def f(x):
y = x**2
if invoke:
if h.cas() == dend and x == 1.0:
1 / 0
if h.cas() == dend and x > 0.6:
sys.exit(0)
print("{}({})".format(h.cas(), x))
return y
def testSectionListIterator(self):
"""As of v8.0, iteration over a SectionList does not change the cas"""
# See issue 509. SectionList iterator bug requires change to
# longstanding behavior
soma = h.Section(name='soma')
soma.push()
sections = [h.Section(name='s%d' % i) for i in range(3)]
assert len([s for s in h.allsec()]) == 4
sl = h.SectionList(sections)
# Iteration over s SectionList does not change the currently accessed section
for s in sl:
assert 1 and h.cas() == soma
# If an iteration does not complete the section stack is still ok.
assert sections[1] in sl
assert 2 and h.cas() == soma
def setup(self):
h.cvode.use_fast_imem(
1
) # enables fast calculation of transmembrane current (nA) at each segment
self.bscallback = h.beforestep_callback(h.cas()(.5))
self.bscallback.set_callback(self.callback)
fih = h.FInitializeHandler(1, self.LFPinit)
def importCell (fileName, cellName, cellArgs = None, cellInstance = False):
h.initnrn()
varList = mechVarList() # list of properties for all density mechanisms and point processes
origGlob = getGlobals(list(varList['mechs'].keys())+list(varList['pointps'].keys()))
origGlob['v_init'] = -65 # add by hand since won't be set unless load h.load_file('stdrun')
if cellArgs is None: cellArgs = [] # Define as empty list if not otherwise defined
''' Import cell from HOC template or python file into framework format (dict of sections, with geom, topol, mechs, syns)'''
if fileName.endswith('.hoc') or fileName.endswith('.tem'):
h.load_file(fileName)
if not cellInstance:
if isinstance(cellArgs, dict):
cell = getattr(h, cellName)(**cellArgs) # create cell using template, passing dict with args
else:
cell = getattr(h, cellName)(*cellArgs) # create cell using template, passing list with args
else:
try:
cell = getattr(h, cellName)
except:
cell = None
elif fileName.endswith('.py'):
filePath,fileNameOnly = os.path.split(fileName) # split path from filename
if filePath not in sys.path: # add to path if not there (need to import module)
sys.path.insert(0, filePath)
removeFilePath = True
else:
removeFilePath = False
moduleName = fileNameOnly.split('.py')[0] # remove .py to obtain module name
tempModule = importlib.import_module(moduleName)
modulePointer = tempModule
if isinstance(cellArgs, dict):
cell = getattr(modulePointer, cellName)(**cellArgs) # create cell using template, passing dict with args
else:
cell = getattr(modulePointer, cellName)(*cellArgs) # create cell using template, passing list with args
if removeFilePath: sys.path.remove(filePath)
else:
print("File name should be either .hoc or .py file")
return
secDic, secListDic, synMechs, globs = getCellParams(cell, varList, origGlob)
if fileName.endswith('.py'):
_delete_module(moduleName)
_delete_module('tempModule')
del modulePointer
elif fileName.endswith('.hoc'):
for sec in h.allsec():
try:
if h.cas()!=sec: sec.push()
h.delete_section()
h.pop_section()
except:
pass
h.initnrn()
setGlobals(origGlob) # restore original globals
return secDic, secListDic, synMechs, globs
def _get_syn_location(self, nc, cell):
if isinstance(cell, BioCell):
sec_x = nc.postloc()
sec = h.cas()
sec_id = self._sec_lookup[cell.gid][
sec] # cell.get_section_id(sec)
h.pop_section()
return sec_id, sec_x
else:
return -1, -1
def _print_nc(self, nc, src_nid, trg_nid, cell, src_pop, trg_pop,
edge_type_id):
if isinstance(cell, BioCell):
sec_x = nc.postloc()
sec = h.cas()
sec_id = self._sec_lookup[cell.gid][
sec] # cell.get_section_id(sec)
h.pop_section()
self._syn_writer.add_bio_conn(edge_type_id, src_nid, src_pop,
trg_nid, trg_pop, nc.weight[0],
sec_id, sec_x)
else:
self._syn_writer.add_point_conn(edge_type_id, src_nid, src_pop,
trg_nid, trg_pop, nc.weight[0])
def pre_synapse(self,j):
'''
search for viable synaptic vesicle sites.
