TreeAnalyzer (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, SciJavaPlugin

Direct Known Subclasses:

PathOrderAnalysisCmd, RoiConverter, TreeStatistics
```
public class TreeAnalyzer
extends ContextCommand
```
Class for analysis of Trees

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`protected DisplayService`	`displayService`
`protected List<Path>`	`innerBranches`
`protected List<Path>`	`primaryBranches`
`protected StatusService`	`statusService`
`protected DefaultGenericTable`	`table`
`protected List<Path>`	`terminalBranches`
`protected Set<PointInImage>`	`tips`
`protected Tree`	`tree`

Constructor Summary

Constructors
Constructor and Description
`TreeAnalyzer(Collection<Path> paths, String label)` Instantiates a new Tree analyzer from a collection of paths.
`TreeAnalyzer(Tree tree)` Instantiates a new Tree analyzer.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static List<String>`	`getAllMetrics()` Gets the list of all supported metrics.
`Set<BrainAnnotation>`	`getAnnotations()`
`Set<BrainAnnotation>`	`getAnnotations(int level)`
`double`	`getAvgBranchLength()` Gets average length for all the branches of the analyzed tree.
`double`	`getAvgContraction()` Gets average `contraction` for all the branches of the analyzed tree.
`double`	`getAvgFractalDimension()` Gets the average fractal dimension of the analyzed tree.
`double`	`getAvgFragmentation()`
`double`	`getAvgPartitionAsymmetry()` Gets the average partition asymmetry of the analyzed tree.
`double`	`getAvgRemoteBifAngle()` Gets the average remote bifurcation angle of the analyzed tree.
`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.
`Set<PointInImage>`	`getBranchPoints(BrainAnnotation annot)` Gets the position of all the branch points in the analyzed tree associated with the specified annotation.
`double`	`getCableLength()` Gets the cable length.
`double`	`getCableLength(BrainAnnotation compartment)` Gets the cable length associated with the specified compartment (neuropil label).
`double`	`getCableLength(BrainAnnotation compartment, boolean includeChildren)` Gets the cable length associated with the specified compartment (neuropil label).
`double`	`getCableLengthNorm(BrainAnnotation compartment)` Gets the cable length associated with the specified compartment (neuropil label) as a ratio of total length.
`protected int`	`getCol(String header)`
`double`	`getDepth()`
`List<Double>`	`getFractalDimension()` Gets the fractal dimension of each branch in the analyzed tree.
`double`	`getHeight()`
`int`	`getHighestPathOrder()` Gets the highest `path order` of 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
`Number`	`getMetric(String metric)` Computes the specified metric.
`protected Number`	`getMetricInternal(String metric)`
`static List<String>`	`getMetrics()` Gets a list of supported metrics.
`protected Number`	`getMetricWithoutChecks(String metric)`
`int`	`getNBranches()` Gets the number of branches in the analyzed tree.
`int`	`getNbranchPoints(BrainAnnotation annot)` Gets the number of branch points in the analyzed tree associated with the specified annotation.
`double`	`getNbranchPointsNorm(BrainAnnotation annot)` Gets the percentage of branch points in the analyzed tree associated with the specified annotation
`protected int`	`getNextRow(String rowHeader)`
`protected int`	`getNFittedPaths()`
`int`	`getNoSpinesOrVaricosities()` Gets the number of spines/varicosities that have been (manually) assigned to tree being analyzed.
`int`	`getNPaths()` Gets the no.
`int`	`getNtips(BrainAnnotation annot)` Gets the number of end points in the analyzed tree associated with the specified annotation.
`double`	`getNtipsNorm(BrainAnnotation annot)` Gets the percentage of end points in the analyzed tree associated with the specified annotation
`Tree`	`getParsedTree()` Returns the set of parsed Paths.
`List<Double>`	`getPartitionAsymmetry()` Gets the partition asymmetry at each bifurcation point in the analyzed tree.
`List<Path>`	`getPrimaryBranches()` Retrieves the primary branches of the analyzed Tree.
