Merge pull request #245 from chaoming0625/master

update apis and examples

Author: chaoming0625

.github/workflows/Sync_branches.yml

@@ -9,10 +9,10 @@ jobs:
     steps:
       - uses: actions/checkout@master
 
-      - name: Merge master -> brainpy-2.x
+      - name: Merge master -> brainpy-2.2.x
         uses: devmasx/merge-branch@master
         with:
           type: now
           from_branch: master
-          target_branch: brainpy-2.x
+          target_branch: brainpy-2.2.x
           github_token: ${{ github.token }}

brainpy/base/base.py

@@ -29,6 +29,8 @@ class Base(object):
 
   """
 
+  _excluded_vars = ()
+
   def __init__(self, name=None):
     # check whether the object has a unique name.
     self._name = None
@@ -120,8 +122,10 @@ def vars(self, method='absolute', level=-1, include_self=True):
     for node_path, node in nodes.items():
       for k in dir(node):
         v = getattr(node, k)
-        if isinstance(v, math.Variable) and not k.startswith('_') and not k.endswith('_'):
-          gather[f'{node_path}.{k}' if node_path else k] = v
+        if isinstance(v, math.Variable):
+          if k not in node._excluded_vars:
+          # if not k.startswith('_') and not k.endswith('_'):
+            gather[f'{node_path}.{k}' if node_path else k] = v
       gather.update({f'{node_path}.{k}': v for k, v in node.implicit_vars.items()})
     return gather
 

brainpy/dyn/neurons/fractional_models.py

@@ -226,7 +226,7 @@ def __init__(
       self,
       size: Shape,
       alpha: Union[float, Sequence[float]],
-      num_step: int,
+      num_memory: int,
       a: Union[float, Tensor, Initializer, Callable] = 0.02,
       b: Union[float, Tensor, Initializer, Callable] = 0.20,
       c: Union[float, Tensor, Initializer, Callable] = -65.,
@@ -272,10 +272,10 @@ def __init__(
     self.spike = bm.Variable(bm.zeros(self.varshape, dtype=bool))
 
     # functions
-    check_integer(num_step, 'num_step', allow_none=False)
+    check_integer(num_memory, 'num_step', allow_none=False)
     self.integral = CaputoL1Schema(f=self.derivative,
                                    alpha=alpha,
-                                   num_memory=num_step,
+                                   num_memory=num_memory,
                                    inits=[self.V, self.u])
 
   def reset_state(self, batch_size=None):

brainpy/inputs/currents.py

@@ -113,12 +113,12 @@ def constant_input(I_and_duration, dt=None):
 
   # get the current
   start = 0
-  I_current = jnp.zeros((int(np.ceil(I_duration / dt)),) + I_shape)
+  I_current = bm.zeros((int(np.ceil(I_duration / dt)),) + I_shape)
   for c_size, duration in I_and_duration:
     length = int(duration / dt)
-    I_current = I_current.at[start: start + length].set(c_size)
+    I_current[start: start + length] = c_size
     start += length
-  return I_current, I_duration
+  return I_current.value, I_duration
 
 
 def constant_current(*args, **kwargs):
@@ -172,12 +172,12 @@ def spike_input(sp_times, sp_lens, sp_sizes, duration, dt=None):
   if isinstance(sp_sizes, (float, int)):
     sp_sizes = [sp_sizes] * len(sp_times)
 
-  current = jnp.zeros(int(np.ceil(duration / dt)))
+  current = bm.zeros(int(np.ceil(duration / dt)))
   for time, dur, size in zip(sp_times, sp_lens, sp_sizes):
     pp = int(time / dt)
     p_len = int(dur / dt)
-    current = current.at[pp: pp + p_len].set(size)
-  return current
+    current[pp: pp + p_len] = size
+  return current.value
 
 
 def spike_current(*args, **kwargs):
@@ -218,12 +218,12 @@ def ramp_input(c_start, c_end, duration, t_start=0, t_end=None, dt=None):
   dt = bm.get_dt() if dt is None else dt
   t_end = duration if t_end is None else t_end
 
