def before_run(self, run_namespace=None, level=0):
# execute code to initalize the data structures
if self._prepare_codeobj is None:
self._prepare_codeobj = create_runner_codeobj(
self.group,
'', # no code,
'spatialneuron_prepare',
name=self.name + '_spatialneuron_prepare',
check_units=False,
additional_variables=self.variables,
run_namespace=run_namespace,
level=level + 1)
self._prepare_codeobj()
# Raise a warning if the slow pure numpy version is used
# For simplicity, we check which CodeObject class the _prepare_codeobj
# is using, this will be the same as the main state updater
from brian2.codegen.runtime.numpy_rt.numpy_rt import NumpyCodeObject
if isinstance(self._prepare_codeobj, NumpyCodeObject):
# If numpy is used, raise a warning if scipy is not present
try:
import scipy
except ImportError:
logger.warn(
('SpatialNeuron will use numpy to do the numerical '
'integration -- this will be very slow. Either '
'switch to a different code generation target '
'(e.g. weave or cython) or install scipy.'),
once=True)
CodeRunner.before_run(self, run_namespace, level=level + 1)
def before_run(self, run_namespace):
# execute code to initalize the data structures
if self._prepare_codeobj is None:
self._prepare_codeobj = create_runner_codeobj(self.group,
'', # no code,
'spatialneuron_prepare',
name=self.name+'_spatialneuron_prepare',
check_units=False,
additional_variables=self.variables,
run_namespace=run_namespace)
self._prepare_codeobj()
# Raise a warning if the slow pure numpy version is used
# For simplicity, we check which CodeObject class the _prepare_codeobj
# is using, this will be the same as the main state updater
from brian2.codegen.runtime.numpy_rt.numpy_rt import NumpyCodeObject
if isinstance(self._prepare_codeobj, NumpyCodeObject):
# If numpy is used, raise a warning if scipy is not present
try:
import scipy
except ImportError:
logger.info(('SpatialNeuron will use numpy to do the numerical '
'integration -- this will be very slow. Either '
'switch to a different code generation target '
'(e.g. weave or cython) or install scipy.'),
once=True)
CodeRunner.before_run(self, run_namespace)
def before_run(self, run_namespace=None, level=0):
# execute code to initalize the data structures
if self._prepare_codeobj is None:
self._prepare_codeobj = create_runner_codeobj(self.group,
'', # no code,
'spatialneuron_prepare',
name=self.name+'_spatialneuron_prepare',
check_units=False,
additional_variables=self.variables,
run_namespace=run_namespace,
level=level+1)
self._prepare_codeobj()
CodeRunner.before_run(self, run_namespace, level=level + 1)
def pre_run(self, namespace):
# Some dummy code so that code generation takes care of the indexing
# and subexpressions
code = ['_to_record_%s = %s' % (v, v)
for v in self.record_variables]
code += ['_recorded_%s = _recorded_%s' % (v, v)
for v in self.record_variables]
code = '\n'.join(code)
self.codeobj = create_runner_codeobj(self.source,
code,
'statemonitor',
name=self.name,
additional_variables=self.variables,
additional_namespace=namespace,
template_kwds={'_variable_names':
self.record_variables},
check_units=False)
def __getitem__(self, index):
'''
Returns synaptic indices for `index`, which can be a tuple of indices
(including arrays and slices), a single index or a string.
