def test_from_graph(self):
p = Pattern('/foo[0:4]', '/bar[0:4]')
p['/foo[0]', '/bar[0]'] = 1
p['/foo[0]', '/bar[1]'] = 1
p['/foo[1]', '/bar[2]'] = 1
p['/bar[3]', '/foo[2]'] = 1
p['/bar[3]', '/foo[3]'] = 1
g = nx.DiGraph()
g.add_node('/bar[0]', interface=1, io='out')
g.add_node('/bar[1]', interface=1, io='out')
g.add_node('/bar[2]', interface=1, io='out')
g.add_node('/bar[3]', interface=1, io='in')
g.add_node('/foo[0]', interface=0, io='in')
g.add_node('/foo[1]', interface=0, io='in')
g.add_node('/foo[2]', interface=0, io='out')
g.add_node('/foo[3]', interface=0, io='out')
g.add_edge('/foo[0]', '/bar[0]')
g.add_edge('/foo[0]', '/bar[1]')
g.add_edge('/foo[1]', '/bar[2]')
g.add_edge('/bar[3]', '/foo[2]')
g.add_edge('/bar[3]', '/foo[3]')
pg = Pattern.from_graph(g)
assert_frame_equal(pg.data.sort_index(), p.data.sort_index())
assert_frame_equal(pg.interface.data.sort_index(),
p.interface.data.sort_index())
p.interface['/foo[0]', 'type'] = 'gpot'
p.interface['/bar[0]', 'type'] = 'gpot'
p.interface['/bar[1]', 'type'] = 'gpot'
p.interface['/foo[1]', 'type'] = 'gpot'
p.interface['/bar[2]', 'type'] = 'gpot'
p.interface['/bar[3]', 'type'] = 'spike'
p.interface['/foo[2]', 'type'] = 'spike'
p.interface['/bar[3]', 'type'] = 'spike'
p.interface['/foo[3]', 'type'] = 'spike'
g = nx.DiGraph()
g.add_node('/bar[0]', interface=1, io='out', type='gpot')
g.add_node('/bar[1]', interface=1, io='out', type='gpot')
g.add_node('/bar[2]', interface=1, io='out', type='gpot')
g.add_node('/bar[3]', interface=1, io='in', type='spike')
g.add_node('/foo[0]', interface=0, io='in', type='gpot')
g.add_node('/foo[1]', interface=0, io='in', type='gpot')
g.add_node('/foo[2]', interface=0, io='out', type='spike')
g.add_node('/foo[3]', interface=0, io='out', type='spike')
g.add_edge('/foo[0]', '/bar[0]')
g.add_edge('/foo[0]', '/bar[1]')
g.add_edge('/foo[1]', '/bar[2]')
g.add_edge('/bar[3]', '/foo[2]')
g.add_edge('/bar[3]', '/foo[3]')
pg = Pattern.from_graph(g)
assert_frame_equal(pg.data.sort_index(), p.data.sort_index())
assert_frame_equal(pg.interface.data.sort_index(),
p.interface.data.sort_index())
def test_from_graph(self):
p = Pattern('/foo[0:4]', '/bar[0:4]')
p['/foo[0]', '/bar[0]'] = 1
p['/foo[0]', '/bar[1]'] = 1
p['/foo[1]', '/bar[2]'] = 1
p['/bar[3]', '/foo[2]'] = 1
p['/bar[3]', '/foo[3]'] = 1
g = nx.DiGraph()
g.add_node('/bar[0]', interface=1, io='out')
g.add_node('/bar[1]', interface=1, io='out')
g.add_node('/bar[2]', interface=1, io='out')
g.add_node('/bar[3]', interface=1, io='in')
g.add_node('/foo[0]', interface=0, io='in')
g.add_node('/foo[1]', interface=0, io='in')
g.add_node('/foo[2]', interface=0, io='out')
g.add_node('/foo[3]', interface=0, io='out')
g.add_edge('/foo[0]', '/bar[0]')
g.add_edge('/foo[0]', '/bar[1]')
g.add_edge('/foo[1]', '/bar[2]')
g.add_edge('/bar[3]', '/foo[2]')
g.add_edge('/bar[3]', '/foo[3]')
pg = Pattern.from_graph(g)
assert_frame_equal(pg.data.sort_index(), p.data.sort_index())
assert_frame_equal(pg.interface.data.sort_index(),
p.interface.data.sort_index())
p.interface['/foo[0]', 'type'] = 'gpot'
p.interface['/bar[0]', 'type'] = 'gpot'
p.interface['/bar[1]', 'type'] = 'gpot'
