def main(config, config_prefix, population, gid, ref_axis, input_file, template_name, output_file, dry_run, verbose):
utils.config_logging(verbose)
logger = utils.get_script_logger(os.path.basename(__file__))
h.load_file("nrngui.hoc")
h.load_file("import3d.hoc")
env = Env(config_file=config, config_prefix=config_prefix)
swc_type_defs = env.SWC_Types
if not os.path.isfile(output_file):
io_utils.make_h5types(env, output_file)
(forest_pop_ranges, _) = read_population_ranges(output_file)
(forest_population_start, forest_population_count) = forest_pop_ranges[population]
forest_population_end = forest_population_start + forest_population_count
h.load_file(input_file)
cell = getattr(h, template_name)(0, 0)
if verbose:
h.topology()
tree_dict = export_swc_dict(cell, ref_axis=ref_axis)
if (gid < forest_population_start) or (gid > forest_population_end):
gid = forest_population_start
trees_dict = { gid : tree_dict }
logger.info(pprint.pformat(trees_dict))
if not dry_run:
append_cell_trees(output_file, population, trees_dict)
def main(spike_events_path, spike_events_namespace, populations,
include_artificial, bin_size, smooth, t_variable, t_max, t_min,
quantity, font_size, graph_type, overlay, save_format, progress,
verbose):
utils.config_logging(verbose)
if t_max is None:
time_range = None
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,
include_artificial=include_artificial,
saveFig=True,
figFormat=save_format)
def main(spike_events_path, spike_events_namespace, populations, max_spikes,
spike_hist_bin, t_variable, t_max, t_min, font_size, fig_size, labels,
save_format, include_artificial, verbose):
utils.config_logging(verbose)
if t_max is None:
time_range = None
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_raster(spike_events_path,
spike_events_namespace,
include=populations,
time_range=time_range,
time_variable=t_variable,
pop_rates=True,
spike_hist='subplot',
max_spikes=max_spikes,
spike_hist_bin=spike_hist_bin,
include_artificial=include_artificial,
fontSize=font_size,
figSize=fig_size,
labels=labels,
saveFig=True,
figFormat=save_format)
def main(config, config_prefix, verbose):
config_logging(verbose)
logger = get_script_logger(script_name)
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
env = Env(comm=comm, config_file=config, config_prefix=config_prefix)
def main(celltype_path, input_path, output_path, output_namespace, output_npy,
verbose, progress):
utils.config_logging(verbose)
io_utils.import_spikeraster(celltype_path,
input_path,
output_path,
namespace=output_namespace,
output_npy=output_npy,
progress=progress)
def main(config_path, input_path, t_max, t_min, window_size, overlap,
frequency_range, dt, font_size, verbose):
utils.config_logging(verbose)
if t_max is None:
time_range = None
else:
if t_min is None:
time_range = [0.0, t_max]
else:
time_range = [t_min, t_max]
plot.plot_lfp_spectrogram (input_path, config_path=config_path, time_range=time_range, \
window_size=window_size, overlap=overlap, frequency_range=frequency_range, \
fontSize=font_size, dt=dt, saveFig=True)
def main(config_path, input_path, t_max, t_min, psd, window_size, overlap,
frequency_range, bandpass_filter, dt, font_size, verbose):
utils.config_logging(verbose)
if t_max is None:
time_range = None
else:
if t_min is None:
time_range = [0.0, t_max]
else:
time_range = [t_min, t_max]
if bandpass_filter[0] is None:
bandpass_filter = None
plot.plot_lfp (input_path, config_path=config_path, time_range=time_range, \
compute_psd=psd, window_size=window_size, \
