def saveConnections(self, file, gather=True, compatible_output=True):
"""
Save connections to file in a format suitable for reading in with a
FromFileConnector.
"""
if isinstance(file, basestring):
file = files.StandardTextFile(file, mode='w')
lines = []
if not compatible_output:
for c in self.connections:
lines.append([c.source, c.target, c.weight, c.delay])
else:
for c in self.connections:
lines.append([self.pre.id_to_index(c.source), self.post.id_to_index(c.target), c.weight, c.delay])
if gather == True and self._simulator.state.num_processes > 1:
all_lines = { self._simulator.state.mpi_rank: lines }
all_lines = recording.gather_dict(all_lines)
if self._simulator.state.mpi_rank == 0:
lines = reduce(operator.add, all_lines.values())
elif self._simulator.state.num_processes > 1:
file.rename('%s.%d' % (file.name, self._simulator.state.mpi_rank))
logger.debug("--- Projection[%s].__saveConnections__() ---" % self.label)
if gather == False or self._simulator.state.mpi_rank == 0:
file.write(lines, {'pre' : self.pre.label, 'post' : self.post.label})
file.close()
def saveConnections(self, file, gather=True, compatible_output=True):
"""
Save connections to file in a format suitable for reading in with a
FromFileConnector.
"""
if isinstance(file, basestring):
file = files.StandardTextFile(file, mode='w')
lines = []
if not compatible_output:
for c in self.connections:
lines.append([c.source, c.target, c.weight, c.delay])
else:
for c in self.connections:
lines.append([
self.pre.id_to_index(c.source),
self.post.id_to_index(c.target), c.weight, c.delay
])
if gather == True and self._simulator.state.num_processes > 1:
all_lines = {self._simulator.state.mpi_rank: lines}
all_lines = recording.gather_dict(all_lines)
if self._simulator.state.mpi_rank == 0:
lines = reduce(operator.add, all_lines.values())
elif self._simulator.state.num_processes > 1:
file.rename('%s.%d' % (file.name, self._simulator.state.mpi_rank))
logger.debug("--- Projection[%s].__saveConnections__() ---" %
self.label)
if gather == False or self._simulator.state.mpi_rank == 0:
file.write(lines, {'pre': self.pre.label, 'post': self.post.label})
file.close()
def saveConnections(self, file, gather=True, compatible_output=True):
"""
Save connections to file in a format suitable for reading in with a
FromFileConnector.
"""
import operator
if isinstance(file, basestring):
file = files.StandardTextFile(file, mode='w')
lines = nest.GetStatus(self.connections,
('source', 'target', 'weight', 'delay'))
if gather == True and num_processes() > 1:
all_lines = {rank(): lines}
all_lines = recording.gather_dict(all_lines)
if rank() == 0:
lines = reduce(operator.add, all_lines.values())
elif num_processes() > 1:
file.rename('%s.%d' % (file.name, rank()))
logger.debug("--- Projection[%s].__saveConnections__() ---" %
self.label)
if gather == False or rank() == 0:
lines = numpy.array(lines, dtype=float)
lines[:, 2] *= 0.001
if compatible_output:
lines[:, 0] = self.pre.id_to_index(lines[:, 0])
lines[:, 1] = self.post.id_to_index(lines[:, 1])
file.write(lines, {'pre': self.pre.label, 'post': self.post.label})
file.close()
def saveConnections(self, file, gather=True, compatible_output=True):
"""
Save connections to file in a format suitable for reading in with a
FromFileConnector.
"""
import operator
if isinstance(file, basestring):
file = files.StandardTextFile(file, mode='w')
lines = nest.GetStatus(self.connections, ('source', 'target', 'weight', 'delay'))
if gather == True and num_processes() > 1:
all_lines = { rank(): lines }
all_lines = recording.gather_dict(all_lines)
if rank() == 0:
lines = reduce(operator.add, all_lines.values())
elif num_processes() > 1:
file.rename('%s.%d' % (file.name, rank()))
logger.debug("--- Projection[%s].__saveConnections__() ---" % self.label)
if gather == False or rank() == 0:
lines = numpy.array(lines, dtype=float)
lines[:,2] *= 0.001
if compatible_output:
lines[:,0] = self.pre.id_to_index(lines[:,0])
lines[:,1] = self.post.id_to_index(lines[:,1])
file.write(lines, {'pre' : self.pre.label, 'post' : self.post.label})
file.close()
def count(self, gather=False, filter=None):
"""
Return the number of data points for each cell, as a dict. This is mainly
useful for spike counts or for variable-time-step integration methods.
