def importCellParams(self, label, conds, fileName, cellName, cellArgs=None, importSynMechs=False, somaAtOrigin=False, cellInstance=False):
if cellArgs is None: cellArgs = {}
if not label:
label = int(self._labelid)
self._labelid += 1
secs, secLists, synMechs, globs = utils.importCell(fileName, cellName, cellArgs, cellInstance)
cellRule = {'conds': conds, 'secs': secs, 'secLists': secLists, 'globals': globs}
# adjust cell 3d points so that soma is at location 0,0,0
if somaAtOrigin:
somaSec = next((sec for sec in cellRule['secs'] if 'soma' in sec), None)
if not somaSec or not 'pt3d' in cellRule['secs'][somaSec]['geom']:
print 'Warning: cannot place soma at origin because soma does not exist or does not contain pt3d'
return
soma3d = cellRule['secs'][somaSec]['geom']['pt3d']
midpoint = int(len(soma3d)/2)
somaX, somaY, somaZ = soma3d[midpoint][0:3]
for sec in cellRule['secs'].values():
for i,pt3d in enumerate(sec['geom']['pt3d']):
sec['geom']['pt3d'][i] = (pt3d[0] - somaX, pt3d[1] - somaY, pt3d[2] - somaZ, pt3d[3])
self.addCellParams(label, cellRule)
if importSynMechs:
for synMech in synMechs: self.addSynMechParams(synMech.pop('label'), synMech)
return self.cellParams[label]
def importCellParams(self, label, conds, fileName, cellName, cellArgs=None, importSynMechs=False):
if cellArgs is None: cellArgs = {}
if not label:
label = int(self._labelid)
self._labelid += 1
secs, secLists, synMechs = utils.importCell(fileName, cellName, cellArgs)
cellRule = {'conds': conds, 'secs': secs, 'secLists': secLists}
self.addCellParams(label, cellRule)
if importSynMechs:
for synMech in synMechs: self.addSynMechParams(synMech.pop('label'), synMech)
return self.cellParams[label]
def importCellParams(self,
label,
conds,
fileName,
cellName,
cellArgs=None,
importSynMechs=False):
if cellArgs is None: cellArgs = {}
if not label:
label = int(self._labelid)
self._labelid += 1
secs, secLists, synMechs = utils.importCell(fileName, cellName,
cellArgs)
cellRule = {'conds': conds, 'secs': secs, 'secLists': secLists}
self.addCellParams(label, cellRule)
if importSynMechs:
for synMech in synMechs:
self.addSynMechParams(synMech.pop('label'), synMech)
return self.cellParams[label]
netParams['popParams'].append({'popLabel': 'HH3D_pop', 'cellType': 'PYR', 'numCells': 5, 'cellModel': 'HH3D'})
netParams['popParams'].append({'popLabel': 'Traub_pop', 'cellType': 'PYR', 'numCells': 5, 'cellModel': 'Traub'})
netParams['popParams'].append({'popLabel': 'Mainen_pop', 'cellType': 'PYR', 'numCells': 5, 'cellModel': 'Mainen'})
netParams['popParams'].append({'popLabel': 'Friesen_pop', 'cellType': 'PYR', 'numCells': 5, 'cellModel': 'Friesen'})
netParams['popParams'].append({'popLabel': 'Izhi03b_pop', 'cellType': 'PYR', 'numCells': 5, 'cellModel': 'Izhi2003a'})
netParams['popParams'].append({'popLabel': 'Izhi03b_pop', 'cellType': 'PYR', 'numCells': 5, 'cellModel': 'Izhi2003b'})
netParams['popParams'].append({'popLabel': 'Izhi07a_pop', 'cellType': 'PYR', 'numCells': 5, 'cellModel': 'Izhi2007a'})
netParams['popParams'].append({'popLabel': 'Izhi07b_pop', 'cellType': 'PYR', 'numCells': 5, 'cellModel': 'Izhi2007b'})
netParams['popParams'].append({'popLabel': 'background', 'rate': 50, 'noise': 0.5, 'source': 'random', 'cellModel': 'NetStim'})
## Cell property rules
netParams['cellParams'] = [] # list of cell property rules - each item will contain dict with cell properties
### HH
cellRule = {'label': 'PYR_HH_rule', 'conditions': {'cellType': 'PYR', 'cellModel': 'HH'}, 'sections': {}} # cell rule dict
cellRule['sections'] = utils.importCell(fileName='HHCellFile.py', cellName='HHCellClass')
netParams['cellParams'].append(cellRule) # add dict to list of cell parameters
### HH3D
cellRule = {'label': 'PYR_HH3D_rule', 'conditions': {'cellType': 'PYR', 'cellModel': 'HH3D'}, 'sections': {}} # cell rule dict
cellRule['sections'] = utils.importCell(fileName='geom.hoc', cellName='E21')
cellRule['sections']['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70} # soma hh mechanism
for secName in cellRule['sections']:
cellRule['sections'][secName]['mechs']['pas'] = {'g': 0.0000357, 'e': -70}
cellRule['sections'][secName]['geom']['cm'] = 10
cellRule['sections']['soma']['syns']['NMDA'] = {'_type': 'Exp2Syn', '_loc': 0.5, 'tau1': 1.0, 'tau2': 5.0, 'e': 0} # soma NMDA synapse
netParams['cellParams'].append(cellRule)
### Traub
cellRule = {'label': 'PYR_Traub_rule', 'conditions': {'cellType': 'PYR', 'cellModel': 'Traub'}, 'sections': {}} # cell rule dict
cellRule['sections'] = utils.importCell(fileName='pyr3_traub.hoc', cellName='pyr3')