of SNT

SNTTable#

getColumnCount()#

Signature: getColumnCount() -> int

Returns: int

getColumnHeader(arg0)#

Signature: getColumnHeader(int) -> String

Parameters:

  • arg0 (int)

Returns: str

getColumnIndex(arg0)#

Signature: getColumnIndex(String) -> int

Parameters:

  • arg0 (str)

Returns: int

getFirst()#

Signature: getFirst() -> Object

Returns: Any

getLast()#

Signature: getLast() -> Object

Returns: Any

getRowCount()#

Signature: getRowCount() -> int

Returns: int

getRowHeader(arg0)#

Signature: getRowHeader(int) -> String

Parameters:

  • arg0 (int)

Returns: str

getRowIndex(arg0)#

Signature: getRowIndex(String) -> int

Parameters:

  • arg0 (str)

Returns: int

getSummaryRow()#

Signature: getSummaryRow() -> int

Returns: int

SWCPoint#

getAnnotation()#

Signature: getAnnotation() -> BrainAnnotation

Returns: (Any) the neuropil annotation assigned to this point

getColor()#

Gets the color of this point.

Signature: getColor() -> Color

Returns: (Any) the color

getCoordinateOnAxis(arg0)#

Signature: getCoordinateOnAxis(int) -> double

Parameters:

  • arg0 (int)

Returns: float

getHemisphere()#

Signature: getHemisphere() -> char

Returns: str

getNextPoints()#

Returns the list holding the subsequent nodes in the reconstructed structure after this one.

Signature: getNextPoints() -> List

Returns: (List[Any]) the list of “next points”

getPath()#

Signature: getPath() -> Path

Returns: Path

getTags()#

Gets the tags associated with this point.

Signature: getTags() -> String

Returns: (str) the tags string

getUnscaledPoint(arg0)#

Signature: getUnscaledPoint(int) -> PointInCanvas

Parameters:

  • arg0 (int)

Returns: Any

getX()#

Signature: getX() -> double

Returns: (float) the X-coordinate of the point

getY()#

Signature: getY() -> double

Returns: (float) the Y-coordinate of the point

getZ()#

Signature: getZ() -> double

Returns: (float) the Z-coordinate of the point

isReal()#

Signature: isReal() -> boolean

Returns: bool

isSameLocation(arg0)#

Signature: isSameLocation(PointInImage) -> boolean

Parameters:

  • arg0 (PointInImage)

Returns: bool

SciViewSNT#

getSciView()#

Gets the SciView instance currently in use.

Signature: getSciView() -> SciView

Returns: (Any) the SciView instance. It is never null: A new instance is created if none has been specified

getTreeAsSceneryNode(arg0)#

Gets the specified Tree as a Scenery Node.

Signature: getTreeAsSceneryNode(Tree) -> Node

Parameters:

  • arg0 (Tree): - the tree previously added to SciView using addTree(Tree)

Returns: (Any) the scenery Node

SearchNode#

getX()#

Signature: getX() -> int

Returns: int

getY()#

Signature: getY() -> int

Returns: int

getZ()#

Signature: getZ() -> int

Returns: int

SearchThread#

getExitReason()#

Signature: getExitReason() -> int

Returns: int

getNodesAsImageFromGoal()#

Signature: getNodesAsImageFromGoal() -> SearchImageStack

Returns: Any

getNodesAsImageFromStart()#

Signature: getNodesAsImageFromStart() -> SearchImageStack

Returns: Any

getResult()#

Signature: getResult() -> Path

Returns: Path

ShollAnalyzer#

getLinearStats()#

Gets the LinearProfileStats associated with this analyzer. By default, it is set to determine the polynomial of ‘best-fit’ (2-20 degree range.)

Signature: getLinearStats() -> LinearProfileStats

Returns: (Any) the LinearProfileStats instance

getMaximaRadii()#

Signature: getMaximaRadii() -> ArrayList

Returns: List[Any]

getNormStats()#

Gets the NormalizedProfileStats associated with this analyzer. By default it is set to determine the regression method of ‘best-fit’ (log-log or semi-log) using shell volume as normalizer (if Tree has a depth component) or shell area if Tree is 2D.