"""
N = {}
if self.variable == 'spikes':
for id in self.filter_recorded(filter):
N[id] = simulator.net.object(self.recorders[id]).spikeCount()
else:
raise Exception("Only implemented for spikes.")
if gather and simulator.state.num_processes > 1:
N = recording.gather_dict(N)
return N
def get(self, attribute_names, format, gather=True, with_address=True):
"""
Get the values of a given attribute (weight or delay) for all
connections in this Projection.
`attribute_names`:
name of the attributes whose values are wanted, or a list of such
names.
`format`:
"list" or "array".
With list format, returns a list of tuples. Each tuple contains the
indices of the pre- and post-synaptic cell followed by the attribute
values in the order given in `attribute_names`. Example::
>>> prj.get(["weight", "delay"], format="list")[:5]
[(TODO)]
With array format, returns a tuple of 2D NumPy arrays, one for each
name in `attribute_names`. The array element X_ij contains the
attribute value for the connection from the ith neuron in the pre-
synaptic Population to the jth neuron in the post-synaptic Population,
if a single such connection exists. If there are no such connections,
X_ij will be NaN. If there are multiple such connections, the summed
value will be given, which makes some sense for weights, but is
pretty meaningless for delays. Example::
>>> weights, delays = prj.get(["weight", "delay"], format="array")
>>> weights.shape
TODO
TODO: document "with_address"
Values will be expressed in the standard PyNN units (i.e. millivolts,
nanoamps, milliseconds, microsiemens, nanofarads, event per second).
"""
if isinstance(attribute_names, basestring):
attribute_names = (attribute_names,)
return_single = True
else:
return_single = False
if isinstance(self.synapse_type, StandardSynapseType):
attribute_names = self.synapse_type.get_native_names(*attribute_names)
if format == 'list':
names = list(attribute_names)
if with_address:
names = ["presynaptic_index", "postsynaptic_index"] + names
values = self._get_attributes_as_list(*names)
if gather and self._simulator.state.num_processes > 1:
all_values = {self._simulator.state.mpi_rank: values}
all_values = recording.gather_dict(all_values, all=(gather == 'all'))
if gather == 'all' or self._simulator.state.mpi_rank == 0:
values = reduce(operator.add, all_values.values())
if not with_address and return_single:
values = [val[0] for val in values]
return values
elif format == 'array':
if gather and self._simulator.state.num_processes > 1:
# Node 0 is the only one creating a full connection matrix, and returning it (saving memory)
# Slaves nodes are returning list of connections, so this may be inconsistent...
names = list(attribute_names)
names = ["presynaptic_index", "postsynaptic_index"] + names
values = self._get_attributes_as_list(*names)
all_values = {self._simulator.state.mpi_rank: values}
all_values = recording.gather_dict(all_values, all=(gather == 'all'))
if gather == 'all' or self._simulator.state.mpi_rank == 0:
tmp_values = reduce(operator.add, all_values.values())
values = self._get_attributes_as_arrays(*attribute_names)
tmp_values = numpy.array(tmp_values)
for i in xrange(len(values)):
values[i][tmp_values[:, 0].astype(int), tmp_values[:, 1].astype(int)] = tmp_values[:, 2 + i]
else:
values = self._get_attributes_as_arrays(*attribute_names)
if return_single:
if gather == 'all' or self._simulator.state.mpi_rank == 0:
assert len(values) == 1, values
return values[0]
else:
return values
else:
raise Exception("format must be 'list' or 'array'")
def get(self,
attribute_names,
format,
gather=True,
with_address=True,
multiple_synapses='sum'):
"""
Get the values of a given attribute (weight or delay) for all
connections in this Projection.
`attribute_names`:
name of the attributes whose values are wanted, or a list of such
names.
