Package sc.fiji.snt.seed

Class SeedRois

java.lang.Object

sc.fiji.snt.seed.SeedRois

public final class SeedRois
extends Object

Bidirectional SeedPoint-Roi converter.

Author:

Tiago Ferreira

Method Summary

Modifier and Type	Method	Description
static List<ij.gui.Roi>	toRois(Collection<SeedPoint> seeds, ij.ImagePlus imp)	Converts the given seeds to ROIs.
static List<SeedPoint>	toSeeds(ij.gui.Roi[] rois, ij.ImagePlus imp, double confidence, String type, String source)	Converts the given ROIs to seeds.

Methods inherited from class java.lang.Object

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

Method Details

toSeeds

public static List<SeedPoint> toSeeds(ij.gui.Roi[] rois,
 ij.ImagePlus imp,
 double confidence,
 String type,
 String source)

Converts the given ROIs to seeds.

Rules per ROI type:

• Area ROIs (oval, polygon, rectangle, freehand, traced): centroid as position, radius derived from the area of the matched circle (r = sqrt(area / pi))
• Line ROIs: midpoint as position, radius = half the path length
• Point ROIs: each contained point becomes its own seed with radius = 0. All points inherit the ROI's hyperstack position.
• Other (e.g. ANGLE, COMPOSITE): bounds center as position, radius = 0.

Parameters:

rois - the input ROIs. null/empty array returns an empty list. null entries are skipped.

imp - provides calibration and default C/T/Z. null yields uncalibrated (voxel-unit) coordinates and unset CT position.

confidence - value assigned to every produced seed, clamped to [0, 1].

type - value assigned to each seed's type field. null -> "".

source - value assigned to each seed's source field (e.g. "roi"). null -> "".

Returns:

a list of seeds. Point ROIs may produce multiple seeds (one per contained point); a ROI with no usable geometry is skipped.

toRois

public static List<ij.gui.Roi> toRois(Collection<SeedPoint> seeds,
 ij.ImagePlus imp)

Converts the given seeds to ROIs.

Seed radius is converted using the geometric mean of pixelWidth and pixelHeight so a 2D seed round-trip preserves the physical area of the equivalent disk

Parameters:

seeds - the input seed points. null/empty array returns an empty list. null entries are skipped.

imp - provides calibration. null yields uncalibrated (voxel-unit) coordinates

Returns:

a list of ROIs (either PointROI (seeds without radius) or OvalRoi.