Signature: getNormStats() -> NormalizedProfileStats

Returns: (Any) the LinearProfileStats instance

getSecondaryMaxima()#

Signature: getSecondaryMaxima() -> ArrayList

Returns: List[Any]

getSingleValueMetrics()#

Signature: getSingleValueMetrics() -> Map

Returns: Dict[str, Any]

SkeletonConverter#

getGraphs()#

Generates a list of DirectedWeightedGraph`s from the skeleton image. Each graph corresponds to one connected component of the graph returned by `SkeletonResult.getGraph().

Signature: getGraphs() -> List

Returns: (List[Any]) the list of skeletonized graphs

getPruneMode()#

Gets the loop pruning strategy.

Signature: getPruneMode() -> int

Returns: int

getRootRoiStrategy()#

Gets the current root ROI strategy.

Returns the strategy used for handling root ROIs during skeleton conversion. If no root ROI is set, returns ROI_UNSET.

Signature: getRootRoiStrategy() -> int

Returns: (int) the root ROI strategy constant

getSingleGraph()#

Generates a single DirectedWeightedGraph`s by combining getGraphs()’s list into a single, combined graph. Typically, this method assumes that the skeletonization handles a known single component (e.g., an image of a single cell). If multiple graphs() do exist, this method requires that setRootRoi(Roi, int) has been called using ROI_CENTROID or `ROI_CENTROID_WEIGHTED.

Signature: getSingleGraph() -> DirectedWeightedGraph

Returns: (DirectedWeightedGraph) the single graph

getSingleTree()#

Generates a single Tree from getSingleGraph(). If a ROI-based centroid has been set, Root is converted to a single node, root path with radius set to that of a circle with the same area of root-defining soma.

Signature: getSingleTree() -> Tree

Returns: (Tree) the single tree

getTrees()#

Generates a list of Trees from the skeleton image. Each Tree corresponds to one connected component of the graph returned by SkeletonResult.getGraph().

Signature: getTrees() -> List

Returns: (List[Any]) the skeleton tree list

setPruneByLength(arg0)#

Sets whether to prune components below a threshold length from the result.

Signature: setPruneByLength(boolean) -> void

Parameters:

  • arg0 (bool)

Returns: None

StrahlerAnalyzer#

getAvgBifurcationRatio()#

Signature: getAvgBifurcationRatio() -> double

Returns: (float) the average bifurcation ratio of the parsed tree. In a complete binary tree, the bifurcation ratio is 2.

getAvgContractions()#

Signature: getAvgContractions() -> Map

Returns: Dict[str, Any]

getAvgExtensionAngle(arg0, arg1)#

Gets the average relative extension angle for branches of a specific Strahler order.

Signature: getAvgExtensionAngle(boolean, int) -> double

Parameters:

  • arg0 (bool): - the Strahler order

  • arg1 (int)

Returns: (float) the average relative extension angle in degrees, or Double.NaN if no valid angles

getAvgExtensionAngles(arg0)#

Gets a map of average relative extension angles for all Strahler orders.

Signature: getAvgExtensionAngles(boolean) -> Map

Parameters:

  • arg0 (bool)

Returns: (Dict[str, Any]) map with Strahler order as key and average relative extension angle as value

getAvgFragmentations()#

Signature: getAvgFragmentations() -> Map

Returns: Dict[str, Any]

getBifurcationRatios()#

Signature: getBifurcationRatios() -> Map

Returns: (Dict[str, Any]) the map containing the bifurcation ratios obtained as the ratio of no. of branches between consecutive orders (Horton-Strahler numbers as key and ratios as value).

getBranchCounts()#

Signature: getBranchCounts() -> Map

Returns: (Dict[str, Any]) the map containing the number of branches on each order (Horton-Strahler numbers as key and branch count as value).

getBranchPointCounts()#

Signature: getBranchPointCounts() -> Map

Returns: (Dict[str, Any]) the map containing the number of branch points on each order (Horton-Strahler numbers as key and branch points count as value).

getBranches()#

Signature: getBranches() -> Map

Returns: Dict[str, Any]

getExtensionAngles(arg0)#

Gets a map of relative extension angles for all branches in each Strahler order.

