AnalyzeSkeleton_ (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

All Implemented Interfaces:

DialogListener, ij.plugin.filter.PlugInFilter
```
public class AnalyzeSkeleton_
extends Object
implements ij.plugin.filter.PlugInFilter, DialogListener
```
Main class of the ImageJ/Fiji plugin for skeleton analysis. This class is a plugin for the ImageJ and Fiji interfaces for analyzing 2D/3D skeleton images.
For more detailed information, visit the AnalyzeSkeleton home page: http://fiji.sc/AnalyzeSkeleton

Author:

Ignacio Arganda-Carreras

Field Summary

Fields
Modifier and Type	Field and Description
`static boolean`	`calculateShortestPath` calculate largest shortest path option
`static boolean`	`displaySkeletons` flag to output the labeled skeletons in a new image
`static byte`	`END_POINT` end point flag
`static byte`	`JUNCTION` junction flag
`static int`	`LOWEST_INTENSITY_BRANCH` lowest intensity branch pruning mode index
`static int`	`LOWEST_INTENSITY_VOXEL` lowest pixel intensity pruning mode index
`static int`	`NONE` no pruning mode index
`static boolean`	`protectRoi` protective-ROI option (branches inside ROI are spared from pruning)
`static String[]`	`pruneCyclesModes` prune cycle options
`static boolean`	`pruneEnds` dead-end pruning option
`static int`	`pruneIndex` prune cycle options index
`static int`	`SHORTEST_BRANCH` shortest branch pruning mode index
`static byte`	`SHORTEST_PATH` shortest path flag
`protected boolean`	`silent` silent run flag, to distinguish between GUI and plugin calls
`static byte`	`SLAB` slab flag
`static boolean`	`verbose` boolean flag to display extra information in result tables

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

AnalyzeSkeleton_()

Constructors
Constructor and Description
`AnalyzeSkeleton_()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected SkeletonResult`	`assembleResults()` Returns the analysis results in a SkeletonResult object.
`double`	`calculateDistance(Point point1, Point point2)` Calculate Euclidean distance between two points in 3D.
`boolean`	`dialogItemChanged(GenericDialog gd, AWTEvent e)` Disables dialog components that are irrelevant to GUI-based analysis.
`Vertex`	`findPointVertex(Vertex[] vertex, Point p)` Find vertex in an array given a specific vertex point.
`static double`	`getAverageNeighborhoodValue(ij.ImageStack image, Point p, int x_offset, int y_offset, int z_offset)` Get average neighborhood pixel value of a given point.
`ArrayList<Point>`	`getEndPoints()` Get the list of endpoints in the skeleton image.
`ArrayList<Point>[]`	`getEndPointsTree()` Get the list of endpoints in the skeleton image per tree.
`Graph[]`	`getGraphs()` Get the graphs of the current skeletons
`ij.ImageStack`	`getLabeledSkeletons()` Get the stack containing all the trees labeld with their corresponding skeleton id.
`static byte[]`	`getNeighborhood(ij.ImageStack image, Point p, int x_offset, int y_offset, int z_offset)` Get neighborhood of a pixel in a 3D image (0 border conditions).
`static byte`	`getPixel(ij.ImageStack image, int x, int y, int z)` Get pixel in 3D image (0 border conditions)
`ij.ImageStack`	`getResultImage(boolean longestShortestPath)` Returns one of the two result images in an ImageStack object.
`ArrayList<Point>[]`	`getShortestPathPoints()` Get the list of points (including junctions and end points) of the largest shortest paths in the skeleton image (one per tree).
`void`	`processSkeleton(ij.ImageStack inputImage2)` Process skeleton: tag image, mark trees and visit.
`SkeletonResult`	`run()` A simpler standalone running method, for analysis without pruning or showing images.
`void`	`run(ij.process.ImageProcessor ip)` Process the image: tag skeleton and show results.
`SkeletonResult`	`run(int pruneIndex, boolean pruneEnds, boolean shortPath, ij.ImagePlus origIP, boolean silent, boolean verbose)` This method is intended for non-interactively using this plugin.
`SkeletonResult`	`run(int pruneIndex, boolean pruneEnds, boolean shortPath, ij.ImagePlus origIP, boolean silent, boolean verbose, Roi roi)` This method is intended for non-interactively using this plugin.
`SkeletonResult`	`run(int pruneIndex, double thresholdLength, boolean shortPath, ij.ImagePlus origIP, boolean silent, boolean verbose)` This method is intended for non-interactively using this plugin.
`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