overlap=overlap, frequency_range=frequency_range,
bandpass_filter=bandpass_filter, dt=dt,
fontSize=font_size, saveFig=True)
def main(config, coords_path, coords_namespace, populations, subpopulation, scale, subvol, mayavi, verbose):
utils.config_logging(verbose)
plot.plot_coords_in_volume (populations, coords_path, coords_namespace, config, \
subpopulation=subpopulation, subvol=subvol, scale=scale, verbose=verbose, mayavi=mayavi)
def main(config, config_prefix, types_path, geometry_path, output_path,
output_namespace, populations, resolution, alpha_radius, nodeiter,
dispersion_delta, snap_delta, io_size, chunk_size, value_chunk_size,
verbose):
config_logging(verbose)
logger = get_script_logger(script_name)
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
np.seterr(all='raise')
if io_size == -1:
io_size = comm.size
if rank == 0:
logger.info('%i ranks have been allocated' % comm.size)
if rank == 0:
if not os.path.isfile(output_path):
input_file = h5py.File(types_path, 'r')
output_file = h5py.File(output_path, 'w')
input_file.copy('/H5Types', output_file)
input_file.close()
output_file.close()
comm.barrier()
env = Env(comm=comm, config_file=config, config_prefix=config_prefix)
random_seed = int(env.model_config['Random Seeds']['Soma Locations'])
random.seed(random_seed)
layer_extents = env.geometry['Parametric Surface']['Layer Extents']
rotate = env.geometry['Parametric Surface']['Rotation']
(extent_u, extent_v, extent_l) = get_total_extents(layer_extents)
vol = make_CA1_volume(extent_u,
extent_v,
extent_l,
rotate=rotate,
resolution=resolution)
layer_alpha_shape_path = 'Layer Alpha Shape/%d/%d/%d' % resolution
if rank == 0:
logger.info("Constructing alpha shape for volume: extents: %s..." %
str((extent_u, extent_v, extent_l)))
vol_alpha_shape_path = '%s/all' % (layer_alpha_shape_path)
if geometry_path:
vol_alpha_shape = load_alpha_shape(geometry_path,
vol_alpha_shape_path)
else:
vol_alpha_shape = make_alpha_shape(vol, alpha_radius=alpha_radius)
if geometry_path:
save_alpha_shape(geometry_path, vol_alpha_shape_path,
vol_alpha_shape)
vert = vol_alpha_shape.points
smp = np.asarray(vol_alpha_shape.bounds, dtype=np.int64)
vol_domain = (vert, smp)
layer_alpha_shapes = {}
layer_extent_vals = {}
layer_extent_transformed_vals = {}
if rank == 0:
for layer, extents in viewitems(layer_extents):
(extent_u, extent_v,
extent_l) = get_layer_extents(layer_extents, layer)
layer_extent_vals[layer] = (extent_u, extent_v, extent_l)
layer_extent_transformed_vals[layer] = CA1_volume_transform(
extent_u, extent_v, extent_l)
has_layer_alpha_shape = False
if geometry_path:
this_layer_alpha_shape_path = '%s/%s' % (
layer_alpha_shape_path, layer)
this_layer_alpha_shape = load_alpha_shape(
geometry_path, this_layer_alpha_shape_path)
layer_alpha_shapes[layer] = this_layer_alpha_shape
if this_layer_alpha_shape is not None:
has_layer_alpha_shape = True
if not has_layer_alpha_shape:
logger.info(
"Constructing alpha shape for layers %s: extents: %s..." %
(layer, str(extents)))
layer_vol = make_CA1_volume(extent_u,
extent_v,
extent_l,
rotate=rotate,
resolution=resolution)
this_layer_alpha_shape = make_alpha_shape(
layer_vol, alpha_radius=alpha_radius)
layer_alpha_shapes[layer] = this_layer_alpha_shape
if geometry_path:
save_alpha_shape(geometry_path,
this_layer_alpha_shape_path,
this_layer_alpha_shape)
comm.barrier()
population_ranges = read_population_ranges(output_path, comm)[0]
if len(populations) == 0:
populations = sorted(population_ranges.keys())
total_count = 0