Signature: getExtensionAngles(boolean) -> Map

Parameters:

  • arg0 (bool)

Returns: (Dict[str, Any]) map with Strahler order as key and list of relative extension angles as values

getGraph()#

Signature: getGraph() -> DirectedWeightedGraph

Returns: (DirectedWeightedGraph) the graph of the tree being parsed.

getHighestBranchOrder()#

Signature: getHighestBranchOrder() -> int

Returns: (int) the highest Horton-Strahler number associated with a branch in the parsed tree. Either getRootNumber() or getRootNumber()-1.

getLengths()#

Signature: getLengths() -> Map

Returns: (Dict[str, Any]) the map containing the cable lengh associated to each order ( Horton-Strahler numbers as key and cable length as value).

getRelativeExtensionAngle(arg0)#

Computes the relative extension angle for a StrahlerAnalyzer branch by finding the parent direction from the graph structure.

Signature: getRelativeExtensionAngle(Path) -> double

Parameters:

  • arg0 (Path): - the branch path to analyze

Returns: (float) the relative extension angle in degrees (0-180°), or Double.NaN if computation fails

getRootAssociatedBranches()#

Signature: getRootAssociatedBranches() -> List

Returns: List[Any]

getRootNumber()#

Signature: getRootNumber() -> int

Returns: (int) the highest Horton-Strahler number in the parsed tree.

TracerCanvas#

getAccessibleContext()#

Signature: getAccessibleContext() -> AccessibleContext

Returns: Any

getAlignmentX()#

Signature: getAlignmentX() -> float

Returns: float

getAlignmentY()#

Signature: getAlignmentY() -> float

Returns: float

getAnnotationsColor()#

Signature: getAnnotationsColor() -> Color

Returns: Any

getBackground()#

Signature: getBackground() -> Color

Returns: Any

getBaseline(arg0, arg1)#

Signature: getBaseline(int, int) -> int

Parameters:

  • arg0 (int)

  • arg1 (int)

Returns: int

TracerThread#

getExitReason()#

Signature: getExitReason() -> int

Returns: int

getNodesAsImageFromGoal()#

Signature: getNodesAsImageFromGoal() -> SearchImageStack

Returns: Any

getNodesAsImageFromStart()#

Signature: getNodesAsImageFromStart() -> SearchImageStack

Returns: Any

getResult()#

Signature: getResult() -> Path

Returns: Path

Tree#

getApproximatedSurface()#

Retrieves an approximate estimate of Tree’s surface are by approximating the surface area of each path, and summing to total. The surface of each path is computed assuming the lateral surface area of a conical frustum between nodes.

Signature: getApproximatedSurface() -> double

Returns: (float) the approximate surface area or NaN if this Tree’s paths have no radius

getApproximatedVolume()#

Retrieves an approximate estimate of Tree’s volume by approximating the volume of each path, and summing to total. The volume of each path is computed assuming the volume of each of inter-node segment to be that of a truncated cone (Frustum).

Signature: getApproximatedVolume() -> double

Returns: (float) the approximate volume or NaN if this Tree’s paths have no radius

getAssignedValue()#

Retrieves the numeric property assigned to this Tree.

Signature: getAssignedValue() -> double

Returns: (float) the assigned value.

getBPs()#

Gets the branch points (junctions) of the graph. This is simply an alias for DirectedWeightedGraph.getBPs().

Signature: getBPs() -> List

Returns: (List[Any]) the list of branch points

getBoundingBox(arg0)#

Gets the bounding box associated with this tree.

