brainstate 0.1.9__py2.py3-none-any.whl → 0.2.0__py2.py3-none-any.whl

brainstate/nn/_inputs.py

@@ -1,608 +0,0 @@
-# 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, Optional, Sequence, Callable
-
-import brainunit as u
-import jax
-import numpy as np
-
-from brainstate import environ, init, random
-from brainstate._state import ShortTermState, State, maybe_state
-from brainstate.compile import while_loop
-from brainstate.typing import ArrayLike, Size, DTypeLike
-from ._dynamics import Dynamics, Prefetch
-from ._module import Module
-
-__all__ = [
-    'SpikeTime',
-    'PoissonSpike',
-    'PoissonEncoder',
-    'PoissonInput',
-    'poisson_input',
-]
-
-
-class SpikeTime(Dynamics):
-    """The input neuron group characterized by spikes emitting at given times.
-
-    >>> # Get 2 neurons, firing spikes at 10 ms and 20 ms.
-    >>> SpikeTime(2, times=[10, 20])
-    >>> # or
-    >>> # Get 2 neurons, the neuron 0 fires spikes at 10 ms and 20 ms.
-    >>> SpikeTime(2, times=[10, 20], indices=[0, 0])
-    >>> # or
-    >>> # Get 2 neurons, neuron 0 fires at 10 ms and 30 ms, neuron 1 fires at 20 ms.
-    >>> SpikeTime(2, times=[10, 20, 30], indices=[0, 1, 0])
-    >>> # or
-    >>> # Get 2 neurons; at 10 ms, neuron 0 fires; at 20 ms, neuron 0 and 1 fire;
-    >>> # at 30 ms, neuron 1 fires.
-    >>> SpikeTime(2, times=[10, 20, 20, 30], indices=[0, 0, 1, 1])
-
-    Parameters
-    ----------
-    in_size : int, tuple, list
-        The neuron group geometry.
-    indices : list, tuple, ArrayType
-        The neuron indices at each time point to emit spikes.
-    times : list, tuple, ArrayType
-        The time points which generate the spikes.
-    name : str, optional
-        The name of the dynamic system.
-    """
-
-    def __init__(
-        self,
-        in_size: Size,
-        indices: Union[Sequence, ArrayLike],
-        times: Union[Sequence, ArrayLike],
-        spk_type: DTypeLike = bool,
-        name: Optional[str] = None,
-        need_sort: bool = True,
-    ):
-        super().__init__(in_size=in_size, name=name)
-
-        # parameters
-        if len(indices) != len(times):
-            raise ValueError(f'The length of "indices" and "times" must be the same. '
-                             f'However, we got {len(indices)} != {len(times)}.')
-        self.num_times = len(times)
-        self.spk_type = spk_type
-
-        # data about times and indices
-        self.times = u.math.asarray(times)
-        self.indices = u.math.asarray(indices, dtype=environ.ditype())
-        if need_sort:
-            sort_idx = u.math.argsort(self.times)
-            self.indices = self.indices[sort_idx]
-            self.times = self.times[sort_idx]
-
-    def init_state(self, *args, **kwargs):
-        self.i = ShortTermState(-1)
-
-    def reset_state(self, batch_size=None, **kwargs):
-        self.i.value = -1
-
-    def update(self):
-        t = environ.get('t')
-
-        def _cond_fun(spikes):
-            i = self.i.value
-            return u.math.logical_and(i < self.num_times, t >= self.times[i])
-
-        def _body_fun(spikes):
-            i = self.i.value
-            spikes = spikes.at[..., self.indices[i]].set(True)
-            self.i.value += 1
-            return spikes
-
-        spike = u.math.zeros(self.varshape, dtype=self.spk_type)
-        spike = while_loop(_cond_fun, _body_fun, spike)
-        return spike
-
-
-class PoissonSpike(Dynamics):
-    """
-    Poisson Neuron Group.
