LongestShortestPath_to_LineSelection.groovy

import ij.IJ
import ij.ImageStack
import ij.ImagePlus
import ij.gui.Line
import ij.gui.OvalRoi
import ij.gui.PolygonRoi
import java.awt.Polygon
import sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

imp = IJ.createImage("Untitled", "8-bit black", 100, 100, 1)
IJ.setForegroundColor(255, 255, 255);
imp.show()

//IJ.run("Set... ", "zoom=400")
Line.setWidth(1)

imp.setRoi(new OvalRoi(11,15,57,35));
IJ.run(imp, "Draw", "slice");
imp.setRoi(new OvalRoi(33,36,57,35));
IJ.run(imp, "Draw", "slice");

imp.setRoi(new Line(20,20,10,10))
IJ.run(imp, "Draw", "slice")
imp.setRoi(new Line(68,71,87,76))
IJ.run(imp, "Draw", "slice")

IJ.run(imp, "Skeletonize (2D/3D)", "");

// Initialize AnalyzeSkeleton_
skel = new AnalyzeSkeleton_()
skel.calculateShortestPath = true
skel.setup("", imp)
 
// Perform analysis in silent mode
skelResult = skel.run(AnalyzeSkeleton_.NONE, false, true, null, true, false)

// Read the results
shortestPaths = skelResult.getShortestPathList().toArray()
sppoints = skel.getShortestPathPoints()

// imps = new ImageStack(imp.getWidth(), imp.getHeight())
poly = new Polygon()
for (p in sppoints[0]) {
    poly.addPoint((int)p.x, (int)p.y)
    imp.setRoi(new PolygonRoi(poly, PolygonRoi.POLYLINE))
    IJ.wait(50)
    // imps.addSlice(imp.flatten().getProcessor())
}

pRoi = new PolygonRoi(poly, PolygonRoi.POLYLINE)
imp.setRoi(pRoi)

IJ.run(imp, "Straighten...", "line=20");

// new ImagePlus("Animation", imps).show()