Signature: getBoundingBox(boolean) -> BoundingBox

Parameters:

  • arg0 (bool): - if

Returns: (BoundingBox) the BoundingBox

getColor()#

Gets the color assigned to this Tree.

Signature: getColor() -> ColorRGB

Returns: (Any) the Tree color, or null if no color has been assigned

getConvexHull()#

Retrieves the convex hull of this tree.

Signature: getConvexHull() -> AbstractConvexHull

Returns: Any

getGraph()#

Assembles a DirectedGraph from this Tree.

Signature: getGraph() -> DirectedWeightedGraph

Returns: DirectedWeightedGraph

getImpContainer(arg0, arg1)#

Gets an empty image capable of holding the skeletonized version of this tree.

Signature: getImpContainer(int, int) -> ImagePlus

Parameters:

  • arg0 (int): - the pane flag indicating the SNT view for this image e.g., MultiDThreePanes.XY_PLANE

  • arg1 (int)

Returns: (Any) the empty ImagePlus container

getLabel()#

Returns the identifying label of this tree. When importing files, the label typically defaults to the imported filename,

Signature: getLabel() -> String

Returns: (str) the Tree label (or null) if none has been set.

getNodes()#

Gets all the nodes (path points) forming this tree.

Signature: getNodes() -> List

Returns: (List[Any]) the points

getNodesAsSWCPoints()#

Signature: getNodesAsSWCPoints() -> List

Returns: List[Any]

getNodesCount()#

Gets the total number of nodes across all paths in this Tree.

Signature: getNodesCount() -> long

Returns: (int) the total node count

getProperties()#

Returns the Properties instance holding the persistent set of properties. Useful to associate metadata to this tree. E.g.

` getProperties().setProperty(Tree.KEY_SPATIAL_UNIT, "um"); String unit = getProperties().getProperty(Tree.KEY_SPATIAL_UNIT); getProperties().setProperty(Tree.KEY_COMPARTMENT, Tree.DENDRITIC); `

Signature: getProperties() -> Properties

Returns: (Any) the Properties instance

Example:

getProperties().setProperty(Tree.KEY_SPATIAL_UNIT, "um");
String unit = getProperties().getProperty(Tree.KEY_SPATIAL_UNIT);
getProperties().setProperty(Tree.KEY_COMPARTMENT, Tree.DENDRITIC);
getRoot()#

Gets the first node of the main primary path of this tree

Signature: getRoot() -> PointInImage

Returns: (PointInImage) the root node, or null if the main primary path is undefined for this tree.

getSWCTypeNames(arg0)#

Gets the set of SWC type labels present in this tree with optional soma inclusion in a readable form.

Signature: getSWCTypeNames(boolean) -> Set

Parameters:

  • arg0 (bool): - if true, includes soma in the returned set; if false, excludes Path.SWC_SOMA from the result

Returns: (Set[Any]) a Set containing the SWC type labels (e.g., Path.SWC_AXON_LABEL, Path.SWC_DENDRITE_LABEL, etc.) present in the tree

getSWCTypes(arg0)#

Gets the set of SWC types present in this tree with optional soma inclusion.

Signature: getSWCTypes(boolean) -> Set

Parameters:

  • arg0 (bool): - if true, includes the soma type in the returned set; if false, excludes Path.SWC_SOMA from the result

Returns: (Set[Any]) a Set containing the SWC type constants (e.g., Path.SWC_AXON, Path.SWC_DENDRITE, etc.) present in the tree

getSkeleton()#

Retrieves the rasterized skeleton of this tree at 1:1 scaling.

Signature: getSkeleton() -> ImagePlus

Returns: Any

getSkeleton2D(arg0)#

Retrieves a 2D projection of the rasterized skeleton of this tree at 1:1 scaling.

Signature: getSkeleton2D(int) -> ImagePlus

Parameters:

  • arg0 (int): - the pixel intensities of the skeleton. If

Returns: (Any) the skeletonized 16-bit binary image

getSomaNodes()#

Gets the list of all nodes tagged as Path.SWC_SOMA.

