TreeStatistics (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

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, SciJavaPlugin

Direct Known Subclasses:

MultiTreeStatistics, PathAnalyzer
```
public class TreeStatistics
extends TreeAnalyzer
```
Computes summary and descriptive statistics from univariate properties of Paths and Nodes in a Tree. For analysis of groups of Trees use MultiTreeStatistics.

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`AVG_SPINE_DENSITY` Flag for "Average spine/varicosity density" statistics.
`static String`	`BRANCH_LENGTH` Flag for "Branch length" analysis.
`static String`	`CONTRACTION` Flag for "Contraction" statistics.
`static String`	`FRACTAL_DIMENSION` Flag for "Fractal dimension" statistics.
`static String`	`INNER_LENGTH` Flag for "Length of inner branches" analysis.
`static String`	`INTER_NODE_DISTANCE` Flag for "Inter-node distance" statistics.
`static String`	`INTER_NODE_DISTANCE_SQUARED` Flag for "Inter-node distance (squared)" statistics.
`protected sc.fiji.snt.analysis.TreeStatistics.LastDstats`	`lastDstats`
`static String`	`MEAN_RADIUS` Flag for "Path mean radius" statistics.
`static String`	`N_BRANCH_POINTS` Flag for "No. of branch points" statistics.
`static String`	`N_NODES` Flag for "No. of branch points" statistics.
`static String`	`N_SPINES` Flag for "No. of spines/varicosities" statistics.
`static String`	`NODE_RADIUS` Flag for "Node radius" statistics.
`static String`	`PARTITION_ASYMMETRY` Flag for "Partition asymmetry" statistics.
`static String`	`PATH_CHANNEL` Flag for "Path channel" statistics.
`static String`	`PATH_FRAME` Flag for "Path frame" statistics.
`static String`	`PATH_LENGTH` Flag for "Path length" analysis.
`static String`	`PATH_ORDER` Flag for "Path order" statistics.
`static String`	`PRIMARY_LENGTH` Flag for "Length of primary branches" analysis.
`static String`	`REMOTE_BIF_ANGLES` Flag for "Remote bif. angles" statistics.
`static String`	`TERMINAL_LENGTH` Flag for "Length of terminal branches" analysis.
`static String`	`VALUES` Flag for analysis of "Node intensity values", an optional numeric property that can be assigned to Path nodes (e.g., voxel intensities, assigned via `PathProfiler`.
`static String`	`X_COORDINATES` Flag for "X coordinates" statistics.
`static String`	`Y_COORDINATES` Flag for "Y coordinates" statistics.
`static String`	`Z_COORDINATES` Flag for "Z coordinates" statistics.

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

Constructor Summary

Constructors
Constructor and Description

TreeStatistics(Tree tree)
Instantiates a new instance from a collection of Paths

Constructors
Constructor and Description
`TreeStatistics(Tree tree)` Instantiates a new instance from a collection of Paths

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 TreeStatistics`	`fromCollection(Collection<Tree> trees, String metric)`
`static List<String>`	`getAllMetrics()` Gets the list of all supported metrics.
`static List<String>`	`getAnalyzerMetrics()` Gets the list of all `TreeAnalyzer` supported metrics.
`protected static Map<BrainAnnotation,Double>`	`getAnnotatedLength(DirectedWeightedGraph graph, int level, char lr)`
`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.
`SNTChart`	`getAnnotatedLengthHistogram()` Retrieves the of cable length frequencies across brain areas.
`SNTChart`	`getAnnotatedLengthHistogram(int depth)` Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level.
`SNTChart`	`getAnnotatedLengthHistogram(int depth, String hemisphere)` Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level across the specified hemisphere.
`protected SNTChart`	`getAnnotatedLengthHistogram(Map<BrainAnnotation,Double> map, int depth, String secondaryLabel)`
`protected static Map<BrainAnnotation,double[]>`	`getAnnotatedLengthsByHemisphere(DirectedWeightedGraph graph, int level)`
`Map<BrainAnnotation,double[]>`	`getAnnotatedLengthsByHemisphere(int level)`
`protected SNTChart`	`getAnnotatedLengthsByHemisphereHistogram(int depth)`
`DescriptiveStatistics`	`getDescriptiveStats(String metric)` Computes the `DescriptiveStatistics` for the specified measurement.
`SNTChart`	`getHistogram(String metric)` Retrieves the histogram of relative frequencies histogram for a univariate measurement.
`protected SNTChart`	`getHistogram(String normMeasurement, sc.fiji.snt.analysis.AnalysisUtils.HistogramDatasetPlus datasetPlus)`
`static List<String>`	`getMetrics()` Gets the list of most commonly used metrics.
`NodeStatistics<SWCPoint>`	`getNodeStatistics()`
`NodeStatistics<SWCPoint>`	`getNodeStatistics(String type)`
`protected static String`	`getNormalizedMeasurement(String measurement)`
`SummaryStatistics`	`getSummaryStats(String metric)` Computes the `SummaryStatistics` for the specified measurement.
`protected boolean`	`lastDstatsCanBeRecycled(String normMeasurement)`
`static void`	`main(String[] args)`
`protected static String`	`tryReallyHardToGuessMetric(String guess)`