'''
#from neuron import h
pc=h.ParallelContext()
shiplist=[]
h('objref coords')
h('coords = new Vector(3)')
#self.celldict.items()[0]
if j in self.celldict.keys():
seglist= iter( (seg, sec, self.celldict[j]) for sec in self.celldict[j].spk_trig_ls for seg in sec )
for (seg,sec, cellc) in seglist:
sec.push()
get_cox = str('coords.x[0]=x_xtra('
+ str(seg.x) + ')')
h(get_cox)
get_coy = str('coords.x[1]=y_xtra('
+ str(seg.x) + ')')
h(get_coy)
get_coz = str('coords.x[2]=z_xtra('
+ str(seg.x) + ')')
h(get_coz)
coordict={}
coordict['hostfrom'] = pc.id()
coordict['coords'] = np.array(h.coords.to_python(),
dtype=np.float64)
coordict['gid']= int(j)
coordict['seg']= seg.x
secnames = h.cas().name()#sec.name()
coordict['secnames'] = str(secnames)
shiplist.append(coordict)
h.pop_section()
'''
total_matrix=np.matrix(( 3,len(shiplist) ))
total_list=[ (x['coords'][0],x['coords'][1],x['coords'][2]) for x in shiplist ]
for i,j in enumerate(total_list):
print type(j)
#pdb.set_trace()
total_matrix[i][0]=j[0]
total_matrix[i][1]=j[1]
total_matrix[i][2]=j[2]
print total_array[:]
'''
return shiplist
def f(a, b, c, d):
l = list()
print h.cas().name()
l.append(h.NetCon(a, b, 0, 0, 1))
soma3.push()
print h.cas().name()
l.append(h.NetCon(c, d, 0, 0, 1))
h.pop_section()
print h.cas().name()
return l
def connect(v1, syn2, v3, syn4):
l = list()
print h.cas().name()
l.append(h.NetCon(v1, syn2, 0, 0, 0.5))
soma3.push()
print h.cas().name()
l.append(h.NetCon(v3, syn4, 0, 0, 1))
h.pop_section()
print h.cas().name()
return l
def p(type, x, y, keystate):
if type == 2:
d = vc.nearest(x, y)
arc = vc.push_selected()
if arc >= 0:
cs = h.cas()
#vc.color(2)
sn = str(cs)
match = re.search('\.(dend|soma)\d*\Z', sn)
if not match == None:
name = match.group(0)[5:]
print '%g from %s' % (d, name)
print "at x=", x, ", y=", y
vc.label(x, y, name, 1, 1, 0.5, 0., 5, 2)
#vc.label(x+378.941,y+457.031,name,1,1,0.5,0.5,2)
#vc.exec_menu("Change Text")
h.pop_section()
vc.flush()
def callback(self, type, x, y, keystate):
#info about nearest section to mouse
if type == 2:
s = self.sh
d = s.nearest(x, y)
arc = s.push_selected()
if arc >= 0:
s.select()
sec = h.cas()
gid = self.sections[sec]
ilayer, icircle, ipt = gid2org(gid)
x, y, z = xyz(ilayer, icircle, ipt)
print(
"gid %d id (%d, %d, %d) prox pt at (%g, %g, %g) length %g"
% (gid, ilayer, icircle, ipt, x, y, z, sec.L))
h.pop_section()
if self.master:
neighborhood(ilayer, icircle, ipt)
def addvar(self, label, var=None):
default_lab = False
if var is None:
var = label
default_lab = True
current_uuid = uuid.uuid4().hex
if (isinstance(var, str)): #retrieve cas
spl = var.split('(')
if len(spl) == 1:
seg = 0.5 #default
else:
seg = float(spl[1][:-1])
ptr = getattr(h.cas()(seg), "_ref_" + spl[0])
self.var_mappings.update({current_uuid: ptr})
if default_lab:
label = spl[0]
else: #TODO: if not a ptr
self.var_mappings.update({current_uuid: var})
self.labels.update({current_uuid: label})
logging.debug("added graph var: " + label)
return 1
def source_var(x, id):
src_var(h.cas()(x), id)
from neuron import h
a = h.Section(name='bob')
b = h.Section(name='bob')
print((a.same(b), a is b, a == b) == (False, False, False))
c = h.cas()
print((c.same(a), c == a, c.same(b), c is a, c is b) == (True, True, False,
True, False))
h('create s, d')
print((h.s.same(h.s), h.s is h.s, h.s == h.s) == (True, False, True))
print(h.s.same(5) == False)
print((h.s == 5) == False)
h('objref vv')
h('vv = new Vector(3)')
print((h.vv == h.vv, h.vv.same(h.vv)) == (False, True))
#now only in HocTopLevelInterpreter
names = ['ref', 'cas', 'allsec', 'Section', 'setpointer']
from neuron import h
o = h
d = dir(o)
for i in names:
assert(i in d)
print((eval("o.%s" % i).__doc__))
o = h.IClamp()
d = dir(o)
for i in names:
assert(i not in d)
assert('get_segment' in d)
print((o.get_segment.__doc__))
print("success")
s = [h.Section(name='s'+str(i)) for i in range(5)]
print(s)
for sec in h.allsec():
print((h.cas()))
r = h.ref("hello")
print((r[0] == 'hello'))
# Tutorial2.py
# Author : Jose Guzman
# Mail : jose.guzman __at__ physiologie.uni-freiburg.de
#! /usr/bin/env python
import neuron
import nrn
from neuron import h
# create soma object
soma = nrn.Section()
# soma attributes
soma.L = 30
soma.nseg = 3
soma.diam = 30
h('''
NDEND = 2
