def __init__(self, N, spiketimes, clock=None, period=None, gather=False, sort=True):
clock = guess_clock(clock)
if gather: # assumes spike times are sorted
spiketimes=self.gather(spiketimes,clock.dt)
sort=False
thresh = SpikeGeneratorThreshold(N, spiketimes, period=period, sort=sort)
self.period = period
NeuronGroup.__init__(self, N, model=LazyStateUpdater(), threshold=thresh, clock=clock)
def __init__(self, threshold=1 * mvolt, refractory=1 * msecond, state=0, clock=None):
self.threshold = threshold # Threshold value
self.state = state
clock = guess_clock(clock)
self.refractory = int(refractory / clock.dt)
# this assumes that if the state stays over the threshold, and say
# refractory=5ms the user wants spiking at 0ms 5ms 10ms 15ms etc.
if is_approx_equal(self.refractory * clock.dt, refractory) and self.refractory > 0:
self.refractory -= 1
def __init__(self, spiketimes, clock=None, period=None):
"""Pass spiketimes
spiketimes is a list of lists, one list for each neuron
in the group. Each sublist consists of the spike times.
"""
clock = guess_clock(clock)
thresh = MultipleSpikeGeneratorThreshold(spiketimes, period=period)
NeuronGroup.__init__(self, len(spiketimes), model=LazyStateUpdater(), threshold=thresh, clock=clock)
def reinit(self, states=True):
'''
Resets the objects and clocks. If ``states=False`` it will not reinit
the state variables.
'''
objs = self.groups + self.connections + self.operations
if self.clock is not None:
objs.append(self.clock)
else:
guess_clock(None).reinit()
if hasattr(self, 'clocks'):
objs.extend(self.clocks)
for P in objs:
if hasattr(P, 'reinit'):
if isinstance(P, NeuronGroup):
try:
P.reinit(states=states)
except TypeError:
P.reinit()
else:
P.reinit()
def set_clock(self):
'''
Sets the clock and checks that clocks of all groups are synchronized.
'''
if self.same_clocks():
groups_and_operations=self.groups + self.operations
if len(groups_and_operations)>0:
self.clock = groups_and_operations[0].clock
else:
self.clock = guess_clock()
else:
raise TypeError, 'Clocks are not synchronized!' # other error type?
def __init__(self, baseupdater, nstate, mu, sigma, clock=None):
'''
baseupdater = source neuron StateUpdater
nstate = index of synaptic state variable
mu = mean synaptic input rate (per ms)
sigma = s.d. of synaptic input per ms^{1/2}
'''
self.baseupdater = baseupdater
self.nstate = nstate
if clock == None:
clock = guess_clock()
if clock:
# TODO: check units
self.mu = mu * clock.dt
self.sigma = sigma * clock.dt ** .5
else:
raise TypeError, "A time reference must be passed."
def __init__(self, baseupdater, nstate, mu, sigma, clock=None):
'''
baseupdater = source neuron StateUpdater
nstate = index of synaptic state variable
mu = mean synaptic input rate (per ms)
sigma = s.d. of synaptic input per ms^{1/2}
'''
self.baseupdater = baseupdater
self.nstate = nstate
if clock == None:
clock = guess_clock()
if clock:
# TODO: check units
self.mu = mu * clock.dt
self.sigma = sigma * clock.dt ** .5
else:
raise TypeError, "A time reference must be passed."
def __init__(self, M, B=None, clock=None):
'''
Initialize a linear model with dynamics dX/dt = M(X-B) or dX/dt = MX,
where B is a column vector.
