Package sc.fiji.snt.analysis

Class MultiTreeStatistics

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.TreeStatistics

sc.fiji.snt.analysis.MultiTreeStatistics

All Implemented Interfaces:

Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.plugin.SciJavaPlugin

public class MultiTreeStatistics
extends TreeStatistics

Computes summary and descriptive statistics from univariate properties of Tree groups. For analysis of individual Trees use TreeStatistics.

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ASSIGNED_VALUE	Flag specifying Tree value statistics
static final String	AVG_BRANCH_LENGTH	Flag for "Average branch length" analysis.
static final String	AVG_CONTRACTION	Flag for "Average contraction" statistics
static final String	AVG_FRACTAL_DIMENSION	Flag specifying "Average fractal dimension" statistics
static final String	AVG_FRAGMENTATION	Flag for "Average fragmentation" statistics
static final String	AVG_PARTITION_ASYMMETRY	Flag specifying "Average partition asymmetry" statistics
static final String	AVG_REMOTE_ANGLE	Flag specifying "Average remote bif. angle" statistics
static final String	HIGHEST_PATH_ORDER	Flag specifying "Highest path order" statistics
static final String	INNER_LENGTH	Flag for "Length of inner branches (sum)" analysis.
static final String	MEAN_RADIUS	Deprecated. use #PATH_MEAN_RADIUS instead
static final String	PRIMARY_LENGTH	Flag for "Length of primary branches (sum)" analysis.
static final String	TERMINAL_LENGTH	Flag for "Length of terminal branches (sum)" analysis.

Fields inherited from class sc.fiji.snt.analysis.TreeStatistics

AVG_SPINE_DENSITY, BRANCH_CONTRACTION, BRANCH_EXTENSION_ANGLE, BRANCH_EXTENSION_ANGLE_REL, BRANCH_EXTENSION_ANGLE_XY, BRANCH_EXTENSION_ANGLE_XZ, BRANCH_EXTENSION_ANGLE_ZY, BRANCH_FRACTAL_DIMENSION, BRANCH_LENGTH, BRANCH_MEAN_RADIUS, BRANCH_SURFACE_AREA, BRANCH_VOLUME, COMPLEXITY_INDEX_ACI, COMPLEXITY_INDEX_DCI, CONTRACTION, CONVEX_HULL_BOUNDARY_SIZE, CONVEX_HULL_BOXIVITY, CONVEX_HULL_CENTROID_ROOT_DISTANCE, CONVEX_HULL_COMPACTNESS_3D, CONVEX_HULL_ECCENTRICITY_2D, CONVEX_HULL_ELONGATION, CONVEX_HULL_ROUNDNESS, CONVEX_HULL_SIZE, DEPTH, FRACTAL_DIMENSION, GRAPH_DIAMETER, GRAPH_DIAMETER_ANGLE, GRAPH_DIAMETER_ANGLE_XY, GRAPH_DIAMETER_ANGLE_XZ, GRAPH_DIAMETER_ANGLE_ZY, HEIGHT, INNER_EXTENSION_ANGLE, INNER_EXTENSION_ANGLE_REL, INNER_EXTENSION_ANGLE_XY, INNER_EXTENSION_ANGLE_XZ, INNER_EXTENSION_ANGLE_ZY, innerBranches, INTER_NODE_ANGLE, INTER_NODE_DISTANCE, INTER_NODE_DISTANCE_SQUARED, lastDstats, LENGTH, N_BRANCH_NODES, N_BRANCH_POINTS, N_BRANCHES, N_FITTED_PATHS, N_INNER_BRANCHES, N_NODES, N_PATH_NODES, N_PATHS, N_PRIMARY_BRANCHES, N_SPINES, N_TERMINAL_BRANCHES, N_TIPS, NODE_RADIUS, PARTITION_ASYMMETRY, PATH_CHANNEL, PATH_CONTRACTION, PATH_EXT_ANGLE, PATH_EXT_ANGLE_REL, PATH_EXT_ANGLE_XY, PATH_EXT_ANGLE_XZ, PATH_EXT_ANGLE_ZY, PATH_FRACTAL_DIMENSION, PATH_FRAME, PATH_LENGTH, PATH_MEAN_RADIUS, PATH_N_SPINES, PATH_ORDER, PATH_SPINE_DENSITY, PATH_SURFACE_AREA, PATH_VOLUME, PRIMARY_EXTENSION_ANGLE, PRIMARY_EXTENSION_ANGLE_XY, PRIMARY_EXTENSION_ANGLE_XZ, PRIMARY_EXTENSION_ANGLE_ZY, primaryBranches, REMOTE_BIF_ANGLES, ROOT_ANGLE_B_FACTOR, ROOT_ANGLE_C_BIAS, ROOT_ANGLE_M_DIRECTION, SHOLL_DECAY, SHOLL_KURTOSIS, SHOLL_MAX_FITTED, SHOLL_MAX_FITTED_RADIUS, SHOLL_MAX_VALUE, SHOLL_MEAN_VALUE, SHOLL_N_MAX, SHOLL_N_SECONDARY_MAX, SHOLL_POLY_FIT_DEGREE, SHOLL_RAMIFICATION_INDEX, SHOLL_SKEWNESS, SHOLL_SUM_VALUE, statusService, STRAHLER_NUMBER, STRAHLER_RATIO, SURFACE_AREA, table, TERMINAL_EXTENSION_ANGLE, TERMINAL_EXTENSION_ANGLE_REL, TERMINAL_EXTENSION_ANGLE_XY, TERMINAL_EXTENSION_ANGLE_XZ, TERMINAL_EXTENSION_ANGLE_ZY, terminalBranches, tips, tree, VALUES, VOLUME, WIDTH, X_COORDINATES, Y_COORDINATES, Z_COORDINATES