Signature: getSomaNodes() -> List

Returns: (List[Any]) the soma nodes or null if no Paths are tagged as soma.

getTips()#

Gets the end points (tips) of the graph. This is simply an alias for DirectedWeightedGraph.getTips().

Signature: getTips() -> List

Returns: (List[Any]) the list of end points

isAnnotated()#

Checks if the nodes of this Tree have been assigned BrainAnnotations (neuropil labels).

Signature: isAnnotated() -> boolean

Returns: (bool) true if at least one node in the Tree has a valid annotation, false otherwise

isEmpty()#

Checks if this Tree is empty.

Signature: isEmpty() -> boolean

Returns: (bool) true if this tree contains no Paths, false otherwise

TreeColorMapper#

getAvailableLuts()#

Gets the available LUTs.

Signature: getAvailableLuts() -> Set

Returns: (Set[Any]) the set of keys, corresponding to the set of LUTs available

getColor(arg0)#

Signature: getColor(double) -> Color

Parameters:

  • arg0 (float)

Returns: Any

getColorRGB(arg0)#

Signature: getColorRGB(double) -> ColorRGB

Parameters:

  • arg0 (float)

Returns: Any

getColorTable(arg0)#

Signature: getColorTable(String) -> ColorTable

Parameters:

  • arg0 (str)

Returns: Any

getMinMax()#

Signature: getMinMax() -> [D

Returns: Any

getMultiViewer()#

Assembles a Multi-pane viewer using all the Trees mapped so far.

Signature: getMultiViewer() -> MultiViewer2D

Returns: (MultiViewer2D) the multi-viewer instance

getNaNColor()#

Signature: getNaNColor() -> Color

Returns: Any

isIntegerScale()#

Signature: isIntegerScale() -> boolean

Returns: bool

isNodeMapping()#

Signature: isNodeMapping() -> boolean

Returns: bool

TreeStatistics#

cancel(arg0)#

Sets the table for this TreeStatistics instance.

Signature: cancel(String) -> void

Parameters:

  • arg0 (str): - the table to be used by this TreeStatistics instance

Returns: None

getAnnotatedLength(arg0, arg1)#

Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.

Signature: getAnnotatedLength(int, String) -> Map

Parameters:

  • arg0 (int)

  • arg1 (str)

Returns: Dict[str, Any]

getAnnotatedLengthHistogram(arg0)#

Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level across the specified hemisphere.

Signature: getAnnotatedLengthHistogram(int) -> SNTChart

Parameters:

  • arg0 (int): - the ontological depth of the compartments to be considered

Returns: (SNTChart) the annotated length histogram

getAnnotatedLengthsByHemisphere(arg0)#

Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron in the two brain hemispheres. Lengths are absolute and not normalized to the cells’ cable length.

Signature: getAnnotatedLengthsByHemisphere(int) -> Map

Parameters:

  • arg0 (int): - the ontological depth of the compartments to be considered

Returns: (Dict[str, Any]) the map containing the brain compartments as keys, and cable lengths per hemisphere as values.

getAnnotations(arg0)#

Retrieves the brain compartments (neuropil labels) associated with the Tree being measured innervated by the analyzed neuron.

Signature: getAnnotations(int) -> Set

Parameters:

  • arg0 (int): - the max. ontological depth of the compartments to be retrieved

Returns: (Set[Any]) the set of brain compartments (BrainAnnotations)

getAvgBranchLength()#

Gets average length for all the branches of the analyzed tree.

Signature: getAvgBranchLength() -> double

Returns: (float) the average branch length

getAvgContraction()#

Gets average contraction for all the branches of the analyzed tree.

Signature: getAvgContraction() -> double

Returns: (float) the average branch contraction

getAvgFractalDimension()#

Gets the average fractal dimension of the analyzed tree. Note that branches with less than 5 points are ignored during the computation.