for population in populations:
(population_start, population_count) = population_ranges[population]
total_count += population_count
all_xyz_coords1 = None
generated_coords_count_dict = defaultdict(int)
if rank == 0:
all_xyz_coords_lst = []
for population in populations:
gc.collect()
(population_start,
population_count) = population_ranges[population]
pop_layers = env.geometry['Cell Distribution'][population]
pop_constraint = None
if 'Cell Constraints' in env.geometry:
if population in env.geometry['Cell Constraints']:
pop_constraint = env.geometry['Cell Constraints'][
population]
if rank == 0:
logger.info("Population %s: layer distribution is %s" %
(population, str(pop_layers)))
pop_layer_count = 0
for layer, count in viewitems(pop_layers):
pop_layer_count += count
assert (population_count == pop_layer_count)
xyz_coords_lst = []
for layer, count in viewitems(pop_layers):
if count <= 0:
continue
alpha = layer_alpha_shapes[layer]
vert = alpha.points
smp = np.asarray(alpha.bounds, dtype=np.int64)
extents_xyz = layer_extent_transformed_vals[layer]
for (vvi, vv) in enumerate(vert):
for (vi, v) in enumerate(vv):
if v < extents_xyz[vi][0]:
vert[vvi][vi] = extents_xyz[vi][0]
elif v > extents_xyz[vi][1]:
vert[vvi][vi] = extents_xyz[vi][1]
N = int(count * 2) # layer-specific number of nodes
node_count = 0
logger.info(
"Generating %i nodes in layer %s for population %s..." %
(N, layer, population))
if verbose:
rbf_logger = logging.Logger.manager.loggerDict[
'rbf.pde.nodes']
rbf_logger.setLevel(logging.DEBUG)
min_energy_constraint = None
if pop_constraint is not None and layer in pop_constraint:
min_energy_constraint = pop_constraint[layer]
nodes = gen_min_energy_nodes(count, (vert, smp),
min_energy_constraint, nodeiter,
dispersion_delta, snap_delta)
#nodes = gen_min_energy_nodes(count, (vert, smp),
# pop_constraint[layer] if pop_constraint is not None else None,
# nodeiter, dispersion_delta, snap_delta)
xyz_coords_lst.append(nodes.reshape(-1, 3))
for this_xyz_coords in xyz_coords_lst:
all_xyz_coords_lst.append(this_xyz_coords)
generated_coords_count_dict[population] += len(this_xyz_coords)
# Additional dispersion step to ensure no overlapping cell positions
all_xyz_coords = np.row_stack(all_xyz_coords_lst)
mask = np.ones((all_xyz_coords.shape[0], ), dtype=np.bool)
# distance to nearest neighbor
while True:
kdt = cKDTree(all_xyz_coords[mask, :])
nndist, nnindices = kdt.query(all_xyz_coords[mask, :], k=2)
nndist, nnindices = nndist[:, 1:], nnindices[:, 1:]
zindices = nnindices[np.argwhere(
np.isclose(nndist, 0.0, atol=1e-3, rtol=1e-3))]
if len(zindices) > 0:
mask[np.argwhere(mask)[zindices]] = False
else:
break
coords_offset = 0
for population in populations:
pop_coords_count = generated_coords_count_dict[population]
pop_mask = mask[coords_offset:coords_offset + pop_coords_count]
generated_coords_count_dict[population] = np.count_nonzero(
pop_mask)
coords_offset += pop_coords_count
logger.info("Dispersion of %i nodes..." % np.count_nonzero(mask))
all_xyz_coords1 = disperse(all_xyz_coords[mask, :],
vol_domain,
delta=dispersion_delta)
if rank == 0:
logger.info("Computing UVL coordinates of %i nodes..." %
len(all_xyz_coords1))
all_xyz_coords_interp = None
all_uvl_coords_interp = None
if rank == 0:
all_uvl_coords_interp = vol.inverse(all_xyz_coords1)
all_xyz_coords_interp = vol(all_uvl_coords_interp[:, 0],
all_uvl_coords_interp[:, 1],
all_uvl_coords_interp[:, 2],
mesh=False).reshape(3, -1).T
if rank == 0:
logger.info("Broadcasting generated nodes...")
