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

brainstate/nn/_projection/_align_post.py

@@ -1,546 +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 Optional, Union
-
-
-import brainunit as u
-from brainstate._module import (register_delay_of_target,
-                                Projection,
-                                Module,
-                                Dynamics,
-                                ReceiveInputProj,
-                                ExtendedUpdateWithBA)
-from brainstate._utils import set_module_as
-from brainstate.mixin import (Mode, JointTypes, DelayedInitializer, BindCondData, AlignPost, UpdateReturn)
-from ._utils import is_instance
-
-__all__ = [
-  'HalfProjAlignPostMg', 'FullProjAlignPostMg',
-  'HalfProjAlignPost', 'FullProjAlignPost',
-]
-
-
-def get_post_repr(out_label, syn, out):
-  return f'{out_label} // {syn.identifier} // {out.identifier}'
-
-
-def align_post_add_bef_update(
-    out_label: str,
-    syn_desc,
-    out_desc,
-    post: JointTypes[ReceiveInputProj, ExtendedUpdateWithBA],
-    proj_name: str
-):
-  # synapse and output initialization
-  _post_repr = get_post_repr(out_label, syn_desc, out_desc)
-  if not post.has_before_update(_post_repr):
-    syn_cls = syn_desc()
-    out_cls = out_desc()
-
-    # synapse and output initialization
-    post.add_input_fun(proj_name, out_cls, label=out_label)
-    post.add_before_update(_post_repr, _AlignPost(syn_cls, out_cls))
-  syn = post.get_before_update(_post_repr).syn
-  out = post.get_before_update(_post_repr).out
-  return syn, out
-
-
-class _AlignPost(Module):
-  def __init__(
-      self,
-      syn: Module,
-      out: JointTypes[Dynamics, BindCondData]
-  ):
-    super().__init__()
-    self.syn = syn
-    self.out = out
-
-  def update(self, *args, **kwargs):
-    self.out.bind_cond(self.syn(*args, **kwargs))
-
-
-@set_module_as('brainstate.nn')
-class HalfProjAlignPostMg(Projection):
-  r"""
-  Defining the half part of synaptic projection with the align-post reduction and the automatic synapse merging.
-
-  The ``half-part`` means that the model only needs to provide half information needed for a projection,
-  including ``comm`` -> ``syn`` -> ``out`` -> ``post``. Therefore, the model's ``update`` function needs
-  the manual providing of the spiking input.
-
-  The ``align-post`` means that the synaptic variables have the same dimension as the post-synaptic neuron group.
-
-  The ``merging`` means that the same delay model is shared by all synapses, and the synapse model with same
-  parameters (such like time constants) will also share the same synaptic variables.
-
-  All align-post projection models prefer to use the event-driven computation mode. This means that the
-  ``comm`` model should be the event-driven model.
-
-  **Code Examples**
-
-  To define an E/I balanced network model.
-  
-  .. code-block:: python
-
-    import brainstate as bp
-    import brainstate.math as bm
-
-    class EINet(bp.DynSysGroup):
-      def __init__(self):
-        super().__init__()
-        self.N = bp.dyn.LifRef(4000, V_rest=-60., V_th=-50., V_reset=-60., tau=20., tau_ref=5.,
-                               V_initializer=bp.init.Normal(-55., 2.))
-        self.delay = bp.VarDelay(self.N.spike, entries={'I': None})
-        self.E = bp.dyn.HalfProjAlignPostMg(comm=bp.dnn.EventJitFPHomoLinear(3200, 4000, prob=0.02, weight=0.6),
-                                         syn=bp.dyn.Expon.desc(size=4000, tau=5.),
-                                         out=bp.dyn.COBA.desc(E=0.),
-                                         post=self.N)
-        self.I = bp.dyn.HalfProjAlignPostMg(comm=bp.dnn.EventJitFPHomoLinear(800, 4000, prob=0.02, weight=6.7),
-                                         syn=bp.dyn.Expon.desc(size=4000, tau=10.),
-                                         out=bp.dyn.COBA.desc(E=-80.),
-                                         post=self.N)
-
-      def update(self, input):
-        spk = self.delay.at('I')
-        self.E(spk[:3200])
-        self.I(spk[3200:])
-        self.delay(self.N(input))
-        return self.N.spike.value
-
-    model = EINet()
-    indices = bm.arange(1000)
-    spks = bm.for_loop(lambda i: model.step_run(i, 20.), indices)
-    bp.visualize.raster_plot(indices, spks, show=True)
-
-  Args:
-    comm: The synaptic communication.
