def __init__(self, seg):
self.seg = seg #dangerous as contents can disappear when nseg changes
self.call = [self.setup, self.initialize,
self.current, self.conductance, self.fixed_step_solve,
self.ode_count, self.ode_reinit, self.ode_fun, self.ode_solve, None,
None
]
self.gkbar = .036
nbs.register(self.call)
def __init__(self, sectionlist=None):
if sectionlist:
self.sl = sectionlist
else:
self.sl = h.SectionList()
for sec in h.allsec():
self.sl.append()
self.call = [self.setup, self.initialize,
self.current, self.conductance, self.fixed_step_solve,
self.ode_count, self.ode_reinit, self.ode_fun, self.ode_solve, None,
None, self.statename
]
self.gkbar = .036
nbs.register(self.call)
def test_nonvint_block_supervisor():
# making sure we can import
from neuron import nonvint_block_supervisor
# and can still use threads (no registered callbacks)
pc = h.ParallelContext()
pc.nthread(2)
h.finitialize()
# but if there is a callback it will fail with threads
nonvint_block_supervisor.register([None for _ in range(11)])
expect_hocerr(h.finitialize, (-65, ))
# but can be cleared
nonvint_block_supervisor.clear()
h.finitialize()
pc.nthread(1)
def _do_nbs_register():
global _has_nbs_registered, _nbs, _fih, _fih2
if not _has_nbs_registered:
from neuron import nonvint_block_supervisor as _nbs
_has_nbs_registered = True
_nbs.register(_callbacks)
#
# register the initialization handler and the ion register handler
#
_fih = h.FInitializeHandler(_init)
_fih2 = h.FInitializeHandler(3, initializer._do_ion_register)
#
# register scatter/gather mechanisms
#
_cvode_object.extra_scatter_gather(0, _after_advance)
def _do_nbs_register():
global _has_nbs_registered, _nbs, _fih, _fih2
if not _has_nbs_registered:
from neuron import nonvint_block_supervisor as _nbs
_has_nbs_registered = True
_nbs.register(_callbacks)
#
# register the initialization handler and the ion register handler
#
_fih = h.FInitializeHandler(_init)
_fih2 = h.FInitializeHandler(3, initializer._do_ion_register)
#
# register scatter/gather mechanisms
#
_cvode_object.extra_scatter_gather(0, _after_advance)
def _conductance(d):
pass
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])
_callbacks = [
_setup, None, _fixed_step_currents, _conductance, _fixed_step_solve,
_ode_count, _ode_reinit, _ode_fun, _ode_solve, _ode_jacobian, None
]
nbs.register(_callbacks)
_curr_ptr_vector = None
_curr_ptr_storage = None
_curr_ptr_storage_nrn = None
def _update_node_data(force=False):
global last_diam_change_cnt, last_structure_change_cnt, _curr_indices, _curr_scales, _curr_ptrs
global _curr_ptr_vector, _curr_ptr_storage, _curr_ptr_storage_nrn
if last_diam_change_cnt != _cvode_object.diam_change_count(
) or _cvode_object.structure_change_count(
) != last_structure_change_cnt or force:
last_diam_change_cnt = _cvode_object.diam_change_count()
last_structure_change_cnt = _cvode_object.structure_change_count()
for sr in species._get_all_species().values():
print(h.f())
h.x = 4
print(h.x)
h.y[2] = 6
print(h.y[2])
a = h.A()
a.call(callback)
from neuron import h, nonvint_block_supervisor
h.load_file('stdrun.hoc')
_callbacks = [None] * 11
_callbacks[1] = callback
nonvint_block_supervisor.register(_callbacks)
#h.cvode_active(0)
h('''
begintemplate B
proc call() {
// anything that ends up calling a nonvint_block_supervisor callback
// that calls 'def callback' within this context
finitialize()
}
endtemplate B
''')
h.finitialize()
print('ok so far')
_react_matrix_solver = lambda x: x
def _setup():
# TODO: this is when I should resetup matrices (structure changed event)
pass
def _conductance(d):
pass
def _ode_jacobian(dt, t, ypred, fpred):
#print '_ode_jacobian: dt = %g, last_dt = %r' % (dt, _last_dt)
_reaction_matrix_setup(dt, fpred)
_callbacks = [_setup, None, _fixed_step_currents, _conductance, _fixed_step_solve,
_ode_count, _ode_reinit, _ode_fun, _ode_solve, _ode_jacobian, None]
nbs.register(_callbacks)
_curr_ptr_vector = None
_curr_ptr_storage = None
_curr_ptr_storage_nrn = None
def _update_node_data(force=False):
global last_diam_change_cnt, last_structure_change_cnt, _curr_indices, _curr_scales, _curr_ptrs
global _curr_ptr_vector, _curr_ptr_storage, _curr_ptr_storage_nrn
if last_diam_change_cnt != _cvode_object.diam_change_count() or _cvode_object.structure_change_count() != last_structure_change_cnt or force:
last_diam_change_cnt = _cvode_object.diam_change_count()
last_structure_change_cnt = _cvode_object.structure_change_count()
for sr in species._get_all_species().values():
s = sr()
if s is not None: s._update_node_data()
for sr in species._get_all_species().values():