Constructor Summary

Constructors

Constructor	Description
MultiTreeStatistics(Collection<Tree> group)	Instantiates a new instance from a collection of Trees.
MultiTreeStatistics(Collection<Tree> group, String... swcTypes)	Instantiates a new instance from a collection of Trees.

Method Summary

Modifier and Type	Method	Description
protected void	assembleStats(sc.fiji.snt.analysis.TreeStatistics.StatisticsInstance stat, String measurement)
Map<BrainAnnotation,Double>	getAnnotatedLength(int level)	Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
Map<BrainAnnotation,Double>	getAnnotatedLength(int level, String hemisphere)	Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
Map<BrainAnnotation,Double>	getAnnotatedLength(int level, String hemisphere, boolean norm)	Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
Map<BrainAnnotation,double[]>	getAnnotatedLengthsByHemisphere(int level)	Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron in the two brain hemispheres.
Set<BrainAnnotation>	getAnnotations()	Retrieves the brain compartments (neuropil labels) associated with the Tree being measured innervated by the analyzed neuron.
Set<BrainAnnotation>	getAnnotations(int level)	Retrieves the brain compartments (neuropil labels) associated with the Tree being measured innervated by the analyzed neuron.
SNTChart	getBoxPlot(String measurement)	Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).
List<Path>	getBranches()	Gets all the branches in the analyzed tree.
Set<PointInImage>	getBranchPoints()	Gets the position of all the branch points in the analyzed tree.
double	getCableLength()	Gets the cable length.
double	getCableLength(BrainAnnotation compartment)	Gets the cable length associated with the specified compartment (neuropil label).
org.apache.commons.math3.stat.descriptive.DescriptiveStatistics	getDescriptiveStats(String metric)	Computes the DescriptiveStatistics for the specified measurement.
SNTChart	getFlowPlot(String feature, int depth)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth.
SNTChart	getFlowPlot(String feature, int depth, double cutoff, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth
SNTChart	getFlowPlot(String feature, Collection<BrainAnnotation> annotations)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.
SNTChart	getFlowPlot(String feature, Collection<BrainAnnotation> annotations, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.
SNTChart	getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature.
Collection<Tree>	getGroup()	Gets the collection of Trees being analyzed.
SNTChart	getHistogram(String metric)	Retrieves the histogram of relative frequencies histogram for a univariate measurement.
List<Path>	getInnerBranches()	Retrieves the branches of highest Strahler order in the Tree.
static List<String>	getMetrics()	Gets the list of metrics supported by MultiTreeStatistics.
SNTChart	getPolarHistogram(String metric)	Assembles a polar histogram for the specified metric (assumed to be an angular measurements (e.g., branch angles, path orientations).