-    syn: The synaptic dynamics.
-    out: The synaptic output.
-    post: The post-synaptic neuron group.
-    out_label: str. The prefix of the output function.
-    name: str. The projection name.
-    mode:  Mode. The computing mode.
-  """
-
-  _invisible_nodes = ['syn', 'out', 'post']
-
-  def __init__(
-      self,
-      comm: Module,
-      syn: DelayedInitializer[AlignPost],
-      out: DelayedInitializer[BindCondData],
-      post: JointTypes[ReceiveInputProj, ExtendedUpdateWithBA],
-      out_label: Optional[str] = None,
-      name: Optional[str] = None,
-      mode: Optional[Mode] = None,
-  ):
-    super().__init__(name=name, mode=mode)
-
-    # synaptic models
-    is_instance(syn, DelayedInitializer[AlignPost])
-    is_instance(out, DelayedInitializer[BindCondData])
-    is_instance(post, JointTypes[ReceiveInputProj, ExtendedUpdateWithBA])
-
-    # synapse and output initialization
-    syn, out = align_post_add_bef_update(out_label, syn_desc=syn, out_desc=out, post=post, proj_name=self.name)
-
-    # references
-    self.post = post
-    self.syn = syn
-    self.out = out
-    self.comm = comm
-
-  def update(self, x):
-    current = self.comm(x)
-    self.syn.align_post_input_add(current)  # synapse post current
-    return current
-
-
-@set_module_as('brainstate.nn')
-class FullProjAlignPostMg(Projection):
-  """Full-chain synaptic projection with the align-post reduction and the automatic synapse merging.
-
-  The ``full-chain`` means that the model needs to provide all information needed for a projection,
-  including ``pre`` -> ``delay`` -> ``comm`` -> ``syn`` -> ``out`` -> ``post``.
-
-  The ``align-post`` means that the synaptic variables have the same dimension as the post-synaptic neuron group.
-
-  The ``merging`` means that the same delay model is shared by all synapses, and the synapse model with same
-  parameters (such like time constants) will also share the same synaptic variables.
-
-  All align-post projection models prefer to use the event-driven computation mode. This means that the
-  ``comm`` model should be the event-driven model.
-
-  Moreover, it's worth noting that ``FullProjAlignPostMg`` has a different updating order with all align-pre
-  projection models. The updating order of align-post projections is ``spikes`` -> ``comm`` -> ``syn`` -> ``out``.
-  While, the updating order of all align-pre projection models is usually ``spikes`` -> ``syn`` -> ``comm`` -> ``out``.
-
-  **Code Examples**
-
-  To define an E/I balanced network model.
-
-  .. code-block:: python
-
-      import brainstate as bp
-      import brainstate.math as bm
-
-      class EINet(bp.DynSysGroup):
-        def __init__(self):
-          super().__init__()
-          ne, ni = 3200, 800
-          self.E = bp.dyn.LifRef(ne, V_rest=-60., V_th=-50., V_reset=-60., tau=20., tau_ref=5.,
-                                 V_initializer=bp.init.Normal(-55., 2.))
-          self.I = bp.dyn.LifRef(ni, V_rest=-60., V_th=-50., V_reset=-60., tau=20., tau_ref=5.,
-                                 V_initializer=bp.init.Normal(-55., 2.))
