How to use the neuron.nrn_dll_sym function in NEURON

numpy.ctypeslib.ndpointer(dtype=int),
    numpy.ctypeslib.ndpointer(dtype=int),
    numpy.ctypeslib.ndpointer(dtype=int),
    ctypes.c_long,
    numpy.ctypeslib.ndpointer(dtype=int),
    ctypes.c_long,
    numpy.ctypeslib.ndpointer(dtype=int),
    ctypes.c_long,
    ctypes.c_double,
    ctypes.c_double,
    ctypes.c_bool,
    ctypes.c_double,
    numpy.ctypeslib.ndpointer(dtype=float),]

#function to change extracellular diffusion
set_diffusion = nrn_dll_sym('set_diffusion')
set_diffusion.argtypes = [ctypes.c_int, ctypes.c_int, ctypes.c_double, ctypes.c_double, ctypes.c_double]
set_diffusion.restype = ctypes.c_int

ICS_insert.restype = ctypes.c_int

species_atolscale = nrn_dll_sym('species_atolscale')
species_atolscale.argtypes = [ctypes.c_int, ctypes.c_double, ctypes.c_int, ctypes.POINTER(ctypes.c_int)]

_set_grid_concentrations = nrn_dll_sym('set_grid_concentrations')
_set_grid_concentrations.argtypes = [ctypes.c_int, ctypes.c_int, ctypes.py_object, ctypes.py_object]

_ics_set_grid_concentrations = nrn_dll_sym('ics_set_grid_concentrations')
_ics_set_grid_concentrations.argtypes = [ctypes.c_int, ctypes.c_int, numpy.ctypeslib.ndpointer(dtype=numpy.int64), numpy.ctypeslib.ndpointer(dtype=numpy.int64), ctypes.py_object]

_set_grid_currents = nrn_dll_sym('set_grid_currents')
_set_grid_currents.argtypes = [ctypes.c_int, ctypes.c_int, ctypes.py_object, ctypes.py_object, ctypes.py_object]

_windows_dll_files = []
_windows_dll = []



make_time_ptr = nrn_dll_sym('make_time_ptr')
make_time_ptr.argtypes = [ctypes.py_object, ctypes.py_object]
make_time_ptr(h._ref_dt, h._ref_t)

_double_ptr = ctypes.POINTER(ctypes.c_double)
_int_ptr = ctypes.POINTER(_ctypes_c_int)
_long_ptr = ctypes.POINTER(ctypes.c_long)


fptr_prototype = ctypes.CFUNCTYPE(None)
set_nonvint_block = nrn_dll_sym('set_nonvint_block')
set_nonvint_block(nrn_dll_sym('rxd_nonvint_block'))

set_setup = nrn_dll_sym('set_setup')
set_setup.argtypes = [fptr_prototype]
set_initialize = nrn_dll_sym('set_initialize')
set_initialize.argtypes = [fptr_prototype]

scatter_concentrations = nrn_dll_sym('scatter_concentrations')

# Transfer extracellular concentrations to NEURON
_fih_transfer_ecs = h.FInitializeHandler(1, scatter_concentrations)


rxd_set_no_diffusion = nrn_dll_sym('rxd_set_no_diffusion')

setup_solver = nrn_dll_sym('setup_solver')

def _ode_jacobian(dt, t, ypred, fpred):
    #print '_ode_jacobian: dt = %g, last_dt = %r' % (dt, _last_dt)
    lo = _rxd_offset
    hi = lo + len(_nonzero_volume_indices)    
    _reaction_matrix_setup(dt, ypred[lo : hi])

_curr_ptr_vector = None
_curr_ptr_storage = None
_curr_ptr_storage_nrn = None
pinverse = None
_cur_map = None
_h_ptrvector = h.PtrVector
_h_vector = h.Vector

_structure_change_count = nrn_dll_sym('structure_change_cnt', _ctypes_c_int)
_diam_change_count = nrn_dll_sym('diam_change_cnt', _ctypes_c_int)

def _donothing(): pass

def _update_node_data(force=False, newspecies=False):
    global last_diam_change_cnt, last_structure_change_cnt, _curr_indices, _cur_node_indices, _curr_scales, _curr_ptrs, _cur_map
    global _curr_ptr_vector, _curr_ptr_storage, _curr_ptr_storage_nrn
    if last_diam_change_cnt != _diam_change_count.value or _structure_change_count.value != last_structure_change_cnt or force:
        _cur_map = {}
        last_diam_change_cnt = _diam_change_count.value
        last_structure_change_cnt = _structure_change_count.value
        #if not species._has_3d:
        # TODO: merge this with the 3d/hybrid case?
        if initializer.is_initialized():
            nsegs_changed = 0
            for sr in _species_get_all_species():
                s = sr()

ICS_insert.restype = ctypes.c_int

species_atolscale = nrn_dll_sym('species_atolscale')
species_atolscale.argtypes = [ctypes.c_int, ctypes.c_double, ctypes.c_int, ctypes.POINTER(ctypes.c_int)]