List<Path>	getPrimaryBranches()	Retrieves the primary branches of the analyzed Tree.
SNTTable	getRawValues(String metric)
ShollAnalyzer	getShollAnalyzer()	Gets the ShollAnalyzer instance associated with this TreeStatistics instance.
protected String	getSpatialUnit()
StrahlerAnalyzer	getStrahlerAnalyzer()	Gets the StrahlerAnalyzer instance associated with this TreeStatistics instance
org.apache.commons.math3.stat.descriptive.SummaryStatistics	getSummaryStats(String metric)	Computes the SummaryStatistics for the specified measurement.
List<Path>	getTerminalBranches()	Retrieves the terminal branches of the analyzed Tree.
Set<PointInImage>	getTips()	Gets the position of all the tips in the analyzed tree.
static void	main(String[] args)	Main method for testing and demonstration purposes.
void	resetRestrictions()	Removes any filtering restrictions that may have been set.
void	restrictToSWCType(int... types)	Restricts analysis to Paths sharing the specified SWC flag(s).
void	setLabel(String groupLabel)	Sets an identifying label for the group of Trees being analyzed.

Methods inherited from class sc.fiji.snt.analysis.TreeStatistics

contains, dispose, fromCollection, getAllMetrics, getAnnotatedLength, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthsByHemisphere, getAnnotatedLengthsByHemisphereHistogram, getAvgBranchLength, getAvgContraction, getAvgFractalDimension, getAvgFragmentation, getAvgPartitionAsymmetry, getAvgRemoteBifAngle, getBranchPoints, getBranchPoints, getCableLength, getCableLengthNorm, getCableLengthNorm, getCol, getConvexAnalyzer, getConvexHullMetric, getDepth, getFractalDimension, getHeight, getHighestPathOrder, getHistogram, getInnerLength, getMetric, getMetrics, getNBranches, getNBranchPoints, getNBranchPoints, getNBranchPointsNorm, getNBranchPointsNorm, getNextRow, getNFittedPaths, getNNodes, getNodeStatistics, getNodeStatistics, getNormalizedMeasurement, getNoSpinesOrVaricosities, getNPaths, getNTips, getNTips, getNTipsNorm, getNTipsNorm, getParsedTree, getPartitionAsymmetry, getPrimaryLength, getPrimaryPaths, getRemoteBifAngles, getRootAngleAnalyzer, getRootAngleMetric, getShollMetric, getSpineOrVaricosityDensity, getStrahlerBifurcationRatio, getStrahlerNumber, getSWCTypesAsString, getTable, getTerminalLength, getTips, getTips, getTips, getTips, getUnit, getWidth, isExactMetricMatch, isValid, lastDstatsCanBeRecycled, measure, measure, run, setExactMetricMatch, setTable, setTable, summarize, summarize, tryReallyHardToGuessMetric, updateAndDisplayTable

Methods inherited from class org.scijava.command.ContextCommand

cancel, getCancelReason, isCanceled

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.scijava.Contextual

setContext

Field Details

TERMINAL_LENGTH

public static final String TERMINAL_LENGTH

Flag for "Length of terminal branches (sum)" analysis.

See Also:

• Constant Field Values

INNER_LENGTH

public static final String INNER_LENGTH

Flag for "Length of inner branches (sum)" analysis.