Methods inherited from class sc.fiji.snt.analysis.TreeAnalyzer
getAnnotations, getAnnotations, getAvgBranchLength, getAvgContraction, getAvgFractalDimension, getAvgFragmentation, getAvgPartitionAsymmetry, getAvgRemoteBifAngle, getBranches, getBranchPoints, getBranchPoints, getCableLength, getCableLength, getCableLength, getCableLengthNorm, getCol, getDepth, getFractalDimension, getHeight, getHighestPathOrder, getInnerBranches, getInnerLength, getMetric, getMetricInternal, getMetricWithoutChecks, getNBranches, getNbranchPoints, getNbranchPointsNorm, getNextRow, getNFittedPaths, getNoSpinesOrVaricosities, getNPaths, getNtips, getNtipsNorm, getParsedTree, getPartitionAsymmetry, getPrimaryBranches, getPrimaryLength, 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, 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
  - PATH_LENGTH
```
public static final String PATH_LENGTH
```
    Flag for "Path length" analysis.
    
    See Also:
    
    Constant Field Values
  - BRANCH_LENGTH
```
public static final String BRANCH_LENGTH
```
    Flag for "Branch length" analysis.
    
    See Also:
    
    Constant Field Values
  - TERMINAL_LENGTH
```
public static final String TERMINAL_LENGTH
```
    Flag for "Length of terminal branches" analysis.
    
    See Also:
    
    Constant Field Values
  - PRIMARY_LENGTH
```
public static final String PRIMARY_LENGTH
```
    Flag for "Length of primary branches" analysis.
    
    See Also:
    
    Constant Field Values
  - INNER_LENGTH
```
public static final String INNER_LENGTH
```
    Flag for "Length of inner branches" analysis.
    
    See Also:
    
    Constant Field Values
  - PATH_ORDER
```
public static final String PATH_ORDER
```
    Flag for "Path order" statistics.
    
    See Also:
    
    Constant Field Values
  - PATH_CHANNEL
```
public static final String PATH_CHANNEL
```
    Flag for "Path channel" statistics.
    
    See Also:
    
    Constant Field Values
  - PATH_FRAME
```
public static final String PATH_FRAME
```
    Flag for "Path frame" statistics.
    
    See Also:
    
    Constant Field Values
  - INTER_NODE_DISTANCE
```
public static final String INTER_NODE_DISTANCE
```
    Flag for "Inter-node distance" statistics.
    
    See Also:
    
    Constant Field Values
  - INTER_NODE_DISTANCE_SQUARED
```
public static final String INTER_NODE_DISTANCE_SQUARED
```
    Flag for "Inter-node distance (squared)" 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_NODES
```
public static final String N_NODES
```
    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
  - NODE_RADIUS
```
public static final String NODE_RADIUS
```
    Flag for "Node radius" statistics.
    
    See Also:
    
    Constant Field Values
  - MEAN_RADIUS
```
public static final String MEAN_RADIUS
```
    Flag for "Path mean radius" 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
  - X_COORDINATES
```
public static final String X_COORDINATES
```
    Flag for "X coordinates" statistics.
    
