sc.fiji.snt.viewer

Class Viewer2D

java.lang.Object

sc.fiji.snt.analysis.ColorMapper

sc.fiji.snt.analysis.TreeColorMapper

sc.fiji.snt.viewer.Viewer2D

public class Viewer2D
extends TreeColorMapper

Class for rendering Trees as 2D plots that can be exported as SVG, PNG or PDF.

Author:

Tiago Ferreira

Field Summary

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

BRANCH_ORDER, LENGTH, MEAN_RADIUS, N_BRANCH_POINTS, N_NODES, NODE_RADIUS, PATH_DISTANCE, TAG_FILENAME, VALUES, X_COORDINATES, Y_COORDINATES, Z_COORDINATES

Constructor Summary

Constructors

Constructor and Description
Viewer2D(org.scijava.Context context) Instantiates an empty 2D viewer.

Method Summary

Modifier and Type	Method and Description
void	addColorBarLegend() Adds a color bar legend (LUT ramp) to the viewer.
void	addColorBarLegend(net.imglib2.display.ColorTable colorTable, double min, double max) Adds a color bar legend (LUT ramp).
void	addTree(Tree tree) Appends a tree to the viewer using default options.
void	addTree(Tree tree, org.scijava.util.ColorRGB color) Appends a tree to the viewer.
void	addTree(Tree tree, java.lang.String measurement, net.imglib2.display.ColorTable colorTable, double min, double max) Appends a tree to the viewer rendered after the specified measurement.
void	addTree(Tree tree, java.lang.String measurement, java.lang.String lut) Appends a tree to the viewer rendered after the specified measurement.
void	addTree(Tree tree, java.lang.String measurement, java.lang.String lut, double min, double max) Appends a tree to the viewer rendered after the specified measurement.
void	addTrees(java.util.List<Tree> trees, java.lang.String lut) Adds a list of trees while assigning each tree to a LUT index.
org.jfree.chart.JFreeChart	getChart() Gets the current viewer as a JFreeChart object
net.imagej.plot.XYPlot	getPlot(boolean show) Gets the current plot as a XYPlot object
java.lang.String	getTitle() Gets the plot display title.
static void	main(java.lang.String... args)
void	setAxesVisible(boolean visible)
void	setDefaultColor(org.scijava.util.ColorRGB color) Sets the default (fallback) color for plotting paths.
void	setGridlinesVisible(boolean visible)
void	setOutlineVisible(boolean visible)
void	setPreferredSize(int width, int height) Sets the preferred size of the plot to a constant value.
void	setTitle(java.lang.String title) Sets the plot display title.
void	showPlot() Displays the current plot on a dedicated frame

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

getAvalailableLuts, getColorTable, getMultiViewer, map, map, map, mapTrees

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

Constructor Detail

Viewer2D

public Viewer2D(org.scijava.Context context)

Instantiates an empty 2D viewer.

Parameters:

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

Method Detail

addColorBarLegend

public void addColorBarLegend(net.imglib2.display.ColorTable colorTable,
                              double min,
                              double max)

Adds a color bar legend (LUT ramp).

Parameters:

colorTable - the color table

min - the minimum value in the color table

max - the maximum value in the color table

addColorBarLegend

public void addColorBarLegend()

Adds a color bar legend (LUT ramp) to the viewer. Does nothing if no measurement mapping occurred successfully. Note that when performing mapping to different measurements, the legend reflects only the last mapped measurement.

addTree

public void addTree(Tree tree)

Appends a tree to the viewer using default options.

Parameters:

tree - the Collection of paths to be plotted

addTrees

public void addTrees(java.util.List<Tree> trees,
                     java.lang.String lut)

Adds a list of trees while assigning each tree to a LUT index.

Parameters:

trees - the list of trees to be plotted

lut - the lookup table specifying the color mapping

addTree

public void addTree(Tree tree,
                    org.scijava.util.ColorRGB color)

Appends a tree to the viewer.

Parameters:

tree - the Collection of paths to be plotted

color - the color to render the Tree

addTree

public void addTree(Tree tree,
                    java.lang.String measurement,
                    net.imglib2.display.ColorTable colorTable,
                    double min,
                    double max)

Appends a tree to the viewer rendered after the specified measurement.

Parameters:

tree - the tree to be plotted

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

colorTable - the color table specifying the color mapping

min - the mapping lower bound (i.e., the highest measurement value for the LUT scale)

max - the mapping upper bound (i.e., the highest measurement value for the LUT scale)

addTree

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

Appends a tree to the viewer rendered after the specified measurement. Mapping bounds are automatically determined.

Parameters:

tree - the tree to be plotted

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

lut - the lookup table specifying the color mapping

addTree

public void addTree(Tree tree,
                    java.lang.String measurement,
                    java.lang.String lut,
                    double min,
                    double max)

Appends a tree to the viewer rendered after the specified measurement.

Parameters:

tree - the tree to be plotted

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

lut - the lookup table specifying the color mapping

min - the mapping lower bound (i.e., the highest measurement value for the LUT scale)

max - the mapping upper bound (i.e., the highest measurement value for the LUT scale)

getChart

public org.jfree.chart.JFreeChart getChart()

Gets the current viewer as a JFreeChart object

Returns:

the converted viewer

getPlot

public net.imagej.plot.XYPlot getPlot(boolean show)

Gets the current plot as a XYPlot object

Parameters:

show - if true, plot is displayed

Returns:

the current plot

setDefaultColor

public void setDefaultColor(org.scijava.util.ColorRGB color)

Sets the default (fallback) color for plotting paths.

Parameters:

color - null not allowed

setPreferredSize

public void setPreferredSize(int width,
                             int height)

Sets the preferred size of the plot to a constant value.

Parameters:

width - the preferred width

height - the preferred height

setTitle

public void setTitle(java.lang.String title)

Sets the plot display title.

Parameters:

title - the new title

getTitle

public java.lang.String getTitle()

Gets the plot display title.

Returns:

the current display title

showPlot

public void showPlot()

Displays the current plot on a dedicated frame

setGridlinesVisible

public void setGridlinesVisible(boolean visible)

setAxesVisible

public void setAxesVisible(boolean visible)

setOutlineVisible

public void setOutlineVisible(boolean visible)

main

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