MultiTreeStatistics (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.AbstractContextual
- - org.scijava.command.ContextCommand
  - - sc.fiji.snt.analysis.TreeAnalyzer
    - - sc.fiji.snt.analysis.TreeStatistics
      - sc.fiji.snt.analysis.MultiTreeStatistics

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, SciJavaPlugin
```
public class MultiTreeStatistics
extends TreeStatistics
```
Computes summary and descriptive statistics from univariate properties of Tree groups. For analysis of individual Trees use TreeStatistics.

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`protected static String[]`	`ALL_FLAGS`
`static String`	`ASSIGNED_VALUE` Flag specifying `Tree value` statistics
`static String`	`AVG_BRANCH_LENGTH` Flag for "Average branch length" analysis.
`static String`	`AVG_CONTRACTION` Flag for "Average contraction" statistics
`static String`	`AVG_FRACTAL_DIMENSION` Flag specifying "Average fractal dimension" statistics
`static String`	`AVG_FRAGMENTATION` Flag for "Average fragmentation" statistics
`static String`	`AVG_PARTITION_ASYMMETRY` Flag specifying "Average partition asymmetry" statistics
`static String`	`AVG_REMOTE_ANGLE` Flag specifying "Average remote bif. angle" statistics
`static String`	`AVG_SPINE_DENSITY` Flag for "Average spine/varicosity density" statistics.
`static String`	`DEPTH` Flag for "Depth" statistics
`static String`	`HEIGHT` Flag for "Height" statistics
`static String`	`HIGHEST_PATH_ORDER` Flag specifying "Highest path order" statistics
`static String`	`INNER_LENGTH` Flag for "Length of inner branches (sum)" analysis.
`static String`	`LENGTH` Flag for "Cable length" analysis.
`static String`	`MEAN_RADIUS` Flag for "Mean radius" statistics
`static String`	`N_BRANCH_POINTS` Flag for "No. of branch points" statistics
`static String`	`N_BRANCHES` Flag specifying "No. of branches" statistics
`static String`	`N_FITTED_PATHS` Flag for "No. of fitted paths" statistics
`static String`	`N_INNER_BRANCHES` Flag specifying "No. of inner branches" statistics
`static String`	`N_NODES` Flag for "No. of nodes" statistics
`static String`	`N_PATHS` Flag for "No. of paths" statistics
`static String`	`N_PRIMARY_BRANCHES` Flag specifying "No. of primary branches" statistics
`static String`	`N_SPINES` Flag for "No of spines/varicosities" statistics
`static String`	`N_TERMINAL_BRANCHES` Flag specifying "No. of terminal branches" statistics
`static String`	`N_TIPS` Flag specifying "No. of tips" statistics
`static String`	`PRIMARY_LENGTH` Flag for "Length of primary branches (sum)" analysis.
`static String`	`STRAHLER_NUMBER` Flag specifying `Horton-Strahler number` statistics
`static String`	`STRAHLER_RATIO` Flag specifying `Horton-Strahler bifurcation ratio` statistics
`static String`	`TERMINAL_LENGTH` Flag for "Length of terminal branches (sum)" analysis.
`static String`	`WIDTH` Flag for "Width" statistics

Fields inherited from class sc.fiji.snt.analysis.TreeStatistics
BRANCH_LENGTH, CONTRACTION, FRACTAL_DIMENSION, INTER_NODE_DISTANCE, INTER_NODE_DISTANCE_SQUARED, lastDstats, NODE_RADIUS, PARTITION_ASYMMETRY, PATH_CHANNEL, PATH_FRAME, PATH_LENGTH, PATH_ORDER, REMOTE_BIF_ANGLES, VALUES, X_COORDINATES, Y_COORDINATES, Z_COORDINATES

Fields inherited from class sc.fiji.snt.analysis.TreeAnalyzer
displayService, innerBranches, primaryBranches, statusService, table, terminalBranches, tips, tree

