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 getSecName(sec, dirCellSecNames=None):
if dirCellSecNames is None: dirCellSecNames = {}
if '>.' in sec.name():
fullSecName = sec.name().split('>.')[1]
elif '.' in sec.name():
fullSecName = sec.name().split('.')[1]
else:
fullSecName = sec.name()
if '[' in fullSecName: # if section is array element
secNameTemp = fullSecName.split('[')[0]
secIndex = int(fullSecName.split('[')[1].split(']')[0])
secName = secNameTemp + '_' + str(secIndex)
else:
secName = fullSecName
secIndex = -1
if secName in dirCellSecNames: # get sec names from python
secName = dirCellSecNames[secName]
return secName
def EMunits(A):
# calculate the number of source observation
Q = []
observation = []
q_number = len(Q)
for i in range(0, q_number):
observation.append(Q[i][1])
observation_set = set(observation)
o_number = len(observation_set)
# calculate units
D0 = 2
O = []
units = 0
for i in range(0,o_number):
m = len(O[i])
n = math.floor(m/D0)
n = math.int(n)
pe = 1 - np.random.binomial(n, A, size=None)
if pe >= 0.5 :
units += 1 - pe * math.log(pe,2) - (1 - pe) * math.log(1-pe,2)
return units
def getCellParams(cell, varList={}, origGlob={}):
dirCell = dir(cell)
if 'all_sec' in dirCell:
secs = cell.all_sec
elif 'sec' in dirCell:
secs = [cell.sec]
elif 'allsec' in dir(h):
secs = [sec for sec in h.allsec()]
elif 'soma' in dirCell:
secs = [cell.soma]
else:
secs = []
# create dict with hname of each element in dir(cell)
dirCellHnames = {}
for dirCellName in dirCell:
try:
dirCellHnames.update(
{getattr(cell, dirCellName).hname(): dirCellName})
except:
pass
# create dict with dir(cell) name corresponding to each hname
dirCellSecNames = {}
for sec in secs:
dirCellSecNames.update({
hname: name
for hname, name in dirCellHnames.iteritems()
if hname == sec.hname()
})
secDic = {}
synMechs = []
for sec in secs:
# create new section dict with name of section
secName = getSecName(sec, dirCellSecNames)
# if len(secs) == 1: secName = 'soma' # if just one section rename to 'soma' -- REMOVED, doesn't always apply
secDic[secName] = {
'geom': {},
'topol': {},
'mechs': {}
} # create dictionary to store sec info
# store geometry properties
standardGeomParams = ['L', 'nseg', 'diam', 'Ra', 'cm']
secDir = dir(sec)
for geomParam in standardGeomParams:
#if geomParam in secDir:
try:
secDic[secName]['geom'][geomParam] = sec.__getattribute__(
geomParam)
except:
pass
# store 3d geometry
sec.push() # access current section so ismembrane() works
numPoints = int(h.n3d())
if numPoints:
points = []
for ipoint in range(numPoints):
x = h.x3d(ipoint)
y = h.y3d(ipoint)
z = h.z3d(ipoint)
diam = h.diam3d(ipoint)
points.append((x, y, z, diam))
secDic[secName]['geom']['pt3d'] = points
# store mechanisms
#varList = mechVarList() # list of properties for all density mechanisms and point processes
ignoreMechs = ['dist'] # dist only used during cell creation
ignoreVars = [] #
mechDic = {}
ionDic = {}
for mech in dir(sec(0.5)):
if h.ismembrane(
mech
) and mech not in ignoreMechs: # check if membrane mechanism
if not mech.endswith('_ion'): # exclude ions
mechDic[mech] = {} # create dic for mechanism properties
varNames = [
varName.replace('_' + mech, '')
for varName in varList['mechs'][mech]
]
varVals = []
for varName in varNames:
if varName not in ignoreVars:
try:
varVals = [
seg.__getattribute__(
mech).__getattribute__(varName)
for seg in sec
]
if len(set(varVals)) == 1:
varVals = varVals[0]
mechDic[mech][varName] = varVals
except:
pass
#print 'Could not read variable %s from mechanism %s'%(varName,mech)
# store ions
elif mech.endswith('_ion'):
ionName = mech.split('_ion')[0]
varNames = [
varName.replace('_' + mech, '').replace(ionName, '')
for varName in varList['mechs'][mech]
]
varNames.append('e')
varVals = []
ionDic[ionName] = {} # create dic for mechanism properties
