brainstate 0.1.8__py2.py3-none-any.whl → 0.1.9__py2.py3-none-any.whl

brainstate/nn/_exp_euler_test.py

@@ -1,35 +1,35 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# ==============================================================================
-
-
-import unittest
-
-import brainunit as u
-
-import brainstate
-
-
-class TestExpEuler(unittest.TestCase):
-    def test1(self):
-        def fun(x, tau):
-            return -x / tau
-
-        with brainstate.environ.context(dt=0.1):
-            with self.assertRaises(AssertionError):
-                r = brainstate.nn.exp_euler_step(fun, 1.0 * u.mV, 1. * u.ms)
-
-        with brainstate.environ.context(dt=1. * u.ms):
-            r = brainstate.nn.exp_euler_step(fun, 1.0 * u.mV, 1. * u.ms)
-            print(r)
+# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+
+import unittest
+
+import brainunit as u
+
+import brainstate
+
+
+class TestExpEuler(unittest.TestCase):
+    def test1(self):
+        def fun(x, tau):
+            return -x / tau
+
+        with brainstate.environ.context(dt=0.1):
+            with self.assertRaises(AssertionError):
+                r = brainstate.nn.exp_euler_step(fun, 1.0 * u.mV, 1. * u.ms)
+
+        with brainstate.environ.context(dt=1. * u.ms):
+            r = brainstate.nn.exp_euler_step(fun, 1.0 * u.mV, 1. * u.ms)
+            print(r)

brainstate/nn/_fixedprob.py

@@ -1,239 +1,239 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# ==============================================================================
-
-
-from typing import Union, Callable, Optional
-
-import brainevent
-import brainunit as u
-import jax
-import jax.numpy as jnp
-import numpy as np
-
-from brainstate import random, augment, environ, init
-from brainstate._state import ParamState, FakeState
-from brainstate.compile import for_loop
-from brainstate.typing import Size, ArrayLike
-from ._module import Module
-
-__all__ = [
-    'FixedNumConn',
-    'EventFixedNumConn',
-    'EventFixedProb',
-]
-
-
-def init_indices_without_replace(
-    conn_num: int,
-    n_pre: int,
-    n_post: int,
-    seed: int | None,
-    method: str
-):
-    rng = random.default_rng(seed)
-
-    if method == 'vmap':
-        @augment.vmap(axis_size=n_pre)
-        def rand_indices():
-            return rng.choice(n_post, size=(conn_num,), replace=False)
-
-        return rand_indices()
-
-    elif method == 'for_loop':
-        return for_loop(
-            lambda *args: rng.choice(n_post, size=(conn_num,), replace=False),
-            length=n_pre
-        )
-
-    else:
-        raise ValueError(f"Unknown method: {method}")
-
-
-class FixedNumConn(Module):
-    """
-    The ``FixedNumConn`` module implements a fixed probability connection with CSR sparse data structure.
-
-    Parameters
-    ----------
-    in_size : Size
-        Number of pre-synaptic neurons, i.e., input size.
-    out_size : Size
-        Number of post-synaptic neurons, i.e., output size.
-    conn_num : float, int
-        If it is a float, representing the probability of connection, i.e., connection probability.
-
-        If it is an integer, representing the number of connections.
-    conn_weight : float or callable or jax.Array or brainunit.Quantity
-        Maximum synaptic conductance, i.e., synaptic weight.
-    efferent_target : str, optional
-        The target of the connection. Default is 'post', meaning that each pre-synaptic neuron connects to
-        a fixed number of post-synaptic neurons. The connection number is determined by the value of ``n_conn``.
-
-        If 'pre', each post-synaptic neuron connects to a fixed number of pre-synaptic neurons.
-    conn_init : str, optional
-        The initialization method of the connection weight. Default is 'vmap', meaning that the connection weight
-        is initialized by parallelized across multiple threads.
-
-        If 'for_loop', the connection weight is initialized by a for loop.