Constructor Summary

Constructors
Constructor and Description
`MultiTreeStatistics(Collection<Tree> group)` Instantiates a new instance from a collection of Trees.
`MultiTreeStatistics(Collection<Tree> group, String... swcTypes)` Instantiates a new instance from a collection of Trees.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`assembleStats(sc.fiji.snt.analysis.TreeStatistics.StatisticsInstance stat, String measurement)`
`static List<String>`	`getAllMetrics()` Gets the list of all supported metrics.
`Map<BrainAnnotation,Double>`	`getAnnotatedLength(int level)` Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
`Map<BrainAnnotation,Double>`	`getAnnotatedLength(int level, String hemisphere)` Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
`Map<BrainAnnotation,double[]>`	`getAnnotatedLengthsByHemisphere(int level)`
`Set<BrainAnnotation>`	`getAnnotations()`
`Set<BrainAnnotation>`	`getAnnotations(int level)`
`List<Path>`	`getBranches()` Gets all the branches in the analyzed tree.
`Set<PointInImage>`	`getBranchPoints()` Gets the position of all the branch points in the analyzed tree.
`double`	`getCableLength(BrainAnnotation compartment)` Gets the cable length associated with the specified compartment (neuropil label).
`DescriptiveStatistics`	`getDescriptiveStats(String metric)` Computes the `DescriptiveStatistics` for the specified measurement.
`Collection<Tree>`	`getGroup()` Gets the collection of Trees being analyzed.
`SNTChart`	`getHistogram(String metric)` Retrieves the histogram of relative frequencies histogram for a univariate measurement.
`List<Path>`	`getInnerBranches()` Retrieves the branches of highest `Strahler order` in the Tree.
`static List<String>`	`getMetrics()` Gets the list of most commonly used metrics.
`protected static String`	`getNormalizedMeasurement(String measurement, boolean defaultToTreeStatistics)`
`List<Path>`	`getPrimaryBranches()` Retrieves the primary branches of the analyzed Tree.
`ShollAnalyzer`	`getShollAnalyzer()` Gets the `ShollAnalyzer` instance associated with this analyzer.
`StrahlerAnalyzer`	`getStrahlerAnalyzer()` Gets the `StrahlerAnalyzer` instance associated with this analyzer
`SummaryStatistics`	`getSummaryStats(String metric)` Computes the `SummaryStatistics` for the specified measurement.
`List<Path>`	`getTerminalBranches()` Retrieves the terminal branches of the analyzed Tree.
`Set<PointInImage>`	`getTips()` Gets the position of all the tips in the analyzed tree.
`static void`	`main(String[] args)`
`void`	`resetRestrictions()` Removes any filtering restrictions that may have been set.
`void`	`restrictToSWCType(int... types)` Restricts analysis to Paths sharing the specified SWC flag(s).
`void`	`setLabel(String groupLabel)` Sets an identifying label for the group of Trees being analyzed.
`protected static String`	`tryReallyHardToGuessMetric(String guess)`

Methods inherited from class sc.fiji.snt.analysis.TreeStatistics
fromCollection, getAnalyzerMetrics, getAnnotatedLength, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthHistogram, getAnnotatedLengthsByHemisphere, getAnnotatedLengthsByHemisphereHistogram, getHistogram, getNodeStatistics, getNodeStatistics, getNormalizedMeasurement, lastDstatsCanBeRecycled

Methods inherited from class sc.fiji.snt.analysis.TreeAnalyzer
getAvgBranchLength, getAvgContraction, getAvgFractalDimension, getAvgFragmentation, getAvgPartitionAsymmetry, getAvgRemoteBifAngle, getBranchPoints, getCableLength, getCableLength, getCableLengthNorm, getCol, getDepth, getFractalDimension, getHeight, getHighestPathOrder, getInnerLength, getMetric, getMetricInternal, getMetricWithoutChecks, getNBranches, getNbranchPoints, getNbranchPointsNorm, getNextRow, getNFittedPaths, getNoSpinesOrVaricosities, getNPaths, getNtips, getNtipsNorm, getParsedTree, getPartitionAsymmetry, getPrimaryLength, getPrimaryPaths, getRemoteBifAngles, getSinglePointPaths, getSpineOrVaricosityDensity, getStrahlerBifurcationRatio, getStrahlerNumber, getSWCTypesAsString, getTable, getTerminalLength, getTips, getWidth, ignoreSWCType, isSameOrParentAnnotation, isValid, measure, measure, restrictToLength, restrictToNamePattern, restrictToOrder, restrictToSize, run, setTable, setTable, summarize, summarize, 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

- Field Detail
  - LENGTH
```
public static final String LENGTH
```
    Flag for "Cable length" analysis.
    
    See Also:
    
    Constant Field Values
  - TERMINAL_LENGTH
```
public static final String TERMINAL_LENGTH
```
    Flag for "Length of terminal branches (sum)" analysis.
    
