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.
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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 -
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, updateAndDisplayTableMethods inherited from class org.scijava.command.ContextCommand
cancel, getCancelReason, isCanceledMethods inherited from class org.scijava.AbstractContextual
context, getContextMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface org.scijava.Contextual
setContext
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Constructor Details
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TreeAnalyzer
Deprecated.UseTreeStatisticsconstructors insteadInstantiates a TreeAnalyzer from a Tree.- Parameters:
tree- the Tree to be analyzed
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TreeStatisticsinstead