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
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();