    See Also:
    
    Constant Field Values
  - INNER_LENGTH
```
public static final String INNER_LENGTH
```
    Flag for "Length of inner branches (sum)" analysis.
    
    See Also:
    
    Constant Field Values
  - PRIMARY_LENGTH
```
public static final String PRIMARY_LENGTH
```
    Flag for "Length of primary branches (sum)" analysis.
    
    See Also:
    
    Constant Field Values
  - AVG_BRANCH_LENGTH
```
public static final String AVG_BRANCH_LENGTH
```
    Flag for "Average branch length" analysis.
    
    See Also:
    
    Constant Field Values
  - ASSIGNED_VALUE
```
public static final String ASSIGNED_VALUE
```
    Flag specifying Tree value statistics
    
    See Also:
    
    Constant Field Values
  - STRAHLER_NUMBER
```
public static final String STRAHLER_NUMBER
```
    Flag specifying Horton-Strahler number statistics
    
    See Also:
    
    Constant Field Values
  - STRAHLER_RATIO
```
public static final String STRAHLER_RATIO
```
    Flag specifying Horton-Strahler bifurcation ratio statistics
    
    See Also:
    
    Constant Field Values
  - HIGHEST_PATH_ORDER
```
public static final String HIGHEST_PATH_ORDER
```
    Flag specifying "Highest path order" statistics
    
    See Also:
    
    Constant Field Values
  - N_BRANCHES
```
public static final String N_BRANCHES
```
    Flag specifying "No. of branches" statistics
    
    See Also:
    
    Constant Field Values
  - N_PRIMARY_BRANCHES
```
public static final String N_PRIMARY_BRANCHES
```
    Flag specifying "No. of primary branches" statistics
    
    See Also:
    
    Constant Field Values
  - N_INNER_BRANCHES
```
public static final String N_INNER_BRANCHES
```
    Flag specifying "No. of inner branches" statistics
    
    See Also:
    
    Constant Field Values
  - N_TERMINAL_BRANCHES
```
public static final String N_TERMINAL_BRANCHES
```
    Flag specifying "No. of terminal branches" statistics
    
    See Also:
    
    Constant Field Values
  - N_BRANCH_POINTS
```
public static final String N_BRANCH_POINTS
```
    Flag for "No. of branch points" statistics
    
    See Also:
    
    Constant Field Values
  - N_SPINES
```
public static final String N_SPINES
```
    Flag for "No of spines/varicosities" statistics
    
    See Also:
    
    Constant Field Values
  - AVG_CONTRACTION
```
public static final String AVG_CONTRACTION
```
    Flag for "Average contraction" statistics
    
    See Also:
    
    Constant Field Values
  - AVG_FRAGMENTATION
```
public static final String AVG_FRAGMENTATION
```
    Flag for "Average fragmentation" statistics
    
    See Also:
    
    Constant Field Values
  - AVG_REMOTE_ANGLE
```
public static final String AVG_REMOTE_ANGLE
```
    Flag specifying "Average remote bif. angle" statistics
    
    See Also:
    
    Constant Field Values
  - AVG_PARTITION_ASYMMETRY
```
public static final String AVG_PARTITION_ASYMMETRY
```
    Flag specifying "Average partition asymmetry" statistics
    
    See Also:
    
    Constant Field Values
  - AVG_FRACTAL_DIMENSION
```
public static final String AVG_FRACTAL_DIMENSION
```
    Flag specifying "Average fractal dimension" statistics
    
    See Also:
    
    Constant Field Values
  - AVG_SPINE_DENSITY
```
public static final String AVG_SPINE_DENSITY
```
    Flag for "Average spine/varicosity density" statistics.
    
    See Also:
    
    Constant Field Values
  - N_PATHS
```
public static final String N_PATHS
```
    Flag for "No. of paths" statistics
    
    See Also:
    
    Constant Field Values
  - MEAN_RADIUS
```
public static final String MEAN_RADIUS
```
    Flag for "Mean radius" statistics
    
    See Also:
    
    Constant Field Values
  - N_NODES
```
public static final String N_NODES
```
    Flag for "No. of nodes" statistics
    
    See Also:
    
    Constant Field Values
  - N_TIPS
```
public static final String N_TIPS
```
    Flag specifying "No. of tips" statistics
    
    See Also:
    
    Constant Field Values
  - WIDTH
```
public static final String WIDTH
```
    Flag for "Width" statistics
    