-          self.E2E = bp.dyn.FullProjAlignPostMg(pre=self.E,
-                                             delay=0.1,
-                                             comm=bp.dnn.EventJitFPHomoLinear(ne, ne, prob=0.02, weight=0.6),
-                                             syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                             out=bp.dyn.COBA.desc(E=0.),
-                                             post=self.E)
-          self.E2I = bp.dyn.FullProjAlignPostMg(pre=self.E,
-                                             delay=0.1,
-                                             comm=bp.dnn.EventJitFPHomoLinear(ne, ni, prob=0.02, weight=0.6),
-                                             syn=bp.dyn.Expon.desc(size=ni, tau=5.),
-                                             out=bp.dyn.COBA.desc(E=0.),
-                                             post=self.I)
-          self.I2E = bp.dyn.FullProjAlignPostMg(pre=self.I,
-                                             delay=0.1,
-                                             comm=bp.dnn.EventJitFPHomoLinear(ni, ne, prob=0.02, weight=6.7),
-                                             syn=bp.dyn.Expon.desc(size=ne, tau=10.),
-                                             out=bp.dyn.COBA.desc(E=-80.),
-                                             post=self.E)
-          self.I2I = bp.dyn.FullProjAlignPostMg(pre=self.I,
-                                             delay=0.1,
-                                             comm=bp.dnn.EventJitFPHomoLinear(ni, ni, prob=0.02, weight=6.7),
-                                             syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                             out=bp.dyn.COBA.desc(E=-80.),
-                                             post=self.I)
-
-        def update(self, inp):
-          self.E2E()
-          self.E2I()
-          self.I2E()
-          self.I2I()
-          self.E(inp)
-          self.I(inp)
-          return self.E.spike
-
-      model = EINet()
-      indices = bm.arange(1000)
-      spks = bm.for_loop(lambda i: model.step_run(i, 20.), indices)
-      bp.visualize.raster_plot(indices, spks, show=True)
-
-  Args:
-    pre: The pre-synaptic neuron group.
-    delay: The synaptic delay.
-    comm: The synaptic communication.
-    syn: The synaptic dynamics.
-    out: The synaptic output.
-    post: The post-synaptic neuron group.
-    name: str. The projection name.
-    mode:  Mode. The computing mode.
-  """
-
-  _invisible_nodes = ['syn', 'out', 'post', 'pre', 'delay']
-
-  def __init__(
-      self,
-      pre: JointTypes[ExtendedUpdateWithBA, UpdateReturn],
-      delay: Union[None, int, float],
-      comm: Module,
-      syn: DelayedInitializer[AlignPost],
-      out: DelayedInitializer[BindCondData],
-      post: JointTypes[ReceiveInputProj, ExtendedUpdateWithBA],
-      out_label: Optional[str] = None,
-      name: Optional[str] = None,
-      mode: Optional[Mode] = None,
-  ):
-    super().__init__(name=name, mode=mode)
-
-    # synaptic models
-    is_instance(pre, JointTypes[ExtendedUpdateWithBA, UpdateReturn])
-    is_instance(comm, Module)
-    is_instance(syn, DelayedInitializer[AlignPost])
-    is_instance(out, DelayedInitializer[BindCondData])
-    is_instance(post, JointTypes[ReceiveInputProj, ExtendedUpdateWithBA])
-    self.comm = comm
-
-    # delay initialization
-    if delay is not None:
-      if isinstance(delay, u.Quantity):
-        has_delay = delay.mantissa > 0.
-      else:
-        has_delay = delay > 0.
-      if has_delay:
-        delay_cls = register_delay_of_target(pre)
-        delay_cls.register_entry(self.name, delay)
-        self.delay = delay_cls
-        self.has_delay = True
-      else:
-        self.delay = None
-        self.has_delay = False
-    else:
-      self.delay = None
-      self.has_delay = False
-
-    # synapse and output initialization
-    syn, out = align_post_add_bef_update(out_label, syn_desc=syn, out_desc=out, post=post, proj_name=self.name)
-
-    # references
-    self.pre = pre
-    self.post = post
-    self.syn = syn
-    self.out = out
-
-  def update(self):
-    if self.has_delay:
-      x = self.delay.at(self.name)
-    else:
-      x = self.pre.update_return()
-    current = self.comm(x)
-    self.syn.align_post_input_add(current)  # synapse post current
-    return current
-
-
-@set_module_as('brainstate.nn')
-class HalfProjAlignPost(Projection):
-  """Defining the half-part of synaptic projection with the align-post reduction.
-
-  The ``half-part`` means that the model only needs to provide half information needed for a projection,
-  including ``comm`` -> ``syn`` -> ``out`` -> ``post``. Therefore, the model's ``update`` function needs
-  the manual providing of the spiking input.
-
-  The ``align-post`` means that the synaptic variables have the same dimension as the post-synaptic neuron group.
-
-  All align-post projection models prefer to use the event-driven computation mode. This means that the
-  ``comm`` model should be the event-driven model.
