io.loader.load2D
Class SampleParts2D

java.lang.Object
  io.loader.load2D.SampleParts2D

public class SampleParts2D
extends java.lang.Object

Sample the skeleton branches emanating from one critical node (end or junction node).

Field Summary

private static org.apache.log4j.Logger

logger logger instance

Constructor Summary

SampleParts2D()

Method Summary

private static SkeletonBranch	createPart(SkeletonNode startnode, SkeletonNode endnode, java.util.List<SkeletonNode> nodesOnPart) If an end node or junction node has been reached, this function can be used to create the part between the startnode and the current node.
private static boolean	isVisited(boolean[][] visited, SkeletonNode node) Test if the speicifed skeleton node has been visited.
private static void	markAsVisited(boolean[][] visited, SkeletonNode node) mark the specified skeleton node as visited.
static java.util.List<SkeletonBranch>	samplePartsPerStartNode(SkeletonNode startnode, ij.ImagePlus skeletonImage, java.util.List<SkeletonNode> endnodes, java.util.List<SkeletonNode> junctionnodes) Sample all skeleton branches emanating from the specified startnode.

Methods inherited from class java.lang.Object

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

Field Detail

logger

private static org.apache.log4j.Logger logger

logger instance

Constructor Detail

SampleParts2D

public SampleParts2D()

Method Detail

markAsVisited

private static void markAsVisited(boolean[][] visited,
                                  SkeletonNode node)

mark the specified skeleton node as visited.

Parameters:

visited - the 3D array to mark visited nodes in

node - the node to be marked as visited

isVisited

private static boolean isVisited(boolean[][] visited,
                                 SkeletonNode node)

Test if the speicifed skeleton node has been visited.

Parameters:

visited - the 3D array where information is saved about visited nodes

node - the node to be tested

Returns:

true if the nodes was already visited, false if not

samplePartsPerStartNode

public static java.util.List<SkeletonBranch> samplePartsPerStartNode(SkeletonNode startnode,
                                                                     ij.ImagePlus skeletonImage,
                                                                     java.util.List<SkeletonNode> endnodes,
                                                                     java.util.List<SkeletonNode> junctionnodes)
                                                              throws InvalidSkeletonException

Sample all skeleton branches emanating from the specified startnode.

Parameters:

startnode - the node for which the emanating parts will be sampled

skeletonImage - the skeleton image

endnodes - a list of all endnodes in the skeleton image

junctionnodes - a list of all junction nodes in the skeleton image

Returns:

a list of all skeleton branches emanating from the specified start node

Throws:

InvalidSkeletonException - if the skeleton seems broken

createPart

private static SkeletonBranch createPart(SkeletonNode startnode,
                                         SkeletonNode endnode,
                                         java.util.List<SkeletonNode> nodesOnPart)

If an end node or junction node has been reached, this function can be used to create the part between the startnode and the current node. A copy of the list of all visited nodes is set as visited nodes in the part, and the original (temporary) list is cleared.

Parameters:

startnode - - the startnode of the new part

endnode - - the endnode of the new part

nodesOnPart - - all nodes lieing on this part, in the order of their occurance. Warning: this list cleared in the function.

Returns:

a skeleton part, starting at startnode and ending at end node, connected by the list of skeleton nodes passed as nodesOnPath