`double`	`getPrimaryLength()` Gets the cable length of primary branches.
`List<Path>`	`getPrimaryPaths()` Retrieves all the Paths in the analyzed Tree tagged as primary.
`List<Double>`	`getRemoteBifAngles()` Gets the angle between each bifurcation point and its children in the simplified graph, which comprise either branch points or terminal nodes.
`ShollAnalyzer`	`getShollAnalyzer()` Gets the `ShollAnalyzer` instance associated with this analyzer.
`protected int`	`getSinglePointPaths()`
`double`	`getSpineOrVaricosityDensity()` Gets the overall density of spines/varicosities associated with this tree
`StrahlerAnalyzer`	`getStrahlerAnalyzer()` Gets the `StrahlerAnalyzer` instance associated with this analyzer
`double`	`getStrahlerBifurcationRatio()` Gets the average `Strahler bifurcation ratio` of the analyzed tree.
`int`	`getStrahlerNumber()` Gets the highest `Strahler number` of the analyzed tree.
`protected String`	`getSWCTypesAsString()`
`DefaultGenericTable`	`getTable()` Gets the table currently being used by the Analyzer
`List<Path>`	`getTerminalBranches()` Retrieves the terminal branches of the analyzed Tree.
`double`	`getTerminalLength()` Gets the cable length of terminal branches
`Set<PointInImage>`	`getTips()` Gets the position of all the tips in the analyzed tree.
`Set<PointInImage>`	`getTips(BrainAnnotation annot)` Gets the position of all the tips in the analyzed tree associated with the specified annotation.
`double`	`getWidth()`
`void`	`ignoreSWCType(int... types)` Ignores Paths sharing the specified SWC flag(s).
`protected boolean`	`isSameOrParentAnnotation(BrainAnnotation annot, BrainAnnotation annotToBeTested)`
`boolean`	`isValid()` Checks whether this tree is topologically valid, i.e., contains only one root and no loops.
`static void`	`main(String[] args)`
`void`	`measure(Collection<String> metrics, boolean groupByType)` Measures this Tree, outputting the result to this Analyzer table using default row labels.
`void`	`measure(String rowHeader, Collection<String> metrics, boolean groupByType)` Measures this Tree, outputting the result to this Analyzer table.
`void`	`resetRestrictions()` Removes any filtering restrictions that may have been set.
`void`	`restrictToLength(double lowerBound, double upperBound)` Restricts analysis to paths sharing the specified length range.
`void`	`restrictToNamePattern(String pattern)` Restricts analysis to Paths containing the specified string in their name.
`void`	`restrictToOrder(int... orders)` Restricts analysis to Paths sharing the specified Path `order`(s).
`void`	`restrictToSize(int minSize, int maxSize)` Restricts analysis to paths having the specified number of nodes.
`void`	`restrictToSWCType(int... types)` Restricts analysis to Paths sharing the specified SWC flag(s).
`void`	`run()` Generates detailed summaries in which measurements are grouped by SWC-type flags
`void`	`setTable(DefaultGenericTable table)` Sets the Analyzer table.
`void`	`setTable(DefaultGenericTable table, String title)` Sets the table.
`void`	`summarize(boolean groupByType)` Outputs a summary of the current analysis to the Analyzer table using the default Tree label.
`void`	`summarize(String rowHeader, boolean groupByType)` Outputs a summary of the current analysis to the Analyzer table.
`void`	`updateAndDisplayTable()` Updates and displays the Analyzer table.

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
  - statusService
```
protected StatusService statusService
```
  - displayService
```
protected DisplayService displayService
```
  - tree
```
protected Tree tree
```
  - primaryBranches
```
protected List<Path> primaryBranches
```
  - innerBranches
```
protected List<Path> innerBranches
```
  - terminalBranches
```
protected List<Path> terminalBranches
```
  - tips
```
protected Set<PointInImage> tips
```
  - table
```
protected DefaultGenericTable table
```
- Constructor Detail
  - TreeAnalyzer
```
public TreeAnalyzer(Collection<Path> paths,
                    String label)
```
    Instantiates a new Tree analyzer from a collection of paths.
    