for varName in varNames:
varNameSplit = varName
if varName not in ignoreVars:
try:
if varNameSplit in [
'i', 'o'
]: # var name after ion name (eg. 'nai', 'nao')
varVals = [
seg.__getattribute__(ionName +
varNameSplit)
for seg in sec
]
else: # var name before ion name (eg. 'ena')
varVals = [
seg.__getattribute__(varNameSplit +
ionName)
for seg in sec
]
if len(set(varVals)) == 1:
varVals = varVals[0]
ionDic[ionName][varNameSplit] = varVals
except:
pass
#print 'Could not read variable %s from mechanism %s'%(varName,mech)
secDic[secName]['mechs'] = mechDic
if len(ionDic) > 0:
secDic[secName]['ions'] = ionDic
# add synapses and point neurons
# for now read fixed params, but need to find way to read only synapse params
pointps = {}
for seg in sec:
for ipoint, point in enumerate(seg.point_processes()):
pointpMod = point.hname().split('[')[0]
varNames = varList['pointps'][pointpMod]
if any([
s in pointpMod.lower()
for s in ['syn', 'ampa', 'gaba', 'nmda', 'glu']
]):
#if 'synMech' in pptype.lower(): # if syn in name of point process then assume synapse
synMech = {}
synMech['label'] = pointpMod + '_' + str(len(synMechs))
synMech['mod'] = pointpMod
#synMech['loc'] = seg.x
for varName in varNames:
try:
synMech[varName] = point.__getattribute__(varName)
except:
print 'Could not read variable %s from synapse %s' % (
varName, synMech['label'])
if not any([
_equal_dicts(
synMech, synMech2, ignore_keys=['label'])
for synMech2 in synMechs
]):
synMechs.append(synMech)
else: # assume its a non-synapse point process
pointpName = pointpMod + '_' + str(len(pointps))
pointps[pointpName] = {}
pointps[pointpName]['mod'] = pointpMod
pointps[pointpName]['loc'] = seg.x
for varName in varNames:
try:
pointps[pointpName][
varName] = point.__getattribute__(varName)
# special condition for Izhi model, to set vinit=vr
# if varName == 'vr': secDic[secName]['vinit'] = point.__getattribute__(varName)
except:
print 'Could not read %s variable from point process %s' % (
varName, pointpName)
if pointps: secDic[secName]['pointps'] = pointps
# store topology (keep at the end since h.SectionRef messes remaining loop)
secRef = h.SectionRef(sec=sec)
if secRef.has_parent():
secDic[secName]['topol']['parentSec'] = getSecName(
secRef.parent().sec, dirCellSecNames)
secDic[secName]['topol']['parentX'] = h.parent_connection()
secDic[secName]['topol']['childX'] = h.section_orientation()
h.pop_section() # to prevent section stack overflow
# store section lists
secLists = h.List('SectionList')
if int(secLists.count()):
secListDic = {}
for i in xrange(int(secLists.count())): # loop over section lists
hname = secLists.o(i).hname()
if hname in dirCellHnames: # use python variable name
secListName = dirCellHnames[hname]
else:
secListName = hname
secListDic[secListName] = [
getSecName(sec, dirCellSecNames) for sec in secLists.o(i)
]
else:
secListDic = {}
# globals
globs = getGlobals(varList['mechs'].keys() + varList['pointps'].keys(),
origGlob=origGlob)
if 'v_init' in globs: # set v_init for each section (allows for cells with differnet vinits)
for sec in secDic.values():
sec['vinit'] = globs['v_init']
# clean
cell = None
for i in range(len(secs)):
tmp = secs.pop()
del tmp
import gc
gc.collect()
return secDic, secListDic, synMechs, globs
x=x/y
except FloatingPointError:
print "FloatingPointError occurs due to zero division of float values"
else:
print "program executed and value of x is:",x
try:
import matrix
a=matrix.sqrt(9)
print a
except ImportError:
print "ImportError occurs"
else:
print "Program executed"
try:
import math
a=math.int(9.0)
print a
except AttributeError:
print "AttributeError occurs"
else:
print "Program executed"
try:
a=open("file.txt","r")
b=a.read()
k=input("enter k value:")
j=len(b)-k
for i in range(j+1):
if i==len(b):
raise EOFError
else:
continue