Package sc.fiji.snt.analysis

Class MultiTreeColorMapper

java.lang.Object

sc.fiji.snt.analysis.ColorMapper

sc.fiji.snt.analysis.TreeColorMapper

sc.fiji.snt.analysis.MultiTreeColorMapper

public class MultiTreeColorMapper
extends TreeColorMapper

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	Description
static final String	ASSIGNED_VALUE	Mapping property: Assigned Tree value
static final String	CABLE_LENGTH	Mapping property: Cable length
static final String	HIGHEST_PATH_ORDER	Mapping property: Highest path order
static final String	ID	Mapping property (dummy): Each Tree in the collection is assigned an incremental LUT entry
static final String	N_BRANCHES	Mapping property: Count of all branches
static final String	N_TIPS	Mapping property: Count of all tips (end points)
static final String	STRAHLER_NUMBER	Mapping property: Horton-Strahler number

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

INTER_NODE_ANGLE, INTER_NODE_DISTANCE, N_BRANCH_POINTS, N_NODES, N_SPINES, NODE_RADIUS, PATH_AVG_SPINE_DENSITY, PATH_DISTANCE, PATH_EXT_ANGLE, PATH_EXT_ANGLE_REL, PATH_EXT_ANGLE_XY, PATH_EXT_ANGLE_XZ, PATH_EXT_ANGLE_ZY, PATH_FRAME, PATH_LENGTH, PATH_MEAN_RADIUS, PATH_ORDER, paths, SHOLL_COUNTS, STRAHLER_ORDERS, TAG_FILENAME, VALUES, X_COORDINATES, Y_COORDINATES, Z_COORDINATES

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

colorTable, integerScale, luts, lutService, max, min

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
static List<String>	getMetrics()	Gets the list of all supported mapping metrics.
static List<String>	getMetrics(String type)	Gets the list of supported mapping metrics.
MultiViewer2D	getMultiViewer()	Assembles a Multi-pane viewer using all the Trees mapped so far.
static List<String>	getSingleValueMetrics()	Gets the list of single-value mapping metrics.
static void	main(String... args)
void	map(String measurement, net.imglib2.display.ColorTable colorTable)	Sets up the color mapping for the specified measurement using the given color table.
void	mapRootDistanceToCentroid(AllenCompartment compartment, net.imglib2.display.ColorTable colorTable)
List<Tree>	sortedMappedTrees()

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

getAvailableLuts, getColorTable, getNormalizedMeasurement, isNodeMapping, map, map, map, map, map, mapToProperty, mapTrees

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

getColor, getColorRGB, getColorTable, getMinMax, getNaNColor, initLuts, isIntegerScale, setMinMax, setNaNColor, unMap, unMap

Methods inherited from class java.lang.Object

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

Field Details

ASSIGNED_VALUE

public static final String ASSIGNED_VALUE

Mapping property: Assigned Tree value

See Also:

• Constant Field Values

CABLE_LENGTH

public static final String CABLE_LENGTH

Mapping property: Cable length

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

HIGHEST_PATH_ORDER

public static final String HIGHEST_PATH_ORDER

Mapping property: Highest path order

See Also:

• Constant Field Values

N_BRANCHES

public static final String N_BRANCHES

Mapping property: Count of all branches

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

STRAHLER_NUMBER

public static final String STRAHLER_NUMBER

Mapping property: Horton-Strahler number

See Also:

• Constant Field Values

Constructor Details

MultiTreeColorMapper

public MultiTreeColorMapper(Collection<Tree> trees)

Instantiates the MultiTreeColorMapper.

Parameters:

trees - the group of trees to be mapped,

Method Details

getMetrics

public static List<String> getMetrics()

Gets the list of all supported mapping metrics.

Returns:

the list of mapping metrics.

getMetrics

public static List<String> getMetrics(String type)

Gets the list of supported mapping metrics.

Parameters:

type - Either 'all' (MultiTreeColorMapper and TreeColorMapper metrics) or 'default' (MultiTreeColorMapper only)

Returns:

the list of mapping metrics.

getSingleValueMetrics

public static List<String> getSingleValueMetrics()

Gets the list of single-value mapping metrics.

Returns:

the list of single-value mapping metrics.

map

public void map(String measurement,
 net.imglib2.display.ColorTable colorTable)

Description copied from class: ColorMapper

Sets up the color mapping for the specified measurement using the given color table.

This method configures the ColorMapper to use the specified measurement and color table for mapping values to colors. The actual mapping implementation is left to extending classes.

Overrides:

map in class ColorMapper

Parameters:

measurement - the measurement to be mapped

colorTable - the color table to use for mapping

mapRootDistanceToCentroid

public void mapRootDistanceToCentroid(AllenCompartment compartment,
 net.imglib2.display.ColorTable colorTable)

sortedMappedTrees

public List<Tree> sortedMappedTrees()

getMultiViewer

public MultiViewer2D getMultiViewer()

Description copied from class: TreeColorMapper

Assembles a Multi-pane viewer using all the Trees mapped so far.

Overrides:

getMultiViewer in class TreeColorMapper

Returns:

the multi-viewer instance

main

public static void main(String... args)