for (t,v1,v2) in zip(h.tlog,h.Vlog1,h.Vlog2):
f.write("%f %f %f\n" % (t,v1,v2))
f.close()
@click.command()
@click.option("--template-path", required=True, type=click.Path(exists=True, file_okay=False, dir_okay=True))
@click.option("--forest-path", required=True, type=click.Path(exists=True, file_okay=True, dir_okay=False))
def main(template_path,forest_path):
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
h('objref nil, pc, tlog, Vlog, spikelog')
h.load_file("nrngui.hoc")
h.xopen("./lib.hoc")
h.xopen ("./tests/rn.hoc")
h.xopen(template_path+'/MOPPCell.hoc')
h.pc = h.ParallelContext()
popName = "MOPP"
(trees,_) = read_tree_selection (comm, forest_path, popName, [1052650])
tree = next(iter(viewvalues(trees)))
passive_test(tree,-60)
ap_rate_test(tree,-60)
if __name__ == '__main__':
main(args=sys.argv[(utils.list_find(lambda s: s.find("MOPPCellTest.py") != -1,sys.argv)+1):])
else:
if t_min is None:
time_range = [0.0, t_max]
else:
time_range = [t_min, t_max]
if not populations:
populations = ['eachPop']
plot.plot_spike_histogram(spike_events_path,
spike_events_namespace,
include=populations,
time_variable=t_variable,
time_range=time_range,
pop_rates=True,
bin_size=bin_size,
smooth=smooth,
quantity=quantity,
fontSize=font_size,
overlay=overlay,
graph_type=graph_type,
progress=progress,
saveFig=True,
figFormat=save_format)
if __name__ == '__main__':
main(args=sys.argv[(
utils.list_find(lambda x: os.path.basename(x) == script_name, sys.argv
) + 1):])
@click.option("--font-size", type=float, default=14)
@click.option("--verbose", "-v", type=bool, default=False, is_flag=True)
def main(config, config_prefix, connectivity_path, coords_path,
vertex_metrics_namespace, distances_namespace, destination, sources,
normed, metric, graph_type, bin_size, font_size, verbose):
utils.config_logging(verbose)
logger = utils.get_script_logger(script_name)
env = Env(config_file=config, config_prefix=config_prefix)
plot.plot_vertex_metrics(env,
connectivity_path,
coords_path,
vertex_metrics_namespace,
distances_namespace,
destination,
sources,
metric=metric,
normed=normed,
bin_size=bin_size,
fontSize=font_size,
graph_type=graph_type,
saveFig=True)
if __name__ == '__main__':
main(args=sys.argv[(utils.list_find(
lambda x: os.path.basename(x) == os.path.basename(script_name), sys.
argv) + 1):])
import click
from dentate import env
from dentate import io_utils
from dentate import utils
from env import Env
@click.command()
@click.option("--config",
'-c',
required=True,
type=click.Path(exists=True, file_okay=True, dir_okay=False))
@click.option("--output-path",
default='dentate_h5types.h5',
type=click.Path(exists=False, file_okay=True, dir_okay=False))
@click.option("--template-path",
required=True,
type=click.Path(exists=True, file_okay=False, dir_okay=True))
@click.option('--gap-junctions', is_flag=True)
def main(config, output_path, template_path, gap_junctions):
env = Env(config_file=config, template_paths=template_path)
io_utils.make_h5types(env, output_path, gap_junctions=gap_junctions)
if __name__ == '__main__':
main(args=sys.argv[(utils.list_find(
lambda x: os.path.basename(x) == os.path.basename(__file__), sys.argv
) + 1):])
@click.option("--distances-namespace", '-t', type=str, default='Arc Distances')
@click.option("--metric", type=str, default='dendrite_length')
@click.option("--metric-index", type=int, default=0)
@click.option("--percentile", type=float)
#@click.option("--normed", type=bool, default=False, is_flag=True)
@click.option("--font-size", type=float, default=14)
@click.option("--verbose", "-v", type=bool, default=False, is_flag=True)
def main(config, config_prefix, forest_path, coords_path, population,
metric_namespace, distances_namespace, metric, metric_index,
percentile, font_size, verbose):
env = Env(config_file=config, config_prefix=config_prefix)
plot.plot_tree_metrics(env,
forest_path,
coords_path,
population,
metric_namespace,
distances_namespace,
metric=metric,
metric_index=metric_index,
percentile=percentile,
fontSize=font_size,
saveFig=True,
verbose=verbose)
if __name__ == '__main__':
main(args=sys.argv[(
utils.list_find(lambda s: s.find(script_name) != -1, sys.argv) + 1):])
if isinstance(param_rst, dict):
for const_name, const_range in sorted(
viewitems(param_rst)):
param_path = (param_fst, const_name)
param_tuples.append(
SynParam(pop_name, source, sec_type,