xyz_coords = comm.bcast(all_xyz_coords1, root=0)
all_xyz_coords_interp = comm.bcast(all_xyz_coords_interp, root=0)
all_uvl_coords_interp = comm.bcast(all_uvl_coords_interp, root=0)
generated_coords_count_dict = comm.bcast(dict(generated_coords_count_dict),
root=0)
coords_offset = 0
pop_coords_dict = {}
for population in populations:
xyz_error = np.asarray([0.0, 0.0, 0.0])
pop_layers = env.geometry['Cell Distribution'][population]
pop_start, pop_count = population_ranges[population]
coords = []
gen_coords_count = generated_coords_count_dict[population]
for i, coord_ind in enumerate(
range(coords_offset, coords_offset + gen_coords_count)):
if i % size == rank:
uvl_coords = all_uvl_coords_interp[coord_ind, :].ravel()
xyz_coords1 = all_xyz_coords_interp[coord_ind, :].ravel()
if uvl_in_bounds(all_uvl_coords_interp[coord_ind, :],
layer_extents, pop_layers):
xyz_error = np.add(
xyz_error,
np.abs(
np.subtract(xyz_coords[coord_ind, :],
xyz_coords1)))
logger.info('Rank %i: %s cell %i: %f %f %f' %
(rank, population, i, uvl_coords[0],
uvl_coords[1], uvl_coords[2]))
coords.append(
(xyz_coords1[0], xyz_coords1[1], xyz_coords1[2],
uvl_coords[0], uvl_coords[1], uvl_coords[2]))
else:
logger.debug(
'Rank %i: %s cell %i not in bounds: %f %f %f' %
(rank, population, i, uvl_coords[0], uvl_coords[1],
uvl_coords[2]))
uvl_coords = None
xyz_coords1 = None
total_xyz_error = np.zeros((3, ))
comm.Allreduce(xyz_error, total_xyz_error, op=MPI.SUM)
coords_count = 0
coords_count = np.sum(np.asarray(comm.allgather(len(coords))))
mean_xyz_error = np.asarray([(total_xyz_error[0] / coords_count), \
(total_xyz_error[1] / coords_count), \
(total_xyz_error[2] / coords_count)])
pop_coords_dict[population] = coords
coords_offset += gen_coords_count
if rank == 0:
logger.info(
'Total %i coordinates generated for population %s: mean XYZ error: %f %f %f'
% (coords_count, population, mean_xyz_error[0],
mean_xyz_error[1], mean_xyz_error[2]))
if rank == 0:
color = 1
else:
color = 0
## comm0 includes only rank 0
comm0 = comm.Split(color, 0)
for population in populations:
pop_start, pop_count = population_ranges[population]
pop_layers = env.geometry['Cell Distribution'][population]
pop_constraint = None
if 'Cell Constraints' in env.geometry:
if population in env.geometry['Cell Constraints']:
pop_constraint = env.geometry['Cell Constraints'][population]
coords_lst = comm.gather(pop_coords_dict[population], root=0)
if rank == 0:
all_coords = []
for sublist in coords_lst:
for item in sublist:
all_coords.append(item)
coords_count = len(all_coords)
if coords_count < pop_count:
logger.warning(
"Generating additional %i coordinates for population %s..."