p.interface['/foo[1]', 'type'] = 'gpot'
p.interface['/bar[2]', 'type'] = 'gpot'
p.interface['/bar[3]', 'type'] = 'spike'
p.interface['/foo[2]', 'type'] = 'spike'
p.interface['/bar[3]', 'type'] = 'spike'
p.interface['/foo[3]', 'type'] = 'spike'
g = nx.DiGraph()
g.add_node('/bar[0]', interface=1, io='out', type='gpot')
g.add_node('/bar[1]', interface=1, io='out', type='gpot')
g.add_node('/bar[2]', interface=1, io='out', type='gpot')
g.add_node('/bar[3]', interface=1, io='in', type='spike')
g.add_node('/foo[0]', interface=0, io='in', type='gpot')
g.add_node('/foo[1]', interface=0, io='in', type='gpot')
g.add_node('/foo[2]', interface=0, io='out', type='spike')
g.add_node('/foo[3]', interface=0, io='out', type='spike')
g.add_edge('/foo[0]', '/bar[0]')
g.add_edge('/foo[0]', '/bar[1]')
g.add_edge('/foo[1]', '/bar[2]')
g.add_edge('/bar[3]', '/foo[2]')
g.add_edge('/bar[3]', '/foo[3]')
pg = Pattern.from_graph(g)
assert_frame_equal(pg.data.sort_index(), p.data.sort_index())
assert_frame_equal(pg.interface.data.sort_index(),
p.interface.data.sort_index())
def launch(self, user_id, task):
neuron_uid_list = [str(a) for a in task['neuron_list']]
conf_obj = get_config_obj()
config = conf_obj.conf
if config['Retina']['intype'] == 'Natural':
coord_file = config['InputType']['Natural']['coord_file']
tmp = os.path.splitext(coord_file)
config['InputType']['Natural']['coord_file'] = '{}_{}{}'.format(
tmp[0], user_id, tmp[1])
setup_logger(file_name='neurokernel_' + user_id + '.log', screen=False)
manager = core.Manager()
lpus = {}
patterns = {}
G = task['success']['data']
# get graph and output_uid_list for each LPU
for k, lpu in G['LPU'].iteritems():
lpus[k] = {}
g_lpu_na = create_graph_from_database_returned(lpu)
lpu_nk_graph = nk.na_lpu_to_nk_new(g_lpu_na)
lpus[k]['graph'] = lpu_nk_graph
lpus[k]['output_uid_list'] = list(
set(lpu_nk_graph.nodes()).intersection(set(neuron_uid_list)))
lpus[k]['output_file'] = '{}_output_{}.h5'.format(k, user_id)
# get graph for each Pattern
for k, pat in G['Pattern'].iteritems():
l1, l2 = k.split('-')
if l1 in lpus and l2 in lpus:
g_pattern_na = create_graph_from_database_returned(pat)
pattern_nk = nk.na_pat_to_nk(g_pattern_na)
lpu_ports = [node[1]['selector'] \
for node in lpus[l1]['graph'].nodes(data=True) \
if node[1]['class']=='Port'] + \
[node[1]['selector'] \
for node in lpus[l2]['graph'].nodes(data=True) \
if node[1]['class']=='Port']
pattern_ports = pattern_nk.nodes()
patterns[k] = {}
patterns[k]['graph'] = pattern_nk.subgraph(
list(set(lpu_ports).intersection(set(pattern_ports))))
dt = config['General']['dt']
# add LPUs to manager
for k, lpu in lpus.iteritems():
graph = lpu['graph']
if k == 'retina':
prs = [node for node in graph.nodes(data=True) \
if node[1]['class'] == 'PhotoreceptorModel']
for pr in prs:
graph.node[pr[0]]['num_microvilli'] = 3000
input_processors = [
RetinaInputIndividual(config, prs, user_id)
]
extra_comps = [PhotoreceptorModel]
retina_input_uids = [a[0] for a in prs]
else:
input_processors = []
extra_comps = [BufferVoltage]
output_processor = FileOutputProcessor(
[('V', lpu['output_uid_list'])],
lpu['output_file'],
sample_interval=10)
(comp_dict, conns) = LPU.graph_to_dicts(graph)
