def get_mech_globals(mechname, var=-1):
ms = h.MechanismStandard(mechname, var)
name = h.ref('')
mech_globals = {}
for j in range(ms.count()):
ms.name(name, j)
mech_globals[name[0]] = getattr(h, name[0])
return mech_globals
def pname(msname):
s = h.ref('')
for i in range(-1, 4):
ms = h.MechanismStandard(msname, i)
print('\n', msname, ' vartype=%d' % i) # vartype = 1 -> PARAMETER
for j in range(int(ms.count())):
k = ms.name(s, j)
print('%-5d %-20s size=%d' % (j, s[0], k))
def cellran(gid, nclist):
r = h.Random()
r.Random123(gid)
r.uniform(1.0, 1.1)
cell = pc.gid2cell(gid)
for sec in cell.all:
sec.L *= r.repick()
for seg in sec:
seg.diam *= r.repick()
seg.cm *= r.repick()
#print 'diam ', seg.diam, 'cm ', seg.cm
#mechanism variables
for mech in seg:
ms = h.MechanismStandard(mech.name(), 1)
for i in range(int(ms.count())):
varname = h.ref("")
sz = ms.name(varname, i)
n = varname[0]
x = seg.__getattribute__(n)
setattr(seg, n, x * r.repick())
#print n, seg.__getattribute__(n)
#point process parameters
for p in seg.point_processes():
n = p.hname()
n = n[:n.index('[')]
if n == 'HalfGap':
continue
ms = h.MechanismStandard(n, 1)
for i in range(int(ms.count())):
varname = h.ref("")
ms.name(varname, i)
x = p.__getattribute__(varname[0])
setattr(p, varname[0], x * r.repick())
#print varname[0], p.__getattribute__(varname[0])
#netcons targeting the cell
for nc in nclist:
if nc.postcell() == cell:
nc.weight[0] *= r.repick()
nc.delay *= r.repick()
pc.threshold(gid, pc.threshold(gid) + r.uniform(-9, 0))
def get_mech_globals(mechname):
ms = h.MechanismStandard(mechname, -1)
name = h.ref('')
mech_globals = []
integer2 = int(ms.count())
for j in range(integer2):
ms.name(name, j)
mech_globals.append(name[0])
return mech_globals
def uses_pointer(mechname):
# do not get involved with POINTER
ms = h.MechanismStandard(mechname, 0)
for i in range(int(ms.count())):
n = h.ref("")
ms.name(n, i)
if ms.get(n[0]) == -1e+300:
return True
return False
def barname(mech='it'):
'''return the name of a gbar (max conductance) for a given mechanism name'''
l = []
pname, ms = h.ref(''), h.MechanismStandard(mech, 1)
for i in range(int(ms.count())):
ms.name(pname, i)
l.append(pname[0])
ll = [x for x in l if 'bar' in x]
if len(ll) != 1:
raise Exception("Can't identify proper parameter for %s: %s" %
(mech, ll))
return ll[0]
def get_rangevars(mech_name):
ms = h.MechanismStandard(mech_name)
suffix = '_' + mech_name
lensuffix = len(suffix)
mname = h.ref('')
result = []
for i in range(int(ms.count())):
ms.name(mname, i)
my_mname = mname[0]
if my_mname.endswith(suffix):
my_mname = my_mname[:-lensuffix]
result.append({'type': 'NEURONMECH', 'mech': mech_name, 'var': my_mname, 'name': mech_name + '.' + my_mname})
return result
def mechVarList ():
msname = h.ref('')
varList = {}
for i, mechtype in enumerate(['mechs','pointps']):
mt = h.MechanismType(i) # either distributed mechs (0) or point process (1)
varList[mechtype] = {}
for j in xrange(int(mt.count())):
mt.select(j)
mt.selected(msname)
ms = h.MechanismStandard(msname[0], 1) # PARAMETER (modifiable)
varList[mechtype][msname[0]] = []
propName = h.ref('')
for var in xrange(int(ms.count())):
k = ms.name(propName, var)
varList[mechtype][msname[0]].append(propName[0])
return varList
def get_rangevars(mech_name):
ms = h.MechanismStandard(mech_name)
suffix = "_" + mech_name
lensuffix = len(suffix)
mname = h.ref("")
result = []
for i in range(int(ms.count())):
ms.name(mname, i)
my_mname = mname[0]
if my_mname.endswith(suffix):
my_mname = my_mname[:-lensuffix]
result.append({
"type": "NEURONMECH",
"mech": mech_name,
"var": my_mname,
"name": mech_name + "." + my_mname,
})
return result
def ptype():
msname = h.ref('')
propList = {}
for i, mechtype in enumerate(['mechs', 'pointps']):
mt = h.MechanismType(
i) # either distributed mechs (0) or point process (1)
propList[mechtype] = {}
for j in range(int(mt.count())):
mt.select(j)
mt.selected(msname)
print('\n\n', msname[0], ' mechanismtype=%d' % j)
pname(msname[0])
ms = h.MechanismStandard(msname[0], 1) # PARAMETER (modifiable)
propList[mechtype][msname[0]] = []
propName = h.ref('')
for prop in range(int(ms.count())):
k = ms.name(propName, prop)
propList[mechtype][msname[0]].append(propName[0])
print(propList)
def setchans(mun=3,
pnafjr=0.0,
gnamult=1.0,
gcabar=None,
gcavfac=1.0,
tyli=['TC', 'RE', 'PY', 'IN']):
it2 = it2l[mun]
ms = h.MechanismStandard(it2, 1)
print "Using %s channels" % it2
gcab = gcabar if gcabar else 3e-3
for k in ['TC', 'RE']:
vals = thalDict[k]
for ce in vals['cel']:
ce.soma[0].gnabar_hh2nafjr = pnafjr * gnamult * vals[
'gnabar'] # what is this??