-    """
-
-    def __init__(
-        self,
-        in_size: Size,
-        freqs: Union[ArrayLike, Callable],
-        spk_type: DTypeLike = bool,
-        name: Optional[str] = None,
-    ):
-        super().__init__(in_size=in_size, name=name)
-
-        self.spk_type = spk_type
-
-        # parameters
-        self.freqs = init.param(freqs, self.varshape, allow_none=False)
-
-    def update(self):
-        spikes = random.rand(*self.varshape) <= (self.freqs * environ.get_dt())
-        spikes = u.math.asarray(spikes, dtype=self.spk_type)
-        return spikes
-
-
-class PoissonEncoder(Dynamics):
-    r"""Poisson spike encoder for converting firing rates to spike trains.
-
-    This class implements a Poisson process to generate spikes based on provided
-    firing rates. Unlike the PoissonSpike class, this encoder accepts firing rates
-    as input during the update step rather than having them fixed at initialization.
-
-    The spike generation follows a Poisson process where the probability of a spike
-    in each time step is proportional to the firing rate and the simulation time step:
-
-    $$
-    P(\text{spike}) = \text{rate} \cdot \text{dt}
-    $$
-
-    For each neuron and time step, the encoder draws a random number from a uniform
-    distribution [0,1] and generates a spike if the number is less than or equal to
-    the spiking probability.
-
-    Parameters
-    ----------
-    in_size : Size
-        Size of the input to the encoder, defining the shape of the output spike train.
-    spk_type : DTypeLike, default=bool
-        Data type for the generated spikes. Typically boolean for binary spikes.
-    name : str, optional
-        Name of the encoder module.
-
-    Examples
-    --------
-    >>> import brainstate as bs
-    >>> import brainunit as u
-    >>> import numpy as np
-    >>>
-    >>> # Create a Poisson encoder for 10 neurons
-    >>> encoder = bs.nn.PoissonEncoder(10)
-    >>>
-    >>> # Generate spikes with varying firing rates
-    >>> rates = np.array([10, 20, 30, 40, 50, 60, 70, 80, 90, 100]) * u.Hz
-    >>> spikes = encoder.update(rates)
-    >>>
-    >>> # Use in a more complex processing pipeline
-    >>> # First, generate rate-coded output from an analog signal
-    >>> analog_values = np.random.rand(10) * 100  # values between 0 and 100
-    >>> firing_rates = analog_values * u.Hz  # convert to firing rates
-    >>> spike_train = encoder.update(firing_rates)
-    >>>
-    >>> # Feed the spikes into a spiking neural network
-    >>> neuron_layer = bs.nn.LIF(10)
-    >>> neuron_layer.init_state(batch_size=1)
-    >>> output_spikes = neuron_layer.update(spike_train)
-
-    Notes
-    -----
-    - This encoder is particularly useful for rate-to-spike conversion in neuromorphic
-      computing applications and sensory encoding tasks.
-    - The statistical properties of the generated spike trains follow a Poisson process,
-      where the inter-spike intervals are exponentially distributed.
-    - For small time steps (dt), the number of spikes in a time window T approximately
-      follows a Poisson distribution with parameter λ = rate * T.
-    - Unlike PoissonSpike which has fixed rates, this encoder allows dynamic rate changes
-      with every update call, making it suitable for encoding time-varying signals.
-    - The independence of spike generation between time steps results in renewal process
-      statistics without memory of previous spiking history.
-    """
-
-    def __init__(
-        self,
-        in_size: Size,
-        spk_type: DTypeLike = bool,
-        name: Optional[str] = None,
-    ):
-        super().__init__(in_size=in_size, name=name)
-        self.spk_type = spk_type
-
-    def update(self, freqs: ArrayLike):
-        spikes = random.rand(*self.varshape) <= (freqs * environ.get_dt())
-        spikes = u.math.asarray(spikes, dtype=self.spk_type)
-        return spikes
-
-
-class PoissonInput(Module):
-    r"""Poisson Input to the given state variable.
-
-    This class provides a way to add independent Poisson-distributed spiking input
-    to a target state variable. For large numbers of inputs, this implementation is
-    computationally more efficient than creating separate Poisson spike generators.
-
-    The synaptic events are generated randomly during simulation runtime and are not
-    preloaded or stored in memory, which improves memory efficiency for large-scale
-    simulations. All inputs target the same variable with the same frequency and
-    synaptic weight.