% (pop_count - len(all_coords), population))
safety = 0.01
delta = pop_count - len(all_coords)
for i in range(delta):
for layer, count in viewitems(pop_layers):
if count > 0:
min_extent = layer_extents[layer][0]
max_extent = layer_extents[layer][1]
coord_u = np.random.uniform(
min_extent[0] + safety, max_extent[0] - safety)
coord_v = np.random.uniform(
min_extent[1] + safety, max_extent[1] - safety)
if pop_constraint is None:
coord_l = np.random.uniform(
min_extent[2] + safety,
max_extent[2] - safety)
else:
coord_l = np.random.uniform(
pop_constraint[layer][0] + safety,
pop_constraint[layer][1] - safety)
xyz_coords = CA1_volume(coord_u,
coord_v,
coord_l,
rotate=rotate).ravel()
all_coords.append(
(xyz_coords[0], xyz_coords[1], xyz_coords[2],
coord_u, coord_v, coord_l))
sampled_coords = random_subset(all_coords, int(pop_count))
sampled_coords.sort(
key=lambda coord: coord[3]) ## sort on U coordinate
coords_dict = {
pop_start + i: {
'X Coordinate': np.asarray([x_coord], dtype=np.float32),
'Y Coordinate': np.asarray([y_coord], dtype=np.float32),
'Z Coordinate': np.asarray([z_coord], dtype=np.float32),
'U Coordinate': np.asarray([u_coord], dtype=np.float32),
'V Coordinate': np.asarray([v_coord], dtype=np.float32),
'L Coordinate': np.asarray([l_coord], dtype=np.float32)
}
for (i, (x_coord, y_coord, z_coord, u_coord, v_coord,
l_coord)) in enumerate(sampled_coords)
}
append_cell_attributes(output_path,
population,
coords_dict,
namespace=output_namespace,
io_size=io_size,
chunk_size=chunk_size,
value_chunk_size=value_chunk_size,
comm=comm0)
comm.barrier()
comm0.Free()
def main(config_file, population, gid, template_paths, dataset_prefix,
config_prefix, data_file, load_synapses, syn_types, syn_sources,
syn_source_threshold, font_size, bgcolor, colormap, plot_method,
verbose):
utils.config_logging(verbose)
logger = utils.get_script_logger(script_name)
if dataset_prefix is None and data_file is None:
raise RuntimeError(
'Either --dataset-prefix or --data-file must be provided.')
params = dict(locals())
env = Env(**params)
configure_hoc_env(env)
if env.data_file_path is None:
env.data_file_path = data_file
env.load_celltypes()
## Determine if a mechanism configuration file exists for this cell type
if 'mech_file_path' in env.celltypes[population]:
mech_file_path = env.celltypes[population]['mech_file_path']
else:
mech_file_path = None
logger.info('loading cell %i' % gid)
load_weights = False
load_edges = False
biophys_cell = make_biophys_cell(env,
population,
gid,
load_synapses=load_synapses,
load_weights=load_weights,
load_edges=load_edges,
mech_file_path=mech_file_path)
cells.init_biophysics(biophys_cell,
reset_cable=True,
correct_cm=False,
correct_g_pas=False,
env=env)
if load_synapses:
init_syn_mech_attrs(biophys_cell, env, update_targets=True)
cells.report_topology(env, biophys_cell)
if len(syn_types) == 0:
syn_types = None
else:
syn_types = list(syn_types)
if len(syn_sources) == 0:
syn_sources = None
else:
syn_sources = list(syn_sources)
plot.plot_biophys_cell_tree(env,
biophys_cell,
saveFig=True,
syn_source_threshold=syn_source_threshold,
synapse_filters={
'syn_types': syn_types,
'sources': syn_sources
},
bgcolor=bgcolor,
colormap=colormap,
plot_method=plot_method)
def main(config, coords_path, coords_namespace, geometry_path, populations, interp_chunk_size, resolution, alpha_radius, nsample, io_size, chunk_size, value_chunk_size, cache_size, verbose):
utils.config_logging(verbose)
logger = utils.get_script_logger(__file__)
comm = MPI.COMM_WORLD
rank = comm.rank
env = Env(comm=comm, config_file=config)
output_path = coords_path
soma_coords = {}
if rank == 0:
logger.info('Reading population coordinates...')
for population in sorted(populations):
coords = bcast_cell_attributes(coords_path, population, 0, \
namespace=coords_namespace, comm=comm)
soma_coords[population] = { k: (v['U Coordinate'][0], v['V Coordinate'][0], v['L Coordinate'][0])
for (k,v) in coords }
del coords
gc.collect()
has_ip_dist=False
origin_ranges=None
ip_dist_u=None
ip_dist_v=None
ip_dist_path = 'Distance Interpolant/%d/%d/%d' % resolution
if rank == 0:
if geometry_path is not None:
f = h5py.File(geometry_path,"a")
pkl_path = f'{ip_dist_path}/ip_dist.pkl'
if pkl_path in f:
has_ip_dist = True
ip_dist_dset = f[pkl_path]
origin_ranges, ip_dist_u, ip_dist_v = pickle.loads(base64.b64decode(ip_dist_dset[()]))
f.close()
has_ip_dist = env.comm.bcast(has_ip_dist, root=0)
if not has_ip_dist:
if rank == 0:
logger.info('Creating distance interpolant...')