    See Also:
    
    Constant Field Values
  - HEIGHT
```
public static final String HEIGHT
```
    Flag for "Height" statistics
    
    See Also:
    
    Constant Field Values
  - DEPTH
```
public static final String DEPTH
```
    Flag for "Depth" statistics
    
    See Also:
    
    Constant Field Values
  - N_FITTED_PATHS
```
public static final String N_FITTED_PATHS
```
    Flag for "No. of fitted paths" statistics
    
    See Also:
    
    Constant Field Values
  - ALL_FLAGS
```
protected static String[] ALL_FLAGS
```
- Constructor Detail
  - MultiTreeStatistics
```
public MultiTreeStatistics(Collection<Tree> group)
```
    Instantiates a new instance from a collection of Trees.
    
    Parameters:
    
    group - the collection of Trees to be analyzed
  - MultiTreeStatistics
```
public MultiTreeStatistics(Collection<Tree> group,
                           String... swcTypes)
                    throws NoSuchElementException
```
    Instantiates a new instance from a collection of Trees.
    
    Parameters:
    
    group - the collection of Trees to be analyzed
    
    swcTypes - SWC type(s) a string with at least 2 characters describing the SWC type allowed in the subtree (e.g., 'axn', or 'dendrite')
    
    Throws:
    
    NoSuchElementException - swcTypes are not applicable to group
- Method Detail
  - getAllMetrics
```
public static List<String> getAllMetrics()
```
    Gets the list of all supported metrics.
    
    Returns:
    
    the list of available metrics
  - getMetrics
```
public static List<String> getMetrics()
```
    Gets the list of most commonly used metrics.
    
    Returns:
    
    the list of commonly used metrics
  - getGroup
```
public Collection<Tree> getGroup()
```
    Gets the collection of Trees being analyzed.
    
    Returns:
    
    the Tree group
  - setLabel
```
public void setLabel(String groupLabel)
```
    Sets an identifying label for the group of Trees being analyzed.
    
    Parameters:
    
    groupLabel - the identifying string for the group.
  - getNormalizedMeasurement
```
protected static String getNormalizedMeasurement(String measurement,
                                                 boolean defaultToTreeStatistics)
                                          throws sc.fiji.snt.analysis.UnknownMetricException
```
    Throws:
    
    sc.fiji.snt.analysis.UnknownMetricException
  - tryReallyHardToGuessMetric
```
protected static String tryReallyHardToGuessMetric(String guess)
```
  - getSummaryStats
```
public SummaryStatistics getSummaryStats(String metric)
```
    Description copied from class: TreeStatistics
    
    Computes the SummaryStatistics for the specified measurement.
    
    Overrides:
    
    getSummaryStats in class TreeStatistics
    
    Parameters:
    
    metric - the measurement (TreeStatistics.N_NODES, TreeStatistics.NODE_RADIUS, etc.)
    
    Returns:
    
    the SummaryStatistics object.
  - getDescriptiveStats
```
public DescriptiveStatistics getDescriptiveStats(String metric)
```
    Description copied from class: TreeStatistics
    
    Computes the DescriptiveStatistics for the specified measurement.
    
    Overrides:
    
    getDescriptiveStats in class TreeStatistics
    
    Parameters:
    
    metric - the measurement (TreeStatistics.N_NODES, TreeStatistics.NODE_RADIUS, etc.)
    
    Returns:
    
    the DescriptiveStatistics object.
  - assembleStats
```
protected void assembleStats(sc.fiji.snt.analysis.TreeStatistics.StatisticsInstance stat,
                             String measurement)
                      throws sc.fiji.snt.analysis.UnknownMetricException
```
    Overrides:
    
    assembleStats in class TreeStatistics
    
    Throws:
    
    sc.fiji.snt.analysis.UnknownMetricException
  - restrictToSWCType
```
public void restrictToSWCType(int... types)
```
    Description copied from class: TreeAnalyzer
    
    Restricts analysis to Paths sharing the specified SWC flag(s).
    
    Overrides:
    
    restrictToSWCType in class TreeAnalyzer
    
    Parameters:
    
    types - the allowed SWC flags (e.g., Path.SWC_AXON, etc.)
  - resetRestrictions
```
public void resetRestrictions()
```
    Description copied from class: TreeAnalyzer
    
    Removes any filtering restrictions that may have been set. Once called, subsequent analysis will use all paths initially parsed by the constructor. Does nothing if no paths are currently being excluded from the analysis.
    