_set_grid_concentrations = nrn_dll_sym('set_grid_concentrations')
_set_grid_concentrations.argtypes = [ctypes.c_int, ctypes.c_int, ctypes.py_object, ctypes.py_object]

_ics_set_grid_concentrations = nrn_dll_sym('ics_set_grid_concentrations')
_ics_set_grid_concentrations.argtypes = [ctypes.c_int, ctypes.c_int, numpy.ctypeslib.ndpointer(dtype=numpy.int64), numpy.ctypeslib.ndpointer(dtype=numpy.int64), ctypes.py_object]

_set_grid_currents = nrn_dll_sym('set_grid_currents')
_set_grid_currents.argtypes = [ctypes.c_int, ctypes.c_int, ctypes.py_object, ctypes.py_object, ctypes.py_object]

_ics_set_grid_currents = nrn_dll_sym('ics_set_grid_currents')
_ics_set_grid_currents.argtypes = [ctypes.c_int, ctypes.c_int, numpy.ctypeslib.ndpointer(dtype=numpy.int64), numpy.ctypeslib.ndpointer(dtype=numpy.int64), ctypes.py_object, numpy.ctypeslib.ndpointer(dtype=numpy.float_)]


_delete_by_id = nrn_dll_sym('delete_by_id')
_delete_by_id.argtypes = [ctypes.c_int]


# The difference here is that defined species only exists after rxd initialization
_all_species = []
_defined_species = {}
def _get_all_species():
    return _defined_species

_extracellular_diffusion_objects = weakref.WeakKeyDictionary()
_intracellular_diffusion_objects = weakref.WeakKeyDictionary()

fptr_prototype = ctypes.CFUNCTYPE(None)
set_nonvint_block = nrn_dll_sym('set_nonvint_block')
set_nonvint_block(nrn_dll_sym('rxd_nonvint_block'))

set_setup = nrn_dll_sym('set_setup')
set_setup.argtypes = [fptr_prototype]
set_initialize = nrn_dll_sym('set_initialize')
set_initialize.argtypes = [fptr_prototype]

scatter_concentrations = nrn_dll_sym('scatter_concentrations')

# Transfer extracellular concentrations to NEURON
_fih_transfer_ecs = h.FInitializeHandler(1, scatter_concentrations)


rxd_set_no_diffusion = nrn_dll_sym('rxd_set_no_diffusion')

setup_solver = nrn_dll_sym('setup_solver')
setup_solver.argtypes = [ndpointer(ctypes.c_double), ctypes.c_int,  numpy.ctypeslib.ndpointer(numpy.int_, flags='contiguous'), ctypes.c_int, ctypes.py_object, ctypes.py_object]

#states = None
_set_num_threads = nrn_dll_sym('set_num_threads')
_set_num_threads.argtypes = [ctypes.c_int]
_get_num_threads = nrn_dll_sym('get_num_threads')
_get_num_threads.restype = ctypes.c_int


clear_rates = nrn_dll_sym('clear_rates')
register_rate = nrn_dll_sym('register_rate')
register_rate.argtypes = [ 
        ctypes.c_int,                                                               #num species
        ctypes.c_int,                                                               #num regions

set_nonvint_block(nrn_dll_sym('rxd_nonvint_block'))

set_setup = nrn_dll_sym('set_setup')
set_setup.argtypes = [fptr_prototype]
set_initialize = nrn_dll_sym('set_initialize')
set_initialize.argtypes = [fptr_prototype]

scatter_concentrations = nrn_dll_sym('scatter_concentrations')

# Transfer extracellular concentrations to NEURON
_fih_transfer_ecs = h.FInitializeHandler(1, scatter_concentrations)


rxd_set_no_diffusion = nrn_dll_sym('rxd_set_no_diffusion')

setup_solver = nrn_dll_sym('setup_solver')
setup_solver.argtypes = [ndpointer(ctypes.c_double), ctypes.c_int,  numpy.ctypeslib.ndpointer(numpy.int_, flags='contiguous'), ctypes.c_int, ctypes.py_object, ctypes.py_object]

#states = None
_set_num_threads = nrn_dll_sym('set_num_threads')
_set_num_threads.argtypes = [ctypes.c_int]
_get_num_threads = nrn_dll_sym('get_num_threads')
_get_num_threads.restype = ctypes.c_int


clear_rates = nrn_dll_sym('clear_rates')
register_rate = nrn_dll_sym('register_rate')
register_rate.argtypes = [ 
        ctypes.c_int,                                                               #num species
        ctypes.c_int,                                                               #num regions
        ctypes.c_int,                                                               #num seg
        numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),                #species ids

_fih_transfer_ecs = h.FInitializeHandler(1, scatter_concentrations)


rxd_set_no_diffusion = nrn_dll_sym('rxd_set_no_diffusion')

setup_solver = nrn_dll_sym('setup_solver')
setup_solver.argtypes = [ndpointer(ctypes.c_double), ctypes.c_int,  numpy.ctypeslib.ndpointer(numpy.int_, flags='contiguous'), ctypes.c_int, ctypes.py_object, ctypes.py_object]

