Fix several bugs, update APIs and docs (#304)

Fix several bugs, update APIs and docs

Author: chaoming0625

brainpy/connect/base.py

@@ -81,8 +81,8 @@ class CSRConn(TwoEndConnector):
   def __init__(self, indices, inptr):
     super(CSRConn, self).__init__()
 
-    self.indices = bm.asarray(indices).astype(IDX_DTYPE)
-    self.inptr = bm.asarray(inptr).astype(IDX_DTYPE)
+    self.indices = bm.asarray(indices, dtype=IDX_DTYPE)
+    self.inptr = bm.asarray(inptr, dtype=IDX_DTYPE)
     self.pre_num = self.inptr.size - 1
     self.max_post = bm.max(self.indices)
 
@@ -110,3 +110,5 @@ def __init__(self, csr_mat):
     self.csr_mat = csr_mat
     super(SparseMatConn, self).__init__(indices=bm.asarray(self.csr_mat.indices, dtype=IDX_DTYPE),
                                         inptr=bm.asarray(self.csr_mat.indptr, dtype=IDX_DTYPE))
+    self.pre_num = csr_mat.shape[0]
+    self.post_num = csr_mat.shape[1]

brainpy/connect/custom_conn.py

@@ -46,7 +46,7 @@ def build_csr(self):
                            f'same size, but {self.pre_num} != {self.post_num}.')
     ind = np.arange(self.pre_num)
     indptr = np.arange(self.pre_num + 1)
-    return np.asarray(ind, dtype=IDX_DTYPE), np.arange(indptr, dtype=IDX_DTYPE),
+    return (np.asarray(ind, dtype=IDX_DTYPE), np.asarray(indptr, dtype=IDX_DTYPE))
 
   def build_mat(self, pre_size=None, post_size=None):
     if self.pre_num != self.post_num:

brainpy/connect/regular_conn.py

@@ -988,15 +988,15 @@ def __init__(
     ltp.register_master(master=self)
     self.ltp: SynLTP = ltp
 
-  def init_weights(
+  def _init_weights(
       self,
       weight: Union[float, Array, Initializer, Callable],
       comp_method: str,
       sparse_data: str = 'csr'
   ) -> Union[float, Array]:
     if comp_method not in ['sparse', 'dense']:
       raise ValueError(f'"comp_method" must be in "sparse" and "dense", but we got {comp_method}')
-    if sparse_data not in ['csr', 'ij']:
+    if sparse_data not in ['csr', 'ij', 'coo']:
       raise ValueError(f'"sparse_data" must be in "csr" and "ij", but we got {sparse_data}')
     if self.conn is None:
       raise ValueError(f'Must provide "conn" when initialize the model {self.name}')
@@ -1014,11 +1014,11 @@ def init_weights(
       if comp_method == 'sparse':
         if sparse_data == 'csr':
           conn_mask = self.conn.require('pre2post')
-        elif sparse_data == 'ij':
+        elif sparse_data in ['ij', 'coo']:
           conn_mask = self.conn.require('post_ids', 'pre_ids')
         else:
           ValueError(f'Unknown sparse data type: {sparse_data}')
-        weight = parameter(weight, conn_mask[1].shape, allow_none=False)
+        weight = parameter(weight, conn_mask[0].shape, allow_none=False)
       elif comp_method == 'dense':
         weight = parameter(weight, (self.pre.num, self.post.num), allow_none=False)
         conn_mask = self.conn.require('conn_mat')
@@ -1030,7 +1030,7 @@ def init_weights(
       weight = bm.TrainVar(weight)
     return weight, conn_mask
 
-  def syn2post_with_all2all(self, syn_value, syn_weight):
+  def _syn2post_with_all2all(self, syn_value, syn_weight):
     if bm.ndim(syn_weight) == 0:
       if isinstance(self.mode, BatchingMode):
         post_vs = bm.sum(syn_value, keepdims=True, axis=tuple(range(syn_value.ndim))[1:])
@@ -1043,10 +1043,10 @@ def syn2post_with_all2all(self, syn_value, syn_weight):
       post_vs = syn_value @ syn_weight
     return post_vs
 
-  def syn2post_with_one2one(self, syn_value, syn_weight):
+  def _syn2post_with_one2one(self, syn_value, syn_weight):
     return syn_value * syn_weight
 