create soma, basal[NDEND], axon
access basal[1]
''')
sec = h.cas()
print (sec(), sec.name())
from neuron import h, gui
from e import e
s = h.Section()
s.insert('hh')
iname = s.hoc_internal_name()
print(iname)
exec('s2 = h.' + iname)
print('s is s2', s is s2)
print('s is h.cas()', s is h.cas())
print('s == h.cas()', s == h.cas())
h('create soma')
s4 = h.soma
print(s4.hoc_internal_name())
exec('s5 = h.' + s4.hoc_internal_name())
print('s5 is s4', s5 is s4)
print('s5 == s4', s5 == s4)
print(s5.name())
s6 = h.Section(name="s6")
s6.name()
h.topology()
h('''__nrnsec_0x { print secname() }''')
e('s7 = h.__nrnsec_0x')
h('''__nrnsec_0xaaaa { print secname() }''')
e('s7 = h.__nrnsec_0xaaaa')
del(s)
print(s2)
def importCell(fileName, cellName, cellArgs=None, cellInstance=False):
"""
Function for/to <short description of `netpyne.conversion.neuronPyHoc.importCell`>
Parameters
----------
fileName : <type>
<Short description of fileName>
**Default:** *required*
cellName : <type>
<Short description of cellName>
**Default:** *required*
cellArgs : <``None``?>
<Short description of cellArgs>
**Default:** ``None``
**Options:** ``<option>`` <description of option>
cellInstance : bool
<Short description of cellInstance>
**Default:** ``False``
**Options:** ``<option>`` <description of option>
"""
h.initnrn()
varList = mechVarList(
) # list of properties for all density mechanisms and point processes
origGlob = getGlobals(
list(varList['mechs'].keys()) + list(varList['pointps'].keys()))
origGlob[
'v_init'] = -65 # add by hand since won't be set unless load h.load_file('stdrun')
if cellArgs is None:
cellArgs = [] # Define as empty list if not otherwise defined
if fileName.endswith('.hoc') or fileName.endswith('.tem'):
h.load_file(fileName)
if not cellInstance:
if isinstance(cellArgs, dict):
cell = getattr(h, cellName)(
**cellArgs
) # create cell using template, passing dict with args
else:
cell = getattr(h, cellName)(
*cellArgs
) # create cell using template, passing list with args
else:
try:
cell = getattr(h, cellName)
except:
cell = None
elif fileName.endswith('.py'):
filePath, fileNameOnly = os.path.split(
fileName) # split path from filename
if filePath not in sys.path: # add to path if not there (need to import module)
sys.path.insert(0, filePath)
removeFilePath = True
else:
removeFilePath = False
moduleName = fileNameOnly.split('.py')[
0] # remove .py to obtain module name
tempModule = importlib.import_module(moduleName)
modulePointer = tempModule
if isinstance(cellArgs, dict):
cell = getattr(
modulePointer, cellName
)(**cellArgs) # create cell using template, passing dict with args
else:
cell = getattr(modulePointer, cellName)(
*cellArgs
) # create cell using template, passing list with args
if removeFilePath: sys.path.remove(filePath)
else:
print("File name should be either .hoc or .py file")
return
secDic, secListDic, synMechs, globs = getCellParams(
cell, varList, origGlob)
if fileName.endswith('.py'):
_delete_module(moduleName)
_delete_module('tempModule')
del modulePointer
elif fileName.endswith('.hoc'):
for sec in h.allsec():
try:
if h.cas() != sec: sec.push()
h.delete_section()
h.pop_section()
except:
pass
h.initnrn()
setGlobals(origGlob) # restore original globals
return secDic, secListDic, synMechs, globs
from neuron import h soma = h.Section(name='soma') dend = h.Section(name='dend') print(soma == h.cas()) sr = h.SectionRef() print(soma == sr.sec) sr = h.SectionRef(sec=dend) print(dend == sr.sec) sr = h.SectionRef(dend) print(dend == sr.sec) print(soma == h.cas())
from neuron import h
import matplotlib.pyplot as plt
import numpy as np
h.load_file("nrngui.hoc") # load standard run system
soma = h.Section(name='soma')
print h.cas().name(), soma.name()
soma2 = h.Section(name='soma2')
print h.cas().name(), soma2.name()
soma.insert('hh_original')
soma2.insert('hh_original')
syn = h.Exp2Syn(0.5, sec=soma2)
syn.e = 0
syn.tau1 = 1
syn.tau2 = 3
net_con = h.NetCon(soma(0.5)._ref_v, syn, 0, 5, 0.07)
stim = h.IClamp(soma(0.5))
stim.delay = 1
stim.dur = 5
stim.amp = 20
rec_cell = h.Vector()
rec_cell.record(soma(0.5)._ref_v)
rec_cell2 = h.Vector()
rec_cell2.record(soma2(0.5)._ref_v)
rec_syn = h.Vector()
def root_section(self):
sref = nrn.SectionRef()
sref.root.push()
cas = nrn.cas()
nrn.pop_section()
return cas