ce.soma[0].gnabar_hh2 = (1 - pnafjr) * gnamult * vals['gnabar']
for ce in thalDict['RE'][
'cel']: # just set the RE one for now; corrD=3.777 for surface correction (Cav32RE3cc.hoc:105:257)
sec = ce.soma[0]
for v in thalDict['RE']['T'].values():
sec.__setattr__(v, 0.0) # turn all off
sec.__setattr__(thalDict['RE']['T'][it2], gcab * gcavfac)
def mechVarList():
"""
Function for/to <short description of `netpyne.conversion.neuronPyHoc.mechVarList`>
"""
msname = h.ref('')
varList = {}
for i, mechtype in enumerate(['mechs', 'pointps']):
mt = h.MechanismType(
i) # either distributed mechs (0) or point process (1)
varList[mechtype] = {}
for j in range(int(mt.count())):
mt.select(j)
mt.selected(msname)
ms = h.MechanismStandard(msname[0], 1) # PARAMETER (modifiable)
varList[mechtype][msname[0]] = []
propName = h.ref('')
for var in range(int(ms.count())):
k = ms.name(propName, var)
varList[mechtype][msname[0]].append(propName[0])
return varList
action['marker_mouseovers'] = pointprocess_mouseovers_by_root[name][root]
except:
pass
child['action'].append(action)
if 'children' in child:
for grandchild in child['children']:
grandchild['noop'] = True
# get the names of mechanism parameters (range_vars)
range_vars = {}
for mech in mech_names:
h.mt = h.MechanismStandard(mech)
range_vars[mech] = []
suffix = '_' + mech
lensuffix = len(suffix)
for i in xrange(int(h.mt.count())):
h('mt.name(mname, %d)' % i)
mname = h.mname
if mname[-lensuffix :] == suffix:
mname = mname[: -lensuffix]
range_vars[mech].append(mname)
if not range_vars[mech]: del range_vars[mech]
#print 'range_vars:', range_vars
def mechs_present(secs):
result = []
def psection(sec):
from neuron import h, _has_rxd
try:
if _has_rxd['crxd']:
from neuron import crxd as rxd
from neuron.crxd import region, species
from neuron.crxd import rxd as rxd_module
else:
from neuron import rxd
from neuron.rxd import region, species
from neuron.rxd import rxd as rxd_module
have_rxd = True
except:
have_rxd = False
results = {}
mname = h.ref('')
# point processes
pps = {}
mt = h.MechanismType(1)
for i in range(int(mt.count())):
mt.select(i)
mypps = set()
pp = mt.pp_begin(sec=sec)
while pp is not None:
mypps.add(pp)
pp = mt.pp_next()
if mypps:
mt.selected(mname)
pps[mname[0]] = mypps
results['point_processes'] = pps
center_seg_dir = dir(sec(0.5))
mechs_present = []
# membrane mechanisms
mt = h.MechanismType(0)
for i in range(int(mt.count())):
mt.select(i)
mt.selected(mname)
name = mname[0]
if name in center_seg_dir:
mechs_present.append(name)
results['density_mechs'] = {}
results['ions'] = {}
for mech in mechs_present:
my_results = {}
ms = h.MechanismStandard(mech, 0)
for j in range(int(ms.count())):
n = int(ms.name(mname, j))
name = mname[0]
pvals = []
# TODO: technically this is assuming everything that ends with _ion
# is an ion. Check this.
if mech.endswith('_ion'):
pvals = [getattr(seg, name) for seg in sec]
else:
mechname = name #+ '_' + mech
for seg in sec:
if n > 1:
pvals.append(
[getattr(seg, mechname)[i] for i in range(n)])
else:
pvals.append(getattr(seg, mechname))
my_results[name[:-(len(mech) +
1)] if name.endswith('_' +
mech) else name] = pvals
# TODO: should be a better way of testing if an ion
if mech.endswith('_ion'):
results['ions'][mech[:-4]] = my_results
else:
results['density_mechs'][mech] = my_results
morphology = {
'L':
sec.L,
'diam': [seg.diam for seg in sec],
'pts3d': [(sec.x3d(i), sec.y3d(i), sec.z3d(i), sec.diam3d(i))
for i in range(sec.n3d())],
'parent':
sec.parentseg(),
'trueparent':
sec.trueparentseg()
}
results['morphology'] = morphology
results['nseg'] = sec.nseg
results['Ra'] = sec.Ra
results['cm'] = [seg.cm for seg in sec]
if have_rxd:
regions = {
r()
for r in region._all_regions if r() is not None and sec in r().secs
}
results['regions'] = regions
my_species = []
for sp in species._all_species:
sp = sp()
if sp is not None:
sp_regions = sp._regions
if not hasattr(sp_regions, '__len__'):
sp_regions = [sp_regions]
if any(r in sp_regions for r in regions):
my_species.append(sp)
results['species'] = set(my_species)
results['name'] = sec.hname()
results['hoc_internal_name'] = sec.hoc_internal_name()
results['cell'] = sec.cell()
#all_active_reactions = [r() for r in rxd_module._all_reactions if r() is not None]
return results
