sc.fiji.snt.analysis

Class TreeColorMapper

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 java.lang.String	BRANCH_ORDER Flag for "Branch order" mapping.
static java.lang.String	LENGTH Flag for "Length" mapping.
static java.lang.String	MEAN_RADIUS Flag for "Path mean radius" mapping.
static java.lang.String	N_BRANCH_POINTS Flag for "No. of branch points" mapping.
static java.lang.String	N_NODES Flag for "No. of nodes" mapping.
static java.lang.String	NODE_RADIUS Flag for "Node radius" mapping.
static java.lang.String	PATH_DISTANCE Flag for "Path distance to soma" mapping.
static java.lang.String	TAG_FILENAME Flag for "Tags/filename" mapping.
static java.lang.String	VALUES See TreeAnalyzer.VALUES.
static java.lang.String	X_COORDINATES Flag for "X coordinates" mapping.
static java.lang.String	Y_COORDINATES Flag for "Y coordinates" mapping.
static java.lang.String	Z_COORDINATES Flag for "Z coordinates" mapping.

Constructor Summary

Constructors

Constructor and Description
TreeColorMapper() Instantiates the Colorizer.
TreeColorMapper(org.scijava.Context context) Instantiates the Colorizer.

Method Summary

Modifier and Type	Method and Description
java.util.Set<java.lang.String>	getAvalailableLuts() Gets the available LUTs.
net.imglib2.display.ColorTable	getColorTable(java.lang.String lut)
MultiViewer2D	getMultiViewer()
static void	main(java.lang.String... args)
void	map(Tree tree, sholl.math.LinearProfileStats stats, net.imglib2.display.ColorTable colorTable) Colorizes a tree using Sholl data.
void	map(Tree tree, java.lang.String measurement, net.imglib2.display.ColorTable colorTable) Colorizes a tree after the specified measurement.
void	map(Tree tree, java.lang.String measurement, java.lang.String lut) Colorizes a tree after the specified measurement.
void	mapTrees(java.util.List<Tree> trees, java.lang.String lut) Colorizes a list of trees, with each tree being assigned a LUT index.

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

getMinMax, map, setMinMax

Methods inherited from class java.lang.Object

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

Field Detail

BRANCH_ORDER

public static final java.lang.String BRANCH_ORDER

Flag for "Branch order" mapping.

See Also:

Constant Field Values

LENGTH

public static final java.lang.String LENGTH

Flag for "Length" mapping.

See Also:

Constant Field Values

N_BRANCH_POINTS

public static final java.lang.String N_BRANCH_POINTS

Flag for "No. of branch points" mapping.

See Also:

Constant Field Values

N_NODES

public static final java.lang.String N_NODES

Flag for "No. of nodes" mapping.

See Also:

Constant Field Values

MEAN_RADIUS

public static final java.lang.String MEAN_RADIUS

Flag for "Path mean radius" mapping.

See Also:

Constant Field Values

NODE_RADIUS

public static final java.lang.String NODE_RADIUS

Flag for "Node radius" mapping.

See Also:

Constant Field Values

X_COORDINATES

public static final java.lang.String X_COORDINATES

Flag for "X coordinates" mapping.

See Also:

Constant Field Values

Y_COORDINATES

public static final java.lang.String Y_COORDINATES

Flag for "Y coordinates" mapping.

See Also:

Constant Field Values

Z_COORDINATES

public static final java.lang.String Z_COORDINATES

Flag for "Z coordinates" mapping.

See Also:

Constant Field Values

VALUES

public static final java.lang.String VALUES

See TreeAnalyzer.VALUES.

See Also:

Constant Field Values

PATH_DISTANCE

public static final java.lang.String PATH_DISTANCE

Flag for "Path distance to soma" mapping.

See Also:

Constant Field Values

TAG_FILENAME

public static final java.lang.String TAG_FILENAME

Flag for "Tags/filename" mapping.

See Also:

Constant Field Values

Constructor Detail

TreeColorMapper

public TreeColorMapper(org.scijava.Context context)

Instantiates the Colorizer.

Parameters:

context - the SciJava application context providing the services required by the class

TreeColorMapper

public TreeColorMapper()

Instantiates the Colorizer. 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

getColorTable

public net.imglib2.display.ColorTable getColorTable(java.lang.String lut)

map

public void map(Tree tree,
                sholl.math.LinearProfileStats stats,
                net.imglib2.display.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,
                java.lang.String measurement,
                net.imglib2.display.ColorTable colorTable)

Colorizes a tree after the specified measurement.

Parameters:

tree - the tree to be colorized

measurement - the measurement (BRANCH_ORDER }LENGTH, etc.)

colorTable - the color table specifying the color mapping. Null not allowed.

map

public void map(Tree tree,
                java.lang.String measurement,
                java.lang.String lut)

Colorizes a tree after the specified measurement. Mapping bounds are automatically determined.

Parameters:

tree - the tree to be plotted

measurement - the measurement (BRANCH_ORDER }LENGTH, etc.)

lut - the lookup table specifying the color mapping

mapTrees

public void mapTrees(java.util.List<Tree> trees,
                     java.lang.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

getAvalailableLuts

public java.util.Set<java.lang.String> getAvalailableLuts()

Gets the available LUTs.

Returns:

the set of keys, corresponding to the set of LUTs available

getMultiViewer

public MultiViewer2D getMultiViewer()

main

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