def maximum_line_profile(imp, roi, pixel_width):
    """return a line profile taking the maximum value over n pixels perpendicular to roi line"""
    imp.setRoi(roi)
    IJ.run(imp, "Interpolate", "interval=1.0 smooth adjust")
    if pixel_width < 1:
        pixel_width = 1
    pixel_width = int(2 * math.ceil(float(pixel_width) / 2))
    ip = Straightener().straightenLine(imp, pixel_width)
    # debug
    #from ij import ImagePlus
    #from ij.gui import WaitForUserDialog
    #debug_imp = ImagePlus("debug", ip);
    #debug_imp.show();
    #WaitForUserDialog("debug").show();
    #debug_imp.close();
    width = ip.getWidth()
    height = ip.getHeight()
    max_profile = []
    poly = roi.getInterpolatedPolygon(1.0, True)
    for idx, (x, y) in enumerate(zip(poly.xpoints, poly.ypoints)):
        pix = ip.getLine(idx, 0, idx, height)
        max_profile.append(((x, y), max(pix)))
    return max_profile
def straighten_vessel(imp, smooth_centres, it=1, save_output=False):
    """use IJ straigtening tool to deal with convoluted vessels"""
    print("straighten vessel input image dims = " + str(imp.getWidth()) + "x" +
          str(imp.getHeight()))
    rot_imp = utils.rot3d(imp, axis='x')
    if it == 1:
        roi = PolygonRoi([x for x, y, z in smooth_centres],
                         [z for x, y, z in smooth_centres], Roi.FREELINE)
        print("len interp polygon = " +
              str(roi.getInterpolatedPolygon().npoints))
    elif it == 2:
        new_zs = [z for z in range(rot_imp.getWidth())]
        new_ys = lin_interp_1d([z for x, y, z in smooth_centres],
                               [y for x, y, z in smooth_centres], new_zs)
        roi = PolygonRoi(new_zs, new_ys, Roi.FREELINE)

    split_ch = ChannelSplitter().split(rot_imp)
    mch_imp = split_ch[0]
    egfp_imp = split_ch[1]
    roi_imp = split_ch[2]

    roi_imp.setRoi(roi)

    for zidx in range(egfp_imp.getNSlices()):
        for chidx in range(3):
            split_ch[chidx].setZ(zidx + 1)
            split_ch[chidx].setRoi(roi)
            ip = Straightener().straightenLine(split_ch[chidx], 150)
            if chidx == 1:
                if zidx == 0:
                    egfp_straight_stack = ImageStack(ip.getWidth(),
                                                     ip.getHeight())
                egfp_straight_stack.addSlice(ip)
            elif chidx == 0:
                if zidx == 0:
                    mch_straight_stack = ImageStack(ip.getWidth(),
                                                    ip.getHeight())
                mch_straight_stack.addSlice(ip)
            else:
                if zidx == 0:
                    roi_straight_stack = ImageStack(ip.getWidth(),
                                                    ip.getHeight())
                roi_straight_stack.addSlice(ip)

    egfp_out_imp = ImagePlus("Straightened EGFP", egfp_straight_stack)
    mch_out_imp = ImagePlus("Straightened mCh", mch_straight_stack)
    roi_out_imp = ImagePlus("Straightened ROI", roi_straight_stack)
    if it == 2:
        egfp_out_imp = utils.rot3d(egfp_out_imp, axis='y')
        mch_out_imp = utils.rot3d(mch_out_imp, axis='y')
        roi_out_imp = utils.rot3d(roi_out_imp, axis='y')
    egfp_out_imp.show()
    mch_out_imp.show()
    roi_out_imp.show()
    IJ.run(
        "Merge Channels...",
        "c1=[" + mch_out_imp.getTitle() + "] c2=[" + egfp_out_imp.getTitle() +
        "] c7=[" + roi_out_imp.getTitle() + "] create keep")
    #	WaitForUserDialog("pause").show();
    #	if it==1:
    egfp_out_imp.close()
    mch_out_imp.close()
    roi_out_imp.close()
    new_composite = IJ.getImage()
    if save_output:
        FileSaver(new_composite).saveAsTiffStack(
            os.path.join(output_path, "after rotation " + str(it) + ".tif"))
    return new_composite
Example #3
0


z_planes = egfp_imp.getNSlices();
#straight_stack = Straightener().straightenStack(egfp_imp, roi, 100);
#out_imp = ImagePlus("Straightened", straight_stack);

for zidx in range(z_planes):
	for chidx in range(3):
		#print("Working on " + str(["egfp", "mCh", "roi"][chidx]));
		split_ch[chidx].setZ(zidx+1);
		split_ch[chidx].setRoi(roi);
		ip = Straightener().straightenLine(split_ch[chidx], 150);
		if chidx==1:
			if zidx==0:
				egfp_straight_stack = ImageStack(ip.getWidth(), ip.getHeight());
			egfp_straight_stack.addSlice(ip);
		elif chidx==0:
			if zidx==0:
				mch_straight_stack = ImageStack(ip.getWidth(), ip.getHeight());
			mch_straight_stack.addSlice(ip);
		else:
			if zidx==0:
				roi_straight_stack = ImageStack(ip.getWidth(), ip.getHeight());
			roi_straight_stack.addSlice(ip);

egfp_out_imp = ImagePlus("Straightened EGFP", egfp_straight_stack);
mch_out_imp = ImagePlus("Straightened mCh", mch_straight_stack);
roi_out_imp = ImagePlus("Straightened ROI", roi_straight_stack);
egfp_out_imp.show();
mch_out_imp.show();