-  def syn2post_with_dense(self, syn_value, syn_weight, conn_mat):
+  def _syn2post_with_dense(self, syn_value, syn_weight, conn_mat):
     if bm.ndim(syn_weight) == 0:
       post_vs = (syn_weight * syn_value) @ conn_mat
     else:

brainpy/dyn/base.py

@@ -1,28 +1,30 @@
-from brainpy.dyn.base import DynamicalSystem
-from typing import Optional
-from brainpy.modes import Mode
 from typing import Callable
+from typing import Optional
+
+from brainpy.dyn.base import DynamicalSystem
+from brainpy.modes import Mode, training
 
 
 class Activation(DynamicalSystem):
-  r"""Applies a activation to the inputs
+  r"""Applies an activation function to the inputs
 
   Parameters:
   ----------
-  activate_fun: Callable
+  activate_fun: Callable, function
     The function of Activation
   name: str, Optional
     The name of the object
   mode: Mode
     Enable training this node or not. (default True).
   """
 
-  def __init__(self,
-               activate_fun: Callable,
-               name: Optional[str] = None,
-               mode: Optional[Mode] = None,
-               **kwargs,
-      ):
+  def __init__(
+      self,
+      activate_fun: Callable,
+      name: Optional[str] = None,
+      mode: Mode = training,
+      **kwargs,
+  ):
     super().__init__(name, mode)
     self.activate_fun = activate_fun
     self.kwargs = kwargs

brainpy/dyn/layers/activate.py

@@ -9,7 +9,7 @@
 from brainpy.dyn.base import DynamicalSystem
 from brainpy.errors import MathError
 from brainpy.initialize import XavierNormal, ZeroInit, Initializer, parameter
-from brainpy.modes import  Mode, TrainingMode, BatchingMode, training, batching
+from brainpy.modes import Mode, TrainingMode, BatchingMode, training, batching
 from brainpy.tools.checking import check_initializer
 from brainpy.types import Array
 
@@ -201,17 +201,19 @@ class Flatten(DynamicalSystem):
   mode: Mode
     Enable training this node or not. (default True)
   """
-  def __init__(self,
-               name: Optional[str] = None,
-               mode: Optional[Mode] = batching,
-      ):
+
+  def __init__(
+      self,
+      name: Optional[str] = None,
+      mode: Optional[Mode] = batching,
+  ):
     super().__init__(name, mode)
-  
+
   def update(self, shr, x):
     if isinstance(self.mode, BatchingMode):
       return x.reshape((x.shape[0], -1))
     else:
       return x.flatten()
-  
+
   def reset_state(self, batch_size=None):
-    pass
+    pass

brainpy/dyn/layers/linear.py

@@ -119,7 +119,7 @@ def __init__(
     self.comp_method = comp_method
 
     # connections and weights
-    self.g_max, self.conn_mask = self.init_weights(g_max, comp_method=comp_method, sparse_data='csr')
+    self.g_max, self.conn_mask = self._init_weights(g_max, comp_method=comp_method, sparse_data='csr')
 
     # register delay
     self.delay_step = self.register_delay(f"{self.pre.name}.spike", delay_step, self.pre.spike)
@@ -143,10 +143,10 @@ def update(self, tdi, pre_spike=None):
     # synaptic values onto the post
     if isinstance(self.conn, All2All):
       syn_value = self.stp(bm.asarray(pre_spike, dtype=bm.dftype()))
-      post_vs = self.syn2post_with_all2all(syn_value, self.g_max)
+      post_vs = self._syn2post_with_all2all(syn_value, self.g_max)
     elif isinstance(self.conn, One2One):
       syn_value = self.stp(bm.asarray(pre_spike, dtype=bm.dftype()))
-      post_vs = self.syn2post_with_one2one(syn_value, self.g_max)
+      post_vs = self._syn2post_with_one2one(syn_value, self.g_max)
     else:
       if self.comp_method == 'sparse':
         f = lambda s: bm.pre2post_event_sum(s, self.conn_mask, self.post.num, self.g_max)
@@ -160,7 +160,7 @@ def update(self, tdi, pre_spike=None):
         #   post_vs *= f2(stp_value)
       else:
         syn_value = self.stp(bm.asarray(pre_spike, dtype=bm.dftype()))
-        post_vs = self.syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
+        post_vs = self._syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
     if self.post_ref_key:
       post_vs = post_vs * (1. - getattr(self.post, self.post_ref_key))
 
@@ -296,7 +296,7 @@ def __init__(
       raise ValueError(f'"tau" must be a scalar or a tensor with size of 1. But we got {self.tau}')
 
