How to use the neuron.h.y3d function in NEURON

for new 3d styles, like soma outlines)
    
    .. warning::
    
        This assumes a 3d style exists. The safest way to call this is to call
        h.define_shape() first
    """
    # TODO: fix the issue described in the warning
    #       (when this was written, these objects were only under development)
    
    n3d = int(h.n3d(sec=sec))
    length = sec.L
    
    arc3d = [h.arc3d(i, sec=sec) for i in range(n3d)]
    x3d = numpy.array([h.x3d(i, sec=sec) for i in range(n3d)])
    y3d = numpy.array([h.y3d(i, sec=sec) for i in range(n3d)])
    z3d = numpy.array([h.z3d(i, sec=sec) for i in range(n3d)])
    diam3d = numpy.array([h.diam3d(i, sec=sec) for i in range(n3d)])
    
    dx = length / sec.nseg
    objs = {}
    for i in range(sec.nseg):
        x_lo = i * dx
        x_hi = (i + 1) * dx
        pts = [x_lo] + _values_strictly_between(x_lo, x_hi, arc3d) + [x_hi]
        local_x3d = numpy.interp(pts, arc3d, x3d)
        local_y3d = numpy.interp(pts, arc3d, y3d)
        local_z3d = numpy.interp(pts, arc3d, z3d)
        local_diam3d = numpy.interp(pts, arc3d, diam3d)
        local_objs = []
        for j in range(len(pts) - 1):
            x0, y0, z0, r0 = local_x3d[j], local_y3d[j], local_z3d[j], local_diam3d[j] / 2.

secDir = dir(sec)
        for geomParam in standardGeomParams:
            #if geomParam in secDir:
            try:
                secDic[secName]['geom'][geomParam] = sec.__getattribute__(geomParam)
            except:
                pass

        # store 3d geometry
        sec.push()  # access current section so ismembrane() works
        numPoints = int(h.n3d())
        if numPoints: 
            points = []
            for ipoint in range(numPoints):
                x = h.x3d(ipoint)
                y = h.y3d(ipoint)
                z = h.z3d(ipoint)
                diam = h.diam3d(ipoint)
                points.append((x, y, z, diam))
            secDic[secName]['geom']['pt3d'] = points

        # store mechanisms
        #varList = mechVarList()  # list of properties for all density mechanisms and point processes
        ignoreMechs = ['dist']  # dist only used during cell creation 
        ignoreVars = []  # 
        mechDic = {}
        ionDic = {}
        
        for mech in dir(sec(0.5)): 
            if h.ismembrane(mech) and mech not in ignoreMechs:  # check if membrane mechanism
                if not mech.endswith('_ion'):  # exclude ions
                    mechDic[mech] = {}  # create dic for mechanism properties

def retrieve_coordinate(self, sec):
        """Retrieve the coordinates of the section"""
        coords = {}
        sec.push()
        coords['x0'] = h.x3d((h.n3d()- h.n3d()))
        coords['x1'] = h.x3d((h.n3d()- 1))
        coords['y0'] = h.y3d((h.n3d()- h.n3d()))
        coords['y1'] = h.y3d((h.n3d()- 1))
        coords['z0'] = h.z3d((h.n3d()- h.n3d()))
        coords['z1'] = h.z3d((h.n3d()- 1))
        h.pop_section()
        return coords

p0 = np.zeros((3, nseg))  # hold the coordinates of segment starting points
        p1 = np.zeros((3, nseg))  # hold the coordinates of segment end points
        d0 = np.zeros(nseg) 
        d1 = np.zeros(nseg) 

        for sec in list(cell.secs.values()):
            hSec = sec['hSec']
            hSec.push()
            n3d = int(h.n3d())  # get number of n3d points in each section
            p3d = np.zeros((3, n3d))  # to hold locations of 3D morphology for the current section
            l3d = np.zeros(n3d)  # to hold locations of 3D morphology for the current section
            diam3d = np.zeros(n3d)  # to diameters

            for i in range(n3d):
                p3d[0, i] = h.x3d(i) - p3dsoma[0]
                p3d[1, i] = h.y3d(i) - p3dsoma[1]  # shift coordinates such to place soma at the origin.
                p3d[2, i] = h.z3d(i) - p3dsoma[2]
                diam3d[i] = h.diam3d(i)
                l3d[i] = h.arc3d(i)

            l3d /= hSec.L                  # normalize
            nseg = hSec.nseg
            
            l0 = np.zeros(nseg)     # keep range of segment starting point 
            l1 = np.zeros(nseg)     # keep range of segment ending point 
            
            for iseg, seg in enumerate(hSec):
                l0[iseg] = seg.x - 0.5*1/nseg   # x (normalized distance along the section) for the beginning of the segment
                l1[iseg] = seg.x + 0.5*1/nseg   # x for the end of the segment

            p0[0, ix:ix+nseg] = np.interp(l0, l3d, p3d[0, :])
            p0[1, ix:ix+nseg] = np.interp(l0, l3d, p3d[1, :])

def _posFromLoc(self, sec, x):
    sec.push()
    s = x * sec.L
    numpts = int(h.n3d())
    b = -1
    for ii in range(numpts):
        if h.arc3d(ii) >= s:
            b = ii
            break
    if b == -1: print("an error occurred in pointFromLoc, SOMETHING IS NOT RIGHT")

    if h.arc3d(b) == s:  # shortcut
        x, y, z = h.x3d(b), h.y3d(b), h.z3d(b)
    else:               # need to interpolate
        a = b-1
        t = (s - h.arc3d(a)) / (h.arc3d(b) - h.arc3d(a))
        x = h.x3d(a) + t * (h.x3d(b) - h.x3d(a))
        y = h.y3d(a) + t * (h.y3d(b) - h.y3d(a))
        z = h.z3d(a) + t * (h.z3d(b) - h.z3d(a))    

    h.pop_section()
    return x, y, z

def retrieve_coordinate(self, sec):
        """Retrieve the coordinates of the section"""
        coords = {}
        sec.push()
        coords['x0'] = h.x3d((h.n3d()- h.n3d()))
        coords['x1'] = h.x3d((h.n3d()- 1))
        coords['y0'] = h.y3d((h.n3d()- h.n3d()))
        coords['y1'] = h.y3d((h.n3d()- 1))
        coords['z0'] = h.z3d((h.n3d()- h.n3d()))
        coords['z1'] = h.z3d((h.n3d()- 1))
        h.pop_section()
        return coords

for geomParam in standardGeomParams:
            # if geomParam in secDir:
            try:
                secDic[secName]['geom'][
                    geomParam] = sec.__getattribute__(geomParam)
            except:
                pass

        # store 3d geometry
        sec.push()  # access current section so ismembrane() works
        numPoints = int(h.n3d())
        if numPoints:
            points = []
            for ipoint in range(numPoints):
                x = h.x3d(ipoint)
                y = h.y3d(ipoint)
                z = h.z3d(ipoint)
                diam = h.diam3d(ipoint)
                points.append((x, y, z, diam))
            secDic[secName]['geom']['pt3d'] = points

        # store mechanisms
        # list of properties for all density mechanisms and point processes
        varList = mechVarList()
        ignoreMechs = ['dist']  # dist only used during cell creation
        ignoreVars = []  #
        mechDic = {}
        ionDic = {}

        for mech in dir(sec(0.5)):
            if h.ismembrane(mech) and mech not in ignoreMechs:  # check if membrane mechanism
                if not mech.endswith('_ion'):  # exclude ions