-
-  To simulate an E/I balanced network:
-
-  .. code-block::
-
-      class EINet(bp.DynSysGroup):
-        def __init__(self):
-          super().__init__()
-          self.N = bp.dyn.LifRef(4000, V_rest=-60., V_th=-50., V_reset=-60., tau=20., tau_ref=5.,
-                                 V_initializer=bp.init.Normal(-55., 2.))
-          self.delay = bp.VarDelay(self.N.spike, entries={'I': None})
-          self.E = bp.dyn.HalfProjAlignPost(comm=bp.dnn.EventJitFPHomoLinear(3200, 4000, prob=0.02, weight=0.6),
-                                         syn=bp.dyn.Expon(size=4000, tau=5.),
-                                         out=bp.dyn.COBA(E=0.),
-                                         post=self.N)
-          self.I = bp.dyn.HalfProjAlignPost(comm=bp.dnn.EventJitFPHomoLinear(800, 4000, prob=0.02, weight=6.7),
-                                         syn=bp.dyn.Expon(size=4000, tau=10.),
-                                         out=bp.dyn.COBA(E=-80.),
-                                         post=self.N)
-
-        def update(self, input):
-          spk = self.delay.at('I')
-          self.E(spk[:3200])
-          self.I(spk[3200:])
-          self.delay(self.N(input))
-          return self.N.spike.value
-
-      model = EINet()
-      indices = bm.arange(1000)
-      spks = bm.for_loop(lambda i: model.step_run(i, 20.), indices)
-      bp.visualize.raster_plot(indices, spks, show=True)
-
-
-  Args:
-    comm: The synaptic communication.
-    syn: The synaptic dynamics.
-    out: The synaptic output.
-    post: The post-synaptic neuron group.
-    name: str. The projection name.
-    mode:  Mode. The computing mode.
-  """
-
-  _invisible_nodes = ['out', 'post']
-
-  def __init__(
-      self,
-      comm: Module,
-      syn: AlignPost,
-      out: BindCondData,
-      post: ReceiveInputProj,
-      out_label: Optional[str] = None,
-      name: Optional[str] = None,
-      mode: Optional[Mode] = None,
-  ):
-    super().__init__(name=name, mode=mode)
-
-    # synaptic models
-    is_instance(comm, Module)
-    is_instance(syn, AlignPost)
-    is_instance(out, BindCondData)
-    is_instance(post, Module)
-    self.comm = comm
-    self.syn = syn
-
-    # synapse and output initialization
-    post.add_input_fun(self.name, out, label=out_label)
-
-    # reference
-    self.post = post
-    self.out = out
-
-  def update(self, x):
-    current = self.comm(x)
-    g = self.syn(current)
-    self.out.bind_cond(g)  # synapse post current
-    return current
-
-
-@set_module_as('brainstate.nn')
-class FullProjAlignPost(Projection):
-  """Full-chain synaptic projection with the align-post reduction.
-
-  The ``full-chain`` means that the model needs to provide all information needed for a projection,
-  including ``pre`` -> ``delay`` -> ``comm`` -> ``syn`` -> ``out`` -> ``post``.
-
-  The ``align-post`` means that the synaptic variables have the same dimension as the post-synaptic neuron group.
-
-  All align-post projection models prefer to use the event-driven computation mode. This means that the
-  ``comm`` model should be the event-driven model.
-
-  Moreover, it's worth noting that ``FullProjAlignPost`` has a different updating order with all align-pre
-  projection models. The updating order of align-post projections is ``spikes`` -> ``comm`` -> ``syn`` -> ``out``.
-  While, the updating order of all align-pre projection models is usually ``spikes`` -> ``syn`` -> ``comm`` -> ``out``.
-
-  To simulate and define an E/I balanced network model:
-
-  .. code-block:: python
-
-      class EINet(bp.DynSysGroup):
-        def __init__(self):
-          super().__init__()
-          ne, ni = 3200, 800
-          self.E = bp.dyn.LifRef(ne, V_rest=-60., V_th=-50., V_reset=-60., tau=20., tau_ref=5.,
-                                 V_initializer=bp.init.Normal(-55., 2.))
