def __init__(self, target, variables):
self.target = target
for mon_var in variables:
if not hasattr(target, mon_var):
raise errors.ModelDefError(
f"Item {mon_var} isn't defined in model {target}, "
f"so it can not be monitored.")
item_names = []
mon_indices = []
item_content = {}
if variables is not None:
if isinstance(variables, (list, tuple)):
for mon_var in variables:
if isinstance(mon_var, str):
var_data = getattr(target, mon_var)
mon_key = mon_var
mon_idx = None
mon_shape = ops.shape(var_data)
elif isinstance(mon_var, (tuple, list)):
mon_key = mon_var[0]
var_data = getattr(target, mon_key)
mon_idx = mon_var[1]
mon_shape = ops.shape(mon_idx) # TODO: matrix index
else:
raise errors.ModelUseError(
f'Unknown monitor item: {str(mon_var)}')
item_names.append(mon_key)
mon_indices.append(mon_idx)
dtype = var_data.dtype if hasattr(var_data,
'dtype') else None
item_content[mon_var] = ops.zeros((1, ) + mon_shape,
dtype=dtype)
elif isinstance(variables, dict):
for k, v in variables.items():
item_names.append(k)
mon_indices.append(v)
if v is None:
shape = ops.shape(getattr(target, k))
else:
shape = ops.shape(v)
val_data = getattr(target, k)
dtype = val_data.dtype if hasattr(val_data,
'dtype') else None
item_content[k] = ops.zeros((1, ) + shape, dtype=dtype)
else:
raise errors.ModelUseError(
f'Unknown monitors type: {type(variables)}')
self.ts = None
self.item_names = item_names
self.item_indices = mon_indices
self.item_contents = item_content
self.num_item = len(item_content)
def __init__(self, v0, delay_len, before_t0=0., t0=0., dt=None):
# size
self.size = ops.shape(v0)
# delay_len
self.delay_len = delay_len
self.dt = backend.get_dt() if dt is None else dt
self.num_delay = int(math.ceil(delay_len / self.dt))
# other variables
self._delay_in = self.num_delay - 1
self._delay_out = 0
self.current_time = t0
# before_t0
self.before_t0 = before_t0
# delay data
self.data = ops.zeros((self.num_delay + 1,) + self.size)
if callable(before_t0):
for i in range(self.num_delay):
self.data[i] = before_t0(t0 + (i - self.num_delay) * self.dt)
else:
self.data[:-1] = before_t0
self.data[-1] = v0
def run(self, duration, inputs=(), report=False, report_percent=0.1):
"""The running function.
Parameters
----------
duration : float, int, tuple, list
The running duration.
inputs : list, tuple
The model inputs with the format of ``[(key, value [operation])]``.
report : bool
Whether report the running progress.
report_percent : float
The percent of progress to report.
"""
# times
# ------
start, end = utils.check_duration(duration)
times = ops.arange(start, end, backend.get_dt())
run_length = ops.shape(times)[0]
# build run function
# ------------------
self.run_func = self.build(inputs, inputs_is_formatted=False, mon_length=run_length, return_code=False)
# run the model
# -------------
res = utils.run_model(self.run_func, times, report, report_percent)
self.mon.ts = times
return res
def period_input(values, durations, dt=None, return_length=False):
"""Format an input current with different periods.
For example:
If you want to get an input where the size is 0 bwteen 0-100 ms,
and the size is 1. between 100-200 ms.
>>> import numpy as np
>>> period_input(values=[0, 1],
>>> durations=[100, 100])
Parameters
----------
values : list, np.ndarray
The current values for each period duration.
durations : list, np.ndarray
The duration for each period.
dt : float
Default is None.
return_length : bool
Return the final duration length.
Returns
-------
current_and_duration : tuple
(The formatted current, total duration)
"""
assert len(durations) == len(values), f'"values" and "durations" must be the same length, while ' \
f'we got {len(values)} != {len(durations)}.'
dt = backend.get_dt() if dt is None else dt
# get input current shape, and duration
I_duration = sum(durations)
I_shape = ()
for val in values:
shape = ops.shape(val)
if len(shape) > len(I_shape):
I_shape = shape
# get the current
start = 0
I_current = ops.zeros((int(math.ceil(I_duration / dt)),) + I_shape)
for c_size, duration in zip(values, durations):
length = int(duration / dt)
I_current[start: start + length] = c_size
start += length
if return_length:
return I_current, I_duration
else:
return I_current
def constant_input(I_and_duration, dt=None):
"""Format constant input in durations.
