def generate_r_image(imp, ring_rois, centres, unwrap_axis, threshold_val):
"""for each point in the projection, calculate the distance to the vessel axis and present as an image"""
fp = imp.getProcessor()
fp.setThreshold(threshold_val, fp.maxValue(), FloatProcessor.NO_LUT_UPDATE)
bp = fp.createMask()
bp.dilate()
bp.erode()
mask_imp = ImagePlus("Mask", bp)
tile_mask = make_tiled_imp(mask_imp)
#tile_mask.show();
#WaitForUserDialog("pasue - generated mask").show();
mask_imp = do_unwrap(tile_mask, unwrap_axis, imp_title=mask_imp.getTitle())
#mask_imp.show();
roi = PolygonRoi([x for (x, y) in unwrap_axis],
[y for (x, y) in unwrap_axis], PolygonRoi.POLYLINE)
mask_imp.setRoi(roi)
#WaitForUserDialog("pasue - unwrapped").show();
IJ.run(mask_imp, "Fill Holes", "")
#WaitForUserDialog("pasue - filled holes").show();
IJ.run(mask_imp, "Divide...", "value=255")
#WaitForUserDialog("pasue - scaled to 0-1").show();
#mask_imp.show();
r_list = []
for lidx, (roi, centre) in enumerate(zip(ring_rois, centres)):
r_sublist = [
math.sqrt((x - centre[0])**2 + (y - centre[1])**2)
for x, y in zip(roi.getPolygon().xpoints,
roi.getPolygon().ypoints)
]
r_list.append(r_sublist)
r_imp = ImagePlus("Radii", FloatProcessor([list(x) for x in zip(*r_list)]))
tile_r_imp = make_tiled_imp(r_imp)
r_imp = do_unwrap(tile_r_imp, unwrap_axis, imp_title=r_imp.getTitle())
r_imp = ImageCalculator().run("Multiply create", r_imp, mask_imp)
IJ.run(r_imp, "Cyan Hot", "")
return r_imp, mask_imp
def getPolygon(self):
xPoints, yPoints = self.getLine()
newRoi = PolygonRoi(xPoints, yPoints, Roi.POLYLINE)
return newRoi.getPolygon()
