TreeColorMapper (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.analysis.ColorMapper
- - sc.fiji.snt.analysis.TreeColorMapper

Direct Known Subclasses:

Viewer2D
```
public class TreeColorMapper
extends ColorMapper
```
Class for color coding Trees.

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`AVG_SPINE_DENSITY` Flag for "Average spine/varicosity density" mapping.
`static String`	`LENGTH` Flag for "Path length" mapping.
`static String`	`MEAN_RADIUS` Flag for "Path mean radius" mapping.
`static String`	`N_BRANCH_POINTS` Flag for "No. of branch points" mapping.
`static String`	`N_NODES` Flag for "No. of nodes" mapping.
`static String`	`N_SPINES` Flag for "No. of spines/varicosities" statistics.
`static String`	`NODE_RADIUS` Flag for "Node radius" mapping.
`static String`	`PATH_DISTANCE` Flag for "Path distance to soma" mapping.
`static String`	`PATH_FRAME` Flag for "Path frame" mapping.
`static String`	`PATH_ORDER` Flag for "Path order" mapping.
`protected ArrayList<Path>`	`paths`
`static String`	`SHOLL_COUNTS` Flag for "Sholl inters. (root centered)" mapping.
`static String`	`STRAHLER_NUMBER` Flag for "Horton-Strahler number" mapping.
`static String`	`TAG_FILENAME` Flag for "Tags/filename" mapping.
`static String`	`VALUES` Flag for "Node intensity values" mapping.
`static String`	`X_COORDINATES` Flag for "X coordinates" mapping.
`static String`	`Y_COORDINATES` Flag for "Y coordinates" mapping.
`static String`	`Z_COORDINATES` Flag for "Z coordinates" mapping.

Fields inherited from class sc.fiji.snt.analysis.ColorMapper
colorTable, integerScale, max, min

Constructor Summary

Constructors
Constructor and Description

TreeColorMapper()
Instantiates the mapper.

TreeColorMapper(Context context)
Instantiates the mapper.

Constructors
Constructor and Description
`TreeColorMapper()` Instantiates the mapper.
`TreeColorMapper(Context context)` Instantiates the mapper.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Set<String>`	`getAvailableLuts()` Gets the available LUTs.
`ColorTable`	`getColorTable(String lut)`
`static List<String>`	`getMetrics()` Gets the list of supported mapping metrics.
`MultiViewer2D`	`getMultiViewer()` Assembles a `Multi-pane viewer` using all the Trees mapped so far.
`protected String`	`getNormalizedMeasurement(String measurement)`
`static void`	`main(String... args)`
`void`	`map(Collection<? extends PointInImage> points, String measurement, String lut)` Colorizes a collection of points after the specified measurement.
`void`	`map(Tree tree, LinearProfileStats stats, ColorTable colorTable)` Colorizes a tree using Sholl data.
`void`	`map(Tree tree, String measurement, ColorTable colorTable)` Colorizes a tree after the specified measurement.
`void`	`map(Tree tree, String measurement, String lut)` Colorizes a tree after the specified measurement.
`protected void`	`mapToProperty(String measurement, ColorTable colorTable)`
`void`	`mapTrees(List<Tree> trees, String lut)` Colorizes a list of trees, with each tree being assigned a LUT index.
`protected String`	`tryReallyHardToGuessMetric(String guess)`

Methods inherited from class sc.fiji.snt.analysis.ColorMapper
getColor, getColorRGB, getColorTable, getMinMax, map, setMinMax

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

- Field Detail
  - SHOLL_COUNTS
```
public static final String SHOLL_COUNTS
```
    Flag for "Sholl inters. (root centered)" mapping.
    
    See Also:
    
    Constant Field Values
  - STRAHLER_NUMBER
```
public static final String STRAHLER_NUMBER
```
    Flag for "Horton-Strahler number" mapping.
    
    See Also:
    
    Constant Field Values
  - PATH_ORDER
```
public static final String PATH_ORDER
```
    Flag for "Path order" mapping.
    
    See Also:
    
    Constant Field Values
  - LENGTH
```
public static final String LENGTH
```
    Flag for "Path length" mapping.
    
    See Also:
    
    Constant Field Values
  - N_BRANCH_POINTS
```
public static final String N_BRANCH_POINTS
```
    Flag for "No. of branch points" mapping.
    
    See Also:
    
    Constant Field Values
  - N_NODES
```
public static final String N_NODES
```
    Flag for "No. of nodes" mapping.
    
    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
  - MEAN_RADIUS
```
public static final String MEAN_RADIUS
```
    Flag for "Path mean radius" mapping.
    
    See Also:
    
    Constant Field Values
  - AVG_SPINE_DENSITY
```
public static final String AVG_SPINE_DENSITY
```
    Flag for "Average spine/varicosity density" mapping.
    
    See Also:
    
    Constant Field Values
  - NODE_RADIUS
```
public static final String NODE_RADIUS
```
    Flag for "Node radius" mapping.
    
    See Also:
    
    Constant Field Values
  - X_COORDINATES
```
public static final String X_COORDINATES
```
    Flag for "X coordinates" mapping.
    