    Parameters:
    
    paths - Collection of Paths to be analyzed. Note that null Paths are discarded. Also, when a Path has been fitted and Path.getUseFitted() is true, its fitted 'flavor' is used.
    
    label - the label describing the path collection
    
    See Also:
    
    getParsedTree()
  - TreeAnalyzer
```
public TreeAnalyzer(Tree tree)
```
    Instantiates a new Tree analyzer.
    
    Parameters:
    
    tree - the Tree to be analyzed.
- Method Detail
  - restrictToSWCType
```
public void restrictToSWCType(int... types)
```
    Restricts analysis to Paths sharing the specified SWC flag(s).
    
    Parameters:
    
    types - the allowed SWC flags (e.g., Path.SWC_AXON, etc.)
  - ignoreSWCType
```
public void ignoreSWCType(int... types)
```
    Ignores Paths sharing the specified SWC flag(s).
    
    Parameters:
    
    types - the SWC flags to be ignored (e.g., Path.SWC_AXON, etc.)
  - restrictToOrder
```
public void restrictToOrder(int... orders)
```
    Restricts analysis to Paths sharing the specified Path order(s).
    
    Parameters:
    
    orders - the allowed Path orders
  - restrictToSize
```
public void restrictToSize(int minSize,
                           int maxSize)
```
    Restricts analysis to paths having the specified number of nodes.
    
    Parameters:
    
    minSize - the smallest number of nodes a path must have in order to be analyzed. Set it to -1 to disable minSize filtering
    
    maxSize - the largest number of nodes a path must have in order to be analyzed. Set it to -1 to disable maxSize filtering
  - restrictToLength
```
public void restrictToLength(double lowerBound,
                             double upperBound)
```
    Restricts analysis to paths sharing the specified length range.
    
    Parameters:
    
    lowerBound - the smallest length a path must have in order to be analyzed. Set it to Double.NaN to disable lowerBound filtering
    
    upperBound - the largest length a path must have in order to be analyzed. Set it to Double.NaN to disable upperBound filtering
  - restrictToNamePattern
```
public void restrictToNamePattern(String pattern)
```
    Restricts analysis to Paths containing the specified string in their name.
    
    Parameters:
    
    pattern - the string to search for
  - resetRestrictions
```
public void resetRestrictions()
```
    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.
  - getParsedTree
```
public Tree getParsedTree()
```
    Returns the set of parsed Paths.
    
    Returns:
    
    the set of paths currently being considered for analysis.
    
    See Also:
    
    resetRestrictions()
  - summarize
```
public void summarize(boolean groupByType)
```
    Outputs a summary of the current analysis to the Analyzer table using the default Tree label.
    
    Parameters:
    
    groupByType - if true measurements are grouped by SWC-type flag
    
    See Also:
    
    run(), setTable(DefaultGenericTable)
  - summarize
```
public void summarize(String rowHeader,
                      boolean groupByType)
```
    Outputs a summary of the current analysis to the Analyzer table.
    
    Parameters:
    
    rowHeader - the String to be used as label for the summary
    
    groupByType - if true measurements are grouped by SWC-type flag
    
    See Also:
    
    run(), setTable(DefaultGenericTable)
  - getNextRow
```
protected int getNextRow(String rowHeader)
```
  - getMetrics
```
public static List<String> getMetrics()
```
    Gets a list of supported metrics. Note that this list will only include commonly used metrics. For a complete list of supported metrics see getAllMetrics()
    
    Returns:
    
    the list of available metrics
    
    See Also:
    
    MultiTreeStatistics.getMetrics()
  - getAllMetrics
```
public static List<String> getAllMetrics()
```
    Gets the list of all supported metrics.
    
    Returns:
    
    the list of available metrics
    
    See Also:
    
    MultiTreeStatistics.getAllMetrics()
  - getMetric
```
public Number getMetric(String metric)
                 throws IllegalArgumentException
```
    Computes the specified metric.
    
