ezmsg-neo 0.1__tar.gz

ezmsg_neo-0.1/.github/workflows/python-publish-ezmsg-neo.yml

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+name: Upload Python Package - ezmsg-neo
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: build and upload release to PyPI
+    runs-on: ubuntu-latest
+    environment: "release"
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v2
+
+      - name: Build Package
+        run: uv build
+
+      - name: Publish package distributions to PyPI
+        run: uv publish

ezmsg_neo-0.1/.github/workflows/python-tests.yml

@@ -0,0 +1,41 @@
+name: Test package
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        python-version: [3.9, "3.10", "3.11", "3.12"]
+        os:
+          - "ubuntu-latest"
+          - "windows-latest"
+          - "macos-latest"
+    runs-on: ${{matrix.os}}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v2
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Lint
+        run:
+          uv tool run ruff check --output-format=github src
+
+#      - name: Run tests
+#        run: uv run pytest tests

ezmsg_neo-0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+src/ezmsg/neo/__version__.py

ezmsg_neo-0.1/.python-version

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+3.9

ezmsg_neo-0.1/LICENSE

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+MIT License
+
+Copyright (c) 2024 ezmsg-org
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ezmsg_neo-0.1/PKG-INFO

@@ -0,0 +1,35 @@
+Metadata-Version: 2.3
+Name: ezmsg-neo
+Version: 0.1
+Summary: Load and stream data from neo files into ezmsg.
+Author-email: Chadwick Boulay <chadwick.boulay@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.9
+Requires-Dist: ezmsg>=3.5.0
+Requires-Dist: neo>=0.13.3
+Provides-Extra: tests
+Requires-Dist: pytest>=8.3.3; extra == 'tests'
+Description-Content-Type: text/markdown
+
+# ezmsg-neo
+
+Load and stream data from [neo](https://github.com/NeuralEnsemble/python-neo) files into [ezmsg](https://github.com/iscoe/ezmsg).
+
+## Installation
+
+TODO: `pip install ezmsg-neo`
+
+For now `pip install ezmsg-neo@git+https://github.com/ezmsg-org/ezmsg-neo`
+
+## Dependencies
+* `ezmsg`
+* `neo`
+
+## Setup (Development)
+
+1. Clone this repo
+2. `uv init`
+3. ezmsg-neo modules are available under `import ezmsg.neo`
+
+TODO: See the `examples` folder for more details.

ezmsg_neo-0.1/README.md

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+# ezmsg-neo
+
+Load and stream data from [neo](https://github.com/NeuralEnsemble/python-neo) files into [ezmsg](https://github.com/iscoe/ezmsg).
+
+## Installation
+
+TODO: `pip install ezmsg-neo`
+
+For now `pip install ezmsg-neo@git+https://github.com/ezmsg-org/ezmsg-neo`
+
+## Dependencies
+* `ezmsg`
+* `neo`
+
+## Setup (Development)
+
+1. Clone this repo
+2. `uv init`
+3. ezmsg-neo modules are available under `import ezmsg.neo`
+
+TODO: See the `examples` folder for more details.

ezmsg_neo-0.1/pyproject.toml

@@ -0,0 +1,39 @@
+[project]
+name = "ezmsg-neo"
+description = "Load and stream data from neo files into ezmsg."
+authors = [
+  { name = "Chadwick Boulay", email = "chadwick.boulay@gmail.com" },
+]
+license = "MIT"
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = [
+    "ezmsg>=3.5.0",
+    "neo>=0.13.3",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+tests = [
+    "pytest>=8.3.3",
+]
+
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/ezmsg/neo/__version__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/ezmsg"]
+
+[tool.uv]
+dev-dependencies = [
+    "ruff>=0.6.8",
+]
+
+[tool.uv.sources]

ezmsg_neo-0.1/src/ezmsg/neo/__init__.py

@@ -0,0 +1 @@
+from .__version__ import __version__ as __version__

ezmsg_neo-0.1/src/ezmsg/neo/__version__.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1'
+__version_tuple__ = version_tuple = (0, 1)

