def main():
"""
Program entry point.
"""
args = process_args()
print('Parsing and resolving model: ' + args.lems_file)
model = Model()
if args.I is not None:
for dir in args.I:
model.add_include_directory(dir)
model.import_from_file(args.lems_file)
resolved_model = model.resolve()
print('Building simulation')
sim = SimulationBuilder(resolved_model).build()
#sim.dump("Afterbuild:")
if args.dlems:
print('Exporting as: ' + dlems_info)
from lems.dlems.exportdlems import export_component
target = model.targets[0]
sim_comp = model.components[target]
target_net = sim_comp.parameters['target']
target_comp = model.components[target_net]
dlems_file_name = args.lems_file.replace('.xml', '.json')
if dlems_file_name == args.lems_file:
dlems_file_name = args.lems_file + '.json'
if target_comp.type == 'network':
for child in target_comp.children:
if child.type == 'population':
comp = model.components[child.parameters['component']]
export_component(model,
comp,
sim_comp,
child.id,
file_name=dlems_file_name)
else:
export_component(model, sim_comp, target_comp)
else:
print('Running simulation')
sim.run()
process_simulation_output(sim, args)
def main(args=None):
"""
Program entry point.
"""
if args is None:
args = process_args()
print('Parsing and resolving model: '+args.lems_file)
model = Model()
if args.I is not None:
for dir in args.I:
model.add_include_directory(dir)
model.import_from_file(args.lems_file)
resolved_model = model.resolve()
print('Building simulation')
sim = SimulationBuilder(resolved_model).build()
#sim.dump("Afterbuild:")
if args.dlems:
print('Exporting as: '+dlems_info)
from lems.dlems.exportdlems import export_component
target = model.targets[0]
sim_comp = model.components[target]
target_net = sim_comp.parameters['target']
target_comp = model.components[target_net]
dlems_file_name = args.lems_file.replace('.xml', '.json')
if dlems_file_name == args.lems_file:
dlems_file_name = args.lems_file + '.json'
if target_comp.type == 'network':
for child in target_comp.children:
if child.type == 'population':
comp = model.components[child.parameters['component']]
export_component(model, comp, sim_comp, child.id, file_name=dlems_file_name)
else:
export_component(model, sim_comp, target_comp)
else:
print('Running simulation')
sim.run()
process_simulation_output(sim, model, args)
def validate_model(filename, name=None, config=None):
""" Check that a model is valid
Args:
filename (:obj:`str`): path to model
name (:obj:`str`, optional): name of model for use in error messages
config (:obj:`Config`, optional): whether to fail on missing includes
Returns:
:obj:`tuple`:
* nested :obj:`list` of :obj:`str`: nested list of errors (e.g., required ids missing or ids not unique)
* nested :obj:`list` of :obj:`str`: nested list of errors (e.g., required ids missing or ids not unique)
* :obj:`Model`: model
"""
config = config or get_config()
errors = []
warnings = []
model = None
with StandardOutputErrorCapturer(relay=False, level=StandardOutputErrorCapturerLevel.c):
valid, output = validate_neuroml2_lems_file(filename, exit_on_fail=False, return_string=True)
if not valid:
errors.append(['`{}` is not a valid LEMS file.'.format(filename), [[output]]])
return (errors, warnings, model)
core_types_dir = tempfile.mkdtemp()
jar_filename = get_path_to_jnml_jar()
with zipfile.ZipFile(jar_filename, 'r') as jar_file:
neuroml2_core_type_members = (name for name in jar_file.namelist() if name.startswith('NeuroML2CoreTypes/'))
jar_file.extractall(core_types_dir, members=neuroml2_core_type_members)
model = Model(include_includes=True, fail_on_missing_includes=config.VALIDATE_IMPORTED_MODEL_FILES)
model.add_include_directory(os.path.join(core_types_dir, 'NeuroML2CoreTypes'))
model.import_from_file(filename)
shutil.rmtree(core_types_dir)
return (errors, warnings, model)
reopen = open(dlems_file_name, 'r')
print(reopen.read())
reopen.close()
print("Written to %s" % dlems_file_name)
if __name__ == '__main__':
model = Model()
try:
lems_file = sys.argv[1]
except:
lems_file = '../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml'
model.add_include_directory('../NeuroML2/NeuroML2CoreTypes')
print('Importing LEMS file from: %s' % lems_file)
model.import_from_file(lems_file)
target = model.targets[0]
sim_comp = model.components[target]
target_net = sim_comp.parameters['target']
target_comp = model.components[target_net]
if target_comp.type == 'network':
for child in target_comp.children:
dlems_file.close()
print(open(dlems_file_name,'r').read())
print("Written to %s"%dlems_file_name)
if __name__ == '__main__':
model = Model()
try:
lems_file = sys.argv[1]
except:
lems_file = '../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml'
model.add_include_directory('../NeuroML2/NeuroML2CoreTypes')
print('Importing LEMS file from: %s'%lems_file)
model.import_from_file(lems_file)
target = model.targets[0]
sim_comp = model.components[target]
target_net = sim_comp.parameters['target']
target_comp = model.components[target_net]
if target_comp.type == 'network':
