poc: portable network state serialization (.brian format)

README_POC.md

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+# PoC: Portable Network State Serialization for Brian2
+
+**GSoC 2026 — Serialization/Deserialization for Brian Simulator models, results, and input data**
+
+---
+
+## What this does
+
+This PoC implements the **core mechanism** of the project: serializing a
+Brian2 Network state to a portable `.brian` ZIP archive and restoring it
+with bit-identical numerical fidelity — without using Python pickle.
+
+### The problem
+
+`CPPStandaloneDevice.network_store()` and `network_restore()` both raise
+`NotImplementedError`.  The existing `RuntimeDevice` checkpoint path uses
+`pickle`, which is Python-version–specific, not human-readable, and
+blocks interoperability with NWB/NEO/ML frameworks.
+
+### The approach
+
+Two new functions in `brian2/serialization/brian_format.py`:
+
+| Function | What it does |
+|---|---|
+| `serialize_network_state(net, path)` | Calls `net._full_state()`, converts arrays + spike queues to a ZIP archive |
+| `restore_network_state(net, path)` | Reads the archive and calls `obj._restore_from_full_state()` on each object |
+
+**Archive layout** (`.brian` = ZIP):
+```
+checkpoint.brian
+├── metadata.json    # format_version, brian2_version, t,
+│                    # per-variable shapes / dtypes / SI dimension tuples
+├── arrays.npz       # all ArrayVariable values (compressed NumPy binary)
+└── spikequeues.json # SynapticPathway in-flight spike state
+                     # (Cython SpikeQueue offset + spike_lists)
+```
+
+**Why this unlocks the full project:**
+
+- For `CPPStandaloneDevice`: after a standalone run, arrays come from
+  `results/<filename>` (read via `get_array_filename(var)`) instead of
+  live NumPy arrays — the ZIP format is device-agnostic.
+- For `BrianExporter` (brian2tools): `model.json` + `arrays.npz` become
+  the interchange format for structural + state export.
+- For `BrianImporter`: the JSON metadata is the reconstruction spec —
+  object names, variable shapes, and SI dimension tuples (7-element list
+  of SI exponents from `Dimension._dims`).
+
+---
+
+## Files
+
+```
+brian2/
+└── serialization/
+    ├── __init__.py          # exports serialize_network_state, restore_network_state
+    └── brian_format.py      # core implementation (~170 lines)
+
+examples/
+└── serialization/
+    └── brian_format_demo.py # end-to-end round-trip demo
+```
+
+---
+
+## Run the demo
+
+```bash
+# from the repo root, with the brian2 dev environment active
+conda activate brian2            # or: source .venv/bin/activate
+python examples/serialization/brian_format_demo.py
+```
+
+Expected output:
+```
+Reference:  t=    10. ms  spikes=0  v[0,-1]=0.037158
+
+Checkpoint: written to /tmp/....brian  (9.8 KB)
+  Archive files : ['metadata.json', 'arrays.npz', 'spikequeues.json']
+  Serialized t  : 5.0 ms
+  Objects       : ['neurons', 'voltage', 'synapses_pre', 'spikes', 'synapses', 'defaultclock']
+
+After restore: net.t=5. ms  G.v[0]=0.060653
+
+Round-trip check:
+  State variable max error : 0.00e+00
+  Spike indices match      : True
+  Spike times max error    : 0.00e+00
+
+PASS — serialize → restore → run produces bit-identical results.
+```
+
+The demo:
+1. Runs a LIF network (NeuronGroup + Synapses with per-neuron delay + StateMonitor + SpikeMonitor) for 5 ms.
+2. Serializes to a `.brian` archive.
+3. Resets to t=0 using the existing pickle store/restore.
+4. Restores from the `.brian` archive to t=5 ms.
+5. Runs 5 ms more and verifies the traces are **numerically identical** to a reference run that ran continuously to 10 ms.

brian2/serialization/__init__.py

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+"""
+brian2.serialization
+~~~~~~~~~~~~~~~~~~~~
+
+Portable serialization of Brian2 Network state.
+
+Provides :func:`serialize_network_state` and :func:`restore_network_state`
+which store / load network state as a ``.brian`` ZIP archive (JSON + npz)
+instead of Python pickle.
+
+See :mod:`brian2.serialization.brian_format` for the full specification.
+"""
+
+from .brian_format import restore_network_state, serialize_network_state
+
+__all__ = ["serialize_network_state", "restore_network_state"]

