def __init__(
self,
file, # @ReservedAssignment
distributed=False,
safe=True,
verbose=False):
self._file = file
real_file = file
opened_file = False
if isinstance(file, basestring):
real_file = self.get_reader(file)
opened_file = True
if distributed:
directory = os.path.dirname(real_file.file)
filename = "{}.".format(os.path.basename(real_file.file))
conns = list()
for found_file in os.listdir(directory):
if found_file.startswith(filename):
file_reader = self.get_reader(found_file)
conns.append(file_reader.read())
file_reader.close()
conn_list = numpy.concatenate(conns)
else:
conn_list = real_file.read()
if opened_file:
real_file.close()
FromListConnector.__init__(self, conn_list, safe, verbose)
def __init__(
self, file, # @ReservedAssignment
distributed=False, safe=True, verbose=False):
real_file = file
opened_file = False
if isinstance(file, basestring):
real_file = files.StandardTextFile(file, mode="r")
opened_file = True
conn_list = None
if distributed:
directory = os.path.dirname(real_file.file)
filename = "{}.".format(os.path.basename(real_file.file))
conns = list()
for found_file in os.listdir(directory):
if found_file.startswith(filename):
file_reader = files.StandardTextFile(found_file, mode="r")
conns.append(file_reader.read())
file_reader.close()
conn_list = numpy.concatenate(conns)
else:
conn_list = real_file.read()
if opened_file:
real_file.close()
FromListConnector.__init__(self, conn_list, safe, verbose)
def __init__(self, conn_list, safe=True, verbose=False):
"""
Creates a new FromListConnector.
"""
if conn_list is None or len(conn_list) == 0:
raise exceptions.InvalidParameterType(
"The connection list for the FromListConnector must contain"
" at least a list of tuples, each of which should contain:"
" (pre_idx, post_idx, weight, delay)")
conn_list, weights, delays, self._extra_conn_data = \
self._split_conn_list(
conn_list, ['pre', 'post', 'weight', 'delay'])
CommonFromListConnector.__init__(self, conn_list, safe, verbose)
self.set_weights_and_delays(weights, delays)
def __init__(self, d_expression, allow_self_connections=True,
weights=0.0, delays=None, space=Space(), safe=True,
verbose=False, n_connections=None):
"""
Creates a new DistanceDependentConnector. Uses the underlying machinery
for FromListConnector.
"""
self.d_expression = d_expression
self.allow_self_connections = allow_self_connections
self.space = space
# weights may be a fixed value, a list of values,
# a RandomDistribution object, or a distance_dependence function.
self.weights = weights
self.delays = delays # and similar for this value
self.connections_per_neuron = n_connections
self.connectionSeeds = SeedInfo()
FromListConnector.__init__(self, conn_list=None, safe=safe,
verbose=verbose)
def generate_synapse_list(self, presynaptic_population,
postsynaptic_population, delay_scale,
weight_scale, synapse_type):
conn_file = open(self._filename, 'r')
file_lines = conn_file.readlines()
for line in file_lines:
line.strip()
form1 = re.match(r"\[(\([^()]*\),\s*)*(\([^()]*\)\s*)\]", line)
# form 1: a list of tuples
if form1:
conn_sublist = [
eval(conn.group(0))
for conn in re.finditer(r"\([^()]*\)", line)
]
else:
form2 = re.match(r"\(.*\)\s*", line)
# form 2: a single tuple per line
if form2:
conn_sublist = [
eval(form2.group(0).rstrip(", \a\b\f\n\r\t\v"))
]
else:
form3 = re.match(
r"((?:\[[^[\]\s]+\])|(?:[^[\],\s]+))((?:,\s*)" +
r"|\s+)((?:\[[^[\]\s]+\])|(?:[^[\],\s]+))" +
r"((?:,\s*)|\s+)((?:\+|\-)?\d+(?:\.\d+)?" +
r"(?:(?:E|e)(?:\+|\-)?\d+)?)((?:,\s*)|\s+)" +
r"((?:\+|\-)?\d+(?:\.\d+)?(?:(?:E|e)" +
r"(?:\+|\-)?\d+)?)\s*", line)
# form 3: a comma- or space-separated set of specifiers per
# line
if form3:
conn_sublist = [
(eval(form3.group(1)), eval(form3.group(3)),
float(form3.group(5)), float(form3.group(7)))
]
else:
raise exceptions.ConfigurationException(
"Invalid connection file format")
self._conn_list.extend(conn_sublist)
return FromListConnector.generate_synapse_list(
self, presynaptic_population, postsynaptic_population, delay_scale,
weight_scale, synapse_type)
def generate_synapse_list(
self, presynaptic_population, postsynaptic_population, delay_scale,
weight_scale, synapse_type):
conn_file = open(self._filename, 'r')
file_lines = conn_file.readlines()
for line in file_lines:
line.strip()
form1 = re.match(r"\[(\([^()]*\),\s*)*(\([^()]*\)\s*)\]", line)
# form 1: a list of tuples
if form1:
conn_sublist = [eval(conn.group(0)) for conn in
re.finditer(r"\([^()]*\)", line)]
else:
form2 = re.match(r"\(.*\)\s*", line)
# form 2: a single tuple per line
if form2:
conn_sublist = [eval(form2.group(0).rstrip(
", \a\b\f\n\r\t\v"))]
else:
form3 = re.match(
r"((?:\[[^[\]\s]+\])|(?:[^[\],\s]+))((?:,\s*)" +
r"|\s+)((?:\[[^[\]\s]+\])|(?:[^[\],\s]+))" +
r"((?:,\s*)|\s+)((?:\+|\-)?\d+(?:\.\d+)?" +
r"(?:(?:E|e)(?:\+|\-)?\d+)?)((?:,\s*)|\s+)" +
r"((?:\+|\-)?\d+(?:\.\d+)?(?:(?:E|e)" +
r"(?:\+|\-)?\d+)?)\s*", line)
# form 3: a comma- or space-separated set of specifiers per
# line
if form3:
conn_sublist = [(eval(form3.group(1)),
eval(form3.group(3)),
float(form3.group(5)),
float(form3.group(7)))]
else:
raise exceptions.ConfigurationException(
"Invalid connection file format")
self._conn_list.extend(conn_sublist)
return FromListConnector.generate_synapse_list(
self, presynaptic_population, postsynaptic_population,
delay_scale, weight_scale, synapse_type)
def __init__(self, conn_file, distributed=False, safe=True, verbose=False):
FromListConnector.__init__(self, safe=safe, verbose=verbose)
if distributed:
logger.warn("distributed loading of FromFileConnector files is "
"not supported and will be ignored")
self._filename = conn_file
def __init__(self, conn_file, distributed=False, safe=True, verbose=False):
FromListConnector.__init__(self, safe=safe, verbose=verbose)
if distributed:
logger.warn("distributed loading of FromFileConnector files is "
"not supported and will be ignored")
self._filename = conn_file