- Field Detail
  - END_POINT
```
public static byte END_POINT
```
    end point flag
  - JUNCTION
```
public static byte JUNCTION
```
    junction flag
  - SLAB
```
public static byte SLAB
```
    slab flag
  - SHORTEST_PATH
```
public static byte SHORTEST_PATH
```
    shortest path flag
  - pruneEnds
```
public static boolean pruneEnds
```
    dead-end pruning option
  - protectRoi
```
public static boolean protectRoi
```
    protective-ROI option (branches inside ROI are spared from pruning)
  - calculateShortestPath
```
public static boolean calculateShortestPath
```
    calculate largest shortest path option
  - pruneCyclesModes
```
public static final String[] pruneCyclesModes
```
    prune cycle options
  - NONE
```
public static final int NONE
```
    no pruning mode index
    
    See Also:
    
    Constant Field Values
  - SHORTEST_BRANCH
```
public static final int SHORTEST_BRANCH
```
    shortest branch pruning mode index
    
    See Also:
    
    Constant Field Values
  - LOWEST_INTENSITY_VOXEL
```
public static final int LOWEST_INTENSITY_VOXEL
```
    lowest pixel intensity pruning mode index
    
    See Also:
    
    Constant Field Values
  - LOWEST_INTENSITY_BRANCH
```
public static final int LOWEST_INTENSITY_BRANCH
```
    lowest intensity branch pruning mode index
    
    See Also:
    
    Constant Field Values
  - pruneIndex
```
public static int pruneIndex
```
    prune cycle options index
  - verbose
```
public static boolean verbose
```
    boolean flag to display extra information in result tables
  - silent
```
protected boolean silent
```
    silent run flag, to distinguish between GUI and plugin calls
  - displaySkeletons
```
public static boolean displaySkeletons
```
    flag to output the labeled skeletons in a new image
- Constructor Detail
  - AnalyzeSkeleton_
```
public AnalyzeSkeleton_()
```
- 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: tag skeleton and show results.
    
    Specified by:
    
    run in interface ij.plugin.filter.PlugInFilter
    
    See Also:
    
    PlugInFilter.run(ij.process.ImageProcessor)
  - dialogItemChanged
```
public boolean dialogItemChanged(GenericDialog gd,
                                 AWTEvent e)
```
    Disables dialog components that are irrelevant to GUI-based analysis.
    
    Specified by:
    
    dialogItemChanged in interface DialogListener
  - run
```
public SkeletonResult run(int pruneIndex,
                          boolean pruneEnds,
                          boolean shortPath,
                          ij.ImagePlus origIP,
                          boolean silent,
                          boolean verbose)
```
    This method is intended for non-interactively using this plugin.
    
    Parameters:
    
    pruneIndex - The pruneIndex, as asked by the initial gui dialog.
    
    pruneEnds - flag to prune end-point-ending branches
    
    shortPath - flag to calculate the longest shortest path
    
    origIP - original grayscale input image (for lowest pixel intensity pruning mode)
    
    silent -
    
    verbose - flag to display running information
  - run
```
public SkeletonResult run(int pruneIndex,
                          boolean pruneEnds,
                          boolean shortPath,
                          ij.ImagePlus origIP,
                          boolean silent,
                          boolean verbose,
                          Roi roi)
```
    This method is intended for non-interactively using this plugin.
    
    Parameters:
    
    pruneIndex - The pruneIndex, as asked by the initial gui dialog.
    
    pruneEnds - flag to prune end-point-ending branches
    
    shortPath - flag to calculate the longest shortest path
    
    origIP - original grayscale input image (for lowest pixel intensity pruning mode)
    
    silent -
    
    verbose - flag to display running information
    
    roi - points inside this region are spared from elimination when pruning end branches. ROI can be associated to a single image in the stack or all images as per ij.gui.Roi.getPosition()
  - run
```
public SkeletonResult run(int pruneIndex,
                          double thresholdLength,
                          boolean shortPath,
                          ij.ImagePlus origIP,
                          boolean silent,
                          boolean verbose)
```
    This method is intended for non-interactively using this plugin.
    
    Parameters:
    
    pruneIndex - The pruneIndex, as asked by the initial gui dialog.
    
    thresholdLength - maximum length of the branches to prune (all branches below that value are removed)
    
    shortPath - flag to calculate the longest shortest path
    
    origIP - original input image
    
    silent -
    
    verbose - flag to display running information
  - getGraphs
```
public Graph[] getGraphs()
```
    Get the graphs of the current skeletons
    
    Returns:
    
    array of graphs (one per tree/skeleton)
  - getShortestPathPoints
```
public ArrayList<Point>[] getShortestPathPoints()
```
    Get the list of points (including junctions and end points) of the largest shortest paths in the skeleton image (one per tree).
    
