public class PathAnalyzer extends TreeStatistics
AVG_SPINE_DENSITY, BRANCH_LENGTH, CONTRACTION, FRACTAL_DIMENSION, INNER_LENGTH, INTER_NODE_DISTANCE, INTER_NODE_DISTANCE_SQUARED, lastDstats, MEAN_RADIUS, N_BRANCH_POINTS, N_NODES, N_SPINES, NODE_RADIUS, PARTITION_ASYMMETRY, PATH_CHANNEL, PATH_FRAME, PATH_LENGTH, PATH_ORDER, PRIMARY_LENGTH, REMOTE_BIF_ANGLES, TERMINAL_LENGTH, VALUES, X_COORDINATES, Y_COORDINATES, Z_COORDINATESdisplayService, innerBranches, primaryBranches, statusService, table, terminalBranches, tips, tree| Constructor and Description |
|---|
PathAnalyzer(Collection<Path> paths,
String label) |
| Modifier and Type | Method and Description |
|---|---|
List<Path> |
getBranches()
Gets all the branches in the analyzed tree.
|
List<Path> |
getInnerBranches()
Retrieves the branches of highest
Strahler order in the Tree. |
double |
getInnerLength()
Gets the cable length of inner branches
|
int |
getNBranches()
Gets the number of branches in the analyzed tree.
|
List<Path> |
getPrimaryBranches()
Retrieves the primary branches of the analyzed Tree.
|
double |
getPrimaryLength()
Gets the cable length of primary branches.
|
void |
measureIndividualPaths(Collection<String> metrics) |
assembleStats, fromCollection, getAllMetrics, getAnalyzerMetrics, getAnnotatedLength, getAnnotatedLength, getAnnotatedLength, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthsByHemisphere, getAnnotatedLengthsByHemisphere, getAnnotatedLengthsByHemisphereHistogram, getDescriptiveStats, getHistogram, getHistogram, getMetrics, getNodeStatistics, getNodeStatistics, getNormalizedMeasurement, getSummaryStats, lastDstatsCanBeRecycled, main, tryReallyHardToGuessMetricgetAnnotations, getAnnotations, getAvgBranchLength, getAvgContraction, getAvgFractalDimension, getAvgFragmentation, getAvgPartitionAsymmetry, getAvgRemoteBifAngle, getBranchPoints, getBranchPoints, getCableLength, getCableLength, getCableLength, getCableLengthNorm, getCol, getDepth, getFractalDimension, getHeight, getHighestPathOrder, getMetric, getMetricInternal, getMetricWithoutChecks, getNbranchPoints, getNbranchPointsNorm, getNextRow, getNFittedPaths, getNoSpinesOrVaricosities, getNPaths, getNtips, getNtipsNorm, getParsedTree, getPartitionAsymmetry, getPrimaryPaths, getRemoteBifAngles, getShollAnalyzer, getSinglePointPaths, getSpineOrVaricosityDensity, getStrahlerAnalyzer, getStrahlerBifurcationRatio, getStrahlerNumber, getSWCTypesAsString, getTable, getTerminalBranches, getTerminalLength, getTips, getTips, getWidth, ignoreSWCType, isSameOrParentAnnotation, isValid, measure, measure, resetRestrictions, restrictToLength, restrictToNamePattern, restrictToOrder, restrictToSize, restrictToSWCType, run, setTable, setTable, summarize, summarize, updateAndDisplayTablecancel, getCancelReason, isCanceledcontext, getContextclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitsetContextpublic PathAnalyzer(Collection<Path> paths, String label)
public List<Path> getBranches()
TreeAnalyzergetBranches in class TreeAnalyzerStrahlerAnalyzer.getBranches()public int getNBranches()
TreeAnalyzergetNBranches in class TreeAnalyzerpublic List<Path> getPrimaryBranches()
TreeAnalyzergetPrimaryBranches in class TreeAnalyzerTreeAnalyzer.getPrimaryPaths(),
StrahlerAnalyzer.getRootAssociatedBranches()public double getPrimaryLength()
TreeAnalyzergetPrimaryLength in class TreeAnalyzerTreeAnalyzer.getPrimaryBranches()public List<Path> getInnerBranches()
TreeAnalyzerStrahler order in the Tree.
This typically correspond to the most 'internal' branches of the Tree in
direct sequence from the root.getInnerBranches in class TreeAnalyzerTreeAnalyzer.getPrimaryPaths(),
StrahlerAnalyzer.getBranches(),
StrahlerAnalyzer.getHighestBranchOrder()public double getInnerLength()
TreeAnalyzergetInnerLength in class TreeAnalyzerTreeAnalyzer.getInnerBranches()public void measureIndividualPaths(Collection<String> metrics)
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