def importCellTemplate(self, modelParameters):
try:
with redirect_stdout(sys.__stdout__):
rule = modelParameters["label"]
# Get Current dir
owd = os.getcwd()
conds = {} if rule not in self.netParams.cellParams else self.netParams.cellParams[
rule]['conds']
compileModMechFiles(modelParameters["compileMod"],
modelParameters["modFolder"])
del modelParameters["modFolder"]
del modelParameters["compileMod"]
# import cell template
self.netParams.importCellParams(**modelParameters, conds=conds)
# convert fron netpyne.specs.dict to dict
self.netParams.cellParams[rule] = self.netParams.cellParams[
rule].todict()
return utils.getJSONReply()
except:
return utils.getJSONError(
"Error while importing the NetPyNE cell template",
sys.exc_info())
finally:
os.chdir(owd)
def importModel(self, modelParameters):
""" Imports a model stored in form of Python files.
:param modelParameters:
:return:
"""
if self.doIhaveInstOrSimData()['haveInstance']:
# TODO: this must be integrated into the general lifecycle of "model change -> simulate"
# Shouldn't be specific to Import
sim.clearAll()
try:
# Get Current dir
owd = os.getcwd()
compileModMechFiles(modelParameters['compileMod'],
modelParameters['modFolder'])
with redirect_stdout(sys.__stdout__):
# NetParams
net_params_path = str(modelParameters["netParamsPath"])
sys.path.append(net_params_path)
os.chdir(net_params_path)
# Import Module
net_params_module_name = importlib.import_module(
str(modelParameters["netParamsModuleName"]))
# Import Model attributes
self.netParams = getattr(
net_params_module_name,
str(modelParameters["netParamsVariable"]))
for key, value in self.netParams.cellParams.items():
if hasattr(value, 'todict'):
self.netParams.cellParams[key] = value.todict()
# SimConfig
sim_config_path = str(modelParameters["simConfigPath"])
sys.path.append(sim_config_path)
os.chdir(sim_config_path)
# Import Module
sim_config_module_name = importlib.import_module(
str(modelParameters["simConfigModuleName"]))
# Import Model attributes
self.simConfig = getattr(
sim_config_module_name,
str(modelParameters["simConfigVariable"]))
# TODO: when should sim.initialize be called?
# Only on import or better before every simulation or network instantiation?
sim.initialize()
return utils.getJSONReply()
except:
return utils.getJSONError(
"Error while importing the NetPyNE model", sys.exc_info())
finally:
os.chdir(owd)
def test_compile_mod():
mod_utils.compileModMechFiles(True, NETPYNE_WORKDIR_PATH)
def loadModel(self, args):
""" Imports a model stored as file in json format.
:param args:
:return:
"""
def remove(dictionary):
# remove reserved keys such as __dict__, __Method__, etc
# they appear when we do sim.loadAll(json_file)
if isinstance(dictionary, dict):
for key, value in list(dictionary.items()):
if key.startswith('__'):
dictionary.pop(key)
else:
remove(value)
if not any([
args[option] for option in
['loadNetParams', 'loadSimCfg', 'loadSimData', 'loadNet']
]):
return utils.getJSONError(
"Error while loading data",
'You have to select at least one option')
try:
owd = os.getcwd()
compileModMechFiles(args['compileMod'], args['modFolder'])
except:
return utils.getJSONError("Error while importing/compiling mods",
sys.exc_info())
finally:
os.chdir(owd)
try:
with redirect_stdout(sys.__stdout__):
sim.initialize()
wake_up_geppetto = False
if all([
args[option] for option in
['loadNetParams', 'loadSimCfg', 'loadSimData', 'loadNet']
]):
wake_up_geppetto = True
if self.doIhaveInstOrSimData()['haveInstance']:
sim.clearAll()
sim.initialize()
sim.loadAll(args['jsonModelFolder'])
self.netParams = sim.net.params
self.simConfig = sim.cfg
remove(self.netParams.todict())
remove(self.simConfig.todict())
