sc.fiji.snt.analysis

Class TreeStatistics

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.TreeAnalyzer

sc.fiji.snt.analysis.TreeStatistics

All Implemented Interfaces:

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

public class TreeStatistics
extends TreeAnalyzer

Computes summary and descriptive statistics from univariate properties of a Tree.

Author:

Tiago Ferreira

Field Summary

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

BRANCH_ORDER, COMMON_MEASUREMENTS, INTER_NODE_DISTANCE, INTER_NODE_DISTANCE_SQUARED, LENGTH, MEAN_RADIUS, N_BRANCH_POINTS, N_NODES, NODE_RADIUS, VALUES, X_COORDINATES, Y_COORDINATES, Z_COORDINATES

Constructor Summary

Constructors

Constructor and Description
TreeStatistics(Tree tree) Instantiates a new instance from a collection of Paths

Method Summary

Modifier and Type	Method and Description
org.apache.commons.math3.stat.descriptive.DescriptiveStatistics	getDescriptiveStats(java.lang.String measurement) Computes the DescriptiveStatistics for the specified measurement.
org.jfree.chart.ChartFrame	getHistogram(java.lang.String measurement) Gets the relative frequencies histogram for a univariate measurement.
org.apache.commons.math3.stat.descriptive.SummaryStatistics	getSummaryStats(java.lang.String measurement) Computes the SummaryStatistics for the specified measurement.
static void	main(java.lang.String[] args)

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

getBranchPoints, getCableLength, getNPaths, getParsedTree, getPrimaryBranches, getPrimaryLength, getPrimaryPaths, getStrahlerRootNumber, getTable, getTerminalBranches, getTerminalLength, getTips, ignoreSWCType, resetRestrictions, restrictToLength, restrictToNamePattern, restrictToOrder, restrictToSize, restrictToSWCType, run, setTable, setTable, summarize, summarize, 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

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

Methods inherited from interface org.scijava.Contextual

setContext

Constructor Detail

TreeStatistics

public TreeStatistics(Tree tree)

Instantiates a new instance from a collection of Paths

Parameters:

tree - the collection of paths to be analyzed

Method Detail

getSummaryStats

public org.apache.commons.math3.stat.descriptive.SummaryStatistics getSummaryStats(java.lang.String measurement)

Computes the SummaryStatistics for the specified measurement.

Parameters:

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

Returns:

the SummaryStatistics object.

getDescriptiveStats

public org.apache.commons.math3.stat.descriptive.DescriptiveStatistics getDescriptiveStats(java.lang.String measurement)

Computes the DescriptiveStatistics for the specified measurement.

Parameters:

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

Returns:

the DescriptiveStatistics object.

getHistogram

public org.jfree.chart.ChartFrame getHistogram(java.lang.String measurement)

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

Parameters:

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

Returns:

the frame holding the histogram

main

public static void main(java.lang.String[] args)