io.loader.load2D
Class SkeletonParser2D

java.lang.Object
  io.loader.shared.SkeletonParser
      io.loader.load2D.SkeletonParser2D

public class SkeletonParser2D
extends SkeletonParser

Given the path to a binary image containing the skeleton, and the path to a binary image containing the object's shape, SkeletonParser2D creates a SkeletonObject from this given input data.

Tested input image types are by now .png and .gif. Example usage:

 
 SkeletonParser parser = new SkeletonParser ("/path/to/skeleton.png", "/path/to/object.png");
 SkeletonObject object = parser.getSkeleton();
 
 

Warning: The assumption is we have unit pixels here.

Field Summary

private java.util.List<java.awt.Point>	allContourPoints list containing all contour points (outer contours as well as inner contours
private org.apache.log4j.Logger	logger logger instance
private java.lang.String	objectfilename the path to the image containing the object shape
private ij.ImagePlus	objectImage image containing the object shape
private ij.io.Opener	opener imagej opener instance, offers more possibilites than ImageIO
private java.lang.String	skeletonfilename the path to the image containing the skeleton
private ij.ImagePlus	skeletonImage image containing the skeleton

Fields inherited from class io.loader.shared.SkeletonParser

allEndnodes, allJunctionNodes, config, skeletonObject

Constructor Summary

SkeletonParser2D(java.lang.String skeletonfilename, java.lang.String objectfilename)
Constructor.

SkeletonParser2D(java.lang.String skeletonfilename, java.lang.String objectfilename, boolean flipped)

SkeletonParser2D(java.lang.String skeletonfilename, java.lang.String objectfilename, Config config)

SkeletonParser2D(java.lang.String skeletonfilename, java.lang.String objectfilename, Config config, boolean flipped)
Constructor.

Method Summary

private SkeletonNode	checkNeighborHood(java.awt.Point cp) check if a skeleton end node is in the 3x3 neighbor hood of the specified contour point.
private void	cleanJunctionNodes(java.util.List<SkeletonNode> junctionnodes) In some constellations, directly adjacent nodes are recognized as junction nodes.
private void	getContour() set the object's inner and outer contours.
protected void	getCriticalNodes() extract all critical nodes, that is, end nodes and junction nodes
protected void	getDistanceTransform() compute and set the shape's distance transform
private boolean	isNeighborOf(java.awt.Point cp, SkeletonNode n) check if the specified skeleton node is in the 3x3 neighborhood of the specified contour point.
private boolean	isSkeleton(int argb) check if the specified color code is encoding a skeleton node
private void	load(java.lang.String skeletonfilename, java.lang.String objectfilename, boolean flipped) load the skeleton image and shape image, specified by the parameters.
private void	loadObjectImage(boolean flipped) load the object image
private void	loadSkeletonImage(boolean flipped) load the skeleton image
private void	prepareImage(ij.ImagePlus objectImage) Prepare the image to make sure some conditions are fullfilled: all pixel values are 0 or 255 tell imagej that this is a binary image invert the image in case the foreground seems to be black, the background seems to be white (by now, this is estimated on the pixel in the upper left corner)
protected java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>>	sampleParts() sample all SkeletonBranches emanating from each critical node.
private void	setAllContourPoints() extract all contour points from the object's contour and save them to a list.
private void	setSize() set skeleton object's width and height, based on the input image's size.
private void	sortEndPoints() sort a list of end nodes by traversing an object's contour in clockwise direction and checking for each contour point if there is a skeleton node in the 3x3 neighborhood.

Methods inherited from class io.loader.shared.SkeletonParser

deleteUnconnectedComponents, deleteUnnecessaryBranches, extractPaths, getSkeleton, parse, preprocessGraph

Methods inherited from class java.lang.Object

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

Field Detail

allContourPoints

private java.util.List<java.awt.Point> allContourPoints

list containing all contour points (outer contours as well as inner contours

logger

private final org.apache.log4j.Logger logger

logger instance

objectfilename

private java.lang.String objectfilename

the path to the image containing the object shape

objectImage

private ij.ImagePlus objectImage

image containing the object shape

opener

private final ij.io.Opener opener

imagej opener instance, offers more possibilites than ImageIO

skeletonfilename

private java.lang.String skeletonfilename

the path to the image containing the skeleton

skeletonImage

private ij.ImagePlus skeletonImage

image containing the skeleton

Constructor Detail

SkeletonParser2D

public SkeletonParser2D(java.lang.String skeletonfilename,
                        java.lang.String objectfilename)
                 throws java.io.IOException,
                        InvalidConfigParameterException

Constructor. Create a new SkeletonParser instance, defined by the path to the shape image and the path to the skeleton image.

Both images should be binary images, with black background and white foreground.

Parameters:

skeletonfilename - the path to the binary image containing the skeleton

objectfilename - the path to the binary image containing the object.

Throws:

java.io.IOException - if one of the images was not found.

