centre = (out.xpoints[0], out.ypoints[0]) ring_roi_xs = [] ring_roi_ys = [] for theta in range(359): # for theta_idx in range(6): # theta = theta_idx * 60 - 90; 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]) egfp_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]) #print("Max val = " + str(max(profile))); egfp_imp.killRoi() ring_roi = PolygonRoi(ring_roi_xs, ring_roi_ys, Roi.FREELINE) ring_rois.append(ring_roi) roi_stack.setZ(zidx + 1) roi_stack.setRoi(ring_roi) IJ.run(roi_stack, "Line to Area", "") IJ.run(roi_stack, "Set...",
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