For example:
If you want to get an input where the size is 0 bwteen 0-100 ms,
and the size is 1. between 100-200 ms.
>>> import numpy as np
>>> constant_input([(0, 100), (1, 100)])
>>> constant_input([(np.zeros(100), 100), (np.random.rand(100), 100)])
Parameters
----------
I_and_duration : list
This parameter receives the current size and the current
duration pairs, like `[(Isize1, duration1), (Isize2, duration2)]`.
dt : float
Default is None.
Returns
-------
current_and_duration : tuple
(The formatted current, total duration)
"""
dt = backend.get_dt() if dt is None else dt
# get input current dimension, shape, and duration
I_duration = 0.
I_dim = 0
I_shape = ()
for I in I_and_duration:
I_duration += I[1]
shape = ops.shape(I[0])
if len(shape) > len(I_shape):
I_shape = shape
# get the current
I_current = ops.zeros((int(math.ceil(I_duration / dt)),) + I_shape)
start = 0
for c_size, duration in I_and_duration:
length = int(duration / dt)
I_current[start: start + length] = c_size
start += length
return I_current, I_duration
def __init__(self, size, delay_time):
if isinstance(size, int):
size = (size, )
self.size = tuple(size)
self.delay_time = delay_time
if isinstance(delay_time, (int, float)):
self.uniform_delay = True
self.delay_num_step = int(math.ceil(
delay_time / backend.get_dt())) + 1
self.delay_data = ops.zeros((self.delay_num_step, ) + self.size)
else:
if not len(self.size) == 1:
raise NotImplementedError(
f'Currently, BrainPy only supports 1D heterogeneous delays, while does '
f'not implement the heterogeneous delay with {len(self.size)}-dimensions.'
)
self.num = size2len(size)
if isinstance(delay_time, type(ops.as_tensor([1]))):
assert ops.shape(delay_time) == self.size
elif callable(delay_time):
delay_time2 = ops.zeros(size)
for i in range(size[0]):
delay_time2[i] = delay_time()
delay_time = delay_time2
else:
raise NotImplementedError(
f'Currently, BrainPy does not support delay type '
f'of {type(delay_time)}: {delay_time}')
self.uniform_delay = False
delay = delay_time / backend.get_dt()
dint = ops.as_tensor(delay_time / backend.get_dt(), dtype=int)
ddiff = (delay - dint) >= 0.5
self.delay_num_step = ops.as_tensor(delay + ddiff, dtype=int) + 1
self.delay_data = ops.zeros((max(self.delay_num_step), ) + size)
self.diag = ops.arange(self.num)
self.delay_in_idx = self.delay_num_step - 1
if self.uniform_delay:
self.delay_out_idx = 0
else:
self.delay_out_idx = ops.zeros(self.num, dtype=int)
self.name = None
def mat2ij(conn_mat):
"""Get the i-j connections from connectivity matrix.
Parameters
----------
conn_mat : np.ndarray
Connectivity matrix with `(num_pre, num_post)` shape.
Returns
-------
conn_tuple : tuple
(Pre-synaptic neuron indexes,
post-synaptic neuron indexes).
"""
if len(ops.shape(conn_mat)) != 2:
raise errors.ModelUseError('Connectivity matrix must be in the '
'shape of (num_pre, num_post).')
pre_ids, post_ids = ops.where(conn_mat > 0)
return ops.as_tensor(pre_ids, dtype=ops.int), \
ops.as_tensor(post_ids, dtype=ops.int)
def run(self, duration, report=False, report_percent=0.1):
if isinstance(duration, (int, float)):
duration = [0, duration]
elif isinstance(duration, (tuple, list)):
assert len(duration) == 2
duration = tuple(duration)
else:
raise ValueError
# get the times
times = ops.arange(duration[0], duration[1], backend.get_dt())
# reshape the monitor
for key in self.mon.keys():
self.mon[key] = ops.zeros((len(times), ) +
ops.shape(self.mon[key])[1:])
# run the model
run_model(run_func=self.run_func,
times=times,
report=report,
report_percent=report_percent)
def format_net_level_inputs(inputs, run_length):
"""Format the inputs of a network.