ezmsg_neo-0.1/src/ezmsg/neo/source.py

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+import asyncio
+from collections import deque
+from dataclasses import replace
+import os
+from pathlib import Path
+import time
+import typing
+
+import ezmsg.core as ez
+
+from .util import AxisArray  # This one has labels field.
+from ezmsg.util.generator import GenState
+import neo.rawio.baserawio
+import numpy as np
+
+
+class NeoIteratorSettings(ez.Settings):
+    """Settings for :obj:`NeoIterator`."""
+
+    filepath: os.PathLike
+    chunk_dur: float = 0.1
+    self_terminating: bool = True
+    t_offset: typing.Optional[float] = None
+
+
+class NeoIterator:
+    def __init__(self, settings: NeoIteratorSettings):
+        self._settings = settings
+        self._reader: typing.Optional[neo.rawio.baserawio.BaseRawIO] = None
+        self._playback_state: typing.Optional[dict] = None
+        self._reset()
+
+    def _reset(self):
+        self._playback_state = {
+            "t_offset": self._settings.t_offset
+            if self._settings.t_offset is not None
+            else time.time(),
+            "t_start": np.inf,
+            "chunk_ix": 0,
+            "msg_queue": deque(),
+            "streams": {},
+        }
+        self._preload()
+
+    def _preload(self):
+        fpath = Path(self._settings.filepath)
+
+        if not fpath.exists():
+            raise FileNotFoundError(f"File not found: {fpath}")
+
+        if fpath.suffix == ".vhdr":
+            from neo.rawio import BrainVisionRawIO as RawIO
+        else:
+            raise ValueError(f"Unsupported file type: {fpath.suffix}")
+
+        self._reader = RawIO(filename=str(fpath))
+        self._reader.parse_header()
+
+        nb_block = self._reader.block_count()
+        if nb_block > 1:
+            raise NotImplementedError("Only single-block files are supported.")
+        nb_seg = [self._reader.segment_count(_) for _ in range(nb_block)][0]
+        if nb_seg > 1:
+            raise NotImplementedError("Only single-segment files are supported.")
+        nb_sig_streams = self._reader.signal_streams_count()
+
+        t_stop = -np.inf
+
+        # Fill out metadata for analogsignal streams
+        for strm_ix in range(nb_sig_streams):
+            t_start = self._reader.get_signal_t_start(0, 0, strm_ix)
+            self._playback_state["t_start"] = min(
+                self._playback_state["t_start"], t_start
+            )
+            nb_chans = self._reader.signal_channels_count(strm_ix)
+            fs = self._reader.get_signal_sampling_rate(strm_ix)
+            nb_samps = self._reader.get_signal_size(0, 0, strm_ix)
+            t_stop = max(t_stop, t_start + nb_samps / fs)
+            chan_struct_arr = self._reader.header["signal_channels"]
+            key = self._reader.header["signal_streams"][strm_ix]["name"]
+            template = AxisArray(
+                data=np.zeros((0, nb_chans), dtype=float),
+                dims=["time", "ch"],
+                axes={
+                    "time": AxisArray.Axis.TimeAxis(fs=fs, offset=0.0),
+                    "ch": AxisArray.Axis(labels=chan_struct_arr["name"].tolist()),
+                },
+                key=key,
+            )
+            self._playback_state["streams"][key] = {
+                "idx": strm_ix,
+                "type": "analogsignal",
+                "t_start": t_start,
+                "template": template,
+                "prev_samp": 0,
+            }
+
+        # Fill out metadata for event streams
+        nb_event_channel = self._reader.event_channels_count()
+        if nb_event_channel > 0:
+            # TODO: Event should probably use SampleTriggerMessage
+            self._playback_state["streams"]["events"] = {
+                "type": "event",
+                "nchan": nb_event_channel,
+                "template": AxisArray(
+                    data=np.array([""]),
+                    dims=["time"],
+                    axes={"time": AxisArray.Axis.TimeAxis(fs=1, offset=0.0)},
+                    key="events",
+                ),
+            }
+
+        # TODO: Add support for spiketrain streams
+        # nb_unit = self._reader.spike_channels_count()
+
+        t_elapsed = t_stop - self._playback_state["t_start"]
+        self._playback_state["n_chunks"] = int(
+            np.ceil(t_elapsed / self._settings.chunk_dur)
+        )
+
+    def __iter__(self):
+        self._reset()
+        return self
+
+    def _chunk_step(self):
+        state = self._playback_state
+        t_range = (
+            state["chunk_ix"] * self._settings.chunk_dur,
+            (state["chunk_ix"] + 1) * self._settings.chunk_dur,
+        )
+
+        for key, strm in state["streams"].items():
+            if strm["type"] == "analogsignal":
+                # Fetch data from last_idx to next_idx = next_time * fs
+                fs = 1 / strm["template"].axes["time"].gain
+                prev_samp = strm["prev_samp"]
+                next_samp = max(0, int((t_range[1] - strm["t_start"]) * fs))
+                dat = self._reader.get_analogsignal_chunk(
+                    seg_index=0,
+                    stream_index=strm["idx"],
+                    i_start=prev_samp,
+                    i_stop=next_samp,
+                )
+                if dat.size:
+                    dat = self._reader.rescale_signal_raw_to_float(dat, dtype=float)
+                    msg = replace(
+                        strm["template"],
+                        data=dat,
+                        axes={
+                            "ch": strm["template"].axes["ch"],
+                            "time": replace(
+                                strm["template"].axes["time"],
+                                offset=t_range[0] + state["t_offset"],
+                            ),
+                        },
+                    )
+                    state["msg_queue"].append(msg)
+                strm["prev_samp"] = next_samp
+            elif strm["type"] == "event":
+                # TODO: Event should probably use SampleTriggerMessage
+                for ev_ch_ix in range(strm["nchan"]):
+                    ev_timestamps, ev_durations, ev_labels = (
+                        self._reader.get_event_timestamps(
+                            block_index=0,
+                            seg_index=0,
+                            event_channel_index=ev_ch_ix,
+                            t_start=t_range[0],
+                            t_stop=t_range[1],
+                        )
+                    )
+                    ev_times = self._reader.rescale_event_timestamp(
+                        ev_timestamps, dtype=float
+                    )
+                    for ev_t, ev_l in zip(ev_times, ev_labels):
+                        msg = replace(
+                            strm["template"],
+                            data=np.array(
+                                [ev_l],
+                            ),
+                            axes={
+                                "time": replace(
+                                    strm["template"].axes["time"],
+                                    offset=ev_t + state["t_offset"],
+                                ),
+                            },
+                        )
+                        state["msg_queue"].append(msg)
+
+            else:
+                # TODO: spiketrain
+                # spike_timestamps = self._reader.get_spike_timestamps(block_index=0, seg_index=0, spike_channel_index=0,
+                #                                                t_start=0, t_stop=10)
+                # spike_timestamps
+                # spike_times = self._reader.rescale_spike_timestamp(spike_timestamps, dtype='float64')
+                # raw_waveforms = reader.get_spike_raw_waveforms(block_index=0, seg_index=0, spike_channel_index=0,
+                #                                                t_start=0, t_stop=10)
+                # float_waveforms = reader.rescale_waveforms_to_float(raw_waveforms, dtype='float32', spike_channel_index=0)
+                raise NotImplementedError(f"Unsupported stream type: {strm['type']}")
+
+        state["chunk_ix"] += 1
+
+    def __next__(self) -> AxisArray:
+        state = self._playback_state
+        if not state["msg_queue"]:
+            if state["chunk_ix"] >= state["n_chunks"]:
+                # TODO Close file
+                raise StopIteration
+            self._chunk_step()
+
+        if not state["msg_queue"]:
+            raise StopIteration
+
+        return state["msg_queue"].popleft()
+
+
+class NeoIteratorUnit(ez.Unit):
+    STATE = GenState
+    SETTINGS = NeoIteratorSettings
+
+    OUTPUT_SIGNAL = ez.OutputStream(AxisArray)
+    OUTPUT_TERM = ez.OutputStream(typing.Any)
+
+    def initialize(self) -> None:
+        self.construct_generator()
+
+    def construct_generator(self):
+        self.STATE.gen = NeoIterator(
+            settings=self.SETTINGS,
+        )
+
+    @ez.publisher(OUTPUT_SIGNAL)
+    async def pub_chunk(self) -> typing.AsyncGenerator:
+        for msg in self.STATE.gen:
+            # TODO: Direct msg to OUTPUT_TRIGGER if type is SampleTriggerMessage
+            yield self.OUTPUT_SIGNAL, msg
+            await asyncio.sleep(0)
+
+        ez.logger.debug(f"File ({self.SETTINGS.filepath}) exhausted.")
+        if self.SETTINGS.self_terminating:
+            raise ez.NormalTermination
+        yield self.OUTPUT_TERM, ez.Flag

