MultiTreeColorMapper (Fiji Javadocs 0-SNAPSHOT API)

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

```
public class MultiTreeColorMapper
extends ColorMapper
```
Class for color coding groups of Trees.
After a mapping property and a color table (LUT) are specified, the mapping proceeds as follows: 1) Each Tree in the group is measured for the mapping property; 2) each measurement is mapped to a LUT entry that is used to color each Tree. Mapping limits can be optionally specified

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`ASSIGNED_VALUE` Mapping property: Assigned Tree value
`static String`	`HIGHEST_PATH_ORDER` Mapping property: Highest `path order`
`static String`	`ID` Mapping property (dummy): Each Tree in the collection is assigned an incremental LUT entry
`static String`	`LENGTH` Mapping property: Cable length
`static String`	`N_BRANCH_POINTS` Mapping property: Count of all branch points
`static String`	`N_BRANCHES` Mapping property: Count of all branches
`static String`	`N_TIPS` Mapping property: Count of all tips (end points)
`static String[]`	`PROPERTIES`
`static String`	`STRAHLER_NUMBER` Mapping property: `Horton-Strahler number`

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

Constructor Summary

Constructors
Constructor and Description

MultiTreeColorMapper(Collection<Tree> trees)
Instantiates the MultiTreeColorMapper.

Constructors
Constructor and Description
`MultiTreeColorMapper(Collection<Tree> trees)` Instantiates the MultiTreeColorMapper.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static List<String>`	`getMetrics()` Gets the list of supported mapping metrics.
`MultiViewer2D`	`getMultiViewer()`
`protected String`	`getNormalizedMeasurement(String measurement)`
`static void`	`main(String... args)`
`void`	`map(String measurement, ColorTable colorTable)`
`void`	`mapRootDistanceToCentroid(AllenCompartment compartment, ColorTable colorTable)`
`List<Tree>`	`sortedMappedTrees()`
`protected String`	`tryReallyHardToGuessMetric(String guess)`

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

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

- Field Detail
  - LENGTH
```
public static final String LENGTH
```
    Mapping property: Cable length
    
    See Also:
    
    Constant Field Values
  - N_BRANCH_POINTS
```
public static final String N_BRANCH_POINTS
```
    Mapping property: Count of all branch points
    
    See Also:
    
    Constant Field Values
  - N_TIPS
```
public static final String N_TIPS
```
    Mapping property: Count of all tips (end points)
    
    See Also:
    
    Constant Field Values
  - N_BRANCHES
```
public static final String N_BRANCHES
```
    Mapping property: Count of all branches
    
    See Also:
    
    Constant Field Values
  - STRAHLER_NUMBER
```
public static final String STRAHLER_NUMBER
```
    Mapping property: Horton-Strahler number
    
    See Also:
    
    Constant Field Values
  - HIGHEST_PATH_ORDER
```
public static final String HIGHEST_PATH_ORDER
```
    Mapping property: Highest path order
    
    See Also:
    
    Constant Field Values
  - ASSIGNED_VALUE
```
public static final String ASSIGNED_VALUE
```
    Mapping property: Assigned Tree value
    
    See Also:
    
    Constant Field Values
  - ID
```
public static final String ID
```
    Mapping property (dummy): Each Tree in the collection is assigned an incremental LUT entry
    
    See Also:
    
    Constant Field Values
  - PROPERTIES
```
public static final String[] PROPERTIES
```
- Constructor Detail
  - MultiTreeColorMapper
```
public MultiTreeColorMapper(Collection<Tree> trees)
```
    Instantiates the MultiTreeColorMapper.
    
    Parameters:
    
    trees - the group of trees to be mapped,
- Method Detail
  - getMetrics
```
public static List<String> getMetrics()
```
    Gets the list of supported mapping metrics.
    
    Returns:
    
    the list of mapping metrics.
  - map
```
public void map(String measurement,
                ColorTable colorTable)
```
    Overrides:
    
    map in class ColorMapper
  - mapRootDistanceToCentroid
```
public void mapRootDistanceToCentroid(AllenCompartment compartment,
                                      ColorTable colorTable)
```
  - tryReallyHardToGuessMetric
```
protected String tryReallyHardToGuessMetric(String guess)
```
  - getNormalizedMeasurement
```
protected String getNormalizedMeasurement(String measurement)
```
  - sortedMappedTrees
```
public List<Tree> sortedMappedTrees()
```
  - getMultiViewer
```
public MultiViewer2D getMultiViewer()
```
  - main
```
public static void main(String... args)
```

Class MultiTreeColorMapper

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

LENGTH

N_BRANCH_POINTS

N_TIPS

N_BRANCHES

STRAHLER_NUMBER

HIGHEST_PATH_ORDER

ASSIGNED_VALUE

ID

PROPERTIES

Constructor Detail

MultiTreeColorMapper

Method Detail

getMetrics

map

mapRootDistanceToCentroid

tryReallyHardToGuessMetric

getNormalizedMeasurement

sortedMappedTrees

getMultiViewer

main