Package sc.fiji.snt.analysis

Class RoiConverter

java.lang.Object

sc.fiji.snt.analysis.RoiConverter

public class RoiConverter
extends Object

Converts SNT Paths into (IJ1) ROIs.

Author:

Tiago Ferreira

See Also:

• ROIExporterCmd

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	Description
RoiConverter(Collection<Path> paths, ij.ImagePlus imp)	Instantiates a new Converter.
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

Modifier and Type	Method	Description
static ij.gui.Roi	combine(List<ij.gui.Roi> rois)
static ij.gui.Roi	convert(Collection<Path> paths, ij.ImagePlus imp)
void	convertBranches(ij.gui.Overlay overlay)
void	convertBranchPoints()	Converts all the branch points associated with the parsed paths into PointRois, adding them to the overlay of the image specified in the constructor.
void	convertBranchPoints(ij.gui.Overlay overlay)	Converts all the branch points associated with the parsed paths into PointRois
void	convertInnerBranches(ij.gui.Overlay overlay)
void	convertPaths()	Converts paths into 2D polyline ROIs (segment paths), adding them to the overlay of the image specified in the constructor.
ij.gui.Overlay	convertPaths(ij.gui.Overlay overlay)	Converts paths into 2D polyline ROIs.
ij.gui.Overlay	convertPaths(ij.gui.Overlay overlay, Collection<Path> paths)	Converts an ad-hoc collection of paths into 2D polyline ROIs.
void	convertPrimaryBranches(ij.gui.Overlay overlay)
void	convertRoots()	Converts the starting nodes of primary paths in the parsed pool into PointRois
void	convertRoots(ij.gui.Overlay overlay)	Converts the starting nodes of primary paths in the parsed pool into PointRois
void	convertTerminalBranches(ij.gui.Overlay overlay)
void	convertTips()	Converts all the tips associated with the parsed paths into PointRois, adding them to the overlay of the image specified in the constructor.
void	convertTips(ij.gui.Overlay overlay)	Converts all the tips associated with the parsed paths into PointRois
static ij.gui.Roi	enlarge(ij.gui.Roi roi, int pixels)
static ij.gui.Roi	get2DBoundingBox(Collection<Path> paths, int exportPlane)
static double[]	get2dCentroid(ij.gui.Roi roi)
static List<long[]>	getCentroids(Collection<ij.gui.Roi> rois)	Extracts centroids from a collection of ROIs as integer pixel coordinates.
static double	getFittedRadius(ij.ImagePlus imp, ij.gui.Roi areaRoi)	Retrieves the radius of a circle with the same area of the specified area ROI.
static List<ij.gui.Roi>	getROIs(ij.gui.Overlay overlay, int channel, int zSlice, int tFrame)	Extracts ROIs associated with a specified CZT position.
List<ij.gui.PolygonRoi>	getROIs(Path path)	Gets ROI representations of the specified path.
List<ij.gui.Roi>	getZplaneROIs(int zSlice)	Extracts all the ROIs converted so far associated with the specified Z-plane.
static List<ij.gui.Roi>	getZplaneROIs(ij.gui.Overlay overlay, int zSlice)	Extracts ROIs associated with a specified Z position.
static List<ij.gui.Roi>	loadRoisFromZip(File zipFile)
static boolean	saveRoisToZip(List<ij.gui.Roi> rois, File file)
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).
static ij.gui.PointRoi	toPointRoi(List<Detection> detections, ij.ImagePlus imp, String name, Color color)	Creates a grouped PointRoi from a list of Detections.
void	useSWCcolors(boolean useSWCcolors)	Specifies coloring of ROIs by SWC type.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

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 Details

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(Collection<Path> paths,
 ij.ImagePlus imp)

Instantiates a new Converter.

Parameters:

paths - the collection of Paths to be converted

imp - the image associated with the collection, 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 Details

convertPaths

public ij.gui.Overlay convertPaths(ij.gui.Overlay overlay)

Converts paths into 2D polyline ROIs.

Parameters:

overlay - the target overlay to hold converted paths

Returns:

a reference to the overlay holding paths

convertPaths

public ij.gui.Overlay convertPaths(ij.gui.Overlay overlay,
 Collection<Path> paths)

Converts an ad-hoc collection of paths into 2D polyline ROIs.

Parameters:

overlay - the target overlay to hold converted paths

paths - the collection of paths to be converted (e.g., a list of branches produced by StrahlerAnalyzer

Returns:

a reference to the overlay holding paths

getROIs

public List<ij.gui.PolygonRoi> getROIs(Path path)

Gets ROI representations of the specified path.

Converts the path to a list of PolygonRoi objects using the path's name as the ROI name. The conversion respects the current view setting.