else:
if args['loadNet']:
wake_up_geppetto = True
if self.doIhaveInstOrSimData()['haveInstance']:
sim.clearAll()
sim.initialize()
sim.loadNet(args['jsonModelFolder'])
if args['loadSimData']: # TODO (https://github.com/Neurosim-lab/netpyne/issues/360)
wake_up_geppetto = True
if not self.doIhaveInstOrSimData()['haveInstance']:
sim.create(specs.NetParams(), specs.SimConfig())
sim.net.defineCellShapes()
sim.gatherData(gatherLFP=False)
sim.loadSimData(args['jsonModelFolder'])
if args['loadSimCfg']:
sim.loadSimCfg(args['jsonModelFolder'])
self.simConfig = sim.cfg
remove(self.simConfig.todict())
if args['loadNetParams']:
if self.doIhaveInstOrSimData()['haveInstance']:
sim.clearAll()
sim.loadNetParams(args['jsonModelFolder'])
self.netParams = sim.net.params
remove(self.netParams.todict())
if wake_up_geppetto:
if len(sim.net.cells) > 0:
section = list(sim.net.cells[0].secs.keys())[0]
if 'pt3d' not in list(
sim.net.cells[0].secs[section].geom.keys()):
sim.net.defineCellShapes()
sim.gatherData()
sim.loadSimData(args['jsonModelFolder'])
sim.gatherData()
self.geppetto_model = self.model_interpreter.getGeppettoModel(
sim)
return json.loads(
GeppettoModelSerializer.serialize(self.geppetto_model))
else:
return utils.getJSONReply()
except:
return utils.getJSONError("Error while loading the NetPyNE model",
sys.exc_info())
def loadModel(self, args):
""" Imports a model stored as file in json format.
:param args:
:return:
"""
if not any([
args[option] for option in
['loadNetParams', 'loadSimCfg', 'loadSimData', 'loadNet']
]):
return utils.getJSONError(
"Error while loading data",
'You have to select at least one option')
try:
owd = os.getcwd()
compileModMechFiles(args['compileMod'], args['modFolder'])
except Exception:
message = "Error while importing/compiling mods"
logging.exception(message)
return utils.getJSONError(message, sys.exc_info())
finally:
os.chdir(owd)
try:
with redirect_stdout(sys.__stdout__):
sim.initialize()
wake_up_geppetto = False
if all([
args[option] for option in
['loadNetParams', 'loadSimCfg', 'loadSimData', 'loadNet']
]):
wake_up_geppetto = True
if self.doIhaveInstOrSimData()['haveInstance']:
sim.clearAll()
sim.initialize()
sim.loadAll(args['jsonModelFolder'])
self.netParams = sim.net.params
self.simConfig = sim.cfg
netpyne_ui_utils.remove(self.netParams.todict())
netpyne_ui_utils.remove(self.simConfig.todict())
else:
if args['loadNet']:
wake_up_geppetto = True
if self.doIhaveInstOrSimData()['haveInstance']:
sim.clearAll()
sim.initialize()
sim.loadNet(args['jsonModelFolder'])
# TODO (https://github.com/Neurosim-lab/netpyne/issues/360)
if args['loadSimData']:
wake_up_geppetto = True
if not self.doIhaveInstOrSimData()['haveInstance']:
sim.create(specs.NetParams(), specs.SimConfig())
sim.net.defineCellShapes()
sim.gatherData(gatherLFP=False)
sim.loadSimData(args['jsonModelFolder'])
if args['loadSimCfg']:
sim.loadSimCfg(args['jsonModelFolder'])
self.simConfig = sim.cfg
netpyne_ui_utils.remove(self.simConfig.todict())
if args['loadNetParams']:
if self.doIhaveInstOrSimData()['haveInstance']:
sim.clearAll()
sim.loadNetParams(args['jsonModelFolder'])
self.netParams = sim.net.params
netpyne_ui_utils.remove(self.netParams.todict())
if wake_up_geppetto:
self._create3D_shapes(args['jsonModelFolder'])
# TODO: Fix me - gatherData will remove allSimData!
sim.gatherData()
self.geppetto_model = self.model_interpreter.getGeppettoModel(
sim)
return json.loads(
GeppettoModelSerializer.serialize(self.geppetto_model))
else:
return utils.getJSONReply()
except Exception:
message = "Error while loading the NetPyNE model"
logging.exception(message)
return utils.getJSONError(message, sys.exc_info())
