brainstate 0.0.2.post20241009__py2.py3-none-any.whl → 0.1.0__py2.py3-none-any.whl

brainstate/nn/_dynamics/_dynamics_base.py

@@ -0,0 +1,631 @@
+# 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.
+# ==============================================================================
+
+# -*- coding: utf-8 -*-
+
+
+"""
+All the basic dynamics class for the ``brainstate``.
+
+For handling dynamical systems:
+
+- ``DynamicsGroup``: The class for a group of modules, which update ``Projection`` first,
+                   then ``Dynamics``, finally others.
+- ``Projection``: The class for the synaptic projection.
+- ``Dynamics``: The class for the dynamical system.
+
+For handling the delays:
+
+- ``Delay``: The class for all delays.
+- ``DelayAccess``: The class for the delay access.
+
+"""
+from __future__ import annotations
+
+from typing import Any, Dict, Callable, Hashable, Optional, Union, TypeVar, TYPE_CHECKING
+
+import brainunit as u
+import numpy as np
+
+from brainstate import environ
+from brainstate._state import State
+from brainstate.graph import Node
+from brainstate.mixin import ParamDescriber
+from brainstate.nn._module import Module
+from brainstate.typing import Size, ArrayLike
+from ._state_delay import StateWithDelay, Delay
+
+__all__ = [
+    'DynamicsGroup', 'Projection', 'Dynamics', 'Prefetch',
+]
+
+T = TypeVar('T')
+_max_order = 10
+
+
+class Projection(Module):
+    """
+    Base class to model synaptic projections.
+    """
+
+    __module__ = 'brainstate.nn'
+
+    def update(self, *args, **kwargs):
+        sub_nodes = tuple(self.nodes(allowed_hierarchy=(1, 1)).values())
+        if len(sub_nodes):
+            for node in sub_nodes:
+                node(*args, **kwargs)
+        else:
+            raise ValueError('Do not implement the update() function.')
+
+
+class Dynamics(Module):
+    """
+    Base class to model dynamics.
+
+    .. note::
+       In general, every instance of :py:class:`~.Module` implemented in
+       BrainPy only defines the evolving function at each time step :math:`t`.
+
+       If users want to define the logic of running models across multiple steps,
+       we recommend users to use :py:func:`~.for_loop`, :py:class:`~.LoopOverTime`,
+       :py:class:`~.DSRunner`, or :py:class:`~.DSTrainer`.
+
+       To be compatible with previous APIs, :py:class:`~.Module` inherits
+       from the :py:class:`~.DelayRegister`. It's worthy to note that the methods of
+       :py:class:`~.DelayRegister` will be removed in the future, including:
+
+       - ``.register_delay()``
+       - ``.get_delay_data()``
+       - ``.update_local_delays()``
+       - ``.reset_local_delays()``
+
+    There are several essential attributes:
+
+    - ``size``: the geometry of the neuron group. For example, `(10, )` denotes a line of
+      neurons, `(10, 10)` denotes a neuron group aligned in a 2D space, `(10, 15, 4)` denotes
+      a 3-dimensional neuron group.
+    - ``num``: the flattened number of neurons in the group. For example, `size=(10, )` => \
+      `num=10`, `size=(10, 10)` => `num=100`, `size=(10, 15, 4)` => `num=600`.
+
+    Args:
+      in_size: The neuron group geometry.
+      name: The name of the dynamic system.
+    """
+
+    __module__ = 'brainstate.nn'
+
+    # before updates
+    _before_updates: Optional[Dict[Hashable, Callable]]
+
+    # after updates
+    _after_updates: Optional[Dict[Hashable, Callable]]
+
+    # current inputs
+    _current_inputs: Optional[Dict[str, ArrayLike | Callable]]
+
+    # delta inputs
+    _delta_inputs: Optional[Dict[str, ArrayLike | Callable]]
+
+    def __init__(
+        self,
+        in_size: Size,
+        name: Optional[str] = None,
+    ):
+        # initialize
+        super().__init__(name=name)
+
+        # geometry size of neuron population
+        if isinstance(in_size, (list, tuple)):
+            if len(in_size) <= 0:
+                raise ValueError(f'"in_size" must be int, or a tuple/list of int. But we got {type(in_size)}')
+            if not isinstance(in_size[0], (int, np.integer)):
+                raise ValueError(f'"in_size" must be int, or a tuple/list of int. But we got {type(in_size)}')
+            in_size = tuple(in_size)
+        elif isinstance(in_size, (int, np.integer)):
+            in_size = (in_size,)
+        else:
+            raise ValueError(f'"in_size" must be int, or a tuple/list of int. But we got {type(in_size)}')
+        self.in_size = in_size
+
+        # current inputs
+        self._current_inputs = None
+
+        # delta inputs
+        self._delta_inputs = None
+
+        # before updates
+        self._before_updates = None
+
+        # after updates
+        self._after_updates = None
+
+        # in-/out- size of neuron population
+        self.out_size = self.in_size
+
+    @property
+    def varshape(self):
+        """The shape of variables in the neuron group."""
