brainstate 0.0.2.post20241010__py2.py3-none-any.whl → 0.1.0.post20241122__py2.py3-none-any.whl

brainstate/nn/_projection/_align_pre.py

@@ -1,599 +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
-
-from brainstate._module import (Module, DelayAccess, Projection,
-                                ExtendedUpdateWithBA, ReceiveInputProj,
-                                register_delay_of_target)
-from brainstate._utils import set_module_as
-from brainstate.mixin import (DelayedInitializer, BindCondData, UpdateReturn, Mode, JointTypes)
-from ._utils import is_instance
-
-__all__ = [
-  'FullProjAlignPreSDMg', 'FullProjAlignPreDSMg',
-  'FullProjAlignPreSD', 'FullProjAlignPreDS',
-]
-
-
-def align_pre_add_bef_update(
-    syn_desc: DelayedInitializer,
-    delay_at,
-    delay_cls: ExtendedUpdateWithBA,
-    proj_name: str = None
-):
-  _syn_id = f'Delay({str(delay_at)}) // {syn_desc.identifier}'
-  if not delay_cls.has_before_update(_syn_id):
-    # delay
-    delay_access = DelayAccess(delay_cls, delay_at, delay_entry=proj_name)
-    # synapse
-    syn_cls = syn_desc()
-    # add to "after_updates"
-    delay_cls.add_before_update(_syn_id, _AlignPreMg(delay_access, syn_cls))
-  syn = delay_cls.get_before_update(_syn_id).syn
-  return syn
-
-
-class _AlignPreMg(Module):
-  def __init__(self, access, syn):
-    super().__init__()
-    self.access = access
-    self.syn = syn
-
-  def update(self, *args, **kwargs):
-    return self.syn(self.access())
-
-
-@set_module_as('brainstate.nn')
-class FullProjAlignPreSDMg(Projection):
-  """Full-chain synaptic projection with the align-pre reduction and synapse+delay updating and merging.
-
-  The ``full-chain`` means that the model needs to provide all information needed for a projection,
-  including ``pre`` -> ``syn`` -> ``delay`` -> ``comm`` -> ``out`` -> ``post``.
-
-  The ``align-pre`` means that the synaptic variables have the same dimension as the pre-synaptic neuron group.
-
-  The ``synapse+delay updating`` means that the projection first computes the synapse states, then delivers the
-  synapse states to the delay model, and finally computes the synaptic current.
-
-  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.
-
-  Neither ``FullProjAlignPreSDMg`` nor ``FullProjAlignPreDSMg`` facilitates the event-driven computation.
-  This is because the ``comm`` is computed after the synapse state, which is a floating-point number, rather
-  than the spiking. To facilitate the event-driven computation, please use align post projections.
-
-  To simulate 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.FullProjAlignPreSDMg(pre=self.E,
-                                                syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                                delay=0.1,
-                                                comm=bp.dnn.JitFPHomoLinear(ne, ne, prob=0.02, weight=0.6),
-                                                out=bp.dyn.COBA(E=0.),
-                                                post=self.E)
-          self.E2I = bp.dyn.FullProjAlignPreSDMg(pre=self.E,
-                                                syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                                delay=0.1,
-                                                comm=bp.dnn.JitFPHomoLinear(ne, ni, prob=0.02, weight=0.6),
-                                                out=bp.dyn.COBA(E=0.),
-                                                post=self.I)
-          self.I2E = bp.dyn.FullProjAlignPreSDMg(pre=self.I,
-                                                syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                                delay=0.1,
-                                                comm=bp.dnn.JitFPHomoLinear(ni, ne, prob=0.02, weight=6.7),
-                                                out=bp.dyn.COBA(E=-80.),
-                                                post=self.E)
-          self.I2I = bp.dyn.FullProjAlignPreSDMg(pre=self.I,
-                                                syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                                delay=0.1,
-                                                comm=bp.dnn.JitFPHomoLinear(ni, ni, prob=0.02, weight=6.7),
-                                                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.
-    syn: The synaptic dynamics.
-    delay: The synaptic delay.
-    comm: The synaptic communication.
-    out: The synaptic output.
-    post: The post-synaptic neuron group.
-    name: str. The projection name.
-    mode: Mode. The computing mode.