Parameters:

path - the path to convert

Returns:

a list of PolygonRoi objects representing the path

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:

• TreeStatistics.getTips()

convertRoots

public void convertRoots(ij.gui.Overlay overlay)

Converts the starting nodes of primary paths in the parsed pool into PointRois

Parameters:

overlay - the target overlay to hold converted point

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)

convertBranches

public void convertBranches(ij.gui.Overlay overlay)

convertInnerBranches

public void convertInnerBranches(ij.gui.Overlay overlay)

convertPrimaryBranches

public void convertPrimaryBranches(ij.gui.Overlay overlay)

convertTerminalBranches

public void convertTerminalBranches(ij.gui.Overlay 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 points 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)

convertRoots

public void convertRoots()
                  throws IllegalArgumentException

Converts the starting nodes of primary paths in the parsed pool into PointRois

Throws:

IllegalArgumentException - if this RoiConverter instance is not aware of any image

See Also:

• convertRoots(Overlay)

getZplaneROIs

public List<ij.gui.Roi> getZplaneROIs(int zSlice)

Extracts all the ROIs converted so far associated with the specified Z-plane. It is assumed that ROIs are stored in the overlay of the image specified in the constructor.

Throws:

IllegalArgumentException - if this RoiConverter instance is not aware of any image

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:

• TreeStatistics.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()

getZplaneROIs

public static List<ij.gui.Roi> getZplaneROIs(ij.gui.Overlay overlay,
 int zSlice)

Extracts ROIs associated with a specified Z position.

Parameters:

overlay - the overlay holding ROIs

zSlice - the z-plane (1-based index)

Returns:

the sub-list of ROIs associated with the specified Z position. Note that ROIs with a ZPosition of 0 are considered to be associated with all Z-slices of a stack

getROIs

public static List<ij.gui.Roi> getROIs(ij.gui.Overlay overlay,
 int channel,
 int zSlice,
 int tFrame)

Extracts ROIs associated with a specified CZT position. Only ROIS with known hyperstackPosition are considered.

Parameters:

overlay - the overlay holding ROIs

channel - the channel (1-based index)

zSlice - the z-plane (1-based index)

tFrame - the t-frame (1-based index)

Returns:

the sub-list of ROIs associated with the specified CZT position

See Also:

• Roi.hasHyperStackPosition()

enlarge

public static ij.gui.Roi enlarge(ij.gui.Roi roi,
 int pixels)

combine

public static ij.gui.Roi combine(List<ij.gui.Roi> rois)

convert

public static ij.gui.Roi convert(Collection<Path> paths,
 ij.ImagePlus imp)

toPointRoi

public static ij.gui.PointRoi toPointRoi(List<Detection> detections,
 ij.ImagePlus imp,
 String name,
 Color color)

Creates a grouped PointRoi from a list of Detections. Each detection's pixel coordinates and stack position are computed via Detection.xyzct().

Parameters:

detections - the detections to convert

imp - the image used to resolve stack positions (channel, Z, frame)

name - the ROI name, or null for no name

color - the stroke color, or null for default

Returns:

a PointRoi containing all detection points with per-point Z positions

Throws:

IllegalArgumentException - if detections or imp is null

get2DBoundingBox

public static ij.gui.Roi get2DBoundingBox(Collection<Path> paths,
 int exportPlane)

getFittedRadius

public static double getFittedRadius(ij.ImagePlus imp,
 ij.gui.Roi areaRoi)

Retrieves the radius of a circle with the same area of the specified area ROI.

Parameters:

imp - The image associated with the ROI

areaRoi - The input area ROI

Returns:

the radius (in calibrated units) of a circle with the same area of areaRoi

get2dCentroid

public static double[] get2dCentroid(ij.gui.Roi roi)

getCentroids

public static List<long[]> getCentroids(Collection<ij.gui.Roi> rois)

Extracts centroids from a collection of ROIs as integer pixel coordinates. Each centroid is computed via get2dCentroid(Roi) and rounded to the nearest pixel. The Z coordinate is derived from Roi.getZPosition(): ROIs associated with a specific slice produce a 0-indexed Z value (getZPosition() - 1); ROIs not associated with a particular slice (getZPosition() == 0) produce z = -1, indicating that the Z position is unresolved and should be determined by the caller. Null ROIs or ROIs whose centroid cannot be determined are silently skipped.

Parameters:

rois - the ROIs to extract centroids from

Returns:

list of long[]{x, y, z} pixel coordinates (z is 0-indexed, or -1 if the ROI has no slice association), one per valid ROI (may be smaller than input if some ROIs are null/invalid)

See Also:

• get2dCentroid(Roi)
• Roi.getZPosition()

saveRoisToZip

public static boolean saveRoisToZip(List<ij.gui.Roi> rois,
 File file)

loadRoisFromZip

public static List<ij.gui.Roi> loadRoisFromZip(File zipFile)