manager.add(LPU,
k,
dt,
comp_dict,
conns,
device=0,
input_processors=input_processors,
output_processors=[output_processor],
extra_comps=extra_comps)
# connect LPUs by Patterns
for k, pattern in patterns.iteritems():
l1, l2 = k.split('-')
if l1 in lpus and l2 in lpus:
print('Connecting {} and {}'.format(l1, l2))
pat, key_order = Pattern.from_graph(
nx.DiGraph(pattern['graph']))
with Timer('update of connections in Manager'):
manager.connect(l1,
l2,
pat,
int_0=key_order.index(l1),
int_1=key_order.index(l2))
# start simulation
steps = config['General']['steps']
ignored_steps = config['General']['ignored_steps']
manager.spawn()
manager.start(steps=steps)
manager.wait()
time.sleep(5)
# post-processing inputs (hard coded, can be better organized)
inputs = {
u'ydomain': 1.0,
u'xdomain': dt * (steps - ignored_steps),
u'dt': dt * 10,
u'data': {}
}
if 'retina' in lpus:
input_array = si.read_array('{}_{}.h5'.format(
config['Retina']['input_file'], user_id))
inputs[u'ydomain'] = input_array.max()
for i, item in enumerate(retina_input_uids):
inputs['data'][item] = np.hstack(
(np.arange(int((steps - ignored_steps) / 10)).reshape(
(-1, 1)) * dt * 10, input_array[ignored_steps::10,
i:i + 1])).tolist()
del input_array
# post-processing outputs from all LPUs and combine them into one dictionary
result = {
u'ydomain': 1,
u'xdomain': dt * (steps - ignored_steps),
u'dt': dt * 10,
u'data': {}
}
for k, lpu in lpus.iteritems():
with h5py.File(lpu['output_file']) as output_file:
uids = output_file['V']['uids'][:]
output_array = output_file['V']['data'][:]
for i, item in enumerate(uids):
output = output_array[int(ignored_steps / 10):, i:i + 1]
tmp = output.max() - output.min()
if tmp <= 0.01: #mV
output = (output - output.min()) + 0.5
else:
output = (output - output.min()) / tmp * 0.9 + 0.1
result['data'][item] = np.hstack(
(np.arange(int((steps - ignored_steps) / 10)).reshape(
(-1, 1)) * dt * 10, output)).tolist()
return inputs, result
def launch(self, user_id, task):
neuron_uid_list = [str(a) for a in task['neuron_list']]
conf_obj = get_config_obj()
config = conf_obj.conf
if config['Retina']['intype'] == 'Natural':
coord_file = config['InputType']['Natural']['coord_file']
tmp = os.path.splitext(coord_file)
config['InputType']['Natural']['coord_file'] = '{}_{}{}'.format(
tmp[0], user_id, tmp[1])
setup_logger(file_name='neurokernel_' + user_id + '.log', screen=True)
manager = core.Manager()
lpus = {}
patterns = {}
G = task['data']
with open('G.pickle', 'wb') as f:
pickle.dump(G, f, protocol=pickle.HIGHEST_PROTOCOL)
print(G)
print(G.keys())
print(G['LPU'])
print(G['LPU'].keys())
# get graph and output_uid_list for each LPU
for k, lpu in G['LPU'].items():
lpus[k] = {}
g_lpu_na = create_graph_from_database_returned(lpu)
lpu_nk_graph = nk.na_lpu_to_nk_new(g_lpu_na)
lpus[k]['graph'] = lpu_nk_graph
lpus[k]['output_uid_list'] = list(
set(lpu_nk_graph.nodes()).intersection(set(neuron_uid_list)))
lpus[k]['output_file'] = '{}_output_{}.h5'.format(k, user_id)
for kkey, lpu in lpus.items():
graph = lpu['graph']
for uid, comp in graph.node.items():
if 'attr_dict' in comp:
print('Found attr_dict; fixing...')