-  """
-
-  _invisible_nodes = ['pre', 'syn', 'delay', 'post']
-
-  def __init__(
-      self,
-      pre: ExtendedUpdateWithBA,
-      syn: DelayedInitializer[UpdateReturn],
-      delay: Union[None, int, float],
-      comm: Module,
-      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, ExtendedUpdateWithBA)
-    is_instance(syn, DelayedInitializer[UpdateReturn])
-    is_instance(comm, Module)
-    is_instance(out, BindCondData)
-    is_instance(post, ReceiveInputProj)
-    self.comm = comm
-    self.out = out
-
-    # synapse initialization
-    if not pre.has_after_update(syn.identifier):
-      syn_cls = syn()
-      pre.add_after_update(syn.identifier, syn_cls)
-    self.syn = pre.get_after_update(syn.identifier)
-
-    # delay initialization
-    if delay is not None and delay > 0.:
-      delay_cls = register_delay_of_target(self.syn)
-      self.has_delay = True
-      self.delay = delay_cls
-    else:
-      self.has_delay = False
-      self.delay = None
-
-    # output initialization
-    post.add_input_fun(self.name, out, label=out_label)
-
-    # references
-    self.pre = pre
-    self.post = post
-
-  def update(self, x=None):
-    if x is None:
-      if self.has_delay:
-        x = self.delay.at(self.name)
-      else:
-        x = self.syn.update_return()
-    current = self.comm(x)
-    self.out.bind_cond(current)
-    return current
-
-
-@set_module_as('brainstate.nn')
-class FullProjAlignPreDSMg(Projection):
-  """Full-chain synaptic projection with the align-pre reduction and delay+synapse updating and merging.
-
-  The ``full-chain`` means that the model needs to provide all information needed for a projection,
-  including ``pre`` -> ``delay`` -> ``syn`` -> ``comm`` -> ``out`` -> ``post``.
-  Note here, compared to ``FullProjAlignPreSDMg``, the ``delay`` and ``syn`` are exchanged.
-
-  The ``align-pre`` means that the synaptic variables have the same dimension as the pre-synaptic neuron group.
-
-  The ``delay+synapse updating`` means that the projection first delivers the pre neuron output (usually the
-  spiking)  to the delay model, then computes the synapse states, and finally computes the synaptic current.
-
-  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.
-
-  Neither ``FullProjAlignPreDSMg`` nor ``FullProjAlignPreSDMg`` facilitates the event-driven computation.
-  This is because the ``comm`` is computed after the synapse state, which is a floating-point number, rather
-  than the spiking. To facilitate the event-driven computation, please use align post projections.
-
-
-  To simulate 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.FullProjAlignPreDSMg(pre=self.E,
-                                                delay=0.1,
-                                                syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                                comm=bp.dnn.JitFPHomoLinear(ne, ne, prob=0.02, weight=0.6),
-                                                out=bp.dyn.COBA(E=0.),
-                                                post=self.E)
-          self.E2I = bp.dyn.FullProjAlignPreDSMg(pre=self.E,
-                                                delay=0.1,
-                                                syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                                comm=bp.dnn.JitFPHomoLinear(ne, ni, prob=0.02, weight=0.6),
-                                                out=bp.dyn.COBA(E=0.),
-                                                post=self.I)
-          self.I2E = bp.dyn.FullProjAlignPreDSMg(pre=self.I,
-                                                delay=0.1,
-                                                syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                                comm=bp.dnn.JitFPHomoLinear(ni, ne, prob=0.02, weight=6.7),
-                                                out=bp.dyn.COBA(E=-80.),
-                                                post=self.E)
-          self.I2I = bp.dyn.FullProjAlignPreDSMg(pre=self.I,
-                                                delay=0.1,
-                                                syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                                comm=bp.dnn.JitFPHomoLinear(ni, ni, prob=0.02, weight=6.7),
-                                                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.
-    syn: The synaptic dynamics.
-    comm: The synaptic communication.
-    out: The synaptic output.
-    post: The post-synaptic neuron group.
-    name: str. The projection name.
-    mode: Mode. The computing mode.