    See Also:
    
    Constant Field Values
  - Y_COORDINATES
```
public static final String Y_COORDINATES
```
    Flag for "Y coordinates" statistics.
    
    See Also:
    
    Constant Field Values
  - Z_COORDINATES
```
public static final String Z_COORDINATES
```
    Flag for "Z coordinates" statistics.
    
    See Also:
    
    Constant Field Values
  - CONTRACTION
```
public static final String CONTRACTION
```
    Flag for "Contraction" statistics.
    
    See Also:
    
    Constant Field Values
  - REMOTE_BIF_ANGLES
```
public static final String REMOTE_BIF_ANGLES
```
    Flag for "Remote bif. angles" statistics.
    
    See Also:
    
    Constant Field Values
  - PARTITION_ASYMMETRY
```
public static final String PARTITION_ASYMMETRY
```
    Flag for "Partition asymmetry" statistics.
    
    See Also:
    
    Constant Field Values
  - FRACTAL_DIMENSION
```
public static final String FRACTAL_DIMENSION
```
    Flag for "Fractal dimension" statistics.
    
    See Also:
    
    Constant Field Values
  - VALUES
```
public static final String VALUES
```
    Flag for analysis of "Node intensity values", an optional numeric property that can be assigned to Path nodes (e.g., voxel intensities, assigned via PathProfiler. Note that an IllegalArgumentException is triggered if no values have been assigned to the tree being analyzed.
    
    See Also:
    
    Path.hasNodeValues(), PathProfiler.assignValues(), Constant Field Values
  - lastDstats
```
protected sc.fiji.snt.analysis.TreeStatistics.LastDstats lastDstats
```
- Constructor Detail
  - TreeStatistics
```
public TreeStatistics(Tree tree)
```
    Instantiates a new instance from a collection of Paths
    
    Parameters:
    
    tree - the collection of paths to be analyzed
- Method Detail
  - getAnalyzerMetrics
```
public static List<String> getAnalyzerMetrics()
```
    Gets the list of all TreeAnalyzer supported metrics.
    
    Returns:
    
    the list of all TreeAnalyzer's metrics
    
    See Also:
    
    TreeAnalyzer.getAllMetrics()
  - 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
  - getSummaryStats
```
public SummaryStatistics getSummaryStats(String metric)
```
    Computes the SummaryStatistics for the specified measurement.
    
    Parameters:
    
    metric - the measurement (N_NODES, NODE_RADIUS, etc.)
    
    Returns:
    
    the SummaryStatistics object.
  - getDescriptiveStats
```
public DescriptiveStatistics getDescriptiveStats(String metric)
```
    Computes the DescriptiveStatistics for the specified measurement.
    
    Parameters:
    
    metric - the measurement (N_NODES, NODE_RADIUS, etc.)
    
    Returns:
    
    the DescriptiveStatistics object.
  - getAnnotatedLength
```
public Map<BrainAnnotation,Double> getAnnotatedLength(int level)
```
    Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
    
    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()
  - getAnnotatedLength
```
public Map<BrainAnnotation,Double> getAnnotatedLength(int level,
                                                      String hemisphere)
```
    Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
    
    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
```
protected static Map<BrainAnnotation,Double> getAnnotatedLength(DirectedWeightedGraph graph,
                                                                int level,
                                                                char lr)
```
  - getAnnotatedLengthsByHemisphere
```
public Map<BrainAnnotation,double[]> getAnnotatedLengthsByHemisphere(int level)
```
  - getAnnotatedLengthsByHemisphere
```
protected static Map<BrainAnnotation,double[]> getAnnotatedLengthsByHemisphere(DirectedWeightedGraph graph,
                                                                               int level)
```
  - getAnnotatedLengthHistogram
```
public SNTChart getAnnotatedLengthHistogram()
```
    Retrieves the of cable length frequencies across brain areas.
    
    Returns:
    
    the histogram of cable length frequencies.
  - getAnnotatedLengthHistogram
```
public SNTChart getAnnotatedLengthHistogram(int depth)
```
    Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level.
    
