sc.fiji.snt.plugin

Class StrahlerCmd

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.TreeAnalyzer

sc.fiji.snt.plugin.StrahlerCmd

All Implemented Interfaces:

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

public class StrahlerCmd
extends TreeAnalyzer

Command to perform Horton-Strahler analysis on 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
StrahlerCmd(Tree tree)

Method Summary

Modifier and Type	Method and Description
void	compute()
void	displayPlot()
java.util.Map<java.lang.Integer,java.lang.Double>	getBranchPointMap()
java.util.Map<java.lang.Integer,java.lang.Double>	getCountMap()
java.util.Map<java.lang.Integer,java.lang.Double>	getLengthMap()
java.util.Map<java.lang.Integer,java.lang.Double>	getRatioMap()
int	getRootNumber()
void	run() Generates detailed summaries in which measurements are grouped by SWC-type flags
void	updateAndDisplayTable() Updates and displays the Analyzer table.

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

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

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

StrahlerCmd

public StrahlerCmd(Tree tree)

Method Detail

run

public void run()

Description copied from class: TreeAnalyzer

Generates detailed summaries in which measurements are grouped by SWC-type flags

Specified by:

run in interface java.lang.Runnable

Overrides:

run in class TreeAnalyzer

See Also:

TreeAnalyzer.summarize(String, boolean)

compute

public void compute()

updateAndDisplayTable

public void updateAndDisplayTable()

Description copied from class: TreeAnalyzer

Updates and displays the Analyzer table.

Overrides:

updateAndDisplayTable in class TreeAnalyzer

displayPlot

public void displayPlot()

getCountMap

public java.util.Map<java.lang.Integer,java.lang.Double> getCountMap()

Returns:

the map containing the number of paths on each order (reverse Horton-Strahler number as key and counts as value). Single-point paths are ignored. An empty map will be returned if {compute() has not been called.

getBranchPointMap

public java.util.Map<java.lang.Integer,java.lang.Double> getBranchPointMap()

Returns:

the map containing the number of branch points on each order (reverse Horton-Strahler number as key and branch point count as value). Single-point paths are ignored. An empty map will be returned if {compute() has not been called.

getRootNumber

public int getRootNumber()

Returns:

the highest Horton-Strahler number of the parsed tree.

getLengthMap

public java.util.Map<java.lang.Integer,java.lang.Double> getLengthMap()

Returns:

the map containing the total path lengh on each order (reverse Horton-Strahler number as key and sum length as value). Single-point paths are ignored. An empty map will be returned if {compute() has not been called.

getRatioMap

public java.util.Map<java.lang.Integer,java.lang.Double> getRatioMap()

Returns:

the map containing th bifurcation ratios between orders (reverse Horton-Strahler numbers as key and ratios as value). Single-point paths are ignored. An empty map will be returned if {compute() has not been called.