'''
if (not isinstance(index, (tuple, basestring)) and
isinstance(index, (int, np.ndarray, slice,
collections.Sequence))):
index = (index, slice(None), slice(None))
if isinstance(index, tuple):
if len(index) == 2: # two indices (pre- and postsynaptic cell)
index = (index[0], index[1], slice(None))
elif len(index) > 3:
raise IndexError('Need 1, 2 or 3 indices, got %d.' % len(index))
I, J, K = index
pre_synapses = find_synapses(I, self.pre_synaptic,
self.synaptic_pre)
post_synapses = find_synapses(J, self.post_synaptic,
self.synaptic_post)
matching_synapses = np.intersect1d(pre_synapses, post_synapses,
assume_unique=True)
if K == slice(None):
return matching_synapses
elif isinstance(K, (int, slice)):
test_k = slice_to_test(K)
else:
raise NotImplementedError(('Indexing synapses with arrays not'
'implemented yet'))
pre_neurons = self.synaptic_pre[pre_synapses]
post_neurons = self.synaptic_post[post_synapses]
synapse_numbers = _synapse_numbers(pre_neurons,
post_neurons)
return np.intersect1d(matching_synapses,
np.flatnonzero(test_k(synapse_numbers)),
assume_unique=True)
elif isinstance(index, basestring):
# interpret the string expression
identifiers = get_identifiers(index)
variables = dict(self.variables)
if 'k' in identifiers:
synapse_numbers = _synapse_numbers(self.synaptic_pre[:],
self.synaptic_post[:])
variables['k'] = ArrayVariable('k', Unit(1),
synapse_numbers)
namespace = get_local_namespace(1)
additional_namespace = ('implicit-namespace', namespace)
abstract_code = '_cond = ' + index
codeobj = create_runner_codeobj(self.synapses,
abstract_code,
'state_variable_indexing',
additional_variables=variables,
additional_namespace=additional_namespace,
)
result = codeobj()
return result
else:
raise IndexError('Unsupported index type {itype}'.format(itype=type(index)))
def _add_synapses(self, sources, targets, n, p, condition=None,
level=0):
if condition is None:
sources = np.atleast_1d(sources)
targets = np.atleast_1d(targets)
n = np.atleast_1d(n)
p = np.atleast_1d(p)
if not len(p) == 1 or p != 1:
use_connections = np.random.rand(len(sources)) < p
sources = sources[use_connections]
targets = targets[use_connections]
n = n[use_connections]
sources = sources.repeat(n)
targets = targets.repeat(n)
new_synapses = len(sources)
old_N = self.N
new_N = old_N + new_synapses
self._resize(new_N)
self.synaptic_pre[old_N:new_N] = sources
self.synaptic_post[old_N:new_N] = targets
synapse_idx = old_N
for source, target in zip(sources, targets):
synapses = self.pre_synaptic[source]
synapses.resize(len(synapses) + 1)
synapses[-1] = synapse_idx
synapses = self.post_synaptic[target]
synapses.resize(len(synapses) + 1)
synapses[-1] = synapse_idx
synapse_idx += 1
else:
abstract_code = '_cond = ' + condition + '\n'
abstract_code += '_n = ' + str(n) + '\n'
abstract_code += '_p = ' + str(p)
namespace = get_local_namespace(level + 1)
additional_namespace = ('implicit-namespace', namespace)
variables = {
'_source_neurons': ArrayVariable('_source_neurons', Unit(1),
self.source.item_mapping[:] -
self.source.offset,
constant=True),
'_target_neurons': ArrayVariable('_target_neurons', Unit(1),
self.target.item_mapping[:] -
self.target.offset,
constant=True),
# The template needs to have access to the DynamicArray here,
# having access to the underlying array (which would be much
# faster), is not enough
'_synaptic_pre': Variable(Unit(1),
self.synaptic_pre, constant=True),
'_synaptic_post': Variable(Unit(1),
self.synaptic_post, constant=True),
'_pre_synaptic': Variable(Unit(1),
self.pre_synaptic, constant=True),
'_post_synaptic': Variable(Unit(1),
self.post_synaptic, constant=True),
# Will be set in the template
'i': Variable(unit=Unit(1), constant=True),
'j': Variable(unit=Unit(1), constant=True)
}
codeobj = create_runner_codeobj(self.synapses,
abstract_code,
'synapses_create',
additional_variables=variables,
additional_namespace=additional_namespace,
check_units=False
)
codeobj()
number = len(self.synaptic_pre)
for variable in self._registered_variables:
variable.resize(number)
def __getitem__(self, index):
'''
Returns synaptic indices for `index`, which can be a tuple of indices
(including arrays and slices), a single index or a string.