-    allow_multi_conn : bool, optional
-        Whether multiple connections are allowed from a single pre-synaptic neuron.
-        Default is True, meaning that a value of ``a`` can be selected multiple times.
-    seed: int, optional
-        Random seed. Default is None. If None, the default random seed will be used.
-    name : str, optional
-        Name of the module.
-    """
-
-    __module__ = 'brainstate.nn'
-
-    def __init__(
-        self,
-        in_size: Size,
-        out_size: Size,
-        conn_num: Union[int, float],
-        conn_weight: Union[Callable, ArrayLike],
-        efferent_target: str = 'post',  # 'pre' or 'post'
-        afferent_ratio: Union[int, float] = 1.,
-        allow_multi_conn: bool = True,
-        seed: Optional[int] = None,
-        name: Optional[str] = None,
-        conn_init: str = 'vmap',  # 'vmap' or 'for_loop'
-        param_type: type = ParamState,
-    ):
-        super().__init__(name=name)
-
-        # network parameters
-        self.in_size = in_size
-        self.out_size = out_size
-        self.efferent_target = efferent_target
-        assert efferent_target in ('pre', 'post'), 'The target of the connection must be either "pre" or "post".'
-        assert 0. <= afferent_ratio <= 1., 'Afferent ratio must be in [0, 1].'
-        if isinstance(conn_num, float):
-            assert 0. <= conn_num <= 1., 'Connection probability must be in [0, 1].'
-            conn_num = (int(self.out_size[-1] * conn_num)
-                        if efferent_target == 'post' else
-                        int(self.in_size[-1] * conn_num))
-        assert isinstance(conn_num, int), 'Connection number must be an integer.'
-        self.conn_num = conn_num
-        self.seed = seed
-        self.allow_multi_conn = allow_multi_conn
-
-        # connections
-        if self.conn_num >= 1:
-            if self.efferent_target == 'post':
-                n_post = self.out_size[-1]
-                n_pre = self.in_size[-1]
-            else:
-                n_post = self.in_size[-1]
-                n_pre = self.out_size[-1]
-
-            with jax.ensure_compile_time_eval():
-                if allow_multi_conn:
-                    rng = np.random if seed is None else np.random.RandomState(seed)
-                    indices = rng.randint(0, n_post, size=(n_pre, self.conn_num))
-                else:
-                    indices = init_indices_without_replace(self.conn_num, n_pre, n_post, seed, conn_init)
-                indices = u.math.asarray(indices, dtype=environ.ditype())
-
-            if afferent_ratio == 1.:
-                conn_weight = u.math.asarray(init.param(conn_weight, (n_pre, self.conn_num), allow_none=False))
-                self.weight = param_type(conn_weight)
-                csr = (
-                    brainevent.FixedPostNumConn((conn_weight, indices), shape=(n_pre, n_post))
-                    if self.efferent_target == 'post' else
-                    brainevent.FixedPreNumConn((conn_weight, indices), shape=(n_pre, n_post))
-                )
-                self.conn = csr
-
-            else:
-                self.pre_selected = np.random.random(n_pre) < afferent_ratio
-                indices = indices[self.pre_selected].flatten()
-                conn_weight = u.math.asarray(init.param(conn_weight, (indices.size,), allow_none=False))
-                self.weight = param_type(conn_weight)
-                indptr = (jnp.arange(1, n_pre + 1) * self.conn_num -
-                          jnp.cumsum(~self.pre_selected) * self.conn_num)
-                indptr = jnp.insert(indptr, 0, 0)  # insert 0 at the beginning
-                csr = (
-                    brainevent.CSR((conn_weight, indices, indptr), shape=(n_pre, n_post))
-                    if self.efferent_target == 'post' else
-                    brainevent.CSC((conn_weight, indices, indptr), shape=(n_pre, n_post))
-                )
-                self.conn = csr
-
-        else:
-            conn_weight = u.math.asarray(init.param(conn_weight, (), allow_none=False))
-            self.weight = FakeState(conn_weight)
-
-    def update(self, x: jax.Array) -> Union[jax.Array, u.Quantity]:
-        if self.conn_num >= 1:
-            csr = self.conn.with_data(self.weight.value)
-            return x @ csr
-        else:
-            weight = self.weight.value
-            r = u.math.zeros(x.shape[:-1] + (self.out_size[-1],), dtype=weight.dtype)
-            r = u.maybe_decimal(u.Quantity(r, unit=u.get_unit(weight)))
-            return u.math.asarray(r, dtype=environ.dftype())
-
-
-class EventFixedNumConn(FixedNumConn):
-    """
-    The FixedProb module implements a fixed probability connection with CSR sparse data structure.
