ezmsg-event 0.1.1__tar.gz

ezmsg_event-0.1.1/.github/workflows/python-publish-ezmsg-event.yml

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+name: Upload Python Package - ezmsg-event
+
+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_event-0.1.1/.github/workflows/python-tests.yml

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+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_event-0.1.1/.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/event/__version__.py

ezmsg_event-0.1.1/.python-version

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+3.9

ezmsg_event-0.1.1/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_event-0.1.1/PKG-INFO

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+Metadata-Version: 2.3
+Name: ezmsg-event
+Version: 0.1.1
+Summary: Namespace package for ezmsg to work with signal events like neural spikes and heartbeats
+Author-email: Chadwick Boulay <chadwick.boulay@gmail.com>
+License-File: LICENSE
+Requires-Python: >=3.9
+Requires-Dist: ezmsg-sigproc>=1.3.3
+Requires-Dist: ezmsg>=3.5.0
+Requires-Dist: numpy>=2.0.2
+Requires-Dist: sparse>=0.15.4
+Provides-Extra: test
+Requires-Dist: pytest>=8.3.3; extra == 'test'
+Description-Content-Type: text/markdown
+
+# ezmsg-event
+
+ezmsg namespace package for working with signal events like neural spikes and heartbeats

ezmsg_event-0.1.1/README.md

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+# ezmsg-event
+
+ezmsg namespace package for working with signal events like neural spikes and heartbeats

ezmsg_event-0.1.1/docs/scripts_nbs/event_rates_system_compact.py

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+import ezmsg.core as ez
+from ezmsg.sigproc.math.log import Log
+from ezmsg.util.debuglog import DebugLog
+from ezmsg.util.messages.chunker import ArrayChunker
+from ezmsg.util.terminate import TerminateOnTotal
+import typer
+
+from ezmsg.event.util.simulate import generate_white_noise_with_events
+from ezmsg.event.peak import ThresholdCrossing
+from ezmsg.event.rate import EventRate
+
+
+def main(bin_duration: float = 0.05):
+    fs = 30_000.0
+    dur = 10.0
+    n_chans = 128
+    threshold = 2.5
+    rate_range = (10, 100)
+    chunk_dur = bin_duration / 2
+    chunk_len = int(fs * chunk_dur)
+    data = generate_white_noise_with_events(
+        fs, dur, n_chans, rate_range, chunk_dur, threshold
+    )
+    n_chunks = int(dur / bin_duration)
+
+    comps = {
+        "SOURCE": ArrayChunker(data, chunk_len, fs=fs),
+        "THRESH": ThresholdCrossing(threshold=threshold),
+        "RATE": EventRate(bin_duration=bin_duration),
+        "LOG10": Log(10, clip_zero=True),
+        "SINK": DebugLog(),
+        "TERM": TerminateOnTotal(n_chunks),
+    }
+    conns = (
+        (comps["SOURCE"].OUTPUT_SIGNAL, comps["THRESH"].INPUT_SIGNAL),
+        (comps["THRESH"].OUTPUT_SIGNAL, comps["RATE"].INPUT_SIGNAL),
+        (comps["RATE"].OUTPUT_SIGNAL, comps["LOG10"].INPUT_SIGNAL),
+        (comps["LOG10"].OUTPUT_SIGNAL, comps["SINK"].INPUT),
+        (comps["SINK"].OUTPUT, comps["TERM"].INPUT_MESSAGE),
+    )
+    ez.run(components=comps, connections=conns)
+
+
+if __name__ == "__main__":
+    typer.run(main)