syn_name, param_path,
const_range))
param_key = '%s.%s.%s.%s.%s.%s' % (
pop_name, str(source), sec_type, syn_name,
param_fst, const_name)
param_names.append(param_key)
else:
param_name = param_fst
param_range = param_rst
param_tuples.append(
SynParam(pop_name, source, sec_type, syn_name,
param_name, param_range))
param_key = '%s.%s.%s.%s.%s' % (pop_name, source,
sec_type, syn_name,
param_name)
param_names.append(param_key)
return ParamSpec(param_names=param_names, param_tuples=param_tuples)
if __name__ == '__main__':
main(args=sys.argv[(
list_find(lambda x: os.path.basename(x) == os.path.basename(__file__),
sys.argv) + 1):])
(trees, _) = read_tree_selection(forest_path, popName, [gid], comm=comm)
if synapses_path is not None:
synapses_iter = read_cell_attribute_selection (synapses_path, popName, [gid], \
"Synapse Attributes", comm=comm)
else:
synapses_iter = None
gid, tree = next(trees)
if synapses_iter is not None:
(_, synapses) = next(synapses_iter)
else:
synapses = None
if 'mech_file' in env.celltypes[popName]:
mech_file_path = env.config_prefix + '/' + env.celltypes[popName][
'mech_file']
else:
mech_file_path = None
template_class = getattr(h, "MossyCell")
if (synapses is not None):
synapse_test(template_class, mech_file_path, gid, tree, synapses,
v_init, env)
if __name__ == '__main__':
main(args=sys.argv[(
utils.list_find(lambda s: s.find("MossyCellTest.py") != -1, sys.argv) +
1):])
gid=gid,
load_edges=load_edges,
load_weights=load_weights,
mech_file_path=mech_file_path)
context.update(locals())
init_biophysics(cell,
reset_cable=True,
correct_cm=correct_for_spines,
correct_g_pas=correct_for_spines,
env=env,
verbose=verbose)
init_syn_mech_attrs(cell, env)
config_biophys_cell_syns(env,
gid,
pop_name,
insert=True,
insert_netcons=True,
insert_vecstims=True,
verbose=verbose)
if verbose:
report_topology(cell, env)
if __name__ == '__main__':
main(args=sys.argv[(
list_find(lambda s: s.find(os.path.basename(__file__)) != -1, sys.argv
) + 1):],
standalone_mode=False)
pop_name = "BC"
gid = 1039000
(trees_dict, _) = read_tree_selection(forest_path,
pop_name, [gid],
comm=env.comm)
synapses_dict = read_cell_attribute_selection(synapses_path,
pop_name, [gid],
"Synapse Attributes",
comm=env.comm)
(_, tree) = next(trees_dict)
(_, synapses) = next(synapses_dict)
v_init = -60
template_class = getattr(h, "BasketCell")
ap_test(template_class, tree, v_init)
passive_test(template_class, tree, v_init)
ap_rate_test(template_class, tree, v_init)
fi_test(template_class, tree, v_init)
gap_junction_test(env, template_class, tree, v_init)
synapse_test(template_class, gid, tree, synapses, v_init, env)
if __name__ == '__main__':
main(args=sys.argv[(
utils.list_find(lambda s: s.find("BasketCellTest.py") != -1, sys.argv
) + 1):])
(trees, _) = read_tree_selection(forest_path, pop_name, [gid], comm=comm)
if synapses_path is not None:
synapses_dict = read_cell_attribute_selection (synapses_path, pop_name, [gid], \
"Synapse Attributes", comm=comm)
else:
synapses_dict = None
gid, tree = next(trees)
if synapses_dict is not None:
(_, synapses) = next(synapses_dict)
else:
synapses = None
if 'mech_file' in env.celltypes[pop_name]:
mech_file_path = env.config_prefix + '/' + env.celltypes[pop_name][
'mech_file']
else:
mech_file_path = None
template_class = getattr(h, "DGC")
if (synapses is not None):
synapse_test(template_class, mech_file_path, gid, tree, synapses,
v_init, env)
if __name__ == '__main__':
main(args=sys.argv[(
utils.list_find(lambda s: s.find("GranuleCellTest.py") != -1, sys.argv
) + 1):])
type=click.Path(exists=True, file_okay=False, dir_okay=True))
@click.option("--forest-path",
required=True,
type=click.Path(exists=True, file_okay=True, dir_okay=False))
def main(template_path, forest_path):
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
h('objref nil, pc, tlog, Vlog, spikelog')
h.load_file("nrngui.hoc")
h.xopen("./lib.hoc")
h.xopen("./tests/rn.hoc")
h.xopen(template_path + '/AxoAxonicCell.hoc')
h.pc = h.ParallelContext()
popName = "AAC"
(trees, _) = read_tree_selection(comm, forest_path, popName, [1042800])
tree = next(iter(viewvalues(trees)))
passive_test(tree, -60)
ap_rate_test(tree, -60)
gap_junction_test(tree, -60)
if __name__ == '__main__':
main(args=sys.argv[(
utils.list_find(lambda s: s.find("AxoAxonicCellTest.py") != -1, sys.
argv) + 1):])
