def main():
import neurokernel.mpi_relaunch
# default limit is low for pickling
# the data structures passed through mpi
sys.setrecursionlimit(RECURSION_LIMIT)
resource.setrlimit(resource.RLIMIT_STACK,
(resource.RLIM_INFINITY, resource.RLIM_INFINITY))
parser = argparse.ArgumentParser()
parser.add_argument('-c',
'--config',
default='default',
help='configuration file')
parser.add_argument('-v',
'--value',
type=int,
default=-1,
help='Value that can overwrite configuration '
'by changing this script accordingly. '
'It is useful when need to run this script '
'repeatedly for different configuration')
args = parser.parse_args()
with Timer('getting configuration'):
conf_obj = get_config_obj(args)
config = conf_obj.conf
change_config(config, args.value)
setup_logging(config)
worker_num = config['Retina']['worker_num']
num_rings = config['Retina']['rings']
radius = config['Retina']['radius']
eulerangles = config['Retina']['eulerangles']
manager = core.Manager()
with Timer('instantiation of retina'):
transform = AlbersProjectionMap(radius, eulerangles).invmap
hexagon = hx.HexagonArray(num_rings=num_rings,
radius=radius,
transform=transform)
retina = ret.RetinaArray(hexagon, config)
# sets retina attribute which is required for the generation of
# receptive fields
#if generator is not None:
# generator.generate_datafiles(0, retina)
add_master_LPU(config, 0, retina, manager)
for j in range(worker_num):
add_worker_LPU(config, j, retina, manager)
connect_master_worker(config, j, retina, manager)
start_simulation(config, manager)
def main():
import neurokernel.mpi_relaunch
# default limit is low for pickling
# the data structures passed through mpi
sys.setrecursionlimit(RECURSION_LIMIT)
resource.setrlimit(resource.RLIMIT_STACK,
(resource.RLIM_INFINITY, resource.RLIM_INFINITY))
parser = argparse.ArgumentParser()
parser.add_argument('-c', '--config', default='default',
help='configuration file')
parser.add_argument('-v', '--value', type=int, default=-1,
help='Value that can overwrite configuration '
'by changing this script accordingly. '
'It is useful when need to run this script '
'repeatedly for different configuration')
args = parser.parse_args()
with Timer('getting configuration'):
conf_obj = get_config_obj(args)
config = conf_obj.conf
change_config(config, args.value)
setup_logging(config)
num_rings = config['Retina']['rings']
eulerangles = config['Retina']['eulerangles']
radius = config['Retina']['radius']
manager = core.Manager()
with Timer('instantiation of retina and lamina'):
transform = AlbersProjectionMap(radius, eulerangles).invmap
r_hexagon = r_hx.HexagonArray(num_rings=num_rings, radius=radius,
transform=transform)
l_hexagon = l_hx.HexagonArray(num_rings=num_rings, radius=radius,
transform=transform)
retina = ret.RetinaArray(r_hexagon, config)
lamina = lam.LaminaArray(l_hexagon, config)
add_retina_LPU(config, 0, retina, manager)
add_lamina_LPU(config, 0, lamina, manager)
connect_retina_lamina(config, 0, retina, lamina, manager)
start_simulation(config, manager)
def main():
from retina.screen.map.mapimpl import AlbersProjectionMap
import retina.geometry.hexagon as hex
from retina.configreader import ConfigReader
import retina.retina as ret
import networkx as nx
config = ConfigReader('retlam_default.cfg', '../template_spec.cfg').conf
transform = AlbersProjectionMap(config['Retina']['radius'],
config['Retina']['eulerangles']).invmap
hexarray = hex.HexagonArray(num_rings=14,
radius=config['Retina']['radius'],
transform=transform)
a = ret.RetinaArray(hexarray, config)
G = a.generate_neuroarch_gexf()
nx.write_gexf(G, 'retina_neuroarch.gexf.gz')
def gen_input(config):
cuda.init()
ctx = cuda.Device(0).make_context()
atexit.register(ctx.pop)
suffix = config['General']['file_suffix']
eye_num = config['General']['eye_num']
rings = config['Retina']['rings']
steps = config['General']['steps']
input_filename = config['Retina']['input_file']
screen_write_step = config['Retina']['screen_write_step']
config['Retina']['screen_write_step'] = 1
screen_type = config['Retina']['screentype']
screen_cls = cls_map.get_screen_cls(screen_type)
eulerangles = config['Retina']['eulerangles']
radius = config['Retina']['radius']
for i in range(eye_num):
screen = screen_cls(config)
screen_file = 'intensities_tmp{}.h5'.format(i)
screen.setup_file(screen_file)
retina_elev_file = 'retina_elev{}.h5'.format(i)
retina_azim_file = 'retina_azim{}.h5'.format(i)
screen_dima_file = 'grid_dima{}.h5'.format(i)
screen_dimb_file = 'grid_dimb{}.h5'.format(i)
retina_dima_file = 'retina_dima{}.h5'.format(i)
retina_dimb_file = 'retina_dimb{}.h5'.format(i)
input_file = '{}{}{}.h5'.format(input_filename, i, suffix)
transform = AlbersProjectionMap(radius,
eulerangles[3*i:3*(i+1)]).invmap
hexagon = hx.HexagonArray(num_rings=rings, radius=radius,
transform=transform)
retina = ret.RetinaArray(hexagon, config=config)
print('Acceptance angle: {}'.format(retina.acceptance_angle))
print('Neurons: {}'.format(retina.num_photoreceptors))
elev_v, azim_v = retina.get_ommatidia_pos()
rfs = _get_receptive_fields(retina, screen, screen_type)
steps_count = steps
write_mode = 'w'
while (steps_count > 0):
steps_batch = min(100, steps_count)
im = screen.get_screen_intensity_steps(steps_batch)
photor_inputs = rfs.filter(im)
sio.write_array(photor_inputs, filename=input_file, mode=write_mode)
steps_count -= steps_batch
write_mode = 'a'
tmp = sio.read_array(screen_file)
sio.write_array(tmp[::screen_write_step],
'intensities{}{}.h5'.format(suffix, i),
complevel = 9)
del tmp
os.remove(screen_file)
for data, filename in [(elev_v, retina_elev_file),
(azim_v, retina_azim_file),
(screen.grid[0], screen_dima_file),
(screen.grid[1], screen_dimb_file),
(rfs.refa, retina_dima_file),
(rfs.refb, retina_dimb_file)]:
sio.write_array(data, filename)