sc.fiji.snt.analysis

Class RoiConverter

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.TreeAnalyzer

sc.fiji.snt.analysis.RoiConverter

All Implemented Interfaces:

java.lang.Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.plugin.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

BRANCH_ORDER, COMMON_MEASUREMENTS, INTER_NODE_DISTANCE, INTER_NODE_DISTANCE_SQUARED, LENGTH, MEAN_RADIUS, N_BRANCH_POINTS, N_NODES, NODE_RADIUS, VALUES, X_COORDINATES, Y_COORDINATES, Z_COORDINATES

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
void	convertBranchPoints(ij.gui.Overlay overlay) Converts all the branch points associated with the parsed paths into PointRois
void	convertPaths(ij.gui.Overlay overlay) Converts paths into 2D polyline ROIs (segment paths)
void	convertTips(ij.gui.Overlay overlay) Converts all the tips associated with the parsed paths into PointRois
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

getBranchPoints, getCableLength, getNPaths, getParsedTree, getPrimaryBranches, getPrimaryLength, getPrimaryPaths, getStrahlerRootNumber, getTable, getTerminalBranches, getTerminalLength, getTips, ignoreSWCType, main, 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

equals, 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(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(ij.gui.Overlay overlay)

Converts paths into 2D polyline ROIs (segment paths)

Parameters:

overlay - the target overlay to hold converted paths

convertTips

public void convertTips(ij.gui.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()

convertBranchPoints

public void convertBranchPoints(ij.gui.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()