+        return self.in_size
+
+    @property
+    def current_inputs(self):
+        """
+        The current inputs of the model. It should be a dictionary of the input data.
+        """
+        return self._current_inputs
+
+    @property
+    def delta_inputs(self):
+        """
+        The delta inputs of the model. It should be a dictionary of the input data.
+        """
+        return self._delta_inputs
+
+    def add_current_input(
+        self,
+        key: str,
+        inp: Union[Callable, ArrayLike],
+        label: Optional[str] = None
+    ):
+        """
+        Add a current input function.
+
+        Args:
+          key: str. The dict key.
+          inp: Callable, ArrayLike. The currents or the function to generate currents.
+          label: str. The input label.
+        """
+        key = _input_label_repr(key, label)
+        if self._current_inputs is None:
+            self._current_inputs = dict()
+        if key in self._current_inputs:
+            if id(self._current_inputs[key]) != id(inp):
+                raise ValueError(f'Key "{key}" has been defined and used in the current inputs of {self}.')
+        self._current_inputs[key] = inp
+
+    def add_delta_input(
+        self,
+        key: str,
+        inp: Union[Callable, ArrayLike],
+        label: Optional[str] = None
+    ):
+        """
+        Add a delta input function.
+
+        Args:
+          key: str. The dict key.
+          inp: Callable, ArrayLike. The currents or the function to generate currents.
+          label: str. The input label.
+        """
+        key = _input_label_repr(key, label)
+        if self._delta_inputs is None:
+            self._delta_inputs = dict()
+        if key in self._delta_inputs:
+            if id(self._delta_inputs[key]) != id(inp):
+                raise ValueError(f'Key "{key}" has been defined and used.')
+        self._delta_inputs[key] = inp
+
+    def get_input(self, key: str):
+        """Get the input function.
+
+        Args:
+          key: str. The key.
+
+        Returns:
+          The input function which generates currents.
+        """
+        if self._current_inputs is not None and key in self._current_inputs:
+            return self._current_inputs[key]
+        elif self._delta_inputs is not None and key in self._delta_inputs:
+            return self._delta_inputs[key]
+        else:
+            raise ValueError(f'Input key {key} is not in current/delta inputs of the module {self}.')
+
+    def sum_current_inputs(
+        self,
+        init: Any,
+        *args,
+        label: Optional[str] = None,
+        **kwargs
+    ):
+        """
+        Summarize all current inputs by the defined input functions ``.current_inputs``.
+
+        Args:
+          init: The initial input data.
+          *args: The arguments for input functions.
+          **kwargs: The arguments for input functions.
+          label: str. The input label.
+
+        Returns:
+          The total currents.
+        """
+        if self._current_inputs is None:
+            return init
+        if label is None:
+            # no label
+            for key in tuple(self._current_inputs.keys()):
+                out = self._current_inputs[key]
+                init = init + (out(*args, **kwargs) if callable(out) else out)
+                if not callable(out):
+                    self._current_inputs.pop(key)
+        else:
+            # has label
+            label_repr = _input_label_start(label)
+            for key in tuple(self._current_inputs.keys()):
+                if key.startswith(label_repr):
+                    out = self._current_inputs[key]
+                    init = init + (out(*args, **kwargs) if callable(out) else out)
+                    if not callable(out):
+                        self._current_inputs.pop(key)
+        return init
+
+    def sum_delta_inputs(
+        self,
+        init: Any,
+        *args,
+        label: Optional[str] = None,
+        **kwargs
+    ):
+        """
+        Summarize all delta inputs by the defined input functions ``.delta_inputs``.
+
+        Args:
+          init: The initial input data.
+          *args: The arguments for input functions.
+          **kwargs: The arguments for input functions.
+          label: str. The input label.
+
+        Returns:
+          The total currents.