(origin_ranges, ip_dist_u, ip_dist_v) = make_distance_interpolant(env.comm, geometry_config=env.geometry,
make_volume=make_CA1_volume,
resolution=resolution, nsample=nsample)
if rank == 0:
if geometry_path is not None:
f = h5py.File(geometry_path, 'a')
pkl_path = f'{ip_dist_path}/ip_dist.pkl'
pkl = pickle.dumps((origin_ranges, ip_dist_u, ip_dist_v))
pklstr = base64.b64encode(pkl)
f[pkl_path] = pklstr
f.close()
ip_dist = (origin_ranges, ip_dist_u, ip_dist_v)
if rank == 0:
logger.info('Measuring soma distances...')
soma_distances = measure_distances(env.comm, env.geometry, soma_coords, ip_dist, resolution=resolution)
for population in list(sorted(soma_distances.keys())):
if rank == 0:
logger.info(f'Writing distances for population {population}...')
dist_dict = soma_distances[population]
attr_dict = {}
for k, v in viewitems(dist_dict):
attr_dict[k] = { 'U Distance': np.asarray([v[0]],dtype=np.float32), \
'V Distance': np.asarray([v[1]],dtype=np.float32) }
append_cell_attributes(output_path, population, attr_dict,
namespace='Arc Distances', comm=comm,
io_size=io_size, chunk_size=chunk_size,
value_chunk_size=value_chunk_size, cache_size=cache_size)
if rank == 0:
f = h5py.File(output_path, 'a')
f['Populations'][population]['Arc Distances'].attrs['Reference U Min'] = origin_ranges[0][0]
f['Populations'][population]['Arc Distances'].attrs['Reference U Max'] = origin_ranges[0][1]
f['Populations'][population]['Arc Distances'].attrs['Reference V Min'] = origin_ranges[1][0]
f['Populations'][population]['Arc Distances'].attrs['Reference V Max'] = origin_ranges[1][1]
f.close()
comm.Barrier()
def main(config, config_prefix, include, forest_path, connectivity_path,
connectivity_namespace, coords_path, coords_namespace,
synapses_namespace, distances_namespace, resolution,
interp_chunk_size, io_size, chunk_size, value_chunk_size, cache_size,
write_size, verbose, dry_run, debug):
utils.config_logging(verbose)
logger = utils.get_script_logger(os.path.basename(__file__))
comm = MPI.COMM_WORLD
rank = comm.rank
env = Env(comm=comm, config_file=config, config_prefix=config_prefix)
configure_hoc_env(env)
connection_config = env.connection_config
extent = {}
if (not dry_run) and (rank == 0):
if not os.path.isfile(connectivity_path):
input_file = h5py.File(coords_path, 'r')
output_file = h5py.File(connectivity_path, 'w')
input_file.copy('/H5Types', output_file)
input_file.close()
output_file.close()
comm.barrier()
population_ranges = read_population_ranges(coords_path)[0]
populations = sorted(list(population_ranges.keys()))
color = 0
if rank == 0:
color = 1
comm0 = comm.Split(color, 0)
soma_distances = {}
soma_coords = {}
for population in populations:
if rank == 0:
logger.info(f'Reading {population} coordinates...')