    Parameters:
    
    metric - the metric to be computed (case insensitive). While it is expected to be an element of getMetrics(), it can be specified in a "loose" manner: If metric is not initially recognized, an heuristic will match it to the closest entry in the list of possible metrics. E.g., "# bps", "n junctions", will be both mapped to MultiTreeStatistics.N_BRANCH_POINTS. Details on the matching are printed to the Console when in debug mode.
    
    Returns:
    
    the computed value
    
    Throws:
    
    IllegalArgumentException - if metric is not recognized
    
    See Also:
    
    getMetrics()
  - getMetricInternal
```
protected Number getMetricInternal(String metric)
```
  - getMetricWithoutChecks
```
protected Number getMetricWithoutChecks(String metric)
                                 throws sc.fiji.snt.analysis.UnknownMetricException
```
    Throws:
    
    sc.fiji.snt.analysis.UnknownMetricException
  - measure
```
public void measure(Collection<String> metrics,
                    boolean groupByType)
```
    Measures this Tree, outputting the result to this Analyzer table using default row labels. If a Context has been specified, the table is updated. Otherwise, table contents are printed to Console.
    
    Parameters:
    
    metrics - the list of metrics to be computed. When null or an empty collection is specified, getMetrics() is used.
    
    groupByType - if false, metrics are computed to all branches in the Tree. If true, measurements will be split by SWC type annotations (axon, dendrite, etc.)
  - measure
```
public void measure(String rowHeader,
                    Collection<String> metrics,
                    boolean groupByType)
```
    Measures this Tree, outputting the result to this Analyzer table. If a Context has been specified, the table is updated. Otherwise, table contents are printed to Console.
    
    Parameters:
    
    rowHeader - the row header label
    
    metrics - the list of metrics to be computed. When null or an empty collection is specified, getMetrics() is used.
    
    groupByType - if false, metrics are computed to all branches in the Tree. If true, measurements will be split by SWC type annotations (axon, dendrite, etc.)
  - getSWCTypesAsString
```
protected String getSWCTypesAsString()
```
  - setTable
```
public void setTable(DefaultGenericTable table)
```
    Sets the Analyzer table.
    
    Parameters:
    
    table - the table to be used by the analyzer
    
    See Also:
    
    summarize(boolean)
  - setTable
```
public void setTable(DefaultGenericTable table,
                     String title)
```
    Sets the table.
    
    Parameters:
    
    table - the table to be used by the analyzer
    
    title - the title of the table display window
  - getTable
```
public DefaultGenericTable getTable()
```
    Gets the table currently being used by the Analyzer
    
    Returns:
    
    the table
  - run
```
public void run()
```
    Generates detailed summaries in which measurements are grouped by SWC-type flags
    
    See Also:
    
    summarize(String, boolean)
  - updateAndDisplayTable
```
public void updateAndDisplayTable()
```
    Updates and displays the Analyzer table.
  - getCol
```
protected int getCol(String header)
```
  - getSinglePointPaths
```
protected int getSinglePointPaths()
```
  - getNPaths
```
public int getNPaths()
```
    Gets the no. of paths parsed by the Analyzer.
    
    Returns:
    
    the number of paths
  - getNFittedPaths
```
protected int getNFittedPaths()
```
  - getWidth
```
public double getWidth()
```
  - getHeight
```
public double getHeight()
```
  - getDepth
```
public double getDepth()
```
  - getPrimaryPaths
```
public List<Path> getPrimaryPaths()
```
    Retrieves all the Paths in the analyzed Tree tagged as primary.
    
    Returns:
    
    the list of primary paths.
    
    See Also:
    
    getPrimaryBranches()
  - getInnerBranches
```
public List<Path> getInnerBranches()
```
    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.
    
    Returns:
    
    the list containing the "inner" branches. Note that these branches (Path segments) will not carry any connectivity information.
    
    See Also:
    
    getPrimaryPaths(), StrahlerAnalyzer.getBranches(), StrahlerAnalyzer.getHighestBranchOrder()
  - getPrimaryBranches
```
public List<Path> getPrimaryBranches()
```
    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.
    
