Field Detail

• FUNC_UNKNOWN

  protected static final int FUNC_UNKNOWN

  See Also:

  Constant Field Values

• FUNC_0_GEODESIC

  protected static final int FUNC_0_GEODESIC

  The geodesic (i.e., "path") distance from a node to the tree root

  See Also:

  Constant Field Values

• FUNC_1_RADIAL

  protected static final int FUNC_1_RADIAL

  The euclidean (i.e., "straight line") distance between a node and the tree root

  See Also:

  Constant Field Values

• FUNC_2_CENTRIFUGAL

  protected static final int FUNC_2_CENTRIFUGAL

  The centrifugal branch order of a node

  See Also:

  Constant Field Values

• FUNC_3_PATH_ORDER

  protected static final int FUNC_3_PATH_ORDER

  The Path order of a node.

  See Also:

  Path.getOrder(), Constant Field Values

• FUNC_4_X

  protected static final int FUNC_4_X

  The X coordinate of a node

  See Also:

  Constant Field Values

• FUNC_5_Y

  protected static final int FUNC_5_Y

  The Y coordinate of a node

  See Also:

  Constant Field Values

• FUNC_6_Z

  protected static final int FUNC_6_Z

  The Z coordinate of a node

  See Also:

  Constant Field Values

Constructor Detail

• PersistenceAnalyzer

  public PersistenceAnalyzer(Tree tree)

Method Detail

• getDescriptors

  public static List<String> getDescriptors()

  Gets a list of supported descriptor functions.

  Returns:

  the list of available descriptors.

• getDiagram

  public ArrayList<ArrayList<Double>> getDiagram(String descriptor)
                                          throws sc.fiji.snt.analysis.UnknownMetricException,
                                                 IllegalArgumentException

  Gets the persistence diagram.

  Parameters:

  descriptor - A descriptor for the filter function as per getDescriptors() (case insensitive), such as radial, geodesic, centrifugal (reverse Strahler), etc.

  Returns:

  the persistence diagram

  Throws:

  UnknownMetricException - If descriptor is not valid

  IllegalArgumentException - If the tree's graph could not be obtained

• getBarcode

  public ArrayList<Double> getBarcode(String descriptor)
                               throws sc.fiji.snt.analysis.UnknownMetricException,
                                      IllegalArgumentException

  Gets the 'barcode' for the specified filter function.

  Parameters:

  descriptor - A descriptor for the filter function as per getDescriptors() (case insensitive), such as radial, geodesic, centrifugal (reverse Strahler), etc.

  Returns:

  the barcode

  Throws:

  UnknownMetricException - If descriptor is not valid

  IllegalArgumentException - If the tree's graph could not be obtained

• getDiagramNodes

  public ArrayList<ArrayList<SWCPoint>> getDiagramNodes(String descriptor)

  Gets the persistence diagram nodes.

  Parameters:

  descriptor - A descriptor for the filter function as per getDescriptors() (case insensitive), such as radial, geodesic, centrifugal (reverse Strahler), etc.

  Returns:

  the persistence diagram nodes.

  Throws:

  UnknownMetricException - If descriptor is not valid.

  IllegalArgumentException - If the tree's graph could not be obtained

• getLandscape

  public double[] getLandscape(String descriptor,
                               int numLandscapes,
                               int resolution)

  Gets the persistence landscape as an N-dimensional vector, where N == numLandscapes x resolution. For an overview of persistence landscapes, see Bubenik, P.. (2015). Statistical topological data analysis using persistence landscapes. Journal of Machine Learning Research. 16. 77-102.

  Parameters:

  descriptor - A descriptor for the filter function as per getDescriptors() (case insensitive), such as radial, geodesic, centrifugal (reverse Strahler), etc.

  numLandscapes - the number of piecewise-linear functions to output.

  resolution - the number of samples for all piecewise-linear functions.

• main

  public static void main(String[] args)