RoiConverter (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.AbstractContextual
- - org.scijava.command.ContextCommand
  - - sc.fiji.snt.analysis.TreeAnalyzer
    - - sc.fiji.snt.analysis.RoiConverter

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, SciJavaPlugin
```
public class RoiConverter
extends TreeAnalyzer
```
Converts SNT Paths into (IJ1) ROIs.

Author:

Tiago Ferreira

See Also:

ROIExporterCmd

Field Summary

Fields
Modifier and Type Field and Description

static int XY_PLANE
SNT's XY view (the default export plane)

static int XZ_PLANE
SNT's XZ view

static int ZY_PLANE
SNT's ZY view
- Fields inherited from class sc.fiji.snt.analysis.TreeAnalyzer
  displayService, innerBranches, primaryBranches, statusService, table, terminalBranches, tips, tree

Fields
Modifier and Type	Field and Description
`static int`	`XY_PLANE` SNT's XY view (the default export plane)
`static int`	`XZ_PLANE` SNT's XZ view
`static int`	`ZY_PLANE` SNT's ZY view

Constructor Summary

Constructors
Constructor and Description
`RoiConverter(Path path, ij.ImagePlus imp)` Instantiates a new Converter.
`RoiConverter(Tree tree)` Instantiates a new Converter.
`RoiConverter(Tree tree, ij.ImagePlus imp)` Instantiates a new Converter.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`convertBranchPoints()` Converts all the branch poisnts associated with the parsed paths into `PointRoi`s, adding them to the overlay of the image specified in the constructor.
`void`	`convertBranchPoints(Overlay overlay)` Converts all the branch points associated with the parsed paths into `PointRoi`s
`void`	`convertPaths()` Converts paths into 2D polyline ROIs (segment paths), adding them to the overlay of the image specified in the constructor.
`void`	`convertPaths(Overlay overlay)` Converts paths into 2D polyline ROIs (segment paths)
`void`	`convertTips()` Converts all the tips associated with the parsed paths into `PointRoi`s, adding them to the overlay of the image specified in the constructor.
`void`	`convertTips(Overlay overlay)` Converts all the tips associated with the parsed paths into `PointRoi`s
`List<PolygonRoi>`	`getROIs(Path path)`
`void`	`setStrokeWidth(int width)` Sets the line width of converted segment paths.
`void`	`setView(int view)` Sets the exporting view for segment paths (XY by default).
`void`	`useSWCcolors(boolean useSWCcolors)` Specifies coloring of ROIs by SWC type.

Methods inherited from class sc.fiji.snt.analysis.TreeAnalyzer
getAllMetrics, getAnnotations, getAnnotations, getAvgBranchLength, getAvgContraction, getAvgFractalDimension, getAvgFragmentation, getAvgPartitionAsymmetry, getAvgRemoteBifAngle, getBranches, getBranchPoints, getBranchPoints, getCableLength, getCableLength, getCableLength, getCableLengthNorm, getCol, getDepth, getFractalDimension, getHeight, getHighestPathOrder, getInnerBranches, getInnerLength, getMetric, getMetricInternal, getMetrics, getMetricWithoutChecks, getNBranches, getNbranchPoints, getNbranchPointsNorm, getNextRow, getNFittedPaths, getNoSpinesOrVaricosities, getNPaths, getNtips, getNtipsNorm, getParsedTree, getPartitionAsymmetry, getPrimaryBranches, getPrimaryLength, getPrimaryPaths, getRemoteBifAngles, getShollAnalyzer, getSinglePointPaths, getSpineOrVaricosityDensity, getStrahlerAnalyzer, getStrahlerBifurcationRatio, getStrahlerNumber, getSWCTypesAsString, getTable, getTerminalBranches, getTerminalLength, getTips, getTips, getWidth, ignoreSWCType, isSameOrParentAnnotation, isValid, main, measure, measure, resetRestrictions, restrictToLength, restrictToNamePattern, restrictToOrder, restrictToSize, restrictToSWCType, run, setTable, setTable, summarize, summarize, updateAndDisplayTable

Methods inherited from class org.scijava.command.ContextCommand
cancel, getCancelReason, isCanceled

Methods inherited from class org.scijava.AbstractContextual
context, getContext

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

Methods inherited from interface org.scijava.Contextual
setContext

- Field Detail
  - XY_PLANE
```
public static final int XY_PLANE
```
    SNT's XY view (the default export plane)
    
    See Also:
    
    Constant Field Values
  - ZY_PLANE
```
public static final int ZY_PLANE
```
    SNT's ZY view
    
    See Also:
    
    Constant Field Values
  - XZ_PLANE
```
public static final int XZ_PLANE
```
    SNT's XZ view
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - RoiConverter
```
public RoiConverter(Tree tree)
```
    Instantiates a new Converter. Since an image has not been specified, C,Z,T positions may not be properly for converted nodes.
    