-
-    The Poisson process generates spikes with probability based on the frequency and
-    simulation time step:
-
-    $$
-    P(\text{spike}) = \text{freq} \cdot \text{dt}
-    $$
-
-    For computational efficiency, two different methods are used for spike generation:
-
-    1. For large numbers of inputs, a normal approximation:
-       $$
-       \text{inputs} \sim \mathcal{N}(\mu, \sigma^2)
-       $$
-       where $\mu = \text{num\_input} \cdot p$ and $\sigma^2 = \text{num\_input} \cdot p \cdot (1-p)$
-
-    2. For smaller numbers, a direct binomial sampling:
-       $$
-       \text{inputs} \sim \text{Binomial}(\text{num\_input}, p)
-       $$
-
-    where $p = \text{freq} \cdot \text{dt}$ in both cases.
-
-    Parameters
-    ----------
-    target : Prefetch
-        The variable that is targeted by this input. Should be an instance of
-        :py:class:`brainstate.State` that's prefetched via the target mechanism.
-    indices : Union[np.ndarray, jax.Array]
-        Indices of the target to receive input. If None, input is applied to the entire target.
-    num_input : int
-        The number of independent Poisson input sources.
-    freq : Union[int, float]
-        The firing frequency of each input source in Hz.
-    weight :  ndarray, float, or brainunit.Quantity
-        The synaptic weight of each input spike.
-    name : Optional[str], optional
-        The name of this module.
-
-    Examples
-    --------
-    >>> import brainstate as bs
-    >>> import brainunit as u
-    >>> import numpy as np
-    >>>
-    >>> # Create a neuron group with membrane potential
-    >>> neuron = bs.nn.LIF(100)
-    >>> neuron.init_state(batch_size=1)
-    >>>
-    >>> # Add Poisson input to all neurons
-    >>> poisson_in = bs.nn.PoissonInput(
-    ...     target=neuron.V,
-    ...     indices=None,
-    ...     num_input=200,
-    ...     freq=50 * u.Hz,
-    ...     weight=0.1 * u.mV
-    ... )
-    >>>
-    >>> # Add Poisson input only to specific neurons
-    >>> indices = np.array([0, 10, 20, 30])
-    >>> specific_input = bs.nn.PoissonInput(
-    ...     target=neuron.V,
-    ...     indices=indices,
-    ...     num_input=50,
-    ...     freq=100 * u.Hz,
-    ...     weight=0.2 * u.mV
-    ... )
-    >>>
-    >>> # Run simulation with the inputs
-    >>> for t in range(100):
-    ...     poisson_in.update()
-    ...     specific_input.update()
-    ...     neuron.update()
-
-    Notes
-    -----
-    - The Poisson inputs are statistically independent between update steps and across
-      target neurons.
-    - This implementation is particularly efficient for large numbers of inputs or targets.
-    - For very sparse connectivity patterns, consider using individual PoissonSpike neurons
-      with specific connectivity patterns instead.
-    - The update method internally calls the poisson_input function which handles the
-      spike generation and target state updates.
-    """
-
-    def __init__(
-        self,
-        target: Prefetch,
-        indices: Union[np.ndarray, jax.Array],
-        num_input: int,
-        freq: u.Quantity[u.Hz],
-        weight: Union[jax.typing.ArrayLike, u.Quantity],
-        name: Optional[str] = None,
-    ):
-        super().__init__(name=name)
-
-        self.target = target
-        self.indices = indices
-        self.num_input = num_input
-        self.freq = freq
-        self.weight = weight
-
-    def update(self):
-        target_state = getattr(self.target.module, self.target.item)
-
-        # generate Poisson input
-        poisson_input(
-            self.freq,
-            self.num_input,
-            self.weight,
-            target_state,
-            self.indices,
-        )
-
-
-def poisson_input(
-    freq: u.Quantity[u.Hz],
-    num_input: int,
-    weight: Union[jax.typing.ArrayLike, u.Quantity],
-    target: State,
-    indices: Optional[Union[np.ndarray, jax.Array]] = None,
-    refractory: Optional[Union[jax.Array]] = None,
-):
-    r"""Generates Poisson-distributed input spikes to a target state variable.