    Parameters:
    
    depth - the ontological depth of the compartments to be considered
    
    Returns:
    
    the annotated length histogram
    
    See Also:
    
    AllenCompartment.getOntologyDepth()
  - getAnnotatedLengthHistogram
```
public SNTChart getAnnotatedLengthHistogram(int depth,
                                            String hemisphere)
```
    Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level across the specified hemisphere.
    
    Parameters:
    
    depth - the ontological depth of the compartments to be considered
    
    hemisphere - 'left', 'right' or 'ratio' (case insensitive). Ignored if not a recognized option
    
    Returns:
    
    the annotated length histogram
    
    See Also:
    
    AllenCompartment.getOntologyDepth()
  - getAnnotatedLengthsByHemisphereHistogram
```
protected SNTChart getAnnotatedLengthsByHemisphereHistogram(int depth)
```
  - getAnnotatedLengthHistogram
```
protected SNTChart getAnnotatedLengthHistogram(Map<BrainAnnotation,Double> map,
                                               int depth,
                                               String secondaryLabel)
```
  - getHistogram
```
public SNTChart getHistogram(String metric)
```
    Retrieves the histogram of relative frequencies histogram for a univariate measurement. The number of bins is determined using the Freedman-Diaconis rule.
    
    Parameters:
    
    metric - the measurement (N_NODES, NODE_RADIUS, etc.)
    
    Returns:
    
    the frame holding the histogram
  - fromCollection
```
public static TreeStatistics fromCollection(Collection<Tree> trees,
                                            String metric)
```
  - getHistogram
```
protected SNTChart getHistogram(String normMeasurement,
                                sc.fiji.snt.analysis.AnalysisUtils.HistogramDatasetPlus datasetPlus)
```
  - tryReallyHardToGuessMetric
```
protected static String tryReallyHardToGuessMetric(String guess)
```
  - getNormalizedMeasurement
```
protected static String getNormalizedMeasurement(String measurement)
```
  - assembleStats
```
protected void assembleStats(sc.fiji.snt.analysis.TreeStatistics.StatisticsInstance stat,
                             String measurement)
```
  - lastDstatsCanBeRecycled
```
protected boolean lastDstatsCanBeRecycled(String normMeasurement)
```
  - getNodeStatistics
```
public NodeStatistics<SWCPoint> getNodeStatistics()
```
  - getNodeStatistics
```
public NodeStatistics<SWCPoint> getNodeStatistics(String type)
```
  - main
```
public static void main(String[] args)
```

Class TreeStatistics

Field Summary

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

Constructor Summary

Method Summary

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

PATH_LENGTH

BRANCH_LENGTH

TERMINAL_LENGTH

PRIMARY_LENGTH

INNER_LENGTH

PATH_ORDER

PATH_CHANNEL

PATH_FRAME

INTER_NODE_DISTANCE

INTER_NODE_DISTANCE_SQUARED

N_BRANCH_POINTS

N_NODES

N_SPINES

NODE_RADIUS

MEAN_RADIUS

AVG_SPINE_DENSITY

X_COORDINATES

Y_COORDINATES

Z_COORDINATES

CONTRACTION

REMOTE_BIF_ANGLES

PARTITION_ASYMMETRY

FRACTAL_DIMENSION

VALUES

lastDstats

Constructor Detail

TreeStatistics

Method Detail

getAnalyzerMetrics

getAllMetrics

getMetrics

getSummaryStats

getDescriptiveStats

getAnnotatedLength

getAnnotatedLength

getAnnotatedLength

getAnnotatedLengthsByHemisphere

getAnnotatedLengthsByHemisphere

getAnnotatedLengthHistogram

getAnnotatedLengthHistogram

getAnnotatedLengthHistogram

getAnnotatedLengthsByHemisphereHistogram

getAnnotatedLengthHistogram

getHistogram

fromCollection

getHistogram

tryReallyHardToGuessMetric

getNormalizedMeasurement

assembleStats

lastDstatsCanBeRecycled

getNodeStatistics

getNodeStatistics

main