Parameters
----------
inputs : tuple
The inputs.
run_length : int
The running length.
Returns
-------
formatted_input : dict
The formatted input.
"""
from brainpy.simulation.dynamic_system import DynamicSystem
# 1. format the inputs to standard
# formats and check the inputs
if not isinstance(inputs, (tuple, list)):
raise errors.ModelUseError('"inputs" must be a tuple/list.')
if len(inputs) > 0 and not isinstance(inputs[0], (list, tuple)):
if isinstance(inputs[0], DynamicSystem):
inputs = [inputs]
else:
raise errors.ModelUseError('Unknown input structure. Only supports '
'"(target, key, value, [operation])".')
for input in inputs:
if not 3 <= len(input) <= 4:
raise errors.ModelUseError('For each target, you must specify '
'"(target, key, value, [operation])".')
if len(input) == 4:
if input[3] not in SUPPORTED_INPUT_OPS:
raise errors.ModelUseError(f'Input operation only supports '
f'"{SUPPORTED_INPUT_OPS}", '
f'not "{input[3]}".')
# 2. format inputs
formatted_inputs = {}
for input in inputs:
# target
if isinstance(input[0], DynamicSystem):
target = input[0]
target_name = input[0].name
else:
raise KeyError(f'Unknown input target: {str(input[0])}')
# key
key = input[1]
if not isinstance(key, str):
raise errors.ModelUseError('For each input, input[1] must be a string '
'to specify variable of the target.')
if not hasattr(target, key):
raise errors.ModelUseError(f'Target {target} does not have key {key}. '
f'So, it can not assign input to it.')
# value and data type
val = input[2]
if isinstance(input[2], (int, float)):
data_type = 'fix'
else:
shape = ops.shape(val)
if shape[0] == run_length:
data_type = 'iter'
else:
data_type = 'fix'
# operation
if len(input) == 4:
operation = input[3]
else:
operation = '+'
# final result
if target_name not in formatted_inputs:
formatted_inputs[target_name] = []
format_inp = (key, val, operation, data_type)
formatted_inputs[target_name].append(format_inp)
return formatted_inputs
def format_pop_level_inputs(inputs, host, mon_length):
"""Format the inputs of a population.
Parameters
----------
inputs : tuple, list
The inputs of the population.
host : Population
The host which contains all data.
mon_length : int
The monitor length.
Returns
-------
formatted_inputs : tuple, list
The formatted inputs of the population.
"""
if inputs is None:
inputs = []
if not isinstance(inputs, (tuple, list)):
raise errors.ModelUseError('"inputs" must be a tuple/list.')
if len(inputs) > 0 and not isinstance(inputs[0], (list, tuple)):
if isinstance(inputs[0], str):
inputs = [inputs]
else:
raise errors.ModelUseError('Unknown input structure, only support inputs '
'with format of "(key, value, [operation])".')
for input in inputs:
if not 2 <= len(input) <= 3:
raise errors.ModelUseError('For each target, you must specify "(key, value, [operation])".')
if len(input) == 3 and input[2] not in SUPPORTED_INPUT_OPS:
raise errors.ModelUseError(f'Input operation only supports '
f'"{SUPPORTED_INPUT_OPS}", '
f'not "{input[2]}".')
# format inputs
# -------------
formatted_inputs = []
for input in inputs:
# key
if not isinstance(input[0], str):
raise errors.ModelUseError('For each input, input[0] must be a string '
'to specify variable of the target.')
key = input[0]
if not hasattr(host, key):
raise errors.ModelUseError(f'Input target key "{key}" is not defined in {host}.')
# value and data type
val = input[1]
if isinstance(input[1], (int, float)):
data_type = 'fix'
else:
shape = ops.shape(input[1])
if shape[0] == mon_length:
data_type = 'iter'
else:
data_type = 'fix'
# operation
if len(input) == 3:
operation = input[2]
else:
operation = '+'
if operation not in SUPPORTED_INPUT_OPS:
raise errors.ModelUseError(f'Currently, BrainPy only support operations '
f'{SUPPORTED_INPUT_OPS}, '
f'not {operation}')
# input
format_inp = (key, val, operation, data_type)
formatted_inputs.append(format_inp)
return formatted_inputs