-
-    This function simulates Poisson input to a given state, updating the target
-    variable with generated spikes based on the specified frequency, number of inputs,
-    and synaptic weight. The input can be applied to specific indices of the target
-    or to the entire target if indices are not provided.
-
-    The function uses two different methods to generate the Poisson-distributed input:
-    1. For large numbers of inputs (a > 5 and b > 5), a normal approximation is used
-    2. For smaller numbers, a direct binomial sampling approach is used
-
-    Mathematical model for Poisson input:
-    $$
-    P(\text{spike}) = \text{freq} \cdot \text{dt}
-    $$
-
-    For the normal approximation (when a > 5 and b > 5):
-    $$
-    \text{inputs} \sim \mathcal{N}(a, b \cdot p)
-    $$
-    where:
-    $$
-    a = \text{num\_input} \cdot p
-    $$
-    $$
-    b = \text{num\_input} \cdot (1 - p)
-    $$
-    $$
-    p = \text{freq} \cdot \text{dt}
-    $$
-
-    For direct binomial sampling (when a ≤ 5 or b ≤ 5):
-    $$
-    \text{inputs} \sim \text{Binomial}(\text{num\_input}, p)
-    $$
-
-    Parameters
-    ----------
-    freq : u.Quantity[u.Hz]
-        The frequency of the Poisson input in Hertz.
-    num_input : int
-        The number of input channels or neurons generating the Poisson spikes.
-    weight : u.Quantity
-        The synaptic weight applied to each spike.
-    target : State
-        The target state variable to which the Poisson input is applied.
-    indices : Optional[Union[np.ndarray, jax.Array]], optional
-        Specific indices of the target to apply the input. If None, the input is applied
-        to the entire target.
-    refractory : Optional[Union[jax.Array]], optional
-        A boolean array indicating which parts of the target are in a refractory state
-        and should not be updated. Should be the same length as the target.
-
-    Examples
-    --------
-    >>> import brainstate as bs
-    >>> import brainunit as u
-    >>> import numpy as np
-    >>>
-    >>> # Create a membrane potential state
-    >>> V = bs.HiddenState(np.zeros(100) * u.mV)
-    >>>
-    >>> # Add Poisson input to all neurons at 50 Hz
-    >>> bs.nn.poisson_input(
-    ...     freq=50 * u.Hz,
-    ...     num_input=200,
-    ...     weight=0.1 * u.mV,
-    ...     target=V
-    ... )
-    >>>
-    >>> # Apply Poisson input only to a subset of neurons
-    >>> indices = np.array([0, 10, 20, 30])
-    >>> bs.nn.poisson_input(
-    ...     freq=100 * u.Hz,
-    ...     num_input=50,
-    ...     weight=0.2 * u.mV,
-    ...     target=V,
-    ...     indices=indices
-    ... )
-    >>>
-    >>> # Apply input with refractory mask
-    >>> refractory = np.zeros(100, dtype=bool)
-    >>> refractory[40:60] = True  # neurons 40-59 are in refractory period
-    >>> bs.nn.poisson_input(
-    ...     freq=75 * u.Hz,
-    ...     num_input=100,
-    ...     weight=0.15 * u.mV,
-    ...     target=V,
-    ...     refractory=refractory
-    ... )
-
-    Notes
-    -----
-    - The function automatically switches between normal approximation and binomial
-      sampling based on the input parameters to optimize computation efficiency.
-    - For large numbers of inputs, the normal approximation provides significant
-      performance improvements.
-    - The weight parameter is applied uniformly to all generated spikes.
-    - When refractory is provided, the corresponding target elements are not updated.
-    """
-    freq = maybe_state(freq)
-    weight = maybe_state(weight)
-
-    assert isinstance(target, State), 'The target must be a State.'
