sc.fiji.snt.analysis

Class TreeAnalyzer

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.TreeAnalyzer

All Implemented Interfaces:

java.lang.Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.plugin.SciJavaPlugin

Direct Known Subclasses:

RoiConverter, StrahlerCmd, TreeStatistics

public class TreeAnalyzer
extends org.scijava.command.ContextCommand

Class for analysis of Trees

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BRANCH_ORDER Flag for "Branch order" analysis.
static java.lang.String[]	COMMON_MEASUREMENTS
static java.lang.String	INTER_NODE_DISTANCE Flag for "Inter-node distance" analysis.
static java.lang.String	INTER_NODE_DISTANCE_SQUARED Flag for "Inter-node distance (squared)" analysis.
static java.lang.String	LENGTH Flag for "Length" analysis.
static java.lang.String	MEAN_RADIUS Flag for "Path mean radius" analysis.
static java.lang.String	N_BRANCH_POINTS Flag for "No. of branch points" analysis.
static java.lang.String	N_NODES Flag for "No. of nodes" analysis.
static java.lang.String	NODE_RADIUS Flag for "Node radius" analysis.
static java.lang.String	VALUES Flag for analysis of "Node intensity values", an optional numeric property that can be assigned to Path nodes (typically voxel intensities, assigned via PathProfiler.
static java.lang.String	X_COORDINATES Flag for "X coordinates" analysis.
static java.lang.String	Y_COORDINATES Flag for "Y coordinates" analysis.
static java.lang.String	Z_COORDINATES Flag for "Z coordinates" analysis.

Constructor Summary

Constructors

Constructor and Description
TreeAnalyzer(Tree tree) Instantiates a new Tree analyzer.

Method Summary

Modifier and Type	Method and Description
java.util.Set<PointInImage>	getBranchPoints() Gets the position of all the branch points in the analyzed tree.
double	getCableLength() Gets the cable length.
int	getNPaths() Gets the no.
Tree	getParsedTree() Returns the set of parsed Paths.
java.util.Set<Path>	getPrimaryBranches() Retrieves the primary branches of the analyzed Tree.
double	getPrimaryLength() Gets the cable length of primary branches.
java.util.Set<Path>	getPrimaryPaths() Retrieves all the Paths in the analyzed Tree tagged as primary.
int	getStrahlerRootNumber() Gets the Strahler-Horton root number of the analyzed tree
org.scijava.table.DefaultGenericTable	getTable() Gets the table currently being used by the Analyzer
java.util.Set<Path>	getTerminalBranches() Retrieves the terminal branches of the analyzed Tree.
double	getTerminalLength() Gets the cable length of terminal branches
java.util.Set<PointInImage>	getTips() Gets the position of all the tips in the analyzed tree.
void	ignoreSWCType(int... types) Ignores Paths sharing the specified SWC flag(s).
static void	main(java.lang.String[] args)
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(java.lang.String pattern) Restricts analysis to Paths containing the specified string in their name.
void	restrictToOrder(int... orders) Restricts analysis to Paths sharing the specified branching 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(org.scijava.table.DefaultGenericTable table) Sets the Analyzer table.
void	setTable(org.scijava.table.DefaultGenericTable table, java.lang.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(java.lang.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

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.scijava.Contextual

setContext

Field Detail

BRANCH_ORDER

public static final java.lang.String BRANCH_ORDER

Flag for "Branch order" analysis.

See Also:

Constant Field Values

INTER_NODE_DISTANCE

public static final java.lang.String INTER_NODE_DISTANCE

Flag for "Inter-node distance" analysis.

See Also:

Constant Field Values

INTER_NODE_DISTANCE_SQUARED

public static final java.lang.String INTER_NODE_DISTANCE_SQUARED

Flag for "Inter-node distance (squared)" analysis.

See Also:

Constant Field Values

LENGTH

public static final java.lang.String LENGTH

Flag for "Length" analysis.

See Also:

Constant Field Values

N_BRANCH_POINTS

public static final java.lang.String N_BRANCH_POINTS

Flag for "No. of branch points" analysis.

See Also:

Constant Field Values

N_NODES

public static final java.lang.String N_NODES

Flag for "No. of nodes" analysis.

See Also:

Constant Field Values

NODE_RADIUS

public static final java.lang.String NODE_RADIUS

Flag for "Node radius" analysis.

See Also:

Constant Field Values

MEAN_RADIUS

public static final java.lang.String MEAN_RADIUS

Flag for "Path mean radius" analysis.

See Also:

Constant Field Values

X_COORDINATES

public static final java.lang.String X_COORDINATES

Flag for "X coordinates" analysis.

See Also:

Constant Field Values

Y_COORDINATES

public static final java.lang.String Y_COORDINATES

Flag for "Y coordinates" analysis.

See Also:

Constant Field Values

Z_COORDINATES

public static final java.lang.String Z_COORDINATES

Flag for "Z coordinates" analysis.

See Also:

Constant Field Values

VALUES

public static final java.lang.String VALUES

Flag for analysis of "Node intensity values", an optional numeric property that can be assigned to Path nodes (typically 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

COMMON_MEASUREMENTS

public static final java.lang.String[] COMMON_MEASUREMENTS

Constructor Detail

TreeAnalyzer

public TreeAnalyzer(Tree tree)

Instantiates a new Tree analyzer.

Parameters:

tree - 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.

See Also:

getParsedTree()

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 branching order(s).

Parameters:

orders - the allowed branching 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(java.lang.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(java.lang.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)

setTable

public void setTable(org.scijava.table.DefaultGenericTable table)

Sets the Analyzer table.

Parameters:

table - the table to be used by the analyzer

See Also:

summarize(boolean)

setTable

public void setTable(org.scijava.table.DefaultGenericTable table,
                     java.lang.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 org.scijava.table.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.

getNPaths

public int getNPaths()

Gets the no. of paths parsed by the Analyzer.

Returns:

the number of paths

getPrimaryPaths

public java.util.Set<Path> getPrimaryPaths()

Retrieves all the Paths in the analyzed Tree tagged as primary.

Returns:

the set of primary paths.

See Also:

getPrimaryBranches()

getPrimaryBranches

public java.util.Set<Path> getPrimaryBranches()

Retrieves the primary branches of the analyzed Tree. A primary branch corresponds to the section of a primary Path between its origin and its closest branch-point.

Returns:

the set containing the primary branches. Note that as per Path.getSection(int, int), these branches will not carry any connectivity information.

See Also:

getPrimaryPaths(), restrictToOrder(int...)

getTerminalBranches

public java.util.Set<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).

Returns:

the set containing 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 java.util.Set<PointInImage> getTips()

Gets the position of all the tips in the analyzed tree.

Returns:

the set of terminal points

getBranchPoints

public java.util.Set<PointInImage> getBranchPoints()

Gets the position of all the branch points in the analyzed tree.

Returns:

the branch points positions

getCableLength

public double getCableLength()

Gets the cable length.

Returns:

the cable length of the tree

getPrimaryLength

public double getPrimaryLength()

Gets the cable length of primary branches.

Returns:

the length sum of all primary branches

See Also:

getPrimaryBranches()

getTerminalLength

public double getTerminalLength()

Gets the cable length of terminal branches

Returns:

the length sum of all terminal branches

See Also:

getTerminalBranches()

getStrahlerRootNumber

public int getStrahlerRootNumber()

Gets the Strahler-Horton root number of the analyzed tree

Returns:

the Strahler root number, or -1 if tree has no defined order

main

public static void main(java.lang.String[] args)
                 throws java.lang.InterruptedException

Throws:

java.lang.InterruptedException