coords_iter = read_cell_attributes(
coords_path,
population,
comm=comm0,
mask=set(['U Coordinate', 'V Coordinate', 'L Coordinate']),
namespace=coords_namespace)
distances_iter = read_cell_attributes(
coords_path,
population,
comm=comm0,
mask=set(['U Distance', 'V Distance']),
namespace=distances_namespace)
soma_coords[population] = {
k: (float(v['U Coordinate'][0]), float(v['V Coordinate'][0]),
float(v['L Coordinate'][0]))
for (k, v) in coords_iter
}
distances = {
k: (float(v['U Distance'][0]), float(v['V Distance'][0]))
for (k, v) in distances_iter
}
if len(distances) > 0:
soma_distances[population] = distances
gc.collect()
comm.barrier()
comm0.Free()
soma_distances = comm.bcast(soma_distances, root=0)
soma_coords = comm.bcast(soma_coords, root=0)
forest_populations = sorted(read_population_names(forest_path))
if (include is None) or (len(include) == 0):
destination_populations = forest_populations
else:
destination_populations = []
for p in include:
if p in forest_populations:
destination_populations.append(p)
if rank == 0:
logger.info(
f'Generating connectivity for populations {destination_populations}...'
)
if len(soma_distances) == 0:
(origin_ranges, ip_dist_u,
ip_dist_v) = make_distance_interpolant(env,
resolution=resolution,
nsample=nsample)
ip_dist = (origin_ranges, ip_dist_u, ip_dist_v)
soma_distances = measure_distances(env,
soma_coords,
ip_dist,
resolution=resolution)
for destination_population in destination_populations:
if rank == 0:
logger.info(
f'Generating connection probabilities for population {destination_population}...'
)
connection_prob = ConnectionProb(destination_population, soma_coords, soma_distances, \
env.connection_extents)
synapse_seed = int(
env.model_config['Random Seeds']['Synapse Projection Partitions'])
connectivity_seed = int(env.model_config['Random Seeds']
['Distance-Dependent Connectivity'])
cluster_seed = int(
env.model_config['Random Seeds']['Connectivity Clustering'])
if rank == 0:
logger.info(
f'Generating connections for population {destination_population}...'
)
populations_dict = env.model_config['Definitions']['Populations']
generate_uv_distance_connections(comm,
populations_dict,
connection_config,
connection_prob,
forest_path,
synapse_seed,
connectivity_seed,
cluster_seed,
synapses_namespace,
connectivity_namespace,
connectivity_path,
io_size,
chunk_size,
value_chunk_size,
cache_size,
write_size,
dry_run=dry_run,
debug=debug)
MPI.Finalize()
def main(config, config_prefix, template_path, output_path, forest_path,
populations, distribution, io_size, chunk_size, value_chunk_size,
write_size, verbose, dry_run, debug):
"""
:param config:
:param config_prefix:
:param template_path:
:param forest_path:
:param populations:
:param distribution:
:param io_size:
:param chunk_size:
:param value_chunk_size:
"""
utils.config_logging(verbose)
logger = utils.get_script_logger(os.path.basename(__file__))
comm = MPI.COMM_WORLD
rank = comm.rank
if rank == 0:
logger.info(f'{comm.size} ranks have been allocated')
env = Env(comm=comm,
config_file=config,
config_prefix=config_prefix,
template_paths=template_path)
configure_hoc_env(env)
if io_size == -1:
io_size = comm.size
if output_path is None:
output_path = forest_path
if not dry_run:
if rank == 0:
if not os.path.isfile(output_path):
input_file = h5py.File(forest_path, 'r')
output_file = h5py.File(output_path, 'w')
input_file.copy('/H5Types', output_file)
input_file.close()
output_file.close()
comm.barrier()
(pop_ranges, _) = read_population_ranges(forest_path, comm=comm)
start_time = time.time()
syn_stats = dict()
for population in populations:
syn_stats[population] = { 'section': defaultdict(lambda: { 'excitatory': 0, 'inhibitory': 0 }), \