`format`:
"list" or "array".
`gather`:
if True, get connection information from all MPI nodes, otherwise
only from connections that exist in this node.
With list format, returns a list of tuples. By default, each tuple
contains the indices of the pre- and post-synaptic cell followed by
the attribute values in the order given in `attribute_names`.
Example::
>>> prj.get(["weight", "delay"], format="list")[:5]
[(0.0, 0.0, 0.3401892507507171, 0.1),
(0.0, 1.0, 0.7990713166233654, 0.30000000000000004),
(0.0, 2.0, 0.6180841812877726, 0.5),
(0.0, 3.0, 0.6758149775627305, 0.7000000000000001),
(0.0, 4.0, 0.7166906726862953, 0.9)]
If `with_address` is set to False, then the tuples will contain only the
attribute values, not the cell indices.
With array format, returns a tuple of 2D NumPy arrays, one for each
name in `attribute_names`. The array element X_ij contains the
attribute value for the connection from the ith neuron in the pre-
synaptic Population to the jth neuron in the post-synaptic Population,
if a single such connection exists. If there are no such connections,
X_ij will be NaN. Example::
>>> weights, delays = prj.get(["weight", "delay"], format="array")
>>> weights
array([[ 0.66210438, nan, 0.10744555, 0.54557088],
[ 0.3676134 , nan, 0.41463193, nan],
[ 0.57434871, 0.4329354 , 0.58482943, 0.42863916]])
If there are multiple such connections, the action to take is
controlled by the `multiple_synapses` argument, which must be one of
{'last', 'first', 'sum', 'min', 'max'}.
Values will be expressed in the standard PyNN units (i.e. millivolts,
nanoamps, milliseconds, microsiemens, nanofarads, event per second).
"""
if isinstance(attribute_names, basestring):
attribute_names = (attribute_names, )
return_single = True
else:
return_single = False
if isinstance(self.synapse_type, StandardSynapseType):
attribute_names = self.synapse_type.get_native_names(
*attribute_names)
if format == 'list':
names = list(attribute_names)
if with_address:
names = ["presynaptic_index", "postsynaptic_index"] + names
values = self._get_attributes_as_list(names)
if gather and self._simulator.state.num_processes > 1:
all_values = {self._simulator.state.mpi_rank: values}
all_values = recording.gather_dict(all_values,
all=(gather == 'all'))
if gather == 'all' or self._simulator.state.mpi_rank == 0:
values = reduce(operator.add, all_values.values())
if not with_address and return_single:
values = [val[0] for val in values]
return values
elif format == 'array':
if multiple_synapses not in Projection.MULTI_SYNAPSE_OPERATIONS:
raise ValueError(
"`multiple_synapses` argument must be one of {}".format(
list(Projection.MULTI_SYNAPSE_OPERATIONS)))
if gather and self._simulator.state.num_processes > 1:
# Node 0 is the only one creating a full connection matrix, and returning it (saving memory)
# Slaves nodes are returning list of connections, so this may be inconsistent...
names = list(attribute_names)
names = ["presynaptic_index", "postsynaptic_index"] + names
values = self._get_attributes_as_list(names)
all_values = {self._simulator.state.mpi_rank: values}
all_values = recording.gather_dict(all_values,
all=(gather == 'all'))
if gather == 'all' or self._simulator.state.mpi_rank == 0:
tmp_values = reduce(operator.add, all_values.values())
values = self._get_attributes_as_arrays(
attribute_names, multiple_synapses=multiple_synapses)
tmp_values = numpy.array(tmp_values)
for i in xrange(len(values)):
values[i][tmp_values[:, 0].astype(int),
tmp_values[:,
1].astype(int)] = tmp_values[:,
2 +
i]
else:
values = self._get_attributes_as_arrays(
attribute_names, multiple_synapses=multiple_synapses)
if return_single:
if gather == 'all' or self._simulator.state.mpi_rank == 0:
assert len(values) == 1, values
return values[0]
else:
return values
else:
raise Exception("format must be 'list' or 'array'")
def get(self, attribute_names, format, gather=True, with_address=True,
multiple_synapses='sum'):
"""
Get the values of a given attribute (weight or delay) for all
connections in this Projection.