-
-    Parameters
-    ----------
-    in_size : Size
-        Number of pre-synaptic neurons, i.e., input size.
-    out_size : Size
-        Number of post-synaptic neurons, i.e., output size.
-    conn_num : float, int
-        If it is a float, representing the probability of connection, i.e., connection probability.
-
-        If it is an integer, representing the number of connections.
-    conn_weight : float or callable or jax.Array or brainunit.Quantity
-        Maximum synaptic conductance, i.e., synaptic weight.
-    conn_target : str, optional
-        The target of the connection. Default is 'post', meaning that each pre-synaptic neuron connects to
-        a fixed number of post-synaptic neurons. The connection number is determined by the value of ``n_conn``.
-
-        If 'pre', each post-synaptic neuron connects to a fixed number of pre-synaptic neurons.
-    conn_init : str, optional
-        The initialization method of the connection weight. Default is 'vmap', meaning that the connection weight
-        is initialized by parallelized across multiple threads.
-
-        If 'for_loop', the connection weight is initialized by a for loop.
-    allow_multi_conn : bool, optional
-        Whether multiple connections are allowed from a single pre-synaptic neuron.
-        Default is True, meaning that a value of ``a`` can be selected multiple times.
-    seed: int, optional
-        Random seed. Default is None. If None, the default random seed will be used.
-    name : str, optional
-        Name of the module.
-    """
-
-    __module__ = 'brainstate.nn'
-
-    def update(self, spk: jax.Array) -> Union[jax.Array, u.Quantity]:
-        if self.conn_num >= 1:
-            csr = self.conn.with_data(self.weight.value)
-            return brainevent.EventArray(spk) @ csr
-        else:
-            weight = self.weight.value
-            unit = u.get_unit(weight)
-            r = jnp.zeros(spk.shape[:-1] + (self.out_size[-1],), dtype=weight.dtype)
-            r = u.maybe_decimal(u.Quantity(r, unit=unit))
-            return u.math.asarray(r, dtype=environ.dftype())
-
-
-EventFixedProb = EventFixedNumConn
+# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+
+from typing import Union, Callable, Optional
+
+import brainevent
+import brainunit as u
+import jax
+import jax.numpy as jnp
+import numpy as np
+
+from brainstate import random, augment, environ, init
+from brainstate._state import ParamState, FakeState
+from brainstate.compile import for_loop
+from brainstate.typing import Size, ArrayLike
+from ._module import Module
+
+__all__ = [
+    'FixedNumConn',
+    'EventFixedNumConn',
+    'EventFixedProb',
+]
+
+
+def init_indices_without_replace(
+    conn_num: int,
+    n_pre: int,
+    n_post: int,
+    seed: int | None,
+    method: str
+):
+    rng = random.default_rng(seed)
+
+    if method == 'vmap':
+        @augment.vmap(axis_size=n_pre)
+        def rand_indices():
+            return rng.choice(n_post, size=(conn_num,), replace=False)
+
+        return rand_indices()
+
+    elif method == 'for_loop':
+        return for_loop(
+            lambda *args: rng.choice(n_post, size=(conn_num,), replace=False),
+            length=n_pre
+        )
+
+    else:
+        raise ValueError(f"Unknown method: {method}")
+
+
+class FixedNumConn(Module):
+    """
+    The ``FixedNumConn`` module implements a fixed probability connection with CSR sparse data structure.