Signature: getAvgFractalDimension() -> double

Returns: (float) the average fractal dimension

getAvgFragmentation()#

Gets the average no. of nodes (fragmentation) for all the branches of the analyzed tree.

Signature: getAvgFragmentation() -> double

Returns: (float) the average no. of branch nodes (average branch fragmentation)

getAvgPartitionAsymmetry()#

Gets the average partition asymmetry of the analyzed tree. Note that branch points with more than 2 children are ignored during the computation.

Signature: getAvgPartitionAsymmetry() -> double

Returns: (float) the average partition asymmetry

getAvgRemoteBifAngle()#

Gets the average remote bifurcation angle of the analyzed tree. Note that branch points with more than 2 children are ignored during the computation.

Signature: getAvgRemoteBifAngle() -> double

Returns: (float) the average remote bifurcation angle

getBranchPoints(arg0, arg1)#

Gets the position of all the branch points in the analyzed tree associated with the specified annotation.

Signature: getBranchPoints(BrainAnnotation, boolean) -> Set

Parameters:

  • arg0 (Any)

  • arg1 (bool)

Returns: Set[Any]

getBranches()#

Gets all the branches in the analyzed tree. A branch is defined as the Path composed of all the nodes between two branching points or between one branching point and a termination point.

Signature: getBranches() -> List

Returns: (List[Any]) the list of branches as Path objects.

getCableLength(arg0)#

Gets the cable length associated with the specified compartment (neuropil label).

Signature: getCableLength(BrainAnnotation) -> double

Parameters:

  • arg0 (Any): - the query compartment (null not allowed)

Returns: (float) the filtered cable length

getCableLengthNorm(arg0)#

Gets the cable length associated with the specified compartment (neuropil label) as a ratio of total length.

Signature: getCableLengthNorm(BrainAnnotation) -> double

Parameters:

  • arg0 (Any): - the query compartment (null not allowed)

Returns: (float) the filtered cable length normalized to total cable length

getCancelReason()#

Signature: getCancelReason() -> String

Returns: str

getContext()#

Signature: getContext() -> Context

Returns: Any

getConvexAnalyzer()#

Gets the ConvexHullAnalyzer instance associated with this TreeStatistics instance.

Signature: getConvexAnalyzer() -> ConvexHullAnalyzer

Returns: (Any) the ConvexHullAnalyzer instance

getConvexHullMetric(arg0)#

Convenience method to obtain a single-value metric from ConvexHullAnalyzer

Signature: getConvexHullMetric(String) -> double

Parameters:

  • arg0 (str): - the metric to be retrieved, one of ConvexHullAnalyzer.supportedMetrics()

Returns: (float) the convex hull metric

getDepth()#

Returns the depth of the BoundingBox box of the tree being measured

Signature: getDepth() -> double

Returns: (float) the bounding box depth

getDescriptiveStats(arg0)#

Computes the DescriptiveStatistics for the specified measurement.

Signature: getDescriptiveStats(String) -> DescriptiveStatistics

Parameters:

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

Returns: (Any) the DescriptiveStatistics object.

getFlowPlot(arg0, arg1)#

Assembles a Flow plot (aka Sankey diagram) for the specified feature.

Signature: getFlowPlot(String, Collection) -> SNTChart

Parameters:

  • arg0 (str): - the feature (“Cable length”, “No. of branch points”, “No. of tips”, etc.). Note that the majority of getAllMetrics() metrics are currently not supported.

  • arg1 (List[Any])

Returns: (SNTChart) the SNTChart holding the flow plot

getFractalDimension()#

Gets the fractal dimension of each branch in the analyzed tree. Note that branches with less than 5 points are ignored.