-          self.I = bp.dyn.LifRef(ni, V_rest=-60., V_th=-50., V_reset=-60., tau=20., tau_ref=5.,
-                                 V_initializer=bp.init.Normal(-55., 2.))
-          self.E2E = bp.dyn.FullProjAlignPost(pre=self.E,
-                                           delay=0.1,
-                                           comm=bp.dnn.EventJitFPHomoLinear(ne, ne, prob=0.02, weight=0.6),
-                                           syn=bp.dyn.Expon(size=ne, tau=5.),
-                                           out=bp.dyn.COBA(E=0.),
-                                           post=self.E)
-          self.E2I = bp.dyn.FullProjAlignPost(pre=self.E,
-                                           delay=0.1,
-                                           comm=bp.dnn.EventJitFPHomoLinear(ne, ni, prob=0.02, weight=0.6),
-                                           syn=bp.dyn.Expon(size=ni, tau=5.),
-                                           out=bp.dyn.COBA(E=0.),
-                                           post=self.I)
-          self.I2E = bp.dyn.FullProjAlignPost(pre=self.I,
-                                           delay=0.1,
-                                           comm=bp.dnn.EventJitFPHomoLinear(ni, ne, prob=0.02, weight=6.7),
-                                           syn=bp.dyn.Expon(size=ne, tau=10.),
-                                           out=bp.dyn.COBA(E=-80.),
-                                           post=self.E)
-          self.I2I = bp.dyn.FullProjAlignPost(pre=self.I,
-                                           delay=0.1,
-                                           comm=bp.dnn.EventJitFPHomoLinear(ni, ni, prob=0.02, weight=6.7),
-                                           syn=bp.dyn.Expon(size=ni, tau=10.),
-                                           out=bp.dyn.COBA(E=-80.),
-                                           post=self.I)
-
-        def update(self, inp):
-          self.E2E()
-          self.E2I()
-          self.I2E()
-          self.I2I()
-          self.E(inp)
-          self.I(inp)
-          return self.E.spike
-
-      model = EINet()
-      indices = bm.arange(1000)
-      spks = bm.for_loop(lambda i: model.step_run(i, 20.), indices)
-      bp.visualize.raster_plot(indices, spks, show=True)
-
-
-  Args:
-    pre: The pre-synaptic neuron group.
-    delay: The synaptic delay.
-    comm: The synaptic communication.
-    syn: The synaptic dynamics.
-    out: The synaptic output.
-    post: The post-synaptic neuron group.
-    name: str. The projection name.
-    mode:  Mode. The computing mode.
-  """
-
-  _invisible_nodes = ['post', 'pre', 'delay']
-
-  def __init__(
-      self,
-      pre: UpdateReturn,
-      delay: Union[None, int, float],
-      comm: Module,
-      syn: AlignPost,
-      out: BindCondData,
-      post: ReceiveInputProj,
-      out_label: Optional[str] = None,
-      name: Optional[str] = None,
-      mode: Optional[Mode] = None,
-  ):
-    super().__init__(name=name, mode=mode)
-
-    # synaptic models
-    is_instance(pre, UpdateReturn)
-    is_instance(comm, Module)
-    is_instance(syn, JointTypes[Dynamics, AlignPost])
-    is_instance(out, JointTypes[Dynamics, BindCondData])
-    is_instance(post, ReceiveInputProj)
-    self.comm = comm
-    self.syn = syn
-    self.out = out
-
-    # delay initialization
-    if delay is not None:
-      if isinstance(delay, u.Quantity):
-        has_delay = delay.mantissa > 0.
-      else:
-        has_delay = delay > 0.
-      if has_delay:
-        delay_cls = register_delay_of_target(pre)
-        delay_cls.register_entry(self.name, delay)
-        self.delay = delay_cls
-        self.has_delay = True
-      else:
-        self.delay = None
-        self.has_delay = False
-    else:
-      self.delay = None
-      self.has_delay = False
-
-    # synapse and output initialization
-    post.add_input_fun(self.name, out, label=out_label)
-
-    # references
-    self.post = post
-    self.pre = pre
-
-  def update(self):
-    if self.has_delay:
-      x = self.delay.at(self.name)
-    else:
-      x = self.pre.update_return()
-    g = self.syn(self.comm(x))
-    self.out.bind_cond(g)  # synapse post current
-    return g