See Also:

• Constant Field Values

PRIMARY_LENGTH

public static final String PRIMARY_LENGTH

Flag for "Length of primary branches (sum)" analysis.

See Also:

• Constant Field Values

AVG_BRANCH_LENGTH

public static final String AVG_BRANCH_LENGTH

Flag for "Average branch length" analysis.

See Also:

• Constant Field Values

ASSIGNED_VALUE

public static final String ASSIGNED_VALUE

Flag specifying Tree value statistics

See Also:

• Constant Field Values

HIGHEST_PATH_ORDER

public static final String HIGHEST_PATH_ORDER

Flag specifying "Highest path order" statistics

See Also:

• Constant Field Values

AVG_CONTRACTION

public static final String AVG_CONTRACTION

Flag for "Average contraction" statistics

See Also:

• Constant Field Values

AVG_FRAGMENTATION

public static final String AVG_FRAGMENTATION

Flag for "Average fragmentation" statistics

See Also:

• Constant Field Values

AVG_REMOTE_ANGLE

public static final String AVG_REMOTE_ANGLE

Flag specifying "Average remote bif. angle" statistics

See Also:

• Constant Field Values

AVG_PARTITION_ASYMMETRY

public static final String AVG_PARTITION_ASYMMETRY

Flag specifying "Average partition asymmetry" statistics

See Also:

• Constant Field Values

AVG_FRACTAL_DIMENSION

public static final String AVG_FRACTAL_DIMENSION

Flag specifying "Average fractal dimension" statistics

See Also:

• Constant Field Values

MEAN_RADIUS

@Deprecated
public static final String MEAN_RADIUS

Deprecated.

use #PATH_MEAN_RADIUS instead

Flag for "Mean radius" statistics

See Also:

• Constant Field Values

Constructor Details

MultiTreeStatistics

public MultiTreeStatistics(Collection<Tree> group)

Instantiates a new instance from a collection of Trees.

Parameters:

group - the collection of Trees to be analyzed

MultiTreeStatistics

public MultiTreeStatistics(Collection<Tree> group,
 String... swcTypes)
                    throws NoSuchElementException

Instantiates a new instance from a collection of Trees.

Parameters:

group - the collection of Trees to be analyzed

swcTypes - SWC type(s) a string with at least 2 characters describing the SWC type allowed in the subtree (e.g., 'axn', or 'dendrite')

Throws:

NoSuchElementException - swcTypes are not applicable to group

Method Details

getGroup

public Collection<Tree> getGroup()

Gets the collection of Trees being analyzed.

Returns:

the Tree group

setLabel

public void setLabel(String groupLabel)

Sets an identifying label for the group of Trees being analyzed.

Parameters:

groupLabel - the identifying string for the group.

getSummaryStats

public org.apache.commons.math3.stat.descriptive.SummaryStatistics getSummaryStats(String metric)

Description copied from class: TreeStatistics

Computes the SummaryStatistics for the specified measurement.

Overrides:

getSummaryStats in class TreeStatistics

Parameters:

metric - the measurement (TreeStatistics.N_NODES, TreeStatistics.NODE_RADIUS, etc.)

Returns:

the SummaryStatistics object.

getDescriptiveStats

public org.apache.commons.math3.stat.descriptive.DescriptiveStatistics getDescriptiveStats(String metric)

Description copied from class: TreeStatistics

Computes the DescriptiveStatistics for the specified measurement.

Overrides:

getDescriptiveStats in class TreeStatistics

Parameters:

metric - the measurement (TreeStatistics.N_NODES, TreeStatistics.NODE_RADIUS, etc.)

