def basicRxD3D():
from neuron import h, rxd
s = h.Section(name='s')
s.L = s.diam = 1
cyt = rxd.Region([s])
ca = rxd.Species(cyt)
rxd.set_solve_type(dimension=3)
h.finitialize(-65)
h.fadvance()
return 1
def neuron_instance(neuron_import):
"""Sets/Resets the rxd test environment.
Provides 'data', a dictionary used to store voltages and rxd node
values for comparisons with the 'correct_data'.
"""
h, rxd, save_path = neuron_import
data = {'record_count': 0, 'data': []}
h.load_file('stdrun.hoc')
h.nrnunit_use_legacy(True)
# pytest fixtures at the function scope that require neuron_instance will go # out of scope after neuron_instance. So species, sections, etc. will go
# out of scope after neuron_instance is torn down.
# Here we assert that no section left alive. If the assertion fails it is
# due to a problem with the previous test, not the test which failed.
gc.collect()
for sec in h.allsec():
assert (False)
cvode = h.CVode()
cvode.active(False)
cvode.atol(1e-3)
h.dt = 0.025
h.stoprun = False
def gather():
return collect_data(h, rxd, data, save_path)
cvode.extra_scatter_gather(0, gather)
yield (h, rxd, data)
for r in rxd.rxd._all_reactions[:]:
if r():
rxd.rxd._unregister_reaction(r)
for s in rxd.species._all_species:
if s():
s().__del__()
rxd.region._all_regions = []
rxd.region._region_count = 0
rxd.region._c_region_lookup = None
rxd.species._species_counts = 0
rxd.section1d._purge_cptrs()
rxd.initializer.has_initialized = False
rxd.rxd.free_conc_ptrs()
rxd.rxd.free_curr_ptrs()
rxd.rxd.rxd_include_node_flux1D(0, None, None, None)
rxd.species._has_1d = False
rxd.species._has_3d = False
rxd.rxd._zero_volume_indices = numpy.ndarray(0, dtype=numpy.int_)
rxd.set_solve_type(dimension=1)
cvode.extra_scatter_gather_remove(gather)
def neuron_instance(neuron_import):
"""Sets/Resets the rxd test environment.
Provides 'data', a dictionary used to store voltages and rxd node
values for comparisons with the 'correct_data'.
"""
h, rxd = neuron_import
data = {'record_count': 0, 'data': []}
h.load_file('stdrun.hoc')
cvode = h.CVode()
cvode.active(False)
cvode.atol(1e-3)
h.dt = 0.025
h.stoprun = False
def gather():
return collect_data(h, rxd, data)
cvode.extra_scatter_gather(0, gather)
yield (h, rxd, data)
rxd.region._all_regions = []
rxd.region._region_count = 0
rxd.region._c_region_lookup = None
for r in rxd.rxd._all_reactions[:]:
if r():
rxd.rxd._unregister_reaction(r)
for s in rxd.species._all_species:
if s():
s().__del__()
rxd.species._species_counts = 0
rxd.section1d._rxd_sec_lookup = {}
rxd.section1d._purge_cptrs()
rxd.initializer.has_initialized = False
rxd.rxd.free_conc_ptrs()
rxd.rxd.free_curr_ptrs()
rxd.rxd.rxd_include_node_flux1D(0, None, None, None)
for sec in h.allsec():
h.disconnect(sec=sec)
sref = h.SectionRef(sec=sec)
sref.rename('delete')
h.delete_section(sec=sec)
rxd.species._has_1d = False
rxd.species._has_3d = False
rxd.rxd._memb_cur_ptrs = []
rxd.rxd._rxd_induced_currents = None
rxd.rxd._curr_indices = None
rxd.rxd._zero_volume_indices = numpy.ndarray(0, dtype=numpy.int_)
rxd.set_solve_type(dimension=1)
cvode.extra_scatter_gather_remove(gather)
def neuron_nosave_instance(neuron_import):
"""Sets/Resets the rxd test environment."""
h, rxd, save_path = neuron_import
h.load_file("stdrun.hoc")
h.load_file("import3d.hoc")
h.nrnunit_use_legacy(True)
# pytest fixtures at the function scope that require neuron_instance will go # out of scope after neuron_instance. So species, sections, etc. will go
# out of scope after neuron_instance is torn down.
# Here we assert that no section left alive. If the assertion fails it is
# due to a problem with the previous test, not the test which failed.
gc.collect()
for sec in h.allsec():
assert False
cvode = h.CVode()
cvode.active(False)
cvode.atol(1e-3)
h.dt = 0.025
h.stoprun = False
yield (h, rxd, save_path)
for r in rxd.rxd._all_reactions[:]:
if r():
rxd.rxd._unregister_reaction(r)
for s in rxd.species._all_species:
if s():
s().__del__()
rxd.region._all_regions = []
rxd.region._region_count = 0
rxd.region._c_region_lookup = None
rxd.species._species_counts = 0
rxd.section1d._purge_cptrs()
rxd.initializer.has_initialized = False
rxd.rxd.free_conc_ptrs()
rxd.rxd.free_curr_ptrs()
rxd.rxd.rxd_include_node_flux1D(0, None, None, None)
rxd.species._has_1d = False
rxd.species._has_3d = False
rxd.rxd._zero_volume_indices = numpy.ndarray(0, dtype=numpy.int_)
rxd.set_solve_type(dimension=1)
def setnsubseg():
global mGLURRWM
if nsubseg > 0:
print 'setting rxd nsubseg to ', dconf['nsubseg']
rxd.set_solve_type(nsubseg=dconf['nsubseg'])
mGLURRWM /= float(nsubseg)
print 'adjusted mGLURRWM to ', mGLURRWM
elif subsegum > 0.0:
for sec in cell.all_sec:
ns = int(sec.L / subsegum)
if ns > 1:
if ns % 2 == 0: ns += 1
print 'L = ', sec.L, ' subseg = ', ns
rxd.set_solve_type(sec, nsubseg=ns)
if sec == cell.Adend3:
mGLURRWM /= float(ns)
print 'adjusted mGLURRWM to ', mGLURRWM
else:
print 'L = ', sec.L, ' not using subseg'
rxd.options.subseg_interpolation = 1
rxd.options.subseg_averaging = 1
from neuron import h, rxd
h.load_file("stdrun.hoc")
sec = h.Section(name="sec")
sec.L = 10
sec.nseg = 11
sec.diam = 5
rxd.set_solve_type(dimension=3)
cyt = rxd.Region(h.allsec(), name="cyt", nrn_region="i")
ip3 = rxd.Species(cyt,
name="ip3",
initial=lambda nd: 1000 if nd.segment == sec(0.3) else 0)
def callbackfun():
return 1000
for nd in ip3.nodes(sec(0.1)):
nd.include_flux(1000)
for nd in ip3.nodes(sec(0.5)):
nd.include_flux(callbackfun)
for nd in ip3.nodes(sec(0.9)):
nd.include_flux(sec(0.3)._ref_ip3i)
h.finitialize(-70)
h.continuerun(10)
import numpy