#states = None
_set_num_threads = nrn_dll_sym('set_num_threads')
_set_num_threads.argtypes = [ctypes.c_int]
_get_num_threads = nrn_dll_sym('get_num_threads')
_get_num_threads.restype = ctypes.c_int


clear_rates = nrn_dll_sym('clear_rates')
register_rate = nrn_dll_sym('register_rate')
register_rate.argtypes = [ 
        ctypes.c_int,                                                               #num species
        ctypes.c_int,                                                               #num parameters
        ctypes.c_int,                                                               #num regions
        ctypes.c_int,                                                               #num seg
        numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),                #species ids
        ctypes.c_int,                                                               #num ecs species
        ctypes.c_int,                                                               #num ecs parameters
        numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),                #ecs species ids
        numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),                #ecs indices
        ctypes.c_int,                                                               #num multicompartment reactions
        numpy.ctypeslib.ndpointer(ctypes.c_double, flags='contiguous'),             #multicompartment multipliers
        ctypes.POINTER(ctypes.py_object),                                           #voltage pointers
        ]                                                                           #Reaction rate function

set_initialize = nrn_dll_sym('set_initialize')
set_initialize.argtypes = [fptr_prototype]

scatter_concentrations = nrn_dll_sym('scatter_concentrations')

# Transfer extracellular concentrations to NEURON
_fih_transfer_ecs = h.FInitializeHandler(1, scatter_concentrations)


rxd_set_no_diffusion = nrn_dll_sym('rxd_set_no_diffusion')

setup_solver = nrn_dll_sym('setup_solver')
setup_solver.argtypes = [ndpointer(ctypes.c_double), ctypes.c_int,  numpy.ctypeslib.ndpointer(numpy.int_, flags='contiguous'), ctypes.c_int, ctypes.py_object, ctypes.py_object]

#states = None
_set_num_threads = nrn_dll_sym('set_num_threads')
_set_num_threads.argtypes = [ctypes.c_int]
_get_num_threads = nrn_dll_sym('get_num_threads')
_get_num_threads.restype = ctypes.c_int


clear_rates = nrn_dll_sym('clear_rates')
register_rate = nrn_dll_sym('register_rate')
register_rate.argtypes = [ 
        ctypes.c_int,                                                               #num species
        ctypes.c_int,                                                               #num regions
        ctypes.c_int,                                                               #num seg
        numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),                #species ids
        ctypes.c_int, numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),  #num ecs species
        numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),                #ecs species ids
        ctypes.c_int,                                                               #num multicompartment reactions
        numpy.ctypeslib.ndpointer(ctypes.c_double, flags='contiguous'),             #multicompartment multipliers

clear_rates = nrn_dll_sym('clear_rates')
register_rate = nrn_dll_sym('register_rate')
register_rate.argtypes = [ 
        ctypes.c_int,                                                               #num species
        ctypes.c_int,                                                               #num regions
        ctypes.c_int,                                                               #num seg
        numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),                #species ids
        ctypes.c_int, numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),  #num ecs species
        numpy.ctypeslib.ndpointer(ctypes.c_int, flags='contiguous'),                #ecs species ids
        ctypes.c_int,                                                               #num multicompartment reactions
        numpy.ctypeslib.ndpointer(ctypes.c_double, flags='contiguous'),             #multicompartment multipliers
        ctypes.POINTER(ctypes.py_object),                                           #voltage pointers
        ]                                                                           #Reaction rate function

setup_currents = nrn_dll_sym('setup_currents')
setup_currents.argtypes = [
    ctypes.c_int,   #number of membrane currents
    ctypes.c_int,   #number induced currents
    ctypes.c_int,   #number of nodes with membrane currents
    _int_ptr,       #number of species involved in each membrane current
    _int_ptr,       #charges of the species involved in each membrane current
    _int_ptr,       #node indices
    _int_ptr,       #node indices
    _double_ptr,    #scaling (areas) of the fluxes
    _int_ptr,       #charges for each species in each reation
    ctypes.POINTER(ctypes.py_object),    #hoc pointers
    _int_ptr,       #maps for membrane fluxes
    _int_ptr        #maps for ecs fluxes
]

def _do_nbs_register():
    global _has_nbs_registered, _nbs, _fih, _fih2, _fih3, do_setup_matrices_fptr
    
    if not _has_nbs_registered:
        #from neuron import nonvint_block_supervisor as _nbs

        _has_nbs_registered = True
        #_nbs.register(_callbacks)  not used by crxd
    
        #
        # register the initialization handler and the ion register handler
        #
        _fih = h.FInitializeHandler(_init_concentration)
        _fih3 = h.FInitializeHandler(3, _init)

        set_setup_matrices = nrn_dll_sym('set_setup_matrices')
        set_setup_matrices.argtypes = [fptr_prototype]
        do_setup_matrices_fptr = fptr_prototype(_setup_matrices)
        set_setup_matrices(do_setup_matrices_fptr)

        _fih2 = h.FInitializeHandler(3, initializer._do_ion_register)


        #
        # register scatter/gather mechanisms
        #
        _cvode_object.extra_scatter_gather(0, _after_advance)