     # connections and weights
-    self.g_max, self.conn_mask = self.init_weights(g_max, comp_method, sparse_data='csr')
+    self.g_max, self.conn_mask = self._init_weights(g_max, comp_method, sparse_data='csr')
 
     # variables
     self.g = variable_(bm.zeros, self.post.num, mode)
@@ -328,11 +328,11 @@ def update(self, tdi, pre_spike=None):
     if isinstance(self.conn, All2All):
       syn_value = bm.asarray(pre_spike, dtype=bm.dftype())
       if self.stp is not None: syn_value = self.stp(syn_value)
-      post_vs = self.syn2post_with_all2all(syn_value, self.g_max)
+      post_vs = self._syn2post_with_all2all(syn_value, self.g_max)
     elif isinstance(self.conn, One2One):
       syn_value = bm.asarray(pre_spike, dtype=bm.dftype())
       if self.stp is not None: syn_value = self.stp(syn_value)
-      post_vs = self.syn2post_with_one2one(syn_value, self.g_max)
+      post_vs = self._syn2post_with_one2one(syn_value, self.g_max)
     else:
       if self.comp_method == 'sparse':
         f = lambda s: bm.pre2post_event_sum(s, self.conn_mask, self.post.num, self.g_max)
@@ -343,7 +343,7 @@ def update(self, tdi, pre_spike=None):
       else:
         syn_value = bm.asarray(pre_spike, dtype=bm.dftype())
         if self.stp is not None: syn_value = self.stp(syn_value)
-        post_vs = self.syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
+        post_vs = self._syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
     # updates
     self.g.value = self.integral(self.g.value, t, dt) + post_vs
 
@@ -487,7 +487,7 @@ def __init__(
                        f'But we got {self.tau_decay}')
 
     # connections
-    self.g_max, self.conn_mask = self.init_weights(g_max, comp_method, sparse_data='ij')
+    self.g_max, self.conn_mask = self._init_weights(g_max, comp_method, sparse_data='ij')
 
     # variables
     self.h = variable_(bm.zeros, self.pre.num, mode)
@@ -531,16 +531,16 @@ def update(self, tdi, pre_spike=None):
     syn_value = self.g.value
     if self.stp is not None: syn_value = self.stp(syn_value)
     if isinstance(self.conn, All2All):
-      post_vs = self.syn2post_with_all2all(syn_value, self.g_max)
+      post_vs = self._syn2post_with_all2all(syn_value, self.g_max)
     elif isinstance(self.conn, One2One):
-      post_vs = self.syn2post_with_one2one(syn_value, self.g_max)
+      post_vs = self._syn2post_with_one2one(syn_value, self.g_max)
     else:
       if self.comp_method == 'sparse':
         f = lambda s: bm.pre2post_sum(s, self.post.num, *self.conn_mask)
         if isinstance(self.mode, BatchingMode): f = vmap(f)
         post_vs = f(syn_value)
       else:
-        post_vs = self.syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
+        post_vs = self._syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
 
     # output
     return self.output(post_vs)
@@ -829,7 +829,7 @@ def __init__(
     self.stop_spike_gradient = stop_spike_gradient
 
     # connections and weights
-    self.g_max, self.conn_mask = self.init_weights(g_max, comp_method, sparse_data='ij')
+    self.g_max, self.conn_mask = self._init_weights(g_max, comp_method, sparse_data='ij')
 
     # variables
     self.g = variable_(bm.zeros, self.pre.num, mode)
@@ -872,16 +872,16 @@ def update(self, tdi, pre_spike=None):
     syn_value = self.g.value
     if self.stp is not None: syn_value = self.stp(syn_value)
     if isinstance(self.conn, All2All):
-      post_vs = self.syn2post_with_all2all(syn_value, self.g_max)
+      post_vs = self._syn2post_with_all2all(syn_value, self.g_max)
     elif isinstance(self.conn, One2One):
-      post_vs = self.syn2post_with_one2one(syn_value, self.g_max)
+      post_vs = self._syn2post_with_one2one(syn_value, self.g_max)
     else:
       if self.comp_method == 'sparse':
         f = lambda s: bm.pre2post_sum(s, self.post.num, *self.conn_mask)
         if isinstance(self.mode, BatchingMode): f = vmap(f)
         post_vs = f(syn_value)
       else:
-        post_vs = self.syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
+        post_vs = self._syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
 
