def importCell (fileName, cellName, cellArgs = None):
h.initnrn()
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'):
h.load_file(fileName)
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
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)
moduleName = fileNameOnly.split('.py')[0] # remove .py to obtain module name
exec('import ' + moduleName + ' as tempModule') in globals(), locals() # import module dynamically
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
sys.path.remove(filePath)
else:
print "File name should be either .hoc or .py file"
return
secDic, secListDic, synMechs = getCellParams(cell)
return secDic, secListDic, synMechs
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 importCellsFromNet(netParams, fileName, labelList, condsList,
cellNamesList, importSynMechs):
"""
importCellsFromNet
Import cell from HOC template or python file into framework format (dict of sections, with geom, topol, mechs, syns)
"""
h.initnrn()
if fileName.endswith('.hoc') or fileName.endswith('.tem'):
print('Importing from .hoc network not yet supported')
return
# h.load_file(fileName)
# for cellName in cellNames:
# cell = getattr(h, cellName) # create cell using template, passing dict with args
# secDic, secListDic, synMechs = getCellParams(cell)
elif fileName.endswith('.py'):
origDir = os.getcwd()
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
os.chdir(filePath)
print('\nRunning network in %s to import cells into NetPyNE ...\n' %
(fileName))
from neuron import load_mechanisms
load_mechanisms(filePath)
tempModule = importlib.import_module(moduleName)
modulePointer = tempModule
if removeFilePath: sys.path.remove(filePath)
else:
print("File name should be either .hoc or .py file")
return
for label, conds, cellName in zip(labelList, condsList, cellNamesList):
print('\nImporting %s from %s ...' % (cellName, fileName))
exec('cell = tempModule' + '.' + cellName)
#cell = getattr(modulePointer, cellName) # get cell object
varList = mechVarList()
origGlob = getGlobals(
list(varList['mechs'].keys()) + list(varList['pointps'].keys()))
secs, secLists, synMechs = getCellParams(cell, varList, origGlob)
cellRule = {'conds': conds, 'secs': secs, 'secLists': secLists}
netParams.addCellParams(label, cellRule)
if importSynMechs:
for synMech in synMechs:
netParams.addSynMechParams(synMech.pop('label'), synMech)
def reset(self):
print("Simulation initialization.")
h.initnrn()
h.frecord_init()
h.finitialize(self.init_v * mV)
if self.init_sleep > 0:
print("sleep before run for: %s seconds" % self.init_sleep)
time.sleep(self.init_sleep)
if self.warmup > 0:
h.dt = self.warmup / 10
h.continuerun(self.warmup * ms)
h.dt = self.dt
def importCellsFromNet(netParams, fileName, labelList, condsList,
cellNamesList, importSynMechs):
h.initnrn()
''' Import cell from HOC template or python file into framework format (dict of sections, with geom, topol, mechs, syns)'''
if fileName.endswith('.hoc'):
print 'Importing from .hoc network not yet supported'
return
# h.load_file(fileName)
# for cellName in cellNames:
# cell = getattr(h, cellName) # create cell using template, passing dict with args
# secDic, secListDic, synMechs = getCellParams(cell)
elif fileName.endswith('.py'):
origDir = os.getcwd()
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)
moduleName = fileNameOnly.split('.py')[
0] # remove .py to obtain module name
os.chdir(filePath)
print '\nRunning network in %s to import cells into NetPyNE ...\n' % (
fileName)
print h.name_declared('hcurrent')
from neuron import load_mechanisms
load_mechanisms(filePath)
exec('import ' + moduleName + ' as tempModule'
) in globals(), locals() # import module dynamically
modulePointer = tempModule
sys.path.remove(filePath)
else:
print "File name should be either .hoc or .py file"
return
for label, conds, cellName in zip(labelList, condsList, cellNamesList):
print '\nImporting %s from %s ...' % (cellName, fileName)
exec('cell = tempModule' + '.' + cellName)
#cell = getattr(modulePointer, cellName) # get cell object
secs, secLists, synMechs = getCellParams(cell)
cellRule = {'conds': conds, 'secs': secs, 'secLists': secLists}
netParams.addCellParams(label, cellRule)
if importSynMechs:
for synMech in synMechs:
netParams.addSynMechParams(synMech.pop('label'), synMech)
def importCell (fileName, cellName, cellArgs = None, cellInstance = False):
h.initnrn()
varList = mechVarList() # list of properties for all density mechanisms and point processes
origGlob = getGlobals(varList['mechs'].keys()+varList['pointps'].keys())
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'):
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:
cell = getattr(h, cellName)
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)
moduleName = fileNameOnly.split('.py')[0] # remove .py to obtain module name
exec('import ' + moduleName + ' as tempModule') in globals(), locals() # import module dynamically
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
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
setGlobals(origGlob) # restore original globals
return secDic, secListDic, synMechs, globs
def importCell(fileName, cellName, cellArgs=None):
h.initnrn()
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'):
h.load_file(fileName)
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
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)
moduleName = fileNameOnly.split('.py')[
0] # remove .py to obtain module name
exec('import ' + moduleName + ' as tempModule'
) in globals(), locals() # import module dynamically
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
sys.path.remove(filePath)
else:
print "File name should be either .hoc or .py file"
return
secDic, secListDic, synMechs = getCellParams(cell)
return secDic, secListDic, synMechs
def importCellsFromNet (netParams, fileName, labelList, condsList, cellNamesList, importSynMechs):
h.initnrn()
''' Import cell from HOC template or python file into framework format (dict of sections, with geom, topol, mechs, syns)'''
if fileName.endswith('.hoc'):
print 'Importing from .hoc network not yet supported'
return
# h.load_file(fileName)
# for cellName in cellNames:
# cell = getattr(h, cellName) # create cell using template, passing dict with args
# secDic, secListDic, synMechs = getCellParams(cell)
elif fileName.endswith('.py'):
origDir = os.getcwd()
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)
moduleName = fileNameOnly.split('.py')[0] # remove .py to obtain module name
os.chdir(filePath)
print '\nRunning network in %s to import cells into NetPyNE ...\n'%(fileName)
from neuron import load_mechanisms
load_mechanisms(filePath)
exec('import ' + moduleName + ' as tempModule') in globals(), locals() # import module dynamically
modulePointer = tempModule
sys.path.remove(filePath)
else:
print "File name should be either .hoc or .py file"
return
for label, conds, cellName in zip(labelList, condsList, cellNamesList):
print '\nImporting %s from %s ...'%(cellName, fileName)
exec('cell = tempModule' + '.' + cellName)
#cell = getattr(modulePointer, cellName) # get cell object
secs, secLists, synMechs = getCellParams(cell)
cellRule = {'conds': conds, 'secs': secs, 'secLists': secLists}
netParams.addCellParams(label, cellRule)
if importSynMechs:
for synMech in synMechs: netParams.addSynMechParams(synMech.pop('label'), synMech)
def getCellParams(cell):
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'
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:
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 [
_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 = {}
# celsius warning
if hasattr(h, 'celsius'):
if h.celsius != 6.3: # if not default value
print "Warning: h.celsius=%.4g in imported file -- you can set this value in simConfig['hParams']['celsius']" % (
h.celsius)
# clean
h.initnrn()
del (cell) # delete cell
import gc
gc.collect()
return secDic, secListDic, synMechs
def getCellParams(cell):
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'
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:
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 [_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 = {}
# celsius warning
if hasattr(h, 'celsius'):
if h.celsius != 6.3: # if not default value
print "Warning: h.celsius=%.4g in imported file -- you can set this value in simConfig['hParams']['celsius']"%(h.celsius)
# clean
h.initnrn()
del(cell) # delete cell
import gc; gc.collect()
return secDic, secListDic, synMechs
from neuron import h h.initnrn()
def importCell (fileName, cellName, cellArgs = None):
h.initnrn()
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'):
h.load_file(fileName)
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
secs = list(cell.allsec())
dirCell = dir(cell)
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)
moduleName = fileNameOnly.split('.py')[0] # remove .py to obtain module name
exec('import ' + moduleName + ' as tempModule') in globals(), locals() # import module dynamically
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
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 = []
sys.path.remove(filePath)
else:
print "File name should be either .hoc or .py file"
return