nx.set_node_attributes(graph, {uid: comp['attr_dict']})
# print('changed',uid)
graph.nodes[uid].pop('attr_dict')
for i, j, k, v in graph.edges(keys=True, data=True):
if 'attr_dict' in v:
for key in v['attr_dict']:
nx.set_edge_attributes(
graph, {(i, j, k): {
key: v['attr_dict'][key]
}})
graph.edges[(i, j, k)].pop('attr_dict')
lpus[kkey]['graph'] = graph
# get graph for each Pattern
for k, pat in G['Pattern'].items():
l1, l2 = k.split('-')
if l1 in lpus and l2 in lpus:
g_pattern_na = create_graph_from_database_returned(pat)
pattern_nk = nk.na_pat_to_nk(g_pattern_na)
print(lpus[l1]['graph'].nodes(data=True))
lpu_ports = [node[1]['selector'] \
for node in lpus[l1]['graph'].nodes(data=True) \
if node[1]['class']=='Port'] + \
[node[1]['selector'] \
for node in lpus[l2]['graph'].nodes(data=True) \
if node[1]['class']=='Port']
pattern_ports = pattern_nk.nodes()
patterns[k] = {}
patterns[k]['graph'] = pattern_nk.subgraph(
list(set(lpu_ports).intersection(set(pattern_ports))))
dt = config['General']['dt']
if 'dt' in task:
dt = task['dt']
print(dt)
# add LPUs to manager
for k, lpu in lpus.items():
lpu_name = k
graph = lpu['graph']
for uid, comp in graph.node.items():
if 'attr_dict' in comp:
nx.set_node_attributes(graph, {uid: comp['attr_dict']})
# print('changed',uid)
graph.nodes[uid].pop('attr_dict')
for i, j, ko, v in graph.edges(keys=True, data=True):
if 'attr_dict' in v:
for key in v['attr_dict']:
nx.set_edge_attributes(
graph, {(i, j, ko): {
key: v['attr_dict'][key]
}})
graph.edges[(i, j, ko)].pop('attr_dict')
nx.write_gexf(graph, 'name.gexf')
with open(lpu_name + '.pickle', 'wb') as f:
pickle.dump(graph, f, protocol=pickle.HIGHEST_PROTOCOL)
comps = graph.node.items()
#for uid, comp in comps:
# if 'attr_dict' in comp:
# nx.set_node_attributes(graph, {uid: comp['attr_dict']})
# print('changed',uid)
# if 'class' in comp:
if k == 'retina':
prs = [node for node in graph.nodes(data=True) \
if node[1]['class'] == 'PhotoreceptorModel']
for pr in prs:
graph.node[pr[0]]['num_microvilli'] = 3000
input_processors = [
RetinaInputIndividual(config, prs, user_id)
]
extra_comps = [PhotoreceptorModel]
retina_input_uids = [a[0] for a in prs]
elif k == 'EB':
input_processor = StepInputProcessor('I', [node[0] for node in graph.nodes(data=True) \
if node[1]['class'] == 'LeakyIAF'], 40.0, 0.0, 1.0)
input_processors = [input_processor]
extra_comps = [BufferVoltage]
else:
input_processors = []
extra_comps = [BufferVoltage]
if 'inputProcessors' in task:
input_processors = loadExperimentSettings(
task['inputProcessors'])
output_processor = FileOutputProcessor(
[('V', lpu['output_uid_list'])],
lpu['output_file'],
sample_interval=10)
(comp_dict, conns) = LPU.graph_to_dicts(graph)
# print(comp_dict)
# print(conns)
print(k)
manager.add(LPU,
k,
dt,
comp_dict,
conns,
device=0,
input_processors=input_processors,
output_processors=[output_processor],
extra_comps=extra_comps,
debug=True)
# connect LPUs by Patterns
for k, pattern in patterns.items():
l1, l2 = k.split('-')
if l1 in lpus and l2 in lpus:
print('Connecting {} and {}'.format(l1, l2))
