def do_angular_projection(imp,
max_r_pix=60,
min_r_pix=10,
generate_roi_stack=True):
"""perform ray-based projection of vessel wall, c.f. ICY TubeSkinner (Lancino 2018)"""
Prefs.blackBackground = True
print("do angular projection input imp = " + str(imp))
split_chs = ChannelSplitter().split(imp)
mch_imp = split_chs[0]
IJ.setAutoThreshold(mch_imp, "IsoData dark stack")
egfp_imp = split_chs[1]
proj_imp = Duplicator().run(egfp_imp)
cl_imp = split_chs[2]
if generate_roi_stack:
egfp_imp_disp = Duplicator().run(egfp_imp)
roi_stack = IJ.createImage("rois", egfp_imp.getWidth(),
egfp_imp.getHeight(), egfp_imp.getNSlices(),
16)
centres = []
projected_im_pix = []
ring_rois = []
for zidx in range(cl_imp.getNSlices()):
if ((zidx + 1) % 100) == 0:
print("Progress = " +
str(round(100 * (float(zidx + 1) / cl_imp.getNSlices()))))
projected_im_row = []
proj_imp.setZ(zidx + 1)
mch_imp.setZ(zidx + 1)
bp = mch_imp.createThresholdMask()
bp.dilate()
bp.erode()
bp.erode()
bp.erode()
mask_imp = ImagePlus("mask", bp)
IJ.run(mask_imp, "Create Selection", "")
roi = mask_imp.getRoi()
proj_imp.setRoi(roi)
IJ.run(proj_imp, "Set...", "value=0 slice")
IJ.run(proj_imp, "Make Inverse", "")
roi = proj_imp.getRoi()
centre = (roi.getStatistics().xCentroid, roi.getStatistics().yCentroid)
centres.append(centre)
ring_roi_xs = []
ring_roi_ys = []
for theta in range(360):
pt1 = (centre[0] + min_r_pix * math.cos(math.radians(theta)),
centre[1] + min_r_pix * math.sin(math.radians(theta)))
pt2 = (centre[0] + max_r_pix * math.cos(math.radians(theta)),
centre[1] + max_r_pix * math.sin(math.radians(theta)))
roi = Line(pt1[0], pt1[1], pt2[0], pt2[1])
proj_imp.setRoi(roi)
profile = roi.getPixels()
projected_im_row.append(max(profile))
try:
ring_roi_xs.append(roi.getContainedPoints()[profile.index(
max(profile))].x)
except IndexError:
ring_roi_xs.append(pt2[0])
try:
ring_roi_ys.append(roi.getContainedPoints()[profile.index(
max(profile))].y)
except IndexError:
ring_roi_ys.append(pt2[1])
proj_imp.killRoi()
ring_roi = PolygonRoi(ring_roi_xs, ring_roi_ys, Roi.FREELINE)
ring_rois.append(ring_roi)
if generate_roi_stack:
roi_stack.setZ(zidx + 1)
roi_stack.setRoi(ring_roi)
IJ.run(roi_stack, "Line to Area", "")
IJ.run(
roi_stack, "Set...",
"value=" + str(roi_stack.getProcessor().maxValue()) + " slice")
#egfp_imp.setRoi(ring_roi);
projected_im_pix.append(projected_im_row)
# for ch in split_chs:
# ch.close();
out_imp = ImagePlus(
"projected", FloatProcessor([list(x) for x in zip(*projected_im_pix)]))
if generate_roi_stack:
roi_stack.show()
egfp_imp_disp.show()
# merge?
else:
roi_stack = None
return out_imp, roi_stack, ring_rois, centres