    See Also:
    
    Constant Field Values
  - Y_COORDINATES
```
public static final String Y_COORDINATES
```
    Flag for "Y coordinates" mapping.
    
    See Also:
    
    Constant Field Values
  - Z_COORDINATES
```
public static final String Z_COORDINATES
```
    Flag for "Z coordinates" mapping.
    
    See Also:
    
    Constant Field Values
  - VALUES
```
public static final String VALUES
```
    Flag for "Node intensity values" mapping.
    
    See Also:
    
    Constant Field Values
  - PATH_DISTANCE
```
public static final String PATH_DISTANCE
```
    Flag for "Path distance to soma" mapping.
    
    See Also:
    
    Constant Field Values
  - TAG_FILENAME
```
public static final String TAG_FILENAME
```
    Flag for "Tags/filename" mapping.
    
    See Also:
    
    Constant Field Values
  - PATH_FRAME
```
public static final String PATH_FRAME
```
    Flag for "Path frame" mapping.
    
    See Also:
    
    Constant Field Values
  - paths
```
protected ArrayList<Path> paths
```
- Constructor Detail
  - TreeColorMapper
```
public TreeColorMapper(Context context)
```
    Instantiates the mapper.
    
    Parameters:
    
    context - the SciJava application context providing the services required by the class
  - TreeColorMapper
```
public TreeColorMapper()
```
    Instantiates the mapper. Note that because the instance is not aware of any context, script-friendly methods that use string as arguments may fail to retrieve referenced Scijava objects.
- Method Detail
  - getMetrics
```
public static List<String> getMetrics()
```
    Gets the list of supported mapping metrics.
    
    Returns:
    
    the list of mapping metrics.
  - getColorTable
```
public ColorTable getColorTable(String lut)
```
  - mapToProperty
```
protected void mapToProperty(String measurement,
                             ColorTable colorTable)
```
  - map
```
public void map(Tree tree,
                LinearProfileStats stats,
                ColorTable colorTable)
```
    Colorizes a tree using Sholl data.
    
    Parameters:
    
    tree - the tree to be colorized
    
    stats - the LinearProfileStats instance containing the mapping profile. if a polynomial fit has been successfully performed, mapping is done against the fitted data, otherwise sampled intersections are used.
    
    colorTable - the color table specifying the color mapping. Null not allowed.
  - map
```
public void map(Tree tree,
                String measurement,
                ColorTable colorTable)
```
    Colorizes a tree after the specified measurement.
    
    Parameters:
    
    tree - the tree to be mapped
    
    measurement - the measurement (PATH_ORDER }LENGTH, etc.)
    
    colorTable - the color table specifying the color mapping. Null not allowed.
  - map
```
public void map(Collection<? extends PointInImage> points,
                String measurement,
                String lut)
```
    Colorizes a collection of points after the specified measurement. Mapping bounds are automatically determined. This is a convenience method to extend color mapping to point clouds.
    
    Parameters:
    
    points - the points to be mapped
    
    measurement - the measurement (Z_COORDINATES, etc.). Note that if points do note encode a valid Tree. only metrics applicable to coordinates are expected.
    
    lut - the lookup table specifying the color mapping
  - tryReallyHardToGuessMetric
```
protected String tryReallyHardToGuessMetric(String guess)
```
  - getNormalizedMeasurement
```
protected String getNormalizedMeasurement(String measurement)
```
  - map
```
public void map(Tree tree,
                String measurement,
                String lut)
```
    Colorizes a tree after the specified measurement. Mapping bounds are automatically determined.
    
    Parameters:
    
    tree - the tree to be mapped
    
    measurement - the measurement (PATH_ORDER }LENGTH, etc.)
    
    lut - the lookup table specifying the color mapping
  - mapTrees
```
public void mapTrees(List<Tree> trees,
                     String lut)
```
    Colorizes a list of trees, with each tree being assigned a LUT index.
    
    Parameters:
    
    trees - the list of trees to be colorized
    
    lut - the lookup table specifying the color mapping
  - getAvailableLuts
```
public Set<String> getAvailableLuts()
```
    Gets the available LUTs.
    
    Returns:
    
    the set of keys, corresponding to the set of LUTs available
  - getMultiViewer
```
public MultiViewer2D getMultiViewer()
```
    Assembles a Multi-pane viewer using all the Trees mapped so far.
    
    Returns:
    
    the multi-viewer instance
  - main
```
public static void main(String... args)
```

Class TreeColorMapper

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class sc.fiji.snt.analysis.ColorMapper

Methods inherited from class java.lang.Object

Field Detail

SHOLL_COUNTS

STRAHLER_NUMBER

PATH_ORDER

LENGTH

N_BRANCH_POINTS

N_NODES

N_SPINES

MEAN_RADIUS

AVG_SPINE_DENSITY

NODE_RADIUS

X_COORDINATES

Y_COORDINATES

Z_COORDINATES

VALUES

PATH_DISTANCE

TAG_FILENAME

PATH_FRAME

paths

Constructor Detail

TreeColorMapper

TreeColorMapper

Method Detail

getMetrics

getColorTable

mapToProperty

map

map

map

tryReallyHardToGuessMetric

getNormalizedMeasurement

map

mapTrees

getAvailableLuts

getMultiViewer

main