io.loader.load3D
Class SkeletonParser3D

java.lang.Object
  io.loader.shared.SkeletonParser
      io.loader.load3D.SkeletonParser3D

public class SkeletonParser3D
extends SkeletonParser

Load a skeleton from the input data.

To load one 3D skeleton, 4 input files are needed:

• The raw binary data containing the shape's volume, where the shape is marked by a value bigger than 0, the background is labeled with 0.
• An info file for the raw data, containing meta information about the shape's volume, for example:

                          
                          Width 123
                          Height 95
                          Depth 379
                          WidthDim 1.46875
                          HeightDim 1.46875
                          DepthDim 1.00134
                          MinVal ^@
                          MaxVal ^@
                          BitsUsed 16
                          
   

• The raw data containing the shape's skeleton, where the skeleton is marked by a value bigger than 0, the background is labeled with 0.
• An info file for the skeleton raw data, containing meta information about the shape's skeleton, as shown above.

Field Summary

private double	depthDim the voxelsÄ z dimension
private double	heightDim the voxels' y dimension
private org.apache.log4j.Logger	logger the logger instance
private int[][][]	segmentationcube the cube containing the volume information
private java.lang.String	shapeinfoPath the path to the volume meta information file
private java.lang.String	shapePath the path to the volume data
private int[][][]	thinningcube the cube containing the skeleton information
private java.lang.String	thinninginfoPath the path tp the skeleton meta information file
private java.lang.String	thinningPath the path to the skeleton data
private double	widthDim the voxels' x dimension

Fields inherited from class io.loader.shared.SkeletonParser

allEndnodes, allJunctionNodes, config, skeletonObject

Constructor Summary

SkeletonParser3D(java.lang.String thinningPath, java.lang.String thinninginfoPath, java.lang.String shapePath, java.lang.String shapeinfoPath, Config config)
Constructor.

Method Summary

private void	cleanJunctionNodes(java.util.List<SkeletonNode> junctionnodes, int[][][] thinningcube) Clean the list of junction nodes.
protected void	getCriticalNodes() extract all critical nodes, that is, end nodes and junction nodes
void	getDistanceTransform() compute and set the shape's distance transform
int[][][]	getSegmentationcube() Get the 3D cube containing the volume data (0 = background, 255 = foreground)
int[][][]	getThinningCube() Read the thinning cube.
private int[][][]	readBin(java.lang.String file, int width, int height, int depth) read raw data and save it to 1D-array
private void	readThinningInfo() read thinning info file
protected java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>>	sampleParts() sample all SkeletonBranches emanating from each critical node.
void	setSegmentationcube(int[][][] segmentationcube) Set the volume data.

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

widthDim

private double widthDim

the voxels' x dimension

heightDim

private double heightDim

the voxels' y dimension

depthDim

private double depthDim

the voxelsÄ z dimension

thinningPath

private final java.lang.String thinningPath

the path to the skeleton data

thinninginfoPath

private final java.lang.String thinninginfoPath

the path tp the skeleton meta information file

shapePath

private final java.lang.String shapePath

the path to the volume data

shapeinfoPath

private final java.lang.String shapeinfoPath

the path to the volume meta information file

thinningcube

private final int[][][] thinningcube

the cube containing the skeleton information

segmentationcube

private int[][][] segmentationcube

the cube containing the volume information

logger

private final org.apache.log4j.Logger logger

the logger instance

Constructor Detail

SkeletonParser3D

public SkeletonParser3D(java.lang.String thinningPath,
                        java.lang.String thinninginfoPath,
                        java.lang.String shapePath,
                        java.lang.String shapeinfoPath,
                        Config config)
                 throws java.io.IOException

Constructor.

Parameters:

thinningPath - - path to the skeleton data file

thinninginfoPath - - path to the skeleton meta data file (like width, height)

shapePath - - path to the shape data file

shapeinfoPath - - path to the meta data shape file (like width, height)

Throws:

java.io.IOException

Method Detail

getDistanceTransform

public void getDistanceTransform()
                          throws java.io.IOException

Description copied from class: SkeletonParser

compute and set the shape's distance transform

Specified by:

getDistanceTransform in class SkeletonParser

Throws:

java.io.IOException - if the shape file could not be found

getSegmentationcube

public int[][][] getSegmentationcube()
                              throws java.io.IOException

Get the 3D cube containing the volume data (0 = background, 255 = foreground)

Returns:

the segmentationcube the volume data

Throws:

java.io.IOException - if the shape path could not be found

setSegmentationcube

public void setSegmentationcube(int[][][] segmentationcube)

Set the volume data.

Parameters:

segmentationcube - the segmentationcube to set

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

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

cleanJunctionNodes

private void cleanJunctionNodes(java.util.List<SkeletonNode> junctionnodes,
                                int[][][] thinningcube)
                         throws InvalidSkeletonException

Clean the list of junction nodes.

In some constellations, it might happen that "wrong" junction nodes are recognized as juncion nodes, such that multiple junction nodes are directly adjacent. This is information we have no use for, so one of the adjacent junction nodes has to be selected as "real" junction nodes. In this function, the junction node with the most surface neighbors is selected as the real junction node.

The class member SkeletonParser.allJunctionNodes is manipulated directly, so no return type is needed.

Parameters:

junctionnodes - - list of all junction nodes - probably containing "wrong" junction nodes

thinningcube - - 3D array containing skeleton information

Throws:

InvalidSkeletonException - - if skeleton seems to be broken

getThinningCube

public int[][][] getThinningCube()
                          throws java.io.IOException

Read the thinning cube.

Returns:

1d-array, containing the data read in the thinning file specified by thinningPath

Throws:

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

readBin

private int[][][] readBin(java.lang.String file,
                          int width,
                          int height,
                          int depth)
                   throws java.io.IOException

read raw data and save it to 1D-array

Parameters:

file - - path to file

Returns:

1D array containing all entries in the specified file

Throws:

java.io.IOException - - if file could not be found

readThinningInfo

private void readThinningInfo()
                       throws java.io.IOException

read thinning info file

Throws:

java.io.IOException