Returns:

the DescriptiveStatistics object.

assembleStats

protected void assembleStats(sc.fiji.snt.analysis.TreeStatistics.StatisticsInstance stat,
 String measurement)
                      throws UnknownMetricException

Overrides:

assembleStats in class TreeStatistics

Throws:

UnknownMetricException

getSpatialUnit

protected String getSpatialUnit()

Overrides:

getSpatialUnit in class TreeStatistics

restrictToSWCType

public void restrictToSWCType(int... types)

Description copied from class: TreeStatistics

Restricts analysis to Paths sharing the specified SWC flag(s).

Overrides:

restrictToSWCType in class TreeStatistics

Parameters:

types - the allowed SWC flags (e.g., Path.SWC_AXON, etc.)

resetRestrictions

public void resetRestrictions()

Description copied from class: TreeStatistics

Removes any filtering restrictions that may have been set. Once called, subsequent analysis will use all paths initially parsed by the constructor. Does nothing if no paths are currently being excluded from the analysis.

Overrides:

resetRestrictions in class TreeStatistics

getStrahlerAnalyzer

public StrahlerAnalyzer getStrahlerAnalyzer()
                                     throws IllegalArgumentException

Description copied from class: TreeStatistics

Gets the StrahlerAnalyzer instance associated with this TreeStatistics instance

Overrides:

getStrahlerAnalyzer in class TreeStatistics

Returns:

the StrahlerAnalyzer instance associated with this TreeStatistics instance

Throws:

IllegalArgumentException - if tree contains multiple roots or loops

getShollAnalyzer

public ShollAnalyzer getShollAnalyzer()

Description copied from class: TreeStatistics

Gets the ShollAnalyzer instance associated with this TreeStatistics instance. Note that changes to ShollAnalyzer must be performed before retrieving Sholl related metrics, i.e., before calling TreeStatistics.measure(Collection, boolean), etc.

Overrides:

getShollAnalyzer in class TreeStatistics

Returns:

the ShollAnalyzer instance associated with this TreeStatistics instance

getAnnotations

public Set<BrainAnnotation> getAnnotations()

Description copied from class: TreeStatistics

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

Overrides:

getAnnotations in class TreeStatistics

Returns:

the set of brain compartments (BrainAnnotations)

See Also:

• AllenCompartment

getAnnotations

public Set<BrainAnnotation> getAnnotations(int level)

Description copied from class: TreeStatistics

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

Overrides:

getAnnotations in class TreeStatistics

Parameters:

level - the max. ontological depth of the compartments to be retrieved

Returns:

the set of brain compartments (BrainAnnotations)

See Also:

• AllenCompartment

getCableLength

public double getCableLength()

Description copied from class: TreeStatistics

Gets the cable length.

Overrides:

getCableLength in class TreeStatistics

Returns:

the cable length of the tree

getCableLength

public double getCableLength(BrainAnnotation compartment)

Description copied from class: TreeStatistics

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

Overrides:

getCableLength in class TreeStatistics

Parameters:

compartment - the query compartment (null not allowed). All of its children will be considered

Returns:

the filtered cable length

getAnnotatedLength

public Map<BrainAnnotation,Double> getAnnotatedLength(int level,
 String hemisphere)

Description copied from class: TreeStatistics

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

Overrides:

getAnnotatedLength in class TreeStatistics

Parameters:

level - the ontological depth of the compartments to be considered

hemisphere - typically 'left' or 'right'. The hemisphere flag ( BrainAnnotation.LEFT_HEMISPHERE or BrainAnnotation.RIGHT_HEMISPHERE) is extracted from the first character of the string (case-insensitive). Ignored if not a recognized option

Returns:

the map containing the brain compartments as keys, and cable lengths as values.

See Also:

• AllenCompartment.getOntologyDepth()

getAnnotatedLength

public Map<BrainAnnotation,Double> getAnnotatedLength(int level,
 String hemisphere,
 boolean norm)

Description copied from class: TreeStatistics

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

Overrides:

getAnnotatedLength in class TreeStatistics

Parameters:

level - the ontological depth of the compartments to be considered

hemisphere - typically 'left' or 'right'. The hemisphere flag ( BrainAnnotation.LEFT_HEMISPHERE or BrainAnnotation.RIGHT_HEMISPHERE) is extracted from the first character of the string (case-insensitive). Ignored if not a recognized option

norm - whether length should be normalized to the cells' cable length

Returns:

the map containing the brain compartments as keys, and cable lengths as values.