-  """
-  _invisible_nodes = ['pre', 'syn', 'delay', 'post']
-
-  def __init__(
-      self,
-      pre: JointTypes[ExtendedUpdateWithBA, UpdateReturn],
-      delay: Union[None, int, float],
-      syn: DelayedInitializer[UpdateReturn],
-      comm: Module,
-      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, JointTypes[ExtendedUpdateWithBA, UpdateReturn])
-    is_instance(syn, DelayedInitializer[Module])
-    is_instance(comm, Module)
-    is_instance(out, BindCondData)
-    is_instance(post, ReceiveInputProj)
-    self.comm = comm
-    self.out = out
-
-    # delay initialization
-    if delay is not None and delay > 0.:
-      delay_cls = register_delay_of_target(pre)
-      self.has_delay = True
-      self.delay = delay_cls
-      # synapse initialization
-      self.syn = align_pre_add_bef_update(syn, delay, delay_cls, self.name)
-    else:
-      self.has_delay = False
-      self.delay = None
-      if not pre.has_after_update(syn.identifier):
-        syn_cls = syn()
-        pre.add_after_update(syn.identifier, syn_cls)
-      self.syn = pre.get_after_update(syn.identifier)
-
-    # output initialization
-    post.add_input_fun(self.name, out, label=out_label)
-
-    # references
-    self.pre = pre
-    self.post = post
-
-  def update(self):
-    x = self.syn.update_return()
-    current = self.comm(x)
-    self.out.bind_cond(current)
-    return current
-
-
-@set_module_as('brainstate.nn')
-class FullProjAlignPreSD(Projection):
-  """Full-chain synaptic projection with the align-pre reduction and synapse+delay updating.
-
-  The ``full-chain`` means that the model needs to provide all information needed for a projection,
-  including ``pre`` -> ``syn`` -> ``delay`` -> ``comm`` -> ``out`` -> ``post``.
-
-  The ``align-pre`` means that the synaptic variables have the same dimension as the pre-synaptic neuron group.
-
-  The ``synapse+delay updating`` means that the projection first computes the synapse states, then delivers the
-  synapse states to the delay model, and finally computes the synaptic current.
-
-  Neither ``FullProjAlignPreSD`` nor ``FullProjAlignPreDS`` facilitates the event-driven computation.
-  This is because the ``comm`` is computed after the synapse state, which is a floating-point number, rather
-  than the spiking. To facilitate the event-driven computation, please use align post projections.
-
-
-  To simulate 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.FullProjAlignPreSD(pre=self.E,
-                                              syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                              delay=0.1,
-                                              comm=bp.dnn.JitFPHomoLinear(ne, ne, prob=0.02, weight=0.6),
-                                              out=bp.dyn.COBA(E=0.),
-                                              post=self.E)
-          self.E2I = bp.dyn.FullProjAlignPreSD(pre=self.E,
-                                              syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                              delay=0.1,
-                                              comm=bp.dnn.JitFPHomoLinear(ne, ni, prob=0.02, weight=0.6),
-                                              out=bp.dyn.COBA(E=0.),
-                                              post=self.I)
-          self.I2E = bp.dyn.FullProjAlignPreSD(pre=self.I,
-                                              syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                              delay=0.1,
-                                              comm=bp.dnn.JitFPHomoLinear(ni, ne, prob=0.02, weight=6.7),
-                                              out=bp.dyn.COBA(E=-80.),
-                                              post=self.E)
-          self.I2I = bp.dyn.FullProjAlignPreSD(pre=self.I,
-                                              syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                              delay=0.1,
-                                              comm=bp.dnn.JitFPHomoLinear(ni, ni, prob=0.02, weight=6.7),
-                                              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.
-    syn: The synaptic dynamics.
-    delay: The synaptic delay.
-    comm: The synaptic communication.
-    out: The synaptic output.
-    post: The post-synaptic neuron group.
-    name: str. The projection name.
-    mode: Mode. The computing mode.
-  """
-
-  _invisible_nodes = ['pre', 'post']
-
-  def __init__(
-      self,
-      pre: ExtendedUpdateWithBA,
-      syn: UpdateReturn,
-      delay: Union[None, int, float],
-      comm: Module,
-      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, ExtendedUpdateWithBA)
-    is_instance(syn, UpdateReturn)
-    is_instance(comm, Module)
-    is_instance(out, BindCondData)
-    is_instance(post, ReceiveInputProj)
-    self.comm = comm
-    self.syn = syn
-    self.out = out
-
-    # delay initialization
-    if delay is not None and delay > 0.:
-      delay_cls = register_delay_of_target(syn)
-      delay_cls.register_entry(self.name, delay)
-      self.delay = delay_cls
-    else:
-      self.delay = None
-
-    # output initialization
-    post.add_input_fun(self.name, out, label=out_label)
-
-    # references
-    self.pre = pre
-    self.post = post
-
-  def update(self):
-    if self.delay is not None:
-      self.delay(self.syn(self.pre.update_return()))
-      x = self.delay.at(self.name)
-    else:
-      x = self.syn(self.pre.update_return())
-    current = self.comm(x)
-    self.out.bind_cond(current)
-    return current
-
-
-@set_module_as('brainstate.nn')
-class FullProjAlignPreDS(Projection):
-  """Full-chain synaptic projection with the align-pre reduction and delay+synapse updating.
