TreeParser (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.analysis.sholl.parsers.TreeParser

All Implemented Interfaces:

Parser, ProfileProperties
```
public class TreeParser
extends Object
implements Parser
```
A Parser for extracting Sholl Profiles from a Tree.

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ROOT_NODES_ANY` Flag for defining the profile center as the average position of root nodes of all primary Paths.
`static int`	`ROOT_NODES_APICAL_DENDRITE` Flag for defining the profile center as the average position of root nodes of Paths tagged as Apical Dendrite.
`static int`	`ROOT_NODES_AXON` Flag for defining the profile center as the average position of root nodes of Paths tagged as Axon.
`static int`	`ROOT_NODES_CUSTOM` Flag for defining the profile center as the average position of root nodes of Paths tagged as Custom.
`static int`	`ROOT_NODES_DENDRITE` Flag for defining the profile center as the average position of root nodes of Paths tagged as (Basal) Dendrite
`static int`	`ROOT_NODES_SOMA` Flag for defining the profile center as the average position of root nodes of Paths tagged as Soma
`static int`	`ROOT_NODES_UNDEFINED` Flag for defining the profile center as the average position of root nodes of Paths tagged as Undefined

Fields inherited from interface sc.fiji.snt.analysis.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.

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`PointInImage`	`getCenter()` Returns the center coordinates
`ij.ImagePlus`	`getLabelsImage(ij.ImagePlus templateImg, ColorTable cTable)` Gets the labels image.
`Profile`	`getProfile()`
`Tree`	`getTree()` Returns the tree associated with this parser
`boolean`	`isSkipSomaticSegments()`
`static void`	`main(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`	`setSkipSomaticSegments(boolean skipSomaticSegments)` If primary paths start far-away from the soma (expected to be defined by a single-point (soma centroid)), should segments between the soma and neurite be ignored.
`void`	`setStepSize(double stepSize)` Sets the radius step size.
`boolean`	`successful()`
`void`	`terminate()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - ROOT_NODES_ANY
```
public static final int ROOT_NODES_ANY
```
    Flag for defining the profile center as the average position of root nodes of all primary Paths.
    
    See Also:
    
    Constant Field Values
  - ROOT_NODES_APICAL_DENDRITE
```
public static final int ROOT_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
  - ROOT_NODES_AXON
```
public static final int ROOT_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
  - ROOT_NODES_CUSTOM
```
public static final int ROOT_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
  - ROOT_NODES_DENDRITE
```
public static final int ROOT_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
  - ROOT_NODES_SOMA
```
public static final int ROOT_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
  - ROOT_NODES_UNDEFINED
```
public static final int ROOT_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 IllegalArgumentException
```
    Computes the center of the Profile.
    
    Parameters:
    
    choice - the flag specifying the center (e.g., ROOT_NODES_SOMA, ROOT_NODES_ANY, etc.)
    
    Throws:
    
    IllegalArgumentException - if choice is not a recognized flag or if no Paths in the Tree match the choice criteria
  - getCenter
```
public PointInImage 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()
           throws IllegalArgumentException
```
    Specified by:
    
    parse in interface Parser
    
    Throws:
    
    IllegalArgumentException
  - successful
```
public boolean successful()
```
    Specified by:
    
    successful in interface Parser
  - terminate
```
public void terminate()
```
    Specified by:
    
    terminate in interface Parser
  - getProfile
```
public Profile getProfile()
```
    Specified by:
    
    getProfile in interface Parser
  - getLabelsImage
```
public ij.ImagePlus getLabelsImage(ij.ImagePlus templateImg,
                                   ColorTable cTable)
```
    Gets the labels image.
    
    Parameters:
    
    templateImg - the template img
    
    cTable - the c table
    
    Returns:
    
    the labels image
  - main
```
public static void main(String... args)
```
  - getTree
```
public Tree getTree()
```
    Returns the tree associated with this parser
    
    Returns:
    
    the profiled tree
  - isSkipSomaticSegments
```
public boolean isSkipSomaticSegments()
```
    See Also:
    
    setSkipSomaticSegments(boolean)
  - setSkipSomaticSegments
```
public void setSkipSomaticSegments(boolean skipSomaticSegments)
```
    If primary paths start far-away from the soma (expected to be defined by a single-point (soma centroid)), should segments between the soma and neurite be ignored. Useful when somas are large relatively to the length of arbor, as in microglia cells. See e.g., this forum thread.
    
    Parameters:
    
    skipSomaticSegments - the skipFirsNode to set

Class TreeParser

Field Summary

Fields inherited from interface sc.fiji.snt.analysis.sholl.ProfileProperties

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ROOT_NODES_ANY

ROOT_NODES_APICAL_DENDRITE

ROOT_NODES_AXON

ROOT_NODES_CUSTOM

ROOT_NODES_DENDRITE

ROOT_NODES_SOMA

ROOT_NODES_UNDEFINED

Constructor Detail

TreeParser

Method Detail

setCenter

getCenter

setCenter

setStepSize

parse

successful

terminate

getProfile

getLabelsImage

main

getTree

isSkipSomaticSegments

setSkipSomaticSegments