+        """
+        if self._delta_inputs is None:
+            return init
+        if label is None:
+            # no label
+            for key in tuple(self._delta_inputs.keys()):
+                out = self._delta_inputs[key]
+                init = init + (out(*args, **kwargs) if callable(out) else out)
+                if not callable(out):
+                    self._delta_inputs.pop(key)
+        else:
+            # has label
+            label_repr = _input_label_start(label)
+            for key in tuple(self._delta_inputs.keys()):
+                if key.startswith(label_repr):
+                    out = self._delta_inputs[key]
+                    init = init + (out(*args, **kwargs) if callable(out) else out)
+                    if not callable(out):
+                        self._delta_inputs.pop(key)
+        return init
+
+    @property
+    def before_updates(self):
+        """
+        The before updates of the model. It should be a dictionary of the updating functions.
+        """
+        return self._before_updates
+
+    @property
+    def after_updates(self):
+        """
+        The after updates of the model. It should be a dictionary of the updating functions.
+        """
+        return self._after_updates
+
+    def _add_before_update(self, key: Any, fun: Callable):
+        """
+        Add the before update into this node.
+        """
+        if self._before_updates is None:
+            self._before_updates = dict()
+        if key in self.before_updates:
+            raise KeyError(f'{key} has been registered in before_updates of {self}')
+        self.before_updates[key] = fun
+
+    def _add_after_update(self, key: Any, fun: Callable):
+        """Add the after update into this node"""
+        if self._after_updates is None:
+            self._after_updates = dict()
+        if key in self.after_updates:
+            raise KeyError(f'{key} has been registered in after_updates of {self}')
+        self.after_updates[key] = fun
+
+    def _get_before_update(self, key: Any):
+        """Get the before update of this node by the given ``key``."""
+        if self._before_updates is None:
+            raise KeyError(f'{key} is not registered in before_updates of {self}')
+        if key not in self.before_updates:
+            raise KeyError(f'{key} is not registered in before_updates of {self}')
+        return self.before_updates.get(key)
+
+    def _get_after_update(self, key: Any):
+        """Get the after update of this node by the given ``key``."""
+        if self._after_updates is None:
+            raise KeyError(f'{key} is not registered in after_updates of {self}')
+        if key not in self.after_updates:
+            raise KeyError(f'{key} is not registered in after_updates of {self}')
+        return self.after_updates.get(key)
+
+    def _has_before_update(self, key: Any):
+        """Whether this node has the before update of the given ``key``."""
+        if self._before_updates is None:
+            return False
+        return key in self.before_updates
+
+    def _has_after_update(self, key: Any):
+        """Whether this node has the after update of the given ``key``."""
+        if self._after_updates is None:
+            return False
+        return key in self.after_updates
+
+    def __call__(self, *args, **kwargs):
+        """
+        The shortcut to call ``update`` methods.
+        """
+
+        # ``before_updates``
+        if self.before_updates is not None:
+            for model in self.before_updates.values():
+                if hasattr(model, '_receive_update_input'):
+                    model(*args, **kwargs)
+                else:
+                    model()
+
+        # update the model self
+        ret = self.update(*args, **kwargs)
+
+        # ``after_updates``
+        if self.after_updates is not None:
+            for model in self.after_updates.values():
+                if hasattr(model, '_not_receive_update_output'):
+                    model()
+                else:
+                    model(ret)
+        return ret
+
+    def prefetch(self, item: str) -> 'Prefetch':
+        return Prefetch(self, item)
+
+    def align_pre(
+        self, dyn: Union[ParamDescriber[T], T]
+    ) -> T:
+        """
+        Align the dynamics before the interaction.
+        """
+        if isinstance(dyn, Dynamics):
+            self._add_after_update(dyn.name, dyn)
+            return dyn
+        elif isinstance(dyn, ParamDescriber):
+            if not isinstance(dyn.cls, Dynamics):
+                raise TypeError(f'The input {dyn} should be an instance of {Dynamics}.')
+            if not self._has_after_update(dyn.identifier):
+                self._add_after_update(dyn.identifier, dyn())
+            return self._get_after_update(dyn.identifier)
+        else:
+            raise TypeError(f'The input {dyn} should be an instance of {Dynamics} or a delayed initializer.')
+
+    def __leaf_fn__(self, name, value):
+        if name in ['_in_size', '_out_size', '_name', '_mode',
+                    '_before_updates', '_after_updates', '_current_inputs', '_delta_inputs']:
+            return (name, value) if value is None else (name[1:], value)  # skip the first `_`
+        return name, value
+
+
+class Prefetch(Node):
+    """
+    Prefetch a variable of the given module.