Signature: getFractalDimension() -> List

Returns: (List[Any]) a list containing the fractal dimension of each branch

getHeight()#

Returns the height of the BoundingBox box of the tree being measured

Signature: getHeight() -> double

Returns: (float) the bounding box height

getHighestPathOrder()#

Gets the highest path order of the analyzed tree

Signature: getHighestPathOrder() -> int

Returns: (int) the highest Path order, or -1 if Paths in the Tree have no defined order

getHistogram(arg0)#

Retrieves the histogram of relative frequencies histogram for a univariate measurement. The number of bins is determined using the Freedman-Diaconis rule.

Signature: getHistogram(String) -> SNTChart

Parameters:

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

Returns: (SNTChart) the frame holding the histogram

getInnerBranches()#

Retrieves the branches of highest Strahler order in the Tree. This typically correspond to the most ‘internal’ branches of the Tree in direct sequence from the root.

Signature: getInnerBranches() -> List

Returns: (List[Any]) the list containing the “inner” branches. Note that these branches (Path segments) will not carry any connectivity information.

getInnerLength()#

Gets the cable length of inner branches

Signature: getInnerLength() -> double

Returns: (float) the length sum of all inner branches

getMetric(arg0)#

Computes the specified metric.

Signature: getMetric(String) -> Number

Parameters:

  • arg0 (str): - the single-value metric to be computed (case-insensitive). While it is expected to be an element of getAllMetrics(), if isExactMetricMatch() is set,

Returns: (Union[int, float]) the computed value (average if metric is associated with multiple values)

getNBranchPoints(arg0)#

Gets the number of branch points in the analyzed tree associated with the specified annotation.

Signature: getNBranchPoints(BrainAnnotation) -> int

Parameters:

  • arg0 (Any): - the BrainAnnotation to be queried.

Returns: (int) the number of branch points

Tubeness#

getArity()#

Signature: getArity() -> int

Returns: int

getIndependentInstance()#

Signature: getIndependentInstance() -> UnaryComputerOp

Returns: Any

Viewer2D#

getAvailableLuts()#

Signature: getAvailableLuts() -> Set

Returns: Set[Any]

getChart()#

Gets the current viewer as a SNTChart object

Signature: getChart() -> SNTChart

Returns: (SNTChart) the converted viewer

getColor(arg0)#

Signature: getColor(double) -> Color

Parameters:

  • arg0 (float)

Returns: Any

getColorRGB(arg0)#

Signature: getColorRGB(double) -> ColorRGB

Parameters:

  • arg0 (float)

Returns: Any

getColorTable(arg0)#

Signature: getColorTable(String) -> ColorTable

Parameters:

  • arg0 (str)

Returns: Any

getJFreeChart()#

Gets the current viewer as a JFreeChart object

Signature: getJFreeChart() -> JFreeChart

Returns: (Any) the converted viewer

getMinMax()#

Signature: getMinMax() -> [D

Returns: Any

getMultiViewer()#

Signature: getMultiViewer() -> MultiViewer2D

Returns: MultiViewer2D

getNaNColor()#

Signature: getNaNColor() -> Color

Returns: Any

getPlot()#

Gets the current plot as a XYPlot object

Signature: getPlot() -> XYPlot

Returns: (Any) the current plot

getTitle()#

Gets the plot display title.

Signature: getTitle() -> String

Returns: (str) the current display title

isIntegerScale()#

Signature: isIntegerScale() -> boolean

Returns: bool

isNodeMapping()#

Signature: isNodeMapping() -> boolean

Returns: bool

setPreferredSize(arg0, arg1)#

Sets the preferred size of the plot to a constant value.

Signature: setPreferredSize(int, int) -> void

Parameters:

  • arg0 (int): - the preferred width

  • arg1 (int)

Returns: None

Viewer3D#

getAnnotation(arg0)#

Gets the annotation associated with the specified label.

Signature: getAnnotation(String) -> Annotation3D

Parameters:

  • arg0 (str): - the (unique) label as displayed in Viewer’s list

Returns: (Any) the annotation or null if no annotation is associated with the specified label

getAnnotations()#

Returns all annotations added to this viewer.