pat, key_order = Pattern.from_graph(nx.DiGraph(
pattern['graph']),
return_key_order=True)
print(l1, l2)
print(key_order)
with Timer('update of connections in Manager'):
manager.connect(l1,
l2,
pat,
int_0=key_order.index(l1),
int_1=key_order.index(l2))
# start simulation
steps = config['General']['steps']
ignored_steps = config['General']['ignored_steps']
if 'steps' in task:
steps = task['steps']
if 'ignored_steps' in task:
ignored_steps = task['ignored_steps']
# ignored_steps = 0
# steps = 100
manager.spawn()
manager.start(steps=steps)
manager.wait()
time.sleep(5)
print(task)
# post-processing inputs (hard coded, can be better organized)
inputs = {
u'ydomain': 1.0,
u'xdomain': dt * (steps - ignored_steps),
u'dt': dt * 10,
u'data': {}
}
if 'retina' in lpus:
input_array = si.read_array('{}_{}.h5'.format(
config['Retina']['input_file'], user_id))
inputs[u'ydomain'] = input_array.max()
for i, item in enumerate(retina_input_uids):
inputs['data'][item] = np.hstack(
(np.arange(int((steps - ignored_steps) / 10)).reshape(
(-1, 1)) * dt * 10, input_array[ignored_steps::10,
i:i + 1])).tolist()
del input_array
# post-processing outputs from all LPUs and combine them into one dictionary
result = {
u'ydomain': 1,
u'xdomain': dt * (steps - ignored_steps),
u'dt': dt * 10,
u'data': {}
}
for k, lpu in lpus.items():
with h5py.File(lpu['output_file']) as output_file:
uids = output_file['V']['uids'][:]
output_array = output_file['V']['data'][:]
for i, item in enumerate(uids):
output = output_array[int(ignored_steps / 10):, i:i + 1]
# tmp = output.max()-output.min()
# if tmp <= 0.01: #mV
# output = (output - output.min()) + 0.5
# else:
# output = (output - output.min())/tmp*0.9+0.1
result['data'][item] = np.hstack(
(np.arange(int((steps - ignored_steps) / 10)).reshape(
(-1, 1)) * dt * 10, output)).tolist()
return inputs, result
def launch(self, user_id, task):
# neuron_uid_list = [str(a) for a in task['neuron_list']]
try:
# conf_obj = get_config_obj()
# config = conf_obj.conf
setup_logger(file_name = 'neurokernel_'+user_id+'.log', screen = False)
manager = core.Manager()
lpus = {}
patterns = {}
G = task['data']
for i in list(G['Pattern'].keys()):
a = G['Pattern'][i]['nodes']
if len([k for k,v in a.items() if v['class'] == 'Port']) == 0:
del G['Pattern'][i]
for i in list(G['LPU'].keys()):
a = G['LPU'][i]['nodes']
if len(a) < 3:
del G['LPU'][i]
# with open('G.pickle', 'wb') as f:
# pickle.dump(G, f, protocol=pickle.HIGHEST_PROTOCOL)
# print(G)
# print(G.keys())
# print(G['LPU'])
# print(G['LPU'].keys())
# get graph and output_uid_list for each LPU
for k, lpu in G['LPU'].items():
lpus[k] = {}
g_lpu_na = create_graph_from_database_returned(lpu)
lpu_nk_graph = nk.na_lpu_to_nk_new(g_lpu_na)
lpus[k]['graph'] = lpu_nk_graph
# lpus[k]['output_uid_list'] = list(
# set(lpu_nk_graph.nodes()).intersection(
# set(neuron_uid_list)))
# lpus[k]['output_file'] = '{}_output_{}.h5'.format(k, user_id)
for kkey, lpu in lpus.items():
graph = lpu['graph']
for uid, comp in graph.nodes.items():
if 'attr_dict' in comp:
print('Found attr_dict; fixing...')