+    """
+
+    def __init__(self, module: Module, item: str):
+        super().__init__()
+        self.module = module
+        self.item = item
+
+    @property
+    def delay(self):
+        return PrefetchDelay(self.module, self.item)
+
+    def __call__(self, *args, **kwargs):
+        item = _get_prefetch_item(self)
+        return item.value if isinstance(item, State) else item
+
+
+class PrefetchDelay(Node):
+    def __init__(self, module: Dynamics, item: str):
+        self.module = module
+        self.item = item
+
+    def at(self, time: ArrayLike):
+        return PrefetchDelayAt(self.module, self.item, time)
+
+
+class PrefetchDelayAt(Node):
+    """
+    Prefetch the delay of a variable in the given module at a specific time.
+
+    Args:
+      module: The module that has the item with the name specified by ``item`` argument.
+      item: The item that has the delay.
+      time: The time to retrieve the delay.
+    """
+
+    def __init__(self, module: Dynamics, item: str, time: ArrayLike):
+        super().__init__()
+        assert isinstance(module, Dynamics), ''
+        self.module = module
+        self.item = item
+        self.time = time
+        self.step = u.math.asarray(time / environ.get_dt(), dtype=environ.ditype())
+
+        # register the delay
+        key = _get_delay_key(item)
+        if not module._has_after_update(key):
+            module._add_after_update(key, not_receive_update_output(StateWithDelay(module, item)))
+        self.state_delay: StateWithDelay = module._get_after_update(key)
+        self.state_delay.register_delay(time)
+
+    def __call__(self, *args, **kwargs):
+        # return self.state_delay.retrieve_at_time(self.time)
+        return self.state_delay.retrieve_at_step(self.step)
+
+
+def _get_delay_key(item) -> str:
+    return f'{item}-delay'
+
+
+def _get_prefetch_item(target: Union[Prefetch, PrefetchDelayAt]) -> Any:
+    item = getattr(target.module, target.item, None)
+    if item is None:
+        raise AttributeError(f'The target {target.module} should have an `{target.item}` attribute.')
+    return item
+
+
+def _get_prefetch_item_delay(target: Union[Prefetch, PrefetchDelay, PrefetchDelayAt]) -> Delay:
+    assert isinstance(target.module, Dynamics), (f'The target module should be an instance '
+                                                 f'of Dynamics. But got {target.module}.')
+    delay = target.module._get_after_update(_get_delay_key(target.item))
+    if not isinstance(delay, StateWithDelay):
+        raise TypeError(f'The prefetch target should be a {StateWithDelay.__name__} when accessing '
+                        f'its delay. But got {delay}.')
+    return delay
+
+
+def maybe_init_prefetch(target, *args, **kwargs):
+    if isinstance(target, Prefetch):
+        _get_prefetch_item(target)
+
+    elif isinstance(target, PrefetchDelay):
+        _get_prefetch_item_delay(target)
+
+    elif isinstance(target, PrefetchDelayAt):
+        delay = _get_prefetch_item_delay(target)
+        delay.register_delay(target.time)
+
+
+class DynamicsGroup(Module):
+    """
+    A group of :py:class:`~.Module` in which the updating order does not matter.
+
+    Args:
+      children_as_tuple: The children objects.
+      children_as_dict: The children objects.
+    """
+
+    __module__ = 'brainstate.nn'
+
+    if not TYPE_CHECKING:
+        def __init__(self, *children_as_tuple, **children_as_dict):
+            super().__init__()
+            self.layers_tuple = tuple(children_as_tuple)
+            self.layers_dict = dict(children_as_dict)
+
+    def update(self, *args, **kwargs):
+        """
+        Update function of a network.
+
+        In this update function, the update functions in children systems are iteratively called.
+        """
+        projs, dyns, others = self.nodes(allowed_hierarchy=(1, 1)).split(Projection, Dynamics)
+
+        # update nodes of projections
+        for node in projs.values():
+            node()
+
+        # update nodes of dynamics
+        for node in dyns.values():
+            node()
+
+        # update nodes with other types, including delays, ...
+        for node in others.values():
+            node()
+
+
+def receive_update_output(cls: object):
+    """
+    The decorator to mark the object (as the after updates) to receive the output of the update function.
