Viewer2D (Fiji Javadocs 0-SNAPSHOT API)

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
Modifier and Type Field and Description

protected net.imagej.plot.XYPlot plot
- Fields inherited from class sc.fiji.snt.analysis.TreeColorMapper
  AVG_SPINE_DENSITY, LENGTH, MEAN_RADIUS, N_BRANCH_POINTS, N_NODES, N_SPINES, NODE_RADIUS, PATH_DISTANCE, PATH_FRAME, PATH_ORDER, paths, SHOLL_COUNTS, STRAHLER_NUMBER, TAG_FILENAME, VALUES, X_COORDINATES, Y_COORDINATES, Z_COORDINATES
- Fields inherited from class sc.fiji.snt.analysis.ColorMapper
  colorTable, integerScale, max, min

Fields
Modifier and Type	Field and Description
`protected net.imagej.plot.XYPlot`	`plot`

Constructor Summary

Constructors
Constructor and Description

Viewer2D()
Instantiates an empty 2D viewer.

Viewer2D(Context context)
Instantiates an empty 2D viewer.

Constructors
Constructor and Description
`Viewer2D()` Instantiates an empty 2D viewer.
`Viewer2D(Context context)` Instantiates an empty 2D viewer.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`add(List<Tree> trees, String lut)` Adds a list of trees while assigning each tree to a LUT index.
`void`	`add(Tree tree)` Appends a tree to the viewer using default options.
`void`	`add(Tree tree, ColorRGB color)` Appends a tree to the viewer.
`void`	`add(Tree tree, String color)` Appends a tree to the viewer.
`void`	`add(Tree tree, String measurement, ColorTable colorTable, double min, double max)` Appends a tree to the viewer rendered after the specified measurement.
`void`	`add(Tree tree, String measurement, String lut)` Appends a tree to the viewer rendered after the specified measurement.
`void`	`add(Tree tree, String measurement, String lut, double min, double max)` Appends a tree to the viewer rendered after the specified measurement.
`void`	`addColorBarLegend()` Adds a color bar legend (LUT ramp) to the viewer.
`void`	`addColorBarLegend(ColorTable colorTable, double min, double max)` Adds a color bar legend (LUT ramp).
`protected void`	`addColorBarLegend(String colorTable, double min, double max)`
`<T extends ColorMapper> void`	`addColorBarLegend(T colorMapper)` Adds a color bar legend (LUT ramp) from a `ColorMapper`.
`void`	`addPolygon(Polygon2D poly, String label)`
`void`	`addTree(Tree tree)` Deprecated. Use `add(Tree)` instead
`SNTChart`	`getChart()` Gets the current viewer as a `SNTChart` object
`JFreeChart`	`getJFreeChart()` Gets the current viewer as a `JFreeChart` object
`protected PaintScaleLegend`	`getPaintScaleLegend(ColorTable colorTable, double min, double max)`
`protected PaintScaleLegend`	`getPaintScaleLegend(String colorTable, double min, double max)`
`net.imagej.plot.XYPlot`	`getPlot(boolean show)` Gets the current plot as a `XYPlot` object
`String`	`getTitle()` Gets the plot display title.
`static void`	`main(String... args)`
`void`	`setAxesVisible(boolean visible)`
`void`	`setDefaultColor(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(String title)` Sets the plot display title.
`void`	`show()` Displays the current plot on a dedicated frame
`void`	`showPlot()` Deprecated. Use `show()` instead.

Methods inherited from class sc.fiji.snt.analysis.TreeColorMapper
getAvailableLuts, getColorTable, getMetrics, getMultiViewer, getNormalizedMeasurement, map, map, map, map, mapToProperty, mapTrees, tryReallyHardToGuessMetric

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
  - plot
```
protected net.imagej.plot.XYPlot plot
```
- Constructor Detail
  - Viewer2D
```
public Viewer2D()
```
    Instantiates an empty 2D viewer. 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.
  - Viewer2D
```
public Viewer2D(Context context)
```
    Instantiates an empty 2D viewer.
    
    Parameters:
    
    context - the SciJava application context providing the services required by the viewer.
- Method Detail
  - addPolygon
```
public void addPolygon(Polygon2D poly,
                       String label)
```
  - addColorBarLegend
```
protected void addColorBarLegend(String colorTable,
                                 double min,
                                 double max)
```
  - addColorBarLegend
```
public void addColorBarLegend(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 <T extends ColorMapper> void addColorBarLegend(T colorMapper)
```
    Adds a color bar legend (LUT ramp) from a ColorMapper.
    
    Parameters:
    
    colorMapper - the class extending ColorMapper (TreeColorMapper, etc.)
  - 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.
  - getPaintScaleLegend
```
protected PaintScaleLegend getPaintScaleLegend(String colorTable,
                                               double min,
                                               double max)
```
  - getPaintScaleLegend
```
protected PaintScaleLegend getPaintScaleLegend(ColorTable colorTable,
                                               double min,
                                               double max)
```
  - addTree
```
@Deprecated
public void addTree(Tree tree)
```
    Deprecated. Use add(Tree) instead
    
    Appends a tree to the viewer using default options.
    
    Parameters:
    
    tree - the Collection of paths to be plotted
  - add
```
public void add(Tree tree)
```
    Appends a tree to the viewer using default options.
    
    Parameters:
    
    tree - the Collection of paths to be plotted
  - add
```
public void add(List<Tree> trees,
                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
  - add
```
public void add(Tree tree,
                ColorRGB color)
```
    Appends a tree to the viewer.
    
    Parameters:
    
    tree - the Collection of paths to be plotted
    
    color - the color to render the Tree
  - add
```
public void add(Tree tree,
                String color)
```
    Appends a tree to the viewer.
    
    Parameters:
    
    tree - the Collection of paths to be plotted
    
    color - a string representation of the color to render the Tree
  - add
```
public void add(Tree tree,
                String measurement,
                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.PATH_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)
  - add
```
public void add(Tree tree,
                String measurement,
                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.PATH_ORDER }TreeColorMapper.LENGTH, etc.)
    
    lut - the lookup table specifying the color mapping
  - add
```
public void add(Tree tree,
                String measurement,
                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.PATH_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)
  - getJFreeChart
```
public JFreeChart getJFreeChart()
```
    Gets the current viewer as a JFreeChart object
    
    Returns:
    
    the converted viewer
  - getChart
```
public SNTChart getChart()
```
    Gets the current viewer as a SNTChart 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(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(String title)
```
    Sets the plot display title.
    
    Parameters:
    
    title - the new title
  - getTitle
```
public String getTitle()
```
    Gets the plot display title.
    
    Returns:
    
    the current display title
  - showPlot
```
@Deprecated
public void showPlot()
```
    Deprecated. Use show() instead.
  - show
```
public void show()
```
    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(String... args)
```

Class Viewer2D

Field Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Detail

plot

Constructor Detail

Viewer2D

Viewer2D

Method Detail

addPolygon

addColorBarLegend

addColorBarLegend

addColorBarLegend

addColorBarLegend

getPaintScaleLegend

getPaintScaleLegend

addTree

add

add

add

add

add

add

add

getJFreeChart

getChart

getPlot

setDefaultColor

setPreferredSize

setTitle

getTitle

showPlot

show

setGridlinesVisible

setAxesVisible

setOutlineVisible

main