nx.set_node_attributes(graph, {uid: comp['attr_dict']})
# print('changed',uid)
graph.nodes[uid].pop('attr_dict')
if 'params' in comp:
params = graph.nodes[uid].pop('params')
nx.set_node_attributes(graph, {uid: {k: float(v) for k, v in params.items()}})
if 'states' in comp:
states = graph.nodes[uid].pop('states')
nx.set_node_attributes(graph, {uid: {'init{}'.format(k): float(v) for k, v in states.items()}})
for i,j,k,v in graph.edges(keys=True, data=True):
if 'attr_dict' in v:
for key in v['attr_dict']:
nx.set_edge_attributes(graph, {(i,j,k): {key: v['attr_dict'][key]}})
graph.edges[(i,j,k)].pop('attr_dict')
lpus[kkey]['graph'] = graph
# get graph for each Pattern
for k, pat in G['Pattern'].items():
l1,l2 = k.split('-')
if l1 in lpus and l2 in lpus:
g_pattern_na = create_graph_from_database_returned(pat)
pattern_nk = nk.na_pat_to_nk(g_pattern_na)
#print(lpus[l1]['graph'].nodes(data=True))
lpu_ports = [node[1]['selector'] \
for node in lpus[l1]['graph'].nodes(data=True) \
if node[1]['class']=='Port'] + \
[node[1]['selector'] \
for node in lpus[l2]['graph'].nodes(data=True) \
if node[1]['class']=='Port']
pattern_ports = pattern_nk.nodes()
patterns[k] = {}
patterns[k]['graph'] = pattern_nk.subgraph(
list(set(lpu_ports).intersection(set(pattern_ports))))
# dt = config['General']['dt']
# if 'dt' in task:
dt = task['dt']
print(dt)
device_count = 0
# add LPUs to manager
for k, lpu in lpus.items():
lpu_name = k
graph = lpu['graph']
for uid, comp in graph.nodes.items():
if 'attr_dict' in comp:
nx.set_node_attributes(graph, {uid: comp['attr_dict']})
# print('changed',uid)
graph.nodes[uid].pop('attr_dict')
for i,j,ko,v in graph.edges(keys=True, data=True):
if 'attr_dict' in v:
for key in v['attr_dict']:
nx.set_edge_attributes(graph, {(i,j,ko): {key: v['attr_dict'][key]}})
graph.edges[(i,j,ko)].pop('attr_dict')
# nx.write_gexf(graph,'name.gexf')
# with open(lpu_name + '.pickle', 'wb') as f:
# pickle.dump(graph, f, protocol=pickle.HIGHEST_PROTOCOL)
comps = graph.nodes.items()
#for uid, comp in comps:
# if 'attr_dict' in comp:
# nx.set_node_attributes(graph, {uid: comp['attr_dict']})
# print('changed',uid)
# if 'class' in comp:
# if k == 'retina':
# if config['Retina']['intype'] == 'Natural':
# coord_file = config['InputType']['Natural']['coord_file']
# tmp = os.path.splitext(coord_file)
# config['InputType']['Natural']['coord_file'] = '{}_{}{}'.format(
# tmp[0], user_id, tmp[1])
# prs = [node for node in graph.nodes(data=True) \
# if node[1]['class'] == 'PhotoreceptorModel']
# for pr in prs:
# graph.node[pr[0]]['num_microvilli'] = 3000
# input_processors = [RetinaInputIndividual(config, prs, user_id)]
# extra_comps = [PhotoreceptorModel]
# retina_input_uids = [a[0] for a in prs]
# # elif k == 'EB':
# # input_processor = StepInputProcessor('I', [node[0] for node in graph.nodes(data=True) \
# # if node[1]['class'] == 'LeakyIAF'], 40.0, 0.0, 1.0)
# # input_processors = [input_processor]
# # extra_comps = []#[BufferVoltage]
# else:
# input_processors = []
# extra_comps = [BufferVoltage]
if 'inputProcessors' in task:
if lpu_name in task['inputProcessors']:
input_processors, record = \
loadInputProcessors(task['inputProcessors'][lpu_name])