'layer': defaultdict(lambda: { 'excitatory': 0, 'inhibitory': 0 }), \
'swc_type': defaultdict(lambda: { 'excitatory': 0, 'inhibitory': 0 }), \
'total': { 'excitatory': 0, 'inhibitory': 0 } }
for population in populations:
logger.info(f'Rank {rank} population: {population}')
(population_start, _) = pop_ranges[population]
template_class = load_cell_template(env,
population,
bcast_template=True)
density_dict = env.celltypes[population]['synapses']['density']
layer_set_dict = defaultdict(set)
swc_set_dict = defaultdict(set)
for sec_name, sec_dict in viewitems(density_dict):
for syn_type, syn_dict in viewitems(sec_dict):
swc_set_dict[syn_type].add(env.SWC_Types[sec_name])
for layer_name in syn_dict:
if layer_name != 'default':
layer = env.layers[layer_name]
layer_set_dict[syn_type].add(layer)
syn_stats_dict = { 'section': defaultdict(lambda: { 'excitatory': 0, 'inhibitory': 0 }), \
'layer': defaultdict(lambda: { 'excitatory': 0, 'inhibitory': 0 }), \
'swc_type': defaultdict(lambda: { 'excitatory': 0, 'inhibitory': 0 }), \
'total': { 'excitatory': 0, 'inhibitory': 0 } }
count = 0
gid_count = 0
synapse_dict = {}
for gid, morph_dict in NeuroH5TreeGen(forest_path,
population,
io_size=io_size,
comm=comm,
topology=True):
local_time = time.time()
if gid is not None:
logger.info(f'Rank {rank} gid: {gid}: {morph_dict}')
cell = cells.make_neurotree_hoc_cell(template_class,
neurotree_dict=morph_dict,
gid=gid)
cell_sec_dict = {
'apical': (cell.apical_list, None),
'basal': (cell.basal_list, None),
'soma': (cell.soma_list, None),
'ais': (cell.ais_list, None),
'hillock': (cell.hillock_list, None)
}
cell_secidx_dict = {
'apical': cell.apicalidx,
'basal': cell.basalidx,
'soma': cell.somaidx,
'ais': cell.aisidx,
'hillock': cell.hilidx
}
random_seed = env.model_config['Random Seeds'][
'Synapse Locations'] + gid
if distribution == 'uniform':
syn_dict, seg_density_per_sec = synapses.distribute_uniform_synapses(
random_seed, env.Synapse_Types, env.SWC_Types,
env.layers, density_dict, morph_dict, cell_sec_dict,
cell_secidx_dict)
elif distribution == 'poisson':
syn_dict, seg_density_per_sec = synapses.distribute_poisson_synapses(
random_seed, env.Synapse_Types, env.SWC_Types,
env.layers, density_dict, morph_dict, cell_sec_dict,
cell_secidx_dict)
else:
raise Exception('Unknown distribution type: %s' %
distribution)
synapse_dict[gid] = syn_dict
this_syn_stats = update_syn_stats(env, syn_stats_dict,
syn_dict)
check_syns(gid, morph_dict, this_syn_stats,
seg_density_per_sec, layer_set_dict, swc_set_dict,
env, logger)
del cell
num_syns = len(synapse_dict[gid]['syn_ids'])
logger.info(
f'Rank {rank} took {time.time() - local_time:.2f} s to compute {num_syns} synapse locations for {population} gid: {gid}\n'
f'{local_syn_summary(this_syn_stats)}')
gid_count += 1
else:
logger.info(f'Rank {rank} gid is None')
gc.collect()
if (not dry_run) and (write_size > 0) and (gid_count % write_size
== 0):
append_cell_attributes(output_path,
population,
synapse_dict,
namespace='Synapse Attributes',
comm=comm,
io_size=io_size,
chunk_size=chunk_size,
value_chunk_size=value_chunk_size)
synapse_dict = {}
syn_stats[population] = syn_stats_dict
count += 1
if debug and count == 5:
break
if not dry_run:
append_cell_attributes(output_path,
population,
synapse_dict,
namespace='Synapse Attributes',
comm=comm,
io_size=io_size,
chunk_size=chunk_size,
value_chunk_size=value_chunk_size)
global_count, summary = global_syn_summary(comm,
syn_stats,
gid_count,
root=0)
if rank == 0:
logger.info(
f'Population: {population}, {comm.size} ranks took {time.time() - start_time:.2f} s '
f'to compute synapse locations for {np.sum(global_count)} cells'
)
logger.info(summary)
comm.barrier()
MPI.Finalize()