    Returns:
    
    the primary branches. Note that these branches (Path segments) will not carry any connectivity information.
    
    See Also:
    
    getPrimaryPaths(), StrahlerAnalyzer.getRootAssociatedBranches()
  - getTerminalBranches
```
public List<Path> getTerminalBranches()
```
    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.
    
    Returns:
    
    the terminal branches. Note that as per Path.getSection(int, int), these branches will not carry any connectivity information.
    
    See Also:
    
    getPrimaryBranches(), restrictToOrder(int...)
  - getTips
```
public Set<PointInImage> getTips()
```
    Gets the position of all the tips in the analyzed tree.
    
    Returns:
    
    the set of terminal points
  - getTips
```
public Set<PointInImage> getTips(BrainAnnotation annot)
```
    Gets the position of all the tips in the analyzed tree associated with the specified annotation.
    
    Parameters:
    
    annot - the BrainAnnotation to be queried. Null not allowed.
    
    Returns:
    
    the branch points positions, or an empty set if no tips were retrieved.
  - getNtips
```
public int getNtips(BrainAnnotation annot)
```
    Gets the number of end points in the analyzed tree associated with the specified annotation.
    
    Parameters:
    
    annot - the BrainAnnotation to be queried.
    
    Returns:
    
    the number of end points
  - getNtipsNorm
```
public double getNtipsNorm(BrainAnnotation annot)
```
    Gets the percentage of end points in the analyzed tree associated with the specified annotation
    
    Parameters:
    
    annot - the BrainAnnotation to be queried.
    
    Returns:
    
    the ratio between the no. of branch points associated with annot and the total number of end points in the tree.
  - getBranchPoints
```
public Set<PointInImage> getBranchPoints()
```
    Gets the position of all the branch points in the analyzed tree.
    
    Returns:
    
    the branch points positions
  - getBranchPoints
```
public Set<PointInImage> getBranchPoints(BrainAnnotation annot)
```
    Gets the position of all the branch points in the analyzed tree associated with the specified annotation.
    
    Parameters:
    
    annot - the BrainAnnotation to be queried.
    
    Returns:
    
    the branch points positions, or an empty set if no branch points were retrieved.
  - getNbranchPoints
```
public int getNbranchPoints(BrainAnnotation annot)
```
    Gets the number of branch points in the analyzed tree associated with the specified annotation.
    
    Parameters:
    
    annot - the BrainAnnotation to be queried.
    
    Returns:
    
    the number of branch points
  - getNbranchPointsNorm
```
public double getNbranchPointsNorm(BrainAnnotation annot)
```
    Gets the percentage of branch points in the analyzed tree associated with the specified annotation
    
    Parameters:
    
    annot - the BrainAnnotation to be queried.
    
    Returns:
    
    the ratio between the no. of branch points associated with annot and the total number of branch points in the tree.
  - getCableLength
```
public double getCableLength()
```
    Gets the cable length.
    
    Returns:
    
    the cable length of the tree
  - getCableLength
```
public double getCableLength(BrainAnnotation compartment)
```
    Gets the cable length associated with the specified compartment (neuropil label).
    
    Parameters:
    
    compartment - the query compartment (null not allowed). All of its children will be considered
    
    Returns:
    
    the filtered cable length
  - getCableLengthNorm
```
public double getCableLengthNorm(BrainAnnotation compartment)
```
    Gets the cable length associated with the specified compartment (neuropil label) as a ratio of total length.
    
    Parameters:
    
    compartment - the query compartment (null not allowed). All of its children will be considered
    
    Returns:
    
    the filtered cable length normalized to total cable length
  - getCableLength
```
public double getCableLength(BrainAnnotation compartment,
                             boolean includeChildren)
```
    Gets the cable length associated with the specified compartment (neuropil label).
    