    Overrides:
    
    resetRestrictions in class TreeAnalyzer
  - getStrahlerAnalyzer
```
public StrahlerAnalyzer getStrahlerAnalyzer()
                                     throws IllegalArgumentException
```
    Description copied from class: TreeAnalyzer
    
    Gets the StrahlerAnalyzer instance associated with this analyzer
    
    Overrides:
    
    getStrahlerAnalyzer in class TreeAnalyzer
    
    Returns:
    
    the StrahlerAnalyzer instance associated with this analyzer
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - getShollAnalyzer
```
public ShollAnalyzer getShollAnalyzer()
```
    Description copied from class: TreeAnalyzer
    
    Gets the ShollAnalyzer instance associated with this analyzer. Note that changes to ShollAnalyzer must be performed before calling TreeAnalyzer.getMetric(String), TreeAnalyzer.measure(Collection, boolean), etc.
    
    Overrides:
    
    getShollAnalyzer in class TreeAnalyzer
    
    Returns:
    
    the ShollAnalyzer instance associated with this analyzer
  - getAnnotations
```
public Set<BrainAnnotation> getAnnotations()
```
    Overrides:
    
    getAnnotations in class TreeAnalyzer
  - getAnnotations
```
public Set<BrainAnnotation> getAnnotations(int level)
```
    Overrides:
    
    getAnnotations in class TreeAnalyzer
  - getCableLength
```
public double getCableLength(BrainAnnotation compartment)
```
    Description copied from class: TreeAnalyzer
    
    Gets the cable length associated with the specified compartment (neuropil label).
    
    Overrides:
    
    getCableLength in class TreeAnalyzer
    
    Parameters:
    
    compartment - the query compartment (null not allowed). All of its children will be considered
    
    Returns:
    
    the filtered cable length
  - getAnnotatedLength
```
public Map<BrainAnnotation,Double> getAnnotatedLength(int level,
                                                      String hemisphere)
```
    Description copied from class: TreeStatistics
    
    Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
    
    Overrides:
    
    getAnnotatedLength in class TreeStatistics
    
    Parameters:
    
    level - the ontological depth of the compartments to be considered
    
    hemisphere - typically 'left' or 'right'. The hemisphere flag ( BrainAnnotation.LEFT_HEMISPHERE or BrainAnnotation.RIGHT_HEMISPHERE) is extracted from the first character of the string (case insensitive). Ignored if not a recognized option
    
    Returns:
    
    the map containing the brain compartments as keys, and cable lengths as values.
    
    See Also:
    
    AllenCompartment.getOntologyDepth()
  - getAnnotatedLength
```
public Map<BrainAnnotation,Double> getAnnotatedLength(int level)
```
    Description copied from class: TreeStatistics
    
    Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
    
    Overrides:
    
    getAnnotatedLength in class TreeStatistics
    
    Parameters:
    
    level - the ontological depth of the compartments to be considered
    
    Returns:
    
    the map containing the brain compartments as keys, and cable lengths as values.
    
    See Also:
    
    AllenCompartment.getOntologyDepth()
  - getAnnotatedLengthsByHemisphere
```
public Map<BrainAnnotation,double[]> getAnnotatedLengthsByHemisphere(int level)
```
    Overrides:
    
    getAnnotatedLengthsByHemisphere in class TreeStatistics
  - getHistogram
```
public SNTChart getHistogram(String metric)
```
    Description copied from class: TreeStatistics
    
    Retrieves the histogram of relative frequencies histogram for a univariate measurement. The number of bins is determined using the Freedman-Diaconis rule.
    
    Overrides:
    
    getHistogram in class TreeStatistics
    
    Parameters:
    
    metric - the measurement (TreeStatistics.N_NODES, TreeStatistics.NODE_RADIUS, etc.)
    
    Returns:
    
    the frame holding the histogram
  - getTips
```
public Set<PointInImage> getTips()
```
    Description copied from class: TreeAnalyzer
    
    Gets the position of all the tips in the analyzed tree.
    
    Overrides:
    
    getTips in class TreeAnalyzer
    
    Returns:
    
    the set of terminal points
  - getBranchPoints
```
public Set<PointInImage> getBranchPoints()
```
    Description copied from class: TreeAnalyzer
    
    Gets the position of all the branch points in the analyzed tree.
    