lpus[k]['input_record'] = record
else:
input_processors = []
else:
input_processors = []
# configure output processors
lpus[k]['output_file'] = '{}_output_{}.h5'.format(k, user_id)
output_processors = []
if 'outputProcessors' in task:
if lpu_name in task['outputProcessors']:
output_processors, record = loadOutputProcessors(
lpus[k]['output_file'],
task['outputProcessors'][lpu_name])
if len(record):
lpus[k]['output_uid_dict'] = record
# (comp_dict, conns) = LPU.graph_to_dicts(graph)
manager.add(LPU, k, dt, 'pickle', pickle.dumps(graph),#comp_dict, conns,
device = device_count, input_processors = input_processors,
output_processors = output_processors,
extra_comps = [], debug = False)
device_count = (device_count+1) % self.ngpus
# connect LPUs by Patterns
for k, pattern in patterns.items():
l1,l2 = k.split('-')
if l1 in lpus and l2 in lpus:
print('Connecting {} and {}'.format(l1, l2))
pat, key_order = Pattern.from_graph(nx.DiGraph(pattern['graph']),
return_key_order = True)
print(l1,l2)
print(key_order)
with Timer('update of connections in Manager'):
try:
manager.connect(l1, l2, pat,
int_0 = key_order.index('{}/{}'.format(k,l1)),
int_1 = key_order.index('{}/{}'.format(k,l2)))
except ValueError:
manager.connect(l1, l2, pat,
int_0 = key_order.index(l1),
int_1 = key_order.index(l2))
# start simulation
# steps = config['General']['steps']
# ignored_steps = config['General']['ignored_steps']
# if 'steps' in task:
steps = task['steps']
# if 'ignored_steps' in task:
# ignored_steps = task['ignored_steps']
# ignored_steps = 0
# steps = 100
manager.spawn()
manager.start(steps=steps)
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
tb = ''.join(traceback.format_exception(exc_type, exc_value, exc_traceback))
print('An error occured during the compilation\n' + tb)
return {'error':
{'exception': tb,
'message': 'An error occured during the compilation in execution'}}
try:
manager.wait()
except LPUExecutionError:
ErrorMessage = 'An error occured during execution of LPU {} at step {}:\n'.format(
manager._errors[0][0], manager._errors[0][1]) + \
''.join(manager._errors[0][2])
print(ErrorMessage)
return {'error':
{'exception': ''.join(manager._errors[0][2]),
'message': 'An error occured during execution of LPU {} at step {}:\n'.format(
manager._errors[0][0], manager._errors[0][1])}}
time.sleep(5)
# print(task)
ignored_steps = 0
try:
# post-processing inputs (hard coded, can be better organized)
result = {'sensory': {}, 'input': {}, 'output': {}}
for k, lpu in lpus.items():
records = lpu.get('input_record', [])
for record in records:
if record['sensory_file'] is not None:
if k not in result['sensory']:
result['sensory'][k] = []
with h5py.File(record['sensory_file']) as sensory_file:
result['sensory'][k].append({'dt': record['sensory_interval']*dt,
'data': sensory_file['sensory'][:]})
if record['input_file'] is not None:
with h5py.File(record['input_file']) as input_file:
sample_interval = input_file['metadata'].attrs['sample_interval']
for var in input_file.keys():
if var == 'metadata': continue
uids = [n.decode() for n in input_file[var]['uids'][:]]
input_array = input_file[var]['data'][:]
for i, item in enumerate(uids):
if var == 'spike_state':
