def cloneExperiment(self, payload: dict):
""" Loads experiment from disk and replaces experiment in design with it.
1. Replaces current experiment in design with copy of stored experiment.
2. Replace current model specification with spec of stored experiment.
:param payload: { name: str, replaceModelSpec: bool, replaceExperiment: bool }
"""
name = payload.get('name')
# Creates new Experiment in design based on `name` experiment.
if payload.get('replaceExperiment', True):
experiments.replace_current_with(name)
# Replaces model specification
if payload.get('replaceModelSpec', True):
path = os.path.join(constants.EXPERIMENTS_FOLDER_PATH, name)
if self.doIhaveInstOrSimData()['haveInstance']:
sim.clearAll()
sim.initialize()
sim.loadNetParams(os.path.join(path, experiments.NET_PARAMS_FILE))
sim.loadSimCfg(os.path.join(path, experiments.SIM_CONFIG_FILE))
self.netParams = sim.net.params
self.simConfig = sim.cfg
netpyne_ui_utils.remove(self.simConfig.todict())
netpyne_ui_utils.remove(self.netParams.todict())
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 deleteModel(self, modelParams):
try:
with redirect_stdout(sys.__stdout__):
self.netParams = specs.NetParams()
self.simConfig = specs.SimConfig()
self.netParams.todict()
self.netParams.todict()
if self.doIhaveInstOrSimData()['haveInstance']: sim.clearAll()
self.geppetto_model = None
return utils.getJSONReply()
except:
return utils.getJSONError(
"Error while exporting the NetPyNE model", sys.exc_info())
def deleteModel(self, modelParams):
try:
with redirect_stdout(sys.__stdout__):
self.netParams = specs.NetParams()
self.simConfig = specs.SimConfig()
sim.initialize(specs.NetParams(), specs.SimConfig())
self.geppetto_model = None
except Exception:
message = "Error while exporting the NetPyNE model"
logging.exception(message)
return utils.getJSONError(message, sys.exc_info())
try:
sim.clearAll()
except:
logging.exception("Failed to clear simulation")
return utils.getJSONReply()
def viewExperimentResult(self, payload: dict):
""" Loads the output file of a simulated experiment trial.
:param payload: {name: str, trial: str, onlyModelSpecification: bool}
:return: geppetto model
"""
name = payload.get("name", None)
trial = payload.get("trial", None)
only_model_spec = payload.get("onlyModelSpecification", False)
file = experiments.get_trial_output_path(name, trial)
if file is None or not os.path.exists(file):
return utils.getJSONError(
f"Couldn't find output file of condition. Please take a look at the simulation log.",
"")
if self.doIhaveInstOrSimData()['haveInstance']:
sim.clearAll()
sim.initialize()
if only_model_spec:
# Load only model specification
sim.loadNetParams(file)
sim.loadSimCfg(file)
self.netParams = sim.net.params
self.simConfig = sim.cfg
netpyne_ui_utils.remove(self.simConfig.todict())
netpyne_ui_utils.remove(self.netParams.todict())
return
else:
# Load the complete simulation
sim.loadAll(file)
self._create3D_shapes(file)
self.geppetto_model = self.model_interpreter.getGeppettoModel(sim)
return json.loads(
GeppettoModelSerializer.serialize(self.geppetto_model))
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())