# 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'
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
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
mechDic = {}
sec.push() # access current section so ismembrane() works
for mech in dir(sec(0.5)):
if h.ismembrane(mech) and mech not in ignoreMechs: # check if membrane mechanism
mechDic[mech] = {} # create dic for mechanism properties
varNames = [varName.replace('_'+mech, '') for varName in varList['mechs'][mech]]
varVals = []
for varName in varNames:
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)
secDic[secName]['mechs'] = mechDic
# 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 [_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 synMechs in input argument
# if synMechs:
# for synMech in synMechs: synMechParams.append(synMech)
# 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 = {}
# celsius warning
if hasattr(h, 'celsius'):
if h.celsius != 6.3: # if not default value
print "Warning: h.celsius=%.4g in imported file %s -- you can set this value in simConfig['hParams']['celsius']"%(h.celsius, fileName)
# clean
h.initnrn()
del(cell) # delete cell
import gc; gc.collect()
return secDic, secListDic, synMechs
def createPops(self):
# Get info from nodes files
for n in self.network_config['networks']['nodes']:
nodes_file = self.subs(n['nodes_file'])
node_types_file = self.subs(n['node_types_file'])
print("\nLoading nodes from %s and %s"%(nodes_file, node_types_file))
h5file = tables.open_file(nodes_file,mode='r')
self.parse_group(h5file.root.nodes)
h5file.close()
self.nodes_info[self.current_node] = load_csv_props(node_types_file)
self.current_node = None
pp.pprint(self.nodes_info)
# Use extracted node/cell info to create populations
for sonata_pop in self.cell_info:
# iterate over cell types -- will make one netpyne population per cell type
for type in self.cell_info[sonata_pop]['type_numbers']:
info = self.nodes_info[sonata_pop][type]
pop_name = info['pop_name'] if 'pop_name' in info else None
ref = info['model_name'] if 'model_name' in info else info['model_type']
model_type = info['model_type']
model_template = info['model_template'] if 'model_template' in info else '- None -'
if pop_name:
pop_id = '%s_%s'%(sonata_pop, pop_name)
else:
pop_id = '%s_%s_%s'%(sonata_pop,ref,type)
self.pop_id_from_type[(sonata_pop, type)] = pop_id
print(" - Adding population: %s which has model info: %s"%(pop_id, info))
size = self.cell_info[sonata_pop]['type_numbers'][type]
# create netpyne pop
# Note: alternatively could create sim.net.params.popParams and then call sim.createPops()
popTags = {}
popTags['cellModel'] = model_type
popTags['cellType'] = info['model_name'] if 'model_name' in info else pop_id
popTags['numCells'] = size
popTags['pop'] = pop_id
popTags['ei'] = info['ei'] if 'ei' in info else ''
sim.net.pops[pop_id] = sim.Pop(pop_id, popTags)
sim.net.params.popParams[pop_id] = popTags
# create population cell template (sections) from morphology and dynamics params files
if model_type == 'biophysical':
sim.net.pops[pop_id].cellModelClass = sim.CompartCell
# morphology
morphology_file = self.subs(self.network_config['components']['morphologies_dir']) +'/'+info['morphology'] + '.swc'
cellMorph = EmptyCell()
swcData = h.Import3d_SWC_read()
swcData.input(morphology_file)
swcSecs = h.Import3d_GUI(swcData, 0)
swcSecs.instantiate(cellMorph)
# replace axon with AIS stub
if self.replaceAxon:
fix_axon_peri(cellMorph)
# extract netpyne parameters
secs, secLists, synMechs, globs = neuronPyHoc.getCellParams(cellMorph)
# remove sec vinits since imported temporary cell with morph
for secName in secs:
del secs[secName]['vinit']
# fix nseg based on dL
if self.setdLNseg:
fix_sec_nseg(secs, sim.cfg.dL)
# invert y coordinates
# if self.swapSomaXY:
# swap_soma_xy(secs)
# make soma mid segment (x,y,z) = (0,0,0)
# somaLabel = next((s for s in secs.keys() if 'soma' in s), None)
# somaPtFirst = secs[somaLabel]['geom']['pt3d'][0]
# somaPtLast = secs[somaLabel]['geom']['pt3d'][-1]
# somaPt = [(p1+p2)/2.0 for p1,p2 in zip(somaPtFirst, somaPtLast)]
# for secLabel in secs:
# for ipt3d in range(len(secs[secLabel]['geom']['pt3d'])):
# origPt = secs[secLabel]['geom']['pt3d'][ipt3d]
# offsetX = 0.0
# if 'apic' in secLabel:
# offsetX = 0.0
# newpt = (origPt[0] - somaPt[0] + offsetX, origPt[1] - somaPt[1], origPt[2] - somaPt[2], origPt[3])
# secs[secLabel]['geom']['pt3d'][ipt3d] = newpt
# create mapping of sec ids
secLists['SONATA_sec_id'] = [sim.conversion.getSecName(sec) for sec in cellMorph.all]
cellRule = {'conds': {'pop': pop_id}, 'secs': secs, 'secLists': secLists, 'globals': globs}
# dynamics params
if info['model_template'].startswith('nml'):