input = np.nonzero(input_array[ignored_steps:, i:i+1].reshape(-1))[0]*dt
if item in result['input']:
if 'spike_time' in result['input'][item]:
result['input'][item]['spike_time']['data'].append(input)
result['input'][item]['spike_time']['data'] = \
np.sort(result['input'][item]['spike_time']['data'])
else:
result['input'][item]['spike_time'] = {
'data': input.copy(),
'dt': dt*sample_interval}
else:
result['input'][item] = {'spike_time': {
'data': input.copy(),
'dt': dt*sample_interval}}
else:
input = input_array[ignored_steps:, i:i+1]
if item in result['input']:
if var in result['input'][item]:
result['input'][item][var]['data'] += input
else:
result['input'][item][var] = {
'data': input.copy(),
'dt': dt*sample_interval}
else:
result['input'][item] = {var: {
'data': input.copy(),
'dt': dt*sample_interval}}
# if 'retina' in lpus:
# input_array = si.read_array(
# '{}_{}.h5'.format(config['Retina']['input_file'], user_id))
# inputs[u'ydomain'] = input_array.max()
# for i, item in enumerate(retina_input_uids):
# inputs['data'][item] = np.hstack(
# (np.arange(int((steps-ignored_steps)/10)).reshape((-1,1))*dt*10,
# input_array[ignored_steps::10,i:i+1])).tolist()
#
# del input_array
# post-processing outputs from all LPUs and combine them into one dictionary
# result = {u'data': {}}
for k, lpu in lpus.items():
uid_dict = lpu.get('output_uid_dict', None)
if uid_dict is not None:
with h5py.File(lpu['output_file']) as output_file:
sample_interval = output_file['metadata'].attrs['sample_interval']
for var in uid_dict:
if var == 'spike_state':
uids = [n.decode() for n in output_file[var]['uids'][:]]
spike_times = output_file[var]['data']['time'][:]
index = output_file[var]['data']['index'][:]
for i, item in enumerate(uids):
# output = np.nonzero(output_array[ignored_steps:, i:i+1].reshape(-1))[0]*dt
output = spike_times[index == i]
output = output[output>ignored_steps*dt]-ignored_steps*dt
if item in result['output']:
result['output'][item]['spike_time'] = {
'data': output,
'dt': dt*sample_interval}
else:
result['output'][item] = {'spike_time': {
'data': output,
'dt': dt*sample_interval}}
else:
uids = [n.decode() for n in output_file[var]['uids'][:]]
output_array = output_file[var]['data'][:]
for i, item in enumerate(uids):
# if var == 'spike_state':
# output = np.nonzero(output_array[ignored_steps:, i:i+1].reshape(-1))[0]*dt
# if item in result['output']:
# result['output'][item]['spike_time'] = {
# 'data': output.tolist(),
# 'dt': dt}
# else:
# result['output'][item] = {'spike_time': {
# 'data': output.tolist(),
# 'dt': dt}}
# else:
output = output_array[ignored_steps:, i:i+1]
if item in result['output']:
result['output'][item][var] = {
'data': output.copy(),
'dt': dt*sample_interval}
else:
result['output'][item] = {var: {
'data': output.copy(),
'dt': dt*sample_interval}}
result = {'success': {'result': result, 'meta': {'dur': steps*dt}}}
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
tb = ''.join(traceback.format_exception(exc_type, exc_value, exc_traceback))
print('An error occured postprocessing of results\n' + tb)
return {'error':
{'exception': tb,
'message': 'An error occured when postprocessing of results in execution'}}
return result