Signature: getAnnotations() -> List

Returns: (List[Any]) the annotation list

getFrame()#

Gets the frame containing this viewer, optionally controlling its visibility.

Returns the AWT Frame that contains this viewer’s 3D canvas and UI components. If no frame exists, one will be created with the specified visibility setting. This method is useful when you need to control whether the viewer window appears immediately or remains hidden for programmatic manipulation.

Signature: getFrame() -> Frame

Returns: Any

getID()#

Returns this Viewer’s id.

Signature: getID() -> int

Returns: (int) this Viewer’s unique numeric ID.

getManagerPanel()#

Returns a reference to ‘RV Controls’ panel.

Signature: getManagerPanel() -> Viewer3D$ManagerPanel

Returns: (Any) the ManagerPanel associated with this Viewer, or null if the ‘RV Controls’ dialog is not being displayed.

getMesh(arg0)#

Gets the mesh associated with the specified label.

Signature: getMesh(String) -> OBJMesh

Parameters:

  • arg0 (str): - the (unique) label as displayed in Viewer’s list

Returns: (Any) the mesh or null if no mesh is associated with the specified label

getMeshes()#

Returns all meshes added to this viewer.

Signature: getMeshes() -> List

Returns: List[Any]

getRecorder(arg0)#

Gets the script recorder for this viewer, optionally creating one if needed.

Signature: getRecorder(boolean) -> ScriptRecorder

Parameters:

  • arg0 (bool): - if true, creates a new recorder if one doesn’t exist; if false, returns null when no recorder exists

Returns: (Any) the ScriptRecorder instance, or null if none exists and createIfNeeded is false

getTree(arg0)#

Gets the tree associated with the specified label.

Signature: getTree(String) -> Tree

Parameters:

  • arg0 (str): - the (unique) label as displayed in Viewer’s list

Returns: (Tree) the Tree or null if no Tree is associated with the specified label

getTrees()#

Returns all trees added to this viewer.

Signature: getTrees() -> List

Returns: List[Any]

isActive()#

Checks whether this instance is currently active

Signature: isActive() -> boolean

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

isDarkModeOn()#

Checks if scene is being rendered under dark or light background.

Signature: isDarkModeOn() -> boolean

Returns: (bool) true, if “Dark Mode” is active

isSNTInstance()#

Checks whether this instance is SNT’s Reconstruction Viewer.

Signature: isSNTInstance() -> boolean

Returns: (bool) true, if SNT instance, false otherwise

isSplitDendritesFromAxons()#

Checks whether axons and dendrites of imported Trees are set to be imported as separated objects.

Signature: isSplitDendritesFromAxons() -> boolean

Returns: (bool) if imported trees are set to be split into axonal and dendritic subtrees.

WekaModelLoader#

cancel(arg0)#

Signature: cancel(String) -> void

Parameters:

  • arg0 (str)

Returns: None

getCancelReason()#

Signature: getCancelReason() -> String

Returns: str

getContext()#

Signature: getContext() -> Context

Returns: Any

getDelegateObject()#

Signature: getDelegateObject() -> Object

Returns: Any

getInfo()#

Signature: getInfo() -> DynamicCommandInfo

Returns: Any

getInput(arg0)#

Signature: getInput(String) -> Object

Parameters:

  • arg0 (str)

Returns: Any

getInputs()#

Signature: getInputs() -> Map

Returns: Dict[str, Any]

getOutput(arg0)#

Signature: getOutput(String) -> Object

Parameters:

  • arg0 (str)

Returns: Any

getOutputs()#

Signature: getOutputs() -> Map

Returns: Dict[str, Any]

isCanceled()#

Signature: isCanceled() -> boolean

Returns: bool

isInputResolved(arg0)#

Signature: isInputResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

isOutputResolved(arg0)#

Signature: isOutputResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

isResolved(arg0)#

Signature: isResolved(String) -> boolean

Parameters:

  • arg0 (str)

Returns: bool

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

On this page
Edit on GitHub