-  current = jnp.zeros(int(np.ceil(duration / dt)))
+  current = bm.zeros(int(np.ceil(duration / dt)))
   p1 = int(np.ceil(t_start / dt))
   p2 = int(np.ceil(t_end / dt))
   cc = jnp.array(jnp.linspace(c_start, c_end, p2 - p1))
-  current = current.at[p1: p2].set(cc)
-  return current
+  current[p1: p2] = cc
+  return current.value
 
 
 def ramp_current(*args, **kwargs):
@@ -265,9 +265,9 @@ def wiener_process(duration, dt=None, n=1, t_start=0., t_end=None, seed=None):
   i_start = int(t_start / dt)
   i_end = int(t_end / dt)
   noises = rng.standard_normal((i_end - i_start, n)) * jnp.sqrt(dt)
-  currents = jnp.zeros((int(duration / dt), n))
-  currents = currents.at[i_start: i_end].set(bm.as_device_array(noises))
-  return currents
+  currents = bm.zeros((int(duration / dt), n))
+  currents[i_start: i_end] = noises
+  return currents.value
 
 
 def ou_process(mean, sigma, tau, duration, dt=None, n=1, t_start=0., t_end=None, seed=None):

brainpy/integrators/fde/Caputo.py

@@ -154,7 +154,7 @@ def __init__(
 
   def _check_step(self, args):
     dt, t = args
-    raise ValueError(f'The maximum number of step is {self.num_step}, '
+    raise ValueError(f'The maximum number of step is {self.num_memory}, '
                      f'however, the current time {t} require a time '
                      f'step number {t / dt}.')
 
@@ -164,7 +164,7 @@ def _integral_func(self, *args, **kwargs):
     t = all_args['t']
     dt = all_args.pop(DT, self.dt)
     if check.is_checking():
-      check_error_in_jit(self.num_step * dt < t, self._check_step, (dt, t))
+      check_error_in_jit(self.num_memory * dt < t, self._check_step, (dt, t))
 
     # derivative values
     devs = self.f(**all_args)
@@ -185,11 +185,11 @@ def _integral_func(self, *args, **kwargs):
 
     # integral results
     integrals = []
-    idx = ((self.num_step - 1 - self.idx) + bm.arange(self.num_step)) % self.num_step
+    idx = ((self.num_memory - 1 - self.idx) + bm.arange(self.num_memory)) % self.num_memory
     for i, key in enumerate(self.variables):
       integral = self.inits[key] + self.coef[idx, i] @ self.f_states[key]
       integrals.append(integral * (dt ** self.alpha[i] / self.alpha[i]))
-    self.idx.value = (self.idx + 1) % self.num_step
+    self.idx.value = (self.idx + 1) % self.num_memory
 
     # return integrals
     if len(self.variables) == 1:
@@ -344,19 +344,19 @@ def __init__(
                                                           dtype=self.inits[v].dtype))
                         for v in self.variables}
     self.register_implicit_vars(self.diff_states)
-    self.idx = bm.Variable(bm.asarray([self.num_step - 1]))
+    self.idx = bm.Variable(bm.asarray([self.num_memory - 1]))
 
     # integral function
     self.set_integral(self._integral_func)
 
   def reset(self, inits):
     """Reset function."""
-    self.idx.value = bm.asarray([self.num_step - 1])
+    self.idx.value = bm.asarray([self.num_memory - 1])
     inits = check_inits(inits, self.variables)
     for key, value in inits.items():
       self.inits[key].value = value
     for key, val in inits.items():
-      self.diff_states[key + "_diff"].value = bm.zeros((self.num_step,) + val.shape, dtype=val.dtype)
+      self.diff_states[key + "_diff"].value = bm.zeros((self.num_memory,) + val.shape, dtype=val.dtype)
 
   def hists(self, var=None, numpy=True):
     """Get the recorded history values."""
@@ -378,7 +378,7 @@ def hists(self, var=None, numpy=True):
 
   def _check_step(self, args):
     dt, t = args
-    raise ValueError(f'The maximum number of step is {self.num_step}, '
+    raise ValueError(f'The maximum number of step is {self.num_memory}, '
                      f'however, the current time {t} require a time '
                      f'step number {t / dt}.')
 