`attribute_names`:
name of the attributes whose values are wanted, or a list of such
names.
`format`:
"list" or "array".
`gather`:
if True, get connection information from all MPI nodes, otherwise
only from connections that exist in this node.
With list format, returns a list of tuples. By default, each tuple
contains the indices of the pre- and post-synaptic cell followed by
the attribute values in the order given in `attribute_names`.
Example::
>>> prj.get(["weight", "delay"], format="list")[:5]
[(0.0, 0.0, 0.3401892507507171, 0.1),
(0.0, 1.0, 0.7990713166233654, 0.30000000000000004),
(0.0, 2.0, 0.6180841812877726, 0.5),
(0.0, 3.0, 0.6758149775627305, 0.7000000000000001),
(0.0, 4.0, 0.7166906726862953, 0.9)]
If `with_address` is set to False, then the tuples will contain only the
attribute values, not the cell indices.
With array format, returns a tuple of 2D NumPy arrays, one for each
name in `attribute_names`. The array element X_ij contains the
attribute value for the connection from the ith neuron in the pre-
synaptic Population to the jth neuron in the post-synaptic Population,
if a single such connection exists. If there are no such connections,
X_ij will be NaN. Example::
>>> weights, delays = prj.get(["weight", "delay"], format="array")
>>> weights
array([[ 0.66210438, nan, 0.10744555, 0.54557088],
[ 0.3676134 , nan, 0.41463193, nan],
[ 0.57434871, 0.4329354 , 0.58482943, 0.42863916]])
If there are multiple such connections, the action to take is
controlled by the `multiple_synapses` argument, which must be one of
{'last', 'first', 'sum', 'min', 'max'}.
Values will be expressed in the standard PyNN units (i.e. millivolts,
nanoamps, milliseconds, microsiemens, nanofarads, event per second).
"""
if isinstance(attribute_names, basestring):
attribute_names = (attribute_names,)
return_single = True
else:
return_single = False
if isinstance(self.synapse_type, StandardSynapseType):
attribute_names = self.synapse_type.get_native_names(*attribute_names)
if format == 'list':
names = list(attribute_names)
if with_address:
names = ["presynaptic_index", "postsynaptic_index"] + names
values = self._get_attributes_as_list(names)
if gather and self._simulator.state.num_processes > 1:
all_values = {self._simulator.state.mpi_rank: values}
all_values = recording.gather_dict(all_values, all=(gather == 'all'))
if gather == 'all' or self._simulator.state.mpi_rank == 0:
values = reduce(operator.add, all_values.values())
if not with_address and return_single:
values = [val[0] for val in values]
return values
elif format == 'array':
if multiple_synapses not in Projection.MULTI_SYNAPSE_OPERATIONS:
raise ValueError("`multiple_synapses` argument must be one of {}".format(list(Projection.MULTI_SYNAPSE_OPERATIONS)))
if gather and self._simulator.state.num_processes > 1:
# Node 0 is the only one creating a full connection matrix, and returning it (saving memory)
# Slaves nodes are returning list of connections, so this may be inconsistent...
names = list(attribute_names)
names = ["presynaptic_index", "postsynaptic_index"] + names
values = self._get_attributes_as_list(names)
all_values = {self._simulator.state.mpi_rank: values}
all_values = recording.gather_dict(all_values, all=(gather == 'all'))
if gather == 'all' or self._simulator.state.mpi_rank == 0:
tmp_values = reduce(operator.add, all_values.values())
values = self._get_attributes_as_arrays(attribute_names,
multiple_synapses=multiple_synapses)
tmp_values = numpy.array(tmp_values)
for i in xrange(len(values)):
values[i][tmp_values[:, 0].astype(int), tmp_values[:, 1].astype(int)] = tmp_values[:, 2 + i]
else:
values = self._get_attributes_as_arrays(attribute_names,
multiple_synapses=multiple_synapses)
if return_single:
if gather == 'all' or self._simulator.state.mpi_rank == 0:
assert len(values) == 1, values
return values[0]
else:
return values
else:
raise Exception("format must be 'list' or 'array'")