def create_skeleton(image, name, min_branch_length=10, nuclei_rois=None, sample_width=4):
print "Creating skeleton for %s, new name %s" %(image.getTitle(), name)
# analyze skeleton
skel = AnalyzeSkeleton_()
skel.setup("", image)
skelResult = skel.run(AnalyzeSkeleton_.NONE, False, True, None, True, False)
# create copy of input image
pruned_img = image.duplicate()
outStack = pruned_img.getStack()
# get graphs (one per skeleton in the image)
graph = skelResult.getGraph()
# list of end-points
endPoints = skelResult.getListOfEndPoints()
if graph:
for i in range(len(graph)):
listEdges = graph[i].getEdges()
# go through all branches and remove branches < min_branch_length in duplicate image
for e in listEdges:
p = e.getV1().getPoints();
v1End = endPoints.contains( p.get(0) )
p2 = e.getV2().getPoints();
# print "p=",p, "p2=",p2
v2End = endPoints.contains( p2.get(0) )
# if any of the vertices is end-point
if v1End or v2End :
if e.getLength() < min_branch_length:
if v1End:
outStack.setVoxel( p.get(0).x, p.get(0).y, p.get(0).z, 0 )
if v2End:
outStack.setVoxel( p2.get(0).x, p2.get(0).y, p2.get(0).z, 0 )
for p in e.getSlabs():
outStack.setVoxel( p.x, p.y, p.z, 0 )
pruned_img.setTitle(image.getTitle()+"-longestpath")
sppoints = skel.getShortestPathPoints()
if len(sppoints) == 0:
return None, None, None, None, None, None
ais_skeleton = pruned_img.duplicate()
ais_skeleton.setTitle(name);
IJ.run(ais_skeleton, "Select All", "")
IJ.run(ais_skeleton, "Clear", "slice")
points = []
angle = []
b_length = [len(b) for b in sppoints]
longest_branch_idx = b_length.index(max(b_length))
points = [p for p in sppoints[longest_branch_idx]]
closest_nucleus = None
if nuclei_rois is not None:
nroi1,dist1 = find_closest_roi(points[0].x, points[0].y, nuclei_rois)
nroi2,dist2 = find_closest_roi(points[len(points)-1].x, points[len(points)-1].y, nuclei_rois)
if nroi1 != nroi2 and dist2<dist1:
# reverse order
points = points[::-1]
closest_nucleus = nroi2
else:
closest_nucleus = nroi1
closest_nucleus.setName('%s-nucleus-ROI' % (name))
poly = Polygon()
for p in points:
poly.addPoint(int(p.x), int(p.y))
#for branch in sppoints:
# print "Branch %s, len=%d" % (branch, len(branch))
# for p in branch:
# poly.addPoint(int(p.x), int(p.y))
# points.append(p)
angles,orthogonals = local_angles(points, scope=sample_width//2)
ais_roi = PolygonRoi(poly, PolygonRoi.POLYLINE)
ais_roi.setFillColor(Color(0.0,1.0,1.0,0.5));
ais_roi.setStrokeColor(Color(0.0,1.0,1.0,0.5));
ais_roi.setName('%s-AIS-ROI' % (name))
#ais_roi.setStrokeWidth(sample_width)
IJ.run(ais_skeleton, "Analyze Particles...", "size=20-Infinity pixel exclude clear add");
IJ.run(ais_skeleton, "Clear", "slice")
ip = ais_skeleton.getProcessor()
for n in nuclei_rois:
ais_skeleton.setRoi(n)
if n == closest_nucleus:
ip.setValue(128)
else:
ip.setValue(255)
ip.fill(n.getMask())
ais_skeleton.setRoi(ais_roi)
#ip.setValue(200)
#ip.fill()
#rois = RoiManager.getInstance2().getRoisAsArray()
#for roi in rois:
# ais_skeleton.setRoi(roi)
# ip.setValue(255)
# ip.fill(roi.getMask());
for p,a,o in zip(points,angles,orthogonals):
# print "p=%s, a=%s, o=%s" % (p,a,o)
ip.set(int(p.x), int(p.y), int(33+a/2))
ip.set(int(o[0].x), int(o[0].y),255)
ip.set(int(o[1].x), int(o[1].y),255)
IJ.run(ais_skeleton, "Fire", "")
# pruned_img.setRoi(ais_roi)
print "Created ais=%s" % ais_skeleton.getTitle()
print len(skel.getShortestPathPoints()), len(points), len(orthogonals)
return ais_skeleton, skel.getShortestPathPoints(), points, orthogonals, ais_roi, closest_nucleus
if first:
IJ.run("Remove Overlay", "")
imp = IJ.getImage()
channel = max(1, c);
imp.setC(c);
width = imp.getWidth()
height = imp.getHeight()
with open(aFile, 'r') as textfile:
for line in textfile:
xy = map(int, line.rstrip().split(','))
X = xy[::2]
Y = xy[1::2]
roi = PolygonRoi(X, Y, Roi.POLYGON)
if EXCLUDE_ON_EDGES:
bounds = roi.getBounds()
if (bounds.x<DISTANCE_TO_BORDER or bounds.y<DISTANCE_TO_BORDER or bounds.x+bounds.width>width-DISTANCE_TO_BORDER or bounds.y+bounds.height>height-DISTANCE_TO_BORDER):
continue
imp.setRoi(roi)
roi.setStrokeColor(Color.yellow)
roi = imp.getRoi()
roi.setGroup(g)
rm.addRoi(roi)
rm.runCommand("Associate", "true")
rm.runCommand("Show All with labels")
IJ.run("From ROI Manager", "")
imp.getOverlay().setStrokeColor(COLORS[g-1])
rm.reset()
IJ.save(imp, imageFile)
imp.close()
c = c + 1
first = False