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):])