+
+    Parameters
+    ----------
+    in_size : Size
+        Number of pre-synaptic neurons, i.e., input size.
+    out_size : Size
+        Number of post-synaptic neurons, i.e., output size.
+    conn_num : float, int
+        If it is a float, representing the probability of connection, i.e., connection probability.
+
+        If it is an integer, representing the number of connections.
+    conn_weight : float or callable or jax.Array or brainunit.Quantity
+        Maximum synaptic conductance, i.e., synaptic weight.
+    efferent_target : str, optional
+        The target of the connection. Default is 'post', meaning that each pre-synaptic neuron connects to
+        a fixed number of post-synaptic neurons. The connection number is determined by the value of ``n_conn``.
+
+        If 'pre', each post-synaptic neuron connects to a fixed number of pre-synaptic neurons.
+    conn_init : str, optional
+        The initialization method of the connection weight. Default is 'vmap', meaning that the connection weight
+        is initialized by parallelized across multiple threads.
+
+        If 'for_loop', the connection weight is initialized by a for loop.
+    allow_multi_conn : bool, optional
+        Whether multiple connections are allowed from a single pre-synaptic neuron.
+        Default is True, meaning that a value of ``a`` can be selected multiple times.
+    seed: int, optional
+        Random seed. Default is None. If None, the default random seed will be used.
+    name : str, optional
+        Name of the module.
+    """
+
+    __module__ = 'brainstate.nn'
+
+    def __init__(
+        self,
+        in_size: Size,
+        out_size: Size,
+        conn_num: Union[int, float],
+        conn_weight: Union[Callable, ArrayLike],
+        efferent_target: str = 'post',  # 'pre' or 'post'
+        afferent_ratio: Union[int, float] = 1.,
+        allow_multi_conn: bool = True,
+        seed: Optional[int] = None,
+        name: Optional[str] = None,
+        conn_init: str = 'vmap',  # 'vmap' or 'for_loop'
+        param_type: type = ParamState,
+    ):
+        super().__init__(name=name)
+
+        # network parameters
+        self.in_size = in_size
+        self.out_size = out_size
+        self.efferent_target = efferent_target
+        assert efferent_target in ('pre', 'post'), 'The target of the connection must be either "pre" or "post".'
+        assert 0. <= afferent_ratio <= 1., 'Afferent ratio must be in [0, 1].'
+        if isinstance(conn_num, float):
+            assert 0. <= conn_num <= 1., 'Connection probability must be in [0, 1].'
+            conn_num = (int(self.out_size[-1] * conn_num)
+                        if efferent_target == 'post' else
+                        int(self.in_size[-1] * conn_num))
+        assert isinstance(conn_num, int), 'Connection number must be an integer.'
