Skeletonize3D_ (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.skeletonize3D.Skeletonize3D_

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter
```
public class Skeletonize3D_
extends Object
implements ij.plugin.filter.PlugInFilter
```
Main class. This class is a plugin for the ImageJ interface for 2D and 3D thinning (skeletonization) of binary images (2D/3D).
This work is an implementation by Ignacio Arganda-Carreras of the 3D thinning algorithm from Lee et al. "Building skeleton models via 3-D medial surface/axis thinning algorithms. Computer Vision, Graphics, and Image Processing, 56(6):462–478, 1994." Based on the ITK version from Hanno Homann http://hdl.handle.net/1926/1292
More information at Skeletonize3D homepage: http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:skeletonize3d:start

Version:

1.0 11/19/2008

Author:

Ignacio Arganda-Carreras (iargandacarreras at gmail.com)

Field Summary
- Fields inherited from interface ij.plugin.filter.PlugInFilter
  CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, NO_UNDO_RESET, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors
Constructor and Description

Skeletonize3D_()

Constructors
Constructor and Description
`Skeletonize3D_()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`computeThinImage(ij.ImageStack outputImage)` Post processing for computing thinning.
`void`	`fillnumOfPointsLUT(int[] LUT)` Fill number of points in octant LUT
`byte[]`	`getNeighborhood(ij.ImageStack image, int x, int y, int z)` Get neighborhood of a pixel in a 3D image (0 border conditions)
`int`	`getThinningIterations()`
`char`	`indexOctantNEB(byte[] neighbors)`
`char`	`indexOctantNEU(byte[] neighbors)`
`char`	`indexOctantNWB(byte[] neighbors)`
`char`	`indexOctantNWU(byte[] neighbors)`
`char`	`indexOctantSEU(byte[] neighbors)`
`char`	`indexOctantSWB(byte[] neighbors)`
`char`	`indexOctantSWU(byte[] neighbors)`
`char`	`indextOctantSEB(byte[] neighbors)`
`void`	`prepareData(ij.ImageStack outputImage)` Prepare data for computation.
`void`	`run(ij.process.ImageProcessor ip)` Process the image.
`int`	`setup(String arg, ij.ImagePlus imp)` This method is called once when the filter is loaded.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - Skeletonize3D_
```
public Skeletonize3D_()
```
- Method Detail
  - setup
```
public int setup(String arg,
                 ij.ImagePlus imp)
```
    This method is called once when the filter is loaded.
    
    Specified by:
    
    setup in interface ij.plugin.filter.PlugInFilter
    
    Parameters:
    
    arg - argument specified for this plugin
    
    imp - currently active image
    
    Returns:
    
    flag word that specifies the filters capabilities
  - run
```
public void run(ij.process.ImageProcessor ip)
```
    Process the image.
    
    Specified by:
    
    run in interface ij.plugin.filter.PlugInFilter
    
    See Also:
    
    PlugInFilter.run(ij.process.ImageProcessor)
  - prepareData
```
public void prepareData(ij.ImageStack outputImage)
```
    Prepare data for computation. Copy the input image to the output image, changing from the input type to the output type.
    
    Parameters:
    
    outputImage - output image stack
  - computeThinImage
```
public void computeThinImage(ij.ImageStack outputImage)
```
    Post processing for computing thinning.
    
    Parameters:
    
    outputImage - output image stack
  - getNeighborhood
```
public byte[] getNeighborhood(ij.ImageStack image,
                              int x,
                              int y,
                              int z)
```
    Get neighborhood of a pixel in a 3D image (0 border conditions)
    
    Parameters:
    
    image - 3D image (ImageStack)
    
    x - x- coordinate
    
    y - y- coordinate
    
    z - z- coordinate (in image stacks the indexes start at 1)
    
    Returns:
    
    corresponding 27-pixels neighborhood (0 if out of image)
  - fillnumOfPointsLUT
```
public void fillnumOfPointsLUT(int[] LUT)
```
    Fill number of points in octant LUT
    
    Parameters:
    
    LUT - number of points in octant LUT
  - indexOctantNEB
```
public char indexOctantNEB(byte[] neighbors)
```
  - indexOctantNWB
```
public char indexOctantNWB(byte[] neighbors)
```
  - indextOctantSEB
```
public char indextOctantSEB(byte[] neighbors)
```
  - indexOctantSWB
```
public char indexOctantSWB(byte[] neighbors)
```
  - indexOctantNEU
```
public char indexOctantNEU(byte[] neighbors)
```
  - indexOctantNWU
```
public char indexOctantNWU(byte[] neighbors)
```
  - indexOctantSEU
```
public char indexOctantSEU(byte[] neighbors)
```
  - indexOctantSWU
```
public char indexOctantSWU(byte[] neighbors)
```
  - getThinningIterations
```
public int getThinningIterations()
```
    Returns:
    
    Number of iterations the thinning algorithm completed on the last run If 0 is returned, then the plugin hasn't been run yet

Class Skeletonize3D_

Field Summary

Fields inherited from interface ij.plugin.filter.PlugInFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Skeletonize3D_

Method Detail

setup

run

prepareData

computeThinImage

getNeighborhood

fillnumOfPointsLUT

indexOctantNEB

indexOctantNWB

indextOctantSEB

indexOctantSWB

indexOctantNEU

indexOctantNWU

indexOctantSEU

indexOctantSWU

getThinningIterations