Package sc.fiji.snt.plugin

Class PathOrderAnalysisCmd

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.TreeStatistics

sc.fiji.snt.plugin.PathOrderAnalysisCmd

All Implemented Interfaces:

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

public class PathOrderAnalysisCmd
extends TreeStatistics

Command to perform Path Ordering analysis on a Tree. Albeit related to reverse Horton-Strahler classification, Path ordering is formally distinct, as it classifies Paths rather than branches.

Author:

Tiago Ferreira

See Also:

• StrahlerCmd

Field Summary

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, INNER_LENGTH, innerBranches, INTER_NODE_ANGLE, INTER_NODE_DISTANCE, INTER_NODE_DISTANCE_SQUARED, lastDstats, LENGTH, MEAN_RADIUS, 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, PRIMARY_LENGTH, 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, TERMINAL_LENGTH, terminalBranches, tips, tree, VALUES, VOLUME, WIDTH, X_COORDINATES, Y_COORDINATES, Z_COORDINATES

Constructor Summary

Constructors

Constructor	Description
PathOrderAnalysisCmd(Tree tree)

Method Summary

Modifier and Type	Method	Description
void	compute()
void	displayPlot()
Map<Integer,Double>	getBranchPointMap()
org.scijava.plot.CategoryChart	getCategoryChart()	Returns the analysis chart.
SNTChart	getChart()	A variant of getCategoryChart() that returns the Analysis chart as a SNTChart object.
Map<Integer,Double>	getCountMap()
int	getHighestPathOrder()	Gets the highest path order of the analyzed tree
Map<Integer,Double>	getLengthMap()
Map<Integer,Double>	getRatioMap()
void	run()	Generates detailed summaries in which measurements are grouped by SWC-type flags
void	updateAndDisplayTable()	Updates and displays the measurements table.

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

assembleStats, contains, dispose, fromCollection, getAllMetrics, getAnnotatedLength, getAnnotatedLength, getAnnotatedLength, getAnnotatedLength, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthsByHemisphere, getAnnotatedLengthsByHemisphere, getAnnotatedLengthsByHemisphereHistogram, getAnnotations, getAnnotations, getAvgBranchLength, getAvgContraction, getAvgFractalDimension, getAvgFragmentation, getAvgPartitionAsymmetry, getAvgRemoteBifAngle, getBranches, getBranchPoints, getBranchPoints, getBranchPoints, getCableLength, getCableLength, getCableLength, getCableLengthNorm, getCableLengthNorm, getCol, getConvexAnalyzer, getConvexHullMetric, getDepth, getDescriptiveStats, getFlowPlot, getFlowPlot, getFlowPlot, getFlowPlot, getFlowPlot, getFractalDimension, getHeight, getHistogram, getHistogram, getInnerBranches, getInnerLength, getMetric, getMetrics, getMetrics, getNBranches, getNBranchPoints, getNBranchPoints, getNBranchPointsNorm, getNBranchPointsNorm, getNextRow, getNFittedPaths, getNNodes, getNodeStatistics, getNodeStatistics, getNormalizedMeasurement, getNoSpinesOrVaricosities, getNPaths, getNTips, getNTips, getNTipsNorm, getNTipsNorm, getParsedTree, getPartitionAsymmetry, getPolarHistogram, getPrimaryBranches, getPrimaryLength, getPrimaryPaths, getRemoteBifAngles, getRootAngleAnalyzer, getRootAngleMetric, getShollAnalyzer, getShollMetric, getSpatialUnit, getSpineOrVaricosityDensity, getStrahlerAnalyzer, getStrahlerBifurcationRatio, getStrahlerNumber, getSummaryStats, getSWCTypesAsString, getTable, getTerminalBranches, getTerminalLength, getTips, getTips, getTips, getTips, getTips, getUnit, getWidth, isExactMetricMatch, isValid, lastDstatsCanBeRecycled, main, measure, measure, resetRestrictions, restrictToSWCType, setExactMetricMatch, setTable, setTable, summarize, summarize, tryReallyHardToGuessMetric

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

Constructor Details

PathOrderAnalysisCmd

public PathOrderAnalysisCmd(Tree tree)

Method Details

run

public void run()

Description copied from class: TreeStatistics

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

Specified by:

run in interface Runnable

Overrides:

run in class TreeStatistics

See Also:

• TreeStatistics.summarize(String, boolean)

compute

public void compute()

updateAndDisplayTable

public void updateAndDisplayTable()

Description copied from class: TreeStatistics

Updates and displays the measurements table. If Context has not been set (running headless!?), table is printed to Console.

Overrides:

updateAndDisplayTable in class TreeStatistics

displayPlot

public void displayPlot()

getCategoryChart

public org.scijava.plot.CategoryChart getCategoryChart()
                                                throws IllegalArgumentException

Returns the analysis chart.

Returns:

the analysis chart

Throws:

IllegalArgumentException - if tree contains multiple roots or loops

See Also:

• getChart()

getChart

public SNTChart getChart()
                  throws IllegalArgumentException

A variant of getCategoryChart() that returns the Analysis chart as a SNTChart object.

Returns:

the Strahler chart as a SNTChart object

Throws:

IllegalArgumentException - if tree contains multiple roots or loops

getCountMap

public Map<Integer,Double> getCountMap()

Returns:

the map containing the number of paths on each order (order 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 Map<Integer,Double> getBranchPointMap()

Returns:

the map containing the number of branch points on each order (order 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.

getHighestPathOrder

public int getHighestPathOrder()

Description copied from class: TreeStatistics

Gets the highest path order of the analyzed tree

Overrides:

getHighestPathOrder in class TreeStatistics

Returns:

the highest path order of the parsed tree.

See Also:

• TreeStatistics.getStrahlerNumber()

getLengthMap

public Map<Integer,Double> getLengthMap()

Returns:

the map containing the total path lengh on each order (order 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 Map<Integer,Double> getRatioMap()

Returns:

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