sc.fiji.snt.analysis.sholl

Class TreeParser

java.lang.Object

sc.fiji.snt.analysis.sholl.TreeParser

All Implemented Interfaces:

sholl.parsers.Parser, sholl.ProfileProperties

public class TreeParser
extends java.lang.Object
implements sholl.parsers.Parser

A Parser for extracting Sholl Profiles from a Tree.

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field and Description
static int	PRIMARY_NODES_ANY Flag for defining the profile center as the average position of root nodes of all primary Paths.
static int	PRIMARY_NODES_APICAL_DENDRITE Flag for defining the profile center as the average position of root nodes of Paths tagged as Apical Dendrite.
static int	PRIMARY_NODES_AXON Flag for defining the profile center as the average position of root nodes of Paths tagged as Axon.
static int	PRIMARY_NODES_CUSTOM Flag for defining the profile center as the average position of root nodes of Paths tagged as Custom.
static int	PRIMARY_NODES_DENDRITE Flag for defining the profile center as the average position of root nodes of Paths tagged as (Basal) Dendrite
static int	PRIMARY_NODES_SOMA Flag for defining the profile center as the average position of root nodes of Paths tagged as Soma
static int	PRIMARY_NODES_UNDEFINED Flag for defining the profile center as the average position of root nodes of Paths tagged as Undefined

Fields inherited from interface sholl.ProfileProperties

HEMI_EAST, HEMI_NONE, HEMI_NORTH, HEMI_SOUTH, HEMI_WEST, INTG_MEAN, INTG_MEDIAN, INTG_MODE, KEY_2D3D, KEY_CALIBRATION, KEY_CENTER, KEY_CHANNEL_POS, KEY_FRAME_POS, KEY_HEMISHELLS, KEY_ID, KEY_NSAMPLES, KEY_NSAMPLES_INTG, KEY_SLICE_POS, KEY_SOURCE, KEY_THRESHOLD_RANGE, SRC_IMG, SRC_TABLE, SRC_TRACES, UNSET

Constructor Summary

Constructors

Constructor and Description
TreeParser(Tree tree) Instantiates a new Tree Parser.

Method Summary

Modifier and Type	Method and Description
sholl.UPoint	getCenter() Returns the center coordinates
ij.ImagePlus	getLabelsImage(ij.ImagePlus templateImg, net.imglib2.display.ColorTable cTable) Gets the labels image.
sholl.Profile	getProfile()
static void	main(java.lang.String... args)
void	parse()
void	setCenter(int choice) Computes the center of the Profile.
void	setCenter(PointInImage center) Sets the center of the profile.
void	setStepSize(double stepSize) Sets the radius step size.
boolean	successful()
void	terminate()

Methods inherited from class java.lang.Object

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

Field Detail

PRIMARY_NODES_ANY

public static final int PRIMARY_NODES_ANY

Flag for defining the profile center as the average position of root nodes of all primary Paths.

See Also:

Constant Field Values

PRIMARY_NODES_APICAL_DENDRITE

public static final int PRIMARY_NODES_APICAL_DENDRITE

Flag for defining the profile center as the average position of root nodes of Paths tagged as Apical Dendrite.

See Also:

Constant Field Values

PRIMARY_NODES_AXON

public static final int PRIMARY_NODES_AXON

Flag for defining the profile center as the average position of root nodes of Paths tagged as Axon.

See Also:

Constant Field Values

PRIMARY_NODES_CUSTOM

public static final int PRIMARY_NODES_CUSTOM

Flag for defining the profile center as the average position of root nodes of Paths tagged as Custom.

See Also:

Constant Field Values

PRIMARY_NODES_DENDRITE

public static final int PRIMARY_NODES_DENDRITE

Flag for defining the profile center as the average position of root nodes of Paths tagged as (Basal) Dendrite

See Also:

Constant Field Values

PRIMARY_NODES_SOMA

public static final int PRIMARY_NODES_SOMA

Flag for defining the profile center as the average position of root nodes of Paths tagged as Soma

See Also:

Constant Field Values

PRIMARY_NODES_UNDEFINED

public static final int PRIMARY_NODES_UNDEFINED

Flag for defining the profile center as the average position of root nodes of Paths tagged as Undefined

See Also:

Constant Field Values

Constructor Detail

TreeParser

public TreeParser(Tree tree)

Instantiates a new Tree Parser.

Parameters:

tree - the Tree to be profiled

Method Detail

setCenter

public void setCenter(int choice)
               throws java.lang.IllegalArgumentException

Computes the center of the Profile.

Parameters:

choice - the flag specifying the center (e.g., PRIMARY_NODES_SOMA, PRIMARY_NODES_ANY, etc.)

Throws:

java.lang.IllegalArgumentException - if choice is not a recognized flag or if no Paths in the Tree match the choice criteria

getCenter

public sholl.UPoint getCenter()

Returns the center coordinates

Returns:

the point defining the center, or null if it has not yet been set.

setCenter

public void setCenter(PointInImage center)

Sets the center of the profile.

Parameters:

center - the focal point of the profile

setStepSize

public void setStepSize(double stepSize)

Sets the radius step size.

Parameters:

stepSize - the radius step size

parse

public void parse()

Specified by:

parse in interface sholl.parsers.Parser

successful

public boolean successful()

Specified by:

successful in interface sholl.parsers.Parser

terminate

public void terminate()

Specified by:

terminate in interface sholl.parsers.Parser

getProfile

public sholl.Profile getProfile()

Specified by:

getProfile in interface sholl.parsers.Parser

getLabelsImage

public ij.ImagePlus getLabelsImage(ij.ImagePlus templateImg,
                                   net.imglib2.display.ColorTable cTable)

Gets the labels image.

Parameters:

templateImg - the template img

cTable - the c table

Returns:

the labels image

main

public static void main(java.lang.String... args)