-
-  The ``full-chain`` means that the model needs to provide all information needed for a projection,
-  including ``pre`` -> ``syn`` -> ``delay`` -> ``comm`` -> ``out`` -> ``post``.
-  Note here, compared to ``FullProjAlignPreSD``, the ``delay`` and ``syn`` are exchanged.
-
-  The ``align-pre`` means that the synaptic variables have the same dimension as the pre-synaptic neuron group.
-
-  The ``delay+synapse updating`` means that the projection first delivers the pre neuron output (usually the
-  spiking)  to the delay model, then computes the synapse states, and finally computes the synaptic current.
-
-  Neither ``FullProjAlignPreDS`` nor ``FullProjAlignPreSD`` facilitates the event-driven computation.
-  This is because the ``comm`` is computed after the synapse state, which is a floating-point number, rather
-  than the spiking. To facilitate the event-driven computation, please use align post projections.
-
-
-  To simulate 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.FullProjAlignPreDS(pre=self.E,
-                                              delay=0.1,
-                                              syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                              comm=bp.dnn.JitFPHomoLinear(ne, ne, prob=0.02, weight=0.6),
-                                              out=bp.dyn.COBA(E=0.),
-                                              post=self.E)
-          self.E2I = bp.dyn.FullProjAlignPreDS(pre=self.E,
-                                              delay=0.1,
-                                              syn=bp.dyn.Expon.desc(size=ne, tau=5.),
-                                              comm=bp.dnn.JitFPHomoLinear(ne, ni, prob=0.02, weight=0.6),
-                                              out=bp.dyn.COBA(E=0.),
-                                              post=self.I)
-          self.I2E = bp.dyn.FullProjAlignPreDS(pre=self.I,
-                                              delay=0.1,
-                                              syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                              comm=bp.dnn.JitFPHomoLinear(ni, ne, prob=0.02, weight=6.7),
-                                              out=bp.dyn.COBA(E=-80.),
-                                              post=self.E)
-          self.I2I = bp.dyn.FullProjAlignPreDS(pre=self.I,
-                                              delay=0.1,
-                                              syn=bp.dyn.Expon.desc(size=ni, tau=10.),
-                                              comm=bp.dnn.JitFPHomoLinear(ni, ni, prob=0.02, weight=6.7),
-                                              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.
-    syn: The synaptic dynamics.
-    comm: The synaptic communication.
-    out: The synaptic output.
-    post: The post-synaptic neuron group.
-    name: str. The projection name.
-    mode: Mode. The computing mode.
-  """
-
-  _invisible_nodes = ['pre', 'post', 'delay']
-
-  def __init__(
-      self,
-      pre: UpdateReturn,
-      delay: Union[None, int, float],
-      syn: Module,
-      comm: Module,
-      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(syn, Module)
-    is_instance(comm, Module)
-    is_instance(out, BindCondData)
-    is_instance(post, ReceiveInputProj)
-    self.comm = comm
-    self.syn = syn
-    self.out = out
-
-    # delay initialization
-    if delay is not None and delay > 0.:
-      delay_cls = register_delay_of_target(pre)
-      delay_cls.register_entry(self.name, delay)
-      self.delay = delay_cls
-    else:
-      self.delay = None
-
-    # output initialization
-    post.add_input_fun(self.name, out, label=out_label)
-
-    # references
-    self.pre = pre
-    self.post = post
-
-  def update(self, x=None):
-    if x is None:
-      if self.delay is not None:
-        x = self.delay.at(self.name)
-      else:
-        x = self.pre.update_return()
-    g = self.comm(self.syn(x))
-    self.out.bind_cond(g)
-    return g