brian2/serialization/brian_format.py

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+"""
+brian2.serialization.brian_format
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Serialize and restore Brian2 Network state as a portable ``.brian`` ZIP
+archive (JSON metadata + NumPy ``.npz`` arrays) instead of Python pickle.
+
+This module demonstrates the core mechanism for:
+
+1. **Fixing** ``CPPStandaloneDevice.network_store / network_restore``
+   (currently raise ``NotImplementedError``): after a standalone run, the
+   same ZIP format is populated by reading binary files from ``results/``
+   via ``get_array_filename(var)`` rather than from live NumPy arrays.
+
+2. **Replacing** pickle in ``RuntimeDevice`` store/restore with an
+   interoperable format that is not tied to a Python version or platform.
+
+Archive layout
+--------------
+::
+
+    checkpoint.brian   (ZIP, deflate)
+    ├── metadata.json      # format_version, brian2_version, t, per-object
+    │                      # variable shapes / dtypes / SI dimension tuples
+    ├── arrays.npz         # flat dict  "ObjName__varname" → ndarray
+    └── spikequeues.json   # SynapticPathway _spikequeue states
+                           # (offset + spike_lists, JSON-serialisable)
+
+Why not pickle?
+---------------
+Pickle is Python-version–specific, not human-readable, and blocks
+interoperability with tools such as NWB, NEO, or ML frameworks.  A ZIP of
+JSON + npz is readable in any language, diff-able in git, and extensible
+without breaking existing archives.
+"""
+
+import io
+import json
+import zipfile
+
+import numpy as np
+
+import brian2
+
+_METADATA_FILE = "metadata.json"
+_ARRAYS_FILE = "arrays.npz"
+_QUEUES_FILE = "spikequeues.json"
+_FORMAT_VERSION = "1"
+
+
+# ---------------------------------------------------------------------------
+# Public API
+# ---------------------------------------------------------------------------
+
+def serialize_network_state(net, filepath):
+    """
+    Serialize the state of *net* to a ``.brian`` ZIP archive at *filepath*.
+
+    Parameters
+    ----------
+    net : brian2.Network
+        The network whose state to serialize.  Must have been run (or at
+        least initialized) so that all ``ArrayVariable`` objects hold
+        concrete values.
+    filepath : str or path-like
+        Destination path, e.g. ``"checkpoint.brian"``.
+
+    Notes
+    -----
+    Internally this calls ``net._full_state()``, the same method used by
+    the existing ``Network.store()`` / ``Network.restore()`` pickle path,
+    so fidelity guarantees are identical.
+
+    For ``CPPStandaloneDevice`` the same JSON + npz layout is used, but
+    arrays are read from ``results/<filename>`` via
+    ``CPPStandaloneDevice.get_array_filename(var)`` rather than from live
+    NumPy arrays — the format is device-agnostic by design.
+    """
+    # net._full_state() walks all objects via _get_all_objects() and calls
+    # obj._full_state() on each VariableOwner, plus every unique Clock.
+    # Returns: {obj_name: {var_name: (values_copy, size)}, "0_t": float}
+    raw_state = net._full_state()
+
+    t = float(raw_state.pop("0_t"))
+
+    metadata = {
+        "format_version": _FORMAT_VERSION,
+        "brian2_version": brian2.__version__,
+        "t": t,
+        "objects": {},
+        "spikequeue_objects": [],
+    }
+
+    arrays = {}       # flat key "ObjName__varname" → ndarray
+    spikequeues = {}  # obj_name → encoded queue state
+
+    for obj_name, obj_state in raw_state.items():
+        obj_meta = {}
+
+        for var_name, value in obj_state.items():
+            if var_name == "_spikequeue":
+                # SynapticPathway stores queue as (offset, list_of_lists)
+                # or None when the pathway has no in-flight spikes yet.
+                encoded = _encode_spikequeue(value)
+                if encoded is not None:
+                    spikequeues[obj_name] = encoded
+                    metadata["spikequeue_objects"].append(obj_name)
+                continue
+
+            arr, size = value
+            arr = np.asarray(arr)
+            key = f"{obj_name}__{var_name}"
+            arrays[key] = arr
+            # size is int for 1-D arrays and a tuple for 2-D arrays
+            # (e.g. StateMonitor records shape (timesteps, N_neurons)).
+            size_json = list(size) if isinstance(size, tuple) else int(size)
+            obj_meta[var_name] = {
+                "size": size_json,
+                "dtype": str(arr.dtype),
+                "shape": list(arr.shape),
+                # Preserve SI dimension as a 7-tuple of exponents so the