+        self.conn_num = conn_num
+        self.seed = seed
+        self.allow_multi_conn = allow_multi_conn
+
+        # connections
+        if self.conn_num >= 1:
+            if self.efferent_target == 'post':
+                n_post = self.out_size[-1]
+                n_pre = self.in_size[-1]
+            else:
+                n_post = self.in_size[-1]
+                n_pre = self.out_size[-1]
+
+            with jax.ensure_compile_time_eval():
+                if allow_multi_conn:
+                    rng = np.random if seed is None else np.random.RandomState(seed)
+                    indices = rng.randint(0, n_post, size=(n_pre, self.conn_num))
+                else:
+                    indices = init_indices_without_replace(self.conn_num, n_pre, n_post, seed, conn_init)
+                indices = u.math.asarray(indices, dtype=environ.ditype())
+
+            if afferent_ratio == 1.:
+                conn_weight = u.math.asarray(init.param(conn_weight, (n_pre, self.conn_num), allow_none=False))
+                self.weight = param_type(conn_weight)
+                csr = (
+                    brainevent.FixedPostNumConn((conn_weight, indices), shape=(n_pre, n_post))
+                    if self.efferent_target == 'post' else
+                    brainevent.FixedPreNumConn((conn_weight, indices), shape=(n_pre, n_post))
+                )
+                self.conn = csr
+
+            else:
+                self.pre_selected = np.random.random(n_pre) < afferent_ratio
+                indices = indices[self.pre_selected].flatten()
+                conn_weight = u.math.asarray(init.param(conn_weight, (indices.size,), allow_none=False))
+                self.weight = param_type(conn_weight)
+                indptr = (jnp.arange(1, n_pre + 1) * self.conn_num -
+                          jnp.cumsum(~self.pre_selected) * self.conn_num)
+                indptr = jnp.insert(indptr, 0, 0)  # insert 0 at the beginning
+                csr = (
+                    brainevent.CSR((conn_weight, indices, indptr), shape=(n_pre, n_post))
+                    if self.efferent_target == 'post' else
+                    brainevent.CSC((conn_weight, indices, indptr), shape=(n_pre, n_post))
+                )
+                self.conn = csr
+
+        else:
+            conn_weight = u.math.asarray(init.param(conn_weight, (), allow_none=False))
+            self.weight = FakeState(conn_weight)
+
+    def update(self, x: jax.Array) -> Union[jax.Array, u.Quantity]:
+        if self.conn_num >= 1:
+            csr = self.conn.with_data(self.weight.value)
+            return x @ csr
+        else:
+            weight = self.weight.value
+            r = u.math.zeros(x.shape[:-1] + (self.out_size[-1],), dtype=weight.dtype)
+            r = u.maybe_decimal(u.Quantity(r, unit=u.get_unit(weight)))
+            return u.math.asarray(r, dtype=environ.dftype())
+
+
+class EventFixedNumConn(FixedNumConn):
+    """
+    The FixedProb module implements a fixed probability connection with CSR sparse data structure.
+
+    Parameters
+    ----------
+    in_size : Size
+        Number of pre-synaptic neurons, i.e., input size.
+    out_size : Size
+        Number of post-synaptic neurons, i.e., output size.
+    conn_num : float, int
+        If it is a float, representing the probability of connection, i.e., connection probability.
+
+        If it is an integer, representing the number of connections.
+    conn_weight : float or callable or jax.Array or brainunit.Quantity
+        Maximum synaptic conductance, i.e., synaptic weight.
+    conn_target : str, optional
+        The target of the connection. Default is 'post', meaning that each pre-synaptic neuron connects to
+        a fixed number of post-synaptic neurons. The connection number is determined by the value of ``n_conn``.
+
+        If 'pre', each post-synaptic neuron connects to a fixed number of pre-synaptic neurons.
+    conn_init : str, optional
+        The initialization method of the connection weight. Default is 'vmap', meaning that the connection weight
+        is initialized by parallelized across multiple threads.
+
+        If 'for_loop', the connection weight is initialized by a for loop.
+    allow_multi_conn : bool, optional
+        Whether multiple connections are allowed from a single pre-synaptic neuron.
+        Default is True, meaning that a value of ``a`` can be selected multiple times.
+    seed: int, optional
+        Random seed. Default is None. If None, the default random seed will be used.
+    name : str, optional
+        Name of the module.
+    """
+
+    __module__ = 'brainstate.nn'
+
+    def update(self, spk: jax.Array) -> Union[jax.Array, u.Quantity]:
+        if self.conn_num >= 1:
+            csr = self.conn.with_data(self.weight.value)
+            return brainevent.EventArray(spk) @ csr
+        else:
+            weight = self.weight.value
+            unit = u.get_unit(weight)
+            r = jnp.zeros(spk.shape[:-1] + (self.out_size[-1],), dtype=weight.dtype)
+            r = u.maybe_decimal(u.Quantity(r, unit=unit))
+            return u.math.asarray(r, dtype=environ.dftype())
+
+
+EventFixedProb = EventFixedNumConn