@@ -388,7 +388,7 @@ def _integral_func(self, *args, **kwargs):
     t = all_args['t']
     dt = all_args.pop(DT, self.dt)
     if check.is_checking():
-      check_error_in_jit(self.num_step * dt < t, self._check_step, (dt, t))
+      check_error_in_jit(self.num_memory * dt < t, self._check_step, (dt, t))
 
     # derivative values
     devs = self.f(**all_args)
@@ -405,15 +405,15 @@ def _integral_func(self, *args, **kwargs):
 
     # integral results
     integrals = []
-    idx = ((self.num_step - 1 - self.idx) + bm.arange(self.num_step)) % self.num_step
+    idx = ((self.num_memory - 1 - self.idx) + bm.arange(self.num_memory)) % self.num_memory
     for i, key in enumerate(self.variables):
       self.diff_states[key + '_diff'][self.idx[0]] = all_args[key] - self.inits[key]
       self.inits[key].value = all_args[key]
       markov_term = dt ** self.alpha[i] * self.gamma_alpha[i] * devs[key] + all_args[key]
       memory_trace = self.coef[idx, i] @ self.diff_states[key + '_diff']
       integral = markov_term - memory_trace
       integrals.append(integral)
-    self.idx.value = (self.idx + 1) % self.num_step
+    self.idx.value = (self.idx + 1) % self.num_memory
 
     # return integrals
     if len(self.variables) == 1:

brainpy/integrators/fde/GL.py

@@ -4,7 +4,7 @@
 This module provides numerical solvers for Grünwald–Letnikov derivative FDEs.
 """
 
-from typing import Dict, Union, Callable
+from typing import Dict, Union, Callable, Any
 
 import jax.numpy as jnp
 
@@ -127,8 +127,8 @@ class GLShortMemory(FDEIntegrator):
   def __init__(
       self,
       f: Callable,
-      alpha,
-      inits,
+      alpha: Any,
+      inits: Any,
       num_memory: int,
       dt: float = None,
       name: str = None,
@@ -152,9 +152,9 @@ def __init__(
     # delays
     self.delays = {}
     for key, val in inits.items():
-      delay = bm.Variable(bm.zeros((self.num_step,) + val.shape, dtype=val.dtype))
+      delay = bm.Variable(bm.zeros((self.num_memory,) + val.shape, dtype=val.dtype))
       delay[0] = val
-      self.delays[key] = delay
+      self.delays[key+'_delay'] = delay
     self._idx = bm.Variable(bm.asarray([1]))
     self.register_implicit_vars(self.delays)
 
@@ -171,7 +171,7 @@ def reset(self, inits):
     self._idx.value = bm.asarray([1])
     inits = check_inits(inits, self.variables)
     for key, val in inits.items():
-      delay = bm.zeros((self.num_step,) + val.shape, dtype=val.dtype)
+      delay = bm.zeros((self.num_memory,) + val.shape, dtype=val.dtype)
       delay[0] = val
       self.delays[key].value = delay
 
@@ -199,13 +199,14 @@ def _integral_func(self, *args, **kwargs):
 
     # integral results
     integrals = []
-    idx = (self._idx + bm.arange(self.num_step)) % self.num_step
+    idx = (self._idx + bm.arange(self.num_memory)) % self.num_memory
     for i, var in enumerate(self.variables):
-      summation = self._binomial_coef[:, i] @ self.delays[var][idx]
+      delay_var = var + '_delay'
+      summation = self._binomial_coef[:, i] @ self.delays[delay_var][idx]
       integral = (dt ** self.alpha[i]) * devs[var] - summation
-      self.delays[var][self._idx[0]] = integral
+      self.delays[delay_var][self._idx[0]] = integral
       integrals.append(integral)
-    self._idx.value = (self._idx + 1) % self.num_step
+    self._idx.value = (self._idx + 1) % self.num_memory
 