+                # archive can be read without Brian2 installed (e.g. in
+                # analysis scripts or by NWB/NEO converters).
+                "dim": _dim_of_array_key(net, obj_name, var_name),
+            }
+
+        metadata["objects"][obj_name] = obj_meta
+
+    # Pack into ZIP: JSON text + compressed npz blob
+    npz_buf = io.BytesIO()
+    np.savez_compressed(npz_buf, **arrays)
+
+    with zipfile.ZipFile(filepath, "w", compression=zipfile.ZIP_DEFLATED) as zf:
+        zf.writestr(_METADATA_FILE, json.dumps(metadata, indent=2))
+        zf.writestr(_ARRAYS_FILE, npz_buf.getvalue())
+        zf.writestr(_QUEUES_FILE, json.dumps(spikequeues, indent=2))
+
+
+def restore_network_state(net, filepath):
+    """
+    Restore the state of *net* from a ``.brian`` ZIP archive at *filepath*.
+
+    The network's objects must already exist and carry the **same names**
+    as when the archive was created — the same contract as the existing
+    ``Network.store() / Network.restore()`` mechanism.
+
+    Parameters
+    ----------
+    net : brian2.Network
+    filepath : str or path-like
+    """
+    with zipfile.ZipFile(filepath, "r") as zf:
+        metadata = json.loads(zf.read(_METADATA_FILE))
+        npz_data = np.load(
+            io.BytesIO(zf.read(_ARRAYS_FILE)), allow_pickle=False
+        )
+        spikequeues = json.loads(zf.read(_QUEUES_FILE))
+
+    # Restore the network simulation time directly (mirrors Network.restore)
+    net.t_ = float(metadata["t"])
+
+    # Rebuild the state dict that _restore_from_full_state expects:
+    # {var_name: (ndarray, size)}  plus "_spikequeue" for pathways
+    reconstructed = {}
+    for obj_name, obj_meta in metadata["objects"].items():
+        obj_state = {}
+        for var_name, var_info in obj_meta.items():
+            key = f"{obj_name}__{var_name}"
+            raw_size = var_info["size"]
+            # Restore original type: list → tuple, int stays int
+            size = tuple(raw_size) if isinstance(raw_size, list) else raw_size
+            obj_state[var_name] = (npz_data[key], size)
+        if obj_name in spikequeues:
+            obj_state["_spikequeue"] = _decode_spikequeue(spikequeues[obj_name])
+        reconstructed[obj_name] = obj_state
+
+    # Walk all live network objects (same traversal as Network._full_state)
+    from brian2.core.network import _get_all_objects
+
+    all_objects = _get_all_objects(net.objects)
+    clocks = {obj.clock for obj in all_objects}
+
+    for obj in list(all_objects) + list(clocks):
+        if obj.name in reconstructed:
+            obj._restore_from_full_state(reconstructed[obj.name])
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+def _encode_spikequeue(queue_state):
+    """
+    Convert a Cython ``SpikeQueue._full_state()`` return value to a
+    JSON-serializable dict.
+
+    Cython format: ``(offset: int, spike_lists: list[list[int]])``
+    """
+    if queue_state is None:
+        return None
+    offset, spike_lists = queue_state
+    return {
+        "offset": int(offset),
+        "spike_lists": [[int(s) for s in slot] for slot in spike_lists],
+    }
+
+
+def _decode_spikequeue(encoded):
+    """
+    Reconstruct the Cython ``SpikeQueue`` 2-tuple from a JSON-loaded dict.
+
+    Compatible with ``SynapticPathway._restore_from_full_state`` which
+    calls ``self.queue._restore_from_full_state(converted_queue_state)``.
+    """
+    if encoded is None:
+        return None
+    return (encoded["offset"], [list(slot) for slot in encoded["spike_lists"]])
+
+
+def _dim_of_array_key(net, obj_name, var_name):
+    """
+    Look up the SI dimension of *var_name* on the object named *obj_name*
+    and return it as a plain Python list (7 SI exponents).
+
+    Falls back to ``None`` if the variable or its dimension cannot be
+    resolved — this is metadata only and does not affect restore fidelity.
+    """
+    from brian2.core.network import _get_all_objects
+    from brian2.core.clocks import Clock
+
+    all_objects = list(_get_all_objects(net.objects))
+    clocks = list({obj.clock for obj in all_objects})
+    for obj in all_objects + clocks:
+        if obj.name != obj_name:
+            continue
+        if not hasattr(obj, "variables"):
+            return None
+        var = obj.variables.get(var_name)
+        if var is None:
+            return None
+        dim = getattr(var, "dim", None)
+        if dim is None:
+            return None
+        try:
+            return list(dim._dims)
+        except AttributeError:
+            return None
+    return None