InvalidConfigParameterException

SkeletonParser2D

public SkeletonParser2D(java.lang.String skeletonfilename,
                        java.lang.String objectfilename,
                        boolean flipped)
                 throws java.io.IOException,
                        InvalidConfigParameterException

Throws:

java.io.IOException

InvalidConfigParameterException

SkeletonParser2D

public SkeletonParser2D(java.lang.String skeletonfilename,
                        java.lang.String objectfilename,
                        Config config)
                 throws java.io.IOException,
                        InvalidConfigParameterException

Throws:

java.io.IOException

InvalidConfigParameterException

SkeletonParser2D

public SkeletonParser2D(java.lang.String skeletonfilename,
                        java.lang.String objectfilename,
                        Config config,
                        boolean flipped)
                 throws java.io.IOException

Constructor. Create a new SkeletonParser instance, defined by the path to the shape image and the path to the skeleton image. If the third argument, flipped, is set to true, both the shape image and the skeleton image will be flipped horizontally before they are parsed.

Parameters:

skeletonfilename - - the path to the binary image containing the skeleton

objectfilename - - the path to the binary image containing the object.

flipped - - if true, both images will be flipped horizontally before the skeleton is parsed

Throws:

java.io.IOException - - if one if the images could not be found

Method Detail

load

private void load(java.lang.String skeletonfilename,
                  java.lang.String objectfilename,
                  boolean flipped)
           throws java.io.IOException

load the skeleton image and shape image, specified by the parameters. also set site and contour automatically

Parameters:

skeletonfilename - - path to skeleton image

objectfilename - - path to object image

flipped - - true if the image has to be flipped, false if not

Throws:

java.io.IOException - - if one of the files could not be found

checkNeighborHood

private SkeletonNode checkNeighborHood(java.awt.Point cp)

check if a skeleton end node is in the 3x3 neighbor hood of the specified contour point.

Parameters:

cp - the contour point whose neighborhood will be search for skeleton points

Returns:

the endpoint in the contour point's 3x3 neighborhood, null if there is none

getContour

private void getContour()

set the object's inner and outer contours.

getDistanceTransform

protected void getDistanceTransform()

Description copied from class: SkeletonParser

compute and set the shape's distance transform

Specified by:

getDistanceTransform in class SkeletonParser

sampleParts

protected java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>> sampleParts()
                                                                          throws InvalidSkeletonException

Description copied from class: SkeletonParser

sample all SkeletonBranches emanating from each critical node. For each critical node, a list of all emanating parts is stored. The key in the map is the critical node, the value is the list of all skeleton branches emanating from the node that is the key.

Specified by:

sampleParts in class SkeletonParser

Returns:

a map containing all skeleton branches. The key in the return map is a critical node, the value in the map is a list of all skeleton branches emanating from the node key.

Throws:

InvalidSkeletonException

getCriticalNodes

protected void getCriticalNodes()
                         throws InvalidSkeletonException

Description copied from class: SkeletonParser

extract all critical nodes, that is, end nodes and junction nodes

Specified by:

getCriticalNodes in class SkeletonParser

Throws:

InvalidSkeletonException

cleanJunctionNodes

private void cleanJunctionNodes(java.util.List<SkeletonNode> junctionnodes)
                         throws InvalidSkeletonException

In some constellations, directly adjacent nodes are recognized as junction nodes. This is information we have no use for. Thus, we now have to clean up this mess by selecting one junction node for each of these " NodeArea"s

Parameters:

junctionnodes - - list of all found junction nodes (that is, nodes with more than two neighbors)

Throws:

InvalidSkeletonException - - if the skeleton seems to be broken

isNeighborOf

private boolean isNeighborOf(java.awt.Point cp,
                             SkeletonNode n)

check if the specified skeleton node is in the 3x3 neighborhood of the specified contour point.

Parameters:

cp - the contour point

n - the skeleton node

Returns:

true if the skeleton node is in the 3x3 neighborhood of the skeleton, false if not

isSkeleton

private boolean isSkeleton(int argb)

check if the specified color code is encoding a skeleton node

Parameters:

argb -

Returns:

true if the specified color value is the skeleton color, false otherwise

loadObjectImage

private void loadObjectImage(boolean flipped)
                      throws java.io.IOException

load the object image

Parameters:

flipped -

Throws:

java.io.IOException - if the image was not found

prepareImage

private void prepareImage(ij.ImagePlus objectImage)

Prepare the image to make sure some conditions are fullfilled:

• all pixel values are 0 or 255
• tell imagej that this is a binary image
• invert the image in case the foreground seems to be black, the background seems to be white (by now, this is estimated on the pixel in the upper left corner)

Parameters:

objectImage - the image to be prepared

loadSkeletonImage

private void loadSkeletonImage(boolean flipped)
                        throws java.io.IOException

load the skeleton image

Parameters:

flipped - true if the image shall be flipped horizontally, false if not

Throws:

java.io.IOException - if the image was not found

setAllContourPoints

private void setAllContourPoints()

extract all contour points from the object's contour and save them to a list.

setSize

private void setSize()

set skeleton object's width and height, based on the input image's size.

sortEndPoints

private void sortEndPoints()

sort a list of end nodes by traversing an object's contour in clockwise direction and checking for each contour point if there is a skeleton node in the 3x3 neighborhood.