def setUp(self):
g = self.g = Graph(Config.from_url('test_unicode', 'root', 'root',
initial_drop=True))
g.create_all(UnicodeNode.registry)
def setUp(self):
g = self.g = Graph(Config.from_url('test_embedded', 'root', 'root',
initial_drop=True))
g.create_all(EmbeddedNode.registry)
def setUp(self):
g = self.g = Graph(Config.from_url('classes', 'root', 'root'
, initial_drop=True))
def setUp(self):
g = self.g = Graph(Config.from_url('test_datetime', 'root', 'root',
initial_drop=True))
g.create_all(DateTimeNode.registry)
from neurokernel.tools.logging import setup_logger
import neurokernel.core_gpu as core
from neurokernel.LPU.LPU import LPU
import neurokernel.pattern as pattern
from neurokernel.plsel import Selector
import neuroarch.models as models
import neuroarch.nk as nk
from neurokernel.LPU.InputProcessors.FileInputProcessor import FileInputProcessor
from neurokernel.LPU.OutputProcessors.FileOutputProcessor import FileOutputProcessor
from cx_config import cx_db
from cx_utils import partly_relabel_by_sorted_attr
graph = Graph(Config.from_url(cx_db, 'admin', 'admin', initial_drop=False))
models.create_efficiently(graph, models.Node.registry)
models.create_efficiently(graph, models.Relationship.registry)
logger = setup_logger(screen=True)
lpu_name_list = ['BU', 'bu', 'EB', 'FB', 'PB']
# LPUs:
lpu_name_to_node = {} # LPU name -> pyorient LPU node
lpu_name_to_g_na = {} # LPU name -> NeuroArch-compatible graph
lpu_name_to_g_nk_orig = {} # LPU name -> Neurokernel-compatible graph
lpu_name_to_g_nk = {} # LPU name -> Neurokernel-compatible graph with int IDs
#lpu_name_to_n_dict = {} # LPU name -> n_dict data struct
#lpu_name_to_s_dict = {} # LPU name -> s_dict data struct
lpu_name_to_comp_dict = {} # LPU name -> comp_dict data struct
def setUp(self):
g = self.g = Graph(Config.from_url('money', 'root', 'root'
, initial_drop=True))
g.create_all(MoneyNode.registry)
g.create_all(MoneyRelationship.registry)
connect_lpu_pat(lpu0_ports_sels, lpu0_lpu_ports_data,
lpu0_pat_ports_data)
connect_lpu_pat(lpu1_ports_sels, lpu1_lpu_ports_data,
lpu1_pat_ports_data)
if __name__ == '__main__':
logging.basicConfig(
level=logging.DEBUG,
stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
#g_orient = Graph(Config.from_url('/vision_demo','admin', 'admin', initial_drop=True)) # set to True to erase the database
g_orient = Graph(
Config.from_url('/ampa/bionet/databases/development/na_server',
'admin',
'admin',
initial_drop=False,
serialization_type=OrientSerialization.Binary)
) # set to True to erase the database
g_orient.create_all(Node.registry)
g_orient.create_all(Relationship.registry)
#g_orient.include(Node.registry)
#g_orient.include(Relationship.registry)
vl = NetworkXLoader(g_orient)
# Load LPU data:
vl.logger.info('Loading sample Lamina circuit...')
vl.load_lpu('lamina.gexf.gz', 'LAM')
def connect_database(host, user, password, is_initial_drop=False):
global graph
graph = Graph(Config.from_url(host, user, password, is_initial_drop))
# Connect nodes
self.g_orient.Owns.create(npl, n)
self.g_orient.HasData.create(n, arb)
# self.g_orient.HasData.create(n, nm)
if nt:
self.g_orient.HasData.create(n, nt)
self.g_orient.Owns.create(ds_fc, n)
# self.g_orient.Owns.create(ds_fc, nm)
self.g_orient.Owns.create(ds_fc, arb)
if __name__ == '__main__':
logging.basicConfig(
level=logging.DEBUG,
stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
g_orient = Graph(
Config.from_url('/na_server',
'root',
'root',
initial_drop=False,
serialization_type=OrientSerialization.Binary)
) # set to True to erase the database
g_orient.create_all(Node.registry)
g_orient.create_all(Relationship.registry)
vl = NTHULoader(g_orient)
vl.load_neurons('all_female_neurons.txt', 'flycircuit1.1')
import django
from django.conf import settings
from ngpyorient.queryset import NgQuerySet
from person.models import Borned, Person, Car, Province, Likes, Have, Produced
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "mysite_orientdb.settings")
django.setup()
from pyorient.ogm import Graph, Config
config = Config.from_url(
settings.DATABASES_NG["default"]["URL"],
settings.DATABASES_NG["default"]["USER"],
settings.DATABASES_NG["default"]["PASSWORD"],
)
graph = Graph(config)
def create_vertex():
"""CREATE VERTEX Employee CONTENT { "name" : "Jay", "surname" : "Miner" }"""
records = graph.client.command("create vertex person content{'name':'yuan1','age':1}")
records = graph.client.command("create vertex person content{'name':'yuan2','age':1}")