See Also:

• AllenCompartment.getOntologyDepth()

getAnnotatedLength

public Map<BrainAnnotation,Double> getAnnotatedLength(int level)

Description copied from class: TreeStatistics

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

Overrides:

getAnnotatedLength in class TreeStatistics

Parameters:

level - the ontological depth of the compartments to be considered

Returns:

the map containing the brain compartments as keys, and cable lengths as values.

See Also:

• AllenCompartment.getOntologyDepth()

getAnnotatedLengthsByHemisphere

public Map<BrainAnnotation,double[]> getAnnotatedLengthsByHemisphere(int level)

Description copied from class: TreeStatistics

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.

Overrides:

getAnnotatedLengthsByHemisphere in class TreeStatistics

Parameters:

level - the ontological depth of the compartments to be considered

Returns:

the map containing the brain compartments as keys, and cable lengths per hemisphere as values.

See Also:

• AllenCompartment.getOntologyDepth()

getHistogram

public SNTChart getHistogram(String metric)

Description copied from class: TreeStatistics

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

Overrides:

getHistogram in class TreeStatistics

Parameters:

metric - the measurement (TreeStatistics.N_NODES, TreeStatistics.NODE_RADIUS, etc.)

Returns:

the frame holding the histogram

getPolarHistogram

public SNTChart getPolarHistogram(String metric)

Description copied from class: TreeStatistics

Assembles a polar histogram for the specified metric (assumed to be an angular measurements (e.g., branch angles, path orientations).

Overrides:

getPolarHistogram in class TreeStatistics

Parameters:

metric - the metric to be plotted (e.g., TreeStatistics.BRANCH_EXTENSION_ANGLE_XY, TreeStatistics.PATH_EXT_ANGLE_XY, etc.)

Returns:

the polar histogram chart

See Also:

• TreeStatistics.getHistogram(String)

getRawValues

public SNTTable getRawValues(String metric)

getTips

public Set<PointInImage> getTips()

Description copied from class: TreeStatistics

Gets the position of all the tips in the analyzed tree.

Overrides:

getTips in class TreeStatistics

Returns:

the set of terminal points

getBranchPoints

public Set<PointInImage> getBranchPoints()

Description copied from class: TreeStatistics

Gets the position of all the branch points in the analyzed tree.

Overrides:

getBranchPoints in class TreeStatistics

Returns:

the branch points positions

getBranches

public List<Path> getBranches()
                       throws IllegalArgumentException

Description copied from class: TreeStatistics

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.

Overrides:

getBranches in class TreeStatistics

Returns:

the list of branches as Path objects.

Throws:

IllegalArgumentException - if tree contains multiple roots or loops

See Also:

• StrahlerAnalyzer.getBranches()

getPrimaryBranches

public List<Path> getPrimaryBranches()

Description copied from class: TreeStatistics

Retrieves the primary branches of the analyzed Tree. Primary branches (or root-associated) have origin in the Tree's root, extending to the closest branch/end-point. Note that a primary branch can also be terminal.

Overrides:

getPrimaryBranches in class TreeStatistics

Returns:

the primary branches. Note that these branches (Path segments) will not carry any connectivity information.

See Also:

• TreeStatistics.getPrimaryPaths()
• StrahlerAnalyzer.getRootAssociatedBranches()

getInnerBranches

public List<Path> getInnerBranches()

Description copied from class: TreeStatistics

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.

Overrides:

getInnerBranches in class TreeStatistics

Returns:

the list containing the "inner" branches. Note that these branches (Path segments) will not carry any connectivity information.