    Overrides:
    
    getBranchPoints in class TreeAnalyzer
    
    Returns:
    
    the branch points positions
  - getBranches
```
public List<Path> getBranches()
                       throws IllegalArgumentException
```
    Description copied from class: TreeAnalyzer
    
    Gets all the branches in the analyzed tree. A branch is defined as the Path composed of all the nodes between two branching points or between one branching point and a termination point.
    
    Overrides:
    
    getBranches in class TreeAnalyzer
    
    Returns:
    
    the list of branches as Path objects.
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
    
    See Also:
    
    StrahlerAnalyzer.getBranches()
  - getPrimaryBranches
```
public List<Path> getPrimaryBranches()
```
    Description copied from class: TreeAnalyzer
    
    Retrieves the primary branches of the analyzed Tree. Primary branches (or root-associated) have origin in the Tree's root, extending to the closest branch/end-point. Note that a primary branch can also be terminal.
    
    Overrides:
    
    getPrimaryBranches in class TreeAnalyzer
    
    Returns:
    
    the primary branches. Note that these branches (Path segments) will not carry any connectivity information.
    
    See Also:
    
    TreeAnalyzer.getPrimaryPaths(), StrahlerAnalyzer.getRootAssociatedBranches()
  - getInnerBranches
```
public List<Path> getInnerBranches()
```
    Description copied from class: TreeAnalyzer
    
    Retrieves the branches of highest Strahler order in the Tree. This typically correspond to the most 'internal' branches of the Tree in direct sequence from the root.
    
    Overrides:
    
    getInnerBranches in class TreeAnalyzer
    
    Returns:
    
    the list containing the "inner" branches. Note that these branches (Path segments) will not carry any connectivity information.
    
    See Also:
    
    TreeAnalyzer.getPrimaryPaths(), StrahlerAnalyzer.getBranches(), StrahlerAnalyzer.getHighestBranchOrder()
  - getTerminalBranches
```
public List<Path> getTerminalBranches()
```
    Description copied from class: TreeAnalyzer
    
    Retrieves the terminal branches of the analyzed Tree. A terminal branch corresponds to the section of a terminal Path between its last branch-point and its terminal point (tip). A terminal branch can also be primary.
    
    Overrides:
    
    getTerminalBranches in class TreeAnalyzer
    
    Returns:
    
    the terminal branches. Note that as per Path.getSection(int, int), these branches will not carry any connectivity information.
    
    See Also:
    
    TreeAnalyzer.getPrimaryBranches(), TreeAnalyzer.restrictToOrder(int...)
  - main
```
public static void main(String[] args)
```

Class MultiTreeStatistics

Field Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class org.scijava.command.ContextCommand

Methods inherited from class org.scijava.AbstractContextual

Methods inherited from class java.lang.Object

Methods inherited from interface org.scijava.Contextual

Field Detail

LENGTH

TERMINAL_LENGTH

INNER_LENGTH

PRIMARY_LENGTH

AVG_BRANCH_LENGTH

ASSIGNED_VALUE

STRAHLER_NUMBER

STRAHLER_RATIO

HIGHEST_PATH_ORDER

N_BRANCHES

N_PRIMARY_BRANCHES

N_INNER_BRANCHES

N_TERMINAL_BRANCHES

N_BRANCH_POINTS

N_SPINES

AVG_CONTRACTION

AVG_FRAGMENTATION

AVG_REMOTE_ANGLE

AVG_PARTITION_ASYMMETRY

AVG_FRACTAL_DIMENSION

AVG_SPINE_DENSITY

N_PATHS

MEAN_RADIUS

N_NODES

N_TIPS

WIDTH

HEIGHT

DEPTH

N_FITTED_PATHS

ALL_FLAGS

Constructor Detail

MultiTreeStatistics

MultiTreeStatistics

Method Detail

getAllMetrics

getMetrics

getGroup

setLabel

getNormalizedMeasurement

tryReallyHardToGuessMetric

getSummaryStats

getDescriptiveStats

assembleStats

restrictToSWCType

resetRestrictions

getStrahlerAnalyzer

getShollAnalyzer

getAnnotations

getAnnotations

getCableLength

getAnnotatedLength

getAnnotatedLength

getAnnotatedLengthsByHemisphere

getHistogram

getTips

getBranchPoints

getBranches

getPrimaryBranches

getInnerBranches

getTerminalBranches

main