    Returns:
    
    array with the lists of points of the shortest paths
  - getEndPointsTree
```
public ArrayList<Point>[] getEndPointsTree()
```
    Get the list of endpoints in the skeleton image per tree.
    
    Returns:
    
    array with the lists of endpoints
  - getEndPoints
```
public ArrayList<Point> getEndPoints()
```
    Get the list of endpoints in the skeleton image.
    
    Returns:
    
    array with the endpoints
  - run
```
public SkeletonResult run()
```
    A simpler standalone running method, for analysis without pruning or showing images.
    This one just calls run(AnalyzeSkeleton_.NONE, false, null, true, false)
  - processSkeleton
```
public void processSkeleton(ij.ImageStack inputImage2)
```
    Process skeleton: tag image, mark trees and visit.
    
    Parameters:
    
    inputImage2 - input skeleton image to process
  - getResultImage
```
public ij.ImageStack getResultImage(boolean longestShortestPath)
```
    Returns one of the two result images in an ImageStack object.
    
    Parameters:
    
    longestShortestPath - Get the tagged longest shortest paths instead of the standard tagged image
    
    Returns:
    
    The results image with a tagged skeleton
  - assembleResults
```
protected SkeletonResult assembleResults()
```
    Returns the analysis results in a SkeletonResult object.
    
    Returns:
    
    The results of the skeleton analysis.
  - findPointVertex
```
public Vertex findPointVertex(Vertex[] vertex,
                              Point p)
```
    Find vertex in an array given a specific vertex point.
    
    Parameters:
    
    vertex - array of search
    
    p - vertex point
    
    Returns:
    
    vertex containing that point
  - calculateDistance
```
public double calculateDistance(Point point1,
                                Point point2)
```
    Calculate Euclidean distance between two points in 3D.
    
    Parameters:
    
    point1 - first point coordinates
    
    point2 - second point coordinates
    
    Returns:
    
    distance (in the corresponding units)
  - getAverageNeighborhoodValue
```
public static double getAverageNeighborhoodValue(ij.ImageStack image,
                                                 Point p,
                                                 int x_offset,
                                                 int y_offset,
                                                 int z_offset)
```
    Get average neighborhood pixel value of a given point.
    
    Parameters:
    
    image - input image
    
    p - image coordinates
    
    x_offset - x- neighborhood offset
    
    y_offset - y- neighborhood offset
    
    z_offset - z- neighborhood offset
    
    Returns:
    
    average neighborhood pixel value
  - getNeighborhood
```
public static byte[] getNeighborhood(ij.ImageStack image,
                                     Point p,
                                     int x_offset,
                                     int y_offset,
                                     int z_offset)
```
    Get neighborhood of a pixel in a 3D image (0 border conditions).
    
    Parameters:
    
    image - 3D image (ImageStack)
    
    p - point coordinates
    
    x_offset - x- neighborhood offset
    
    y_offset - y- neighborhood offset
    
    z_offset - z- neighborhood offset
    
    Returns:
    
    corresponding neighborhood (0 if out of image)
  - getPixel
```
public static byte getPixel(ij.ImageStack image,
                            int x,
                            int y,
                            int z)
```
    Get pixel in 3D image (0 border conditions)
    
    Parameters:
    
    image - 3D image
    
    x - x- coordinate
    
    y - y- coordinate
    
    z - z- coordinate (in image stacks the indexes start at 1)
    
    Returns:
    
    corresponding pixel (0 if out of image)
  - getLabeledSkeletons
```
public ij.ImageStack getLabeledSkeletons()
```
    Get the stack containing all the trees labeld with their corresponding skeleton id.
    
    Returns:
    
    labeled-skeleton image stack

Class AnalyzeSkeleton_

Field Summary

Fields inherited from interface ij.plugin.filter.PlugInFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

END_POINT

JUNCTION

SLAB

SHORTEST_PATH

pruneEnds

protectRoi

calculateShortestPath

pruneCyclesModes

NONE

SHORTEST_BRANCH

LOWEST_INTENSITY_VOXEL

LOWEST_INTENSITY_BRANCH

pruneIndex

verbose

silent

displaySkeletons

Constructor Detail

AnalyzeSkeleton_

Method Detail

setup

run

dialogItemChanged

run

run

run

getGraphs

getShortestPathPoints

getEndPointsTree

getEndPoints

run

processSkeleton

getResultImage

assembleResults

findPointVertex

calculateDistance

getAverageNeighborhoodValue

getNeighborhood

getPixel

getLabeledSkeletons