records = graph.client.command("create vertex person content{'name':'yuan3','age':1}")
records = graph.client.command("create vertex person content{'name':'yuan4','age':1}")
records = graph.client.command("create vertex province content{'name':'hubei'}")
records = graph.client.command("create vertex province content{'name':'guangdong'}")
records = graph.client.command("create vertex phone content{'brand':'samsung'}")
records = graph.client.command("create vertex phone content{'brand':'huawei'}")
records = graph.client.command("create vertex phone content{'brand':'xiaomi'}")
def convert_set_to_list(a):
for key in a:
if isinstance(a[key], set):
a[key] = list(a[key])
return a
def convert_complicate_list(a):
tmp = []
for region in a['regions']:
tmp.append(list(region))
a['regions'] = tmp
return a
graph = Graph(Config.from_url(cx_db, 'root', 'root',
initial_drop=initial_drop))
if initial_drop:
graph.create_all(models.Node.registry)
graph.create_all(models.Relationship.registry)
else:
graph.include(models.Node.registry)
graph.include(models.Relationship.registry)
logging.basicConfig(level=logging.DEBUG,
stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
logger = logging.getLogger('cx')
logger.info('Start to Load Biological Data')
CX_Neuropils = ['PB', 'EB', 'NO', 'no', 'LAL', 'lal']
def setUp(self):
g = self.g = Graph(
Config.from_url('animals', 'root', 'root', initial_drop=True))
g.create_all(AnimalsNode.registry)
g.create_all(AnimalsRelationship.registry)
def setUp(self):
g = self.g = Graph(
Config.from_url('test_embedded_defaults',
'root',
'root',
initial_drop=True))
def setUp(self):
g = self.g = Graph(Config.from_url('hardware', 'root', 'root'
, initial_drop=True))
g.create_all(HardwareNode.registry)
g.create_all(HardwareRelationship.registry)
from pyorient.ogm import Graph, Config
from pyorient.ogm.property import String, Float, DateTime
from pyorient.ogm.declarative import declarative_node, declarative_relationship
# Initialize Graph Database
graph = Graph(
Config.from_url('plocal://localhost:2424//DeeBeeTee', 'deebeetee',
'deebeetee'))
Node = declarative_node()
Relationship = declarative_relationship()
class TransactionsRel(Relationship):
element_plural = 'tx'
element_type = 'tx'
since = DateTime()
tx = Float()
class Person(Node):
element_plural = 'person'
element_type = 'person'
uid = String(indexed=True)
name = String(indexed=True)
credit_balance = Float(default=0.0, indexed=True)
debit_balance = Float(default=0.0, indexed=True)
balance = Float(default=0.0, indexed=True)
def setUp(self):
g = self.g = Graph(Config.from_url('abstract_classes', 'root', 'root'
, initial_drop=True))
g.client.command('CREATE CLASS AbstractClass EXTENDS V ABSTRACT')
g.client.command('CREATE CLASS ConcreteClass EXTENDS V')
def main():
logging.basicConfig(level=logging.DEBUG, stream=sys.stdout,
format='%(asctime)s %(name)s %(levelname)s %(message)s')
logger = logging.getLogger('cx')
sys.setrecursionlimit(10000)
### Graph ###
graph = Graph(Config.from_url(cx_db, 'admin', 'admin',
initial_drop=False))
graph.include(models.Node.registry)
graph.include(models.Relationship.registry)
### Retina ###
config=retlam_demo.ConfigReader('retlam_default.cfg','../template_spec.cfg').conf
retina = get_retina(config)
##### Configuration ######
logger = setup_logger(screen=True)
lpu_selectors, to_list = get_cx_selectors_name()
lpu_name_to_comp_dict, lpu_name_to_conn_list, pat_name_list, pat_name_to_pat = cx_component(graph)
man = core.Manager()
dt = 1e-4
dur = 0.2
steps = int(dur/dt)
debug = True
lpu_name_list = ['BU', 'bu', 'EB', 'FB', 'PB']
for name in lpu_name_list:
input_processor = []
output_processor = [FileOutputProcessor([('spike_state', None), ('V',None), ('g',None), ('I', None)], '{}_output.h5'.format(name), sample_interval = 1)]
man.add(LPU, name, dt, lpu_name_to_comp_dict[name],
lpu_name_to_conn_list[name],
input_processors = input_processor,
output_processors = output_processor,
device=0,
debug=debug, time_sync=False)
retlam_demo.add_retina_LPU(config, 0, retina, man)
logger.info('add retina lpu')
for name in pat_name_list:
id_0, id_1 = name.split('-')
man.connect(id_0, id_1, pat_name_to_pat[name][0], pat_name_to_pat[name][1].index('0'), pat_name_to_pat[name][1].index('1'))
logger.info('link lpus among cx lpus')
link_retina_pat_cx(retina, lpu_selectors, to_list, man)
logger.info('link retina and cx lpu')
man.spawn()
man.start(steps)
man.wait()