ezmsg_event-0.1.1/docs/scripts_nbs/event_rates_system_detailed.py

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+import ezmsg.core as ez
+from ezmsg.util.messages.modify import ModifyAxis
+from ezmsg.sigproc.aggregate import RangedAggregate, AggregationFunction
+from ezmsg.sigproc.math.scale import Scale
+from ezmsg.sigproc.math.log import Log
+from ezmsg.util.debuglog import DebugLog
+from ezmsg.util.messages.chunker import ArrayChunker
+from ezmsg.util.terminate import TerminateOnTotal
+import typer
+
+from ezmsg.event.util.simulate import generate_white_noise_with_events
+from ezmsg.event.window import Window
+from ezmsg.event.peak import ThresholdCrossing
+from ezmsg.event.sparse import Densify
+
+
+def main(bin_duration: float = 0.05):
+    fs = 30_000.0
+    dur = 10.0
+    n_chans = 128
+    threshold = 2.5
+    rate_range = (10, 100)
+    chunk_dur = bin_duration / 2
+    chunk_len = int(fs * chunk_dur)
+    data = generate_white_noise_with_events(
+        fs, dur, n_chans, rate_range, chunk_dur, threshold
+    )
+    n_chunks = int(dur / bin_duration)
+
+    comps = {
+        "SOURCE": ArrayChunker(data, chunk_len, fs=fs),
+        "THRESH": ThresholdCrossing(threshold=threshold),
+        "WIN": Window(
+            axis="time",
+            newaxis="win",
+            window_dur=bin_duration,
+            window_shift=bin_duration,
+            zero_pad_until="none",
+        ),
+        "AGG": RangedAggregate(
+            axis="time", bands=[(0, bin_duration)], operation=AggregationFunction.SUM
+        ),
+        "SCALE": Scale(1 / bin_duration),
+        "DENSE": Densify(),
+        "AXIS": ModifyAxis(name_map={"time": None, "win": "time"}),
+        "LOG10": Log(10, clip_zero=True),
+        "SINK": DebugLog(),
+        "TERM": TerminateOnTotal(n_chunks),
+    }
+    conns = (
+        (comps["SOURCE"].OUTPUT_SIGNAL, comps["THRESH"].INPUT_SIGNAL),
+        (comps["THRESH"].OUTPUT_SIGNAL, comps["WIN"].INPUT_SIGNAL),
+        (comps["WIN"].OUTPUT_SIGNAL, comps["AGG"].INPUT_SIGNAL),
+        (comps["AGG"].OUTPUT_SIGNAL, comps["SCALE"].INPUT_SIGNAL),
+        (comps["SCALE"].OUTPUT_SIGNAL, comps["DENSE"].INPUT_SIGNAL),
+        (comps["DENSE"].OUTPUT_SIGNAL, comps["AXIS"].INPUT_SIGNAL),
+        (comps["AXIS"].OUTPUT_SIGNAL, comps["LOG10"].INPUT_SIGNAL),
+        (comps["LOG10"].OUTPUT_SIGNAL, comps["SINK"].INPUT),
+        (comps["SINK"].OUTPUT, comps["TERM"].INPUT_MESSAGE),
+    )
+    ez.run(components=comps, connections=conns)
+
+
+if __name__ == "__main__":
+    typer.run(main)

ezmsg_event-0.1.1/pyproject.toml

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+[project]
+name = "ezmsg-event"
+description = "Namespace package for ezmsg to work with signal events like neural spikes and heartbeats"
+authors = [
+  { name = "Chadwick Boulay", email = "chadwick.boulay@gmail.com" },
+]
+readme = "README.md"
+requires-python = ">=3.9"
+dynamic = ["version"]
+dependencies = [
+    "ezmsg-sigproc>=1.3.3",
+    "ezmsg>=3.5.0",
+    "numpy>=2.0.2",
+    "sparse>=0.15.4",
+]
+
+[project.optional-dependencies]
+test = [
+    "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/event/__version__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/ezmsg"]
+
+[tool.uv]
+dev-dependencies = [
+    "ruff>=0.6.8",
+    "typer>=0.12.5",
+]

ezmsg_event-0.1.1/src/ezmsg/event/__init__.py

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+from .__version__ import __version__ as __version__

ezmsg_event-0.1.1/src/ezmsg/event/__version__.py

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+# 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 = '0.1.1'
+__version_tuple__ = version_tuple = (0, 1, 1)

ezmsg_event-0.1.1/src/ezmsg/event/message.py

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+from dataclasses import dataclass
+from numbers import Number
+
+
+@dataclass
+class EventMessage:
+    offset: float
+    """The temporal offset at which the event occurred. This is a float in seconds. The reference point is
+    unspecified and depends on the clock the application uses. Most applications will use time.time."""
+
+    ch_idx: int
+
+    sub_idx: int = 0
+    """The sub-index of the channel. For Blackrock multi-unit data: 0=unsorted, 1-5 sorted unit, >5=noise"""
+
+    value: Number = 1
+    """The value of the event. This can be any number, but is usually an integer, and is often 1 for spikes."""