-    p = freq * environ.get_dt()
-    p = p.to_decimal() if isinstance(p, u.Quantity) else p
-    a = num_input * p
-    b = num_input * (1 - p)
-    tar_val = target.value
-    cond = u.math.logical_and(a > 5, b > 5)
-
-    if indices is None:
-        # generate Poisson input
-        branch1 = jax.tree.map(
-            lambda tar: random.normal(
-                a,
-                b * p,
-                tar.shape,
-                dtype=tar.dtype
-            ),
-            tar_val,
-            is_leaf=u.math.is_quantity
-        )
-        branch2 = jax.tree.map(
-            lambda tar: random.binomial(
-                num_input,
-                p,
-                tar.shape,
-                check_valid=False,
-                dtype=tar.dtype
-            ),
-            tar_val,
-            is_leaf=u.math.is_quantity,
-        )
-
-        inp = jax.tree.map(
-            lambda b1, b2: u.math.where(cond, b1, b2),
-            branch1,
-            branch2,
-            is_leaf=u.math.is_quantity,
-        )
-
-        # inp = jax.lax.cond(
-        #     cond,
-        #     lambda rand_key: jax.tree.map(
-        #         lambda tar: random.normal(
-        #             a,
-        #             b * p,
-        #             tar.shape,
-        #             key=rand_key,
-        #             dtype=tar.dtype
-        #         ),
-        #         tar_val,
-        #         is_leaf=u.math.is_quantity
-        #     ),
-        #     lambda rand_key: jax.tree.map(
-        #         lambda tar: random.binomial(
-        #             num_input,
-        #             p,
-        #             tar.shape,
-        #             key=rand_key,
-        #             check_valid=False,
-        #             dtype=tar.dtype
-        #         ),
-        #         tar_val,
-        #         is_leaf=u.math.is_quantity,
-        #     ),
-        #     random.split_key()
-        # )
-
-        # update target variable
-        data = jax.tree.map(
-            lambda tar, x: tar + x * weight,
-            target.value,
-            inp,
-            is_leaf=u.math.is_quantity
-        )
-
-    else:
-        # generate Poisson input
-        branch1 = jax.tree.map(
-            lambda tar: random.normal(
-                a,
-                b * p,
-                tar[indices].shape,
-                dtype=tar.dtype
-            ),
-            tar_val,
-            is_leaf=u.math.is_quantity
-        )
-        branch2 = jax.tree.map(
-            lambda tar: random.binomial(
-                num_input,
-                p,
-                tar[indices].shape,
-                check_valid=False,
-                dtype=tar.dtype
-            ),
-            tar_val,
-            is_leaf=u.math.is_quantity
-        )
-
-        inp = jax.tree.map(
-            lambda b1, b2: u.math.where(cond, b1, b2),
-            branch1,
-            branch2,
-            is_leaf=u.math.is_quantity,
-        )
-
-        # inp = jax.lax.cond(
-        #     cond,
-        #     lambda rand_key: jax.tree.map(
-        #         lambda tar: random.normal(
-        #             a,
-        #             b * p,
-        #             tar[indices].shape,
-        #             key=rand_key,
-        #             dtype=tar.dtype
-        #         ),
-        #         tar_val,
-        #         is_leaf=u.math.is_quantity
-        #     ),
-        #     lambda rand_key: jax.tree.map(
-        #         lambda tar: random.binomial(
-        #             num_input,
-        #             p,
-        #             tar[indices].shape,
-        #             key=rand_key,
-        #             check_valid=False,
-        #             dtype=tar.dtype
-        #         ),
-        #         tar_val,
-        #         is_leaf=u.math.is_quantity
-        #     ),
-        #     random.split_key()
-        # )
-
-        # update target variable
-        data = jax.tree.map(
-            lambda x, tar: tar.at[indices].add(x * weight),
-            inp,
-            tar_val,
-            is_leaf=u.math.is_quantity
-        )
-
-    if refractory is not None:
-        target.value = jax.tree.map(
-            lambda x, tar: u.math.where(refractory, tar, x),
-            data,
-            tar_val,
-            is_leaf=u.math.is_quantity
-        )
-    else:
-        target.value = data

brainstate/nn/_ltp.py

@@ -1,28 +0,0 @@
-# Copyright 2025 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.
-# ==============================================================================
-
-# -*- coding: utf-8 -*-
-
-
-from ._synapse import Synapse
-
-__all__ = [
-    'LongTermPlasticity',
-]
-
-
-class LongTermPlasticity(Synapse):
-    pass
-