SkeletonConverter (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.analysis.SkeletonConverter

```
public class SkeletonConverter
extends Object
```
Class for generation of Trees from a skeletonized ImagePlus.

Author:

Cameron Arshadi, Tiago Ferreira

See Also:

Skeletonize3D_, AnalyzeSkeleton_

Constructor Summary

Constructors
Constructor and Description

SkeletonConverter(ij.ImagePlus imagePlus)

SkeletonConverter(ij.ImagePlus imagePlus, boolean skeletonize)

Constructors
Constructor and Description
`SkeletonConverter(ij.ImagePlus imagePlus)`
`SkeletonConverter(ij.ImagePlus imagePlus, boolean skeletonize)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`List<DirectedWeightedGraph>`	`getGraphs()` Generates a list of `DirectedWeightedGraph`s from the skeleton image.
`List<Tree>`	`getTrees()` Generates a list of `Tree`s from the skeleton image.
`static void`	`main(String[] args)`
`void`	`setConnectComponents(boolean connectComponents)` Whether to merge broken components in the skeleton result
`void`	`setLengthThreshold(double lengthThreshold)` The minimum component length necessary to avoid pruning.
`void`	`setMaxConnectDist(double maxConnectDist)` The maximum allowable distance between nearest neighbors to be considered for a merge
`void`	`setOrigIP(ij.ImagePlus origIP)` Sets the original `ImagePlus` to be used during voxel-based loop pruning.
`void`	`setPruneByLength(boolean pruneByLength)` Sets whether or not to prune components below a threshold length from the result.
`void`	`setPruneEnds(boolean pruneEnds)` Sets whether or not to prune branches which end in end-points from the result.
`void`	`setPruneMode(int pruneMode)` Sets the loop pruning strategy.
`void`	`setShortestPath(boolean shortestPath)` Sets whether or not to calculate the longest shortest-path in the skeleton result.
`void`	`setSilent(boolean silent)` Setting this to false will display both the tagged skeleton image and the shortest path image (if the shortest path calculation is enabled).
`void`	`setVerbose(boolean verbose)`
`static void`	`skeletonize(ij.ImagePlus imp)` Convenience method to skeletonize an 8-bit image using `Skeletonize3D_`.

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

- Constructor Detail
  - SkeletonConverter
```
public SkeletonConverter(ij.ImagePlus imagePlus)
```
    Parameters:
    
    imagePlus - The image to be parsed. It is expected to be a topological skeleton (non-zero foreground) (conversion will be nonsensical otherwise).
  - SkeletonConverter
```
public SkeletonConverter(ij.ImagePlus imagePlus,
                         boolean skeletonize)
                  throws IllegalArgumentException
```
    Parameters:
    
    imagePlus - The image to be parsed. It is expected to be binary (non-zero foreground).
    
    skeletonize - If true, image will be skeletonized using Skeletonize3D_ _in place_ prior to the analysis. Conversion will be nonsensical if false and imagePlus is not a topological skeleton
    
    Throws:
    
    IllegalArgumentException - if skeletonize is true and imagePlus is not binary.
- Method Detail
  - skeletonize
```
public static void skeletonize(ij.ImagePlus imp)
```
    Convenience method to skeletonize an 8-bit image using Skeletonize3D_.
    
    Parameters:
    
    imp - The 8-bit image to be skeletonized. All non-zero values are considered to be foreground.
  - getTrees
```
public List<Tree> getTrees()
```
    Generates a list of Trees from the skeleton image. Each Tree corresponds to one connected component of the graph returned by SkeletonResult.getGraph().
    
    Returns:
    
    the skeleton tree list
  - getGraphs
```
public List<DirectedWeightedGraph> getGraphs()
```
    Generates a list of DirectedWeightedGraphs from the skeleton image. Each graph corresponds to one connected component of the graph returned by SkeletonResult.getGraph().
    
    Returns:
    
    the skeleton graph list
  - setOrigIP
```
public void setOrigIP(ij.ImagePlus origIP)
```
    Sets the original ImagePlus to be used during voxel-based loop pruning. See AnalyzeSkeleton documentation
    
    Parameters:
    
    origIP - the original ImagePlus
    
    See Also:
    
    AnalyzeSkeleton_.run(int, boolean, boolean, ImagePlus, boolean, boolean)
  - setPruneMode
```
public void setPruneMode(int pruneMode)
```
    Sets the loop pruning strategy. See AnalyzeSkeleton documentation
    
    Parameters:
    
    pruneMode - the loop prune strategy, e.g., AnalyzeSkeleton_.SHORTEST_BRANCH, AnalyzeSkeleton_.LOWEST_INTENSITY_BRANCH or AnalyzeSkeleton_.LOWEST_INTENSITY_VOXEL
    
    See Also:
    
    AnalyzeSkeleton_.run(int, boolean, boolean, ImagePlus, boolean, boolean)
  - setPruneEnds
```
public void setPruneEnds(boolean pruneEnds)
```
    Sets whether or not to prune branches which end in end-points from the result.
    
    See Also:
    
    AnalyzeSkeleton_.run(int, boolean, boolean, ImagePlus, boolean, boolean)
  - setShortestPath
```
public void setShortestPath(boolean shortestPath)
```
    Sets whether or not to calculate the longest shortest-path in the skeleton result.
    
    See Also:
    
    AnalyzeSkeleton_.run(int, boolean, boolean, ImagePlus, boolean, boolean)
  - setSilent
```
public void setSilent(boolean silent)
```
    Setting this to false will display both the tagged skeleton image and the shortest path image (if the shortest path calculation is enabled).
    
    See Also:
    
    AnalyzeSkeleton_.run(int, boolean, boolean, ImagePlus, boolean, boolean)
  - setVerbose
```
public void setVerbose(boolean verbose)
```
    See Also:
    
    AnalyzeSkeleton_.run(int, boolean, boolean, ImagePlus, boolean, boolean)
  - setPruneByLength
```
public void setPruneByLength(boolean pruneByLength)
```
    Sets whether or not to prune components below a threshold length from the result.
  - setLengthThreshold
```
public void setLengthThreshold(double lengthThreshold)
```
    The minimum component length necessary to avoid pruning. This value is only used if pruneByLength is true.
    
    Parameters:
    
    lengthThreshold - the length threshold
    
    See Also:
    
    setPruneByLength(boolean)
  - setConnectComponents
```
public void setConnectComponents(boolean connectComponents)
```
    Whether to merge broken components in the skeleton result
    
    Parameters:
    
    connectComponents -
    
    See Also:
    
    setMaxConnectDist(double)
  - setMaxConnectDist
```
public void setMaxConnectDist(double maxConnectDist)
```
    The maximum allowable distance between nearest neighbors to be considered for a merge
    
    Parameters:
    
    maxConnectDist -
    
    See Also:
    
    setConnectComponents(boolean)
  - main
```
public static void main(String[] args)
```

Class SkeletonConverter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SkeletonConverter

SkeletonConverter

Method Detail

skeletonize

getTrees

getGraphs

setOrigIP

setPruneMode

setPruneEnds

setShortestPath

setSilent

setVerbose

setPruneByLength

setLengthThreshold

setConnectComponents

setMaxConnectDist

main