dynamics_params_file = self.subs(self.network_config['components']['biophysical_neuron_models_dir']+'/'+info['model_template'])
dynamics_params_file = dynamics_params_file.replace('nml:', '')
#nml_doc = read_neuroml2_file(dynamics_params_file)
#cell_dynamic_params = nml_doc.cells[0]
cell_dynamic_params = NMLTree(dynamics_params_file)
cellRule = self.setCellRuleDynamicParamsFromNeuroml(cell_dynamic_params, cellRule)
elif info['dynamics_params'].endswith('json'):
dynamics_params_file = self.subs(self.network_config['components']['biophysical_neuron_models_dir']+'/'+info['dynamics_params'])
cell_dynamic_params = load_json(dynamics_params_file)
cellRule = self.setCellRuleDynamicParamsFromJson(cell_dynamic_params, cellRule)
# set extracted cell params in cellParams rule
sim.net.params.cellParams[pop_id] = cellRule
# clean up before next import
del swcSecs, cellMorph
h.initnrn()
# create population of virtual cells (VecStims so can add spike times)
elif model_type == 'virtual':
popTags['cellModel'] = 'VecStim'
sim.net.pops[pop_id].cellModelClass = sim.PointCell
def createPops(self):
# Get info from nodes files
for n in self.network_config['networks']['nodes']:
nodes_file = self.subs(n['nodes_file'])
node_types_file = self.subs(n['node_types_file'])
print("\nLoading nodes from %s and %s" %
(nodes_file, node_types_file))
h5file = tables.open_file(nodes_file, mode='r')
self.parse_group(h5file.root.nodes)
h5file.close()
self.nodes_info[self.current_node] = load_csv_props(
node_types_file)
self.current_node = None
pp.pprint(self.nodes_info)
# Use extracted node/cell info to create populations
for sonata_pop in self.cell_info:
# iterate over cell types -- will make one netpyne population per cell type
for type in self.cell_info[sonata_pop]['type_numbers']:
info = self.nodes_info[sonata_pop][type]
pop_name = info['pop_name'] if 'pop_name' in info else None
ref = info['model_name'] if 'model_name' in info else info[
'model_type']
model_type = info['model_type']
model_template = info[
'model_template'] if 'model_template' in info else '- None -'
if pop_name:
pop_id = '%s_%s' % (sonata_pop, pop_name)
else:
pop_id = '%s_%s_%s' % (sonata_pop, ref, type)
self.pop_id_from_type[(sonata_pop, type)] = pop_id
print(" - Adding population: %s which has model info: %s" %
(pop_id, info))
size = self.cell_info[sonata_pop]['type_numbers'][type]
# create netpyne pop
# Note: alternatively could create sim.net.params.popParams and then call sim.createPops()
popTags = {}
popTags['cellModel'] = model_type
popTags['cellType'] = info[
'model_name'] if 'model_name' in info else pop_id
popTags['numCells'] = size
popTags['pop'] = pop_id
popTags['ei'] = info['ei'] if 'ei' in info else ''
sim.net.pops[pop_id] = sim.Pop(pop_id, popTags)
# create population cell template (sections) from morphology and dynamics params files
if model_type == 'biophysical':
sim.net.pops[pop_id].cellModelClass = sim.CompartCell
# morphology
morphology_file = self.subs(
self.network_config['components']['morphologies_dir']
) + '/' + info['morphology'] + '.swc'
cellMorph = EmptyCell()
swcData = h.Import3d_SWC_read()
swcData.input(morphology_file)
swcSecs = h.Import3d_GUI(swcData, 0)
swcSecs.instantiate(cellMorph)
# replace axon with AIS stub
if self.replaceAxon:
fix_axon_peri_v2(cellMorph)
# extract netpyne parameters
secs, secLists, synMechs, globs = neuronPyHoc.getCellParams(
cellMorph)
if self.setdLNseg:
fix_sec_nseg(secs, sim.cfg.dL)
# create mapping of sec ids
secLists['SONATA_sec_id'] = [
sim.conversion.getSecName(sec) for sec in cellMorph.all
]
cellRule = {
'conds': {
'pop': pop_id
},
'secs': secs,
'secLists': secLists,
'globals': globs
}
# dynamics params
dynamics_params_file = self.subs(
self.network_config['components']
['biophysical_neuron_models_dir'] + '/' +
info['model_template'])
if info['model_template'].startswith('nml'):
dynamics_params_file = dynamics_params_file.replace(
'nml:', '')
nml_doc = read_neuroml2_file(dynamics_params_file)
cell_dynamic_params = nml_doc.cells[0]
cellRule = self.setCellRuleDynamicParamsFromNeuroml(
cell_dynamic_params, cellRule)
elif info['dynamics_params'].startswith('json'):
dynamics_params = load_json(dynamics_params_file)
pass
# set extracted cell params in cellParams rule
sim.net.params.cellParams[pop_id] = cellRule
# clean up before next import
del swcSecs, cellMorph
h.initnrn()
# create population of virtual cells (VecStims so can add spike times)
elif model_type == 'virtual':
popTags['cellModel'] = 'VecStim'
sim.net.pops[pop_id].cellModelClass = sim.PointCell
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