See Also:

• TreeStatistics.getPrimaryPaths()
• StrahlerAnalyzer.getBranches()
• StrahlerAnalyzer.getHighestBranchOrder()

getTerminalBranches

public List<Path> getTerminalBranches()

Description copied from class: TreeStatistics

Retrieves the terminal branches of the analyzed Tree. A terminal branch corresponds to the section of a terminal Path between its last branch-point and its terminal point (tip). A terminal branch can also be primary.

Overrides:

getTerminalBranches in class TreeStatistics

Returns:

the terminal branches. Note that as per Path.getSection(int, int), these branches will not carry any connectivity information.

See Also:

• TreeStatistics.getPrimaryBranches()

getBoxPlot

public SNTChart getBoxPlot(String measurement)

Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).

Parameters:

measurement - the measurement (N_NODES, NODE_RADIUS, etc.)

Returns:

the SNTChart holding the box plot

See Also:

• getMetrics()
• TreeStatistics.getMetric(String)

getFlowPlot

public SNTChart getFlowPlot(String feature,
 Collection<BrainAnnotation> annotations,
 boolean normalize)

Description copied from class: TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.

Overrides:

getFlowPlot in class TreeStatistics

See Also:

• TreeStatistics.getFlowPlot(String, Collection, String, double, boolean)

getFlowPlot

public SNTChart getFlowPlot(String feature,
 int depth)

Description copied from class: TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth.

Overrides:

getFlowPlot in class TreeStatistics

Parameters:

feature - the feature ("Cable length", "No. of branch points", "No. of tips", etc.).

depth - the ontological depth of the compartments to be considered

Returns:

the flow plot

See Also:

• TreeStatistics.getFlowPlot(String, Collection, String, double, boolean)

getFlowPlot

public SNTChart getFlowPlot(String feature,
 int depth,
 double cutoff,
 boolean normalize)

Description copied from class: TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth. *

Overrides:

getFlowPlot in class TreeStatistics

Parameters:

feature - the feature ("Cable length", "No. of branch points", "No. of tips", etc.)

depth - the ontological depth of the compartments to be considered

cutoff - a filtering option. If the computed feature for an annotation is below this value, that annotation is excluded from the plot * @param normalize If true, values are retrieved as ratios. E.g., If feature is "Cable length", and cutoff 0.1, BrainAnnotations in annotations associated with less than 10% of cable length are ignored.

Returns:

the flow plot

getFlowPlot

public SNTChart getFlowPlot(String feature,
 Collection<BrainAnnotation> annotations)

Description copied from class: TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.

Overrides:

getFlowPlot in class TreeStatistics

See Also:

• TreeStatistics.getFlowPlot(String, Collection, String, double, boolean)

getFlowPlot

public SNTChart getFlowPlot(String feature,
 Collection<BrainAnnotation> annotations,
 String statistic,
 double cutoff,
 boolean normalize)

Description copied from class: TreeStatistics

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

Overrides:

getFlowPlot in class TreeStatistics

Parameters:

feature - the feature ("Cable length", "No. of branch points", "No. of tips", etc.). Note that the majority of TreeStatistics.getAllMetrics() metrics are currently not supported.

annotations - the BrainAnnotations to be queried. Null not allowed.

statistic - the integration statistic (lower case). Either "mean", "sum", "min" or "max". Null not allowed.

cutoff - a filtering option. If the computed feature for an annotation is below this value, that annotation is excluded from the plot

normalize - If true, values are retrieved as ratios. E.g., If feature is "Cable length", and cutoff 0.1, BrainAnnotations in annotations associated with less than 10% of cable length are ignored.

Returns:

the SNTChart holding the flow plot

getMetrics

public static List<String> getMetrics()

Gets the list of metrics supported by MultiTreeStatistics.

Returns all the metrics that can be computed for groups of trees, including aggregate measures and group-specific statistics.

Returns:

the list of supported metric names

main

public static void main(String[] args)

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.

Parameters:

args - command line arguments (not used)