    Parameters:
    
    compartment - the query compartment (null not allowed)
    
    includeChildren - whether children of compartment should be included
    
    Returns:
    
    the filtered cable length
  - isSameOrParentAnnotation
```
protected boolean isSameOrParentAnnotation(BrainAnnotation annot,
                                           BrainAnnotation annotToBeTested)
```
  - getAnnotations
```
public Set<BrainAnnotation> getAnnotations()
```
  - getAnnotations
```
public Set<BrainAnnotation> getAnnotations(int level)
```
  - getPrimaryLength
```
public double getPrimaryLength()
```
    Gets the cable length of primary branches.
    
    Returns:
    
    the length sum of all primary branches
    
    See Also:
    
    getPrimaryBranches()
  - getInnerLength
```
public double getInnerLength()
```
    Gets the cable length of inner branches
    
    Returns:
    
    the length sum of all inner branches
    
    See Also:
    
    getInnerBranches()
  - getTerminalLength
```
public double getTerminalLength()
```
    Gets the cable length of terminal branches
    
    Returns:
    
    the length sum of all terminal branches
    
    See Also:
    
    getTerminalBranches()
  - getHighestPathOrder
```
public int getHighestPathOrder()
```
    Gets the highest path order of the analyzed tree
    
    Returns:
    
    the highest Path order, or -1 if Paths in the Tree have no defined order
    
    See Also:
    
    getStrahlerNumber()
  - isValid
```
public boolean isValid()
```
    Checks whether this tree is topologically valid, i.e., contains only one root and no loops.
    
    Returns:
    
    true, if Tree is valid, false otherwise
  - getStrahlerNumber
```
public int getStrahlerNumber()
                      throws IllegalArgumentException
```
    Gets the highest Strahler number of the analyzed tree.
    
    Returns:
    
    the highest Strahler (root) number order
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - getStrahlerAnalyzer
```
public StrahlerAnalyzer getStrahlerAnalyzer()
                                     throws IllegalArgumentException
```
    Gets the StrahlerAnalyzer instance associated with this analyzer
    
    Returns:
    
    the StrahlerAnalyzer instance associated with this analyzer
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - getShollAnalyzer
```
public ShollAnalyzer getShollAnalyzer()
```
    Gets the ShollAnalyzer instance associated with this analyzer. Note that changes to ShollAnalyzer must be performed before calling getMetric(String), measure(Collection, boolean), etc.
    
    Returns:
    
    the ShollAnalyzer instance associated with this analyzer
  - getStrahlerBifurcationRatio
```
public double getStrahlerBifurcationRatio()
                                   throws IllegalArgumentException
```
    Gets the average Strahler bifurcation ratio of the analyzed tree.
    
    Returns:
    
    the average bifurcation ratio
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - getNBranches
```
public int getNBranches()
                 throws IllegalArgumentException
```
    Gets the number of branches in the analyzed tree.
    
    Returns:
    
    the number of branches
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - getBranches
```
public List<Path> getBranches()
                       throws IllegalArgumentException
```
    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.
    
    Returns:
    
    the list of branches as Path objects.
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
    
    See Also:
    
    StrahlerAnalyzer.getBranches()
  - getAvgContraction
```
public double getAvgContraction()
                         throws IllegalArgumentException
```
    Gets average contraction for all the branches of the analyzed tree.
    
    Returns:
    
    the average branch contraction
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - getAvgFragmentation
```
public double getAvgFragmentation()
```
  - getAvgBranchLength
```
public double getAvgBranchLength()
                          throws IllegalArgumentException
```
    Gets average length for all the branches of the analyzed tree.
    
    Returns:
    
    the average branch length
    
    Throws:
    
    IllegalArgumentException - if tree contains multiple roots or loops
  - getRemoteBifAngles
```
public List<Double> getRemoteBifAngles()
                                throws IllegalArgumentException
```
    Gets the angle between each bifurcation point and its children in the simplified graph, which comprise either branch points or terminal nodes. Note that branch points with more than 2 children are ignored.
    
