How to use the neuron.h.x3d function in NEURON

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

Does not currently support non-frustum based sections (i.e. no support
        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):

# store geometry properties
        standardGeomParams = ['L', 'nseg', 'diam', 'Ra', 'cm']
        secDir = dir(sec)
        for geomParam in standardGeomParams:
            #if geomParam in secDir:
            try:
                secDic[secName]['geom'][geomParam] = sec.__getattribute__(geomParam)
            except:
                pass

        # store 3d geometry
        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 
        mechDic = {}
        sec.push()  # access current section so ismembrane() works
        for mech in dir(sec(0.5)): 
            if h.ismembrane(mech) and mech not in ignoreMechs:  # check if membrane mechanism
                mechDic[mech] = {}  # create dic for mechanism properties
                varNames = [varName.replace('_'+mech, '') for varName in varList['mechs'][mech]]
                varVals = []

def retrieve_coordinate(self, sec):
        """Retrieve the coordinates of the section avoiding duplicates"""
        
        sec.push()
        x, y, z, d = [],[],[],[]

        tot_points = 0
        connect_next = False
        for i in range(int(h.n3d())):
            present = False
            x_i = h.x3d(i)
            y_i = h.y3d(i)
            z_i = h.z3d(i)
            d_i = h.diam3d(i)
            # Avoiding duplicates in the sec
            if x_i in x:
                ind = len(x) - 1 - x[::-1].index(x_i) # Getting the index of last value
                if y_i == y[ind]:
                    if z_i == z[ind]:
                        present = True
                    
            if not present:
                k =(x_i, y_i, z_i)
                x.append(x_i)
                y.append(y_i)
                z.append(z_i)
                d.append(d_i)

def morphology_to_dict(sections, outfile=None):
    section_map = {sec: i for i, sec in enumerate(sections)}
    result = []
    h.define_shape()

    for sec in sections:
        my_parent = parent(sec)
        my_parent_loc = -1 if my_parent is None else parent_loc(sec, my_parent)
        my_parent = -1 if my_parent is None else section_map[my_parent]
        n3d = int(h.n3d(sec=sec))
        result.append({
            'section_orientation': h.section_orientation(sec=sec),
            'parent': my_parent,
            'parent_loc': my_parent_loc,
            'x': [h.x3d(i, sec=sec) for i in xrange(n3d)],
            'y': [h.y3d(i, sec=sec) for i in xrange(n3d)],
            'z': [h.z3d(i, sec=sec) for i in xrange(n3d)],
            'diam': [h.diam3d(i, sec=sec) for i in xrange(n3d)],
            'name': sec.hname()           
        })

    if outfile is not None:
        with open(outfile, 'w') as f:
            json.dump(result, f)

    return result

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

standardGeomParams = ['L', 'nseg', 'diam', 'Ra', 'cm']
        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