def end(compatible_output=True):
"""Do any necessary cleaning up before exiting."""
for (population, variables, filename) in simulator.state.write_on_end:
io = get_io(filename)
population.write_data(io, variables)
simulator.state.write_on_end = []
nml_doc = simulator._get_nml_doc()
import neuroml.writers as writers
if save_format == 'xml':
nml_file = '%s.net.nml' % nml_doc.id
writers.NeuroMLWriter.write(nml_doc, nml_file)
elif save_format == 'hdf5':
nml_file = '%s.net.nml.h5' % nml_doc.id
writers.NeuroMLHdf5Writer.write(nml_doc, nml_file)
logger.info("Written NeuroML 2 file out to: " + nml_file)
lems_sim = simulator._get_lems_sim()
lems_sim.include_neuroml2_file("PyNN.xml", include_included=False)
lems_sim.include_neuroml2_file(nml_file)
lems_file = lems_sim.save_to_file()
logger.info("Written LEMS file (to simulate NeuroML file) to: " +
lems_file)
def setup(timestep=DEFAULT_TIMESTEP,
min_delay=DEFAULT_MIN_DELAY,
**extra_params):
""" Set up for saving cell models and network structure to NeuroML """
common.setup(timestep, min_delay, **extra_params)
simulator.state.clear()
simulator.state.dt = timestep # move to common.setup?
simulator.state.min_delay = min_delay
simulator.state.max_delay = extra_params.get('max_delay',
DEFAULT_MAX_DELAY)
simulator.state.mpi_rank = extra_params.get('rank', 0)
simulator.state.num_processes = extra_params.get('num_processes', 1)
logger.debug("Creating network in NeuroML document to store structure")
nml_doc = simulator._get_nml_doc(extra_params.get('reference',
"PyNN_NeuroML2_Export"),
reset=True)
global save_format
save_format = extra_params.get('save_format', "xml")
# Create network
net = neuroml.Network(id=nml_doc.id)
nml_doc.networks.append(net)
lems_sim = simulator._get_lems_sim(reset=True)
lems_sim.dt = '%s' % timestep
return rank()
def end(compatible_output=True):
"""Do any necessary cleaning up before exiting."""
for (population, variables, filename) in simulator.state.write_on_end:
io = get_io(filename)
population.write_data(io, variables)
simulator.state.write_on_end = []
nml_doc = simulator._get_nml_doc()
import neuroml.writers as writers
if save_format == 'xml':
nml_file = '%s.net.nml'%nml_doc.id
writers.NeuroMLWriter.write(nml_doc, nml_file)
elif save_format == 'hdf5':
nml_file = '%s.net.nml.h5'%nml_doc.id
writers.NeuroMLHdf5Writer.write(nml_doc, nml_file)
logger.info("Written NeuroML 2 file out to: "+nml_file)
lems_sim = simulator._get_lems_sim()
lems_sim.include_neuroml2_file("PyNN.xml", include_included=False)
lems_sim.include_neuroml2_file(nml_file)
lems_file = lems_sim.save_to_file()
logger.info("Written LEMS file (to simulate NeuroML file) to: "+lems_file)
def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY,
**extra_params):
""" Set up for saving cell models and network structure to NeuroML """
common.setup(timestep, min_delay, **extra_params)
simulator.state.clear()
simulator.state.dt = timestep # move to common.setup?
simulator.state.min_delay = min_delay
simulator.state.max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY)
simulator.state.mpi_rank = extra_params.get('rank', 0)
simulator.state.num_processes = extra_params.get('num_processes', 1)
logger.debug("Creating network in NeuroML document to store structure")
nml_doc = simulator._get_nml_doc(extra_params.get('reference', "PyNN_NeuroML2_Export"),reset=True)
global save_format
save_format = extra_params.get('save_format', "xml")
# Create network
net = neuroml.Network(id="network")
nml_doc.networks.append(net)
lems_sim = simulator._get_lems_sim(reset=True)
lems_sim.dt = '%s'%timestep
return rank()