    Returns:
    
    the list of remote bifurcation angles
    
    Throws:
    
    IllegalArgumentException - if the tree contains multiple roots or loops
  - getAvgRemoteBifAngle
```
public double getAvgRemoteBifAngle()
                            throws IllegalArgumentException
```
    Gets the average remote bifurcation angle of the analyzed tree. Note that branch points with more than 2 children are ignored during the computation.
    
    Returns:
    
    the average remote bifurcation angle
    
    Throws:
    
    IllegalArgumentException - if the tree contains multiple roots or loops
  - getPartitionAsymmetry
```
public List<Double> getPartitionAsymmetry()
                                   throws IllegalArgumentException
```
    Gets the partition asymmetry at each bifurcation point in the analyzed tree. Note that branch points with more than 2 children are ignored.
    
    Returns:
    
    a list containing the partition asymmetry at each bifurcation point
    
    Throws:
    
    IllegalArgumentException - if the tree contains multiple roots or loops
  - getAvgPartitionAsymmetry
```
public double getAvgPartitionAsymmetry()
                                throws IllegalArgumentException
```
    Gets the average partition asymmetry of the analyzed tree. Note that branch points with more than 2 children are ignored during the computation.
    
    Returns:
    
    the average partition asymmetry
    
    Throws:
    
    IllegalArgumentException - if the tree contains multiple roots or loops
  - getFractalDimension
```
public List<Double> getFractalDimension()
                                 throws IllegalArgumentException
```
    Gets the fractal dimension of each branch in the analyzed tree. Note that branches with less than 5 points are ignored.
    
    Returns:
    
    a list containing the fractal dimension of each branch
    
    Throws:
    
    IllegalArgumentException - if the tree contains multiple roots or loops
    
    See Also:
    
    StrahlerAnalyzer.getBranches()
  - getAvgFractalDimension
```
public double getAvgFractalDimension()
                              throws IllegalArgumentException
```
    Gets the average fractal dimension of the analyzed tree. Note that branches with less than 5 points are ignored during the computation.
    
    Returns:
    
    the average fractal dimension
    
    Throws:
    
    IllegalArgumentException - if the tree contains multiple roots or loops
  - getNoSpinesOrVaricosities
```
public int getNoSpinesOrVaricosities()
```
    Gets the number of spines/varicosities that have been (manually) assigned to tree being analyzed.
    
    Returns:
    
    the number of spines/varicosities
  - getSpineOrVaricosityDensity
```
public double getSpineOrVaricosityDensity()
```
    Gets the overall density of spines/varicosities associated with this tree
    
    Returns:
    
    the spine/varicosity density (same as getNoSpinesOrVaricosities()/getCableLength())
  - main
```
public static void main(String[] args)
                 throws InterruptedException
```
    Throws:
    
    InterruptedException

Class TreeAnalyzer

Field Summary

Constructor Summary

Method Summary

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

statusService

displayService

tree

primaryBranches

innerBranches

terminalBranches

tips

table

Constructor Detail

TreeAnalyzer

TreeAnalyzer

Method Detail

restrictToSWCType

ignoreSWCType

restrictToOrder

restrictToSize

restrictToLength

restrictToNamePattern

resetRestrictions

getParsedTree

summarize

summarize

getNextRow

getMetrics

getAllMetrics

getMetric

getMetricInternal

getMetricWithoutChecks

measure

measure

getSWCTypesAsString

setTable

setTable

getTable

run

updateAndDisplayTable

getCol

getSinglePointPaths

getNPaths

getNFittedPaths

getWidth

getHeight

getDepth

getPrimaryPaths

getInnerBranches

getPrimaryBranches

getTerminalBranches

getTips

getTips

getNtips

getNtipsNorm

getBranchPoints

getBranchPoints

getNbranchPoints

getNbranchPointsNorm

getCableLength

getCableLength

getCableLengthNorm

getCableLength

isSameOrParentAnnotation

getAnnotations

getAnnotations

getPrimaryLength

getInnerLength

getTerminalLength

getHighestPathOrder

isValid

getStrahlerNumber

getStrahlerAnalyzer

getShollAnalyzer

getStrahlerBifurcationRatio