ezmsg-neo

Load and stream data from neo files into ezmsg.

Installation

pip install ezmsg-neo

Or install the latest development version:

pip install git+https://github.com/ezmsg-org/ezmsg-neo@dev

Dependencies

• ezmsg
• neo
• sparse

Usage

ezmsg-neo modules are available under import ezmsg.neo

Add the NeoIteratorUnit to your ezmsg graph as a data source. You may be interested in other ezmsg extensions for processing the data, such as ezmsg-sigproc and ezmsg-event.

import ezmsg.core as ez
from ezmsg.neo.source import NeoIteratorUnit
from ezmsg.util.messages.key import FilterOnKey
from ezmsg.util.debuglog import DebugLog
from ezmsg.event.rate import EventRate


comps = {
    "NEO": NeoIteratorUnit(filepath="path/to/file", chunk_dur=0.05),
    "FILTER": FilterOnKey(key="spike"),
    "RATE": EventRate(bin_duration=0.05),
    "LOG": DebugLog()  # Print the output to the console
}
conns = (
    (comps["NEO"].OUTPUT_SIGNAL, comps["FILTER"].INPUT_SIGNAL),
    (comps["FILTER"].OUTPUT_SIGNAL, comps["RATE"].INPUT_SIGNAL),
    (comps["RATE"].OUTPUT_SIGNAL, comps["LOG"].INPUT),
)
ez.run(components=comps, connections=conns)

Standalone

The NeoIterator class can be used outside ezmsg for offline processing:

from ezmsg.neo.source import NeoIterator, NeoIteratorSettings
from ezmsg.util.messages.axisarray import AxisArray

settings = NeoIteratorSettings(filepath="data.nev", chunk_dur=0.05)
neo_iter = NeoIterator(settings)

# Filter messages by key (e.g., "ns3" for analog signals, "spike" for spikes)
sig_msgs = [msg for msg in neo_iter if msg.key.startswith("ns")]

# Concatenate all chunks into a single AxisArray
full_signal = AxisArray.concatenate(*sig_msgs, dim="time")

NeoIterator Messages

The NeuoIteratorUnit and NeoIterator objects, when called, return AxisArray messages with a key attribute identifying the signal type:

• Analog signals - Key matches the stream name (e.g., "ns3"). Data shape: (n_samples, n_channels)
• Spike trains - Key is "spike". Data is a sparse array with shape (n_units, n_samples)
• Events - Key is "events". Data contains event labels and its time axis is irregular (CoordinateAxis) with timestamps associated with each event.

Development

1. Clone this repo and cd into it
2. uv sync to setup your environment
3. uv run pytest tests to run the tests
4. (Optional) Install pre-commit hooks: uv run pre-commit install