ezmsg_neo-0.1/src/ezmsg/neo/util.py

@@ -0,0 +1,21 @@
+from dataclasses import dataclass, field
+import typing
+
+from ezmsg.util.messages.axisarray import AxisArray
+
+
+@dataclass
+class CustomAxis(AxisArray.Axis):
+    labels: typing.List[str] = field(default_factory=lambda: [])
+
+    @classmethod
+    def SpaceAxis(
+        cls,
+        labels: typing.List[str],
+        # locs: typing.Optional[npt.NDArray] = None
+    ):
+        return cls(unit="mm", labels=labels)
+
+
+# Monkey-patch AxisArray with our customized Axis
+AxisArray.Axis = CustomAxis

ezmsg_neo-0.1/tests/test_neo_source.py

@@ -0,0 +1,20 @@
+# import os
+# from pathlib import Path
+
+from ezmsg.neo.source import NeoIterator, NeoIteratorSettings
+
+
+def test_brainvision_playback():
+
+    source_path = None  # TODO - web source.
+    settings = NeoIteratorSettings(filepath=source_path)
+    neo_iter = NeoIterator(settings)
+
+    data_msg_count = 0
+    for msg in neo_iter:
+        if msg.key == "events":
+            print(msg)
+        else:
+            data_msg_count += 1
+
+    print(f"Data messages: {data_msg_count}")

ezmsg_neo-0.1/uv.lock

@@ -0,0 +1,217 @@
+version = 1
+requires-python = ">=3.9"
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/d8/53/6f443c9a4a8358a93a6792e2acffb9d9d5cb0a5cfd8802644b7b1c9a02e4/colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44", size = 27697 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6", size = 25335 },
+]
+
+[[package]]
+name = "exceptiongroup"
+version = "1.2.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/09/35/2495c4ac46b980e4ca1f6ad6db102322ef3ad2410b79fdde159a4b0f3b92/exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc", size = 28883 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/02/cc/b7e31358aac6ed1ef2bb790a9746ac2c69bcb3c8588b41616914eb106eaf/exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b", size = 16453 },
+]
+
+[[package]]
+name = "ezmsg"
+version = "3.5.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "typing-extensions" },
+]
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