'''
if (not isinstance(index, (tuple, basestring)) and isinstance(
index, (int, np.ndarray, slice, collections.Sequence))):
index = (index, slice(None), slice(None))
if isinstance(index, tuple):
if len(index) == 2: # two indices (pre- and postsynaptic cell)
index = (index[0], index[1], slice(None))
elif len(index) > 3:
raise IndexError('Need 1, 2 or 3 indices, got %d.' %
len(index))
I, J, K = index
pre_synapses = find_synapses(I, self.pre_synaptic,
self.synaptic_pre)
post_synapses = find_synapses(J, self.post_synaptic,
self.synaptic_post)
matching_synapses = np.intersect1d(pre_synapses,
post_synapses,
assume_unique=True)
if K == slice(None):
return matching_synapses
elif isinstance(K, (int, slice)):
test_k = slice_to_test(K)
else:
raise NotImplementedError(('Indexing synapses with arrays not'
'implemented yet'))
pre_neurons = self.synaptic_pre[pre_synapses]
post_neurons = self.synaptic_post[post_synapses]
synapse_numbers = _synapse_numbers(pre_neurons, post_neurons)
return np.intersect1d(matching_synapses,
np.flatnonzero(test_k(synapse_numbers)),
assume_unique=True)
elif isinstance(index, basestring):
# interpret the string expression
identifiers = get_identifiers(index)
variables = dict(self.variables)
if 'k' in identifiers:
synapse_numbers = _synapse_numbers(self.synaptic_pre[:],
self.synaptic_post[:])
variables['k'] = ArrayVariable('k', Unit(1), synapse_numbers)
namespace = get_local_namespace(1)
additional_namespace = ('implicit-namespace', namespace)
abstract_code = '_cond = ' + index
codeobj = create_runner_codeobj(
self.synapses,
abstract_code,
'state_variable_indexing',
additional_variables=variables,
additional_namespace=additional_namespace,
)
result = codeobj()
return result
else:
raise IndexError(
'Unsupported index type {itype}'.format(itype=type(index)))
def _add_synapses(self, sources, targets, n, p, condition=None, level=0):
if condition is None:
sources = np.atleast_1d(sources)
targets = np.atleast_1d(targets)
n = np.atleast_1d(n)
p = np.atleast_1d(p)
if not len(p) == 1 or p != 1:
use_connections = np.random.rand(len(sources)) < p
sources = sources[use_connections]
targets = targets[use_connections]
n = n[use_connections]
sources = sources.repeat(n)
targets = targets.repeat(n)
new_synapses = len(sources)
old_N = self.N
new_N = old_N + new_synapses
self._resize(new_N)
self.synaptic_pre[old_N:new_N] = sources
self.synaptic_post[old_N:new_N] = targets
synapse_idx = old_N
for source, target in zip(sources, targets):
synapses = self.pre_synaptic[source]
synapses.resize(len(synapses) + 1)
synapses[-1] = synapse_idx
synapses = self.post_synaptic[target]
synapses.resize(len(synapses) + 1)
synapses[-1] = synapse_idx
synapse_idx += 1
else:
abstract_code = '_cond = ' + condition + '\n'
abstract_code += '_n = ' + str(n) + '\n'
abstract_code += '_p = ' + str(p)
namespace = get_local_namespace(level + 1)
additional_namespace = ('implicit-namespace', namespace)
variables = {
'_source_neurons':
ArrayVariable('_source_neurons',
Unit(1),
self.source.item_mapping[:] - self.source.offset,
constant=True),
'_target_neurons':
ArrayVariable('_target_neurons',
Unit(1),
self.target.item_mapping[:] - self.target.offset,
constant=True),
# The template needs to have access to the DynamicArray here,
# having access to the underlying array (which would be much
# faster), is not enough
'_synaptic_pre':
Variable(Unit(1), self.synaptic_pre, constant=True),
'_synaptic_post':
Variable(Unit(1), self.synaptic_post, constant=True),
'_pre_synaptic':
Variable(Unit(1), self.pre_synaptic, constant=True),
'_post_synaptic':
Variable(Unit(1), self.post_synaptic, constant=True),
# Will be set in the template
'i':
Variable(unit=Unit(1), constant=True),
'j':
Variable(unit=Unit(1), constant=True)
}
codeobj = create_runner_codeobj(
self.synapses,
abstract_code,
'synapses_create',
additional_variables=variables,
additional_namespace=additional_namespace,
check_units=False)
codeobj()
number = len(self.synaptic_pre)
for variable in self._registered_variables:
variable.resize(number)