     # return integrals
     if len(self.variables) == 1:

brainpy/integrators/fde/base.py

@@ -55,8 +55,8 @@ def __init__(
     arguments = parses[2]  # function arguments
 
     # memory length
-    check_integer(num_memory, 'num_step', allow_none=False, min_bound=1)
-    self.num_step = num_memory
+    check_integer(num_memory, 'num_memory', allow_none=False, min_bound=1)
+    self.num_memory = num_memory
 
     # super initialization
     super(FDEIntegrator, self).__init__(name=name,

brainpy/integrators/fde/tests/test_Caputo.py

@@ -25,7 +25,7 @@ def test1(self):
 
       intg.idx[0] = N - 1
       intg.diff_states['a_diff'][:N - 1] = bp.math.asarray(diff)
-      idx = ((intg.num_step - intg.idx) + np.arange(intg.num_step)) % intg.num_step
+      idx = ((intg.num_memory - intg.idx) + np.arange(intg.num_memory)) % intg.num_memory
       memory_trace2 = intg.coef[idx, 0] @ intg.diff_states['a_diff']
 
       print()

brainpy/integrators/runner.py

@@ -134,10 +134,11 @@ def __init__(
     numpy_mon_after_run: bool
     """
 
-    # initialize variables
     if not isinstance(target, Integrator):
       raise TypeError(f'Target must be instance of {Integrator.__name__}, '
                       f'but we got {type(target)}')
+
+    # get maximum size and initial variables
     if inits is not None:
       if isinstance(inits, (list, tuple, bm.JaxArray, jnp.ndarray)):
         assert len(target.variables) == len(inits)
@@ -148,6 +149,8 @@ def __init__(
     else:
       max_size = 1
       inits = dict()
+
+    # initialize variables
     self.variables = TensorCollector({v: bm.Variable(bm.zeros(max_size))
                                       for v in target.variables})
     for k in inits.keys():
@@ -207,7 +210,6 @@ def __init__(
     self.dyn_vars.update(self.target.vars().unique())
 
     # Variables
-
     self.dyn_vars.update(self.variables)
     if len(self._dyn_args) > 0:
       self.idx = bm.Variable(bm.zeros(1, dtype=jnp.int_))
@@ -240,11 +242,6 @@ def _loop_func(times):
         return out_vars, returns
     self.step_func = _loop_func
 
-  def _post(self, times, returns: dict):  # monitor
-    self.mon.ts = times + self.dt
-    for key in returns.keys():
-      self.mon[key] = bm.asarray(returns[key])
-
   def _step(self, t):
     # arguments
     kwargs = dict()
@@ -254,17 +251,21 @@ def _step(self, t):
     if len(self._dyn_args) > 0:
       kwargs.update({k: v[self.idx.value] for k, v in self._dyn_args.items()})
       self.idx += 1
+
     # return of function monitors
     returns = dict()
     for key, func in self.fun_monitors.items():
       returns[key] = func(t, self.dt)
+
     # call integrator function
     update_values = self.target(**kwargs)
     if len(self.target.variables) == 1:
       self.variables[self.target.variables[0]].update(update_values)
     else:
       for i, v in enumerate(self.target.variables):
         self.variables[v].update(update_values[i])
+
+    # progress bar
     if self.progress_bar:
       id_tap(lambda *args: self._pbar.update(), ())
     return returns

brainpy/integrators/sde/normal.py

@@ -114,9 +114,9 @@ def step(self, *args, **kwargs):
     # diffusion values
     diffusions = self.g(**all_args)
     if len(self.variables) == 1:
-      if not isinstance(diffusions, (bm.ndarray, jnp.ndarray)):
-        raise ValueError('Diffusion values must be a tensor when there '
-                         'is only one variable in the equation.')
+      # if not isinstance(diffusions, (bm.ndarray, jnp.ndarray)):
+      #   raise ValueError('Diffusion values must be a tensor when there '
+      #                    'is only one variable in the equation.')
       diffusions = {self.variables[0]: diffusions}
     else:
       if not isinstance(diffusions, (tuple, list)):