Field Detail

• BRANCH_LENGTH

  public static final String BRANCH_LENGTH

  Flag for "Branch length" analysis.

  See Also:

  Constant Field Values

• BRANCH_ORDER

  public static final String BRANCH_ORDER

  Flag for "Branch order" statistics.

  See Also:

  Constant Field Values

• RADIUS

  public static final String RADIUS

  Flag for "Node radius" statistics.

  See Also:

  Constant Field Values

• X_COORDINATES

  public static final String X_COORDINATES

  Flag for "X coordinates" statistics.

  See Also:

  Constant Field Values

• Y_COORDINATES

  public static final String Y_COORDINATES

  Flag for "Y coordinates" statistics.

  See Also:

  Constant Field Values

• Z_COORDINATES

  public static final String Z_COORDINATES

  Flag for "Z coordinates" statistics.

  See Also:

  Constant Field Values

• VALUES

  public static final String VALUES

  Flag for statistics on node "Node intensity values"

  See Also:

  Constant Field Values

Constructor Detail

• NodeColorMapper

  public NodeColorMapper(NodeStatistics<?> nodeStatistics,
                         Context context)

  Instantiates the mapper.

  Parameters:

  nodeStatistics - the NodeStatistics instance holding the nodes to be mapped

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

• NodeColorMapper

  public NodeColorMapper(NodeStatistics<?> nodeStatistics)

  Instantiates the mapper. 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.

  Parameters:

  nodeStatistics - the NodeStatistics instance holding the nodes 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)

  Maps nodes after the specified measurement. Mapping bounds are automatically determined.

  Overrides:

  map in class ColorMapper

  Parameters:

  measurement - the measurement (X_COORDINATES, Y_COORDINATES, etc.)

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

• map

  public void map(String measurement,
                  String lut)

  Maps nodes after the specified measurement. Mapping bounds are automatically determined.

  Parameters:

  measurement - the measurement (X_COORDINATES, Y_COORDINATES, etc.)

  lut - the lookup table specifying the color mapping. Null not allowed.

• getNodes

  public Collection<? extends SNTPoint> getNodes()

• getColorTable

  public ColorTable getColorTable(String lut)

• getAvailableLuts

  public Set<String> getAvailableLuts()

  Gets the available LUTs.

  Returns:

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

• setMinMax

  public void setMinMax(double min,
                        double max)

  Description copied from class: ColorMapper
  Sets the LUT mapping bounds.

  Overrides:

  setMinMax in class ColorMapper

  Parameters:

  min - the mapping lower bound (i.e., the highest measurement value for the LUT scale). It is automatically calculated (the default) when set to Double.NaN

  max - the mapping upper bound (i.e., the highest measurement value for the LUT scale).It is automatically calculated (the default) when set to Double.NaN.

• getMinMax

  public double[] getMinMax()

  Description copied from class: ColorMapper
  Returns the mapping bounds

  Overrides:

  getMinMax in class ColorMapper

  Returns:

  a two-element array with current {minimum, maximum} mapping bounds

• getColorTable

  public ColorTable getColorTable()

  Overrides:

  getColorTable in class ColorMapper

• main

  public static void main(String... args)