     # output
     return self.output(post_vs)

brainpy/dyn/synapses/abstract_models.py

@@ -181,7 +181,7 @@ def __init__(
       raise ValueError(f'"T_duration" must be a scalar or a tensor with size of 1. But we got {T_duration}')
 
     # connection
-    self.g_max, self.conn_mask = self.init_weights(g_max, comp_method, sparse_data='ij')
+    self.g_max, self.conn_mask = self._init_weights(g_max, comp_method, sparse_data='ij')
 
     # variables
     self.g = variable(bm.zeros, mode, self.pre.num)
@@ -226,16 +226,16 @@ def update(self, tdi, pre_spike=None):
     syn_value = self.g.value
     if self.stp is not None: syn_value = self.stp(syn_value)
     if isinstance(self.conn, All2All):
-      post_vs = self.syn2post_with_all2all(syn_value, self.g_max)
+      post_vs = self._syn2post_with_all2all(syn_value, self.g_max)
     elif isinstance(self.conn, One2One):
-      post_vs = self.syn2post_with_one2one(syn_value, self.g_max)
+      post_vs = self._syn2post_with_one2one(syn_value, self.g_max)
     else:
       if self.comp_method == 'sparse':
         f = lambda s: bm.pre2post_sum(s, self.post.num, *self.conn_mask)
         if isinstance(self.mode, BatchingMode): f = vmap(f)
         post_vs = f(syn_value)
       else:
-        post_vs = self.syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
+        post_vs = self._syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
 
     # output
     return self.output(post_vs)
@@ -526,7 +526,7 @@ def __init__(
     self.stop_spike_gradient = stop_spike_gradient
 
     # connections and weights
-    self.g_max, self.conn_mask = self.init_weights(g_max, comp_method, sparse_data='ij')
+    self.g_max, self.conn_mask = self._init_weights(g_max, comp_method, sparse_data='ij')
 
     # variables
     self.g = variable(bm.zeros, mode, self.pre.num)
@@ -575,16 +575,16 @@ def update(self, tdi, pre_spike=None):
     syn_value = self.g.value
     if self.stp is not None: syn_value = self.stp(syn_value)
     if isinstance(self.conn, All2All):
-      post_vs = self.syn2post_with_all2all(syn_value, self.g_max)
+      post_vs = self._syn2post_with_all2all(syn_value, self.g_max)
     elif isinstance(self.conn, One2One):
-      post_vs = self.syn2post_with_one2one(syn_value, self.g_max)
+      post_vs = self._syn2post_with_one2one(syn_value, self.g_max)
     else:
       if self.comp_method == 'sparse':
         f = lambda s: bm.pre2post_sum(s, self.post.num, *self.conn_mask)
         if isinstance(self.mode, BatchingMode): f = vmap(f)
         post_vs = f(syn_value)
       else:
-        post_vs = self.syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
+        post_vs = self._syn2post_with_dense(syn_value, self.g_max, self.conn_mask)
 
     # output
     return self.output(post_vs)

brainpy/dyn/synapses/biological_models.py

@@ -3,13 +3,14 @@
 import os
 import re
 
-from jax import dtypes, config, numpy as jnp
+from jax import dtypes, config, numpy as jnp, devices
 from jax.lib import xla_bridge
 
 __all__ = [
   'enable_x64',
   'disable_x64',
   'set_platform',
+  'get_platform',
   'set_host_device_count',
 
   # device memory
@@ -92,7 +93,7 @@ def disable_x64():
   config.update("jax_enable_x64", False)
 
 
-def set_platform(platform):
+def set_platform(platform: str):
   """
   Changes platform to CPU, GPU, or TPU. This utility only takes
   effect at the beginning of your program.
@@ -101,6 +102,17 @@ def set_platform(platform):
   config.update("jax_platform_name", platform)
 
 
+def get_platform() -> str:
+  """Get the computing platform.
+
+  Returns
+  -------
+  platform: str
+    Either 'cpu', 'gpu' or 'tpu'.
+  """
+  return devices()[0].platform
+
+
 def set_host_device_count(n):
   """
   By default, XLA considers all CPU cores as one device. This utility tells XLA

brainpy/math/setting.py

@@ -69,7 +69,7 @@
   'sphinx.ext.autosummary',
   'sphinx.ext.intersphinx',
   'sphinx.ext.mathjax',
-  'sphinx-mathjax-offline',
+  # 'sphinx-mathjax-offline',
   'sphinx.ext.napoleon',
   'sphinx.ext.viewcode',
   'sphinx_autodoc_typehints',