+
+    That is, the `aft_update` will receive the return of the update function::
+
+      ret = model.update(*args, **kwargs)
+      for fun in model.aft_updates:
+        fun(ret)
+
+    """
+    # assert isinstance(cls, Module), 'The input class should be instance of Module.'
+    if hasattr(cls, '_not_receive_update_output'):
+        delattr(cls, '_not_receive_update_output')
+    return cls
+
+
+def not_receive_update_output(cls: T) -> T:
+    """
+    The decorator to mark the object (as the after updates) to not receive the output of the update function.
+
+    That is, the `aft_update` will not receive the return of the update function::
+
+      ret = model.update(*args, **kwargs)
+      for fun in model.aft_updates:
+        fun()
+
+    """
+    # assert isinstance(cls, Module), 'The input class should be instance of Module.'
+    cls._not_receive_update_output = True
+    return cls
+
+
+def receive_update_input(cls: object):
+    """
+    The decorator to mark the object (as the before updates) to receive the input of the update function.
+
+    That is, the `bef_update` will receive the input of the update function::
+
+
+      for fun in model.bef_updates:
+        fun(*args, **kwargs)
+      model.update(*args, **kwargs)
+
+    """
+    # assert isinstance(cls, Module), 'The input class should be instance of Module.'
+    cls._receive_update_input = True
+    return cls
+
+
+def not_receive_update_input(cls: object):
+    """
+    The decorator to mark the object (as the before updates) to not receive the input of the update function.
+
+    That is, the `bef_update` will not receive the input of the update function::
+
+        for fun in model.bef_updates:
+          fun()
+        model.update()
+
+    """
+    # assert isinstance(cls, Module), 'The input class should be instance of Module.'
+    if hasattr(cls, '_receive_update_input'):
+        delattr(cls, '_receive_update_input')
+    return cls
+
+
+def _input_label_start(label: str):
+    # unify the input label repr.
+    return f'{label} // '
+
+
+def _input_label_repr(name: str, label: Optional[str] = None):
+    # unify the input label repr.
+    return name if label is None else (_input_label_start(label) + str(name))

brainstate/nn/_dynamics/_dynamics_base_test.py

@@ -0,0 +1,79 @@
+# 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.
+# ==============================================================================
+
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+
+import brainstate as bst
+
+
+class TestModuleGroup(unittest.TestCase):
+    def test_initialization(self):
+        group = bst.nn.DynamicsGroup()
+        self.assertIsInstance(group, bst.nn.DynamicsGroup)
+
+
+class TestProjection(unittest.TestCase):
+    def test_initialization(self):
+        proj = bst.nn.Projection()
+        self.assertIsInstance(proj, bst.nn.Projection)
+
+    def test_update_not_implemented(self):
+        proj = bst.nn.Projection()
+        with self.assertRaises(ValueError):
+            proj.update()
+
+
+class TestDynamics(unittest.TestCase):
+    def test_initialization(self):
+        dyn = bst.nn.Dynamics(in_size=10)
+        self.assertIsInstance(dyn, bst.nn.Dynamics)
+        self.assertEqual(dyn.in_size, (10,))
+        self.assertEqual(dyn.out_size, (10,))
+
+    def test_size_validation(self):
+        with self.assertRaises(ValueError):
+            bst.nn.Dynamics(in_size=[])
+        with self.assertRaises(ValueError):
+            bst.nn.Dynamics(in_size="invalid")
+
+    def test_input_handling(self):
+        dyn = bst.nn.Dynamics(in_size=10)
+        dyn.add_current_input("test_current", lambda: np.random.rand(10))
+        dyn.add_delta_input("test_delta", lambda: np.random.rand(10))
+
+        self.assertIn("test_current", dyn.current_inputs)
+        self.assertIn("test_delta", dyn.delta_inputs)
+
+    def test_duplicate_input_key(self):
+        dyn = bst.nn.Dynamics(in_size=10)
+        dyn.add_current_input("test", lambda: np.random.rand(10))
+        with self.assertRaises(ValueError):
+            dyn.add_current_input("test", lambda: np.random.rand(10))
+
+    def test_varshape(self):
+        dyn = bst.nn.Dynamics(in_size=(2, 3))
+        self.assertEqual(dyn.varshape, (2, 3))
+        dyn = bst.nn.Dynamics(in_size=(2, 3))
+        self.assertEqual(dyn.varshape, (2, 3))
+
+
+if __name__ == '__main__':
+    unittest.main()