Package sc.fiji.snt.analysis

Class TreeAnalyzer

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.TreeStatistics

sc.fiji.snt.analysis.TreeAnalyzer

All Implemented Interfaces:

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

@Deprecated
public class TreeAnalyzer
extends TreeStatistics

Deprecated.

Use TreeStatistics instead

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
TreeAnalyzer(Tree tree)	Deprecated. Use TreeStatistics constructors instead

Method Summary

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, getHighestPathOrder, 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, 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

Constructor Details

TreeAnalyzer

@Deprecated
public TreeAnalyzer(Tree tree)

Deprecated.

Use TreeStatistics constructors instead

Instantiates a TreeAnalyzer from a Tree.

Parameters:

tree - the Tree to be analyzed