TODO: more checks
TODO: rest
'''
self._useaccel = get_global_preference('useweave_linear_diffeq')
self._cpp_compiler = get_global_preference('weavecompiler')
self._extra_compile_args = ['-O3']
if self._cpp_compiler == 'gcc':
self._extra_compile_args += get_global_preference(
'gcc_options') # ['-march=native', '-ffast-math']
self._useB = False
if clock == None:
clock = guess_clock()
if isinstance(M, ndarray):
self.A = linalg.expm(M * clock.dt)
self.B = B
elif isinstance(M, Equations):
try:
M, self.B = get_linear_equations(M)
self.A = linalg.expm(M * clock.dt)
#self.A=array(self.A,single)
if self.B is not None:
self._C = -dot(self.A, self.B) + self.B
#self._C=array(self._C,single)
self._useB = True
else:
self._useB = False
except LinAlgError:
log_info('brian.stateupdater',
'Solving linear equations numerically')
self.A, self._C = get_linear_equations_solution_numerically(
M, clock.dt)
self.B = NotImplemented # raises error on trying to use this
self._useB = True
# note the numpy dot command works faster if self.A has C ordering compared
# to fortran ordering (although maybe this depends on which implementation
# of BLAS you're using). The difference is only significant in small
# calculations because making a copy of self.A is usually not serious, its
# size is only the number of variables, not the number of neurons.
self.A = array(self.A, order='C')
if self._useB:
self._C = array(self._C, order='C')
def __init__(self, M, B=None, clock=None):
'''
Initialize a linear model with dynamics dX/dt = M(X-B) or dX/dt = MX,
where B is a column vector.
TODO: more checks
TODO: rest
'''
self._useaccel = get_global_preference('useweave_linear_diffeq')
self._cpp_compiler = get_global_preference('weavecompiler')
self._extra_compile_args = ['-O3']
if self._cpp_compiler == 'gcc':
self._extra_compile_args += get_global_preference('gcc_options') # ['-march=native', '-ffast-math']
self._useB = False
if clock == None:
clock = guess_clock()
if isinstance(M, ndarray):
self.A = linalg.expm(M * clock.dt)
self.B = B
elif isinstance(M, Equations):
try:
M, self.B = get_linear_equations(M)
self.A = linalg.expm(M * clock.dt)
#self.A=array(self.A,single)
if self.B is not None:
self._C = -dot(self.A, self.B) + self.B
#self._C=array(self._C,single)
self._useB = True
else:
self._useB = False
except LinAlgError:
log_info('brian.stateupdater', 'Solving linear equations numerically')
self.A, self._C = get_linear_equations_solution_numerically(M, clock.dt)
self.B = NotImplemented # raises error on trying to use this
self._useB = True
# note the numpy dot command works faster if self.A has C ordering compared
# to fortran ordering (although maybe this depends on which implementation
# of BLAS you're using). The difference is only significant in small
# calculations because making a copy of self.A is usually not serious, its
# size is only the number of variables, not the number of neurons.
self.A = array(self.A, order='C')
if self._useB:
self._C = array(self._C, order='C')
def __init__(self, t, n, sigma, clock=None):
self.clock = guess_clock(clock)
self.generate(t, n, sigma)
def __init__(self, func, numstates, clock=None):
self.clock = guess_clock(clock)
self.func = func
self.numstates = numstates
def __init__(self, N, spiketimes, clock=None, period=None,
sort=True, gather=None):
clock = guess_clock(clock)
self.N = N
self.period = period
if gather:
log_warn('brian.SpikeGeneratorGroup', 'SpikeGeneratorGroup\'s gather keyword use is deprecated')
fallback = False # fall back on old SpikeGeneratorThreshold or not
if isinstance(spiketimes, list):
# spiketimes is a list of (i,t)
if len(spiketimes):
idx, times = zip(*spiketimes)
else:
idx, times = [], []
# the following try ... handles the case where spiketimes has index arrays
# e.g spiketimes = [([0, 1], 0 * msecond), ([0, 1, 2], 2 * msecond)]
# Notes:
# - if there is always the same number of indices by array, its simple, it's just a matter of flattening
# - if not, then it requires a for loop, and it's done in the except
try:
idx = array(idx, dtype = float)
times = array(times, dtype = float)
if idx.ndim > 1:
# simple case
times = tile(times.reshape((len(times), 1)), (idx.shape[1], 1)).flatten()
idx = idx.flatten()
except ValueError:
new_idx = []
new_times = []
for k, item in enumerate(idx):
if isinstance(item, list):
new_idx += item # append indices
new_times += [times[k]]*len(item)
else:
new_times += [times[k]]
new_idx += [item]
idx = array(new_idx, dtype = float)
times = new_times
times = array(times, dtype = float)
elif isinstance(spiketimes, tuple):
# spike times is a tuple with idx, times in arrays
idx = spiketimes[0]
times = spiketimes[1]
elif isinstance(spiketimes, ndarray):
# spiketimes is a ndarray, with first col is index and second time
idx = spiketimes[:,0]
times = spiketimes[:,1]
else:
log_warn('brian.SpikeGeneratorGroup', 'Using (slow) threshold because spiketimes is assumed to be a generator/iterator')
# spiketimes is a callable object, so falling back on old SpikeGeneratorThreshold
fallback = True
if not fallback:
thresh = FastSpikeGeneratorThreshold(N, idx, times, dt=clock.dt, period=period)
else:
thresh = SpikeGeneratorThreshold(N, spiketimes, period=period, sort=sort)
if not hasattr(self, '_initialized'):
NeuronGroup.__init__(self, N, model=LazyStateUpdater(), threshold=thresh, clock=clock)
self._initialized = True
else:
self._threshold = thresh
def __init__(self, function, clock=None, when='end'):
self.clock = guess_clock(clock)
self.when = when
self.function = function
if hasattr(function, 'func_code'):
self._has_arg = (self.function.func_code.co_argcount==1)
def __init__(self, func, numstates, clock=None):
self.clock = guess_clock(clock)
self.func = func
self.numstates = numstates
def __init__(self, t, n, sigma, clock=None):
self.clock = guess_clock(clock)
self.generate(t, n, sigma)
def __init__(self,
N,
spiketimes,
clock=None,
period=None,
sort=True,
gather=None):
clock = guess_clock(clock)
self.N = N
self.period = period
if gather:
log_warn(
'brian.SpikeGeneratorGroup',
'SpikeGeneratorGroup\'s gather keyword use is deprecated')
fallback = False # fall back on old SpikeGeneratorThreshold or not
if isinstance(spiketimes, list):
# spiketimes is a list of (i,t)
if len(spiketimes):
idx, times = zip(*spiketimes)
else:
idx, times = [], []
# the following try ... handles the case where spiketimes has index arrays
# e.g spiketimes = [([0, 1], 0 * msecond), ([0, 1, 2], 2 * msecond)]
# Notes:
# - if there is always the same number of indices by array, its simple, it's just a matter of flattening
# - if not, then it requires a for loop, and it's done in the except
try:
idx = array(idx, dtype=float)
times = array(times, dtype=float)
if idx.ndim > 1:
# simple case
times = tile(times.reshape((len(times), 1)),
(idx.shape[1], 1)).flatten()
idx = idx.flatten()
except ValueError:
new_idx = []
new_times = []
for k, item in enumerate(idx):
if isinstance(item, list):
new_idx += item # append indices
new_times += [times[k]] * len(item)
else:
new_times += [times[k]]
new_idx += [item]
idx = array(new_idx, dtype=float)
times = new_times
times = array(times, dtype=float)
elif isinstance(spiketimes, tuple):
# spike times is a tuple with idx, times in arrays
idx = spiketimes[0]
times = spiketimes[1]
elif isinstance(spiketimes, ndarray):
# spiketimes is a ndarray, with first col is index and second time
idx = spiketimes[:, 0]
times = spiketimes[:, 1]
else:
log_warn(
'brian.SpikeGeneratorGroup',
'Using (slow) threshold because spiketimes is assumed to be a generator/iterator'
)
# spiketimes is a callable object, so falling back on old SpikeGeneratorThreshold
fallback = True
if not fallback:
thresh = FastSpikeGeneratorThreshold(N,
idx,
times,
dt=clock.dt,
period=period)
else:
thresh = SpikeGeneratorThreshold(N,
spiketimes,
period=period,
sort=sort)
if not hasattr(self, '_initialized'):
NeuronGroup.__init__(self,
N,
model=LazyStateUpdater(),
threshold=thresh,
clock=clock)
self._initialized = True
else:
self._threshold = thresh