    Parameters:
    
    tree - the Tree to be converted
  - RoiConverter
```
public RoiConverter(Path path,
                    ij.ImagePlus imp)
```
    Instantiates a new Converter.
    
    Parameters:
    
    path - the Path to be converted
    
    imp - the image associated with the Tree, used to properly assign C,T positions of converted nodes
  - RoiConverter
```
public RoiConverter(Tree tree,
                    ij.ImagePlus imp)
```
    Instantiates a new Converter.
    
    Parameters:
    
    tree - the Tree to be converted
    
    imp - the image associated with the Tree, used to properly assign C,T positions of converted nodes
- Method Detail
  - convertPaths
```
public void convertPaths(Overlay overlay)
```
    Converts paths into 2D polyline ROIs (segment paths)
    
    Parameters:
    
    overlay - the target overlay to hold converted paths
  - getROIs
```
public List<PolygonRoi> getROIs(Path path)
```
  - convertTips
```
public void convertTips(Overlay overlay)
```
    Converts all the tips associated with the parsed paths into PointRois
    
    Parameters:
    
    overlay - the target overlay to hold converted point
    
    See Also:
    
    TreeAnalyzer.getTips()
  - convertPaths
```
public void convertPaths()
                  throws IllegalArgumentException
```
    Converts paths into 2D polyline ROIs (segment paths), adding them to the overlay of the image specified in the constructor.
    
    Throws:
    
    IllegalArgumentException - if this RoiConverter instance is not aware of any image
    
    See Also:
    
    convertPaths(Overlay)
  - convertTips
```
public void convertTips()
                 throws IllegalArgumentException
```
    Converts all the tips associated with the parsed paths into PointRois, adding them to the overlay of the image specified in the constructor.
    
    Throws:
    
    IllegalArgumentException - if this RoiConverter instance is not aware of any image
    
    See Also:
    
    convertTips(Overlay)
  - convertBranchPoints
```
public void convertBranchPoints()
                         throws IllegalArgumentException
```
    Converts all the branch poisnts associated with the parsed paths into PointRois, adding them to the overlay of the image specified in the constructor.
    
    Throws:
    
    IllegalArgumentException - if this RoiConverter instance is not aware of any image
    
    See Also:
    
    convertBranchPoints(Overlay)
  - convertBranchPoints
```
public void convertBranchPoints(Overlay overlay)
```
    Converts all the branch points associated with the parsed paths into PointRois
    
    Parameters:
    
    overlay - the target overlay to hold converted point
    
    See Also:
    
    TreeAnalyzer.getBranchPoints()
  - setView
```
public void setView(int view)
```
    Sets the exporting view for segment paths (XY by default).
    
    Parameters:
    
    view - either XY_PLANE, XZ_PLANE or ZY_PLANE.
  - useSWCcolors
```
public void useSWCcolors(boolean useSWCcolors)
```
    Specifies coloring of ROIs by SWC type.
    
    Parameters:
    
    useSWCcolors - if true converted ROIs are colored according to their SWC type integer flag
  - setStrokeWidth
```
public void setStrokeWidth(int width)
```
    Sets the line width of converted segment paths. Set it to -1 to have ROIs plotted using the average diameter of the path
    
    Parameters:
    
    width - the new stroke width
    
    See Also:
    
    Path.getMeanRadius(), Roi.getStrokeWidth()

Class RoiConverter

Field Summary

Fields inherited from class sc.fiji.snt.analysis.TreeAnalyzer

Constructor Summary

Method Summary

Methods inherited from class sc.fiji.snt.analysis.TreeAnalyzer

Methods inherited from class org.scijava.command.ContextCommand

Methods inherited from class org.scijava.AbstractContextual

Methods inherited from class java.lang.Object

Methods inherited from interface org.scijava.Contextual

Field Detail

XY_PLANE

ZY_PLANE

XZ_PLANE

Constructor Detail

RoiConverter

RoiConverter

RoiConverter

Method Detail

convertPaths

getROIs

convertTips

convertPaths

convertTips

convertBranchPoints

convertBranchPoints

setView

useSWCcolors

setStrokeWidth